Metabolic Biochemistry Notes

Lecture 1-Introduction
1.
2.
3.
4.
5.

Enzymes
bioenergetics
metabolic pathways
compartmentalization of pathways
metabolic adaptations:
a. diabetes
b. endurance sports
c. starvation
6. metabolic disease
7. enzyme analysis
Metabolism- Is the complex combination of physical and chemical processes occurring in
a living cell or organism. It is broken down in two main processes:
1. Catabolism- processes that break down large molecules to yield energy Eg
glycolysis- breakdown of glucose
2. Anabolic synthesis of compounds needed by the cell Eg. Lipids, amino acids
Sources of Energy:
1. Carbohydrates such as (potatoes bread rice)- Starch- Glucose-ATP
2. Protiens such as meat fish eggs- Amino Acids and Nitrogen- ATP
3. Fats and Lipids (animal products)- Fatty acids and Acetyl CoA-ATP
ATP-Adenosine Triphosphate is the energy currency of ALL cells. And is a
ribonucleuotide containing 3 phosphate groups. Energy stored in the phosphate bonds
when one phosphate group is donated 30.5 kJmol-1 of energy to produce ADP
Metabolic Pathways are a series of reactions that are normally catalyzed by enzymes.
Reactants and products share intermediate products. Exergonic energy is normally
produced through the breakdown of metabolites through catabolic reactions.
Types of pathways:
A,B and C linear pathways
D cyclic pathway

Reduced Molecules release more energy ( contain more hydrogen) the more it becomes
oxidized ( more Oxygen on the molecule)less energy it produces.
Example: Methane -196 Kcal mol-1
Carbon dioxide 0 Kcal mol-1
Inherited Metabolic Diseases- Majority is due to defects of single genes that code for
enzymes that facilitate conversions of various substances (substrates) into others
(products). Example albinism is due to the deletion of tyrosinase enzyme that produces
the melanin in pigment in hair skin and eyes.
Metabolomics- cell profiling were cellular activity is determined due to chemical
processes the cell undergoes to determine defects and damages may occur compared to
healthy cellular activities.

Lecture 2- Bioenergetics Metabolism and Enzyme Catalysis

Metabolic PathwaysCatabolism breakdown is the breakdown of large products into smaller more usable
products.
Anabolism is the build up of the catabolic products to make larger and newer products
Laws of Thermodynamics:
Principles that describe the flow and exchange of heat, energy, and matter
Deals with systems at equilibrium
Determine if a system is stable or if a reaction can occur spontaneously
Systems are:
Isolated : No exchange of either energy or matter
Closed : No exchange of matter, may exchange energy
Open: May exchange energy or matter (living systems) HUMANS!!
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Equilibrium:
Le Chatliers Principle- A system at equilibrium will change in order to absorb anything
that has occurred from the outside.
The human body is constantly counteracting effects of the outside environment and
internal environment through food and fluid to keep equilibrium constant and at
homeostasis.
Equilibrium constant= Products/ Reactants

Equilibrium constant Keq = [C][D]/ [A][B]

CD- concentration of products
AB- Concentration of reactants
Keq greater than 1 the reaction will tend to the right (direction of products)
First law of thermodynamics: Conservation of energy

Energy cannot be created nor destroyed but it can be created or transferred.

But the TOTAL energy of the system does not change
Second Law of Thermodynamics: The universe tends towards increasing disorder

Entropy is the measure of disorder.

Human system is highly ordered, we do not break the second law because we decompose
to simple matter. We release heat which generates more disorder.
Free Energy- Gibbs free energy G- this energy is free to do work meaning energy that is
broken between C-H bonds in molecules to create energy (ATP).
G- Change in Gibbs free energy.
+G- Unfavorable reaction (energy has to be supplied in order for reaction to take place)
-G- favorable reaction (Reaction happens with no excess energy supplied to reaction)
Entropy is regarded as favorable reaction as it tends to go relates to disorder which uses
free energy and doesnt require any energy from an outside source.
Examples:
+G- making bacterial cell wall, made of peptidoglycan made of repeating units of NAM
and NAG, building blocks that fits together via bridge to make the cell wall. Disordered
state (NAM and NAG separate blocks) to and ordered state ( bacterial cell wall) against
entropy
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-G- Is the degradation of glycogen to glycogen phosphorylase (GP).

Glycogen string of glycogen units broken down into individual molecules of (GP) with
entropy.
Energy lost to entropy is unusable energy which is mainly heat.
Useable energy- chemical energy can be used to breakdown molecules and do work.
Useable energy + non useable energy = Total energy
Exergonic reactions have a -G ( products have less energy)
Endergonic reactions have a +G (energy of the products is higher than the reactants)
Terminology:
G- Change in free energy
H- Change in enthalpy (heat)
S-Change in entropy
T- Temperature (Kelvins)
G= H- TS
G is the driving force towards equilibrium
Go (Go) prime
Standard transformed constants
Standard biological conditions (buffered solutions)
[H+] = 10-7 M (pH 7)
[H2O] = 55.5M

G 'o = -RTlnK ' eq

G 'o- standard biological condition
R- Gas constant
T- Temperature in Kelvin
Keq- products/ reactants
1n- inverse log10
When
Then
And
K ' eq > 1.0 G 'o = -ve reaction proceeds forwards
K ' eq = 1.0 G 'o = 0 reaction is at equilibrium
K ' eq < 1.0 G 'o = +ve reaction proceeds reverse

Reaction Coupling: Taking an unfavorable reaction with a favorable reaction to power the
unfavorable reaction in order for it to become favorable overall.
Example glycolysis:
Reaction 1 Endergonic- Glucose + Pi (inorganic Phosphate PO4) Glucose 6phosphate (has more energy than reactants)
Reaction 2 Exergonic- ATP ADP + Pi (Pi is a product or reaction 2 and a reactant of
product 1, therefore putting both reactions can be put together to get a favorable
reaction!!!
Reaction 3 Exergonic- Glucose+ ATP Glucose 6 phosphate + ADP
Free energy from reaction 2 is powering reaction 1.
Oxidation is the loss of an electron
Reduction is the gain of an electron
Oxidation-reduction reactions always occur together (coupled).

Succinate donates electrons and becomes oxidized

FAD accepts electrons and becomes reduced

ATP- energy currency of cells
ATP-ADP releases 30kJmol-1 of energy
ATP- is continuously made and broken down in the body
Oxidation and Reduction reaction is the transfer of electrons. Highly reactive and cannot
float around freely as free radicals that cause problems. Use electron carriers to hold the
securely and transfer them some were else were they are needed in the body.An example
of this is NAD- Nicotinamide Adenine Dinucleotide (vitamin B3 niacin).Goes from an
oxidized form and reduced form ( picks up 2 electrons and 2 protons( H atom that lost its
electron))

NAD- Oxidised form electron acceptor

NADH- reduced form electron donor
NAD coenzyme- organic molecule that is free in the cytoplasm and involved in enzyme
function.
NADH carriers electrons to the transport chain, electrons go down electron transport
chain to make ATP Carbon dioxide and water. Within electron transport chain the Oxygen
is known as the terminal electron acceptor.
NADH- electron energy
ATP- breaking bonds to produce energy
Both forms provide energy for the cell.
THE MORE REDUCED THE COMPOUND IS THE MORE C-H BONDS THE MORE
ENERGY THERE IS!!!!!
More oxygen less energy produced eg Methane CH4 high energy, CO2 no energy
Use fat as an energy store opposed to glucose because glucose needs water to react, fat
removes water. Fat is highly reduced. Glucose is less reduced but easier to metabolize.

Lecture 3- Enzymes: Kinetics and Regulation

Enzymes:

Enzymes enable molecules called substrates to undergo a chemical change to

form new substances called products. Each enzyme acts on a specific molecule
or group of molecules called substrates. Each substrate fits into an area of the
enzyme called the active site, the enzyme changes shape a little with the
substrate. In he enzyme substrate complex, the enzyme holds the substrate in a
position were the reaction can occur easily, after the reaction releases the
products and carries out the same reaction again and again.

Catalysts- Catalyze is a biological enzyme that breaks down peroxide bubbles in the
liver, peroxide breaks down into water and CO2 but is very slow add FeCl2 as an
inorganic catalyst and reaction runs 1000X faster. However add catalyze breaks
down peroxide in a biologically relative timeframe which is 140 million reactions
every second.

Almost all enzymes are proteins. Highly specific to one substrate and one reaction
only do not do random things.

Reduce the activation energy of a reaction.

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DO NOT alter equilibrium position

Recognize substrates with high specificity and sensitivity. Dont need much reactant
in cytoplasm in order the enzyme to find it and do its job.

Enzymes dont alter equilibrium constant

ALL enzymes will work with equilibrium and based on le chateliers principle

Activation energy- All reactions go through an intermediate state which is a high

energy molecule. The activation energy is the energy required to get over this
intermediate state. The higher the activation energy ( transition state ) the slower the
reaction and is due to same charges being to close together, or molecular bonds
being held together that is unfavorable, this is a high energy state. In order to get
over the high energy state enzymes stabilize the transition state bring reactants
closer together and control repelling charges and stabilize high energy bonds and
overall reducing the activation energy and increasing the rate of the reaction.

Multiple enzymes can speed up reactions to a relative timeframe example Neurons

can have multiple overlapping reactions in order to generate an impulse.

DOES NOT CHANGE THE G

Enzyme and substrate have an induced fit were the enzyme fits in the substrate to
change its electrochemical charge and shape to make sure its a perfect fit. A
specific enzyme will fit into a specific substrate and bind to its active site. HIGHLY
SPECIFIC!!

Enzyme + Substrate ES EP E + Product

ALL enzymes are stereospecific enantomers and chiral

Classification of Enzymes
Enzymes are classified based on there enzymatic function.
6 Classes:
Oxidoreductases catalyze oxidation-reduction reactions BH2 + A B + AH2
Transferases catalyze transfer of functional groups from one molecule to another D-B +
A-H D-H + A-B
Hydrolases catalyze hydrolytic cleavage A-B + H2O A-H + B-OH Ligases and
Synthetases Bond formation (reverse of hydrolase) coupled to ATP hydrolysis
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Lyases catalyze removal of a group from or addition of a group to a double bond or other
cleavages involving electron rearrangement A-B A + B [ synthases: A + B A-B ]
Isomerases catalyze intramolecular rearrangement R-A-B A-B-R
The theory behind the substrate fitting into the enzyme active site is not accurate as the
enzyme catalytic site might not be the perfect fit for the substrate, so some of it that is in
the wrong charge or hydrophobicity, but when the substrate approaches the enzyme at a
close proximity there is molecular movement to get that that perfect fit. THIS IS
INDUCED FIT!!
However substrates that have a slightly different shape CANNOT INDUCE FIT. This is
what gives us enzyme specificity.
ONE SUBSTRATE ONE ENZYME ONE REACTION
Wrong shaped substrate Substrate binds to enzyme (conformational change) Perfect
match
Non Substrates No conformational change
Substrate enzyme have a slightly different shape as they approach each other they change
shape to allow perfect fit which ultimately changes the substrate and enzyme. BOTH
CAN HAVE CONFORMATIONAL CHANGE!!
Alcohol interacts with neurotransmitter channel called GABA to slow it down. Alcohol
changes the sodium and potassium pump in the neuron.
What causes Hangovers?
Kinetics:
Alcohol dehydrogenase (ADH)- When alcohol reacts with the enzyme produces
acetylaldehyde which is toxic, this is an oxidation reduction reaction.
Technically all reactions are reversible, and all go until equilibrium is reached.
Even if there is a decrease in free energy it has to go over the activation energy which is
were looking at an intermediate (enzyme substrate intermediate) that has unfavorable
bonds or charges. The enzyme decreases the activation energy by stabilizing enzyme
substrate intermediate.
Rate:
Rate is the amount substrate converted to product per unit time. Rate is related to a rate
constant, so the rate of reaction is related to the decrease of reactants = rate constant and
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concentration of products. Rate constant goes in TWO DIRECTIONS- forward reaction=

reverse reaction. This is for a simple react

- (not negative value, decrease value)[A] = k [C] decrease in

[A]
[C] = k [A] increase in [C]
Rate reaction reactants X concentration of products
Enzyme + Substrate ES EP E + Product
ES- substrate intermediate
We can calculate the rate or velocity of the reverse and forward reactions.
Rate constant of forward reaction K+1- lots of reactants (A) little product (C)
Rate constant of reverse reaction K-1-little reactants (A) lots of products(C)
Rate constant at equilibrium K0- equal amount of products and reactants A=C
Enzyme Recycling
Enzyme + Substrate ES EP E + Product
E+S- reversible reaction to ES intermediate
ES- reversible reaction (catalysis has occurred) with EP intermediate
EP- reversible reaction of E+P- enzyme is recycled
Lag phase happens in less than a millisecond was the enzyme is finding the substrate.
Theres a direct linear relationship between product and time. Also known as steady state,
were the ES concentration looks constant. Steady state kinetics is where the reaction
E+SESP happens so quickly it looks constant.

Rate equation: Rate= rate constant X substrate concentration

At equilibrium the rate of forward reaction = rate of reverse reaction.
K+1=K-1
K+1/K-1= concentration of products/ conc of reactants = Keq( equ constant)
Steady state were the ES intermediate remains constant.
The very initial parts of the reaction ( ignore reverse reaction) therefore ES is constant.
Limiting rate factor is the catalysis between E+SES.
V0 = Vmax [S]/(Km + [S]) THIS IS THE MICHAELIS-MENTEN EQUATION !!!!
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V0- initial velocity (rate)

Vmax- maximum velocity
[s]- substrate concentration
Km- michaelis- menten constant
Plot- initial velocity V0 vs. Substrate concentration
When this plotted eventually Vmax will be approached, but is an asymptote were the line
goes forever and will never reach Vmax value. This is an estimated reading.
Km is defined as substrate conc that gives half Vmax both can be estimated by the graph.
Vmax is the point that where increasing the substrate conc does NOT increase rate. This
signifies how fast the enzyme can go and its estimation only via the asymptote.
The higher the Km the greater the amount of substrate needed to half Vmax.
>Km > [S]Vmax
Km- can be a measure of affinity between enzyme and substrate, lower Km indicates
higher affinity between enzyme and substrate binding rate.
Higher the Km the lower affinity and slower binding rate.
Very initial part of the graph we start with a low [S] and slow rate, as we increase the [S]
we increase rate and eventually gets to a time were the enzyme is saturated, the limiting
factor is in the binding and catalysis of the enzyme. The more substrate will not increase
enzyme productivity. THIS IS VMAX
Mitochondria has a low Km therefore has more affinity to bind substrates (acetaldehyde)
and have a faster rate of reactions. With the high Km in the cytosol it takes longer
( increased amount of acetaldehyde to reach half Vmax) In mitochondria there is a low
amount of acetaldehyde. Genetic defects in the enzyme within the mitochondria means that
the enzyme will not work as well and relies on the cytosol enzyme to remove the
acetaldehyde (toxic). This builds up quicker in the body and causes a hangover.
Lineweaver- Burk Plot- allows you to calculate 1/ vmax and -km
Is a linear plot y=mx+b
1/V0= km/vmax X 1/[S] +1/vmax

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Questions
1. The induced fit model of enzyme and substrate interaction involves:
a)Enzyme and substrate fitting exactly and no molecular movement required for binding
b)Enzyme first reacting with substrate in order to induce fit
c)Enzyme and substrate not fitting exactly and some molecular movement required
for binding
d)Enzyme not interacting with substrate as it does not partake in the reaction
2. Enzyme steady state kinetics is when:
a)The reaction is at equilibrium
b)No further product is being made
c)Substrate is being consumed at maximal rate
d)The enzyme-substrate concentration appears constant
3. The Michaelis-Menten plot is
a)A graph that compares substrate concentration to reaction rate
b)A graph from which maximal reaction rate can be estimated
c)A graph from which the Michaelis-Menten constant can be determined
d)All of the above
e)None of the above
4.The Lineweaver-Burk plot is
a)A graph that shows the relationship between the inverse of substrate concentration and
reaction rate
b)A graph from which maximal reaction rate can be calculated
c)A graph from which the Michaelis-Menten constant can be calculated
d)A graph which can be used to investigate enzyme-inhibitor interaction
e)All of the above
Enzyme Inhibitors:
There are 2 types of enzyme inhibitors reversible and irreversible.
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1. Irreversible are those under biological conditions cannot be reversed. They dissociate
very slowly from the target.
2. Reversible are used in metabolism, almost everything in our body is regulated to keep
homeostasis and has rapid dissociation, can turn on and off many times a second. 3
forms enzyme inhibitors: competitive, uncompetitive and mixed (uncompetitive).
Irreversible inhibitors:
Penicillin- prevents the cell wall extension and replication (NAM and NAG) cell wall
is made peptidoglycan, polymer of NAM and NAG and linked together by a peptide
cross bridge, which is done by transpeptidase , -lactans stop the transpeptidase from
acting and therefore cell wall cannot be made stopping the bacteria from dividing,
therefore penicillin inhibits bacterial cell division. It acts on the - lactam ring. The
bacteria produced -lactamase- an enzyme that opens the - lactam ring to open the
ring and stops the penicillin from working. Clavulanic acid is used to destroy lactamase and has been mixed with penicillin so it can take its original effect.
Competitive inhibitors
Bind to the enzyme catalytic site to become an enzyme inhibitor complex, they
compete with the substrate for the catalytic site, when the enzyme and inhibitor are
bound there is no catalysis. Inhibitor is similar to the substrate in shape charge and
hydrophobicity, and it binds to the active site of free enzyme. The substrate and
inhibitor bind to the same site therefore if you add more substrate it out competes the
inhibitor and reaction occurs normally. Used in normal metabolism and drug
development.
Uncompetitive Inhibitors
ONLY bind to the substrate enzyme intermediate, they bind to another site NOT
CATALYTIC SITE. When ES bind opens up another site for the inhibitor to bind. A
free enzyme does not have this site when ES bind it opens up this site. ONLY BINDS
TO ES COMPLEX.
Mixed inhibitors
Combine to the enzyme and ES intermediate and create another site on the enzyme.
NOT the catalytic site. Inhibitor binding site is present in the enzyme alone and ES
intermediate. Binding at another site, increasing the substrate concention will have no
affect as its binding to other site then what the substrate is binding.
Enzyme Regulation

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Feedback control- Allosteric modulation is a mixed or uncompetitive inhibitor

binding to a site that is NOT the catalytic site. Is Negative feedback control were the
product binds to the initial enzyme and stops the chain reaction. This is a
conformational change. The inhibitor DOES NOT fit in the catalytic site so it binds
somewhere else to get a conformational change in the active site and substrate cannot
bind

Allosteric modulation happens at the beginning and branch points of a reaction, so we

dont use up substrate and make too much products that are not needed.
Allosteric Modulators:
Can be positive or negative and proteins (enzymes) can go between the Taut state (less
active) and relaxed state ( more active)
Positive effector tautrelaxed more active
Negative effector relaxed taut less active
Produce a sigmoidal shaped graph with velocity Vs Substrate.
Controlling Enzymes
Cleavage- not all are produced in active forms some are produced as zymogens.
Zymogens are inactive form of the enzyme thats released in the blood and is longer
structure that has to be cleaved in order to become active.. Trypsinogen is an enzyme that
is cleaved by pepsinogen in the stomach to make trypsin. Clotting factors they need to be
turned on and off at certain times, it is turned on by a enzyme cascade and starts initially
as a zymogen that is activated which acts on another enzyme to activate it and so on.
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Phosphorylation system can turn on and off - Kinase phosphorylates and phosphatase
dephosphorylates. Classic system of a phosphorylation is the transduction pathway from
outside the cell to inside the cell.
Questions
1. A competitive inhibitor can
a)Bind to an enzyme active site
b)Be part of allosteric modification
c)Be outcompeted by substrate
d)(a) and (c) only
e)All of the above
2. Feedback control can
a)Only work in a negative fashion
b)Only work in a positive fashion
c)Work in a negative and positive fashion
d)Work only in complex, multi-subunit, multi-step enzyme pathways
3. In enzyme catalysis, allosteric modulation is when an effector binds to a site that
is not the active (catalytic) site and alters the shape of the enzyme
FALSE
4. In enzyme control, covalent modifications include phosphorylation carried out
by enzymes called phosphatases
FALSE

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Lecture 4- Glycolysis and Gluconegenesis

Glycolysis is the breaking of 6 carbon chain to two 3 carbon chains (from glycose, an
older term[1] for glucose + -lysis degradation) is the metabolic pathway that converts
glucose C6H12O6, into pyruvate, CH3COCOO + H+. The free energy released in this
process is used to form the high-energy compounds ATP (adenosine triphosphate) and
NADH (reduced nicotinamide adenine dinucleotide). There are 10 steps involved in this
process. We dont store glucose because it needs water to maintain solubility while
fat doesnt need water.
The GOAL of Respiration- is taking C-C and C-H bonds and oxidizing them to
produce energy. Oxidation is loss of electrons to produce energy, end point ATP,
intermediate electron carriers NADH (power the production of ATP).
Carbon dioxide produces the most energy as a product from the reduction of
pyruvate as it has no C-H bonds and has been completely oxidized.
Preparatory Phase is the phosphorylation of glucose to glyceraldehyde 3-phosphate
(GAP) steps 1-5:
1. Priming action phosphorylation of glucose, traps glucose in the cell and need high
energy phosphate groups to release energy and binding of phosphate groups to the
enzyme lowers activation energy :
a)
b)
c)
d)

Glucose Glucose 6- Phosphate, using Hexokinase enzyme

ATP ADP need energy to start the reaction.
FORWARD REACTION
Enzyme glucokinase aka hexokinase

2. Isomerization :
a) Phosphoglucose isomerase enzyme turns glucose 6- phosphate to fructose 6
phosphate in catalytic reaction.
b) Reversible reaction
3. Seconding Priming action:
a) ATPADP
b) Fructose 6 Phosphate Fructose 1,6- Biphosphate (one phosphate group on
both 1,6 carbons on ring), using the enzyme Fructophosphokinase
c) FORWARD REACTION
4. Cleavage:

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a) Aldolase enzyme BREAKS the Fructose 1,6- Phosphate in two separate 3 carbon
chain molecules:
dihydroxyacetone phosphate (DHAP)
glyceraldehyde 3-phosphate (GAP 1)
b) Reversible reaction
5. (DHAP) is not useful so the Triose Phosphate isomerase enzyme converts it to (GAP
2)
a) DHAP GAP2 using triose phosphate isomerase enzyme.

Pay off Phase: Oxidative conversion of GAP to pyruvate and coupled ATP and NADH
(electron acceptor) (ENERGY)
6. Phosphorylation (of organic phosphate from cell cytoplasm) and Oxidation of BOTH
GAP 1+2 molecules:
a) GAP 1,3 Biphosphoglycerate using enzyme triose phosphate dehydrogenase
b) 2NAD+NADH+ H+ Oxidised (Electron reaction) conserved
c) GAP + 2PO4 high energy phosphate is lost to produce ATP
7. First ATP forming reaction (substrate level Phosphorylation) Dephosphorylation:
a)
b)
c)
d)

Enzyme Phosphoglyceralkinase catalyzes BOTH phosphates to ADP.

GAP 3- phosphoglycerate
ADP ATP
Reversible reaction

8. Enzyme Phosphoglyceratemutase changes position of phosphate group in 3phosphoglycerate to 2- phosphoglycerate.

a) Reversible reaction
9. 2- phosphoglycerate loses water phosphoeonalpyruvate (PEP) using the enzyme
enolase.
a) Revisable reaction
b) Very high energy phosphylated compound, transfer it ADP to make ATP
10. The Second ATP forming reaction:
a) Enzyme pyruvate kinase mediates the transfer of phosphate group from 2phosphoglycerate to an ADP molecule.
b) ADP ATP
c) FORWARD REACTION

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Simple Summary of Glycolysis Reaction:

Steps 1-3- 6 carbon compound with 2 ATP two phosphate groups Conversion of glucose
to fructose 6 phosphateusing a series of enzymes:
a) Hexokinase
b) Phosphohexoisomerase
c) Phosphofructokinase-1
Step 4- Fructose 6 phosphate molecule is cleaved forming 2 X 3 carbon chained moles
GAP and DHAP using Alodolose enzyme.
Step 5- DHAP converted to GAP by Triose phosphate isomerase
Step 6- BOTH GAP molecules are Oxidised by triosephosphate dehydrogenase and gain
a phosphate group.
Step 7- ATP is formed using enzyme phosphoglyceralkinase by transferring the
phosphate groups to ADP.
Step 8- phosphate group moved from 3C to 2C on phosphoglycerate molecule using
phosphoglyceromutase enzyme.
Step 9- Dehydration reaction of 2- phosphoglycerate molecule, using enolase enzyme
and producing phosphoenolpyruvate PEP (high energy phosphate molecule)
Step 10- High energy phosphate group from PEP molecule binds to ADP molecule and
produces ATP and pyruvate.

The body needs a constant supply of ATP in order to power cells. Eg charge
separation between cells
Glycolysis- produces 2 ATP

Glycolysis overall reaction

Glucose + 2ATP + 2NAD+ + 4ADP + 2Pi

2 pyruvate + 2NADH + 4ATP + 2ADP + 2H+ + 2H2O

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Control:

Isozymes- same function but slightly different protein sequence or different tissue
locations. They generally have different catalytic activities.
Blood glucose glucokinase enzyme is at Vmax,

The liver does not rely on glycolysis as energy production for itself

Gluconeogenesis

Gluconeogenesis- making glucose from other sources. Mainly in the liver.

Does not produce ATP but uses it up.

Glucose is the major fuel source for the brain, kidney medulla sperm and red
blood cells. Brain uses 120g of glucose a day which is greater than the liver
glycogen stores.
Synthesis of glucose from pyruvate.
3 reactions that cannot be reversed have high -G, 7 reactions are at equilibrium.
The 3 by pass reactions:

Bypass 1 step 10 of glycolysis

1.
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Bypass 2 Step 3 of glycolysis reaction

2.

3. Bypass 3 step 1 of glycolysis reaction

The first by pass is reaction 10, Take PEP high phosphate molecule and convert it to
pyruvate and generate ATP.
These reactions need different enzymes
Step 1 is a kinase so phosphorylation reaction
Step 2- dephosphorylation reaction
Step 10- 2 step reaction because Forward reaction in favorable. REVERSE
REACTION has too high G so needs 2 reactions that happens in the mitochondria:
Bypass 1- step 10
a) Pyruvate + HCO3- + ATP oxaloacetate + ADP + Pi
b) oxaloacetate + GTP PEP + GDP + CO2

The mitochondria has an excess of NADH, we dont have an excess in the cytoplasm
but we need NADH in the cytoplasm otherwise gluconeogenesis will stop. Therefore
pyruvate enters the mitochondria turns gets turned into oxaloacetate, which
regenerates NAD in the mitochondria. Oxaloacetate cant leave the mitochondria, so
its converted to malate that can transport out. The malate is then regenerated to
oxaloacetate to regenerate NADH in the cytoplasm.

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All related to creating NADH in the cytoplasm so gluconeogenesis can keep going.

Bypass 2 step 3 in glycolysis reaction

The forward reaction is one phosphate two phosphate requires energy input. Not
easily reversed
Phosphofructokinase reaction bypassed by a simple hydrolysis reaction:
Phosphofructokinase (Glycolysis) catalyses:
fructose-6-P + ATP fructose-1,6-bisphosphate + ADP
Fructose-1,6-bisphosphatase-1 (Gluconeogenesis) catalyses and chops a phosphate group
off:
fructose-1,6-bisphosphate + H2O fructose-6-P + Pi
By pass 3- is step 1 of glycolysis.
Hexokinase is only found in the liver and a little bit in the renal medulla. The liver is
involved in maintaining blood glucose, if every tissue had the ability to dephosphrylate
glucose it will become straight glucose and will leave the cell. No transport system for
glucose-6-phosphate
Hexokinase reaction bypassed by a simple hydrolysis reaction:
Hexokinase (Glycolysis) catalyses:
glucose + ATP glucose-6-phosphate + ADP
Glucose-6-Phosphatase (only in the liver) (Gluconeogenesis) catalyses:
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glucose-6-phosphate + H2O glucose + Pi

Glycolysis:
glucose + 2 NAD+ + 2 ADP + 2 Pi
2 pyruvate + 2 NADH + 2 ATP
Gluconeogenesis:
2 pyruvate + 2 NADH + 4 ATP + 2 GTP
glucose + 2 NAD+ + 4 ADP + 2 GDP + 6 Pi
o Gluconeogenesis uses more ATP than what glycolysis produces.
o Glycolysis produces a net of 2 ATP and gluconeogenesis needs an input of 6
phosphate bonds therefore we are wasting 4 phosphate bonds if these reactions
were running in tandem.
o Use more energy then we produce
o When glycolysis in on gluconeogenesis is off and vice versa. This is done by
allosteric modulation (turning enzymes on and off) also known as reciprocal
regulation.
o The 3 bypass reactions have a high -G and are used as the regulatory steps.
o Hexokinase 1st step in glycolysis- product is glucose-6 phosphate and gives it
negative feedback; glucose-6 phosphate turns hexokinase off. Aka product
inhibition. Therefore if there is a lot of glucose in the cell theres no need to keep
trapping more so it goes through the negative feedback system.
o Glucokinase- is not inhibited by its own product, therefore continues to use
glucose to make glycogen. So G6P can continue to be produced in the liver and
be made stored as glycogen. Still active at high blood sugar, continues to produce
glucose in order to reduce blood sugar level to 4.5mmol.
o Hexokinase can be controlled on a DNA level, so high glucose and muscle
exertion turns hexokinase.
o In the liver low blood sugar initiates G6P transcription.
o Regulation at the protein level is the regulation of phosphofructokinase-1

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Pyruvate kinase is acted upon by ATP and actylcoA to turn glycolysis off because the
cell is energy full. However fructose 1,6 biphosphate activates pyruvate kinase. When
there are a lot of metabolites present fructose 1.6 phosphate activates the pyruvate
kinase enzyme to remove the metabolites. Conversely acetyl CoA turns glycolysis off
and turns gluconeogenesis on. This is reciprocal regulation
Pentose Phosphate Pathway- needed to make sugars for DNA and keep NADP
reduced. The reducing power is to keep glutathione reduced and NADPH keep
fatty acids reduced.

NADP and NADPH are needed for several reactions, in order to make nucleotides
and coenzymes we need to be able transfer NADP to NADPH and then these two are
necessary for keeping glutathione reduced and NADPH is used in fatty acid synthesis.
22

Lecture 5- Pyruvate Dehydrogenase (PDH) and Citric Acid Cycle

(CAC)

Does not produce ATP but does produce NADH.

Produce electron carriers that undergo oxidative phosphorylation and produce ATP.
Oxidative respiration- NOTHING TO DO WITH OXYGEN ITS THE REDOX
REACTION!!!
OXIDATION- LOSS OF ELECTRONS
REDUCTION- GAIN OF ELECTRONS
Reaction happens in the mitochondria
Mitochondria has been theorized to come from endosymbiosis based on its double
membrane, circular chromosome and ability to divide by itself. Has an outer and
highly folded inner membrane called cristae. Outer membrane is porous allowing
substance to cross with no issue while the inner membrane is selective (ion channels).
The inner membrane is IMPERMEABLE TO IONS which is very important, without
it oxidative phosphorylation cant happen.
The space created by the cristae creates a matrix that the pyruvate eventually enters.
The matrix is like the cytoplasm of the mitochondria.
In the matrix we have PDH and CAC.
Outer membrane has large channels that are not very selective.
Pyruvate to get into the matrix from the cytoplasm has to go through a symporter. It is
a transmembrane protein channel that takes pyruvate and hydrogen.
Matrix needs a lot of hydrogen for oxidative phosphorylation. And pyruvate for CAC.
Since its impermeable to ions the ions can only get through specific protein channels
eg hydrogen pyruvate symporter channel.
Energy used muscle contraction- ATP is bound the myosin head cannot bind to actin,
ATP is hydrolysed to ADP and phosphate get a conformational change PO4 is released
and binds to a new location on actin. ADP is released and we get a conformational
change that pulls actin along. ATP then binds and dissociates from actin.
Slow twitch fibres- slow oxidative (needs oxygen) rich in blood lots of myoglobin
and mitochondria, slow to contract but long lasting eg postural muscles marathons.
Very red in colour
Oxidative and glycolytic uses ANAEROBIC glycolysis as well as oxidative CAC and
oxidative phosphorylation. Rich in blood, mitochondria and myoglobin (oxygen
storing protein ). Pale pinker colour
Fast twitch oxidative- uses ANAEROBIC glycolysis as well as oxidative aerobic
glycolysis. This is good for sprinting, short fast bursts. Mostly glycolysis, not a lot of
blood, myoglobin and mitochondria. White in colour.

23

Enzymes- acetyl CoA is the crossroads were many metabolic pathways converge such
as fatty acids and proteins. Different substances such as sugar fat and protein are
catabolized to produce acetyl CoA, which is then fed into the CAC, it is a major entry
point for energy production.

Acetyl CoA- cannot go back into glueconeogenesis due to a high G, sugar can go
back into fat under physiological conditions.

Under anaerobic conditions pyruvate does not go into PDH, instead pyruvate goes
into otherterminal electron acceptors (lactate) bacteria (ethanol).
Pyruvate Dehydrogenase complex: Is a massive complex

3 different enzymes- within the massive complex there are multiple copies of each
enzyme. In each complex and have a variety of names.
Highly conserved.
Highly exergonic
5 different coenzymes- coenzyme is something that is needed for the enzyme to work,
and is regenerated at the end as well as the enzyme. Dont partake in the reaction.
coenzyme
Pyruvate AcetylCoA
NAD+NADH
FAD, lipoic acid and thiamine pyrophosphate are permanently bound.
CoenzymeA and NAD+ are free to move around the cytoplasm and need to be
continuously controlled by a kinase which phosphorylates and a phosphatase that
dephosphorylates.
Multiple copies of 3 enzymes:
E1 (pyruvate dehydrogenase, 20-30 copies)
E2 (dihydrolipoyl transacetylase, 60 copies)
E3 (dihydrolipoyl dehydrogenase, 6 copies)
5 coenzymes:
CoenzymeA- carries acetyl groups and acetyl are 2 carbon compounds. It is
able to pick up substance because of the SH group and form an S group. Used
in a lot of biological processes.
NAD+ - from niacin vitamin B3 can pick up 2 electrons forming a hydride
ion (1 proton and 2 electrons) one of the protons bind to NAD and the other is
released to the cytoplasm, have to have H+ in the cytoplasm to act as a buffer.
FAD- Vit B2 permanently bound to PDH same as the hydride ion, both
NAD and FAD are electron carriers. Both go into REDOX reactions.

24

lipoic acid- lipoamide produced from lipoic acid, can go between the
REDOX reactions of lipoamide. Therefore is able to pick up other
compounds. Lysine molecule one cofactor compound enables the movement
from oxidized to reduced form.
thiamine pyrophosphate (TPP)- thiamine vit B1, capable of becoming
ionized were the hydrogen ion can dissoaciate and leaves a negatively charged
ion and called the carbanion ion. Thiamine diffieciency causes beri beri
disease affects the CNS and neural communication is disrupting causing
muscle weakness, thiamine is needed for CAC.
Regulatory enzymes:
kinase
phosphatase

Overall pyruvate dehydrogenase complex

1.
2.
3.
4.
5.
6.

Pyruvate from glycolysis.

Need Acetyl CoA
Need electron donor NAD+ and acceptor NADH
All cofactors TPP, FAD and Lipaote
Produce Acetyl CoA goes to the citric acid cycle and CO2
Has a large -G therefore cannot be reversed back into sugar.

25

Yellow E1
Green E2
Pink E3

E1- pyruvate is decarboxylated and produces carbon dioxide and is released. The 2
carbon compound (acetyl) binds to TPP.
E2- S-S group becomes reduced to SH group and the other S from the S-S group
binds with the 2 carbon group from E1. This 2 carbon compound is transferred to
CoenzymeA to make acetyl CoA- which goes to the CAC, and when that happens we
have 2 SH groups so its reduced. However the SH group has to S-S group.
Acetyl CoA
E3- Takes both hydrogens from SH group and transfers them to FAD to make FADH2
and in turn goes back to SS, which is regenerated to what we need on E2. In order for
electrons to moved has to be turned into NAD and go into NADH which is mobile not
bound like FAD. By doing this FAD is regenerated.
Control of PDH

26

Lots of ATP turn on pyruvate kinase and the kinase phosphorylates pyruvate
dehydrogenase and gets turned off. Same as acetyl CoA if theres fatty acids in the cell
Citric Acid Cycle

Stage 1 steps 1-5- introduction of 2 carbons from acetyl CoA (2 carbons from acetyl
and CoA is regenerated to PDH), loss of 2 carbons to CO2 and production of NADH
and one GTP, which is converted to ATP.
Stage 2 steps 6-8- partial oxidation succinate and oxaloacetate, make NADH and
FADH2 and we regenerate oxaloacetate.

Stage 1
o Reaction 1- citrate synthase (makes citrate) is a dimer, shows induced fit really well
also has very specific binding mechanism.

27

Oxaloacetate (from CAC) is 4 carbons and acetyl CoA (from PDH) is 2 carbons and
forms citryl CoA that is 6 carbons, which is dehydrated and CoA group is removed and
regenerated to form citrate. If acetyl CoA bound first it would be cleaved releasing.
Has very specific binding mechanism were the oxaloacetate has to bind first and the
acetyl CoA binds second in order for the 2 carbon to bind with the 4 carbon and make the
6 carbon chain, if Acetyl CoA bound first it would be catalytically cleaved releasing the
2C and CoA, therefore the 2C will not enter CAC. This order means we dont lose the 2C
group.
o Reaction 2- goes through an intermediate called aconitase

o Isomerization of citrate (isocitrate).

Reaction 3- isocitrate dehydrogenase

o Used to lose hydrogen when oxidizing NADH

o Lose a C to CO2 known as carboxylative dehydration and a reduced electron carrier.
28

Reaction 4- - ketgluterate dehydrogenase complex (very similar to PDH)

o Used to lose hydrogen when oxidizing NADH

o Lose a C to CO2 known as carboxylative dehydration and a reduced electron carrier.
o 2 carbons came in as a carboxyl group and 2 carbons left as carbon dioxide. And left
with a 4 carbon compound using Coenzyme A.
o Very similar to PDH
o Made succinyl CoA
Reactions 1-4
o Condensation (oxaloacetate and Acetyl CoA)
o Isomerization (citrate to isocitrate)
o Decarboxylation of isocitrate: CO2, NADH
o Decarboxylation of -ketoglutarate: CO2, NADH

Reaction 5- Succinyl-CoA synthetase Conversion of succinyl-CoA to succinate

29

o Succinyl CoA is broken down from a 6 carbon chain to a 4 carbon chain with the
addition of energy (GTP) and phosphate to produce succinate coenzyme A and GTP
wich is then rapidly converted to ATP.
Reaction 6- succinate dehydrogenase

o Succinate is transferred to an electron carrier FAD which is permanently bound.

o All citric acid cylcle enzymes are free to move around EXCEPT fumerase.
Reaction 7- Fumarase Hydration fumarate to malate

30

o Fumerate has to be in the trans position to produce L- malate this is know as

stereospecifity and is highly reversible with the G close to 0.
o L malate will keep using these products to keep the CAC going and is the basis of
homeostasis.
Reaction 8- regeneration of oxaloacetate

o Has a huge positive G

o Yet goes in the forward reaction because oxaloacetate is continuously being used by
enzyme 1 to make citrate.
CAC summary

2C acetyl CoA condenses with 4C oxaloacetate to form 6C citrate

Coenzyme A is released
Isomerisation of citrate
Oxidative Decarboxylations (NADH, CO2)
31

4/8 reactions are oxidations

Energy of oxidation efficiently conserved in reduced carriers: NADH and
FADH2
A series of reactions regenerate oxaloacetate
This cycle can be repeated as long as oxygen (for oxidative
phosphorylation) and pyruvate are available
8 successive steps

Amphibolic- to be involved in catabolism and anabolism

Different compounds with the CAC can be used to make other compounds such as
amino acids, nucleotides, heme groups and gluconeogenesis

Red arrows indicate anaplurotic meaning if these compounds are running low then the
CAC cannot turn.
Needs regulation- PDH is turned off when there is plenty of energy in the cell which
is determined by ATP and NADH.
The Presence of fatty acids means alternate energy is available and glucose doesnt
need to used and is stored as glycogen..
CAC is turned on when there is a lot of ADP indicating low level of energy and not
much ATP.
Need to have the system making ATP

Lecture 6 oxidative phosphorylation

32

Oxidative phosphorylation- oxidative refers to redox electron carriers and

reduction of energy as electrons move through a system, which powers the
phosphorylation of ADPATP. Coupling of electron carriers and donating
energy, that energy powers the phosphorylation of ADP ATP.
EXERGONIC AND ENDERGONIC REACTION, final step hydride ions are
used to make water and are oxidized.
OILRIG
OIL- OXIDATION IS LOSS
RIG- REDUCTION IS GAIN
ALWAYS COUPLED because electrons cannot be free to move around.
Electrons binding with hydrogen to produce hydride ion (2 protons and 1
electron) is a 1 electron carrier.
Dehydrogenation- transfer of a hydride ion to NAD NADH
LOTS OF LOST ELECTONS
C-H BONDS RELEASES A LOT ENERGY, THAT ENERGY IS USED TO
FUEL THE CELL IN THE ELECTRON TRANSPORT CHAIN!!!
Common electron carriers:
NADNADH
1.
FADFADH2
2.

As the electron moves down the cascade its losing energy as it reaches water
(green oxidized carrier) lowest energy state and is last electron acceptor and most
oxidized form. Water has no c-h bonds and is fully oxidized.
Electron Transport Chain- in the Matrix of the mitochondria is like the cytoplasm and
contains many enzymes. The matrix is where all the pathways of fuel oxidation meet.
The ETC is basically taking electrons putting them into the ETC and producing
protons across the inner membrane and regenerate NAD to continue the CAC.
33

Start of ETC- Complex I- NADH dehydrogenase takes NADH NADH2

Complex III aka BC1 complex- contains cytochromes B and C1.
Complex IV- contains cytochromes oxidase which oxidizes cytochromes.
Complex II- membrane bound proteins- receive NADH and FADH2 which are
transported and pumped through this complex. Succinate dehydrogenase from
CAC, produces FADH2 which is non mobile and can only be distributed via the
ETC.
Chemiosmotic gradient aka proton gradient- receives ions from complex 11 and
forms the chemiosmotic gradient, powers ATP synthesis.
Q and cytochrome C- are mobile electron carriers. As they pass to carriers protons
are pumped across the membrane. These electrons which are hydride ions bond
with oxygen to produce water.
Last step powers the motor for ATP synthesis- rotational catalysis and proton
gradient where there is more protons in the inner membrane space than the matrix,
they will travel down the concentration gradient, however the membrane is
impermeable to ions therefore they have to transfer down a transmembane protein
ATP synthase. As they travel down the gradient they power rotational catalysis
which leads to ADP ATP.
Cytochrome Oxidase- complex IV pumps hydrogen from the matrix to the inner
membrane space and takes hydrogen from the matrix to make water. Therefore
causing a change in charge in the proton gradient.
Complex I and III are proton pumps
THE ETC PRODUCES A PROTON GRADIENT WITHIN THE INNER MEMBRANE
OF THE MITOCHONDRIA. THEY DUE THIS DUE THE MEMBRANE BEING
IMPERMEABLE TO IONS!!!

34

1. NADH and FADH2 enter via dehydrogenation NADH donates 2 electrons at

complex I (NADH dehydrogenase) and FADH2 donates 2 electrons at complex
II (not shown in diagram).
2. Coenzyme Q (ubiquinone) lipid soluble and can diffuse through the inner
membrane and cytochrome C is mobile and sits at the junction of the inner
membrane and inner membrane space and is a one electron carrier are
membrane bound carriers electron carriers. Coenzyme Q takes electrons from
complex I- Complex III an Complex II Complex III. Cytochrme C complex
II(from CAC and succinate dehydrogenase complex)- complex III (bc1
complex)

Complex I contains FMN- flavin mononucleotide which transports the

electrons.

35

Chemiosomotic gradient- creates a proton motive force from concentration

gradient and a charge separation from the high proton conentraton in the inner
membrane.
ETC- 3 proton pumps and take hydrogen to make water, leads to conc grad and
charge separation.
Chemiosmotic model

ATP synthesis happens at complex and is known as ATPsynthase. Its also an ATPase and
wants to make ADP and Phosphate from ATP, the hydrogen flow and certain affinaity
takes it to the right. Made of 2 componants F0 hydrogen pore and F1 Catalytic Head stork
joins both componants. Catalytic head is in the matrix and hydrogen pore is in the
membrane space.
Whole process is controlled by the needs of the cell and is regulated by the ADP and ATP
and NAD and NADH ratio so turning on off metabolites. 32 ATP generated and about
65% efficient as some energy is lost as heat.

Lecture 7 Glycogen Metabolism

Glycogen main storage of glucose in the liver and some in the skeletal muscles.
Comprised of long chains of glucose subunits.
Carbons 1,4 and 6 form the chains on the glucose molecule. Via glycosidic bonds
carbon 6 and 1 forms branches in the chain
Livers buffers blood glucose levels by distributing glucose to other tissues were
needed whilst muscle glucose is only used in he muscle.
Glycogenolysis- breakdown of gglycogen
Glycogensis- make new glycogen molecules

Glycogen breakdown:
Enzyme 1: Glycogen phosphorylase- main enzyme used to catalyzes the phosphorolytic
cleavage of the (14) glycosidic linkage of glycogen releasing a glucose-1-phosphate
36

can only work on single chains not braches. Stops cleaving at 4 molecules before the
branching at 1,6 carbon molecule.
Enzyme 2: glycogen debranching enzyme- 2 independent acting sites
Transferase activity- transfers 3 of the 4 glucose molecule and transfers them to
the end of the chain while leaving the other glucose molecule at the branch point.
Glucosidase activity- cleaves last glucose molecule freeing up the rest of the chain
to be catalyzed by enzyme 1.
Enzyme 3: phophoglucomutase- catalyzes the conversion of glucose-1-phosphate to
glucose-6-phosphate so it can be used in the production of glucose via glycolysis in
skeletal muscle and dephosphorylated in the liver by glucose 6 phosphatase and is not
found in the skeletal muscle and released in the blood.
Synthesis of Glycogen (glycogenesis):

Prominent in liver and skeletal muscle

Reaction 1: via glucose +ATP ADP+ G6p
Reaction in muscle is catalyzed by enzymes hexokinase I and II
Reaction in liver is catalyzed by enzyme Hexokinase IV
G6p is converted to G1p- reversible reaction
Synthesis of UDP glucose made from UDP-glucose phosphorlyase enzyme (uric
diphosphate) activated sugar nucleotide from G1p and UTP. The UDP glucose is
what creates the long polymer chains of glucose to make glycogen. More
energetic favorable than glucose. Also used in carbohydrate chains.
Glycogen synthase enzyme- catalyzes the transfer of the UDP glucose to the end
of the chain to make the chain longer and UDP as it loses the glucose to the chain.
Continuously does that to grow the chains and forms (14) glycosidic bonds.
Can form 1,6 carbon for branching
Branching of glucose chains increases the solubility of the polymer and creates
free ends for enzymes to cleave when glucose is needed rapidly.
Add branches by glycogen synthase by moving upto 7 glucose residues to the 1,6
carbon and forms a chain, however cannot start a new polymer.
glycogenin enzyme is the primer that starts a new polymer and also catalyzes the
assembly of the polymer. Contains a tyrosine molecule that forms a glycosidic
bond with carbon 1 from UDP glucose molecule. This is added to the glycogenin
until chain is 6-10 glucose molecules long and glycogen synthase can catalyze the
chain.

Regulation of glycogen synthesis and breakdown

Coordinately regulated so both mechanism are coordinated at the same time.

Usually regulated when one is more active the other is less active.
Glycogen synthase enzyme- synthesizes glycogen
Glycogen phosphorylase enzyme breaks down glycogen
37

Both enzymes are reciprocally regulated by:

1. Allosteric effectors- glycogen phosphorylase can either be in relaxed and
active conformations. Molecules such as AMP, ATP and G6p all interact with
this enzyme to alter its function:
AMP-relaxed conformation and binds when ATP is depleted
ATP and G6p- tense conformation inhibit glycogen phosphorylase
When ATP and G6p are in abundance glycogen breakdown is stopped.
These processes are reversed in glycogen synthase enzyme and are active when
G6p and ATP are high.
2. Reversible phosphorylation- when phosphate is added to an enzyme can alter
catalytic activity. Phosphate is added to 3 types of amino acids, serine,
tyrosine and threonine in a protein chain which is donated by ATP.
Phosphorylated by a protein kinase and is a reversible reaction. Each kinase
can activate and deactivate each enzyme. In glycogen phosphorylase and
glycogen synthase can be activated and deactivated by phosphorylation.
3. Hormones-

Insulin induces synthesis of glycogen- initiates dephosphorylation cascade of proteins

opposite effect of glucagon.
Glucagon, epinephrine adrenalin induce breakdown of glycogen.
Hormone regulation 1- ATP is synthesized to cAMP when glucagon binds to
adenylate cyclase after a second message is triggered when hormone binds to
receptor. This happens all in sinew.
Hormone regulation 2- second message binds to PKA (protein kinase A ) which adds
inorganic phosphate to proteins and phosphorylates and modifies activity of the
protein which basis the physiological activities of glucagon.

Introduction to lipids

Organic biomolecules with insolubility in water.

Derived from fatty acids
Major classes:
1. Storage lipids- triaclglycerols
2. Structural and functional (phospholipids and eicosanoids)
Constitute all cells.
Triglycerides major energy source and storage
Signaling molecules paracrine cells eicosanoids
Lipid based hormones
Fatty acids are components of lipids are long hydrocarbon chains various numbers of
double bonds and terminate with a carboxylate group
38

Phospholipids are made of fatty acids.

Double bonds are usually in cis configuration of fatty acid chains
The more unsaturated the more fluid the chain is.
Numbered fro carboxylate group 1 is the carbon on the carboxyl group and methyl
group at the end of the chain is however long the chain is and also named alpha, beta
etc carbon
Tryacyl indicates triglycerides stored as fat in adipose cells high level energy source
and insulation have 2 tryl groups attached to 3 hydrocarbon chains that can contain 3
R groups on each head on the glycerol molecule.
Sterols

Non fatty acid containing lipids such as cholesterol (major sterol) and maintain
structure of membrane.
Signaling molecules in cells eg eicosanoids are paracrine hormones not endocrine and
act close to the tissue their made in and derived from fatty acids, involved in clotting,
inflammation an immune defense. Derived from archidonic acid that is a 20 carbon
chain with 4 double bonds.
3 classes of eicosanoids derived from archandonate:
1. Prostaglandins (prostate gland)- immediating pain and fever and
immunosuppresion
2. Thromboxanes (platelets)- blood clotting
3. Leukotreines (leukocytes)- 3 conjugated double bonds tri-3 enedouble bond and mediate airway constriction
Archadonate is the second chain triglycerides and is cleaved by the enzyme
phospholipase A2 in response to hormonal or other stimuli to synthesize the
eicosanoids through a series of reactions.
Formation of prostaglandins and thromboxanes is produced by PGH2 that is
synthesized in 2 reactions that are catalyzed by cyclooxengase (COX) 2 ioforms of
COX so COX I and COX II, pain relief medication acts on COX. Is both a precursor
to prostaglandins and thromboxanes
Synthesis of luekotrienes begins with enzyme lipooxygenases found in leukocytes
heart, brain lung and spleen
All reactions happen in the phospholipid
COX I- responsible for synthesizing prostaglandins that regulate gastric mucin
COX II- synthesis prostaglandins that mediate pain and fever
Pain medication blocks both COX therefore causing gastric problems such as ulcers
COX is inactivated by aspirin irreversibly until the COX is degraded by the cell and a
new COX is made.
COX 2 drugs were specifically targeted so stomach isnt affected for patients with
chronic pain have found to increase the chance of strokes and heart attack.

Lecture 8 Fatty Acid Metabolism

39

Fuel molecule part of triglycerides are fatty acids.

Are the HYDROCARBON CHAINS!!
Highly reduced and anhydrous, varying degrees of saturation terminate with a
carboxyl group.
Even number of carbon chains most common 16 and 18
Egs Stearic acid 18 carbon chain
Monounsaturated fatty acid single double bond HC chain. Eg (18:1) one double
bond in 18C chain.
Cis configuration
Trans configuration made chemically
Attached to a glycerol molecule and stored in adipose tissue, to utilize molecule has
to be cleaved ester bond from glycerol group.
There is twice the amount of energy in fatty acid than carbohydrates.
Glucose quick energy source
Fats long lasting energy source months
Sources of triglycerides:
1. Dietary fat- high fat consumption in food
2. Fat stored in adipose tissue- make fat synthesis and store triglycerides and
mobilizing triglycerides when energy is needed

40

Utilization of Fatty Acids as Fuel

1.
2.
3.

3 stages
Mobilization of fatty acid from glycerol ester
Activation and transport to mitochondria from the cytosol (for catabolism)
Degradation of fatty acids by oxidation to produce ATP for the cell

Mobilization- triacylglycerols are DEGRADED to fatty acids and glycerol by enzyme

triacylglycerol lipase. Released from adipose tissue and then transported bound to
albumin. Stimulated by hormones epinephrine and glucagon and inhibited by insulin.
Glycerol a byproduct of the breakdown of fatty acid is absorbed by the liver and
converted to glyceraldehyde-3- phosphate thats used in glycolysis or gluconeogenis.

2. Activation and Transport- activated by being attached to Coenzyme A to

form fatty acyl CoA (activated fatty acid that can be transported into the
mitochondria), which is catalyzed by enzyme acyl CoA synthase. Carnitine
transport the acyl CoA cells in the mitochindria

41

Any fatty acid that becomes activated it is transported into the mitochondrial
matrix for degradation via oxidation.
3. Fatty acid degradation by oxidation- degraded by a recurring sequence of
4 reactions:
1. OXIDATION by FAD- oxidation of fatty acid chain by enzyme Acyl CoA
dehydrogenase to give Enoyl CoA. FAD FADH2 reaction is on the BETA
CARBON, 2 hydrogens are removed. Trans form molecule
2. HYDRATION- add water on double bond formed by oxidation of beta carbon,
stereospecific reaction only L isomer is formed
3. 2nd OXIDATION by NAD+- removes 2 hydrogens one from water and one
from carbon to produce C=O bond.
4. THIOLYSIS by Acyl CoA- cleaving off 2 carbon unit in the form of acetyl
CoA, making the chain 2 carbons shorter.
A 16 carbon chain the 4 reactions will happen 7 times to produce 8 molecules of
acetyl CoA, will enter CAC and produce NADH and FADH2 and both electron
carriers enter the electron transport chain to produce ATP. And gives 108ATP
molecules and comes from FAD and NAD being passed in the ETC to produce
the ATP.
8 molecules Acetyl CoA
All move in CAC
Each Acetyl CoA in CAC gives 3 NADH , 1 FADH2 and 1 ATP
Even number carbon chains produce total carbon number/2 acetyl CoA eg 16C=
8 acetyl CoA
Odd number carbon chains produce (carbon number/2) -1 end product 2 carbon
molecule propionyl- CoA. Eg 15C= 6 Acetyl CoA and 1 priopionyl CoA and
formed into succinyl CoA which then goes into CAC.
42

Fatty Acid Synthesis

Occurs in 2 stages:
Stage 1- formation of malonyl CoA (3C unit)
Stage 2- Elongation of Chain (2C units at a time)
Stage 1- acetyl CoA is converted to malonyl CoA, which makes the chain were
2C from the malonyl CoA molecule is added, is catalyzed by the enzyme acetyl
transacylase, this is an irreversible reaction in fatty acid synthesis . This step is a
MAJOR step in regulation.

Step 2- Elongation of chain- occurs in recurring series of 4 reactions, this is

opposite to - Oxidation reaction, one catalytic enzyme that controls all
polypeptide reactions. Long flexible arm of fatty acid chain is attached to ACP,
which is attached to the enzyme. Multienzyme complex with 3 enzyme domains.
1. Condensation- produce 4C using acyl-malonyl ACP condensing enzyme
2. Reduction- - ketoacyl ACP reductase
3. Dehydration- removes water
4. 2nd Reduction- enoyl ACP reductase enzyme

43

End product is palmitate C16 + ACP chain, modifications to the chain such as
extensions and double bonds are done by other enzymes in the cell.

44

Degradation
1. Occurs in mitochondrial
matrix

synthesis
Occurs in the cytosol

45

2. intermediates of - oxidation are

linked to acetyl CoA
3. separate enzymes catalyze each step
4. oxidants NAD+ and FADH used
5. variety of chains can be degraded

Intermediates are attached to ACP

One multienzyme complex (fatty acid
synthase)
Reductant NADPH used
Stops at 16C palmitate is synthesized

Regulation of Fatty Acid Metabolism

Regulated to physiological needs of the cell.

Synthesis is maximal when carbs and energy are plentiful after a big meal.
Acetyl CoA Carboxylase initiates fatty acid synthesis and catalyzes the
committed step and regulated by signals, allosteric effectors and covalent
modification. ACTIVATED BY DEPHOSPHORYLATION,
DEACTIVATED BY PHOSPHORYLATION
INSULIN- SYNTHESIS FATTY ACIDS
GLUCAGON & EPINEPHRINE- INHIBITS SYTHESIS AND INIATES
BREAKDOWN OF FATTY ACIDS.

Lecture 9: Amino Acid Metabolism

Protein metabolism
2 molecules that have nitrogen-amino acids and nucleotides
Amino acids are incorporated into proteins on ribosomes.
Amino acids all contain a -carbon with amino group and carboxyl group
attached to the carbon and a side chain. All have a different side chain.
20 amino acids incorporated into proteins.
3 groups: hydrophobic side chain, hydrophilic side chain and in between side
chains
Peptide bond that joins 2 amino acids together formed on the ribosome during
protein synthesis.
Thousands of amino acid chain.
Amino end start of the chain (N terminus)
Carboxyl end of the chain (C terminus)
Amino acids that are used for energy come from dietary protein (meat and certain
vegetables).
Metabolism- amino acids cant be stored by the body and only used when there is
excess amount of amino acids or a lack of other energy sources.
In order to utilize energy from the amino acids the amino group has to be removed
from the -carbon and the remaining amino acid molecule is used for energy.
Amino group that is removed is toxic and has to be eliminated quickly as the
nitrogen is toxic and this occurs through the urea cycle.
46

Serve as a nitrogen source for other compounds that are nitrogen based molecules
such as heme in Hb, hormones and phospholipids, neurotransmitters and bases of
DNA and RNA.
Proteolytic enzymes cleave long chain proteins into smaller peptides that are
further hydrolysed into individual amino acids. Cleave the end of the amino end.
Aminopeptidases cleave amino end of the amino acid. Work in one direction
Carboxypeptidases cleave the carboxyl end of the amino acid work the
opposite direction to the aminopeptidase.
Endopeptidases hydrolyze specific bonds within a protein chain (trypsin
create new ends).
Degradation of Amino Acids and Urea Cycle

Amino acids are degraded when there is normal protein turnover. body protein is
constantly being renewed which leaves excess amino acids.
Amino acids are utilized for energy. When carbs are scarce such as starvation or
diabetes mellitus.
Amino acids are converted to urea in the liver.
In muscle excess amino groups are picked up by pyruvate and converted to
alanine, and moved to the liver which converted by into pyruvate for glycolysis
and transferred back into the muscle.
Alanine (specific to muscle) and glutamine are carriers on amino acids.
Degradation of amino acids occurs in 2 stages:
1. Removal of NH2 group via aminotransferases enzymes (different enzyme for
amino acids have same mechanism) the reaction entails the -amino group is
transferred to the -carbon of the -ketoglutarate, which is converted to glutamate
and -keto acid. This reaction will happen to any amino of the 20 amino acids.
Urea Cycle 5 steps takes free ammonia and converts it to urea begins in the liver mitochondria, 3 steps in the cytosol, expands 2 cycles
mitochondria and cell cytosol!! AS SOON AS GLUTAMATE ENTERS THE
MITOCHONDRIA ITS DEAMINATED THE FREE N2 IS CONVERTED
TO UREA AND QUICKLY REMOVED BY THE UREA CYCLE
1. Formation of carbamoyl phosphate in mitochondrial matrix ( enzyme
carbamoyl phosphate synthase)
2. Formation of citrulline and passes through the mitochondria into the cytosol.
3. In the cytosol the second amino group of urea is attached from aspartate,
example of an amino acid donating an amine group to another compound to
produce another compound, production of argininosuccinate
4. Cleavage of argininosuccinate produce arginine and fumerate, once fumerate is
formed can reenter the mitochondria CAC intermediates. FUMERATE JOINS
CAC AND UREA CYCLE!!
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5. Arginine is cleaved to produce urea and ornithine.

Image showing the CAC and Urea cycle overlapping each other with
argininosuccinate
2.

Breakdown of carbon skeleton that is left behind when the amino acid is
deaminated.
The 6 products that remain when amino acids are broken down are the 6 (1.Actyl
CoA,2 -ketoglutarate,3. Succinyl CoA, 4. Fumarate,5. Oxyloacetate and 6.
Pyruvate) constituents of the CAC. All products from deamination enter the CAC
at different points, the remaining carbon skeletons are oxidized to CO2 and water.
Glucogenic amino acids degraded to -ketoglutarate, succinyl CoA, Fumarate,
Oxaloacetate and pyruvate. C skeletons used to produce glucose
Ketogenic amino acids- degraded to Acetyl CoA acetylacetate CoA, C skeletons
used to produce ketone bodies (produce under starvation).

Regulation of Urea Cycle:

Flux of N2 through the cycle varies with diet, more protein more active the urea cycle.
Prolonged starvation, breakdown of muscle protein thusly more nitrogen is produced.
Rates of synthesis of enzymes within the urea cycle increase when high amounts of
protein are consumed.
Some organisms excrete nitrogen as nitric acid. (birds and reptiles)
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Biosynthesis of Amino Acids

Synthesis requires nitrogen, which is salvaged or reused.

The nitrogen cycle

Humans rely on plants and microbes to turn nitrogen in a digestible form such as
ammonia to produce amino acids.
2 principle enzymes that convert ammonia into amino acids
1. Glutamate corresponding enzyme Glutamate dehydrogenase forms
glutamine
2. Glutamine corresponding enzyme Glutamine synthetase forms glutamine
Both can be transaminated to produce amino acids and glutamate can transfer its
amide group to other amino acids.
Glutamine synthetase is the most important pathway for incorporating ammonia into
glutamine. Regulated allosterically and covalent modification. Highly regulated as it
synthesizes all amino acids.
Essential amino acids are those that CANNOT be synthesized so we get them from
diet.
Non-essential we can synthesis in the cell.
All amino acids are derived from GLYCOLYSIS, PENTOSE PHOSPHATE
PATHWAY AND CAC.
6 precursors that amin0 acids are made -ketoglutarate, 3- phosphoglycerate,
oxyloacetate, pyruvate, phosphophenolpyruvate & erythrose-4-phosphate and ribose5-phosphate.
Precursor 1- -ketoglutarate
Precursor 2- 3- phosphoglycerate
Precursor 3- oxyloacetate,
Precursor 4- , pyruvate
Precursor 5- phosphophenolpyruvate & erythrose-4-phosphate

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Precursor 6- ribose-5-phosphate

Lecture 10: Nucleotide Metabolism

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