De novo pyrimidine and purine synthesis

PURINES
Start with sugar + phosphate (PRPP)
Add base
Purine ring is built directly on the PRPP
Fcn: To provide purines (A and G) for energy metabolism and for DNA-RNA synthesis

Lcxn: Cytoplasm of most cells

Cnxns: To folate metabolism and one-carbon metabolism in de novo synthesis.
From HMP pathway via ribose and PRPP.
To deoxyribonucleotides through ribonucleotide reductase.
Regulxn: Availability of PRPP.
Activity of the enzyme catalyzing the formation of the 5-phosphoribosyl-1-amine from
PRPP is inhibited by purines.
Synthesis of GMP requires ATP.
Synthesis of AMP requires GTP.
Eqn:
PRPP + glutamine +glycine +formyl-THF + aspartate +some ATP purines

PURINE SALVAGE
HGPRTase :
Hypoxanthine /Guanine + PRPP IMP/ GMP+ PPi
APRTase: Adenine + PRPP AMP + PPi

PYRIMIDINES
Make temporary base (orotic acid)
Add sugar + phosphate (PRPP)
Modify base
Pyrimidine ring is assembled and THEN
added to PRPP
Function: To make pyrimidine nucleotides
(U, T, C) for DNA and RNA synthesis.
Lcxn: Cytoplasm of most cells.
Cnxns: To amino acid metabolism by the
requirement for
glutamine and aspartate.
Regulxn: UTP inhibits synthesis of
carbamoylphosphate.

Eqn:
Gln +CO2 +Asp + PRPP +some ATP UTP
+ CTP
PYRIMIDINE SALVAGE
1. Uracil +PRPP UMP +PPi (only uracil)
2. Nucleoside phosphorylase: U, C, T
+ribose 1-phosphate nucleosides +Pi
(but requires the presence of specific

(hypoxanthine-guanine phosphoribosyltransferase)

PURINE DEGRADATION
GMP guanosine guanine xanthine
urate
AMP adenosine inosine
hypoxanthine xanthine urate
AMP IMP inosine urate

PYRIMIDINE DEGRADATION
CMP cytidine uridine uracil
beta- alanine malonate
semialdehyde CO2
Thymidine thymine betaaminobutyrate methylmalonate
semialdehyde CO2
The nitrogen from the pyrimidine bases is
removed by transamination and dumped
onto glutamate. The carbon skeleton ends
up as CO2

kinases to convert the nucleoside to the

monophosphate. Except for
thymidine kinase, these kinases do not
exist in most cells )

Living organisms require a continuous input of free energy for:

(1) performance of mechanical work in muscle contraction and other cellular movements
(2) active transport of molecules and ions
(3) synthesis of macromolecules and other biomolecules from simple precursors
METABOLIC PROFILE OF ORGANS

CONNECTION OF PATHWAYS
1.ATP - is the universal currency of energy
2.ATP - is generated by oxidation of
glucose, FAs, and AAs ; common
intermediate -> acetyl CoA ; electron
carrier -> NADH and FADH2
3.NADPH is major electron donor in
reductive biosynthesis

4.Biomolecules are constructed from a

small set of building blocks
5.Synthesis and degradation pathways
almost
always
separated
->
Compartmentation !!!

GLYCOLYSIS AND
GLUCONEOGENSIS

GLYCOGEN
SYNTHESIS AND
DEGRADATION

GLYCOLYSIS
FUNCTION

Aerobic
Convert glucose to
pyruvate and ATP.
Pyruvate can be
burned for energy
(TCA) or converted
to fat (fatty acid
synthesis).

Anaerobic
ATP production.
Recycle NADH by
making lactate.

GLUCONEOGENESIS
Gluconeogenesis makes glucose from
pyruvate to help maintain
blood glucose levels.

To store glucose equivalents and

retrieve them on demand
Glycogen is a branched polymer (1-4 and 1-6
connections) of glucose connected in an alpha-linkage at
the anomeric carbon.
Branches are created by forming glycosidic linkages with
both the 4- and 6-hydroxyl groups of the glucose residue
at the branch point. The glycogen polymer is very large
and contains multiple branches.

LOCATION

Cytosol of all cells.

Liver and kidneynot muscle.

CONNECTIONS

Glucose in, pyruvate or lactate out.

Glucose 6-phosphate to glycogen
(reversible).
Glucose 6-phosphate to pentose
phosphates (not reversible).
Pyruvate to TCA via acetyl-CoA (not
reversible).
Pyruvate to fat via acetyl-CoA (not
reversible).

Pyruvate in, glucose out.

Lactate in, glucose out.
Alanine in, glucose and

Primary signals
Insulinturns on.
Glucagonturns off.
Epinephrineturns
onin muscle, offin
liver.
Phosphorylation
turns off in liver,

Primary signals
Insulin turns off.
Glucagon turns on.
Acetyl-CoA turns
on.
Phosphorylationtur
ns onin liver.

REGULATION

GLYCOGEN SYNTHESIS
&DEGRADATION

Secondary signals
Glucose signals
activate (fructose 2,6bisphosphate
activates
phosphofructokinase).
Low-glucose signals
inhibit.

urea

out.

* Alanine, a product of protein degradation, yields

pyruvate by simple transamination and this pyruvate can
be converted to glucose by the liver and kidney

Secondary signals
Glucose signals
turn off. (Fructose
2,6-bisphosphate
inhibits fructose
1,6bisphosphatase.)
Low-glucose

Major deposits in liver for maintaining

blood glucose
Deposits in muscle for providing glucose
for muscle energy requirements
Glycogento and from glucose 1phosphate
Glucose 1-phosphate to glucose 6phosphate
Glucose 6-phosphate to glucose (liver
and kidney only)
Glucose 6-phosphate from glucose
Glucose 6-phosphate to and from
glycolysisand gluconeogenesis
Glucose 6-phosphate to pentose
phosphates (notreversible)
Primary signals
Secondary signals
Insulin turns
Glucose 6synthesis on,
phosphate
degradation off.
activates synthesis.
Glucagonturns
Ca2-Calmodulin
synthesis off,
activates
degradation on.
degradation by
Epinephrineturns
activating

on in
muscle.

ATP
CONSUMPTION/
PRODUCTION

High-energy signals
inhibit.
Low-energy signals
activate.

GLYCOLYSIS ATP YIELDS

Aerobic: 1 glucose 2ATP +2NADH +2
pyruvate
Anaerobic: 1 glucose 2ATP + 2 lactate
Complete: 1 glucose 6CO2 +38ATP
(using malate/aspartate shuttle to oxidize
NADH)
From glycogen: (Glycogen)n 3ATP +
2NADH +2 pyruvate

signals activate.
High-energy
signals activate.
Low-energy signals
inhibit.
GLUCONEOGENESIS ATP COSTS
2 lactate +6ATP (equivalents) glucose

synthesis off,
phosphorylase
degradation
kinase
on.
Phosphorylationtur
ns synthesis off,
degradation on.
ATP YIELD
No ATP is required to remove glucose
from glycogen stores.
Degradation:
(Glycogen)n + Pi glucose 1phosphate +(glycogen)n-1
Glucose 1-phosphate +H2O glucose
+ Pi
Net: (Glycogen)n +H2O (glycogen)n1+ glucose
ATP COST
2 ATPs are required to store each
glucose as glycogen.
Synthesis:
Glucose +ATP glucose 6-phosphate
+ ADP
Glucose 6-phosphateglucose 1phosphate
Glucose 1-phosphate +UTP UDPglucose+2Pi
UDP- glucose +(glycogen)nUDP
+(glycogen)n-1
UDP +ATP UTP +ADP

Net: (Glycogen)n+glucose +2ATP

(glycogen)n+1 +2ADP +2Pi
EQUATIONS

NOTES

GLYCOLYSIS EQUATIONS
Aerobic: Glucose + 2ADP +2Pi + 2NAD
+
+
2 pyruvate + 2ATP + 2NADH +2H

GLUCONEOGENESIS EQUATIONS
2 lactate + 4ATP + 2GTP glucose
+4ADP +2GDP +6Pi

Anaerobic: Glucose + 2ADP + 2Pi 2

lactate + 2ATP
LACTATE OR PYRUVATE
O2 present, pyruvate is oxidized by the
tricarboxylic acid cycle (TCA).
O2 absent, pyruvate is reduced to
lactate.
In muscle, lactate is the usual product

2 pyruvate +4ATP +2GTP +2NADH

+
+2H 4ADP + 2GDP + 6Pi + 2NAD
Formation of oxaloacetate from
pyruvate, requires the presence of
acetyl-CoA. This is a check to make
sure
that the TCA cycle is adequately
fueled. If theres not enough acetylCoA
around, the pyruvate is needed for
energy and gluconeogenesis wont
happen. However, if theres sufficient
acetyl-CoA, the pyruvate is shifted
toward the synthesis of glucose.

Glycerol produced by the action of

hormone-sensitive lipase in adipose
tissue cannot be utilized by adipose
tissue itself. Adipose cells lack the
enzyme glycerol kinase, which
is necessary to convert glycerol to
glycerol phosphate

FATTY ACID SYNTHESIS

TCA CYCLE

TCA CYCLE
FUNCTION

LOCATION

To burn the acetyl-CoA made from fat,

glucose, or
protein in order to make ATP in
cooperation
with oxidative phosphorylation
All cells with mitochondria

FATTY ACID SYNTHESIS

To synthesize fatty acids from acetyl-CoA

BETA-OXIDATION/ FATTY ACID

DEGRADATION
To break down fatty acids to acetyl-CoA
to provide fuel for the
TCA cycle

Liver and adipose cytoplasm

Mitochondria of all tissues

*RBC dont have mitochondria

CONNECTIONS

REGULATION

From glycolysisthrough acetyl-CoA.

Pyruvate makes oxaloacetate and malate
through the anaplerotic reactions.
To boxidationthrough acetyl-CoA.
To amino acid degradationthrough
acetyl-CoA and various intermediates of
the cycle.
Supply and demand of TCA cycle.
Availability of NAD and FAD as
substrates.
Inhibition by NADH.
High-energy signals turn off.
Low-energy signals turn on

CARNITINE SHUTTLE
Transfers fatty acids form cytoplasm to
mitochondria for -oxidation
Inhibited by malonyl-CoA, a precursor for fatty
acid synthesis and slows down oxidation

From TCAand mitochondria through

citrateto C16fatty acid
Through C16
-acyl-CoA to elongationand
desaturationpathways
Through C16
-acyl-CoA to triglycerides
Primary signals
Secondary signals
Insulin turns on.
Citrate activates
Glucagon turns off. (acetyl-CoA
Epinephrineturns
carboxylase).
off.
Phosphorylationtur
ns off.

Fatty acyl-CoA in, acetyl-CoA and NADH,

FADH2
out
Fromtriglycerides through hormonesensitive lipase

Primary signals
(effects on
hormone-sensitive
lipase):
Insulinturns off.
Glucagonturns on.
Epinephrineturns
on.
Phosphorylationtur
ns on.

Secondary signals
Malonyl-CoA
inhibits carnitine
acyltransferase.

ATP
CONSUMPTION/
PRODUCTION

EQUATIONS

ATP yield:
Pyruvate 15ATP
Acetyl-CoA 12ATP

FATTY ACID SYNTHESIS ATP COSTS

(FOR C16)
8 acetyl-CoAmito8 acetyl-CoAcyto (-16
ATP)
7 acetyl-CoA 7 malonyl-CoA (-7 ATP)
+
14NADPH 14NADP (-42 ATP)
Total cost: (-65 ATP)

Pyruvate +GDP +Pi +3NAD +FAD

+
3CO2+GTP+3NADH +FADH2+3H
+

Acetyl-CoA +GDP +Pi +2NAD +FAD

+
2CO2+GTP +2NADH +FADH2+2H

NOTES

Acetyl-CoA +7 Malonyl-CoA+
14NADPH+14H
C16 fatty acid +14NADP +7CO2+8CoA

-OXIDATION ATP YIELD

C16 fatty acid 16CO2 (129 ATP)
C16 fatty acyl-CoA 16CO2+CoA (131
ATP)
Breakdown into steps:
Activation of fatty acid to fatty
acyl-CoA (-2 ATP)
7 FADH2made from forming double
bond at C-2 (7 X2) (14 ATP)
7 NADH made from oxidations during
formation of 3-ketoacyl-CoA (7 X3) (21
ATP)
8 acetyl-CoA (8 X12) through TCA cycle
(96 ATP)
C16 fatty acid +CoA +ATP C16
-acyl-CoA +AMP + PPi
C16 -acyl-CoA+7NAD+7FAD
+
8 acetyl-CoA +7NADH +7FADH2+7H

Requires a phosphopantetheine
cofactor
The major control point : acetyl-CoA
carboxylase. The enzyme is inactivated
by phosphorylation and activated by
high concentrations of citrate
The reactions of fatty acid synthesis all
occur on one enzymefatty
acid synthase.
This enzyme has multiple catalytic
activities on one
polypeptide chain. The intermediates of

The major hormone-sensitive control

point for the mobilization of
fat and the -oxidation pathway is the
effect of phosphorylation on the
activity of the hormone-sensitive lipase
of the adipose tissue. The major
direct control point for oxidation is the
inhibition of carnitine acyl-transferase by
malonyl-CoA. Since the malonyl-CoA
required for fatty acid synthesis inhibits
oxidation, this regulation keeps the
opposed pathways of fatty acid synthesis

the reaction are not released until

and oxidation in check. You dont do

synthesis and degradation at the same
time.

All the ATP comes from oxidative

phosphorylation coupled to the
metabolism of acetyl-CoA by the TCA
cycle. No oxygen, no oxidation.
Each cycle of oxidation reduces the
length of the fatty acid chain
by 2 carbons, produces 1 acetyl-CoA (12
ATP), 1 FADH2(2 ATP), and
1 NADH (3 ATP). Each 2-carbon unit of
the fatty acid then results in the
production of 17 ATPs.
Breaking a C20 fatty acid into 10 acetylCoA units requires only 9 -oxidation
cyclesthe last cycle gives 2 acetyl-CoA
as the product.
What oxidation actually accomplishes is
the removal of a C-2 unit as
acetyl-CoA from the carboxyl end of the
fatty acid. This keeps happening until the
fatty acid is completely converted to
acetyl-CoA.

FATTY ACID SYNTHESIS

The major complication : acetyl-CoA is made in the mitochondria,
but fatty acid synthesis occurs in the cytosolacetyl-CoA cant cross
the mitochondrial membrane.
Acetyl-CoA gets out of the mitochondria disguised as citrate.

Acyl-CoAmito+2ATP +NADH +NADP acyl-CoAcyt+2ADP +2Pi

+NAD+NADPH
In addition to moving acetyl-CoA from the mitochondria to the
cytoplasm, this cycle also converts an NADH to an NADPH. If we
assume that the amount of ATP that we could get from NADH and
NADPH oxidation is the same, making NADPH from NADH and
NADP+ doesnt cost any energy. So we can conclude that the cost of
just moving the acetyl-CoA out of the mitochondria is 2 ATPs per
acetyl-CoA.
The synthesis of C16 fatty acid from acetyl-CoA requires 1 acetylCoA
and 7 malonyl-CoA. The synthesis of each malonyl-CoA requires an
ATP (and the cofactor biotin).

The acetyl-CoA is condensed with oxaloacetate to give citrate, and

the citrate leaves the mitochondria. In the cytosol, the citrate is
cleaved by an ATP-dependent citrate lyase into acetyl-CoA and
oxaloacetate
Citrate+ATP+CoA acetyl-CoA +ADP Pi +oxaloacetate
This reaction and the reactions required to get oxaloacetate back
into the mitochondria

Acyl-CoAmito+2ATP +CoA +NADH +NADP+CO2CoA+acylCoAcyt+2ADP +2Pi+NAD+NADPH+CO2

If we cancel the things that appear on both the left and right:

Acetyl-CoA +CO2+ATP malonyl-CoA +ADP + Pi

Then, reaction catalyzed by fatty acid synthase.
Acetyl-CoA +7 malonyl-CoA +14NADPH C16 fat + 14NADP +
7CO2+8CoA
If we count the NADPH (cytosol) as 3 ATP equivalents, which could
have been oxidized by the TCA cycle if they hadnt been used for
fatty acid synthesis, then the synthesis of C16fat requires:
8 acyl-CoAmito acyl-CoAcyto (-16 ATP)
7 acyl-CoA 7 malonyl-CoA (-7 ATP)
14NADPH 14NADP (-42 ATP)
Total cost: (-65 ATP)

ELONGATION AND DESATURATION

Elongated by 2 carbon atoms at a time.
Cisdouble bonds can be introduced no farther than C-9 from the carboxylate end in
mammals.
Numbers between double bonds are different by 3.
Nomenclaturecounts from carboxylate end.
Nomenclaturecounts from methyl end.
TRIGLYCERIDE AND
PHOSPHOLIPID SYNTHESIS
Glycerol phosphate comes from glycerol (not in adipose) or from
dihydroxyacetone phosphate (in liver and adipose).
Nitrogen-containing phospholipids are made from diglyceride.
Other phospholipids are made from phosphatidic acid

ELECTRON TRANSPORT AND OXIDATIVE PHOSPHORYLATION

Electron Transport
1. Oxidation is a process that involves the loss of electrons. Reduction is a process that involves the gain of electrons.
2. Electrons are carried to the electron transport system in the mitochondria by NADH and FADH2.
3. Mitochondria are the site of electron transport and oxidative phosphorylation.
4. Electrons from NADH enter the electron transport system through complex I.
5. Electrons from FADH2 enter the electron transport system through complex II.
6. Coenzyme Q accepts a pair of electrons from either complex I or complex II and passes electrons singly to cytochrome c through complex III.
7. The sequence of electrons passing from coenzyme Q is as follows: Coenzyme Q goes to Complex III goes to Cytochrome c goes to Complex IV
goes to oxygen (to form water)
8. Oxygen is the terminal electron acceptor and is a limiting compound during periods of heavy exercise.
9. If oxygen is not available, electrons will NOT pass through the electron transport system and NADH and FADH2 will not be reoxidized. This is
part of metabolic control.
10. Several compounds inhibit electron transport - rotenoneand amytal block all action of Complex I. Antimycin A blocks action of Complex III.
Cyanide and carbon monoxide block action of complex IV.
11. Movement of electrons through Complex III is known as the Q cycle. This cycle begins with the binding of two molecules of CoQ (QH2 and Q)
to Complex III. QH2 has two electrons and two protons.
12. After QH2 and Q bind, QH2 sends one electron to Q, creating Q- and one electron to cytochrome C. This converts QH2 to Q. Both cytochrome
C and Q leave the complex, but Q- remains behind.
13. Next, another QH2 and another cytochrome C binds to Complex III. QH2 sends one electron to Q-, creating Q-2 and one electron to
cytochrome C. Then Q-2 extracts two protons from the matrix and becomes QH2. Last, cytochrome C, QH2, and Q all leave the complex.
14. Electron transfer through complex IV occurs one electron at a time (since one electron arrives at a time from cytochrome c). Interruption of
electron flow can result in production of reactive oxygen species.
15. In electron flow through complex IV, the first electron is transferred to copper and the second one is transferred to iron. Oxygen then binds to
the iron first, followed by formation of a peroxide bridge between the iron and copper atoms. Addition of a third electron (to the oxygen on the
copper) and binding of a proton from the matrix causes the O-O bond to be cleaved. A fourth electron then reduces the oxygen on the iron and a
proton binds from the matrix as well.
16. During electron movement through Complex IV, four protons are taken from the matrix and combined with oxygen to form two water
molecules. In addition, four other protons are taken from the matrix by the complex and pumped outside the mitochondrial matrix.

Oxidative Phosphorylation
1. ATP is created in oxidative phosphorylation by the movement of protons back into the mitochondrial matrix through complex V.
2. Two essential functions of electron transport - 1. Pump protons out of mitochondrial matrix and 2. Reoxidize NADH and FADH2
to NAD and FAD. In healthy, normal cells, oxidative phosphorylation is tightly coupled to electron transport.
3. Important aspects of the chemiosmotic process include:
a. Intact inner mitochondrial membrane
b. Electron transport creates a proton gradient
c. ATP is made by movement of protons back into the mitochondria
4. Coupling of electron transport and oxidative phosphorylation at a practical level means that the mitochondrial inner membrane
remains impermeable to protons, except for those that enter via the ATP synthase.
5. The ATP synthase consists of a turbine-like structure containing 3 sites called Loose (L), Tight (T), and Open (O).

THE CENTRAL DOGMA

REPLICATION

biosynthesis of either DNA or RNA, where the parental nucleic acid

serves as a template to direct the structure of the product

TRANSCRIPTION

change in the nature of the nucleic acid from DNA to RNA

REVERSE TRANSCRIPTION

reverse process of transcription

TRANSLATION

change from RNA to polypeptide, the RNA, in this case, mRNA, serving
as a template that directs the primary structure of the polypeptide
polypeptide is modified by hydroxylation, phosphorylation or
glycosylation of the R groups of selected amino acid residues

POST-TRANSLATIONAL
MODIFICATION