GENERAL CONCEPTS, ENZYMES AND

COENZYMES BIOENERGETICS AND

BIOLOGICAL OXIDATION
EARL LOUIS A. SEMPIO, MD

I. BASIC CONCEPTS IN BIOCHEMISTRY Amino Acids with Acidic Side Chains

- proton donor at physiologic pH
A. Proteins - negatively charged at physiologic Ph
- abundant and functionally diverse molecules
- perform specific biological function due to their
unique three-dimensional structures
- composed of linear polymers of amino acids

Amino Acids
- there are only 20 amino acids in human proteins as
coded in the DNA
- composition: α- carbon atom, α-carboxyl group, α-
amino group and distinctive side chain (“R-group”)
- the side chains determine the role amino acids in
proteins Amino Acids with Basic Side Chains
- peptide bond: amide linkage between the α- - accept protons at physiologic pH
carboxyl group and α-amino group of two amino - positively charged at physiologic pH
acid residues

Amino Acids with Nonpolar Side Chains

- do not participate in hydrogen or ionic bonds
- do not lose or gain protons
- promotes hydrophobic interactions

Titration of Amino Acids

- amino acids contain weakly acidic α-carboxyl
groups and weakly basic α-amino groups as well as
ionizable R-groups
- act as buffers (i.e. resists change in pH following
addition of an acid or base)
- dissociation of the α-carboxyl group in alkaline pH
and dissociation of the α-amino group in acidic pH
- titration of alanine

Amino Acids with Uncharged Polar Side Chains

- at physiological pH, has a zero-net charge

- at alkaline pH, may donate proton (e.g. cysteine,
tyrosine)
- the hydroxyl, amide and carbonyl groups can
participate in hydrogen bond formation and be sites
of attachment of other compounds (i.e.
oligosaccharide in glycoproteins)
- sulfhydryl group of 2 cysteine molecules can - zwitterion: amino acid form with a zero zwitterion:
oxidize and form a dimer, cystine amino acid form with a zero-net charge

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pH = pK1: equal amount of Forms I and II
- pH < pK1: predominantly Form I
- pH = pK2: equal amount of Forms II and III
- pH > pK2: predominantly Form III
- Isoelectric point (pI): predominantly Form II, net
charge is zero
- Buffering occurs within ± pH unit of the pKa
Primary Structure of Proteins
- consists of the sequence of amino acids along a
polypeptide chain
-Ser-Ala-Glu-Val-Leu-Arg-Gly-
Secondary Structure of Proteins
- formed by regular repeating pattern of hydrogen
bond formation between peptide bond carbonyl
oxygen and amide hydrogens
- atoms of the side chain are not involved
α-helix
- Spiral configuration consisting of tightly packed,
coiled polypeptide
- carbonyl of a peptide bond forms a hydrogen bond
with an amide four amino acid residues further
along the chain
- the side chains extend outward
- disrupted by proline, and amino acids with bulky or
charged side chains
β-sheet
- formed by hydrogen bonds between two extended
polypeptide chains or between two regions of a
single folded chai
- the surface appears “pleated”
- the hydrogen bond are perpendicular to the
polypeptide backbone
- chains may run parallel or antiparallel
Tertiary Structure of Proteins
- refers to the unique three-dimensional
conformation of the protein determined by its amino
acid sequence
- protein folding produced by the interactions
between amino acid residues that may be located at
a considerable distance from each other
- domains are the fundamental functional and
structural unit of polypeptides
- stabilize by electrostatic interactions, hydrogen
bond, hydrophobic interactions, disulfide bonds
Quaternary Structure of Proteins
- refers to the spatial arrangement of subunits in a
protein consisting of more than one polypeptide
chain
Additional notes: pKa of side chains of amino acids
UST FMS MEDICAL BOARD REVIEW 2019
GENERAL CONCEPTS, ENZYMES AND
COENZYMES BIOENERGETICS AND
BIOLOGICAL OXIDATION
EARL LOUIS A. SEMPIO, MD
B. Carbohydrates
- contain at least three carbon atoms, hydroxyl
groups and an aldehyde or ketone group
- empirical formula: (CH2O)n
- functions: main source of dietary energy (i.e.
glucose), storage of energy (i.e. glycogen),
intracellular communication
Classification of Carbohydrates
Monosaccharides
-these are simple sugars containing one saccharide
group
-can be further classified according to the number of
carbons and whether they have an aldehyde or
ketone group in their backbone structures
Oligosaccharide
-composed of two to ten saccharide groups
Polysaccharide
-composed of ten or more saccharide groups that
may be linear or branched
Isomerism
- isomers have the same chemical formula (e.g.
fructose and glucose)
- epimers are isomers that differ around one specific
carbon atom (e.g. glucose is a C2- epimer of
mannose)
- enantiomers: the configuration of the asymmetric
carbon atom farthest from the aldehyde or ketone
group determines whether it is a D- (i.e. hydroxyl
group on the right) or L-sugar (i.e. hydroxyl group
on the left)
- Anomers: the hydroxyl group on the anomeric
carbon may be in the α (i.e. below the plane of the
ring in the Hayworth projection or on the right in the
Fischer projection) or β (i.e. above the plane of the
ring or on the left in the Fischer projection)
configuration
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 GENERAL CONCEPTS, ENZYMES AND
COENZYMES BIOENERGETICS AND
BIOLOGICAL OXIDATION
EARL LOUIS A. SEMPIO, MD

- oxidized to provide energy, structural components

- glycosidic bonds form when the hydroxyl group on
the anomeric carbon reacts with an –OH (i.e.O-
glycoside) or –NH group (i.e. N-glycoside) of
another compound
of triacylgycerols, cholesteryl esters, phospholipids
and glycosphingolipids
- in humans, fatty acids have an even number of
carbon atoms, are 16 to 20 carbon atoms in length,
and may be saturated (i.e. contains no double
bonds) or unsaturated (i.e. contains one or more
double bonds)
- essential fatty acids (cannot be synthesized by
mammals): linoleic acid and linolenic acid
- linoleic acid is the precursor of arachidonic acid

- Reducing properties: If the hydroxyl group on the

anomeric carbon of a cyclized sugar is not linked to
another compound the ring could open and act as a
reducing agent

Complex sugars
- includes the glycosaminoglycans, proteoglycans,
glycoprotein and glycolipids

Glycosaminoglycans (GAGs)
- aka mucopolysaccharides
- long, unbranched, negatively charged,
heteropolysaccharide chain composed of repeating
disaccharide unit [acidic sugar-amino sugar] n
- amino sugar is either D-glucosamine or D-
galactosamine, usually sulfated or acetylated
- acidic sugar is either D-glucuronic acid or
L-iduronic acid which contain carboxyl group
- the negative charge is due to the ionized carboxyl
and sulfate groups at physiologic pH and cause
GAGs to repel each other and bind water
- form most of the ground substance of extracellular
matrices and mucus secretions

Proteoglycans
- consist of a core protein with glycosaminoglycans
attached
- bottle brush appearance
- all GAGs form proteoglycans except hyaluronic acid

Glycoproteins
- proteins to which oligosaccharides are attached
- the carbohydrate moiety has no serial repeats, are
branched and may not be charged
- serves as enzymes, hormones, antibodies and
structural proteins

C. Lipids
- diverse group of molecules but are similar in that
they are water insoluble
- major source of energy, provide hydrophobic
partition, fat- soluble vitamins as coenzymes and
precursor of
prostaglandins and steroid hormones

Free or unesterified fatty acids

- empiric formula: CH3(CH2)nCOO-
- consists of a hydrophobic hydrocarbon chain with a
terminal carboxyl group that ionizes at physiologic
pH hence its amphipathic nature

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 GENERAL CONCEPTS, ENZYMES AND
COENZYMES BIOENERGETICS AND
BIOLOGICAL OXIDATION
EARL LOUIS A. SEMPIO, MD

Triacylglycerols Sphingophospholipids
- 3 molecules of fatty acid esterified to a molecule of
glycerol - sphingomyelin: the only significant
- esterification of fatty acid results in loss of negative sphingophospholipid in human as it is an important
charge constituent of the myelin sheath
- “neutral fat”- stored in adipose tissue as oily
droplet (i.e.body’s major fuel storage reserve) - backbone is the amino alcohol sphingosine
- the fatty acid in carbon 1 is typically saturated
- the fatty acid in carbon 2 is typically unsaturated
- the fatty acid in carbon 3 can be either

Phospholipids
- polar, ionic molecules composed of an alcohol that
is attached by a phosphodiester bridge to either
diacylglycerol or spingosine Glycosphingolipids
- amphipathic with a hydrophilic head and long,
hydrophobic tail - aka glycolipids
- predominant lipids of cell membrane, component
of lung surfactant and bile - differ from sphingophospholipid in that they do not
- classes depend on the backbone: glycerol (i.e. contain phosphate and the polar head function is
glycerophospholipids) and sphingosine (i.e. provided by a monosaccharide or oligosaccharide
glycosphingolipids)
attached directly to the ceramide
Glycerophospholipids
- classified as either neutral or acidic
- aka phosphoglycerides
glycosphingolipids
- Phosphatidic acid acid is the simplest
phosphoglyceride; contains fatty acids esterified to
- the cerebrosides are the simplest neutral
carbons 1 and 2 of the glycerol moiety and a
phosphate group at carbon 3 glycosphingolipids with the alcohol group attached
to monosaccharides

- rest of phosphoglycerides are formed from

phosphatidic acid and an alcohol [e.g.
phosphatidylserine, phosphatidylethanolamine
(cephalin), phosphatidylcholine (lecithin),
phosphatidylglycerol, phosphatidylinositol]

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(e.g. galactocerebrosides) or oligosaccharides
(i.e. globosides)
- acidic glycosphingolipids are negatively
charged at physiologic pH due to the presence
of N-acetylneuraminic acid (NANA) in
gangliosides or by sulfate groups in sulfatides
- gangliosides are derivatives of ceramide
oligosaccharides and contain one or more NANA
- sulfatides (or sulfoglycosphingolipids) are
cerebrosides that contained sulfated galactosyl
residues
Cholesterol
- structural component of cell membrane, precursor
of hormones, bile and vitamins
- consists of four fused hydrocarbon rings (A-D) and
has an eight-carbon, branched hydrocarbon
attached to carbon 17 of the D ring, a hydroxyl
group at carbon 3 of ring A and a double bond
between carbon 5 and 6 in ring B
Plasma lipoproteins
- spherical macromolecules of lipid and
apolipoproteins
- chylomicrons, VLDL, LDL and HDL differ in lipid
and protein composition, size, density and site of
origin
- function to transport lipids (e.g. cholesterol,
triacylglycerol) in the plasma and transport their lipid
content to (and from) the tissues
- lipid core: triacylglycerol and cholesteryl esters
UST FMS MEDICAL BOARD REVIEW 2019
GENERAL CONCEPTS, ENZYMES AND
COENZYMES BIOENERGETICS AND
BIOLOGICAL OXIDATION
EARL LOUIS A. SEMPIO, MD
- shell: unesterified cholesterol, phospholipid,
apolipoproteins
Chylomicrons
-assembled in intestinal mucosal cells and carry
dietary triacylglycerol, cholesterol, and fat-soluble
vitamins to the peripheral tissues
VLDL
-produced in the liver and transport endogenous
triacylglycerol to the peripheral tissues
LDL
- derived from VLDL
- provide cholesterol to the peripheral tissues
- oxidized LDL are taken up by macrophages,
transformed into foam cell which participate in the
development of atherosclerotic plaque
HDL
- formed in the blood by the addition of lipid to apo
A-1, an apolipoprotein made by the liver and
intestine
- reservoir of apolipoproteins (apo C-II and apo E)
and take up cholesterol from peripheral tissues and
return it to the liver
II. ENZYMES
A. General Features of Enzymes
1. Biological catalysts that accelerate
chemical reactions by lowering the
energy of activation of the reaction.
2. Conjugated proteins consisting of
protein portion (apoenzyme) and
nonprotein portion (cofactor, coenzyme,
prosthestic group); Apoenzyme + non
protein portion = Holoenzyme
3. Enzyme specificity resides in the active
site, where substrate binds. Models of
active site:
a. Rigid Template theory (Lock and
Key)- substrate fits snuggly into a
fixed active site
b. Induced Fit theory (Flexible)-
enzyme undergoes conformational
change to accommodate the
substrate into its active site.
4. Classification of enzymes based on type
of reaction catalyzed. Nomenclature
based on an Enzyme commission
number (4-digit numbers) depicting
general class, sub class and sub-
subclass and serial number in the list
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 GENERAL CONCEPTS, ENZYMES AND
COENZYMES BIOENERGETICS AND
BIOLOGICAL OXIDATION
EARL LOUIS A. SEMPIO, MD

D. Enzyme Kinetics Principles based on studies

General Class Function of Michaelis and Menten

I. Oxido- Oxidation-reduction reactions e.g. 1. Study of reaction rates with

reductase dehydrogenase varying concentration of substrate
2. Km and Vmax are kinetic parameters
2.Transferases Transfers functional groups e.g. that characterize enzymes
transaminases  Km is a measure of affinity of
the E to S (affinity inversely
3. Hydrolases Split molecules in the presence of prpoprtional to Km value); is
water. e.g. peptidases equal to the [S] at half Vmax
 Vmax- velocity (vo) when the
4. Lyases Split molecules non hydrolytically active site is fully saturated
with S
e.g. aldolases

5.Isomerases Interconvert isomeric molecules 3. Michaelis Menten Equation:

e.g. epimerases

6. Ligases Join molecules creating bonds

using energy e.g. synthases

1. Enzymes are also classified based on

chemical nature of enzymes
a. Enzyme complex
b. Allosteric enzymes
c. Inducible/repressible enzymes vs
constitutive enzymes

B. Mechanisms of Catalysis explain how

enzymes are able to lower energy of
activation and reach the transitions state.
1. Proximity and orientation effects 4. Lineweaver Burke Equation and Plot
2. Desolvation Effects a. Equation is derived from Michaelis
3. Acid Base catalysis Menten equation
4. Covalent catalysis
5. Strain or bond distortion effects
6. Metal coordination effects

C. Factors Affecting Enzyme Activity

1. pH- extremes of pH denature enzymes b. double reciprocal plot of Michaelis
2. Temperature – high temperatures Menten
denature enzymes and low temperature
inactivate enzyme
3. Enzyme concentration- activity increases
with [E]
4. Substrate concentration- velocity
increases to maximum velocity (Vmax)
representing substrate saturation of
active site of Enzyme
5. Inhibitors
a. Irreversible- Inhibitors become
tightly bound to the enzyme
b. Reversible:
 Competitive- Inhibitor binds
to active site can differentiate different types of inhibition
 Noncompetitive – Inhibitor
binds to another site other
than active site
 Uncompetitive- Inhibitor
only binds to E-S complex

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 GENERAL CONCEPTS, ENZYMES AND
COENZYMES BIOENERGETICS AND
BIOLOGICAL OXIDATION
EARL LOUIS A. SEMPIO, MD

1. Small organic molecules required for the

activity of the enzymes, usually involved in
the transfer of chemical groups.
2. Maybe bound loosely near the active site
and act as second substrates or may be
tightly bound to the enzyme as a prosthetic
group
3. Many are derived from vitamins.

B. Cofactors
1. Small inorganic ions required for proper
structure or to aid in catalysis
2. Metal ions may serve as metal ions bridges
between enzyme and substrate
(metalloenzymes), electron sinks, proton
donors (acids).

Inhibition Km Vmax Coenzyme Vitamin Function

Competitive increased same component
NAD, NADP niacin Redox reactions
Non same decreased (transfer of electrons
competitive and H+)
Uncompetitive decreased decreased FAD, FMN riboflavin Redox
(transfer of electrons
and H+)
E. Regulation of Enzyme activity Coenzyme none Redox (transfer of
Q (Ubiqui- electrons in ETC)
1. Allosteric regulation. Positive and negative none)
effectors bind to allosteric sites and can Tetrahy- none Redox (hydroxylation)
increase and decrease activity, respectively. drobiop-
Allosteric enzymes give sigmoidal curves. terin
2. Covalent modification. Covalent attachment Thiamine Thiamine Transfers of acyl or
of chemical groups to enzymes render Pyrophos- active aldehyde,
enzyme active or inactive, e.g. phate decarboxylation of 
Phosphorylation and dephoshorylation (TPP) keto acids
3. Stimulation and inhibition of control Lipoic acid none Transfer of acyl group
proteins. Formation of Calcium-calmodulin Coenzyme Pantothenic Acyl group transfer
complex activates certain enzymes A acid
4. Proteolytic activation Pyridoxal Pyridoxine Transamination,
Proenzymes or zymogens get activated phosphate decarboxylation,
when peptide bonds in the molecule are isomerization of amino
cleaved. E.g. activation of blood coagulation acids
proteins Biotin biocytin carboxylation
Tetrahy- Folic acid One carbon group
drofolate transfer
F. Applications of Enzymes in Medicine
Cobamide Cobalamine Alkyl group transfer
coenzyme (vitamin
1. Clinical diagnosis and prognosis. B12)
Cell death release enzymes in the circulation
e.g. LDH and CPK isoenzymes in myocardial IV. BIOENERGETICS AND BIOLOGICAL
infarction OXIDATIONS
2. Enzymes as therapeutic agents
Enzymes as medications for treatment of A. Bioenergetics and Concept of Free Energy
certain medical problems. e.g. streptokinase 1. Bioenergetics is the study of energy changes
for blood clots that accompany chemical reactions. (energy
requiring vs energy liberating reactions)
3. Immobilized enzymes as reagents in desk
2. Bioenergetics is governed by Laws of
top clinical analyzers. e.g. glucose oxidase
Thermodynamics:
blood glucose kits
a. First Law- conservation of energy
4. Enzymes as indicators in laboratory
b. Second Law- law on entropy
procedures. e.g. ELISA
B. Free Energy Change ( G)
III. COENZYMES AND COFACTORS
1. Represents amount of energy available for
A. Coenzymes useful work

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 GENERAL CONCEPTS, ENZYMES AND
COENZYMES BIOENERGETICS AND
BIOLOGICAL OXIDATION
EARL LOUIS A. SEMPIO, MD

2. Calculated quantitative value determines 2. Oxidative phosphorylation is the

type of reaction phosphorylation of ADP to ATP coupled with
a) Exergonic-  G < 0; spontaneous oxidation of substrates via the Electron
reaction, Transport Chain
b) Endergonic –  G > than 0; Non
spontaneous; energy requiring. May be D. The Electron Transport Chain
coupled with exergonic reaction to 1. The ETC is composed of enzymes (oxidases
proceed and dehydrogenases) and coenzymes as
c) Equibrium  G=0 electron carriers within the inner membrane
of the mitochondria
3.  G0 is the standard free energy change at
2. The ETC is organized into complexes
standard conditions of T, pressure, at 1M
arranged in a chain like fashion with oxygen
reactants.
as final acceptor of electrons to form water:
4. Quantitative value of DG of reaction
a. Complex I- NADH CoQ dehydrogenase
determines whether compound is high
b. Complex II- Succinate CoQ reductase
energy or low energy.
c. Complex III- Cytochrome b-c1 oxidase
a. High energy compounds –  G0 of -7 to
d. Complex IV – Cytochrome aa3 oxidase
-15 kcal/mole
e. Complex V- ATPase (ATP synthetase)
b. Low energy counds-  G0 less than -7 3. Substrates donate electrons to the ETC via 2
kcal/mole points:
a. Complex I- NADH CoQ dehydrogenase
Compounds Examples DG0 producing a P/O ratio of 2.5/1
(kcal/mole) equivalent to 3 ATPs produced
Phosphoric acid ATP -7.3 b. Complex II- Succinate dehydrogenase
anhydride producing a P/O ratio of 1.5/1
Thiol esters AcetylCoA -7.7 equivalent to 2 ATPs produced
4. Three sites of oxidative phosphorylation in
the ETC where Go > -7.3 kcal/mole
a. Complex I- site 1
b. Complex III- site 2
c. Complex IV – site 3

Phosphoguanides Creatine -10.3

phosphate

Phosphoric-carboxylic - 1,3 BPG -10.1

acid anhydrides - acetyl -10.3
phosphate
- carbamoyl -12.3
phosphate

Enol phosphates Phosphoenol -14

pyruvate 5. Mechanism of oxidative phosphorylation
based on Chemiosmotic Coupling Hypothesis
Phosphate Esters - AMP -3.4 of Peter Mitchell. The oxidation of substrates
- glucose-6 - 3.3 in the ETC is accompanied by release of
phosphate protons in the mitochondrial matrix creating
- glycerol–3 - 3.2 a proton gradient between the matrix and
phosphate intermembranous space, with the
intermembranous space becoming acidic.
Movement of protons from the
C. Cellular Synthesis of ATP intermembranous space back to the matrix,
1. Substrate level phosphorylation via Fo and F1 complex of Complex V
Is direct cleavage of high energy bonds, produces ATP
coupled to synthesis of ATP by transfer of 6. Substances that affect the ETC
high energy group to ADP a. Site/Complex specific
e.g. pyruvate kinase reaction:  Complex I- barbiturates, rotenone,
piericidin A, guanethidine
phosphoenol pyruvate + ADP  pyruvate +
 Complex II- malonate, carboxin
ATP

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 GENERAL CONCEPTS, ENZYMES AND
COENZYMES BIOENERGETICS AND
BIOLOGICAL OXIDATION
EARL LOUIS A. SEMPIO, MD

 Complex III- antimycin A, phenformin,

dimercaprol
 Complex IV – carbon monoxide,
cyanide, azide, H2S
 Complex IV – Oligomycin binds to the
Fo fraction of ATPase
b. Non site specific
 Inhibitor of ADP-ATP carrier-
bongkrekic acid, atractyloside
 Uncouplers – dissociates respiration
(electron flow) from phosphorylation
e.g. 2,4 dinitrophenol, gramicidin,
dicoumarol, valinomycin, thermogenin

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CHOOSE THE BEST ANSWER:
_____1. Which of the following is an essential amino
acid?
A. Glycine
B. Valine
C. Alanine
D. Serine
_____2. A polypeptide chain with an amino acid
sequence of Pro-Gly-Glu would have which of the
following properties at physiologic pH?
A. No net charge
B. Negative charge
C. Positive charge
D. Non-polar
_____3. Which of the following defines the
quaternary structure of a protein?
A. Spatial arrangement of subunits
consisting of more than one polypeptide
chain
B. Unique 3-dimensional conformation of
the protein determined by its amino acid
sequence
C. May run parallel or antiparallel
D. Consists of the sequence of amino acids
along a polypeptide chain
_____4. Which component of the amino acid leucine
is deprotonated at pH 7.4?
A. alpha-carbon
B. alpha-carboxyl group
C. alpha-amino group
D. R-group
_____5. Which among the following is TRUE
regarding carbohydrates?
A. Contain at least 3 carbon atoms
B. Empirical formula (CH2OH)
C. Should contain both aldehyde and
ketone group
D. Have reducing property if the hydroxyl
group on the non-anomeric carbon is
not linked to another compound
_____6. Which of the following is TRUE regarding
Glycosaminoglycans?
A. The positive charge is due to ionized
carboxyl and sulfate groups at
physiologic Ph
B. They are long unbranched charged
heteropolysaccharide chains
C. They repel each other and bind water
due to the net positive charge at
physiologic pH
D. repeating disaccharide units of [basic
sugar-carboxyl sugar
_____7. These are the simplest neutral
glycosphingolipids with the alcohol group attached
to monosaccharides?
A. cerebrosides
B. ceramides
C. sphingomyelin
D. sulfoglycosphingolipids
UST FMS MEDICAL BOARD REVIEW 2019
REVIEW TEST
EARL LOUIS A. SEMPIO, MD
_____8. Which of the following is formed in the
blood by addition of lipid to apo A-1?
A. LDL
B. Chylomicrons
C. VLDL
D. HDL
_____9. Which of the following is TRUE regarding
enzyme activity?
A. activation energy is higher with the
enzyme
B. change in free energy is lower without
the enzyme
C. free energy of the reactants is always
lower than free energy of products
D. reaction is facilitated by lowering
_____10. Which of the following is TRUE regarding
the activity of Lyases?
A. Split molecules in the presence of water
B. They join molecules by creating bonds
C. They transfer functional groups
D. Non-hydrolytic splitting
_____11. Enzymes are affected by temperature,
which among the following statements correctly
states the effect of temperature on enzymes?
A. The higher the temperature the slower
the reaction
B. Reaction rates are similar in high and low
temperatures
C. High temperatures denature enzymes
D. Low temperatures activate enzymes
_____12. In enzyme kinetics, which of the following
is considered as the measure of affinity of E to S
A. Vmax
B. Km
C. V0
D. ½ Vmax
_____13. In which type of enzyme activity inhibition
would both Km and Vmax be decreased?
A. Competitive
B. Non-Competitive
C. Uncompetitive
D. Partly Competive
_____14. Which of the following is defined as small
organic molecules required for the activity of
enzymes?
A. Cofactors
B. Coenzymes
C. Minerals
D. Apoenzyme
_____15. Which if the following characterizes the
reaction facilitated by tetrahydrofolate?
A. transfer of acyl group
B. alkyl group transfer
C. one carbon transfer
D. hydroxylation
| BIOCHEMISTRY
 REVIEW TEST
EARL LOUIS A. SEMPIO, MD

_____16. Free energy change is

A. The amount of energy unavailable for work
B. less than 0 in exergonic reactions
C. is more than 0 in energy releasing reactions
D. is 1 at equilibrium

_____17. Which of the following is defined as the

phosphorylation of ADP to ATP coupled with
oxidation of substrates via the ETC?
A. Substrate level phosphorylation
B. Oxidative phosphorylation
C. ATP phosphorylation
D. Cytosolic-Mitochondrial Phosphorylation

_____18. Carbon monoxide affect the electron

transport chain through which complex?
A. Complex I
B. Complex II
C. Complex III
D. Complex IV

_____19. Which of the following is described as a

substance affecting the electron transport chain by
dissociating electron flow from phosphorylation?
A. Inhibitor
B. Antimycin
C. Uncoupler
D. Ubiquinol

_____20. Which of the following is responsible for

producing ATP?
A. Movement of protons from the matrix to
the intermembranous space
B. Sequestration of protons outside the
mitochondrial matrix
C. Creation of proton gradient between the
matrix and intermembranous space
D. Making the intermembranous space
basic

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INTRODUCTION
Glucose, the major dietary sugar is the
universal source of fuel for human cells. It is likewise
the form of sugar brought in the circulation to
ensure a continuous supply of fuel.
I. DIGESTION, ABSORPTION AND TRANSPORT
OF CARBOHYDRATES
1. Carbohydrates are the largest source of dietary
calories. Major dietary forms are starch, lactose and
sucrose
2. Main sites for digestion are the mouth and
duodenum.
3. Salivary amylase acts on masticated food to break
some  1, 4 glycosidic bonds of starch.
4. Pancreatic amylase in the duodenum completes
the digestion and produces a mixture of
monosaccharides, disaccharides and
oligosaccharides.
5. Disaccharides are hydrolyzed into
monosaccharides by specific disaccharidases in the
brush border of the small intestines e.g.
 Sucrose- isomaltase
 Lactase-glucosylceramidases
 Trehalase
6. Uptake of monosaccharides by intestinal mucosal
cells is mediated by various transporters
 Na dependent active transport for
glucose and galactose
 Facilitative diffusion for fructose and
mannose
7. Transport of absorbed monosaccharides from
intestinal cells into the blood and circulate to the
liver and peripheral tissues by facilitative
transporters (GLUT I to V) in specific tissues.
8. Dietary fibers, (e.g. cellulose) are not digestible
by human intestinal enzymes due to inherent lack of
 1,4 glucosidases
II.
UST FMS MEDICAL BOARD REVIEW 2019
CARBOHYDRATE METABOLISM
JOSE S. BLAS, MD
GLYCOLYSIS
1. Glycolysis is the metabolic pathway utilized by the
cells to oxidize glucose to provide energy as ATP
and intermediates of other metabolic pathways.
2. The glycolytic pathway is central to carbohydrate
metabolism because sugars, whether obtained from
the diet or from the breakdown of other substrates
in the body, can eventually be chemically converted
to glucose.
3. The ten reactions of glycolysis that produces
pyruvate from glucose can be subdivided into the
preparatory (energy investment phase) and pay-off
phase.
4. The energy investment phase utilizes 2ATPS to
phosphorylate glucose and fructose and form 2
triose (DHAP and glyceraldehyde 3 Phosphate. The
payoff phase oxidizes 2 molecules of glyceraldehyde
3 phosphate and generates ATP via substrate level
phosphorylation and NADH which is a potential
source of ATP when oxidized in the ETC (aerobic
glycolysis).
5. Anaerobic condition regenerates NAD when
pyruvate is reduced by LDH to lactate e.g.
erythrocytes and exercising skeletal muscles.
6. Many enzymes and intermediates of glycolysis
operate in gluconeogenesis.
7. Key enzymes in glycolysis include
hexokinase/glucokinase, phosphofructokinase-1
(PFK-1,) and pyruvate kinase which catalyze
irreversible reactions, while the rest catalyze
reversible reactions. Irreversible reactions have
counterparts in gluconeogenesis.
Hexokinase Glucokinase
Most tissues Liver
(hexokinase I, II, III)
(hexokinase IV)
Inhibited by Glucose- Not inhibited by
6-phosphate glucose-6-phosphate
Low Km (high High Km (lower
Affinity) affinity)
Not induced by insulin Induced by insulin
8. The key regulatory enzyme PFK-1 catalyzes the
committed and rate limiting step is allosterically
inhibited by ATP, citrate and phosphoenol pyruvate.
It is activated by AMP (indicating a low energy
charge) and Fructose 2,6 bisphosphate.
9. Pyruvate Kinase (PK) is activated by fructose 1,6
bisphosphate, the product of the PFK-1
 Covalent Modification thru Phosphorylation
by a Camp - dependent protein kinase leads
to inactivation of the hepatic isozyme of PK.
Dephosphorylation of PK by a phosphatase
results in reactivation of the enzyme.
 Glucagon and insulin can affect the levels of
cAMP and covalent modification of PK
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10. Two moles of pyruvate are formed from a
molecule of glucose because the energy investment
phase generates 2 triose phosphates as the 2 moles
of glyceraldehyde 3 phosphate and continues in the
payoff phase.
11. Stoichiometry of energy production produces a
gross yield of 2 ATPs from 2 substrate level
phosphorylations with 2 ATPs used in the investment
phase producing a net of 2 ATPs
12. NADH generated can be oxidized in the ETC and
generates additional ATPs the amount depending on
the Shuttle System used:
 Malate Aspartate shuttle: 3ATPs / NADH
 Alpha glycerophosphate Shuttle: 2 ATPs
/NADH
13. The pyruvate dehydrogenase reaction (PDH) in
the mitochondria oxidatively decarboxylates
pyruvate into acetylCoA is a preparatory reaction to
the TCA Cycle for complete oxidation of glucose into
CO2 and H2O. PDH is an enzyme complex composed
of 3 enzymes:
E1- Pyruvate decarboxylase bound to TPP
E2- Dihydrolipoyl transacetylase bound to
lipoic acid and CoASH
E3- Dihydrolipoyl dehydrogenase
bound to FAD and NAD
 NADH enters the ETC and generates 3 ATPs/NADH
oxidized
 PDH is inhibited by acetylCoA, NADH, ATP and by
covalent modification by phosphorylation by PDH
kinase
Alternate Fates of Pyruvate
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CARBOHYDRATE METABOLISM
JOSE S. BLAS, MD
III. TRICARBOXYLIC ACID CYCLE
The TCA Cycle or Citric Acid Cycle (Krebs cycle) is
the final common pathway for the oxidation of the
major macro-- molecules, carbohydrates, fats and
proteins. Their metabolism results in the formation
of Acetyl CoA or other intermediates of the cycle.
1. Occurring in the mitochondrial matrix the cycle
starts with the entry of acetylCoA which
condenses with oxaloacetate to form citrate,
followed by series of reactions that removes 2
carbon dioxide molecules by dehydrogenases
and generates reduced coenzymes NADH and
FADH2, GTP (via substrate level
phosphorylation) and regeneration of
oxaloacetate to complete the cycle.
2. Intermediates of the cycle include isocitrate,
a keto glutarate, succinylCoA, fumarate and
malate. These intermediates plus oxaloacetate
are points of entry of amino acid catabolites for
gluconeogenesis and can also be used as
precursors of amino acids and other
compounds. AcetylCoA can be a source of
carbons for fatty acid synthesis via citrate.
3. The TCA cycle is controlled by the regulation of
several enzymes: citrate synthase, isocitrate
dehydrogenase, and α- Keto glutarate:
a. NADH inhibits the dehydrogenase
reactions.
b. SuccinylCoA inhibits KG
dehydrogenase and citrate synthase
c. Ciitrate blocks citrate synthase
d. ATP inhibits citrate synthase and ADP
relieves inhibition
e. Ca++ activates KG dehydrogenase
and isocitrate dehydrogenase
4. Energetics of the TCA Cycle
a. Each turn of the TCA cycle
produces three NADH, one FADH2, one
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 CARBOHYDRATE METABOLISM
JOSE S. BLAS, MD

GTP (or ATP) and two CO2 released in 2 PEP to 2 pyruvate 2 ATP 2
oxidative decarboxylation reactions and 2 Pyruvate to 2 Acetyl 2 NADH 6
regeneration of oxaloacetic acid CoA
b. Each NADH oxidized in the ETC 2 Isocitrate to 2 a- KG 2 NADH 6
produces 3 ATPs and each FADH2 2 a-KG to 2 succinyl CoA 2 NADH 6
oxidized in the ETC produces 2 ATP 2 Succinyl CoA to 2 2 ATP (or 2
c. One GTP molecule is equivalent to one succinate 2 GTP)
ATP produced by substrate level 2 Succinate to 2 2 FADH2 4
phosphorylation fumarate
d. A total of 12 ATPs produced per 2 Malate to 2 2 NADH 6
acetylCoA entering the cycle with 2 CO2 oxaloacetate
produced number is either 4 or 6, 36-38
depending Shuttle
- Malate Aspartate= 6
-  Glycero PO4 = 4

IV. GLUCONEOGENESIS

Gluconeogenesis is the synthesis of

glucose from non-carbohydrate sources in order to
provide glucose to glucose dependent tissues. The
liver is the major organ for gluconeogenesis and
kidneys being a minor organ

1. Substrates for gluconeogenesis

a. Lactate produced from exercising muscles
and red blood cells is transported to the liver
and kidneys and converted to pyruvate and
eventually to glucose. The cycle is called
Lactic Acid Cycle or Cori Cycle.
b. Glucogenic amino acids derived from
hydrolysis of tissue proteins are the major
sources of glucose when catabolized to any of
5. Anaplerotic Reactions replenish intermediates of
these intermediates: pyruvate, -Keto
the TCA cycle which are siphoned off to serve
glutarate, succinylCoA, fumarate and
as biosynthetic precursors in other pathways
oxaloacetate.
such as amino acid synthesis and fatty acid
c. Glycerol released from the hydrolysis of
synthesis via citrate. Important anaplerotic
triacylglycerol in adipose is delivered to the
reactions:
liver. Glycerol is phosphorylated to Glycerol 3-
a. Pyruvate carboxylase reaction by
PO4, which is oxidized by Glycerol 3-PO4
pyruvate carboxylase to replenish
dehydrogenase to DHAP, an intermediate of
oxaloacetate (OXAA) is the major
glycolysis and gluconeogenesis
anaplerotic reaction.
b. Catabolism of glucogenic amino acids
2. Reactions in glycolysis and gluconeogenesis
generates intermediates of the TCA Cycle.
are the same except for those irreversible
c. Purine nucleotide cycle supplies fumarate.
reaction in glycolysis which have counterparts
unique to gluconeogenesis. These reactions
Stoichiometry of Coenzyme reduction and ATP
bypass the irreversible steps of glycolysis:
Formation in the Aerobic Oxidation of Glucose via
a. Pyruvate carboxylase converts pyruvate
Glycolysis, PDH Complex Reaction, the TCA Cycle
to OXAA in the mitochondria by passes
and Oxidative Phosphorylation the ETC
pyruvate kinase (PK)
b. Phosphoenolpyruvate (PEP)
Number Number
carboxykinase converts OXAA to PEP in
of ATP or of ATP
the cytosol, requiring GTP- by passes
Reactions reduced formed
PK.
coenzyme
c. Fructose 1,6 bisPhosphatase hydrolyzes
e directly
Fructose1,6 bisP to Fructose 6 P in the
formed
cytosol (by passes PFK-1)
Glucose to Glucose-6- -1 ATP -1 d. Glucose 6 phosphatase converts Glucose
PO4 6 P to Glucose in the cytosol (by passes
Fructose-6-PO4 to -1 ATP -1 Glucose 6 phosphatase)
Fructose 1,6-bisPO4
2 Glyceraldehyde 3-PO4 2 NADH 4 or 6 *
to 2 1,3 BPG
2 1,3- BPG to 2 3-BPG 2 ATP 2
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Glycolysis Gluconeogenesis
Hexokinase/gluco- Glucose- 6 phosphatase
kinase
Phosphofructokinase- Fructose 1,6 bis-
1 phosphatase
Pyruvate kinase - Pyruvate carboxylase
- PEP carboxykinase
3. Regulation of Gluconeogenesis
a. Regulation by compartmentation. First
reaction (pyruvate carboxylase) takes place
in the mitochondria and the rest in the
cytosol to prevent a futile cycle
b. Hormonal Regulation by Glucagon- lowers
the level of fructose 2,6-bisphosphate,
favoring gluconeogenesis over glycolysis.
Glucagon increases the transcription of the
gene for PEP-carboxykinase. Decreased
insulin levels favor mobilization of amino
acids from muscle protein
c. Substrate availability of gluconeogenic
cursors particularly glucogenic amino acids.
d. Allosteric Regulation of Gluconeogenesis
o AMP, Fructose 2,6 bisP inhibit
gluconeogenesis
o ATP (high energy charge) activate
gluconeogenesis
o High insulin/glucagon ratio inhibit
gluconeogenesis
V. GLYCOGEN METABOLISM
In vertebrates, glycogen is formed primarily in
the liver and skeletal muscle, representing
approximately 20% and 1-2% of the weight of liver
and of the weight of muscle, respectively. Liver
glycogen serves as a reservoir of glucose for other
tissues when dietary glucose is not available
(between meals or during a fast; for about 10-18
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CARBOHYDRATE METABOLISM
JOSE S. BLAS, MD
hours). Muscle glycogen provides a quick source of
energy during vigorous activity (strenuous exercise).
1. GLYCOGENESIS
Glycogen synthesis takes place in the cytosol of
virtually all animal tissues but is essentially
prominent in the liver and skeletal muscle. Enzymes
involved are Glycogen phosphorylase and branching
Enzyme
a. UDP Glucose (derived from reaction of
Glucose 6 P + UTP) in the presence of
glycogen synthase adds or transfers glucosyl
units to the non-reducing end of a branched
glycogen molecule or glycogen primer and
forms an 1,4 glycosidic bond
b. Branching enzyme, Amylo (14) to (16
transglycosylase or glycogen (46)
transferase creates the branch points of
glycogen through the formation of (16)
bond. It catalyzes the transfer of a terminal
fragment of 6 or 7 glucose residues from
the non-reducing end of a glycogen branch
having at least 11 residues to the C-6 OH
group of a glucose residue at a more interior
position of the same or another glycogen
chain, thus creating a new branch. The
process is repeated by glycogen synthase
and branching enzyme.
GLYCOGENOLYSIS
Glycogen degradation occurs in the liver and
skeletal muscles involving the enzymes, glycogen
phosphorylase, debranching enzyme and,
phosphoglucomutase.
a. Glycogen phosphorylase hydrolyzes (
14) glycosidic linkage between two
glucose residues at a non-reducing end of
glycogen with an attack to an Inorganic PO4
(Pi), removing the terminal glucose residue
as glucose-1-PO4. Pyridoxal PO4 is an
essential cofactor in the glycogen
phosphorylase reaction.
b. Glycogen phosphorylase acts repetitively on
the non-reducing ends of glycogen branches
until it reaches a point four glucose residues
away from an ( 16) branch point where
its action stops.
c. Debranching enzyme also called oligo (
16) to ( 14) glucan-transferase
transfers a block of 3 glucosyl units to a
nearby non-reducing end to which they are
attached in  1,4 linkage. The  1,6
glucosidase activity of the enzyme releases
a free glucose from the branched point.
d. Phosphoglucomutase converts the glucose-1
PO released from phosphorylase action into
glucose 6-PO4. In the liver, glucose 6- PO4
is transported into the endoplasmic
reticulum (ER) by glucose 6-PO4
translocase. There it is converted to glucose
by glucose phosphatase (same enzyme used
in gluconeogenesis. The glucose is
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 CARBOHYDRATE METABOLISM
JOSE S. BLAS, MD

transported from the ER to the cytosol.

Glucose 6-phosphatase, the same enzyme in
gluconeogenesis is inherently absent in
skeletal muscles.

3. REGULATION OF GLYCOGEN METABOLISM

a. Hormonal Regulation via Covalent
Modification of the Enzymes. The hormones
that affect activity of the enzymes include
glucagon, epinephrine and insulin
(Phosphorylation Dephosphorylation)
 Glucagon and epinephrine binds specific
hepatocyte G protein coupled receptors
(GPCRs) and activates adenylyl cyclase
which in turn catalyzes the synthesis of the
second messenger, cAMP.
 Cyclic AMP-dependent protein kinase A
(PKA) is activated and leads to activation of
phosphorylase kinase and glycogen
phosphorylase b to phosphorylase a
 Phosphorylation of glycogen phosphorylase
activates glycogenolysis and
dephosphorylation leads to inactivation of
glycogenolysis.
 Cyclic AMP is decreased phosphodiesterase
into 5’AMP and inhibits the phosphorylation
cascade of glycogenolysis. Insulin activates
phosphodiesterase opposing the effects of - Cascade Mechanism of Glucagon and Epinephrine
glucagon and epinephrine favoring b. Allosteric Regulation
glycogenesis and inhibiting glycogenolysis.  Glycogenesis is stimulated when substrate
 Protein kinase phosphorylates glycogen availability and energy levels are high,
synthase a (active) to glycogen synthase b whereas glycogenolysis is increased when
Glycogen synthase b can b reconverted to glucose and energy levels are low.
the active form by dephosphorylation.  Glycogen synthase b in both liver and
muscle is activated by glucose 6-P
 Glycogen phosphorylase a is
 inhibited by glucose 6-P as well as by ATP, a
high energy signal in the cell.
 In liver, but not muscle, free glucose is also
an allosteric inhibitor of glycogen
phosphorylase a.
 In muscle glycogen phosphorylase is active
in the presence of the high AMP.
 AMP binds to glycogen phosphorylase b,
causing Its activation with phosphorylation.
AMP also activates PFK-1 of glycolysis
allowing glucose from glycogenolysis to be
oxidized in the muscle

c. Activation of glycogen degradation by Calcium.

 Ca2+ is released into the cytoplasm in
muscle in response to neural stimulation
and in liver in response to epinephrine
binding to  1- adrenergic receptors.
 Calcium released from the sarcoplasmic
reticulum during contraction binds to
calmodulin and binds to Calmodulin. The
Ca- Calmodulin complex (Ca-CaM) activates
muscle phosphorylase kinase which
phosphorylates glycogen phosphorylase and
promote muscle glycogen degradation
producing glucose 6-P which then can enter
muscle glycolysis (Note: Epinephrine at β-

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adrenergic receptors signals through a rise
in cAMP, not Ca2+)
 Calcium activation of liver phosphorylase kinase.
Epinephrine released during stress binds to 1
adrenergic GPCR in hepatocytes leading to activation
of phospholipase C that hydrolyzes PIP 2 to
diacylglycerol (DAG) and IP3. IP3 causes movement
of Ca++ from the sarcoplasmic reticulum and forms
a Ca++-Calmodulin complex. DAG and Ca++
stimulates Protein kinase C.
Ca-Calmodulin complex stimulates phosphorylase
kinase and calmodulin dependent protein kinase.
These three kinases phosphorylate glycogen
synthase at different sites and decrease its activity
while increasing activity of glycogen phosphorylase
thereby promoting glycogenolysis.
4. Glycogen Storage Diseases
These are a group of genetic diseases that are
caused by defects in enzymes required for glycogen
degradation or, more rarely, glycogen synthesis.
They result either in formation of glycogen that has
an abnormal structure or in the accumulation of
excessive amounts of normal glycogen in specific
tissues as a result of impaired degradation.
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CARBOHYDRATE METABOLISM
JOSE S. BLAS, MD
A particular enzyme may be defective in a single
tissue, such as liver (resulting in hypoglycemia) or
muscle (causing muscle weakness), or the defect
may be more generalized, affecting a variety of
tissue. Important glycogen storage diseases include:
 Von Gierke’s (GS I) – Glucose 6
phosphatase deficiency
 Pompe’s Disease (GS II) – lysosomal
glucosidase deficiency
 Cori or Forbe’s (GS III) – Debranching
enzyme deficiency
 Andersen’s (GS IV), branching enzyme
deficiency
 McArdle’s (GS V) – muscle phosphorylase
deficiency
 Her’s (GS VI)- liver phosphorylase deficiency
VI. HEXOSE MONOPHOSPHATE
SHUNT (Pentose Phosphate Pathway)
1. Functions of the HMP Shunt The pentose
phosphate pathway is an alternative route for
the metabolism of glucose. It does not lead to
formation of ATP but has two major functions:
a. the formation of NADPH for reductive
synthesis of fatty acids, hydroxylation
reactions of steroids, detoxification
reactions.
b. the synthesis of ribose phosphate for
nucleotide and nucleic acid formation
2. The HMP Shunt operates in 2 phases:
a. Irreversible Oxidative phase - Glucose 6-
P is oxidized by G-6P dehydrogenase,
the rate limiting step of the reaction
resulting in formation of NADPH, CO2
and ribulose 5 phosphate.
b. Reversible Non oxidative phase
consisting of series of sugar - phosphate
interconversions resulting in
isomerization of ribulose-5 phosphate to
ribose-5 phosphate and xylulose 5-
phosphate. Series of transketolation and
transaldolation yield fructose 6-
phosphate and glyceraldehyde 3
phosphate that may enter glycolysis or
converted back to glucose-6 phosphate
and re-enter the oxidative phase of the
HMP Shunt.
3. The regulation of the HMP Shunt is dependent on
the metabolic demand of the cell for NADPH for
reductive reactions and ribose phosphates for
nucleotide synthesis:
a. NADPH is an inhibitor of G6PD and
increased demand for NADP stimulates the
oxidative phase via G6PD stimulation. e.g.
exposure to oxidizing agents
b. Increased demand for ribose 5
phosphates stimulates the non-oxidative
phase
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VI. Uronic Acid Pathway
1. In the liver, the Uronic acid pathway, like the
HMP Shunt is an alternative oxidative pathway
for glucose that does not lead to the formation
of ATP.
2. The initial reactions in the Uronic Acid is similar
to glycogenesis when glucose 6-phosphate is
somerized to glucose-1 phosphate. Glucose-1
phosphate is activated by UTP to form
UDPGlucose. Oxidation of UDP Glucose forms
UDPGlucuronic acid, the active form of
glucuronic acid used in various reactions.
3. UDP Glucuronic acid is the source of glucuronate
for reactions involving its incorporation into
proteoglycans or for reaction with substrates
such as steroid hormones, bilirubin, and a
number of drugs that are excreted in urine or
bile as glucuronide conjugates. UDPGlucose acid
may be isomerized to UDP Galactose which is
used in the synthesis of lactose.
4. Glucuronate is reduced to L-gulonate, the direct
precursor of ascorbate in those animals capable
of synthesizing this vitamin, in an NADPH-
dependent reaction. In humans and other
primates, as well as guinea pigs, bats, and some
birds and fishes, -ascorbic acid cannot be
synthesized because of the absence of L-
gulonolactone oxidase.
5. L-gulonate continues with the pathway
ultimately forming xylulose 5 phosphate to link
the pathway to the non-oxidative phase of the
HMP shunt.
VII. Metabolism of other Monosaccharides
1. Fructose Metabolism
a. Fructose, is derived from the disaccharide
sucrose which when cleaved in the intestine,
releases equimolar amounts of fructose and
glucose. Fructose transport into cells is not
insulin dependent (unlike that of glucose into
certain tissues), and, in contrast to glucose,
fructose does not promote the secretion of
insulin.
b. Fructokinase primarily phosphorylates
fructose to fructose 1- PO4 because of its low
Km (high affinity for fructose) and high
Vmax. Deficiency of fructokinase causes
Essential fructosuria. Cleavage by aldolase b
forms DHAP and glyceraldehyde. Deficiency
aldolase b leads to Hereditary Fructose
Intolerance.
c. DHAP enters glycolysis or gluconeogenesis
and glyceraldehyde upon phosphorylation to-
glyceraldehyde 3-phosphate likewise enters
the glycolytic and gluconeogenetic pathway
d. The rate of fructose metabolism is more
rapid than that of glucose because the
trioses formed from fructose 1-PO4 bypass
PFK-1, the major rate-limiting step in
glycolysis.
e. Fructose can be synthesized from other
monosaccharide (glucose) via the sorbitol
pathway. Aldose reductase, which reduces
glucose, producing sorbitol, is found in many
tissues, including the lens, retina, Schwann
UST FMS MEDICAL BOARD REVIEW 2019
CARBOHYDRATE METABOLISM
JOSE S. BLAS, MD
cells of peripheral nerves, liver, kidney,
placenta, RBCs, and cells of the ovaries and
seminal vesicles. Sperm cells use fructose for
energy.
f. The pathway from sorbitol to fructose in the
liver provides a mechanism by which any
available sorbitol is converted into a
substrate that can enter glycolysis or
gluconeogenesis.
g. The accumulation of sorbitol in cells due to
increase glucose and NADPH results in
strong osmotic effects and, therefore, cell
swelling as a result of water retention. Some
of the pathologic alterations associated with
diabetes can be attributed, in part, to this
phenomenon, including cataract formation,
peripheral neuropathy, and microvascular
problems leading to nephropathy and
retinopathy.
2. Galactose Metabolism
a. The major dietary source of galactose is
lactose (galactosyl β-1,4-glucose) obtained
from milk and milk products. Some lactose
can also be obtained by lysosomal
degradation of complex carbohydrates, such
as glycoproteins and glycolipids, which are
important membrane components. Like
fructose, the transport of galactose into cells
is not insulin dependent.
b. Phosphorylation of galactose by
galactokinase to galactose -1- phosphate is
the initial reaction followed by formation of
UDP galactose thru an exchange reaction
with UDP Glucose catalyzed by galactose 1-
phosphate uridyltransferase (GALT).
Deficiency of this enzyme causes
galactosemia.
c. UDP Galactose can be epimerized to UDP
Glucose and find its way in Glycogenesis.
UDP Galactose may be used as sugar donor
in lactose synthesis.
d. In lactose intolerance, galactose cannot be
produced from lactose due to deficiency of
lactase which leads to osmotic diarrhea and
flatulence, production of organic acids due
to lactose fermentation by intestinal
bacteria.
3. Mannose Metabolism
a. Mannose is initially phosphorylated to
Mannose-6 P and then isomerized to
Fructose 6-P, which then enters the EMP.
b. GDP Mannose is used in substances
requiring mannose.
REFERENCES:
 Greenstein, Ben, Greenstein Adam, Medical
Biochemistry at a Glance. University Press, Cambridge
1996
 Liebermann, Michael et al. Marks’ Basic Medical
Biochemistry, A Clinical Approach, 4th edition
Lippincott Williams and Wilkins, 2013
 Rodwell Victor, Bender David et al. Harper’s
Illustrated Biochemistry 31sr edition, International
edition. Lange.
 Wilcox. R. Bruce. High Yield Biochemistry. Lippincott
Williams and Wilkins.
7 | BIOCHEMISTRY

CHOOSE THE BEST ANSWER:
_____ 1. Which of the following statements is
correct of carbohydrate digestion?
A. Salivary amylase acts on  1,4 and 1,6
glycosidic bonds of starch
B. Specific disaccharidases in the brush
border of the intestines produce
monosaccharides as final products
C. Cellulose are degraded into dextrins and
oligosaccharides upon digestion
D. The acidic pH of the stomach helps in
digestion by denaturing dietary
saccharides
_____ 2. The absorption and transport of glucose
across the lumen of the gastrointestinal tract is:
A. Through facilitative diffusion
B. Co-transported with sodium, coupled
with Na-K ATPase pump
C. Dependent on insulin
D. Enhanced by phosphorylation of glucose
to glucose -6 phosphate
_____ 3. Hexokinase differs from glucokinase in
which of the following points?
A. Hexokinase is an insulin inducible
enzyme
B. Glucokinase is inhibited by its product,
glucose-6-phosphate
C. Hexokinase has a higher Km for glucose
D. Glucokinase phosphorylates glucose
when glucose concentration is high
_____ 4. The rate limiting and committed step in
glycolysis is:
A. In the energy investment phase of
glycolysis
B. catalyzed by phosphofructokinase-2
C. activated by ATP and a high energy
charge
D. coupled with substrate level
phosphorylation
_____ 5. In the presence of limiting amounts of
oxygen, pyruvate is metabolized into:
A. Oxaloacetic acid
B. acetylCoA
C. Lactic acid
D. Alanine
_____ 6. This glycolytic intermediate in the
erythrocyte enhances the oxygen delivery to the
peripheral tissues:
A. Phosphoenolpyruvate
B. 1,3 bisphosphogylcerate
C. 2,3 bisphosphoglycerate
D. dihydrohyacetone phosphate (DHAP)
_____ 7. Which of the following is true of the
pyruvate dehydrogenase reaction?
A. A mitochondrial enzyme complex
B. Active when covalently modified by
phosphorylation
C. Starts the TCA Cycle
D. Catalyzes a reversible reaction
UST FMS MEDICAL BOARD REVIEW 2019
REVIEW TEST
JOSE S. BLAS, MD
_____ 8. The total number of ATPs produced per
turn of the TCA Cycle per mole of glucose is:
A. 15
B. 12
C. 30
D. 24
_____ 9. The complete oxidation of a mole of
glucose-6- phosphate into carbon dioxide and water,
using the Malate Aspartate Shuttle is:
A. 36
B. 37
C. 38
D. 39
_____ 10. Which of the following reactions in the
TCA Cycle is coupled with substrate level
phosphorylation?
A. malate dehydrogenase
B. succinylCoA synthase (thiokinase)
C. - keto glutarate dehydrogenase
D. succinate dehydrogenase
_____ 11. Which of the following is the major
anaplerotic reaction?
A. Fumarase
B. Pyruvate carboxylase
C. Glutamate dehydrogenase
D. Pyruvate kinase
_____ 12. Which of the following cannot be used as
substrate for glucose synthesis?
A. Lactate
B. Acetate
C. Glycerol
D. Pyruvate
_____ 13. All of the following enzymes are unique to
gluconeogenesis, EXCEPT?
A. Pyruvate carboxylase
B. PEP carboxykinase
C. Fructose 2,6 bisphosphatase
D. Glucose-6 phosphatase
_____ 14. Which of the following conditions will
favor gluconeogenesis over glycolysis?
A. High energy charge
B. Fructose 2,6 bisphosphate
C. Hyperglycemia
D. High insulin/ glucagon ratio
_____ 15. Which is the difference between liver
glycogen and muscle glycogen?
A. Muscle glycogen concentration is higher
per dry weight of tissue
B. Liver glycogen maintains blood glucose
level during fasting
C. Muscle glycogen is structurally different
from liver glycogen
D. Liver glycogen synthesis involves
addition of glucosyl units to nonreducing
end of glycogen primer
| BIOCHEMISTRY
 REVIEW TEST
JOSE S. BLAS, MD

_____ 16. Which of the following cellular conditions _____ 22. Which of the following is true of fructose
or scenarios is compatible with increased metabolism?
glycogenolysis and decreased glycogenesis? A. Enters glycolysis as dihydroxyacetone 3
A. Increased 3’5’ cAMP dependent protein phosphate
kinase activity B. Slower rate of metabolism compared to
B. Dephosphorylation of glycogen synthase glucose
enzyme C. Initially phosphorylated to fructose 6
C. Decreased glucagon/insulin ratio phosphate
D. Increased glucose -6-phosphate D. Intestinal absorption via Na-symport
system.
_____ 17. Epinephrine can promote liver
glycogenolysis upon binding to  adrenergic _____ 23. Galactose enters glucose metabolism as:
receptors and cause: A. Glucose- 6 phosphate
A. Increased cyclic AMP dependent protein B. Uridine Diphosphate Glucose (UDPG)
kinase activity C. Galactose -1- phosphate
B. Inositol triphosphate (IP3)- mediated D. Fructose 1,6 bisphosphate
calcium - Calmodulin stimulation of
phosphorylase kinase _____ 24. Mannose enters the mainstream of
C. Increase 5’ AMP concentration glycolysis thru:
D. Phosphorylation of glycogen synthase A. glucose-6 phosphate
enzyme B. fructose-6-phosphate
C. fructose-1-phosphate
_____ 18. Which of the following Glycogen Storage D. glucose-1-phosphate
diseases is characterized by fasting hypoglycemia,
acidosis, lipemia, hyperuricemia but with normal
liver glycogen structure?
A. Von Gierke’s disease
B. Andersen’s disease
C. Pompe’s disease
D. Mc Ardle’s Disease

_____ 19. The Hexose Monophosphate Shunt is

important in nucleotide metabolism because it
provides:
A. Ribose 5 phosphate
B. NADPH
C. C and N atoms in purine/pyrimidine ring
de novo synthesis
D. Intermediates for glycolysis

_____ 20. Intake of oxidant drugs by Glucose-6-

Phosphate dehydrogenase deficient patents leads to
hemolytic anemia. Decreased levels of which of the
following is a consequence of the enzyme deficiency
and the cause of hemolysis?
A. Glucose – 6-phosphate
B. NADP
C. Reduced glutathione
D. Ribose-5 phosphate

_____ 21. The important function of the Uronic Acid

Pathway in man:
A. Synthesis of ascorbic acid
B. Alternate pathway of glycolysis
C. Source of sugar acids for proteoglycan
D. Provision of sugar alcohols for synthesis
of monosaccharides

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 LIPID METABOLISM
JUDELYN T. UY, MD

GENERAL CHARACTERISTICS OF FATTY ACIDS

1. ‘Free’’ or esterified to glycerol
2. Usually have an even number of Carbon atoms,
(16 to 20), saturated or unsaturated (containing
double bonds).
3. Described by the number of carbons and the
positions of the double bonds (e.g., arachidonic
acid, which has 20 carbons and 4 double bonds,
is 20:4,Δ5,8,11,14).

Figure 2. The Citrate Cleavage Pathway.

C. Fatty Acid Synthesis

1. Glucose is the major precursor via acetyl CoA.
FATTY ACID SYNTHESIS
2. Synthesis involves a sequential addition of 2
A. Glucose is the Major Precursor for Fatty
carbon units, as Acetyl CoA, to the growing
Acid Synthesis (Figure 1)
chain.
1. Dietary carbohydrates in excess of that needed
for energy production and glycerol synthesis
3. Fatty acid synthase (FAS) is a multi-enzyme
is converted to fatty acids in the liver during
complex located in the cytosol composed of
the fed state.
two large identical subunits with 7 catalytic
activities.
2. Glucose provides the carbon (via acetyl-CoA)
for fatty acid synthesis and the reducing
4. This enzyme contains a phosphopantetheine
equivalents in the form of NADPH (pentose
residue, derived from the vitamin pantothenic
phosphate pathway) required for the process.
acid (B5), and a cysteine residue; both contain
sulfhydryl groups that can form thioesters with
acyl groups.

5. The growing fatty acyl chain moves during the

synthesis of two carbon units from one to the
other of these sulfhydryl residues as it is
elongated.

6. The initial step is the formation of Malonyl CoA

– rate limiting step catalyzed by Acetyl CoA
carboxylase (ACC; Figure 3 and 4)

Figure 1. Lipogenesis, the synthesis of fatty acids

(FA) and triacylglycerols (TAG) from glucose, occurs
Fig 3. Formation of Malonyl CoA by Acetyl CoA
mainly in the liver. (BRS, Biochemistry, Molecular
Carboxylase
Biology and Genetics 5th Edition)

B. The Citrate Cleavage Pathway provides

Acetyl CoA and NADPH for Lipogenesis in
the cytosol (Figure 2)
1. Citrate from the TCA is transported across the
mitochondrial inner membrane via the
tricarboxylate or citrate transporter. It is then
cleaved in the cytosol by ATP-citrate lyase
(citrate cleaving enzyme) to form acetyl CoA
and oxaloacetate.
Acetyl CoA carboxylase
2. The oxaloacetate formed is then reduced to is regulated by
Malate by the cytosolic form of NAD Malate phosphorylation and
dehydrogenase. Malate then undergoes allosteric controls
oxidative decarboxylation to pyruvate,
catalyzed by NADP Malate dehydrogenase
Figure 4. Regulation of Acetyl CoA Carboxylase
(malic enzyme).
(ACC)
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7. Addition of two-carbon units (Figure 5)
a. Initially, a priming molecule of acetyl CoA
reacts with the phosphopantetheinyl
residue, and then the acetyl group is
transferred to the cysteinyl residue.
b. The acetyl group on the FAS complex
condenses with the malonyl group; the CO2
that was added to the malonyl group by
- provides the glycerol moiety that reacts with 2
ketoacyl group, now containing four
carbons, is produced.
Figure 5. Synthesis of Palmitic Acid
8. Reduction of the β-ketoacyl group
a. The β-ketogroup is reduced by NADPH to a
β-hydroxyl group.
b. Then dehydration occurs, producing a double
bond between carbons 2 and 3.
c. Finally, the double bond is reduced by
NADPH, and a four-carbon acyl group is
formed.
d. NADPH is generated from the pentose
phosphate pathway and malic enzyme.
9. Elongation of the growing fatty acyl chain
(Figure 6)
a. The acyl group is transferred to the cysteinyl
sulfhydryl group, and malonylCoA reacts
with the phosphopantetheinyl group.
b. Condensation of the acyl and malonyl
groups releases CO2, followed by 3 reactions
reducing the β-keto group. The chain grows
by two carbons.
c. This sequence of reactions repeats until the
growing chain is 16 carbons in length.
d. Palmitate, a 16-carbon saturated fatty acid,
is the final product released by hydrolysis
from the fatty acid synthase complex.
Figure 6. Elongation of the growing fatty acyl chain
UST FMS MEDICAL BOARD REVIEW 2019
LIPID METABOLISM
JUDELYN T. UY, MD
SYNTHESIS OF TRIACYLGLYCEROL (TAG)
A. In intestinal epithelial cells, TAG synthesis occurs
by a different pathway than in other tissues
becoming a component of chylomicrons.
Ultimately, the fatty acyl groups are stored in
adipose TAGs.
B. In liver and adipose tissue, glycerol 3-PO4
fatty acyl CoA molecules to form phosphatidic
acid. The phosphate group is cleaved to form a
diacylglycerol, which reacts with another fatty
acyl CoA to form a TAG.
1. The liver can use glycerol to produce glycerol
3-phosphate by a reaction that requires ATP
and is catalyzed by glycerol kinase.
2. Adipose tissue, which lacks glycerol kinase,
cannot generate glycerol 3-phosphate from
glycerol.
3. Both liver and adipose tissue can convert
glucose, through glycolysis, to DHAP, which is
reduced by NADH to glycerol 3-PO4 (Figure 7).
TAG is stored in adipose tissue.
4. In the liver, TAG is incorporated into very low-
density lipoprotein (VLDL), entering blood.
Ultimately, fatty acyl groups are stored in
adipose TAGs.
5. Fatty acids released from chylomicrons and
VLDL by lipoprotein lipase are taken up by
adipose cells and converted to TAGs, but
glycerol is not used because adipose tissue
lacks glycerol kinase.
6. Glucose, transported into adipose cells as
influenced by insulin, is converted to DHAP
and reduced by NADH to form glycerol 3-PO4,
which produces the glycerol moiety of the
TAG. The TAGs are stored in large fat globules
in adipose cells.
Figure 7. Glycerol 3-PO4 from liver and adipose
7. In the fasted state in adipose tissue and liver,
glycerol 3-PO4 is derived from
glyceroneogenesis. The key enzyme in this
process is phosphoenolpyruvate (PEP)
carboxykinase, which is induced in the liver
and adipose tissue in the fasted state. PEP
carboxykinase converts oxaloacetate from TCA
to phosphoenolpyruvate (PEP). PEP is
converted to DHAP and then to glycerol-3-PO4
which is used for TAG synthesis. (Figure 8)
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Figure 8. Glyceroneogenesis in the liver and adipose
FATTY ACID OXIDATION
A. Initial step involves activation of the fatty acid in
the cytoplasm prior to oxidation in the
mitochondria.
Fatty acid + ATP + CoA ----> Acyl-CoA + PPi
+AMP
B. Cytosolic fatty acyl CoA reacts with carnitine in
the outer mitochondrial membrane, forming fatty
acyl carnitine via carnitine acyl transferase I (CAT
I), also called carnitine palmitoyl transferase I
(CPT I). Fatty acyl carnitine passes to the inner
membrane, where it reacts with carnitine acyl
transferase II (CAT II) to reform fatty acyl CoA,
which enters the mitochondrial matrix. (Figure 9)
Figure 9. Transport of long chain Fatty Acyl CoAs in
mitochondria
C. Beta (β)-Oxidation of even chain fatty acids
is a four-step spiral (Figure 10)
1. Dehydrogenation- the first step is the removal
of two hydrogen atoms (dehydrogenation)
catalyzed by acyl-CoA dehydrogenase and
requiring FAD. This results in the formation of
Δ2-trans-enoyl-CoA and FADH2.
2. Hydration - water is then added to saturate
the double bonds (hydration) and form 3-
hydroxyacyl-CoA, catalyzed by Δ2-enoyl-CoA
hydratase.
3. Dehydrogenation - the 3-hydroxy derivative
undergoes further dehydrogenation on the 3-
carbon catalyzed by L-β-3-hydroxyacyl-CoA
dehydrogenase to form the corresponding 3-
ketoacyl-CoA compound. The coenzyme
utilized in this reaction step is NAD+ which is
reduced to NADH + H+.
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LIPID METABOLISM
JUDELYN T. UY, MD
4. Thiolysis - in the final step, 3-ketoacyl-CoA is
split at the 2,3 position by 3-ketoacyl-CoA-
thiolase, forming acetyl-CoA and a new acyl-
CoA which is two carbons shorter than the
original acyl-CoA molecule.
Each round of β-oxidation produces one mole of
NADH, one mole of FADH2 and one mole of acetyl-
CoA. The acetyl-CoA, the end product of each round
of β-oxidation, then enters the TCA cycle, where it is
further oxidized to CO2 with the concomitant
generation of three moles of NADH, one mole of
FADH2 and one mole of ATP. The NADH and FADH 2
generated during the lipid oxidation and acetyl-CoA
oxidation in the TCA cycle then can enter the
respiratory pathway for the production of ATP. The
oxidation of fatty acids yields significantly more
energy per carbon atom than does the oxidation of
carbohydrates.
Figure 10. Beta (β)-Oxidation of even chain fatty
acids
KETONE BODY SYNTHESIS AND UTILIZATION
A. Occurs in liver mitochondria when fatty acids are
in high concentration in the blood (during fasting,
starvation, or as a result of a high-fat diet).
B. Ketone bodies: (Figure 11)
a. Acetoacetate  Acetone
b. β-hydroxybutyrate
C. STEPS:
1. Two molecules of acetyl CoA condense to
produce acetoacetyl CoA. This reaction is
catalyzed by thiolase.
2. Acetoacetyl CoA and acetyl CoA form
hydroxymethylglutaryl CoA (HMG-CoA) in a
reaction catalyzed by HMG-CoA synthase.
3. HMG-CoA is cleaved by HMG-CoA lyase to
form acetyl CoA and acetoacetate.
4. Acetoacetate can be reduced by an NAD-
requiring dehydrogenase (3-hydroxybutyrate
dehydrogenase) to 3-hydroxybutyrate (also
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 LIPID METABOLISM
JUDELYN T. UY, MD

known as b-hydroxybutyrate). This is a

reversible reaction.

5. Acetoacetate is also spontaneously

decarboxylated in a nonenzymatic reaction,
forming acetone (the source of the odor on
the breath of ketotic diabetic patients).

Figure 12. Ketone Body Utilization

LIPID METABOLISM IN FASTING STATE

A. Mobilization of stored TAGs in the adipose is
initiated by hormone-sensitive lipase. This
enzyme is activated when it is phosphorylated by
cAMP-dependent protein kinase A. Conversely,
insulin inhibits the activity of this enzyme by
inducing dephosphorylation. (Figure 13)

B. Increase in epinephrine and glucagon elevates

Figure 11. Ketone Body Synthesis
D. The liver lacks the enzyme needed to metabolize
ketone bodies (succinyl CoA-acetoacetate- CoA
transferase, so it cannot use the ketone bodies
it produces. Therefore, acetoacetate and 3-
hydroxybutyrate are released into the blood by
the liver.
cAMP and activates protein kinase A.
1. Adipose – activation of hormone sensitive
lipase and perilipin by phosphorylation
2. Liver – decrease in fatty acid synthesis due to
inhibition of ACC via cAMP-dependent
phosphorylation
3. Glycolysis – inhibited which decreases supply
of acetyl CoA
4. Ketogenesis - stimulated due to increased FA
oxidation and increased enzymes for
ketogenesis

E. During starvation, ketone bodies released from

the liver in the blood increase to a level that
permits entry into brain cells, muscle and kidney
where they are oxidized.

F. Acetoacetate can enter cells directly, or it can be

produced from the oxidation of 3-
hydroxybutyrate by 3-hydroxybutyrate
dehydrogenase. NADH is produced by this
reaction and can generate adenosine
triphosphate (ATP).

G. Acetoacetate is activated by reacting with

Succinyl CoA to form acetoacetylCoA and
succinate. The enzyme is succinyl CoA-
acetoacetate-CoA transferase. Finally,
acetoacetyl CoA is cleaved by thiolase to form
two acetyl CoA’s, which enter the TCA cycle and Figure 13. Hormone-induced fatty acid mobilization
are oxidized to molecules of CO2. (Figure 12) in adipocytes

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 LIPID METABOLISM
JUDELYN T. UY, MD

LIPID METABOLISM IN FED STATE

A. After a meal that contains lipids, carbohydrates
and proteins, the dietary lipid is deposited as TAG
in adipose tissue. The dietary carbohydrates and
proteins in excess of that required for energy or
for protein synthesis are converted into fatty
acids and deposited in adipose tissue as TAGs.
F. The ring structure of cholesterol cannot be
degraded in the body. The bile salts in the feces
are the major form in which the steroid nucleus is
excreted.

B. Insulin, the major anabolic hormone is required

for both fatty acid synthesis and for the formation
of TAG in adipose tissue. This hormone acts at
two levels:
1. Long term regulation
a. Promotes fatty acid synthesis through
increase in the levels of key enzymes in the
liver:
 Fatty acid synthase
 NADP-malate dehydrogenase (malic
enzyme)
 Acetyl CoA carboxylase
b. Stimulates synthesis of oxidative enzymes
in HMP to generate NADPH for fatty acid
synthesis.
c. Promotes glucose uptake via GLUT 4
transporter in adipose to provide glycerol-
3-PO4 for TAG synthesis

2. Short term regulation

a. Promotes activation of phosphoprotein Figure 14 Synthesis of Mevalonate
phosphatase in the liver, which activates
ACC through dephosphorylation.
b. Dephosphorylation of key enzymes in the
adipose inactivates the hormone sensitive
lipase and perilipin

CHOLESTEROL AND BILE SALT METABOLISM

A. Cholesterol is synthesized from cytosolic acetyl
coenzyme A (CoA) derived from Glucose. (Figure
14) Cytosolic acetyl CoA forms acetoacetyl CoA,
which condenses with another acetyl CoA to form
HMG-CoA.

B. Cytosolic HMG-CoA, a key intermediate in

cholesterol biosynthesis, is reduced in the
endoplasmic reticulum to mevalonic acid by the
regulatory enzyme HMG-CoA reductase.

C. HMG-CoA reductase is inhibited by cholesterol,

and phosphorylation by (AMP)-activated protein
kinase. In the liver, HMG-CoA reductase is also
inhibited by bile salts and is induced when blood
insulin levels are elevated. (Figure 16)

D. Mevalonic acid is phosphorylated and

decarboxylated to form the five-carbon (C-5)
isoprenoid, isopentenyl pyrophosphate. Two
isopentenyl pyrophosphate units condense, Figure 15a. Synthesis of Squalene
forming a C-10 compound, geranyl
pyrophosphate, which reacts with another C-5
unit to form a C-15 compound, farnesyl
pyrophosphate.

E. Squalene is formed from two C-15 units and then

oxidized and cyclized, forming lanosterol which is
converted to cholesterol in a series of steps.
(Figure 15a and 15b)
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Figure 15b. Synthesis of Cholesterol
Figure 16. Regulation of HMG CoA reductase activity
G. Bile acids are synthesized in the liver from
cholesterol through the rate-limiting step
catalyzed by 7α-hydroxylase forming 7α-hydroxyl
cholesterol.
H. The primary bile acids, chenodeoxycholic acid
and cholic acid are acted upon by bacteria and
converted to the secondary bile acids in the
intestines. The secondary bile acids are
deoxycholate (from cholate) and lithocholate
(from chenodeoxycholate). Both primary and
secondary bile acids are reabsorbed by the
intestines and delivered back to the liver via the
portal circulation.
I. Bile salts are formed by conjugation of the
carboxyl groups of bile acids via an amide bond
to either glycine or taurine prior to secretion into
the bile canaliculi.
LIPOPROTEIN METABOLISM (FIGURE 17)
A. Four major groups of lipoproteins
1. CHYLOMICRONS
2. VLDL or (pre-β-lipoprotein)
3. LDL or (β-lipoprotein)
4. HDL or (α-lipoprotein)
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LIPID METABOLISM
JUDELYN T. UY, MD
B. Chylomicrons are synthesized in intestinal
epithelial cells. Their triacylglycerols are derived
from dietary lipid, and their major apoprotein is
apo B-48.
1. Chylomicrons travel through the lymph into
the blood. Apo C-II, the activator of
lipoprotein lipase, and apo E are transferred to
nascent chylomicrons from HDL, and mature
chylomicrons are formed.
2. In peripheral tissues, particularly adipose and
muscle, the triacylglycerols are digested by
lipoprotein lipase. As the chylomicron loses
triacylglycerol, a chylomicron remnant is
formed. The chylomicron remnants interact
with receptors on liver cells and are taken up
by endocytosis. The contents are degraded by
lysosomal enzymes, and the products (amino
acids, fatty acids, glycerol, cholesterol, and
phosphate) are released into the cytosol and
reused.
C. VLDL is synthesized in the liver, particularly after
a high-carbohydrate meal. It is formed from
TAGs that are packaged with cholesterol,
apoproteins (particularly apo B-100), and
phospholipids, and it is released into the blood.
1. In peripheral tissues, particularly adipose and
muscle, VLDL triacylglycerols are digested by
lipoprotein lipase, and VLDL is converted to
IDL.
2. IDL returns to the liver, is taken up by
endocytosis, and is degraded by lysosomal
enzymes. IDL can also be further degraded,
forming LDL.
D. LDL reacts with receptors on various cells, is
taken up by endocytosis, and is digested by
lysosomal enzymes.
1. Cholesterol, released from cholesterol esters
by a lysosomal esterase, can be used for the
synthesis of cell membranes or for the
synthesis of bile salts in the liver or steroid
hormones in endocrine tissue.
2. Cholesterol inhibits HMG-CoA reductase and,
thus, decreases the rate of cholesterol
synthesis by the cell.
3. Cholesterol inhibits synthesis of LDL receptors
(downregulation) and, thus, reduces the
amount of cholesterol taken up by cells.
4. Cholesterol activates acyl: cholesterol
acyltransferase (ACAT), which converts
cholesterol to cholesterol esters for storage in
cells.
E. HDL is synthesized by the liver and released into
the blood as small, disk-shaped particles. The
major protein of HDL is apo A.
1. ApoC-II, which is transferred by HDL to
chylomicrons and VLDL, serves as an activator
of lipoprotein lipase.
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 LIPID METABOLISM
JUDELYN T. UY, MD

2. Apo E is also transferred and serves as a B. Degradation of phosphoglycerides (Figure

recognition factor for cell surface receptors. 18)
Apo C-II and apo E are transferred back to
HDL after digestion of triacylglycerols of
chylomicrons and VLDL.

3. Cholesterol, obtained by HDL from cell

membranes or from other lipoproteins, is
converted to cholesterol esters within the HDL
particle by the lecithin:cholesterol
acyltransferase (LCAT) reaction, which is
activated by apo A-I.

4. As cholesterol esters accumulate in the core of

the lipoprotein, HDL particles become
spheroidal. Figure 18. Degradation of Phosphoglycerides

C. Sphingolipidoses (Table 1)
5. HDL transfers cholesterol esters to other
lipoproteins in exchange for various lipids via
Cholesterol ester transfer protein (CETP). Table 1. Sphingolipidoses
VLDL and other lipoproteins carry the Disease Enzyme Major Symptoms
cholesterol esters back to the liver. Deficiency
GM1 GM1 Mental retardation, liver
6. HDL particles and other lipoproteins are taken Gangliosid β- enlargement, skeletal
up by the liver by endocytosis and hydrolyzed osis Galactosidas involvement, death by
by lysosomal enzymes. e age 2
Tay-Sachs Hexosamini- Mental retardation,
7. Cholesterol, released from cholesterol esters, Disease dase A blindness death by age
can be packaged by the liver in VLDL and 3
released into the blood or converted to bile Fabry’s α- Skin rash, kidney
salts and secreted into the bile. Disease Galactosidas failure, pain in lower
e extremities
Sandhoff’s Hexosamini Similar to Tay-Sach’s
Disease da-ses A Disease but more
and B rapidly progressing
Gaucher’s Glucocerebr Liver and Spleen
Disease osidase enlarge-ment, long
bone erosion, infantile
mental retardation
Niemann- Sphingomye Liver and Spleen
Pick li-nase enlarge-ment, mental
Disease retardation
Farber’s Ceramidase Painful and
Lipogranul progressively deformed
o-matosis joints, skin nodules,
early death
Krabbe’s Galactocere- Loss of myelin, mental
Disease brosidase retardation, death by
age 2
Sulfatide Arylsulfatas Mental retardation,
Lipidosis eA death in first decade
Figure 17. Transport of Cholesterol between Tissues
IMPORTANT ASPECTS OF EICOSANOID
IMPORTANT ASPECTS OF METABOLISM
PHOSPHOGLYCERIDE AND SPHINGOLIPID
METABOLISM A. Prostaglandins, Prostacyclins, and
A. Respiratory distress syndrome (RDS) of the Thromboxanes (Figure 19)
newborn occurs in premature infants due to a 1. Arachidonic acid, derived from membrane
deficiency of surfactant in the lungs, which leads phospholipids, is the major precursor for
to a decrease in lung compliance. Dipalmitoyl synthesis of the Prostaglandins.
phosphatidylcholine (DPPC, also called lecithin),
is the primary phospholipid in surfactant, which 2. The polyunsaturated fatty acid is cleaved from
lowers surface tension at the alveolar air–fluid the membrane phospholipid by phospholipase
interface. Surfactant is normally produced at A2, which is inhibited by the steroidal anti-
gestational week 30. inflammatory agents (steroids).

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 LIPID METABOLISM
JUDELYN T. UY, MD

3. Oxygen is added, and a five-carbon ring is

formed by the enzyme cyclooxygenase, which
produces the initial prostaglandin. The initial
prostaglandin is converted to other classes of
prostaglandins and to the thromboxanes.
Aspirin, acetaminophen, and other NSAIDS
inhibit this isozyme of cyclo-oxygenase.

4. The prostaglandins are identified as PG and

the thromboxanes as TX. Prostaglandin PGI2 is
also known as prostacyclin. The subscript 2 in
each molecule refers to the number of -C=C-
present.

5. Certain prostacyclins (PGI2), produced by

vascular endothelial cells, inhibit platelet
aggregation, whereas certain thromboxanes
(TXA2) promote platelet aggregation. Aspirin
has been shown to be cardioprotective in
myocardial infarction. Although PGI2 is also
inhibited, the cardioprotective effect is
mediated by inhibiting TXA2.
B. Leukotrienes (Figure 20)
1. Arachidonic acid, derived from membrane
phospholipids, is the major precursor for
synthesis of the leukotrienes.
2. In the first step, oxygen is added by
lipoxygenases, and a family of linear
molecules, hydroperoxyeicosatetraenoic acids
(HPETEs), is formed. A series of compounds,
comprising the family of leukotrienes, is
produced from these HPETEs. The
leukotrienes are involved in allergic reactions.
Figure 20. Synthesis of the clinically relevant
leukotrienes from arachidonic acid through the
Lipoxygenase Pathway.
REFERENCE:
SWANSON, et al. Basic Review Series Biochemistry,
Molecular Biology and Genetics 5th edition.
Lierberman, and Ricer. BRS Biochemistry, Molecular
Biology and Genetics, 6th ed copyright 2014
Ferrier. Lippincott’s Illustrated Review Biochemistry
6th ed copyright 2014
Murray et al. Harper’s Illustrated Biochemistry, 29th
ed copyright 2012
Nelson and Cox. Lehninger Principles of Biochemistry
5th edition copyright 2008

3. The leukotrienes are identified as LT. The Nelson and Cox. Lehninger Principles of Biochemistry
leukotrienes, LTC4, LTD4, LTE4 and LTF4 are 6th edition
known as the peptidoleukotrienes because of
the presence of amino acids. The Lieberman and Mark’s Basic Medical Biochemistry, A
peptidoleukotrienes, LTC4, LTD4 and LTE4 are Clinical Approach, 3rd ed copyright 2009
components of slow-reacting substance of
anaphylaxis The subscript 4 in each molecule
refers to the number of -C=C- present.

Figure 19. Synthesis of the clinically relevant

prostaglandins and thromboxanes from arachidonic
acid through the Cyclooxygenase Pathway.

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CHOOSE THE BEST ANSWER:
1. _____ CH3(CH2)4CH=CHCH2CH=CH(CH2)7COOH
What can be deduced from the structural formula of
this fatty acid?
A. Conjugated double bonds exist either in cis
or trans configuration.
B. Delta system of nomenclature reads the
fatty acid as C18:2 Δ (9,12)
C. Hydrocarbon chain is entirely linear in
arrangement
D. Omega (Ω) carbon is also the carboxylic
carbon
2. _____ Which statement is true regarding Citrate
Cleavage Pathway in relation to lipogenesis?
A. Acetyl CoA generated from the pathway
enters the krebs cycle in the mitochondria
B. Citrate is transported and cleaved in the
cytosol to provide acetyl CoA for
biosynthesis of fats
C. It provides the reducing equivalents, NADH
+ H+ required for lipogenesis
D. Malic enzyme utilizes NADPH from the
hexose monophosphate shunt
3. _____ What is the activity of acetyl-CoA
carboxylase?
A. Controlled by the presence of citrate
B. Inhibited by carnitine
C. Increased by epinephrine and glucagon
D. Unregulated at all times
4. _____ Which of the following statements correctly
describes lipogenesis?
A. Primary source of carbons for fatty acid
synthesis is glycerol
B. Fatty acids are synthesized from acetyl CoA
in the mitochondria
C. Fatty acid synthesis and esterification occurs
primarily in muscle cells
D. Fatty acyl chain on the fatty acid synthase
complex is elongated two carbons at a time
5. _____ Glyceroneogenesis is an important source
of glycerol-3-PO4 in the liver and adipose during
fasting. Which key enzyme is involved?
A. Glycerol-3-phosphatase
B. Glycerol-3-phosphate dehydrogenase
C. Glycerol kinase
D. Phosphoenolpyruvate carboxykinase
6. _____ Prior to betaoxidation, what does activation
of fatty acids to fatty acyl-CoAs require?
A. Breakdown of long chain fatty acids into
short and medium chains
B. Condensation with an acyl carrier protein
(ACP)
C. Hydrolysis of ATP to AMP + PPi
D. Transport of free fatty acids into the inner
mitochondrial membrane
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REVIEW TEST
JUDELYN T. UY, MD
7. _____ The first dehydrogenation step in
betaoxidation involves:
A. Addition of water to trans Δ2 enoyl CoA
B. Condensation of malonyl CoA with an acetyl
CoA primer
C. Formation of a double bond between the α
and β carbons of acyl CoA
D. Thiolytic cleavage β-ketoacyl CoA to yield
acetyl CoA.
8. _____ How many moles of acetyl CoA will be
produced from the complete degradation of a 16-
carbon fatty acid such as palmitic acid?
A. 7
B. 8
C. 9
D. 10
9. _____ How many moles of ATP are generated by
the complete oxidation of 1 mole of Palmitate?
A. 35
B. 96
C. 129
D. 131
10. _____ "Ketone Bodies" are produced:
A. In the liver by the condensation of acetyl-CoA
and acetoacetyl-CoA
B. In the liver from α-ketoglutarate by excessive
stimulation of the TCA cycle
C. In the muscle as a result of the incomplete
oxidation of fatty acids
D. Only under abnormal conditions such as
starvation and diabetes
11. _____ Which metabolic process correctly
describes Lipid metabolism when the cell is in the
“Fed state”?
A. Accelerated rate of fatty acid degradation
B. Increased fatty acid and triacylglycerol
synthesis in the liver and adipose
C. Inhibition of fatty acid synthesis due
inactivation of the rate limiting enzyme
D. Rapid utilization of ketone bodies by the
extra-hepatic tissues
12. _____ Insulin affects Lipid metabolism by
activation of this metabolic process:
A. Fatty Acid mobilization from the adipocytes to
the brain and muscle cells
B. Glyceroneogenesis in the hepatocytes
C. Lipogenesis in the liver and adipose tissues
D. Triaclyglycerol hydrolysis in the adipose by
the Hormone Sensitive Lipase
13. _____ HDL is considered as good cholesterol
because it:
A. Inhibits formation of LDL from VLDL and IDL
B. Promotes degradation of cholesterol into bile
acids
C. Transports cholesterol from peripheral tissue
back to the liver
D. Transports cholesterol from the liver to the
peripheral tissues
| BIOCHEMISTRY
 REVIEW TEST
JUDELYN T. UY, MD

14. _____ The cholesterol lowering effect of the
Statins directly involves:
A. Decreased formation of foam cells by the
macrophages
B. Enhanced uptake of LDL-cholesterol by
peripheral cells
C. Increased production of HDL in the liver
D. Inhibits activity of HMGCoA reductase
15. _____ Which lipoproteins are the major carriers
of triacylglycerols?
A. Chylomicrons and VLDL
B. HDL and LDL
C. IDL and LDL
D. VLDL and LDL
16. _____ Apoprotein C-II is important in the
metabolism of chylomicrons and VLDL because:
A. Activates hepatic lipase
B. Acts as ligand for LDL-receptor-mediated
endocytosis
C. Helps clear the lipoproteins into remnants by
lipoprotein lipase
D. Promotes esterification of cholesterol into
esters by LCAT
17. _____ A 30-year-old man is diagnosed with an
acute middle cerebral artery stroke secondary to
atherosclerosis. Genetic studies show that he has
familial hypercholesterolemia, type II. Which defect
is seen in this type of hypercholesterolemia?
A. Defect in Apoprotein E2 synthesis
B. Deficiency of LDL receptor
C. Lipoprotein lipase deficiency
D. Overproduction of VLDL associated with
glucose intolerance
21. _____ An 11-year-old Ashkenazi Jewish girl
presents with an enlarged liver and spleen, low
white and red blood cell counts, bone pain, and
bruising. She is diagnosed with Gaucher disease.
Which of the following compounds is accumulating
in her lysosomes?
A. Ceramide
B. Galactocerebroside
C. Glucocerebroside
D. Sphingosine
22. _____ Aspirin is a nonsteroidal anti-inflammatory
drug that inhibits cyclooxygenase, an enzyme
required for the conversion of this compound from
arachidonic acid
A. HPETEs
B. Leukotrienes
C. Peptidoleukotrienes
D. Thromboxanes
23. _____ A 40-year-old woman has rheumatoid
arthritis and was prescribed prednisone. What is the
mechanism of action of this drug?
A. Inhibits conversion of arachidonic acid to
epoxides
B. Inhibits phospholipase A2
C. Promote activation of prostacyclins
D. Promote leukotriene formation from HPETEs

18. _____ A 25-year-old woman is diagnosed with

LCAT deficiency. LCAT is involved in which of the
following processes?
A. Converting cholesterol to cholesterol esters
B. Decreased uptake of cholesterol by
hepatocytes
C. Endocytosis of HDL particles into
hepatocytes
D. Transfer of cholesterol esters from HDL to
other lipoproteins

19. _____ What is the rate limiting step in the

biosynthesis of bile acids from cholesterol?
A. 7-α hydroxylation of the steroid nucleus
B. C-17 side chain cleavage to propionyl CoA
C. Conjugation with taurine and glycine
D. Esterification of C-3 OH group with a fatty
acid

20. _____ An infant born prematurely at 28 weeks is

diagnosed with respiratory distress syndrome due to
a deficiency of surfactant. Which type of
phospholipid is deficient in the surfactant of the
infant’s lung?
A. Dipalmitoyl phosphatidylcholine
B. Dipalmitoyl phosphatidylethanolamine
C. Dipalmitoyl phosphatidylglycerol
D. Dipalmitoyl phosphatidylserine

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I. STRUCTURE, CLASSIFICATION AND
FUNCTIONS OF AMINO ACIDS
A. Structure
B. Nomenclature
C. Classification
Essential Amino Acids: PVT TIM HALL
(Phenylalanine, Valine, Threonine,
Tryptophan, Isoleucine, Methionine,
Histidine, Arginine*, Leucine, Lysine)
D. Architecture: Levels of Structure
UST FMS MEDICAL BOARD REVIEW 2019
AMINO ACID METABOLISM
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS
E. The synthesis of new proteins
- requires amino acids. The primary source of
amino acids is dietary protein. Breakdown of
tissue proteins also provides amino acids.
F. Amino acids provide nitrogen-containing
substrates for the biosynthesis of:
1. Non-essential amino acids
2. Purines and pyrimidines
3. Porphyrins
4. Neurotransmitters and hormones
G. The carbon skeletons of the surplus amino
acids not needed for synthetic pathways
serve as fuel. They may be:
1. Oxidized in the tricarboxylic acid (TCA)
cycle to produce energy.
2. Used as substrates for gluconeogenesis.
3. Used as substrates for fatty acid
synthesis.
II. DIGESTION OF PROTEINS
A. Proteolytic enzymes (proteases) break down
dietary proteins into their constituent amino
acids in the stomach and the intestine. Many
of these digestive proteases are synthesized as
larger, inactive forms known as zymogens.
B. In the stomach, pepsin begins the digestion of
proteins by hydrolyzing them to smaller
polypeptides. The contents of the stomach pass
into the small intestine, where enzymes
produced by the exocrine pancreas act. The
pancreatic proteases (trypsin, chymotrypsin,
elastase, and the carboxypeptidases) cleave
the polypeptides into oligopeptides and amino
acids.
1 | BIOCHEMISTRY

C. Further cleavage of the oligopeptides to amino
acids is accomplished by intestinal enzymes that
include aminopeptidases located on the brush
border and other peptidases located within the
cells. Ultimately, the amino acids produced by
protein digestion are absorbed through the
intestinal epithelial cells and enter the
blood.
D. A large number of overlapping transport systems
exist for amino acids in cells: facilitative
transporters, sodium-linked tranporters,
which allow the active transport of amino
acids into cells.
E. Defects in amino acid transport can lead to
disease.
III. ADDITION AND REMOVAL OF AMINO
ACID NITROGEN
A. Transamination involves the transfer of an
amino group from one amino acid (which
is converted to its corresponding a-ketoacid)
to an a-ketoacid (which is converted to its
-amino acid). Thus, the
nitrogen from one amino acid appears in
another amino acid.
B. The enzymes that catalyze transamination
reactions are known as transaminases or
aminotransferases.
C. C. Glutamate and -ketoglutarate are
often involved in transamination reactions,
-ketoacid
pairs.
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AMINO ACID METABOLISM
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS
D. Transamination reactions are readily reversible
and can be used in the synthesis or the
degradation of amino acids.
E. Most amino acids participate in transamination
reactions. Lysine is an exception; it is not
transaminated.
F. Pyridoxal phosphate (PLP) serves as the
cofactor for transamination reactions. PLP is
derived from vitamin B6.
IV. REMOVAL OF AMINO ACID AS AMMONIA
- In comparison with carbohydrate and lipid
metabolism, the metabolism of amino acids
is complex. The body is concerned not only
with the fate of the carbon atoms of the
amino acids but also with the fate of the
nitrogen. During their metabolism, amino
acids travel in the blood from one tissue to
another. Ultimately, most of the nitrogen is
converted to urea in the liver
A. A number of amino acids undergo reactions in
which their nitrogen is released as ammonia
(NH3) or ammonium ion (NH4+).
B. Glutamate dehydrogenase catalyzes the
oxidative deamination of glutamate. Ammonium
ion is released, and -ketoglutarate is formed.
The glutamate dehydrogenase reaction, which is
readily reversible, requires NAD or NADP.
Glutamate
Dehydrogenase
C. Histidine is deaminated by histidase to form NH 4
+
and urocanate.
D. Serine and threonine are deaminated by serine
dehydratase, which requires PLP. Serine is
converted to pyruvate, and threonine is
-ketobutyrate; NH4+ is released.
E. The amide groups of glutamine and asparagine
are released as ammonium ions by hydrolysis.
Glutaminase converts glutamine to glutamate
and NH4+. Asparaginase converts asparagine to
aspartate and NH4+.
F. The purine nucleotide cycle serves to release
NH4+ from amino acids, particularly in muscle.
2 | BIOCHEMISTRY

1. Glutamate collects nitrogen from other amino
acids and transfers it to aspartate by a
transamination reaction.
2. Aspartate reacts with inosine monophosphate
(IMP) to form adenosine monophosphate (AMP)
and generate fumarate.
3. NH4+ is released from AMP, and IMP is re-
formed.
V. ROLE OF GLUTAMATE
A. Glutamate provides nitrogen for synthesis
of many amino acids.
1. NH4+ provides the nitrogen for amino acid
-
ketoglutarate to form glutamate in the
glutamate dehydrogenase reaction.
2. Glutamate transfers nitrogen by
-ketoacids
-amino
acids.
B. Glutamate plays a key role in removing
nitrogen from amino acids.
-Ketoglutarate collects nitrogen from
other amino acids by means of
transamination reactions, forming
glutamate.
2. The nitrogen of glutamate is released as
NH4+ via the glutamate dehydrogenase
reaction.
3. NH4+ and aspartate provide nitrogen for
urea synthesis via the urea cycle.
Aspartate obtains its nitrogen from
glutamate by transamination of
oxaloacetate.
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NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS
VI. FATE OF AMINO ACID NITROGEN
A. Deamination, the first step in metabolizing
surplus amino acids, yields an -keto acid
and an ammonium ion (NH4).
B. Transdeamination effects deamination
through the sequential actions of the
enzymes transaminase
(aminotransferase) and glutamate
dehydrogenase.
C. The appearance of aspartate
aminotransferase (AST) or alanine
aminotransferase (ALT) in the blood is an
indication of tissue damage, especially
cardiac muscle (AST) and liver (AST and
ALT).
VII. UREA CYCLE AND DETOXIFICATION OF
NH4+
A. NH4+ is toxic to the human body,
particularly the central nervous system
(CNS).
B. Conversion of NH4+ to urea occurs in the
liver via the urea cycle. Urea is excreted in
the urine.
C. The concentration of ammonia and
ammonium ions in the blood is normally
very low. Ammonia is in equilibrium with
ammonium ion (NH3 + H+  NH4+), with
a pKa of 9.3. NH3 is freely diffusible across
membranes, but at physiologic pH, the
concentration of ammonia is 1/100 the
concentration of the NH4+ ion (Henderson-
Hasselbach equation).
D. Ammonia travels to the liver from other
tissues, mainly in the form of alanine and
glutamine. It is released from amino acids in
the liver by a series of transamination and
deamination reactions.
3 | BIOCHEMISTRY

E. Ammonia is also produced by bacteria in the gut
and travels to the liver via the hepatic portal vein.
The agent lactulose is used to treat this condition
and is thought to work to reduce ammonia levels by
either increasing bacterial assimilation of ammonia
or reducing deamination of nitrogenous compounds.
F. In peripheral tissues, detoxification of NH4+,
which is ultimately converted to urea in the liver,
occurs by different mechanisms.
1. In most tissues, the enzyme glutamine
synthetase incorporates NH4+ into
glutamate to form glutamine,
which is carried by the circulation to
the liver. There the enzyme
glutaminase hydrolyzes glutamine
back to NH4+ and glutamate.
2. In skeletal muscle, sequential action of
the enzymes glutamate
dehydrogenase and glutamate-
pyruvate aminotransferase can
lead to the incorporation of NH4+
into alanine. The alanine is carried
to the liver, where
transdeamination results in the
conversion of the alanine back to
pyruvate and NH4+.
G. Regulation of the Urea Cycle
1. N-Acetylglutamate is an activator of
CPS I, the first enzyme of the urea
cycle.
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MARY ANNE D. CHIONG, MD, MSC, FPPS
2. Arginine stimulates the synthesis of N-
acetylglutamate from acetyl coenzyme A
(CoA) and glutamate.
3. Although the liver normally has a great
capacity for urea synthesis, the enzymes
of the urea cycle are induced if a high-
protein diet is consumed for 4 days or
more.
4. The key relationship between the urea
cycle and the tricarboxylic acid (TCA)
cycle is that one of the urea nitrogen
molecules is supplied to the urea cycle
as aspartic acid, which is formed from
the TCA cycle intermediate oxaloacetic
acid.
H. Hyperammonemia
1. This condition may be caused by
insufficient removal of NH4+,
resulting from disorders that involve
one of the enzymes in the urea
cycle.
2. Blood ammonia concentrations above the
normal range (30-60 uM) may cause
coma due to ammonia intoxication.
3. Ammonia intoxication can lead to mental
retardation, seizure, coma, and
death.
4. Enzyme defects:
a. When the activity of the enzyme
carbamoyl phosphate
synthetase or ornithine-
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 AMINO ACID METABOLISM
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS

carbamoyl transferase is low,

ammonia concentrations in the
blood and urine rise, and
ammonia intoxication occurs.
b. When any of the enzymes
argininosuccinate synthetase,
argininosuccinase, or arginase is
defective, blood levels of the
metabolite immediately preceding
the defect increase. Ammonia
levels may also rise.
5. Treatment consists of restriction of
dietary protein, intake of mixtures of
keto acids that correspond to essential
amino acids and feeding benzoate and
phenylacetate to provide an alternate
pathway for ammonia excretion.

VIII. DEGRADATION OF AMINO ACIDS

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NOEL MARTIN S. BAUTISTA, MD, MBAH
The amino acids can be grouped into families based
on the point where their carbon skeletons, the
structural portions that remain after deamination,
enter the TCA cycle.
A. The amino acid carbon skeletons
undergo a series of reactions whose
products may be glucogenic,
ketogenic, or both.
Leu, Lys
Degraded to acetyl-CoA.
Ketogenic
Glucose cannot be made from
these.
Glucogenic
Phe, Ile, Tyr, Trp, Thr
and
Goes both ways.
Ketogenic
Everything else
Degraded to pyruvate or a
Glucogenic
member of the TCA cycle
Glucose can be made from these.
B. Degradation of amino acids
(Glucogenic) Amino acids that produce
pyruvate or intermediates of the TCA
cycle. These amino acids are considered
glucogenic because they can produce
glucose in the liver. The fumarate group
of amino acids produces cytoplasmic
fumarate. Potential mechanisms
whereby the cytoplasmic fumarate can
be oxidized.
1. Amino acids that are converted to pyruvate
a. The amino acids that are synthesized
from intermediates of glycolysis
(serine, glycine, cysteine, and
alanine) are degraded to form
pyruvate.
b. Serine is converted to 2-
phosphoglycerate, an intermediate
of glycolysis, or directly to pyruvate
and NH4+ by serine dehydratase, -
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MARY ANNE D. CHIONG, MD, MSC, FPPS
which is an enzyme that requires
PLP.
c. Glycine, in a reversal of the reaction
used for its synthesis, reacts with
methylene FH4 to form serine.
- Glycine also reacts with FH4 and NAD+
to produce CO2 and NH4+.
- Glycine can be converted to glyoxylate,
which can be oxidized to CO2 and
H2O, or converted to oxalate.
d. Cysteine forms pyruvate. Its sulfur,
which was derived from methionine,
is converted to sulfuric acid
(H2SO4), which is excreted by the
kidneys.
e. Alanine can be transaminated to
pyruvate.
- Glutamate can be deaminated by
glutamate dehydrogenase or
-
ketoglutarate.
- Glutamine is converted by glutaminase
to glutamate with the release of its
amide nitrogen as NH4+.
- Proline is oxidized so that its ring
opens, forming glutamate
semialdehyde, which is reduced to
glutamate.
- Arginine is cleaved by arginase in the
liver to form urea and ornithine.
Ornithine is transaminated to
glutamate semialdehyde, which is
oxidized to glutamate.
- Histidine is converted to
formiminoglutamate (FIGLU). The
formimino group is transferred to
FH4, and the remaining five carbons
form glutamate.
6 | BIOCHEMISTRY

c. Amino acids that form succinyl CoA
- Four amino acids (threonine,
methionine, valine, and
isoleucine) are converted to
propionyl CoA.
- Propionyl CoA is carboxylated in a
biotin-requiring reaction to
formmethylmalonyl CoA.
- Methylmalonyl CoA is rearranged to
form succinyl CoA in a reaction
that requires vitamin B12.
- Isoleucine also forms succinyl CoA after two of its
carbons are released as acetyl CoA.
(1) Threonine is converted by a
dehydratase to NH4+ -
ketobutyrate, which is oxidatively
decarboxylated to propionyl CoA. In
a different set of reactions,
threonine is converted to glycine
and acetyl CoA.
(2) Methionine provides methyl groups for
the synthesis of various compounds;
d. Amino acids that form fumarate
its sulfur is incorporated into
cysteine; and the remaining carbons
form succinyl CoA.
- Methionine and ATP form S-
adenosylmethionine (SAM), which
donates a methyl group and forms
homocysteine.
- Homocysteine is reconverted to
methionine by accepting a methyl-
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AMINO ACID METABOLISM
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS
group from the FH4 pool via vitamin
B12.
- Homocysteine can also react with
serine to form cystathionine. The
cleavage of cystathionine produces
cysteine, NH4+, and a-ketobutyrate,
which is converted to propionyl CoA.
(3) Valine and (4) isoleucine, two of the
three branched-chain amino acids,
form succinyl CoA:
- Degradation of all three branched-
chain amino acids begins with a
transamination, followed by an
oxidative decarboxylation catalyzed
by the branched- -ketoacid
dehydrogenase complex. This
enzyme, like pyruvate
-ketoglutarate
dehydrogenase, requires thiamine
pyrophosphate, lipoic acid, CoA,
flavin adenine dinucleotide (FAD),
and NAD+.
- Valine is eventually converted to
succinyl CoA via propionyl CoA and
methylmalonyl CoA.
(1) Three amino acids (phenylalanine,
tyrosine, and aspartate) are
converted to fumarate
(2) Phenylalanine is converted to
tyrosine by phenylalanine
hydroxylase in a reaction requiring
tetrahydrobiopterin and O2.
7 | BIOCHEMISTRY

(3) Tyrosine, which is obtained from the
diet or by hydroxylation of
phenylalanine, is converted to
homogentisic acid. The aromatic
ring is opened and cleaved, forming
fumarate and acetoacetate.
(4) Aspartate is converted to fumarate
through reactions of the urea cycle
and the purine nucleotide cycle.
Aspartate reacts with IMP to form
AMP and fumarate in the purine
nucleotide cycle.
e. Amino acids that form oxaloacetate
(1) Aspartate is transaminated to form
oxaloacetate.
(2) Asparagine loses its amide nitrogen as
NH4+, forming aspartate in a reaction
catalyzed by asparaginase.
C. Degradation of amino acids (Ketogenic)
Amino acids that produce acetyl CoA or
ketone bodies. These amino acids are
considered ketogenic.
1. Acetyl CoA family (also called the
ketogenic amino acid family)
[isoleucine, leucine, lysine,
phenylalanine, tryptophan, and tyrosine]
a. Acetyl CoA is the starting point for
ketogenesis but cannot be used for
net gluconeogenesis. Leucine and
lysine are the only ketogenic
amino acids. The other four amino
acids that form acetyl CoA are both
ketogenic and glucogenic.
b. Phenylalanine and tyrosine form
acetoacetate.
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NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS
c. Leucine is degraded to form both
acetyl CoA and acetoacetate.
D. Generalities of Amino Acid Catabolism
- If a vitamin or cofactor is involved in amino
acid metabolism, it’s most likely pyridoxal
phosphate (B6), unless it involves serine,
and then its B6 and folic acid.
- Nitrogen is dumped into the urea cycle by
transamination to make Asp or Glu or by
deamination to make ammonia.
IX. SYNTHESIS OF NON-ESSENTIAL AMINO
ACIDS
Synthesis of the amino acids: Eleven of the
twenty common amino acids can be synthesized
in the body. The other nine are considered
“essential” and must be obtained from the
diet. Almost all of the amino acids that can be
synthesized by humans are amino acids used for
the synthesis of additional nitrogen-containing
compounds. Examples include glycine, which is
used for porphyrin and purine synthesis;
glutamate, which is required for
neurotransmitter and purine synthesis; and
aspartate, which is required for both purine and
pyrimidine biosynthesis.
Nine of the eleven “nonessential” amino acids
can be produced from glucose plus, of course, a
source of nitrogen, such as another amino acid
or ammonia. The other two nonessential amino
acids, tyrosine and cysteine, require an
essential amino acid for their synthesis
(phenylalanine for tyrosine, and methionine for
cysteine). The carbons for cysteine synthesis
come from glucose; the methionine only
donates the sulfur.
1. Messenger RNA contains codons for 20 amino
acids. Eleven of these amino acids can
be synthesized in the body. The carbon
skeletons of 10 of these amino acids can
be derived from glucose. These 10 are
serine, glycine, cysteine, alanine,
glutamic acid, glutamine, aspartic
acid, asparagine, proline, and
arginine. The essential amino acids
derived from diet are histidine,
isoleucine, leucine, lysine, methionine,
phenylalanine, threonine, tryptophan,
and valine. Note that tyrosine is derived
from phenylalanine.
2. Amino acids derived from intermediates of
glycolysis
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 AMINO ACID METABOLISM
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS

a. Intermediates of glycolysis serve as

precursors for serine, glycine,
cysteine, and alanine.
b. Serine can be synthesized from the
glycolytic intermediate 3-
phosphoglycerate, which is oxidized,
transaminated by glutamate, and
dephosphorylated.
c. Glycine and cysteine can be derived
from serine.
(1) Glycine can be produced from serine
by a reaction in which a methylene
group is transferred to
tetrahydrofolate (FH4).
(2) Cysteine derives its carbon and
nitrogen from serine. The essential
amino acid methionine supplies the
sulfur.
d. Alanine can be derived by
transamination of pyruvate.

3. Amino acids derived from TCA cycle

intermediates

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NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS

Glu  Glu-semialdehyde 
Arg
ornithine  Arg
Pro Glu  Glu-semialdehyde  Pro
Phe  Tyr (phenylalanine
Tyr
hydroxylase)
Met  homoCys + Ser 
Cys
cystathionine  Cys

The regulation of individual amino acid

biosynthesis can be quite complex, but the
overriding feature is that the pathways are
feedback regulated such that as the
concentration of free amino acid
increases, a key biosynthetic enzyme is
allosterically or transcriptionally inhibited.
Amino acid levels, however, are always
maintained at a level such that the aminoacyl-
a. Aspartate can be derived from
tRNA synthetases can remain active, and protein
oxaloacetate by transamination.
synthesis can continue.
b. Asparagine is produced from
X. CLINICAL RELEVANCE: INHERITED
aspartate by amidation.
(INBORN) ERRORS OF AMINO ACID
METABOLISM
c. Glutamate -
ketoglutarate by the addition of NH4+
A. Phenylketonuria (PKU)
via the glutamate dehydrogenase
1. Phenylalanine accumulates in the
reaction or by transamination.
blood (hyperphenylalaninemia).
Glutamine, proline, and arginine
a. Phenylalanine builds up to toxic
can be derived from glutamate.
concentrations in body fluids,
resulting in CNS damage with
(1) Glutamine is produced by amidation
mental retardation.
of glutamate.
b. Elevated phenylalanine inhibits
(2) Proline and arginine can be derived
melanin synthesis, leading to
from glutamate semialdehyde,
hypopigmentation.
which is formed by reduction of
2. This condition results from a deficiency
glutamate.
of phenylalanine hydroxylase or
(3) Proline can be produced by
dihydropterine reductase
cyclization of glutamate
3. An alternative pathway for phenylalanine
semialdehyde.
breakdown produces
(4) Arginine, via three reactions of the
phenylketones (phenylpyruvic,
urea cycle, can be derived from
phenyllactic, and phenylacetic
ornithine, which is produced by
acids), which spill into the urine.
transamination of glutamate
4. In affected individuals, tyrosine is an
semialdehyde.
essential dietary amino acid.
5. Treatment consists of restricting dietary
4. Tyrosine, the 11th nonessential amino acid,
protein (phenylaknine).
is synthesized by hydroxylation of the
essential amino acid phenylalanine in a
B. Albinism
reaction that requires
1. Tyrosinase, the first enzyme on the
tetrahydrobiopterin.
pathway to melanin, is absent.
2. Albinos have little or no melanin (skin
Summary of Synthesis of Non-Essential Amino
pigment). They sunburn easily,
Acids
and are:
Amino Acid Synthetic Route
a. Particularly susceptible to skin
Ala from pyruvate by transamination
carcinoma.
-ketoglutarate by
Glu b. Photophobic because of lack of
transamination
pigment in the iris of the eye.
Asp from oxaloacetate by transamination
Gln Glu + NH4 + ATP  Gln C. Homocystinuria
Asp + Gln + ATP  Asn + 1. In this disorder, homocysteine, which
Asn
AMP + PPi + Glu accumulates in blood and body
Glucose  hydroxypyruvate  Ser; fluids, appears in the urine.
Ser Glucose  phosphohydroxypyruvate 2. Homocystinuria may result from several
 Ser defects
Ser + THfolate  Gly + Ch2- a. Cystathionine synthase deficiency
Gly
THfolate b. Reduced affinity of cystathionine
UST FMS MEDICAL BOARD REVIEW 2019 10 | BIOCHEMISTRY
 AMINO ACID METABOLISM
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS

synthase for its coenzyme,
pyridoxal phosphate (PLP)
[This form may respond to
megadoses of pyridoxine
(vitamin B6).]
5
c. N -Methyl tetrahydrofolate
homocysteine
methyltransferase deficiency
d. Vitamin B12 coenzyme
(methylcobalamin) deficiency
[This form may respond to
vitamin B12 supplements]
3. Pathologic changes
a. Dislocation of the optic lens
b. Mental retardation
c. Osteoporosis and other skeletal
abnormalities
d. Atherosclerosis and thromboembolism
4. Patients who are unresponsive to vitamin
therapy may be treated with
synthetic diet low in methionine,
and by administering betaine (N,
N, N-trimethylglycine) as an
alternative methyl group donor.
D. Maple-syrup urine disease
1. In this disorder, the branched chain keto
acids derived from isoleucine,
leucine and valine appear in the
urine, giving it a maply syrup-like
odor.
2. This condition results from a deficiency in
the branched-chain 2-keto acid
decarboxylase.
3. The elevated keto acids cause severe
brain damage, with death in the first
year of life.
4. Treatment. A few cases respond to
megadoses of thiamine (vitamin B1).
Otherwise, synthetic diets low in
branched-chain amino acids are
given.
2. Creatine travels from the liver to other
tissues, where it is converted to creatine
phosphate. Adenosine triphosphate (ATP)
phosphorylates creatine to form creatine
phosphate in a reaction catalyzed by
creatine kinase (CK).
a. Muscle and brain contain large amounts of
creatine phosphate.
b. Creatine phosphate provides a small
reservoir of high-energy phosphate that
readily regenerates ATP from adenosine
diphosphate (ADP). It plays a particularly
important role during the early stages of
exercise in muscle, where the largest
quantities of creatine phosphate are found.
c. Creatine also transports high-energy
phosphate from mitochondria to actomyosin
fibers.
3. Creatine phosphate spontaneously cyclizes,
forming creatinine, which is excreted by
the kidney.
B. Glutathione
1. Structure
- GSH is a tripeptide synthesized from
glutamate, cysteine, and glycine. It contains
an unusual linkage between the glutamate
side-chain carboxylate group and the
nitrogen of cysteine.

E. Histidinemia
1. This disorder is characterized by elevated
histidine in the blood plasma and
excessive histidine metabolites in the
urine.
2. The enzyme histidine- -deaminase,
the first enzyme in histidine
catabolism, is deficient.
3. Mental retardation and speech defects
may occur but are rare.
4. Treatment is not usually indicated.

XI. SPECIAL PRODUCTS DERIVED FROM

AMINO ACIDS

A. Creatine
2. Function
1. Creatine is produced from glycine, arginine,
a. Involved in the transport of amino acids
and S-adenosylmethionine (SAM). Glycine
across the cell membranes (the c-
combines with arginine to form ornithine -
glutamyl cycle)
and guanidinoacetate, which is methylated
by SAM to form creatine.

UST FMS MEDICAL BOARD REVIEW 2019 11 | BIOCHEMISTRY


b. Aids in the rearrangement of protein
disulfide bonds under oxidizing
conditions and detoxification reactions
(1) The sulfhydryl groups of GSH are
used to reduce oxidized proteins,
resulting in the oxidation of two
molecules of GSH to form GSSG
(two glutathione molecules linked by
a disulfide bond).
(2) GSSG is reduced back to two
molecules of GSH through the
action of glutathione reductase, an
NADPH-requiring enzyme.
C. Nitric Oxide (NO)
1. Synthesis
a. Liberated in the conversion of L-arginine
to citrulline
b. The enzyme nitric oxide synthase (NOS)
is a complex enzyme requiring NADPH,
flavin adenine dinucleotide (FAD), flavin
mononucleotide (FMN), and
tetrahydrobiopterin (BH4).
c. NOS is found in three major isoforms.
(1) Neuronal NOS (nNOS or NOS-1).
(2) Macrophage or inducible NOS (iNOS
or NOS-2).
(3) Endothelial NOS (eNOS or NOS-3).
2. Function
a. iNOS is important in macrophages for
creating NO for the generation of free
radicals, which are bactericidal.
b. NO stimulates the influx of Ca2+ into
vascular endothelial cells, with the
activation of cyclic guanosine
monophosphate (cGMP) resulting in
relaxation of vascular smooth muscle
(NO is also known as endothelium-
derived relaxation factor [EDRF]).
UST FMS MEDICAL BOARD REVIEW 2019
AMINO ACID METABOLISM
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS
D. Products formed by amino acid
decarboxylations
1. Amines are produced by decarboxylation of
amino acids in reactions that use pyridoxal
phosphate (PLP) as a cofactor.
2. -Aminobutyric acid (GABA), an inhibitory
neurotransmitter, is produced by
decarboxylation of glutamate
3. Histamine is produced by decarboxylation of
histidine.
a. Histamine causes vasodilation and
bronchoconstriction.
b. In the stomach, it stimulates the
secretion of hydrochloric acid (HCl).
4. The initial step in ceramide formation
involves the condensation of palmitoyl
coenzyme A (CoA) with serine, which
undergoes a simultaneous decarboxylation.
Ceramide forms the sphingolipids (e.g.,
sphingomyelin, cerebrosides, and
gangliosides).
5. The production of serotonin from tryptophan
and of dopamine from tyrosine involves
decarboxylations of amino acids.
E. Products derived from tryptophan
1. Serotonin, melatonin, and the
nicotinamide moiety of NAD and NADP are
formed from tryptophan
12 | BIOCHEMISTRY
 AMINO ACID METABOLISM
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS

H. S-Adenosylmethionine (SAM)

- synthesized from methionine and ATP

- supplies methyl groups

2. Tryptophan is hydroxylated in a BH4-requiring

reaction similar to the hydroxylation of
phenylalanine. The product, 5-
hydroxytryptophan, is decarboxylated to
form serotonin.

3. Serotonin undergoes acetylation by acetyl

CoA and methylation by SAM to form
melatonin in the pineal gland.

4. Tryptophan can be converted to the

nicotinamide moiety of NAD and NADP
although the major precursor of
nicotinamide is the vitamin niacin (nicotinic
acid). Thus, to a limited extent, tryptophan
can spare the dietary requirement for niacin.

F. Products derived from phenylalanine and

tyrosine

1. Phenylalanine can be hydroxylated to form

tyrosine in a reaction that requires BH4.
Tyrosine can be hydroxylated to form dopa
(3,4-dihydroxyphenylalanine)

2. Thyroid hormones

3. Melanins, which are pigments in skin and

hair, are formed by polymerization of
oxidation products (quinones) of dopa.

4. The catecholamines (dopamine,

norepinephrine, and epinephrine) are
derived from tyrosine in a series of reactions

G. Tetrahydrofolate

- Serine, glycine, and formaldehyde produce

N5,N10-methylene-FH4
UST FMS MEDICAL BOARD REVIEW 2019 13 | BIOCHEMISTRY

CHOOSE THE BEST ANSWER:
_____1. Which one of the following statements
concerning the peptide shown below is correct?
V–C–E–S–D–R–C
A. The peptide contains asparagine
B. The peptide contains a side chain with a
secondary amino group
C. The peptide would move to the cathode
during electrophoresis at pH5
D. The peptide contains a side chain that
can form hydrogen bond with another
amino acid
_____2. The principal function of amino acids in
intermediary metabolism is to:
A. synthesize tissue and blood proteins
B. furnish energy to the cell
C. provide intermediates for synthesis of
specialized products
D. provide nitrogen for urea synthesis
_____3. Which of the following statements is TRUE
regarding trypsin, a major enzyme in the pancreatic
phase of protein digestion?
A. an exopeptidase
B. is activated by H+ ions released from the
stomach
C. is activated by an enzyme (enterokinase)
secreted from the brush border of the
small intestine
D. activation of its zymogen form involves
addition of more amino acid residues to
the polypeptide
_____4. Presence of these enzymes explains why
practically only free amino acids are found in the
portal blood after a meal:
A. endopeptidases (trypsin, chymotrypsin, etc)
B. cytoplasmic dipeptidases and tripeptidases
C. carboxypeptidases B
D. aminopeptidases
_____5. Means of transepithelial transport of amino
acids from the lumen to the intestinal cell involving
an ion pump that creates a gradient of ions between
the lumen and the intestinal cell.
A. facilitated diffusion
B. active transport
C. simple diffusion
D. Na+-dependent co-transport
UST FMS MEDICAL BOARD REVIEW 2019
REVIEW TEST
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS
_____6. Which of the following statements
concerning amino acids is correct?
A. Alanine is ketogenic
B. Amino acids that are catabolized to acetyl
coenzyme A are glucogenic
C. Branched-chain amino acids are
catabolized primarily in the liver
D. Cysteine is essential for individuals
consuming a diet severely limited in
methionine
_____7. This vitamin cofactor is required for
transamination reactions?
A. cobamide
B. nicotinic acid
C. tetrahydrofolic acid
D. pyridoxal phosphate
_____8. The molecule of urea is synthesized in
which compartment of the cell?
A. mitochondria
B. peroxisomes
C. cytosol
D. microsomes
_____9. Which of the following metabolites of the
urea cycle links it to the citric acid cycle?
A. arginine
B. fumarate
C. aspartic acid
D. malate
_____10. A 3-month-old child presents with
vomiting and convulsions. Notable findings include
hepatomegaly and hyperammonemia. A deficiency in
which of the following enzymes would most likely
cause an elevation of blood ammonia levels?
A. CPS I
B. Glutaminase
C. Argininosuccinate lyase
D. Asparagine synthetase
_____11. Which of the following amino acids can be
synthesized in the Krebs-Henseleit Cycle?
A. fumarate
B. arginine
C. aspartate
D. alanine
_____12. N-acetlyglutamate (NAG) is a positive
allosteric effector of which enzyme of the urea
cycle?
A. ornithine transcarbamoylase
B. carbamoyl phosphate synthetase I
C. arginase
D. arginosuccinase
| BIOCHEMISTRY
 REVIEW TEST
NOEL MARTIN S. BAUTISTA, MD, MBAH
MARY ANNE D. CHIONG, MD, MSC, FPPS

_____13. When the carbon skeletons of amino acids _____19. A 1-week old infant, who was born at
are metabolized to any glycolytic and TCA cycle home in a rural area, has undetected classic
intermediates, the amino acid can be used for any of phenylketonuria. Which statement about this baby
the following EXCEPT: and/or her treatment is correct?
A. synthesis of some non-essential amino acids A. A diet devoid of phenylalanine should be
B. complete oxidation to provide energy to the cell initiated immediately
C. synthesis of ketone bodies B. Dietary treatment will be recommended
D. maintenance of glucose through gluconeogenesis to be discontinued in adulthood
C. Supplementation with vitamin B6 is required
_____14. Which of the following amino acids when D. Tyrosine is an essential amino acid
catabolized may be converted to ketone bodies and
fatty acids? _____20. A 56-year-old man with long-standing,
A. aspartate poorly controlled diabetes visits his primary
care physician for a follow-up after a recent
B. histidine
hospitalization. The patient experienced an episode
C. valine of acute renal failure while in the hospital, and his
D. leucine creatinine level rose to 3.4 (normal, 0.7 to
1.5). Creatinine, a marker of kidney function, is
_____15. All of the following amino acids when produced from which of the following precursors?
catabolized enter through the Citric Acid Cycle, A. Glycine, arginine, and SAM
EXCEPT: B. Glutamine, aspartic acid, and CO2
A. histidine C. Glutamine, cysteine, and glycine
D. Serine and palmityl CoA
B. methionine
C. asparagine
D. alanine

_____16. A new test is developed that can non-

radioactively ‘‘label’’ compounds in the human body.
As a physician with a background in the new field of
metabolomics, you assess a 21-year-old with classic
PKU. The patient is fed phenylalanine with a label in
the phenyl ring, and a 24-hour urine sample is
collected. Which of the following compounds would
you expect to contain the greatest amount of label
in this urine sample?
A. Tyrosine
B. Tryptophan
C. Epinephrine
D. Phenylketone

_____17. If an individual has a vitamin B6

deficiency, which of the following amino acids could
still be synthesized and be considered non-essential?
A. Tyrosine
B. Serine
C. Cysteine
D. Aspartate

_____18. In Hartnup’s Disease, pellagra-like

manifestations are seen because of relative
deficiency of nicotinic acid coenzyme derived from:
A. tryptophan
B. phenylalanine
C. tyrosine
D. threonine

UST FMS MEDICAL BOARD REVIEW 2019 | BIOCHEMISTRY


I. PRINCIPAL FUELS OF METABOLISM
The body’s major fuel depots are glycogen in liver and
muscle, triacylglycerols (TAGs) in adipose tissue, and
protein in skeletal muscle. Ketone bodies form a
secondary source particularly in the starved state.
A. Carbohydrate
1. Glucose is stored as glycogen in liver and
muscle.
a. Liver glycogen maintains blood glucose
concentrations between meals. There is
approximately 200 grams of liver glycogen
during the post-absorptive state and this
amount may go down to as low as 80
grams after an overnight fast.
b. Muscle glycogen furnishes energy for
muscle contraction during exercise. The
glycogen content of muscle is about 150
grams.
B. Fat
1. TAGs in adipose tissue serve as the chief fuel
store in the body.
2. About 15 kg. of TAGs accounts for 85% of
total stored calories.
C. Protein
1. Unlike glycogen and fat, protein is not
primarily a fuel reserve.
2. Only about 6 kg. can be oxidized before the
body functions become compromised.
D. Ketone Bodies
1. -hydroxybutyrate, acetoacetate, and acetone
are synthesized from acetyl CoA in the liver
and are normally found at 3 mg/dl in the
blood; they are used by the heart, muscle, and
brain tissues especially during prolonged
fasting or starvation.
2. One gram supplies 4 kcal upon oxidation.
E. Alcohol
1. While it is not a dietary essential, each gram of
ethanol yields 7kcal.
2. Ethanol is catabolized in the liver, by two NAD+-
linked enzymes: alcohol dehydrogenase and
acetaldehyde dehydrogenase.
II. NUTRITIONAL ASPECTS OF DIETARY FUELS
A. Definitions
1.Philippine Dietary Reference Intake (PDRI)
is the collective term comprising reference
values for energy and nutrient levels of
intakes. It has four components:
a. Estimated Average Requirement
(EAR) is the daily nutrient intake level
that meets the median or average
requirement of healthy individuals in a
particular life stage and sex group,
corrected for incomplete utilization or
dietary nutrient bioavailability.
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METABOLIC INTEGRATION
ASSOC. PROF. IMELDA A. DAKIS M.D.
b. Recommended Nutrient Intake (RNI)
is the level of intake of a specific nutrient
which is adequate for the maintenance of
health and well-being of nearly all healthy
persons in the population.
It defines the quantity of essential
nutrients needed to meet the minimal
requirement to maintain health and
provide reasonable levels of reserves plus
an added amount to allow for incomplete
digestion.
c. Adequate Intake (AI) is the daily
nutrient intake level that is based on
observed or experimentally determined
approximation of the average nutrient
intake by a group (or groups) of
apparently healthy people that is assumed
to sustain a defined nutritional state. It is
used when there is insufficient data to
establish the EAR.
d. Tolerable Upper Intake Level or
Upper Limit (UL) is the highest average
daily nutrient intake level likely to pose no
adverse health effects to almost all
individuals in the general population.
2. Minimum Daily Requirement (MDR) refers
to the least amount of a nutrient needed by the
body to prevent manifestations of deficiency.
3. Essential Nutrients are substances which the
body cannot synthesize in sufficient amounts
to meet the demands of the body and
therefore, must be included in the diet.
4. Food Guides are tools to interpret and apply
sound nutrient standards for use in food
planning of individuals and families.
5. Basal Metabolic Rate is the energy required
by an individual in the awake state, during
physical, digestive, and emotional rest to
sustain the metabolic activities of the body and
to maintain circulatory, respiratory,
gastrointestinal, and renal processes.
6. Energy Requirement is the level of energy
intake that will balance energy expenditure
when the individual has a body size and
composition, and a level of physical activity,
consistent with long-term good health.
B. Carbohydrates
1. Each gram yields 4 kcal of energy.
2. 55% to 70% of dietary energy should come
from carbohydrates, 70% of which should
come from complex carbohydrate, and not
more than 10% should come from simple
sugars.
3. A daily intake of 20-25 grams of dietary fiber is
recommended.
1 | BIOCHEMISTRY

C. Lipids
1. A gram of fat provides 9 kcal of energy.
2. The recommended intake is 20%-25% of total
daily dietary energy, with 10% each of
monounsaturated, polyunsaturated, and
saturated fatty acids.
3. Daily cholesterol consumption should be
limited to 300mg or less.
4. Linoleic acid, the only absolute essential fatty
acid should be taken at 1%-2% of total daily
calories.
D. Proteins
1. Protein provides 4 kcal of energy per gram.
2. Recommended daily intake for Filipinos is
1.14grams/kilogram of desirable body weight
(DBW), or 10%-15% of the Total Caloric
Allowance (TCA).
3. Threonine, tryptophan, lysine, leucine,
isoleucine, methionine, valine, phenylalanine
and histidine are indispensable amino acids.
III. CENTRAL THEMES OF METABOLIC
PATHWAYS
A. Acetyl CoA is a common intermediate of all
metabolic pathways.
B. Oxidation of dietary fuel leads to the capture of
energy in the form of ATP and NADH/ FADH2.
C. NADH and FADH2 transfer their electrons to O2
via the ETC. The energy released is used to
synthesize ATP.
D. ATP is the biochemical currency of energy.
E. Biosynthesis involves the reduction of simple
carbon compounds to complex polymers.
F. Most biosynthetic processes use NADPH as the
electron donor.
G. Biosynthetic and degradative pathways are
distinct and coordinately regulated.
IV. KEY JUNCTIONS IN INTEGRATED
METABOLISM
A. Glucose 6-Phosphate
1. When glucose is transported into the cell, it is
rapidly phosphorylated to glucose 6-phosphate.
Glucose 6-phosphate may be catabolized into
pyruvate, stored as glycogen, or converted to
ribose 5-phosphate by the HMP Shunt.
2. Glucose 6-phosphate is also formed when
glycogen is mobilized in liver and muscle, or it
can be synthesized from pyruvate and
glucogenic amino acids by the gluconeogenic
route.
B. Pyruvate
1. The primary source of pyruvate is glycolysis.
Other important origins are alanine and lactate.
2. On the other hand, pyruvate may be converted
to lactate, alanine, oxaloacetic acid, and acetyl
CoA.
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METABOLIC INTEGRATION
ASSOC. PROF. IMELDA A. DAKIS M.D.
C. Acetyl CoA
1. Acetyl CoA is produced by oxidative
decarboxylation of pyruvate or by the -
oxidation of fatty acids and oxidation of
ketogenic amino acids.
2. Acetyl CoA may be completely oxidized to CO2
and H2O, converted to HMGCoA
(hydroxymethylglutaryl CoA), or used in the
synthesis of fatty acids.
V. THE INFLUENCE OF HORMONES ON FUEL
METABOLISM
A. Insulin
1. The pancreatic -cells sense glucose levels and
secrete insulin in response to elevation of
blood glucose concentration.
2. Insulin signals the fed state. It promotes
uptake of fuel substrates into skeletal muscle
and adipose cells, storage of glycogen and
TAGs, and biosynthesis of proteins and nucleic
acids.
B. Glucagon
1. The -cells of the pancreas sense the blood
glucose level and release glucagon in
response to low levels.
2. The foremost target of glucagon is the liver;
its principal effect is to increase cyclic AMP
(cAMP) levels in liver cells. The resulting
cascades promote glycogenolysis.
3. Glucagon raises cAMP levels in adipose tissue,
in which TAG mobilization is favored, yielding
glycerol and fatty acids.
C. Epinephrine
1. It is released from the adrenal medulla in
response to low blood glucose. It then
interacts with second-messenger systems in
many tissues.
2. Epinephrine also holds back the secretion of
insulin and stimulates glucagon secretion.
VI. METABOLIC PROFILES OF MAJOR TISSUES
AND ORGANS
A. Brain
1. The primary fuel for the brain is glucose. Only
under prolonged starvation does the brain use
ketone bodies as fuel source, to spare proteins.
2. The average brain consumes 120 grams of
glucose in a day or 60% of the utilization of
glucose by the body in the resting state.
3. Glucose gains entry into the brain via GLUT3
whose Km for glucose is 1.6mM. This transporter
is saturated under normal blood glucose-
4. conditions of 5mM, thus the brain has a steady
share of glucose.
5. Fatty acids cannot cross the blood-brain barrier
as they are bound to albumin in plasma. Ketone-
bodies are the transportable equivalents of fatty
acids.
2 | BIOCHEMISTRY

B. Skeletal Muscle
1. The muscles can use glucose, fatty acids, and
ketone bodies for fuel.
2. Muscle has stores of glycogen (1200 kcal) or
75% of all the glycogen stored in the body.
3. During vigorous muscle activity, the muscles
account for 90% of the total O2 consumption of
the body (against the 50% consumption at rest).
4. The rate of glycolysis exceeds that of the TCA
Cycle so that much of the pyruvate is reduced to
lactate. Lactate is readily brought to the liver for
conversion to glucose.
5. Protein in muscle is not an efficient fuel store
and its degradation proves deleterious.
6. Skeletal muscle contains 10–30 mM
phosphocreatine which rapidly regenerates ATP
from ADP using phosphocreatine kinase.
C. Liver
1. The liver is the center of metabolism, providing
fuel to the brain, muscle, and other peripheral
tissues.
2. It stores glucose as glycogen. It carries out
glycogenolysis and gluconeogenesis to release
glucose into the blood, being the primary organ
that maintains blood glucose level.
3. The liver processes lipoproteins and ketone body
formation from fatty acids.
4. It is the site of disposal of nitrogen derived from
amino acid degradation, by means of urea
formation.
5. Keto acids from amino acid degradation are
preferred to glucose for its own fuel.
D. Adipose Tissue
1. Adipose tissue stores TAGs and releases fatty
acids as needed.
2. Fatty acids are synthesized in the liver, while in
adipose tissue fatty acids become activated to
acyl-CoA which, in turn, esterifies to glycerol to
form TAG.
3. Adipose tissue is dependent on glucose for the
supply of glycerol 3-phosphate in TAG
production.
4. TAG stores in adipose tissue are hydrolyzed by
hormone-sensitive lipases releasing free fatty
acids and glycerol.
E. Heart
1. Heart muscle, in contrast to skeletal muscle,
functions only under aerobic conditions.
2. There are virtually no glycogen reserves in heart
muscle.
3. The fuel of choice is fatty acids while the least
preferred fuel is glucose. Ketone bodies and
lactate are used under stress.
VII. METABOLIC ADAPTATIONS IN
NUTRITIONAL STATES
A. Well-fed State
1. For about four hours after a meal, there is an
abundant supply of metabolic fuels.
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2. Blood glucose levels rise, stimulating insulin
release from the pancreatic -cells creating a
high insulin-to-glucagon ratio.
3. Because of an increased rate of glucose uptake
by the tissues, glucose becomes the major fuel
for oxidation in the liver, muscle, and adipose
tissue.
4. Activation of the following pathways occurs:
a. glycogen synthesis in liver and muscle
b. glycolysis in liver
c. HMP Shunt
d. TAG synthesis and storage in adipose
e. protein synthesis
5. Glycogenolysis, gluconeogenesis, Cori Cycle, -
oxidation of fatty acid and lipolysis are inhibited.
B. Early Fasting
1. This is represented by an overnight fast, which
begins 4 hours after the evening meal and lasts
for 16 to 24 hours.
2. Fuel stops coming in from the digestive tract,
blood glucose level falls and glucagon release
from the pancreas is stimulated.
3. Glucose uptake and utilization by the cells is
suppressed, except in the brain.
4. Glucagon stimulates the cAMP-dependent
protein kinase A, activating glycogenolysis in the
liver to maintain normal blood glucose
concentration.
5. Gluconeogenesis is activated: lactate, pyruvate,
and alanine are diverted to glucose production
through the Cori Cycle and Glucose-Alanine
Cycle.
6. -oxidation of fatty acids is increased to fuel
muscle in order to spare glucose for brain
activity; consequent increase in ketogenesis
occurs.
7. Hydrolysis of TAG stores in adipose tissue is
stimulated by hormone-sensitive lipase.
8. Hydrolysis of muscle protein is stimulated to
harvest energy from amino acid carbons.
9. Glycogenesis, glycolysis, lipogenesis, and amino
acid degradation are inactivated.
C. Starvation/Prolonged Fasting
1. After 2 to 3 days without food, the body enters
the starvation state.
2. Persistence of a low insulin-glucagon ratio
exaggerates metabolic events of early fasting.
3. Even during starvation, blood glucose levels
have to be maintained at 40mg/dl to offer fuel to
the brain. Glycogen stores have been depleted
at this stage and the liver can no longer keep up
with gluconeogenesis because of lack of
substrates (glycerol, lactate, pyruvate, etc.)
4. Most of the stored energy is in the form of fat
which cannot be converted to glucose (except
the glycerol from TAGs); accelerated lipolysis
and -oxidation of fatty acids in the liver
produce high levels of acetyl CoA and increased
NADH/NAD+ ratio – events that retard the TCA
Cycle.
3 | BIOCHEMISTRY

5. Increased acetyl CoA but lack of oxaloacetic acid
results in exaggerated production of ketone
bodies whose levels go up steadily about 3 days
into starvation.
6. The brain switches to ketone bodies, sparing
proteins from being used for gluconeogenesis.
7. The heart and skeletal muscle rely on ketone
bodies for energy.
8. During this state, fatty acids are fuelling every
tissue except the red blood cells, which still
depend on glucose.
9. Starvation can be fatal because of eventual
protein loss as well as ketoacidosis.
D. Early Re-fed State
1. This state sets in soon after fuels are again
absorbed in the gut after an absence of food.
2. Fat is metabolized normally while normal glucose
metabolism is gradually reestablished.
3. The liver remains in gluconeogenic mode for a
few hours after feeding, but this
gluconeogenesis does not provide blood glucose
but rather glucose 6-phosphate for glycogenesis
(“indirect glycogenesis”). Also, gluconeogenesis
from amino acids coming in from the gut assists
in relaunching glycogen reserves.
4. After maintenance of a well-fed state for a few
hours, the metabolic inter-connections of the
well-fed state become sustained.
Gluconeogenesis decelerates, glycolysis
predominates as a means of glucose utilization
and liver glycogen stores are maintained by
“direct” synthesis from glucose.
E. Obesity
1. It is characterized by an excessive accumulation
of body fat, with an actual body weight of over
20% beyond the desirable body weight.
2. It is similar to a “prolonged well-fed state”, with
a too short fasting phase during which stored fat
is incompletely used up.
3. Insulin-glucagon ratio is high.
4. Glycolysis and glycogenesis are increased;
glycogenolysis and gluconeogenesis are
suppressed.
5. Acetyl CoA is produced in increased amounts
due to increased availability of pyruvate from
glycolysis; excess acetyl CoA is diverted towards
fatty acid and TAG synthesis.
6. Lactate from muscle and red blood cell is also
converted to acetyl CoA and into fat through
pyruvate; lipolysis is inhibited.
7. Other contributors to exaggerated fat synthesis
are dietary fat (chylomicrons) and endogenous
TAGs (VLDL) as well as ketogenic amino acids.
F. Dieting
1. Consuming less food with the same macronutrient
composition has little effect upon the starve-feed
cycle.
 The roles of the tissues remain the same in
the well-fed state.
 There less glycogen and TAGs stored.
2. Consuming less fat to cut calories is another way to
lose weight.
UST FMS MEDICAL BOARD REVIEW 2019
METABOLIC INTEGRATION
ASSOC. PROF. IMELDA A. DAKIS M.D.
 The well-fed state of tissues stays the same
except for a reduction in TAGs.
 The switch to fasting state occurs sooner
after meals.
3. Another way of losing weight is to have an
extremely low carbohydrate-high protein-moderate-fat
diet.
 The fasting state is little changed from that
of other diets.
 The liver remains gluconeogenic as well as
ketogenic in the fed state.
 Little rise in blood glucose occurs and insulin
exhibits a less than normal elevation in response
to meals.
 The excess amino acids are converted to liver
glycogen, blood glucose, and ketone bodies.
 Fatty acids delivered to the liver are converted to
ketone bodies.
 Glucose and ketone bodies are produced in both
the fed and fasted states.
 The need for a supply of energy in the form
ketone bodies in peripheral tissues largely balances
the production of ketone bodies by the liver.
G. Alcohol Ingestion
1. Ethanol is primarily catabolized in the liver, by
two NAD+-linked enzymes: alcohol
dehydrogenase, and acetaldehyde
dehydrogenase. The two-step process produces
acetaldehyde and acetate, respectively, with
concomitant generation of NADH.
2. The major portion of acetate is released into the
blood and delivered to the extrahepatic tissues.
Some of this acetate is changed to acetyl CoA in
the liver. The extra acetyl CoA is stored as long-
chain fatty acids in the liver that may later
become deposited in the hepatocytes (fatty
liver). Little acetyl CoA enters the TCA Cycle
because of a surplus in NADH.
3. Aerobic glycolysis is likewise inactivated because
of the high NADH/NAD+ ratio. Pyruvate then
becomes transformed to lactate and may lead to
acidosis.
4. Gluconeogenesis is also inhibited because an
elevated NADH/NAD+ ratio depresses TCA cycle
enzymes thus restricting the supply of
oxaloacetate and PEP for gluconeogenesis.
5. Glucose 6-phosphate is shifted to the HMP shunt
because of accumulation of glycolytic
intermediates brought about by a high
NADH/NAD+ ratio. Flooding of the HMP shunt
with glucose 6-phosphate increases the
production of NADPH for fatty acid synthesis as
well as of ribose 5-phosphate for nucleotide
synthesis.
6. Chronic and excessive ethanol ingestion
associated with malnutrition is a stimulus for
glycogenolysis in the liver.
4 | BIOCHEMISTRY

VIII. METABOLIC ADAPTATIONS IN
PHYSIOLOGICAL STATES
A. Aerobic Exercise
1. As in the starved state, liver and adipose
tissue adapt to supply fuel for muscle
contraction.
2. With a low insulin-glucagon ratio, lipolysis is
stimulated, the liberated fatty acids fueling the
muscle.
3. Glycogenolysis in liver and muscle, and
ketogenesis in liver furnish the muscle with-
more glucose and ketone bodies. Cori Cycle
supplies additional glucose to muscle.
B. Anaerobic Exercise
1. Anaerobic exercise involves little inter-organ
interaction because the blood vessels within
the muscles are compressed during peak
contraction. This causes the muscle cells to
become separated from the rest of the body.
2. Muscle relies for the most part on its own
glycogen reserve and phosphocreatine for
energy. Phosphocreatine provides high-energy
phosphate bonds for synthesis of ATP until
glycogenolysis and glycolysis are stimulated.
C. Pregnancy
1. The fetus has high demands for nutrients. It
mainly uses glucose but may also derive energy
from amino acids, lactate, and ketone bodies.
2. Fatty acids are not a source of fuel for the fetus
because these compounds cannot cross the
placental barrier.
3. Placental lactogen activates lipolysis in adipose
tissue; placental estradiol and progesterone
induce insulin resistance.
4. Pregnant women enter the starved state more
rapidly.
D. Lactation
1. In late pregnancy, progesterone and prolactin
induce lipoprotein lipase in the mammary gland
to promote the development of milk-secreting
tissues.
2. During this period, the major energy source of
breast tissue is glucose.
3. Amino acids are taken up for protein synthesis.
Chylomicrons and VLDL furnish fatty acids for
TAG production.
IX. METABOLIC ADAPTATIONS IN
PATHOLOGICAL STATES
A. Diabetes Mellitus
1. This complex metabolic derangement is
characterized by a grossly abnormal usage of-
fuel. In untreated diabetes, the level of insulin is
inappropriately low while that of glucagon is too
high relative to the needs of the body. This
deficiency in insulin impairs the entry of glucose
into the cells.
2. As in starvation, glucose utilization in diabetes is
poor, but glucose is actually present in excessive
UST FMS MEDICAL BOARD REVIEW 2019
METABOLIC INTEGRATION
ASSOC. PROF. IMELDA A. DAKIS M.D.
amounts. This is truly a form of “starvation in
the midst of plenty.”
3. With failure of insulin to promote glucose
consumption, the sugar accumulates in the
blood and starves the cells of nutrients,
producing metabolic responses similar to those
of fasting.
a. Glycolysis and glycogenesis are inhibited
in all major tissues.
b. Liver cells attempt to generate more
glucose through gluconeogenesis. This
increases further the blood glucose level
in a well-fed state.
c. TAG depots are mobilized. Fatty acid
oxidation is enhanced, with concomitant
increase in production of acetyl CoA and
ketone bodies, which can eventually lead
to ketoacidosis.
d. Increase in blood fatty acid levels leads
to an increased intake of fatty acids by
the liver. The excess is exported as VLDL
and this leads to hypertriglyceridemia.
4. Type I (insulin-dependent) diabetes mellitus is
characterized by a defect in -cell production of
insulin in the presence of high blood glucose
concentration. Since insulin-glucagon ratio
cannot increase, the liver is always
gluconeogenic and ketogenic. Ketoacidosis
develops from accumulation of ketone bodies
and H+ ions.
5. Type II (insulin-independent) diabetes mellitus is
caused by -cell failure and insulin resistance is
characteristic. The amount of insulin produced is
inadequate to control glucose production by the
liver or promote glucose uptake by muscle.
Ketoacidosis rarely develops because enough
insulin is available to prevent uncontrolled fatty
acid release from adipose tissue.
B. Liver Disease
1. Liver damage, especially in the advanced-
stages, is coupled with major metabolic
derangements, particularly involving the amino
acids.
2. In liver cirrhosis, for example, the hepatocytes
are not capable of converting ammonia to urea-
and glutamine rapidly enough, and the blood
ammonia rises.
C. Cancer
1. Tumor cells function independently of the
starve-feed cycle. They exhibit an incessant
demand for glucose as a source of energy and
amino acids for protein synthesis.
2. Glucose is the preferred fuel of tumor tissues.
3. Cancer cells rarely adapt in the fasting state to
use fatty acids and ketone bodies.
4. They are unresponsive to hormonal changes
that influence metabolic processes in normal
tissues.
5 | BIOCHEMISTRY
 METABOLIC INTEGRATION
ASSOC. PROF. IMELDA A. DAKIS M.D.

X. REGULATION OF APPETITE, ENERGY

CONSUMPTION, AND BODY WEIGHT

A. Neuronal Control of Appetite

 The arcuate nucleus contains two types of
cells that influence the intake of food and the
utilization of energy:
a. Neuropeptide Y (NPY) and Agouti-related
peptide (AgRP) are potent stimulators of
food intake and inhibitors of energy
expenditure.
b. Pro-opiomelanocortin (POMC) and
Cocaine-Amphetamine-Regulated
Transcript (CART).

B. Hormonal Control of Appetite

1. Leptin is the protein product of the Ob gene.

Secreted by the adipose cells, it informs the
brain of the body fat store level. It acts on the
hypothalamus to directly stimulate the oxidation
of fatty acids and inhibit accumulation of lipids
in non-adipose tissue.
2. Insulin stimulates the uptake of glucose by
muscle and adipose cells and storage of glucose
as glycogen in liver and muscle. It stimulates
POMC/CART neurons that will inhibit food intake
and stimulate energy expenditure.
3. Ghrelin, secreted by an empty stomach and a
short-term regulator of appetite, is a gastric
peptide containing 28 amino acid residues. It is
the only known appetite-stimulating hormone.
4. PYY3-36 is secreted in the gastrointestinal tract
proportionally with caloric intake. As a short-
term regulator of appetite, it inhibits further
food intake.

-------------------------------------------------------------------

REFERENCES
1. Devlin TM, Textbook of Biochemistry with Clinical
Correlations, John Wiley Sons, Inc.
2. Murray RK, Granner DK, Rodwell VW, Harper’s
Illustrated Biochemistry
McGraw-Hill Companies, Inc.
3. Marks DB, Marks AD, Smith CM, Basic Medical
Biochemistry A Clinical Approach
Williams & Wilkins Company
4. Gilbert HF, Basic Concepts in Biochemistry McGraw-
Hill Companies
5. FNRI-DOST, PDRI 2015 Philippine Dietary
Reference Intakes Summary of
Recommendations

UST FMS MEDICAL BOARD REVIEW 2019 6 | BIOCHEMISTRY


CHOOSE THE BEST ANSWER:
_____ 1. Which metabolic enzyme does not promote
fuel storage?
A. acetyl CoA carboxylase
B. branching enzyme
C. glucose 6-phosphatase
D. glycogen synthase
_____ 2. Which metabolic intermediate interlocks
glycolysis, fatty acid degradation, and oxidation of
ketogenic amino acids?
A. acetyl CoA
B. citrate
C. glucose 6-phosphate
D. oxaloacetic acid
_____ 3. The reason for protein not being an
efficient metabolic fuel is that:
A. a gram of protein provides only 2 kcal of
energy
B. it is the chief source of fuel for muscle
tissues only
C. its only function is to build up and repair
tissues
D. only limited amounts of it can be oxidized
for energy
_____ 4. Glycogen that is stored in skeletal muscle
is chiefly intended for:
A. allowing the recycling of metabolic
intermediates during muscle activity
B. maintaining normal blood glucose
concentration
C. providing immediate fuel supply during
muscle activity
D. saving phosphocreatine for future ATP
synthesis
_____ 5. The chief role of glycogen stored in the
liver is to:
A. abort hyperglycemia after a meal
B. furnish energy to the skeletal muscles
during physical activity
C. keep blood glucose levels between meals
within normal range
D. sustain adequate energy reserve for at
least three days
_____ 6. Which is correct regarding lipid as a major
metabolic fuel?
A. Around 85% of the total body fuel
reserves is triacylglycerol.
B. Each gram of fat yields less energy than a
gram of glucose does.
C. A huge portion of dietary fat is
transformed to glucose in the liver.
D. Its storage form is mobilized to keep the
energy needs of the brain in sleep.
_____ 7. A low insulin-glucagon ratio promotes:
A. glucose uptake of adipose and muscle
B. production of glucose from lactate,
glycerol, and alanine
C. storage of fat as triacylglycerols in adipose
D. synthesis of liver and muscle glycogen
UST FMS MEDICAL BOARD REVIEW 2019
REVIEW TEST
ASSOC. PROF. IMELDA A. DAKIS M.D.
_____ 8. Which metabolic characteristic is typical of
fuel utilization by the heart muscle cells?
A. fuel substrate metabolism regardless of
availability of oxygen
B. storage of significant amounts of fuel
reserve
C. preference for fatty acids for primary fuel
D. mobilization of triacylglerol stores by
hormone-sensitive lipase
_____ 9. A young man slept from 11:00 p.m. to
6:00 a.m. the following day. It is most likely that
during the hours that he was asleep:
A. glucose generation from lactate, pyruvate
and alanine was significantly rapid
B. glycogen degradation in liver was the
main source of fuel of the tissues
C. triacylglycerol stores in adipose tissue
were increased to a great extent
D. uptake and utilization of glucose in most
cells were activated
_____ 10. The alcohol intake of an individual should
be counted in the daily planning of meals because:
A. alcohol is metabolized slowly in the liver
B. ethanol is directly converted to glucose
and fatty acids during metabolism
C. each gram of ethanol yields 7kcal of
energy
D. starch and alcohol provide equal amounts
of calories per gram
_____ 11. A healthy and non-diabetic 25-year old
office secretary goes into a very low carbohydrate,
moderate fat, high protein diet. Which metabolic
effect is expected while she is on this dietary
regimen?
A. a less than normal insulin response
B. a long well-fed state
C. a pronounced elevation of blood glucose
D. ketogenesis that leads to ketoacidosis
_____ 12. A 29-year old ex-ramp model whose
desirable body weight is 56 kg, presently weighs 70
kg. Becoming less attractive than before, she
becomes depressed and binges on fast-food meals
and takes in-between meals about every two hours.
In her current nutritional state:
A. glucagon is the predominant hormonal signal
B. glycolysis and glycogenesis are inactive
C. stored fat is incompletely used up during
the too short fasting phase
D. there is lack of acetyl CoA for energy
generation
_____ 13. A 57-year old company executive, a
diabetic, is non-compliant with his medications and
prescribed dietary program for over a year now.
Recent laboratory tests show elevated FBS and
HbA1c values. Which metabolic event is expected to
supply the fuel needs of his tissues?
A. inhibition of ketone body synthesis
B. inactivation of gluconeogenesis
C. mobilization of TAG depot
D. promotion of glycolysis and glycogenesis
| BIOCHEMISTRY
 REVIEW TEST
ASSOC. PROF. IMELDA A. DAKIS M.D.

For nos. 20-21. A 25-year old call center agent,

For nos. 14-15. A 52-year old traffic enforcer is whose desirable body weight is 60kg, consumes, on
found stuporous, with face flushed, breath strongly the average, 300 grams of carbohydrate each day.
smelling of alcohol. His blood pressure is 170/90 mm
Hg., cardiac rate 115/min, respiration shallow, _____ 20. How many calories from carbohydrate
respiratory rate 15/min; plasma glucose 2.5 mmol/L does he actually obtain daily?
(normal 3.3-8.4 mmol/L); blood lactate 2.9 mmol/L A. 2700
(normal 0.7-2.0 mmol/L); plasma alcohol B. 2100
concentration 98 mmol/L (normal 17.4 mmol/L). C. 1800
D. 1200
_____ 14. The blood glucose level of the patient is a
result of: _____ 21. Approximately, in what amount (in
A. activation of triacylglycerol synthesis into grams) should he take in protein from his diet
VLDL according to the recommended intake for a normal
B. hyperactivity of the Krebs cycle in the Filipino adult?
peripheral tissues A. 100
C. inhibition of gluconeogenesis in the liver B. 70
D. stimulation of beta-oxidation inside the C. 50
mitochondria D. 30

_____ 15. The blood lactate concentration is _____ 22. Which feature is correct about leptin?
explained by: A. enhances food intake
A. a high NADH-NAD+ ratio B. inhibits fatty acid oxidation
B. an excess of intermediates from muscle C. promotes lipid storage in non-adipose
glycogenolysis tissues
C. failure of fatty acid biosynthesis in D. secreted by the adipose cells
adipose
D. lack of substrate for the Cori cycle _____ 23. Ghrelin is a peptide that stimulates the
intake of food by:
_____ 16. Because of the increased availability of A. accelerating energy consumption by the
glycolytic enzymes and glucose transporters in body
cancer tissue, tumor cells exhibit an incessant B. activating the NPY/AgRP neurons in the
demand for: arcuate nucleus of the hypothalamus
A. acetyl CoA C. blocking the action of appetite-reducing
B. fatty acids hormones in the brain
C. glucose D. causing the release of melanocyte-
D. oxaloacetic acid stimulating hormone

_____ 17. Which amino acid must be supplied in the

diet?
A. alanine
B. aspartic acid
C. glutamic acid
D. threonine

_____ 18. Which recommendation is correct for

dietary intake of lipids?
A. Linolenic acid and arachidonic acid should
always be present in the diet.
B. Saturated fats must comprise 50% of the
total fat intake.
C. The daily consumption of cholesterol
should be less than 300mg/day.
D. Trans-fatty acids may replace saturated
fat in the daily meals.

_____ 19. An individual who is watchful of his blood

cholesterol levels should avoid:
A. avocado
B. cheese from skim milk
C. egg white
D. fish roe

UST FMS MEDICAL BOARD REVIEW 2019 | BIOCHEMISTRY

 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
JOSE S. BLAS, MD

I. CHEMISTRY OF NUCLEIC ACIDS E. Structure of Nucleic Acids

1. DNA Structure (Watson and Crick model)
A. Nucleic acids, DNA and RNA are polymers of a. Polymer of deoxyribonucleotides
nucleotides, the basic building blocks of nucleic acids linked by 3’-5’ phosphodiester
bonds; sugar- phosphate as
B. Nucleotides contain three units: backbone; Bases found include
1. Sugar (ribose or deoxyribose) A, G, C and T
2. Base
a. purines: adenine (A), guanine (G), b. Double stranded right handed
hypoxanthine (H) helix, with antiparallel complementary
b. pyrimidines: cytosine (C), thymine strands. One chain runs in a 5’ to 3’
(T), uracil (U) direction while the other in a 3’ to 5’
3. Phosphate group direction. Adenine (A) always base
pairs thru hydrogen bonding with
C. Nucleoside consists of a sugar with a base in thymine (T) and guanine (G) with
glycosidic linkage to C1 and a nucleotide is a cytosine(C); there are 10 bases per
nucleoside with one or more phosphate groups in an turn of the helix and makes a
ester linkage to C5. complete turn every 3.4 nm; bases
are perpendicular to the helix;
Purine nucleoside - root word + osine,
e.g. Adenine + osine = adenosine; c. Base pairing is reflected by
Pyrimidine nucleoside – root word + idine Chargaff’s rule that states:
e.g. cytosine + idine = cytidine Purines (A +G) = pyrimidines (C+T)
and purine/ pyrimidine = 1 (A/T = 1;
G/C = 1)

d. DNA helix is stabilized by hydrogen

bonding between bases on complementary
strands as well as stacking and hydrophobic,
Van der Waals forces between bases, and
ion-ion interactions, AT base pairs have two
H bonds and GC have three H bonds.

D. Function of Nucleic Acids/ Nucleotides:

1. Nucleic acids are repository molecules for
genetic information.
2. Nucleotides are substrates for DNA synthesis
(replication) and RNA synthesis
(transcription)
3. Nucleotides are carriers of high energy
groups e.g. ATP, UDP glucose, CDP choline
acetylCoA, acylCoA S- adenosylmethionine.
4. Nucleotides are components of
coenzymes: NAD, NADP, FAD, CoASH.
5. Nucleotides as regulatory molecules: e. Eukaryotic DNA is stabilized and bound to
cyclic AMP, cyclic GMP. basic proteins called histones. Their basic
charge enables the histones to bind to the
phosphate backbone of DNA. DNA wraps
around a core of eight histone molecules,
(two molecules each of H4, H3, H2B and
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 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
JOSE S. BLAS, MD

H2A) producing a nucleosome. The translated into proteins; considered an adapter-

polynucleosome consists of several
nucleosome joined by a linker histone H1.
The arrangement produces an appearance
of beads on a string. The chromatin formed
from the DNA-protein complex is condensed
into chromosomes.
molecule that binds to mRNA through its
anticodon arm.
III. rRNA in eukaryotes constitutes 65% of
ribosomes; contains a large (60S) and smaller
subunit (40S) to form an 80S molecule with other
protein molecules; prokaryotes have 50S (larger)
and 30S (smaller), collectively called the 70S
rRNA.

E. Denaturation of DNA:
I. Unwinding of double stranded DNA when
subjected to high temperatures, pH extremes
and certain chemicals.

II. Produces a hyper chromic effect, which is

increased in ultraviolet (UV)absorption at 260nm II. NUCLEOTIDE METABOLISM
and a decrease in viscosity.
A. Purine Nucleotide Synthesis
III. Polynucleotides denature at certain 1. De Novo Pathway of purine synthesis involves
temperatures called melting temperature (Tm). the assembly of all the C and N atoms from
GC rich regions form more stable double helices various precursor
than AT rich regions, thus GC rich DNA has molecules: glycine (C4, C5, N7), glutamine (N3,
higher Tm than AT rich DNA. N9), aspartate (N1), Carbon dioxide (C6), and
formyltetrahydrofolate (C2, C8)
IV. When denatured polynucleotides are cooled
or when denaturing agents are removed,
complementary single stranded regions
reassociate in a process called annealing.
Annealing is the basis for hybridization
(DNA/RNA) in the use of probes in recombinant
DNA technology, e.g. Southern Blot

2. RNA Structure
a. Polymer of ribonucleotides linked by 3’-5’
phosphodiester bonds; single stranded but may
form internal double stranded regions
sometimes called hairpin loops.
2. Synthesis of 5’ phosphoribosyl-1-pyrophosphate
b. Bases found are A, G, C and uracil (U) instead of (PRPP) occurs at the beginning of the process
T catalyzed by ribose phosphate
pyrophosphokinase or PRPP synthase from ATP
c. Three classes of RNA: and ribose-5-phosphate. IMP, AMP and GMP
I. mRNA: carries genetic information (codon) to inhibit this step.
be translated into proteins;
unique base sequences and a 7-methyl 3. The committed step involves the conversion of
guanosine cap at the 5’ end and a polyadenylic PRPP to 5’ phosphoribosyl-1- amine. PRPP
acid tail at 3’ end. activates the enzyme glutamine PRPP
amidotransferase and the products of the
II. tRNA: smallest RNA which assumes pathway inhibit the enzyme. The end products
secondary structure similar to a cloverleaf are:
appearance; contains atypical bases; carries the
specific amino acid to the ribosomes to be
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 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
a. IMP- formed on the amino group of
phosphoribosylamine by a 9-reaction
sequence
b. GMP, formed by the addition of an amino
group to C2 of IMP
c. AMP, formed by the substitution of
an amino group for the oxygen at C6.
4. Regulation of Purine Synthesis
a. Regulation occurs at the final branches
of the de novo pathway to provide a
steady supply of purine nucleotides
- GMP and AMP both inhibit the first step
in their own synthesis from IMP
- GTP is a substrate in AMP synthesis and
ATP is a substrate in GMP synthesis.
Reciprocal substrate effect balances the
supply of adenine and guanine
ribonucleotides
b. Interconversion among purine
nucleotides ensures control of the
levels of adenine and guanine
nucleotides
- IMP is the starting point for synthesis of
AMP and GMP
- AMP deaminase converts AMP back to
IMP
- GMP reductase converts GMP back to
IMP
5. Salvage pathway involves the synthesis of
purine nucleotides from preformed bases
through two enzymes:
a. Hypoxanthine-guanine
phosphoribosyltransferase (HGPRT). IMP
and GMP are competitive inhibitors of
HGPRT
Mg++
Guanine + PRPP  GMP + PPi
Mg++
Hypoxanthine + PRPP  IMP +PPi
b. Adenine phosphoribosyl transferase. AMP
inhibits this enzyme
Mg++
Adenine + PRPP  AMP + PP
A. Pyrimidine Nucleotide Synthesis
1. Synthesis of pyrimidines differs from that
of purines in that the pyrimidine ring is
synthesized first and is then attached to
ribose phosphate.
2. The origin of the atoms in the pyrimidine
ring are carbon dioxide and glutamine
via carbamoyl phosphate (C2, N3) and
aspartate (C4, C5, C6, N1)
UST FMS MEDICAL BOARD REVIEW 2019
JOSE S. BLAS, MD
3. De novo synthesis starts with the synthesis of
carbamoyl phosphate (CAP) using carbon dioxide,
glutamine and ATP by the action of cytosolic enzyme
carbamoyl phosphate synthase II. (CPS II)
4. Synthesis of dihydroorotic acid, a pyrimidine,
involves a 2-step process.
a. The committed step is the addition
aspartate to CAP, catalyzed by
transcarbamoylase, to form carbamoyl
aspartate.
b. Ring closure with a loss of water, catalyzed
by dihydroorotase produces dihydroorotic
acid.
5. Dihydroorotate forms UMP
a. Addition of ribose-phosphate
moiety from PRPP by orotate
phosphoribosyl transferase
produces orotidylate (OMP)
b. Decarboxylation of OMP produces
uridylate (UMP)
c. From UMP the other pyrimidine
nucleotides (CTP and TMP) are
synthesized
6. Regulation of pyrimidine synthesis occurs at
several levels:
a. UTP inhibits carbamoyl phosphate
synthase II while ATP and PRPP
activate this enzyme
b. UMP and CMP inhibit OMP
decarboxylase
c. CTP inhibits CTP synthase
7. Salvage of pyrimidines is accomplished by
the enzyme pyrimidine phosphoribosyl which can
use orotic acid, uracil or thymine but not cytosine,
with PRPP as source of the ribose phosphate
Orotic acid + PRPP  OMP + PPi
Uracil + PRPP UMP +PPi
Thymine +PRPP  TMP + PPi
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 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
JOSE S. BLAS, MD

e. Reaction is inhibited by anticancer

agents:
- 5 fluorouracil (5FU) inhibits
thymidylate synthase
- aminopterin and methotrexate
inhibit dihydrofolate reductase

D. Nucleotide Degradation
1. Purine degradation in man involves uric acid
formation and its urinary excretion; other species
excrete different forms e.g. allantoin, ammonia.
a. Sequential actions of nucleases and
nucleotidases lead to hydrolysis of nucleic
acids to nucleosides.
b. Adenosine deaminase converts adenosine
and deoxyadenosine to inosine or
deoxyinosine
c. Purine nucleoside phosphorylase splits
inosine and guanosine to ribose- 1-phoshate
and the free bases, hypoxanthine and
guanine.
d. Guanine is deaminated to xanthine.
e. Hypoxanthine and xanthine are oxidized to
uric acid by xanthine oxidase.
f. Xanthine oxidase is inhibited by allopurinol

C. Deoxyribonucleotide Synthesis
1. Formation of deoxyribonucleotides, required for
DNA synthesis, involves reduction of the ribose
moiety of ribonucleoside diphosphates
a. Ribonucleotide reductase converts ADP,
GDP, CDP, and UDP to dADP, dGDP, dCDP,
and dUDP, respectively.
b. Thioredoxin with sulfhydryl groups acts as
reducing agent.
c. Thioredoxin reductase converts oxidized
thioredoxin back to reduced form, using
NADPH + H.
d. Reduction requires presence of
nucleoside triphosphate as allosteric
activator, with dATP as an allosteric
inhibitor.

2. Thymidylate synthase catalyzes the formation of

deoxythymidylate (dTMP) from dUMP,
2. Pyrimidine degradation produces amino
a. Transfer of a one-carbon unit from
acids, CO2 and NH4+
N5, N10- methylene etrahydrofolate
a. Excess nucleotides are degraded to
(THF) to C5 of the uracil ring
the free bases uracil or thymine
b. Reduction of methylene group to
b. Reaction sequence consisting of
methyl group and oxidation of THF
reduction, ring opening and
to dihydrofolate (DHF)
deamination- decarboxylation converts
c. Reduction of dihydrofolate back to
uracil to CO2, NH4+ and -alanine.
THF by dihydrofolate reductase
Thymine is converted to CO2, NH4+
(DHFR), requiring NADPH as cofactor
and -amino isobutyrate, an indicator
d. Remethylation of FH4 at the expense
or DNA turnover.
of serine, by enzyme serine
hydroxymethyl transferase
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 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
E. Clinical Disorders of Purine and Pyrimidine
Metabolism
1. Hereditary Orotic Aciduria: deficiency of
orotate phosphoribosyl transferase and/or
OMP decarboxylase leads to increased
urinary excretion of orotic acid and
decreased production of pyridine nucleotides
needed for both RNA and DNA synthesis,
characterized by retarded growth, severe
anemia (megaloblastic).
2. Purine nucleoside phosphorylase deficiency
leads to increased levels of purine
nucleosides with decreased uric acid
formation and impaired T cell function
3. Severe combined immunodeficiency (SCID)
caused by adenosine deaminase deficiency.
It leads to impaired T and B cell dysfunction
with death due to overwhelming infection.
SCID has been treated using gene therapy
4. Lesch-Nyhan Syndrome. Partial or absence
of HGPRT, salvage enzyme leads to
excessive purine synthesis, hyperuricemia,
severe neurologic problems like spasticity,
mental retardation, self-mutilation.
Unsalvaged hypoxanthine and guanine leads
to decreased IMP and GMP and de novo
pathway becomes stimulated due to
increased levels of PRPP. Unsalvaged
purines are then degraded to uric acid.
5. Gout, a form of arthritis associated with
hyperuricemia could be primary due to
defects in enzymes of purine metabolism or
secondary to other clinical disorders
a. Uric acid which is not very soluble in body
fluids are deposited in joints and soft tissues
causing the inflammation characteristic of
gouty arthritis. Crystals can also be
deposited in the kidneys leading to renal
damage (gouty nephropathy)
b. Primary gout involves overproduction
of purine nucleotides via de novo
pathway which could be due to:
- mutations in PRPP synthase with
loss of feedback inhibition by
purine nucleotides
- partial HGPRTase which causes
accumulation of PRPP that
activates PRPP amidotransferase
- abnormal structure of PRPP
Amidotransferase
c. Secondary Gout may be due to excessive
turnover of purines due to cancer
chemotherapy, radiation therapy, leukemia.
d. Gout is frequently treated with allopurinol, a
structural analog of that inhibits xanthine
oxidase Xanthine oxidase can convert
allopurinol to alloxanthine.
UST FMS MEDICAL BOARD REVIEW 2019
JOSE S. BLAS, MD
III. GENE EXPRESSION (INFORMATION
METABOLISM)
A. Genetic information found in DNA is
ultimately expressed into proteins,
following the Central Dogma of Molecular
Biology. The flow of genetic information
proceeds from DNA replication,transcription
into RNA and translation into proteins.
DNA  RNA  Proteins:
Replication Transcription Translation
B. The three major processes (replication,
transcription, translation) consist of
subprocesses which includes initiation,
elongation and termination
C. The genetic code describes the relationship
between the polynucleotide alphabet of
the four bases (A, G, T, C) in DNA and the 20
amino acids in proteins. The base
sequences in one strand of parental DNA
dictate the amino acid sequences of
proteins. Characteristics and properties of
the genetic code:
1. Universal- same in all organisms
2. Contiguous- the codons do not overlap
and are not separated by spacers
3. Specific or unambiguous – the three
nucleotide sense codon specifies only
one amino acid
4. Degenerate- there is more than one
codon for the same amino acids
D. DNA synthesis (Replication) which takes
place during the S phase of the cell cycle is
the production of two double stranded DNA
molecules that are identical in every way to
the parent DNA. Eukaryotic replication is
semiconservative. i.e. each daughter DNA
contains one strand of parental DNA and
one newly synthesized daughter strand.
Replication is unidirectional.
Stages:
1. Pre-priming stage involves a ssDNA
binding proteins and DNA unwinding
proteins or helicases that unwind the
DNA duplex. Topoisomerases (DNA
gyrase) relieve the strain imposed by
unwinding.
2. Initiation involves the use of primase
Which makes RNA primers that are
complementary to the DNA template
strand. This process moves in the 5’-to
3’ direction on the newly synthesized
primer.
3. Elongation involves the addition of
nucleotides (dNTPs) at the 3’ end of
the primer by DNA polymerase (DNAP)
III in prokaryotes ( and  in
eukaryotes). DNAP III possesses
editing function due to its 3’-5
exonuclease activity, i.e. detects and
removes mismatched base pairs and
5 | BIOCHEMISTRY
 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
JOSE S. BLAS, MD

replaces correct bases. DNAP  in

eukaryotes carries out repair. PPi is
released during polymerization.
4. Replication is continuous in the leading
strand and discontinuous in the lagging
strand. DNAP  in eukayotes copies
the lagging strand and DNAP copies
the leading strand RNA primers are
removed with nick translation by
DNAP I. DNAP  carries out
mitochondrial replication in
eukaryotes. Segments of newly
synthesized DNA, in the lagging
strand are called Okazaki fragments
5. Termination involves the joining of the
ends of the synthesized Okazaki
fragments by DNA ligase. (sealing of
nicks)
6. In eukaryotes, DNA is associated with
nucleoprotein histones.
7. Replication is inhibited by the Ara-A and
Ara-C and by Actinomycin D which
intercalates between GC sequences,
blocking the elongation.process;
Ofloxacin inhibits gyrase.

E. Transcription is the process that leads to

synthesis of RNA, with a sequence that is
complementary to that of the DNA template.

1. RNA polymerase (RNAP) is the main

enzyme that synthesizes RNA from DNA.
In eukaryotes several types of RNAP exist:
a. RNAP I: synthesizes rRNA
b. RNAP II: synthesizes mRNA
c. RNAP III:synthesizes tRNA and 5S Rrna
d. mitochondrial RNAP: transcribes RNA
from mitochondrial genes

2. Transcription Cycle occurs as follows:

a. Binding: RNAP binds to specific promoter

sequences on the DNA, which orients the
RNAP on the sense strand in apposition to
begin transcription. Both prokaryotic and
eukaryotic promoters have consensus
sequences “upstream” of the start site.
 Promoter regions in eukaryotes include a -25
TATA box (Hogness box) and a -75 CAAT
region.
 Promoter regions in prokaryotes include a -10
TATAAT region (Pribnow box) and a -75
TTGACA region. A short stretch of DNA duplex
unwinds to form a transcription bubble.
 Unlike DNA replication, no RNA primers are
needed for transcription, and only one DNA
strand is transcribed.
 RNAP holoenzyme is composed of ’
subunits. Polymerase activity resides in the
’; the  subunit recognizes the promoter
region

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 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
b. Initiation involves the formation of the first
phosphodiester bond. ATP or GTP forms a
base pair with the template base on the
antisense strand at the origin, and then the
base of the next nucleoside triphosphate
pairs with the next template base and
forms a phosphodiester bond with the ATP or
GTP, eliminating PPi
c. Elongation proceeds along the DNA sense
strand, with the RNA growing in the 5’-to-3’
direction. NTPs are added with release of PPi
The DNA duplex reforms behind the
enzyme, and the 5’ end of the RNA is
released as a single strand.
d. Termination. In prokaryotes, this occurs at
the site of a stem loop (hairpin loop followed
by a string of Uracils). The presence of a
rho protein makes this process more
efficient. Termination signals in eukaryotes
are poorly understood.
3. RNA processing or post transcriptional
processing involves modification of RNA in
eukaryotes. Unprocessed eukaryotic mRNA
is also called heterogenous nuclear RNA
(hnRNA)
a. 7 methyl guanosine cap at the 5’ end of
mRNA provides protection against nuclease
digestion and help in alignment of the mRNA
during translation.
b. Poly (A) tail in the 3’ end of mRNA
c. RNA splicing removes introns or intervening
segments in mRNA and joining of exons.
Small nuclear RNA helps in splicing
d. Addition of ACC at 3’ end and modification
of bases in tRNA.
4. Certain drugs that inhibit transcription
include rifampicin and streptolydigin which
binds and inhibits RNAP. Actinomycin D
binds to DNA template and inhibits
elongation process. Coumermycin, Nalidixic
acid and Novobiocin are antibiotics that
inhibit topoisomerases
UST FMS MEDICAL BOARD REVIEW 2019
JOSE S. BLAS, MD
F. Translation (Protein Synthesis) involves the
polymerization of amino acids in a precise
sequence directed by the sequence of bases
in mRNA. Steps consist of the following:
1. Activation of amino acids. An amino acid is
activated by binding to the 3’ end of a tRNA
catalyzed by aminoacyltRNA synthase at
the expense of ATP producing an
aminoacyltRNA + AMP + PPi. The first
amino acid to be translated is methionine
(fmet in prokaryotes) as would be indicated
by the first codon AUG, in the mRNA.
2. Formation of the Initiation complex.
a. The 40S initiation complex is formed
when the 40S rRNA binds to initiation
factors (eIFs), GTP and met- tRNA. The
binding enables the mRNA to bind to the
40S subunit.
b. As certain initiation factors are released
and GTP is hydrolyzed, the 40S initiation
complex joins the 60S subunit.
c. The met- tRNA occupies the P site of
the ribosome with the AUG codon and
with an empty A site, the resulting
complex is called 80S initiation complex.
In prokaryotes a purine rich region in
the mRNA called Shine Dalgarno
sequence binds to the 16S subunit of
the 30S rRNA to stabilize the binding of
the mRNA to the 30S subunit.
The 7-methyl guanosine cap in
eukaryotes is its counterpart
3. Elongation phase is a three-step cycle that
repeats each time an amino acid is added.
a. The incoming AA-tRNA binds to the
aminoacyl (A) site of the large 80S
subunit, requiring several elongation
factors (EFs) and the hydrolysis of GTP.
b. Peptidyl transferase catalyzes the transfer
of the amino acid or the peptide from the
P site to the AA-tRNA on the A site, with
The formation of the peptide bond. The
“uncharged” tRNA dissociates from the
complex.
c. The new peptidyl t-RNA moves to the P
site (i.e., the ribosome moves three
nucleotides over on the mRNA), requiring
EF-2 and GTP hydrolysis. The ribosome
moves along the mRNA in the 5’-to-3’
direction and the peptide chain grows
from the N terminus to the C terminus.
d. After the ribosome has “moved” out of
the way, another ribosome can begin
translation at the initiation codon. An
mRNA with several attached ribosomes
are carrying out translation is known as a
polyribosome or polysome.
4. Termination. The process occurs when the
ribosome encounters a nonsense
(termination) codon, i.e. UAA, UAG, UGA,
which signals termination and release of
the polypeptide.
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 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
a. A protein releasing factor (RF)
together with GTP binds to the A site,
instead of a AA-tRNA)
b. Peptidyl transferase hydrolyzes the
peptidyl-tRNA, with the release of
the completed polypeptide. GTP is
hydrolyzed to GDP and Pi occurs.
c. The ribosomes, dissociate into subunits
5. Wobble. The codon in mRNA (3’ base) and
the anticodon in tRNA (5’ base), can
“wobble” at the nucleotide –nucleotide
pairing site. In the tRNA anticodon, the
wobble base is often inosine, which can
pair with U, C, or A in the mRNA. In
mRNA, G in the wobble position can pair
with U or C; U in the wobble position can
pair with A or G. Because of wobble fewer
than 61 tRNAs are needed to translate
the 61 sense codons of the genetic code.
6. Post-translational modifications. The first
amino acid translated, methionine
(f-met in prokaryotes) are removed. The
amino acid sequence, e.g. signal
recognition sequence, and conformational
shape of a protein will determine its fate,
whether it is to be targeted to a particular
site or to be a substrate for modifying
enzymes. They will also determine its half
life. Proteins can also be co-translationally
modified. Modifications include:
a. crosslinking by disulfide bonds
b. excision of a polypeptide chain.
e.g. proinsulin to insulin
c. glycosylation
7. Various antibiotics inhibit translation in
prokaryotes. Tetracyclines inhibit binding
of tRNA to the 30S ribosomal subunit.
Streptomycin affects all phases of
translation, Erythromycin inhibits the
function of 50S rRNA, Chloraphenicol
inhibits peptidyl transferase and
Puromycin mimics an aminoacylt RNA
causing premature termination.
UST FMS MEDICAL BOARD REVIEW 2019
JOSE S. BLAS, MD
G. Regulation of Gene Expression. Regulation
can take place in all phases of gene
expression, from replication through
translation but major control takes place
during the transcription process.
Regulation in prokaryotes differ that
that of eukaryotes.
1. Prokaryotic gene regulation.
a. An operon refers to the prokaryotic
genetic unit in which several genes are
clustered and transcribed into a
polycistronic mRNA.
b. Regulatory genes code for proteins that
in turn control the expression of genes
by binding to control elements at sites
on the DNA near the structural gene.
Regulatory proteins control the degree
of access that the enzyme RNA
polymerase has to its binding site on
the gene. Two types of regulatory
protein have been found
- negatively acting which represses the
operon by binding to the operator
- positively acting which enhance the
affinity of RNAP for its binding sites
on the gene.
c. A good example of an operon is the
lactose operon in E. coli. Expression of
the operon is regulated by an inducer
(lactose or allo lactose) and by a
repressor protein, expressed by the
i gene. The i gene, situated just
before the controlling element for the
cluster of genes coding for three
enzymes is important for lactose
utilization by the cell. The i gene is
continually expressed into a repressor
protein which binds to a specific DNA
sequence between the promoter and
operator gene. This binding blocks the
binding of RNA to the promoter, and
the operon is said to be repressed,
especially so if glucose is abundant in
the cell.
d. Derepression of the operon could be
achieved by an inducer, lactose or
allolactose in the case of lactose
operon. Lactose (and
isopropylthiogalactose)
binds to the repressor protein causing it
to change in conformation which
drastically lowers its affinity to the DNA
sequence to which it usually binds,
paving way to the binding of RNAP to
the promoter.
e. The lac operon is repressed if there is
plenty of glucose even despite
abundance of lactose. This is called
catabolite repression. The cell will only
turn to lactose as a substrate when
glucose concentrations fall. When
glucose concentration is high, the
second messenger cyclic AMP are low.
When glucose concentrations are low,
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 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
cAMP rises and binds to a protein called
catabolite activator protein (CAP.). CAP
undergoes a conformational change as a
result of the binding reaction. This
enables CAP to bind to the promoter,
and this in turn facilitates binding of
RNA polymerase to the promoter
f. Another regulation using the operon
model is the regulation thru repression.
A co- repressor needs to bind to the
repressor in order to inhibit the RNAP
from binding to the promoter. This
model is exemplified by the tryptophan
(trp) operon with tryptophan as a co-
repressor for expression of enzymes for
trp synthesis.
2. Eukaryotic gene regulation. Gene control
has three main components namely,
signals, levels of regulation, and mechanisms
of transcriptional control.
a. Signals include hormones, protein factors
and environmental conditions such as
heat shock.
b. Control in the levels of regulation
involve, nuclear RNA synthesis,
differential processing of primary
transcripts, and alteration in mRNA
stability in the cytoplasm.
i. Control of nuclear RNA synthesis is
effected mainly at the initiation stage
Initiation is activated by transcription
factors (activators) which may
interact with genomic promoters, in
order to guide the RNA polymerase II
to the correct expression of an mRNA
species
ii. Differential nuclear processing of
transcripts involves differential
choice of polyA sites on the primary
transcripts which will determine
tissue specificity of gene expression.
iii. Cytoplasmic gene control involves
The rate of protein synthesis which
could be affected by the rate of
transport of mRNA into the
cytoplasm, half-life of the mRNA,
frequency of mRNA translation, and
post translational control.
UST FMS MEDICAL BOARD REVIEW 2019
JOSE S. BLAS, MD
IV. MUTATIONS AND REPAIR
A. Mutations are heritable, unrepaired
alteration in nucleotide sequence in DNA.
Mutations can be spontaneous or induced
and may or may not be phenotypically
expressed. Gene alterations are an
important factor in biological evolution.
On the other hand, when mutation rates
are too high, they can threaten the
survival of individual organisms or entire
species. This is why cells possess repair
mechanisms that correct most of the DNA
alterations caused by mutations.
B. Various mutagenic agents can cause gene
alterations. This could arise as a result of
physical or chemical damage, from errors
during DNA replication and recombination,
and post replication errors. Viruses can also
lead to mutations and cancer.
C. Mutations may cause cellular death and if
unrepaired may affect surviving cells
undergoing organogenesis and cause
physical malformations in the organism.
Affected germ cells may lead to sterility or
genetic disorders while growth regulation
in somatic cells may be lost and lead to
cancer. Mutagenic agents causing cancer
can also be classified as carcinogen.
D. Tumors can arise when mutations occur
in proto- oncogenes and tumor suppressor
genes. Proto-oncogenes code for proteins
involved in normal cell growth and
differentiation but are converted to
oncogenes when mutated. e.g. ras, abl,
src, myc, jun. Tumor suppressor genes or
anti –oncogenes regulate cell growth but
upon mutation their suppressor function is
lost. Tumor suppressor genes are involved
in regulation of cell cycle, apoptosis and
DNA repair.e, g. p53, Rb.
E. Types of mutations include base substitution and
frameshift mutation.
1. Base substitution
a. Transition- a change from a purine
base to another purine base or a
pyrimidine to another pyrimidine. e.g.
adenine to guanine; cytosine to
thymine.
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b. Transversion – a change from purine to
pyrimidine or a pyrimidine to a
purine. e.g. adenine to thymine; .
guanine to cytosine
2. Frameshift mutation; a base deletion or
base insertion alters the reading frame
of the codon in the mRNA.
F. Base substitution and frameshift mutations
lead to:
1. Missense mutation. A different protein
may be translated with a different
protein and function. e.g. sickle cell
anemia
2. Nonsense mutation. Fomation of a stop
codon prematurely terminates protein
synthesis
3. Silent mutation. No change in amino acid
being translated due to degeneracy of
the genetic code, and no change in
protein structure and function.
G. Spontaneous mutations may be caused by
tautomeric base mispairs, simple
misalignment of repeated bases,
palindromic misalignment and
insertional mutagenesis (jumping genes or
transposons) among others.
H. Induced mutations are frequently caused
by various agents such as ionizing
radiation and chemical agents.
1. Ionizing radiation results in the
production of free radicals and can
damage DNA., with thymine the most
radiosensitive and adenine the least
radiosensitive. Short wavelength
ultraviolet light also has a mutagenic
effect on the skin cells, particularly
formation of thymine dimers. Such
dimers results in errors when DNA is
read during replication and
transcription
2. Chemical agents can be directly
mutagenic or indirectly mutagenic
when metabolized by the body to a
mutagen (promutagenic).
a. Intercalating agents such as
polycyclic aromatic hydrocarbons
insert between successive GC base
pairs and distorts the helix. This
interferes with unwinding during
replication.
b. Alkylating agents carry reactive
groups than can form covalent bonds
with DNA bases, e.g.
methylnitrosoamines, benzo(A)
pyrenes, aflatoxin, ethylene
dibromide
c. Deaminating and oxidizing agents
such as nitrous acid and
hydroxylamine converts cytosine to
uracil and adenine to inosine.
UST FMS MEDICAL BOARD REVIEW 2019
NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
JOSE S. BLAS, MD
I. DNA repair mechanisms are efficient and aim
to maintain cellular function of both germ
cells to preserve species and of somatic cells
to prevent cancer formation. Repair
mechanisms include:
1. Excision repair- nuclease removes a
complete segment of DNA on both sides
of the error site. The segment is
replaced by DNA polymerase using
the opposite strand as template. DNA
ligase closes the gaps
2. Photoreactivation- a photolyase binds at
the site of the defect (thymine dimer)
and upon illumination, cleaves dimer
to yield two single bases.
3. Recombinational repair- the region
containing the defect is omitted during
replication. The resultant gap is closed
by shifting the corresponding segment
from the correctly replicated strand. The
new gap formed is then filled by
polymerases and ligases. Finally, the
original defect is corrected by excision.
J. Protective mechanisms against mutations
could be inherently present such as the
protective structural function of cellular and
nuclear membranes. Protective enzymes
such as superoxide dismutase, glutathione
peroxidase, catalase protects the cell from
the damaging effects of reactive oxygen
species and radicals. Compounds with
protective groups such as glutathione,
acetylCoA, some amino acids and antioxidant
vitamins and minerals prevent DNA
damage.
VI. GENE TECHNOLOGY
A. Techniques for isolating and amplifying
genes and studying and manipulating DNA
sequences involve the use of restriction
enzymes, cloning, polymerase chain
reaction, gel electrophoresis, Southern
blotting and gene sequencing.
1. Restriction Analysis involves the use of
restriction endonucleases. This cuts
DNA into reproducible pieces of
manageable size. These enzymes, derived
from bacteria, cleave DNA at specific
palindromic restriction sites of 4 to 8
base pairs. e.g. EcoRI, SmaI, HaeIII
2. Gel Electrophoresis is used to separate
DNA fragments on the basis of size.
a. Agarose Gel Electrophoresis is used to
separate larger fragments,
b. Polyachrylamide Gel Electrophoresis
separates smaller fragments.; used
for sequencing DNA and preferred-
technique for protein separation
(SDS-PAGE).
3. Southern Blotting is used to detect DNA
fragments that contain specific base
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 NUCLEOTIDE METABOLISM AND MOLECULAR BIOLOGY
JOSE S. BLAS, MD

sequences. After denaturing the DNA in -number of cycles in the program. Each cycle
the gel, fragments are transferred to is programmed to denature the target DNA.
nitrocellulose and the latter is hybridized by high temperature of 90 degrees, followed
with a DNA or RNA probe. The by lowering to 60 degrees to allow the forward
hybridized DNA is detected by auto- and reverse primers to anneal at the 3’ ends
radiography if using a radioactive probe. of the target DNA to be amplified. The
temperature is raised to 72 degrees to allow
4. Restriction Fragment Length extension of primers by polymerization using
Polymorphism (RFLP) uses restriction dNTPs by using heat stable enzyme usually
enzymes to cut DNA from different Taq polymerase.
individuals having different DNA
sequences, followed by probe
hybridization. This results in DNA
fragments of different lengths due to
polymorphisms that exist among
individuals. The technique may use PCR
to amplify DNA prior to digestion by
RE, and gel electrophoresis to separate
DNA fragments and Southern blotting.

5. Cloning is a process of producing

multiple copies of identical DNA. This
could be by use of recombinant DNA in
bacteria (in vivo) or by use of PCR (in
vitro). Cloning in vivo involves production
of DNA inside genetically engineered
cultured bacteria such as E. coli by
recombinant vectors such as plasmids,
thru transformation. This is followed by
selection of recombinant clones inside
the bacteria. The recombinant DNA B. Application of Recombinant DNA
can be isolated from the bacterial colones 1. Production of vaccines and other useful
and can be propagated to create gene proteins, e.g. hormones, growth factors
libraries 2. Genetic counseling
3. Gene therapy
In Vivo Cloning: 4. Production of transgenic animals
5. Production of genetically modified
organisms (GMOs)
5. DNA fingerprinting (forensic applications)

REFERENCES:

Greenstein, Ben, Greenstein Adam, Medical Biochemistry

at a Glance.University Press, Cambridge 1996 pp 38-
39,42-45,52-55 ,90-93,
Koolman, Jan, ; Rohm, Klaus. Color Atlas of
Biochemistry.Thieme- Stuttgart, New York 1996. pp
174- 177; 218-241
Liebermann, Michael et al. Marks’ Basic Medical
Biochemistry, A Clinical Approach, 4th edition
Lippincott Williams and Wilkins, 2013
Rodwell Victor, Bender David et al. Harper’s Illustrated
Biochemistry 31sr edition, International edition.
6. DNA sequencing involves two methods.
Lange.
a. The Sanger-dideoxy method (chain
Swanson, Todd, Kim Sandra,et al BRS Review Series in
termination or enzymatic) Sanger which
Biochemistry, Molecular Biology and Genetics. Fifth
is used frequently and is the technique
Edition, Lippincott pp 203- 210; 251-276; 319-331
in automated sequencing machines.
Wilcox. R. Bruce. High Yield Biochemistry. Lippincott
b. Maxam-Gilbert method (chemical
Williams and Wilkins. pp 54-63; 77-99
method)

7. Polymerase Chain Reaction (PCR) is an

automated in vitro method of cloning
DNA fragments. Introduced by Karl Mullis.
It is used to amplify DNA exponentially
within a short period of time, based on the

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 REVIEW TEST
JOSE S. BLAS, MD

CHOOSE THE BEST ANSWER: _____ 9. Synthesis de novo of pyrimidine

nucleotides differs from that of purine nucleotides in
_____ 1. The basic building block or unit of nucleic that:
acid: A. PRPP is added after synthesis of the
A. nitrogenous base pyrimidine ring
B. nucleotide B. the C and N atoms are built around the
C. sugar phosphate backbone PRPP molecule
D. nucleoside C. there are more energy requiring steps
D. PRPP is the source of the sugar and
_____ 2. Which of the following is NOT a function of phosphate
nucleotides?
A. Substrate for RNA and DNA synthesis _____ 10. The final end product of purine
B. carriers of high energy groups catabolism in man is:
C. Components of coenzymes A. ammonia
D. Major energy source of metabolic fuel B. allantoin
C. urea
_____ 3. Which of the following is considered a D. uric acid
nucleoside?
A. adenosine _____ 11. In treatment of gout, allopurinol lowers
B. cytosine the blood level of uric acid by inhibiting:
C. guanine A. Xanthine oxidase
D. thymine B. HGPRTase
C. PRPP synthetase
_____ 4. Which of the following best describes the D. uricase
Watson Crick Model of DNA?
A. right-handed double helix with both _____ 12. The anticancer agents, aminopterin and
strands running in parallel direction methotrexate can inhibit DNA synthesis and cellular
B. hydrogen base pairing between purine proliferation by inhibiting:
and pyrimidine A. PRPP amidotransferase
C. adenine + thymine = cytosine + guanine B. dihydrofolate reductase
D. 11 base pairs per helical turn with 2.6nm C. thymidylate synthase
distance D. cabamoyl phosphate synthetase II

_____ 5. Which of the following is true of the RNA
molecule?
A. double stranded nucleic acid in a left
handed twist or coil
B. mRNA is derived from DNA thru reverse
transcription
C. tRNA is the smallest RNA
D. eukaryotic rRNA is called 70S with 50S
and 30S subunits
_____ 6. In de novo nucleotide synthesis, which of
the following are sources of atoms common to both
purine and pyrimidine rings?
A. formyl tetrahydrofolate
B. glycine
C. aspartate
D. glutamate
_____ 13. The final end product of gene expression:
A. DNA
B. RNA
C. Proteins
D. glycoproteins
_____ 14. All of the following is a correct statement
about DNA replication EXCEPT:
A. Both strands of paternal DNA are copied,
and daughter DNAs are synthesized in
the 5’  3’ direction
B. Replication is continuous in the leading
strands while discontinuous in the lagging
strand
C. Replication in eukaryotes is semi
conservative
D. Replication is an error free process

_____ 7. The sugar and phosphate moieties in both _____ 15. A type of point mutation wherein an
purine and pyrimidine nucleotide synthesis comes adenine is replaced by a thymine:
from: A. transition
A. phosphoribosyl pyrophosphate (PRPP) B. transversion
B. carbamoyl phosphate C. transformation
C. glucose 6 phosphate D. transfection
D. adenosine triphosphate
_____ 16. An error free type of DNA repair:
_____ 8. The committed step in purine nucleotide A. Excision repair
synthesis de novo is the synthesis of: B. Recombination repair
A. carbamoyl phosphate C. Photoreactivation repair
B. phosphoribosyl pyrophosphate (PRPP) D. Deletion repair
C. phosphoribosyl amine
D. carbamoyl aspartate

UST FMS MEDICAL BOARD REVIEW 2019 | BIOCHEMISTRY

 REVIEW TEST
JOSE S. BLAS, MD

_____ 17. Which of the following statements is

correct of gene transcription?
A. Both parental DNA stands are
transcribed into daughter RNAs in the 5’
 3’ direction
B. Initiation of transcription is signaled by
release of rho factor
C. RNA polymerase recognizes promoters’
regions to start RNA synthesis
D. RNA primers are required for elongation
of RNA
_____ 18. Which of the following is NOT a post
transcriptional processing of mRNA?
A. polyadenylation
B. ligation of exons
C. addition of 7 methyl guanosine cap
D. addition of histones
_____ 24. The standard method used in separating
and identification of large DNA fragments in the
laboratory:
A. polyachrylamide gel electrophoresis
B. SDS- PAGE
C. agarose gel electrophoresis
D. paper chromatography
_____ 25. This automated technique can amplify or
clone DNA exponentially in a short period of time:
A. Polymerase Chain reaction (PCR)
B. Maxam-Gilbert method
C. Sanger technique
D. Southern Blot technique

_____ 19. During protein synthesis (translation),

which of the following is a correct statement?
A. Amino acyl-tRNA binds to the smaller
subunit of the ribosome while the mRNA
binds to the larger subunit
B. Incoming amino acyl-tRNA binds to the P
site of the large ribosomal subunit
B. Peptidyl transferase forms a peptide
bond between the amino acid in the A
and P sites
D. Termination of translation occurs when
the codon AUG is encountered in the mRNA

_____ 20. Degeneracy of the genetic code means

that:
A. the genetic code used by all prokaryotes
and eukaryotes is one and the same
B. an amino acid may have more than one
triplet codon
C. a triplet codon can be coded by more
than one amino acid
D. more than one codon can be read by
one tRNA

_____ 21. All of the following have been found to

inhibit translation process of gene expression,
EXCEPT:
A. Chloramphenicol
B. Tetracyline
C. Erythromycin
D. Ofloxacin

_____ 22. All of the following molecular mechanisms

can promote proto-oncogene activation and
carcinogenesis, EXCEPT?
A. point mutation
B. genetic rearrangement
C. activation of p53 gene
D. promoter and enhancer insertion

_____ 23. Enzymes that are used in recombinant

DNA technology, that recognizes and cut palindromic
sequences:
A. Restriction endonucleases
B. DNA exonucleases
C. Taq polymerase
D. T4 DNA ligase
UST FMS MEDICAL BOARD REVIEW 2019 | BIOCHEMISTRY