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Metabolism
MCD Year 1
Anil Chopra
Contents
Metabolism 1 - Introduction to Protein Structure .................................................... 1
Metabolism 2 - Energetics and Enzymes ................................................................... 5
Metabolism 3 - Metabolic Pathways and ATP Production I ................................. 12
Metabolism 4 -Metabolic Pathways and ATP Production II ................................. 22
Metabolism 5 - Mitochondria and Oxidative Phosphorylation ............................. 30
Metabolism 6 - Lipids & Membranes ...................................................................... 35
Metabolism 7 - Cholesterol ....................................................................................... 44
Metabolism 8 - Membrane Trafficking.................................................................... 52
Metabolism 9 – Integration of Metabolism ............................................................. 55
Metabolism 1 - Introduction to Protein Structure
Anil Chopra
1. Outline the reaction by which amino acids are joined together.
Chirality
Anatomy of an Amino Acid
H
H
amino
group
N
C
H
The central C carbon atom is a chiral centre (from the
Greek, meaning "handed") i.e. it has four different
substituents bound to it.
O
carboxyl
group
C
mirror
OH
-carbon
side chain
C
R
Substitutions at the R position or side chain, give rise to
the 20 different amino acids e.g. R=CH3 in alanine.
The whole of the amino acid minus the side chains is known
as the backbone.

H
H
R
NH2
COOH
L-enantiomer
H2N C
HOOC
R
This gives rise to optical
isomers (enantiomers) of
each amino acids each
of which is a mirror
image of the other.
D-enantiomer
Glycine (Gly) has no side chain (only an H atom)
and is therefore the only non-chiral amino acid.
Side chains can be polar of non-polar – this is vital to the properties of the protein
Eg.
proline – non polar
asparagine - polar





They can also be acidic or basic eg. glutamic acid
The state of ionisation of an amino acid provides vital biological properties to
many proteins and enzymes, and for this reason cells cannot generally tolerate
wide changes in pH.
Consequently, If the ionisation state of key amino acids within a protein is altered,
a loss of biological activity often results.
The ability to take up and release protons gives amino acids some buffering
capacity to resist some changes in pH.
Individual amino acids are joined in condensation reactions (water is lost) to form
peptide chains.
2. Sketch a trimeric peptide, illustrating the amino -terminus, carboxyl terminus
and side chains.
1
Anatomy of a Peptide
peptide bond
amino
terminus
H
N
H
O
C
C
H
N
C
H
R2
O
C
OH
H
R1
carboxyl
terminus
side chains



The polypeptide chain of a protein rarely forms a disordered structure (random
coil) as proteins generally have functions to fulfil, and these functions rely upon
specificity.
In turn, functionality requires a definite 3D structure or conformation of the
polypeptide chain.
Proteins generally possess a degree of flexibility necessary for function e.g.
muscle fibres
3. Give examples of the post translation modifications of amino acids, with
reference to glycosylation, hydroxylation and carboxylation.








Even after synthesis, (post translation), the starting set of 20 amino acids can be
modified to create novel amino acids, enhancing the capabilities of the protein.
Proline can be modified to produce hydroxyproline e.g. collagen fibres, a major
constituent of skin, cartilage, teeth & bones.
These additional hydroxyl groups help to stabilise the fibres.
The addition of sugar residues to the asparagine residues of proteins (N-linked
glycosylation) increases their solubility and also protects them from enzymatic
degradation.
Deficiency of N-linked sugar chain transfer is detected in congenital
carbohydrate-deficient glycoprotein (CGD) syndrome which affects multiple
tissues and has life threatening complications.
Similarly, g-carboxyglutamate is produced by the carboxylation of glutamate.
The formation of g-carboxyglutamate residues within several proteins of the blood
clotting cascade (e.g. factor IX) is critical for their normal function by increasing
their calcium binding capabilities.
The anticoagulant warfarin works by inhibiting the carboxylation reaction.
4. Understand the concepts of primary structure, secondary structure, tertiary
structure & quaternary structure with respect to proteins.
Folding of Proteins




Proteins generally fold into a single conformation of lowest energy.
This can occur spontaneous or involve other molecules known as chaperones,
which bind to the partly folded polypeptide chain and ensure that the folding
continues along the most energetically favourable pathway.
By breaking the bonds that hold the protein together, we can denature the protein
into the original flexible polypeptide.
Common denaturants used within the laboratory are urea (breaks hydrogen bonds)
and 2-mercaptoethanol (breaks disulphide bonds).
2




Primary structure is the linear sequence of amino acids that make up the protein.
Secondary structure is defined as local structural motifs within a protein, e.g. αhelices and β-pleated sheets.
Tertiary structure is the arrangement of the secondary structure motifs into
compact domains.
Quaternary structure is the three dimensional structure of a multimeric protein
composed of several subunits
5. Distinguish between a α-helix and a ß-pleated sheet and appreciate the bonds
that stabilise their formation.

Neutralisation of the polar groups in amino acids is achieved by their hydrogen
bonding to each other in one of two regular structures – α helix and β pleated
sheet.
The α helix

Hydrogen Bonds between the C=O of one residue and the N-H of another residue,
4 amino acids along the helix, stabilise the entire structure.


The side chains of individual amino acids project out from within the a –helix.
Although theoretically helices can be either right-handed or left handed, the usage
of L-amino acids in proteins means that right-handed helices are favoured.
In proline, the last atom of the side chain is bonded to the main chain N atom.
This prevents the N atom from hydrogen bonding with the C=O groups of another
residue within the helix, thereby distorting the helical conformation, putting a
‘kink’ into it.


The β pleated sheet

As with the alpha helix, hydrogen bonds between the N-H and C=O groups of two
or more b-strands hold the b -pleated sheet sheet together.
3



In the b-pleated sheet, the NH and C=O groups point out at right angles to the line
of the backbone. This almost two dimensional sheet is pleated, like the bellows of
an accordion.
Alternate b -strands can run in the same direction to give a parallel b-pleated sheet
or in opposite directions to give an antiparallel b -pleated sheet.
The pleating in each case allows for the best alignment of the hydrogen bonded
groups.
6. Appreciate the different types of bond that combine to stabilise a particular
protein conformation.





Covalent bonds (in which two atoms share electrons) are the strongest bonds
within protein and exist in the primary structure itself. Covalent bonds can also
exist as disulphide bridges. These occur when cysteine side chains within a
protein are oxidised resulting in a covalent link between the two amino acids.
Hydrogen Bonds occur when two atoms bearing partial negative charges share a
partially positively charged hydrogen, the atoms are engaged in a hydrogen bond
(H-bond).
Ionic interactions arise form the electrostatic attraction between charged side
chains e.g. Glu, Asp, Lys and Arg. They are relatively strong bonds, particularly
when the ion pairs are within the protein interior and excluded from water.
Van der Waals Forces are transient, weak electrostatic attractions between two
atoms, due to the fluctuating electron cloud surrounding each atom which has a
temporary electric dipole. Although relatively weak and transient in nature,
because of the sheer number of these interactions within a protein, they can still
have a large part to say in the overall conformation of a protein.
Hydrophobic Interactions are a major force driving the folding of proteins into
their correct conformation. They juxtapose hydrophobic side chains by packing
them into the interior of the protein. This creates a hydrophobic core and a
hydrophilic surface to the majority of proteins
Summary





Proteins are chains of amino acids linked by peptide bonds which have evolved to
fulfil specific functions within the cell.
Such functions are reliant upon the 3D structure or conformation of the protein
which is held together by a variety of forces.
The a-helix and b-pleated sheet are the two staple motifs that define the
conformation of a protein.
The nature of the amino acid side chain dictates its position within the
conformation of the protein.
Post-translational modifications of proteins add yet more diversity to protein
structure.
4
Metabolism 2 - Energetics and Enzymes
Anil Chopra
1. Define the 1st and 2nd Laws of thermodynamics.
The First Law of Thermodynamics

Energy can neither be created nor destroyed. i.e. it is simply converted from one
form to another.
The Second Law of Thermodynamics


In any isolated system, e.g. a single cell or the universe, the degree of disorder
can only increase.
The amount of disorder in a particular system can be quantified as its entropy.
Reactions proceed spontaneously towards products with greater entropy (i.e. more
disorder).
2. Explain the concept of free energy and how we can use changes in free energy
to predict the outcome of a reaction.


However, biological systems are very well ordered.
This is achieved by investing taking energy from the environment surrounding the
cell and investing it in chemical reactions which maintain order.
At The Single Cell Level
At Single Cell Level
Increased
disorder
cell
Increased
order
HEAT
Surrounding environment
In this scenario, both the 1st and 2nd Laws of
thermodynamics are obeyed
5








Entropy changes during a chemical reaction are very difficult to measure.
This lead Josiah Gibbs to create the function known as Free Energy.
(Gibb’s) Free Energy is defined as the amount of energy within a molecule that
could perform useful work at a constant temperature.
It is denoted by the letter G and has units of kilojoules/moles (kJ/mole).
The free energy function combines both the 1st and 2nd Laws of thermodynamics.
Changes in G (DG) measure the amount of disorder that results from a particular
reaction.
i.e. In the above scenario, DG measures both the change in order within the cell
and also upon the change in entropy of the system.
Lets consider the reaction:
A+B
C+D
reactants
products




The changes in free energy for this reaction (DG) can be defined by:
DG = free energy (C+D) - free energy (A+B)
A reaction can only occur spontaneously if DG is negative.
Conversely, a reaction cannot occur spontaneously if DG for the reaction is
positive.
3. Draw the chemical structure of ATP and explain how it acts as a carrier of free
energy and is used to couple energetically unfavourable reactions.
Adenosine Triphosphate (ATP):







Phosphoanhydride bonds have a large negative DG of hydrolysis, and are thus
said to be "high energy" bonds.
ATP
ADP + Pi
DG°'= - 31 kJ/mole !!!
(ΔG°' = standard free energy change at pH 7)
Pathways within the cell that synthesise molecules are generally energetically
unfavourable e.g. peptide synthesis
They take place because they are coupled to an energetically favourable one.
Providing that the sum of the DG for the overall reaction is still negative, the
reaction will proceed.
The majority of energetically unfavourable biochemical reactions rely on the
hydrolysis of high-energy phosphate bonds such as those found in ATP.
6








4. Describe how enzymes act as catalysts of reactions with reference to the
reaction catalysed by lysozyme.
In a biological setting, most energetically favourable reactions will not occur at a
rate useful for life, unless catalysed by enzymes. Enzymes function by lowering
the barriers that block a particular reaction.
Enzymes bind one or more substrate molecules tightly within a part of the protein
known as the active site. Enzymes arrange the substrate(s) in such a way that
certain bonds are strained.
Key residues within the enzyme participate in either the making or breaking of
bonds by altering the arrangement of electrons within the substrate(s).
This can often take the form of either oxidation reactions, (in which electrons are
removed from a molecule) or reduction reactions (in which electrons are added
to a molecule).
Since the cellular environment is generally aqueous, often, when a molecule gains
an electron, it also simultaneously gains a proton.
The transition state is the particular conformation of the substrate in which the
atoms of the molecule are rearranged both geometrically and electronically so that
the reaction can proceed.
Enzymes work by bending their substrates in such a way that the bonds to be
broken are stressed and the substrate molecule resembles the transition state. This
makes them more amenable to reaction with other molecules.
Enzymes function by lowering the barriers that block a particular reaction. Put
graphically:
Transition State
of Substrate
Free energy
Substrate
Transition State
of Substrate
Activation Energy
Substrate
Activation Energy
Product
Product
reaction
Lysozome
 Lysozyme is a component of tears and nasal secretions and is one of the first lines
of defence against bacteria.
 It catalyses the hydrolysis of sugar molecules within bacterial cell walls that are
necessary for their structure. With this bond broken, the bacteria lyse and die.
 The activity of lysozyme was discovered by Sir Alexander Fleming, who suffering
from a cold, allowed some of his nasal secretions to drip into a bacterial culture.
This results in lysed bacteria.
 Lysozyme hydrolyzes alternating polysaccharide copolymers of N-acetyl
glucosamine (NAG) and N-acetyl muramic acid (NAM) which represent the
"unit" polysaccharide structure of many bacterial cell walls.
 Lysozyme cleaves at the b(1-4) glycosidic linkage, connecting the C1 carbon of
NAM to the C4 carbon of NAG.
7
How Lysozome Works
 Glu35 protonates the oxygen in the glycosidic bond breaking the bond holding the
two sugar molecules together.
 A water molecule enters and is de-protonated by Glu35.
 Asp52 stabilises the positive charge in the transition state.
 The hydroxide ion attacks the remaining sugar molecule adding an OH group.
Both Glu35 and Asp52 are in their original state to continue catalysis.
 Glu35 protonates the oxygen in the glycosidic bond breaking the bond holding the
two sugar molecules together.
 A water molecule enters and is de-protonated by Glu35.
 Asp52 stabilises the positive charge in the transition state.
 The hydroxide ion attacks the remaining sugar molecule adding an OH group.
Both Glu35 and Asp52 are in their original state to continue catalysis.
5. Outline the reaction catalysed by glucose-6-phosphatase and explain what
clinical symptoms are linked to inherited deficiencies of this enzyme.
Glucose-6-Phosphatase
H2O
+ Pi
Glucose-6-phosphatase
Glucose-6-phosphate


Glucose
G-6-Pase is predominantly a liver enzyme that catalyses the above reaction,
releasing glucose from the large stores of glycogen within the liver, when blood
glucose levels are low.
On leaving the liver, the glucose is rapidly taken up by the brain and muscle.
Glucose-6-Phosphatase Deficiency



A deficiency in G-6-Pase characteristically leads to:
- low blood sugar levels
- slow growth
- large liver
- short stature
The disease is known as Von Gierke’s disease and sufferers have inherited two
mutant copies of the G6Pase gene, one from each parent.
Thankfully, only around 1 in 100,000 individuals are affected.
6. Outline the differences between lock and key and induced fit models of
substrate-enzyme interactions.
8
Lock and Key Model
+
enzyme


substrate
enzyme-substrate complex
In this model, the shape of the substrate (key) matches that of the active site (lock)
of the enzyme.
This model explains the specificity of most enzymes for a single substrate.
Induced Fit Model

In this model, the substrate induces a change in the conformation of the enzyme
which results in the formation of the active site. Upon release of products, the
enzyme reverts back to its original conformation.
+
enzyme


substrate
enzyme-substrate complex
From crystallographic analysis of enzymes with and without substrate bound, we
now hold the induced fit model to be valid.
Proteins generally possess a degree of flexibility necessary for function. e.g.
muscle fibres
7. Describe graphically, the effects of a) substrate concentration, b) temperature
and c) pH on enzyme catalysed reactions.
Substrate Concentration
Vmax
½ Vmax
rate of reaction
substrate concentration
Km
9





The reaction rates of enzymes vary considerably and can be measured
experimentally. This is useful if we are testing an enyme inhibitor e.g. captopril
Km is known as the Michaelis Constant ands is defined as the concentration of
substrate at which a particular enzyme works at half its maximal velocity.
Biochemically, the Km value is useful as a means of comparing the strength of
Enzyme-Substrate complexes.
Generally a low Km indicates tight binding of a substrate to an enzyme.
Conversely, a high Km is indicative of weak binding.
Temperature
rate of reaction
temperature


Chemical reactions speed up as temperature is increased, so, in general, catalysis
increases at higher temperatures.
However, each enzyme has a temperature optimum, beyond which its
conformation is said to be denatured and the enzyme is inactive.
pH Level
rate of reaction
pH


Enzymes have an optimum pH
This is due to the catalytic side chains in the active site being in the correct state of
ionisation.
8. Illustrate the role of the coenzyme NAD in the reactions catalysed by
glyceraldehyde-3-phosphate dehydrogenase, lactate dehydrogenase and malate
dehydrogenase, referring to the biochemical changes involved in its reduction
to NADH
10

NAD+ (Nicotinamide
adenine dinucleotide) is a
vital component of many
dehydrogenation reactions
within the body.
 It can be described as a coenzyme as it has no
catalytic activity of its own
and functions only after
binding to a enzyme.
NAD+ catalyses the dehydrogenation of substrates by readily accepting a
hydrogen atom and two electrons.
+ H+ + 2e-
H- (hydride ion)
NAD+

NADH
substrate glyceraldehyde-3-phosphate reaction is oxidised (hydrogen removed)
and also phosphorylated in a coupled reaction.
Lactate Dehydrogenase


During intense exercise, skeletal muscles have to function anaerobically, as
oxygen is a limiting factor. As such, the metabolite pyruvate is converted into
lactate. This also generates free NAD+ which is needed by the muscle for other
reactions.
Lactate diffuses from the muscle into the blood stream and is picked up by the
liver, where the high levels of NAD+ can be used by lactate dehydrogenase to
regenerate pyruvate.
Malate Dehdrogenase

Malate dehydrogenase oxidises malate to give oxaloacetate, a key metabolite of
the TCA cycle.
11
Metabolism 3 - Metabolic Pathways and ATP Production I
Anil Chopra
1. Sketch a cartoon of the three stages of cellular metabolism that convert food to
waste products in higher organisms, illustrating the cellular location of each
stage.
Metabolism



Digestion – large to small molecules
Cellular metabolism I – oxidation of small molecules in cytosol to produce ATP
and NADH
Cellular metabolism II – oxidation of small molecules in mitochondria
The Three stages of Cellular Metabolism
cytosol
Proteins
NH2
Amino Acids
TCA cycle
Glucose
ATP
Pyruvate
NADH
Acetyl
CoA
Oxidative
Phosphoryation
NADH
ATP
H20
O2
Glycolysis
mitochondrion
Simple sugars
CO2
Polysaccharides
Fatty Acids
&Glycerol
Fats
12
Glucose
Free
Ener
gy
Free energy
released as heat
Relatively large
activation energy
overcome by heat
source
CO2
+ H20
Reaction
Free energy liberated is
invested in carrier
molecules such as ATP
Glucose
Free
Ener
gy
Relatively small activation energies
overcome by enzymes and body
temperature
CO2
+ H20
Reaction
Reaction
This is around 50% efficient, c.f. car engines which on
average are only 20% efficient
13
2. Outline the metabolism of glucose by the process of glycolysis, listing the key
reactions, in particular those reactions that consume ATP and those that
generate ATP.
Overview of Glycolysis
 1x 6C glucose
2x 3C pyruvate – 2x ATP produced
 Essentially an anaerobic process
 Occurs in cytoplasm of cells
 Ten reactions that make up glycolysis pathway can be split into two main
concepts:
- formation of a high energy compound – involves the investment of energy
in the form of ATP
- susbsequent splitting of compound – produces useful energy in the form of
ATP generation
Glycolytic Pathway
hexokinase
1.
glucose
glucose-6-phosphate
ATP
-
ADP
all kinases transfer a phosphate group
reaction irreversible – commits cell to subsequent reactions
phosphoglucose isomerase
2.
glucose-6-phostphate
-
fructose-6-phosphate
the isomerisation shuffles the glucose chair to give fructose.
the logic behind this reaction is that fructose can be split into equal halves
when subsequently cleaved
phosphofructokinase
3.
fructose-6-phosphate
fructose-1,6-bisphosphate
ATP
-
ADP
here a highly symmetrical, high energy compound is generated
regulation of phosphofructokinase exquisitely controls the entry of sugars
into the glycolysis pathway
adolase
4.
fructose-1,6-bisphosphate
glyceraldehyde-3-phosphate
dihydroxyacetone phosphate
14
-
opening of the fructose ring to generate two high energy compounds, one
of which, (dihydroxyacetone phosphate) subsequently undergoes
isomerisation.
triose phosphate isomerase
5.
dihydroxyacetone phosphate
phosphate
-


glyceraldehyde-3-
deficiency in TPI is extremely rare (only 29 documented cases worldwide)
since its diagnosis 35 years ago. Most sufferers die within the first 6 years
of their lives.
At this half-way point in the pathway one mole of glucose has given rise to two
moles of glyceraldehyde-3-phosphate.
So far, no energy has yet been produced but two moles of ATP have been used.
glyceraldehyde
3-phosphate dehydrogenase
6.
2x glyceraldehyde-3-phosphate
bisphosphoglycerate
2x 1,3-
NAD+ + Pi
-
NADH
NADH is generated here which can be later used to generate yet more ATP
within the mitochondria in a process known as oxidative phosphorylation.
phosphoglycerate kinase
7.
2x 1,3-bisphosphoglycerate
2x 3-phosphoglycerate
ADP
-
ATP
A phosphate group is transferred to an ADP molecule to give ATP.
phosphoglycerate mutase
8.
2x 3-phosphoglycerate
-
2x 2-phosphoglycerate
Shuffling of the phosphate group from the 3 to the 2 position
enolase
9.
2x 2-phosphoglycerate
2x phosphoenolpyruvate
dehydration
pyruvate kinase
10.
2x phosphoenolpyruvate
2x pyruvate
15
ADP

ATP
transfer of the high energy phosphate group to ADP, generating one ATP
molecule in the process.
There is are 2 molecules of pyruvate produced and a net gain of 2 ATP per
molecule of glucose commited to the glycolytic pathway.
3. Distinguish between the aerobic and anaerobic metabolism of glucose with
reference to the enzymes involved and the comparative efficiencies of each
pathway with respect to ATP generation.
Substrate Level Phosphorylation

Substrate-level phosphorylation can be defined as the production of ATP by the
direct transfer of a high-energy phosphate group from an intermediate substrate in
a biochemical pathway to ADP, such as occurs in glycolysis.
phosphoglycerate kinase
e.g. 1,3-bisphosphoglycerate
3-phosphoglycerate
ADP

ATP
This is in contrast to oxidative phosphorylation, where ATP is produced using
energy derived from the transfer of electrons in an electron transport system
Pyruvate has Two Possible Fates in Anaerobic Conditions

Alcoholic fermentation:
.
pyruvate decarboxylase
pyruvate
acetaldehyde
H+
CO2
alcohol dehydrogenase
acetaldehyde
ethanol
NADH + H+

NAD+
this is characteristic of yeasts and can occur under anaerobic conditions
Generation of lactate:
lactate dehydrogenase
16
pyruvate
lactate
NADH + H+
-
NAD+
this is also anaerobic and is characteristic of mammalian muscle during
intense activity when oxygen is a limiting factor
Regeneration of NAD+


Both alcoholic fermentation and the generation of lactate serve one common
purpose:
They allow NAD+ to be regenerated and thus glycolysis to continue, in conditions
of oxygen deprivation. i.e. conditions in which the rate of NADH formation by
glycolysis is greater than its rate of oxidation by the respiratory chain.
Anaerobic vs Aerobic Metabolism


From the anaerobic metabolism of glucose we only generate 2 molecules of
pyruvate and 2ATP molecules (net).
This contrasts poorly to the complete oxidative phosphorylation of glucose which
can yield 38 molecules of ATP.
4. Describe the reactions catalysed by lactate dehydrogenase and creatine kinase
and explain the diagnostic relevance of their appearance in plasma.
Lactate Dehydrogenase as a Diagnostic Tool



Lactate dehydrogenase catalyses the inter-conversion of pyruvate and lactate.
LDH is present in many body tissues, especially the heart, liver, kidney, skeletal
muscle, brain blood cells and lungs.
Elevated levels can be used to diagnose several disorders including:
-
stroke
heart attack
liver disease (eg. hepatitis)
muscle injury
muscular dystrophy
pulmonary infarction
Creatine Kinase as a Diagnostic Tool
 In muscle, the amount of ATP needed during exercise is only enough to sustain
contraction for around one second.
 Thankfully a large reservoir of creatine phosphate is on hand to buffer demands
for phosphate (25mM creatine phosphate c.f. 4mM ATP in resting muscle).
 DG (hydrolysis) = -31 kJ/mole (ATP) & -43.1 kJ/mole (CP)
Creatine kinase
creatine phosphate
creatine +ATP
17
ADP + H+


When a muscle is damaged, creatine kinase leaks into the bloodstream. Either
total levels of creatine kinase or the tissue specific isoform can be measured to
help to determine which tissue has been damaged.
Elevated levels can be used to:
-

ATP
diagnose myocardial infarction (heart attack)
determine the extent of muscular disease
evaluate the cause of chest pain
help discover the carriers of muscular dystrophy (Duchenne)
The total creatine kinase test is about 70% accurate whilst isoenzyme testing is
about 90% accurate.
5. Outline the oxidative decarboxylation reaction catalysed by pyruvate
dehydrogenase, with reference to the product and the five co-enzymes required
by this enzyme complex.
Generation of Acetyl CoA
Pyruvate dehydrogenase
complex
pyruvate + HS-CoA
acetyl CoA + CO2
NAD+




NADH
This series of reactions occurs in the mitochondria of the cell.
The acetyl CoA thus formed is committed to entry into the citric acid cycle and
can ultimately produce ATP by the process of oxidative phosphorylation
This is the committed step for entry of pyruvate into the TCA cycle although in
reality there is a lot more happening.
The pyruvate dehydrogenase complex is gigantic (in molecular terms) and not
only consists of three individual enzymes but also five co-factors:
Enzyme
Prosthetic Group
pyruvate decarboxylase
(E1)
thiamine pyrophosphate (TPP)
lipoamide reductase-transacetylase (E2) lipoamide
dihydrolipoyl dehydrogenase (E3)
FAD (Flavine Adenine Dinucleotide)
 Prosthetic groups such as lipoamide are a permanent part of the complex, whereas
NAD+ and CoA bind reversibly to enzymes.
Thiamine Pyrophosphate (TPP)
 Derivative of the B1 vitamin (thyamine)
 Readily loses a proton and the resulting carbanion attacks that of pyruvate to yield
hydroxyethyl-TPP.
 A deficiency of thiamine (vitamin B1) is the cause of Beri-Beri , whose symptoms
include damage to the peripheral nervous system, weakness of the musculature
18
and decreased cardiac output. The brain is particularly vulnerable as it relies
heavily on glucose metabolism.
Lipoamide


The long flexible arm of the molecule allows the dithiol group to swing from one
active site to another within the complex.
Arsenite (AsO33-) and mercury have a high affinity for neighbouring sulphydryl
groups, such as those that occur in reduced lipoamide and will readily inhibit
pyruvate dehydrogenase.
Flavine Adenine Dinucleotide

FAD accepts and donates 2 electrons with 2 protons (2 H):
FAD + 2 e- + 2 H+
FADH2
The Pyruvate Dehydrogenase Complex





Decarboxylation of pyruvate to give hydroxyethyl TPP.
Oxidation & transfer to lipoamide to give acetylipoamide.
Transfer of the acetyl group to CoA to give acetyl CoA.
Regeneration of oxidised lipoamide.
Regeneration of oxidised FAD, generating NADH.
6. Describe the different processes by which the fatty acid palmitate and the
amino acid alanine are converted into acetyl-CoA.
19


Acetyl CoA is produced from both types of major food molecules within the
mitochondria of cells.
Thus it is the location where most of the cell's oxidation reactions occur and also
where the majority of the cell’s ATP is made.
Fatty Acid Metabolism



By virtue of being fully reduced (i.e carbon skeletons 'saturated' with hydrogens)
the oxidation of fatty acids constitutes the most compact fuel for the body's energy
requirements and as a result, fatty acid oxidation yields several times the usable
chemical energy that carbohydrates can deliver.
On a weight basis, the caloric yield from fatty acids is about double that from
carbohydrates. More than half of the body's energy needs including the liver, but
not the brain, comes from fatty acid oxidation and this is enhanced during fasting
over long periods of time.
Fatty Acids are metabolised in the mitochondria in several stages. Firstly, they are
converted into an acyl CoA species:
Fatty acid + + ATP + HS
i.e. ATP




Acyl CoA + AMP + PPi
AMP, 2 high energy bonds are used.
The acyl coA species then undergoes a sequence of dehydration, hydration,
oxidation and thiolysis reactions (collectively called b-oxidation) resulting in
production of one molecule of acetyl CoA and an acyl CoA species which is 2
carbons shorter than the original.
Eg. Palmitic acid (16C)

CoA
myristyl-CoA (14C) + acetyl CoA (2C)
The -oxidation reactions continue to consecutively remove 2-carbon units from
the acyl CoA therby producing acetyl CoA.
On the final cycle (4-carbon fatty acyl CoA intermediate), two acetyl CoA
molecules are formed.
From just 7 b-oxidation reactions, the 16-carbon palmitoyl CoA molecule
produces 8 molecules of acetyl CoA.
During each cycle one molecule each of FADH2 and NADH are produced. The
overall reaction of -oxidation of palmitoyl CoA is:
palmitoyl CoA + 7 FAD + 7 NAD+ + 7 H2O + 7 CoA
8 acetyl CoA + 7 FADH2 + 7 NADH
Amino Acid Metabolism



Amino acid metabolism can be 'separated' into pathways depending on the number
of carbon atoms the amino acid possesses. All of the degradation pathways
produce common end products which can enter the TCA. The majority of the
degradation takes place in the liver.
C3 family e.g. alanine, serine (glycine), and cysteine are all degraded to pyruvate.
C4 family e.g. aspartate and asparagine are degraded to oxaloacetate.
20

C5 family e.g. glutamine, proline, arginine, and histidine, all of which are
converted to a-ketoglutarate.
Protein Metabolism

Alanine (C3) undergoes transamination by the action of the enzyme alanine
aminotransferase.

Pyruvate can enter the TCA cycle, while glutamate is re-converted to aketoglutarate by glutamate dehydrogenase, generating NH4+ which is ultimately
converted to urea.
Persistently elevated levels of alanine aminotransferase are a diagnostic for
hepatic disorders such as Hepatitis C.

Summary



Glycolysis is central to metabolism in mammals, producing 2 moles of ATP for
every mole of glucose and it relies upon the formation of a high energy compound
which is subsequently split to liberate energy.
Under aerobic conditions, pyruvate produced by glycolysis can be dehydrogenated
by the actions of a giant multimeric enzyme, PDH, to generate acetyl CoA, a
substrate for the TCA cycle in mitochondria and a prelude to oxidative
phosphorylation.
Both amino acids and fatty acids can be oxidised to generate metabollically useful
components such as pyruvate and acetyl CoA.
21
Metabolism 4 -Metabolic Pathways and ATP Production II
Anil Chopra
1. Outline the Krebs or TCA (tricarboxylic acid cycle) with particular reference to
the steps involved in the oxidation of acetyl Co-A and the formation of NADH
and FADH2 and the cellular location of these reactions.
The Three stages of Cellular Metabolism
cytosol
Proteins
NH2
Amino Acids
TCA cycle
Glucose
ATP
Pyruvate
NADH
Acetyl
CoA
Oxidative
Phosphoryation
NADH
ATP
H20
O2
Glycolysis
mitochondrion
Simple sugars
CO2
Polysaccharides
Fatty Acids
&Glycerol
Fats
The Manufacture of Acetyl Co Enzyme A
 Entry to the TCA cycle via conversion into acetyl CoA:



The thioester bond is a high-energy linkage, so it is readily hydrolysed, enabling
acetyl CoA to donate the acetate (2C) to other molecules.
RNA ancestry suggests it is of primeval origin.
The pyruvate dehydrogenase complex:
pyruvate dehydrogenase
complex
Pyruvate + HS-CoA
acetyl CoA + CO2
22
NAD+
NADH
1. Decarboxylation of pyruvate to
give hydroxyethyl TPP.
2. Oxidation & transfer to
lipoamide to give
acetylipoamide.
3. Transfer of the acetyl group to
CoA to give acetyl CoA.
4. Regeneration of oxidised
lipoamide.
5. Regeneration of oxidised FAD,
generating NADH.





Acetyl CoA can also be manufactured from palmitic acid (a fatty acid).
The -oxidation reactions continue to consecutively remove 2-carbon units from
the acyl CoA therby producing acetyl CoA.
On the final cycle (4-carbon fatty acyl CoA intermediate), two acetyl CoA
molecules are formed.
From just 7 b-oxidation reactions, the 16-carbon palmitoyl CoA molecule
produces 8 molecules of acetyl CoA.
During each cycle one molecule each of FADH2 and NADH are produced. The
overall reaction of -oxidation of palmitoyl CoA is:
palmitoyl CoA + 7 FAD + 7 NAD+ + 7 H2O + 7 CoA
8 acetyl CoA + 7 FADH2 + 7 NADH
The TCA Cycle




a.k.a. The Tricarboxylic Acid (TCA) cycle or The Citric Acid Cycle.
A continuous cycle of eight reactions, starting with 2 carbon atoms from acetyl
CoA being condensed with the 4 carbon unit of oxaloacetate to give a 6 carbon
unit , citrate.
The thio-ester linkage of the acetyl
CoA allows it to be readily donated
to oxaloacetate.
Each turn of the cycle produces two
molecules of CO2 (waste) plus
three molecules of NADH, one
molecule of GTP and one molecule
of FADH2.

23

Step 1:
citrate synthase
oxaloacetate (4C)
citrate (6C)
HS-CoA + H+
Acetyl CoA (2C)
- transfer to the oxaloacetate of 2C from acetyl CoA

Step 2:
aconitase
citrate (6C)
isocitrate (6C)
- isomerisation of citrate to give isocitrate

Step 3:
isocitrate dehydrogenase
α-ketogluterate (5C)
isocitrate (4C)
NAD+

NADH + H+ + CO2
-
oxidation of isocitrate to give α-ketoglutarate
dehydrogenation and decarboxylation
Step 4:
α-ketoglutarate
dehydrogenase complex
α-ketoglutarate (5C) + HS-CoA
succinyl-CoA
(4C)
NAD+

similar to reaction catalysed by PDH
dehydrogenation and decarboxylation
Step 5:
succinyl CoA synthetase
succinyl CoA (4C)
H2O + GDP + Pi
-
NADH + H+ + CO2
succinate (4C) + HS-CoA
GTP (guanisone triphosphate)
CoA is displaced by a phosphate molecule which is subsequently
transferred to GTP
only stage that directly forms GTP / ATP (in bacteria and plants)
GTP itself can act as a phophoryl donor in protein synthesis or signal
transduction processes
Alternatively a phosphate grou can be transferred to that of ADP to
generate ATP – catalysed by nucleoside diphosphokinase
24

Step 6:
succinate dehydrogenase
succinate (4C)
fumarate (4C)
FAD

FADH2
oxidation of succinate generating some FADH2
dehydrogenation
Step 7:
fumerase
fumerate (4C)
malate (4C)
H2O

addition of a water molecule – breaking a double bond
Step 8:
malate dehydrogenase
malate (4C)
oxaloacetate (4C)
NAD+
-
NADH + H+
the last step – dehydrogenation of malate to give oxaloacetate, the
starting point of the cycle
Location of the TCA Cycle Enzymes



The Krebs cycle enzymes are soluble proteins located in the mitochondrial matrix
space, except for succinate dehydrogenase, which is an integral membrane protein
that is firmly attached to the inner surface of the inner mitochondrial membrane.
Here, it can communicate directly with components in the respiratory chain, as we
shall see in the next lecture.
The majority of the energy that derives from the metabolism of food is generated
when the reduced coenzymes are re-oxidised by the respiratory chain in the
mitochondrial inner membrane in a process known as oxidative phosphorylation.
The Krebs cycle only operates under aerobic conditions, as the NAD+ and FAD
needed are only regenerated via the transfer of electrons to O2 during oxidative
phosphorylation.
Importance of the TCA Cycle


ATP production by glycolysis and the Krebs cycle is only a prelude to oxidative
phosphorylation.
The function of the Krebs cycle is to produce the reduced co-factors NADH and
FADH2 which are re-oxidised during osidative phosphorylation to yield the
following:
25

three ATP molecules formed by the re-oxidation of each NADH
molecule
two ATP molecules formed by the re-oxidation of each FADH2
molecule.
Therefore from the Krebs cycle – oxidation of 1x acetyl coA gives:
-
3x NADH + 1x FADH2 + 1x GTP = 12x ATP
2. Outline the glycerol phosphate shuttle and the malate-aspartate shuttle, in
particular stating why these mechanisms are required and understand the concept
of transamination with reference to the malate-aspartate shuttle.



NADH produced in glycolysis needs to enter the mitochondria to be utilised by
the process of oxidative phosphorylation and to regenerate NAD+.
Remember, there is only a finite amount of NAD+ and unless it is regenerated,
glycolysis will very quickly grind to a halt.
NADH, or more accurately, its high-energy electrons, crosses from the cytosol
into the matrix of the mitochondria by two methods:
-
the glycerol phosphate shuttle – skeletal muscle, brain
the malate- aspartate shuttle – liver, kidney, heart
The Glycerol Phosphate Shuttle



Electrons from NADH, rather than NADH itself
are carried across the mitochondrial membrane via
the carrier glycerol-3-phosphate.
A cytosolic glycerol dehydrogenase (G-DH)
transfers electrons from NADH to glycerol 3phosphate, which can diffuse into the
mitochondria.
There, a membrane bound form of the same
enzyme transfers them to FAD.
The Malate-Aspartate Shuffle


This takes place primarily in the heart and liver and uses two membrane carriers
and four enzymes.
The net reaction in terms of NADH is:
NADHcytoplasmic + NAD+mitochondrial


NAD+cytoplasmic + NADHmitochondrial
Hydrogen is transferred from cytoplasmic NADH to oxaloacetate to give malate, a
reaction catalysed by cytosolic malate dehydrogenase (MDH).
Malate can be transported into the mitochondria where it is rapidly re-oxidised by
NAD+ to give oxaloacetate and NADH (catalysed by mitochondrial MDH).
26






However, oxaloacetate has now been
being depleted from the cytoplasm and is
accumulating within the mitochondrial
matrix.
Since it cannot cross the matrix
membrane, the problem cannot be solved
by by simply transferring oxaloacetate
back to the cytoplasm.
Instead, the cell uses a transamination
reaction to take an amino group from glutamate and transfer it to oxaloacetate,
giving aspartate.
This aspartate then crosses the matrix membrane, via an amino acid transporter,
and is duly converted by the same transamination reaction in reverse, back to
oxaloacetate.
Transamination is therefore pivotal to the malate-aspartate shuttle – it is defined as
a reaction in which an amine group is transferred from one amino acid to a keto
acid, thereby forming a new pair of amino and keto acids.
A more accurate diagram of the malate-aspartate shuffle is therefore:
A
B


A = alpha-ketoglutarate transporter – exchanges alpha-ketoglutarate for malate
B = glutamate/aspartate transporter – exchanges glutamate for aspartate
3. Explain in general terms the relationship between TCA intermediates and those
pathways involved in amino acids synthesis and breakdown.


The general strategy of amino acid degradation is to remove the amino group
(which is eventually excreted as urea) whilst the carbon skeleton is either
funnelled into the production of glucose or fed into the Krebs cycle
Degradation of all twenty amino acids gives rise to only seven molecules,
pyruvate, acetyl CoA, acetoacetyl CoA, a-ketoglutarate, succinyl CoA, fumarate
and oxaloacetate.
27
4. Calculate the total yield of ATP obtained from the complete oxidation of one
glucose molecule.
glycolysis

glucose
2x pyruvate (net 2x ATP + 2x NADH)
PDH

2x pyruvate + CoA + NAD
+
2x acetyl CoA + 2x NADH
TCA cycle

2x acetyl CoA
6x NADH + 2x FADH2 + 2x GTP
This gives 2x ATP + 10x NADH (3x ATP each) + 2x FADH2 (2x ATP each) + 2x
GTP
= 38x ATP from one molecule of glucose
5. Compare the complete oxidation of one glucose molecule, with the beta oxidation
of palmitic acid with reference to the ATP produced per molecule of each
substrate.

1st step
palmitate + ATP + HS-CoA
(loss 2xATP)
palmitoyl CoA + AMP + PPi
β-oxidation

palmitoyl CoA + 7x FAD + 7x NAD+ + 7H2O + 7x CoA
CoA + 7x FADH2 + 7x NADH
8x acetyl
TCA cycle

8x acetyl CoA
24x NADH + 8x FADH2 + 8x GTP
This gives 31xNADH (3x ATP each) + 15x FADH2 (2xATP each) + 8x GTP –
2xATP
= 129x ATP from one molecule of plamitate – about 5 times that from
glucose
6. Give two examples of the use of NADPH in reductive biosynthesis.


Glycolysis and the Krebs cycle provide
the starting point for many biosynthetic
reactions.
The amino acids, nucleotides, lipids,
sugars, and other molecules shown here
as products, in turn, become the
precursors for the many of the
macromolecules of the cell.
28



Each black arrow in this diagram denotes a single enzyme-catalysed reaction. Red
arrows generally represent multi-step pathways.
If Krebs cycle intermediates are drawn off for biosynthesis then they must be
replenished, otherwise the cycle will grind to a halt. e.g. If oxaloacetate is
removed, acetyl CoA cannot enter and glycolysis backs up.
Thankfully some enzymes can catalyse anaplerotic reactions (from the Greek to
fill up) which can regenerate Krebs cycle intermediates.
Nicotinamide Adenine Dinucleotide Phosphate (NADP+)







This is a relative of NAD+ differing only by a phosphate group attached to one of
the ribose rings
NADP+ is also an electron carrier.
Like NAD+, NADP+ can pick up two high energy electrons and in the process, a
proton (H+) collectively known as a hydride ion (H-). It then forms NADPH.
The phosphate group of NADP+ does not participate in electron transfer, but gives
it a slightly different conformation, meaning that it will bind to different enzymes
than NAD+.
The hydride ion is held in a high-energy linkage, allowing it to be easily
transferred to other molecules.
NADPH takes part in anabolic reactions, whereas NADH takes place in catabolic
reactions. The use of different co-factors for sets of reactions is a classical
“division of labour”a common theme throughout biology.
It allows electron transport in catabolism to be kept separate to that of anabolism.
NADPH is a Co-factor in the Biosynthesis of
Cholesterol


NADPH helps to catalyse the final reaction of
several, that lead to cholesterol synthesis.
The C=C bond is reduced by the transfer of a hydride
ion (two electrons plus a proton from solution, H-).
NADPH is a Co-factor in the Biosynthesis of RNA
29
Metabolism 5 - Mitochondria and Oxidative
Phosphorylation
1. Outline the proposed evolutionary origins of mitochondria.



Mitochondria are believed to be the evolutionary descendants of a prokaryote that
established an endosymbiotic relationship with the ancestors of eukaryotic cells.
This is thought to have occurred early in the history of life on earth and that
following this, many of the genes needed for mitochondrial function were moved
(translocated) to the nuclear genome.
More recently, the elucidation of the complete genome of Rickettsia prowazekii
has revealed that several genes are closely related to those found today in
mitochondria.
Support for the Theory:





Mitochondria can only arise from pre-existing mitochondria and chloroplasts.
Mitochondria possess their own genome and it resembles that of prokaryotes,
being a single circular molecule of DNA, with no associated histones.
Mitochondria have their own protein-synthesizing machinery, which again
resembles that of prokaryotes not that of eukaryotes.
The first amino acid of their transcripts is always fMet as it is in bacteria and not
methionine (Met) that is the first amino acid in eukaryotic proteins).
A number of antibiotics (e.g., streptomycin) that act by blocking protein synthesis
in bacteria also block protein synthesis within mitochondria and chloroplasts.
They do not interfere with protein synthesis in the cytoplasm of the eukaryotes.
2. Draw a cross sectional representation of a mitochondrion, and label its component
parts.


The reactions of oxidative phosphorylation take place on the inner membrane.
The folds of the christae increase the surface area for these reactions to take place.
30
3. Describle the electron transport chain in mitochondria with reference to the
functions of coenzyme Q (ubiquinone) and cyctochrome c.
Two Steps of Oxidative Phosphorylation:
 The translocation or movement of protons from within the matrix of the
mitochondria – controlled by the electron transport chain.
 The pumped protons are allowed back into the mitochondria through a specific
channel, which is coupled to an enzyme which can synthesise ATP known as ATP
synthase.
The Electron Transport Chain







The electron transport chain is a chain of three complexes and two mobile carriers
whih act as electron carriers.
Membrane complexes
- NADH dehydrogenase complex
- cytochrome b-c1 complex
- cytochrome oxidase complex
Mobile carriers
- ubiquinone (co-enzyme Q)
- cytochrome C
These proteins accept electrons and in doing so, a proton (H+) from the aqueous
solution.
As electrons pass through each of the complexes, protons are pumped to the
intermembrane space.
Each unit of the chain has a higher affinity for electrons than the previous unit,
allowing them to flow in a logical order.
The transfer of electrons from one complex to another is energetically favourable
and so the electrons lose energy as they progress along the chain.
Ubiquinone




Ubiquinone can pick up either one or two electrons (with an H+ from solution) and
pass them to cytochrome b-c1 complex.
Its hydrophobic tail confines it to the lipid bilayer of the membrane where it is
needed.
It is the entry point for electrons donated by FADH2 since succinate
dehydrogenase can communicate directly with it.
As fewer protons are pumped to the intermembrane space than for NADH, less
ATP is produced.
Cytochrome Oxidase


Cytochrome oxidase is involved in the final electron transfer step.
It receives 4 electrons from cytochrome c and passes them to oxygen to generate
water:
4e- + 4H+ + O2
2H2O
31

In addition, 4 protons are pumped to the intermembrane space, enhancing the
proton gradient.
Redox Reactions




The reactions that take place in the electron transport chain are redox reactions
since a reduced substrate donates electrons and an oxidised substrate accepts them
(thus electrons move along the transport chain).
The ability of a redox couple to accept of donate electrons is known as the
reduction potential, or redox potential.
Standard redox potential is given the symbol E’0.
Positive E’0 value shows redox couple has a tendency to donate electrons and vice
versa.
4. Outline the chemiosmotic theory.
Two Steps of Oxidative Phosphorylation:


The translocation or movement of protons from within the matrix of the
mitochondria – controlled by the electron transport chain.
The pumped protons are allowed back into the mitochondria through a specific
channel, which is coupled to an enzyme which can synthesise ATP known as ATP
synthase.
Chemiosmosis:



The proton motive force that drives H+ back into the matrix space consists of a pH
gradient and a transmembrane electrical potential.
This flow of protons back into the matrix is coupled to ATP synthesis.
Protons flow back into the matrix through the ATP synthase molecule, which
produces ATP from ADP + Pi.
ATP Synthase:





ATP synthase is a multimeric enzyme consisting of
a membrane bound part (F0) and a part which
projects into the matrix space (F1).
Each part consists of three different sub units.
When hydrogen ions flow through the membrane
via a pore, the disc of c subunits is compelled to
rotate.
The γ-subunit in the F1 unit is fixed to the disc and
therefore rotates with it.
However, the α and β subunits in the F1 unit cannot
rotate because they are locked in a fixed position by
the b subunit, which is anchored to subunit a in the
membrane.
32




As the γ subunit functions as an asymmetrical axle, the β subunits are compelled
to undergo structural changes.
This rotation drives the transitions of the catalytic portions of the β subunits,
which in turn, alters their affinities for ATP and ADP.
As a consequence, torsional energy flows from the catalytic subunit into the bound
ADP and Pi to promote the formation of ATP.
The direction of proton flow dictates ATP synthesis vs ATP hydrolysis.
5. Explain why carbon monoxide, cyanide, malonate and oliogomycin are poisonous
in terms of their effects on specific componenets of the electron transport chain.
ATP Consumption and Cell Death
 Human body synthesises about 70kg of ATP a day.
 Each ATP molecule has a life span of 1-5 mins.
 Any interruption of oxidative phosphorylation and therefore ATP synthesis means
that the cell rapidly becomes depleted of ATP and is likely to die.
 Most common cause of this is lack of oxygen – hypoxia (diminished) or apoxia
(total).
 Death of cell may be within a few minutes (neurons) or a few hours (muscles).
Cyanide and Carbon Monoxide Poisoning
 Classified as supertoxic – a few drops ingested can kill.
 Cyanide (CN-) and azide (N3-) bind with high affinity to the ferric (Fe3+) form of
the haem group in the cytochrome oxidase complex.
 This blocks the flow of electrons through electron transport chain and
consequently the production of ATP.
 In a similar way, CO binds to the ferrous (Fe2+) form of the haem group, also
blocking the flow of electrons.
Malonate Poisoning
 Malonate closely resembles succinate and acts as a competitive inhibitor of
succinate dehydrogenase.
 This Kreb’s Cycle enzyme resides in the the inner membrance and passes FADH2
directly to ubiquinone.
 Malonate therefore slows down the flow of electrons from succinate to
ubiquinone, slowing down ATP production.
Oliogomycin Poisoning
 Oliogomycin is an antibiotic that inhibits oxidative phosphorylation by binding
within the ‘stalk’ of ATP synthase
 This blocks the flow of protons through the enzyme.
 ATP synthesis is inhibited and a backlog of protons builds up in the
intermembrane space.
 This inhibits the flow of electrons through the electron transport chain as the H+
concentration in the intermembrane space reaches saturation point – no more can
be pumped out.
33
6. Describe how oxidative phosphorylation can be measured experimentally.
The Oxygen Electrode
 The oxygen electrode measures the concentration of oxygen in a solution
contained in the chamber of the apparatus.
 The base of the chamber is formed by a Teflon membrane permeable to oxygen.
Underneath this membrane is a compartment containing two electrodes – a
platinum cathode and a silver anode.
 A small voltage is applied between the silver anode and the platinum cathode.
 Oxygen diffuses through the Teflon membrane and is reduced to water at the
cathode.
 The circuit is completed at the anode, which is slowly corroded by the KCl
electrolyte.
 The resulting current is proportional to the oxygen concentration in the sample
chamber.
Measuring Oxidative Phosphorylation
 A suspension of mitochondria from homogenised tissue are incubated within a
sealed incubation chamber containing and isotonic medium containing substrate
eg succinate and Pi.
 The addition of ADP causes a sudden burst of oxygen uptake as the ADP s
converted into ATP – this is termed coupled respiration
 By adding various substances to the camber we can determine their effects on
oxidative phosphorylation.
Summary





Mitochondria are present in almost all eukaryotic cells and are believed to be
evolutionary descendants of an earlier prokaryote life form.
The majority of ATP produced within the body occurs a result of oxidative
phosphorylation, a process which takes place within the mitochondria.
In this process, electrons from the reduced co-enzymes NADH and FADH2 are
passed via a series of enzyme complexes, called the electron transport chain,
which ultimately results in the reduction of oxygen to water and the pumping of
protons out of the mitochondrial matrix, to generate a proton gradient.
These protons re-enter the matrix via the molecular turbine ATP synthase, which
couples the resultant kinetic energy to ATP production.
Compounds which inhibit either the electron transport chain or the proton
gradient, disrupt oxidative phosphorylation which be measured experimentally
with an oxygen electrode.
34
Metabolism 6 - Lipids & Membranes
Objectives:
 Describe the structure of: fatty acids, triglycerides, phospholipids,
cholesterol and sphingomyelin.
 Give examples of how the lipid composition can differ for different
cellular membranes, and indicate the significance of this.
 Outline the pathway for synthesis of fatty acids.
 Distinguish between the pathways for synthesis and metabolism of
fatty acids in terms of: substrates and products, coenzymes used,
carrier molecules and cellular location.
● Describe the structure of: fatty acids, triglycerides, phospholipids,
cholesterol and sphingomyelin:
 Fatty acids:
Fatty acids are the simplest
of all lipids and are constituents of
more complex lipids.
They have hydrophilic
(“water-liking”)
heads,
and
hydrophobic (“water-disliking”)
tails.
The fatty acid chain can
either be composed of saturated
bonds (as is the case with Stearic
acid, shown in diagram). The acid
chain
can
also
contain
unsaturated bonds (as is the case
with Oleic acid, also shown in the
diagram).
 Triglycerides:
As the name suggests, triglycerides contain
three fatty acids attached to a glycerol backbone.
Their main function is that of an energy store.
35
R1, R2 and R3 indicate the three fatty acids.
 Phospholipids:
Phospholipids
are
essentially the same as
triglycerides, but one of the
fatty acids has been replaced
by a phosphate group.
The phosphate group
is very hydrophilic, and the
fatty acid tails are as always
hydrophobic. This gives rise
to
the
formation
of
phospholipids bilayers –
important in the structure of cell membranes.
 Cholesterol:
The structure of cholesterol
is given in more detail in the next
lecture.
The main point to note
about its structure is that all
cyclohexane rings are in the
chair conformation; this gives
cholesterol
a
planar,
rigid
structure.
 Sphingomyelin:
This
is
the
composition
of
sphingomyelin. As can be
seen
it
has
two
36
components; phosphocholine and ceramide.
Sphingomyelin is a common membrane lipid.
● Give examples of how the lipid composition can differ for different
cellular membranes, and indicate the significance of this:
 The cell or plasma membrane is best described as a 2-D fluid
structure or orientated proteins and lipids. It is a continuous double
layer (bilayer) about 5nm thick. The lipids and proteins in the
membrane are held non-covalently, and the proteins the bilayer
contains may be either integral (part of the membrane) or
peripheral (on the outside of the membrane)…
 The degree of fluidity of the cell membrane (the ease with which
its lipid molecules can move about) is important for membrane
function, and thus must be maintained within certain limits.
 The fluidity of a lipid bilayer at a given temperature depends on its
phospholipids composition, and especially on the nature of the
37
hydrocarbon tails: the closer and more regular the packing of the
tails, the more viscous the and less fluid the bilayer will be. There
are two major properties of hydrocarbon tails that affect their
packing in the bilayer –one is their length, and the other is their
unsaturation (that is the number of double bonds they contain).
 Hydrocarbon tails of phospholipids vary in length between 14 and
20 carbon atoms, 18-20 being the most usual. A shorter chain
reduces the tendency of the hydrocarbon tails to interact with one
another, therefore increasing the fluidity of the membrane.
 Each double bond in a hydrocarbon tail creates a kink in the tail,
making it harder for the tails to pack closely together. Thus, lipid
bilayers that contain a large proportion of unsaturated
hydrocarbon tails are more fluid than those with lower proportions.
 Membrane fluidity is important in cells for many reasons. It (the
cell membrane) enables membrane proteins to diffuse rapidly in the
plane of the bilayer and to interact with one another (which is
crucial in cell signalling for example). It also provides a simple
means of distributing membrane lipids and proteins by diffusion
from sites where they are inserted into the bilayer (after their
synthesis) to other regions of the cell. It allows membranes to fuse
with one another and mix their molecules, and it ensures membrane
molecules are evenly distributed between daughter cells when a
cell divides.
 In animal cells, membrane fluidity is regulated by the sterol
cholesterol (which is absent in yeasts, plants and bacteria). These
short, rigid molecules are present in especially large amounts in the
plasma membrane where they fill the space between neighbouring
phospholipid molecules that are caused by kinks in unsaturated
fatty acids. In this way, cholesterol has the ability to stiffen the
bilayer making it less fluid and permeable.
● Outline the pathway for synthesis of fatty acids (Lipogenesis):
38
AcetylCoA
is the key
intermediate between fat and carbohydrate metabolism.
 Essentially, the overall reaction occurring is:
But there are many steps in between…
 1st STEP: PRODUCTION OF MALONYL CoA (catalysed by
the enzyme Acetyl CoA carboxylase):
39
 2nd STEP: ACTIVATION BY ACYL CARRIER PROTEIN
(similar to CoA activation in β-oxidation).
 3rd STEP: ELONGATION BY SUCCESSIVE ADDITION OF
2-CARBON UNITS (this is catalysed by the enzyme FA
Synthase):
Note how the
oxidative degradation
(all of the reactions
on the left-hand side
of
the
diagram
(pink)) is very similar
to the synthesis (all
of the reactions on
the right-hand side of
the diagram (blue))
of a fatty acid.
40
 Fatty acid synthase – mechanism of reaction…
41
 The overall reaction is given as…
 Palmitate can undergo further metabolism:
1. Esterification to form triacylglycerols.
2. Formation of other fatty acids, unsaturated and longer
chains…
Desaturation, elongation, formation of monounsaturated
FA’s - catalysed in different cellular compartments.
 Lipogenesis is regulated:
1. Feedback
inhibition of
palmitoyl
CoA to:
A) AcetylCoA
carboxylase.
B) FA
synthase.
C) Pentose
phosphate
pathway.
2. Acetyl
CoA
carboxylase
regulation
by
hormones.
42
3. Transcriptional regulation of acetyl CoA carboxylase and FA
synthase (activated by insulin and inhibited by glucagon.
 Metabolism of fatty acids:
The pathway for the metabolism of fats is given below (the actual
pathway is highlighted in the pale yellow colour)…
43
Metabolism 7 - Cholesterol
Objectives:
 Explain the physiological functions of cholesterol in membrane
stability.
 Outline the synthesis of cholesterol from acetate.
 Outline the synthesis of bile acids and steroid hormones from
cholesterol.
 Describe the mechanism of transport of cholesterol around the
body and its uptake into cells.
 Draw a diagram of low density lipoprotein (LDL).
 Explain why disturbances in cholesterol homeostasis cause disease.
 Give an example of how a selective enzyme inhibitor can be used
as a pharmacological agent in controlling cholesterol metabolism.
● Explain the physiological functions of cholesterol in membrane
stability:
 In animal cells, membrane fluidity is regulated by the sterol
cholesterol (which is absent in yeasts, plants and bacteria). These
short, rigid molecules are present in especially large amounts in the
plasma membrane where they fill the space between neighbouring
phospholipid molecules that are caused by kinks in unsaturated
fatty acids. In this way, cholesterol has the ability to stiffen the
bilayer making it less fluid and permeable.
● Outline the synthesis of cholesterol from acetate:
 Step 1: Formation of Mevalonate…
See next page…
44
1.1
HMGCoA
Reductase as
the regulated
step in
cholesterol
synthesis
1.2
1.3
 Step 2: Mevalonate to Squalene (Isoprenoid metabolism):
Again, there are 3 stages to this step of the synthesis of cholesterol:
1) Mevalonate to C5 units (isoprene units)
2) Head-to-tail condensations of isoprene units
3) Branched pathway at farnesyl pyrophosphate
see next page…
45
46
 Step 3: Squalene to Cholesterol:
C5
C10
C15
C30
47
● Outline the synthesis of bile acids and steroid hormones from
cholesterol:
 The synthesis of Steroid Hormones…
48
 Levels of steroid hormone controlled by the rate of synthesis.
 Cholesterol desmolase generates pregnenolone the precursor of all
steroid hormones.
 There are 5 classes of steroid hormone:
1. Progestins (progesterone, 17-Hydroxypregnenolone, 17Hydroxyprogesterone)
2. Glucocorticoids
3. Mineralocorticoids
4. Androgens
5. Estrogens
 The synthesis of Bile Acids…
Conjugated
bile acids
49
 This pathway represents the major route for elimination of
cholesterol via the GI tract.
● Describe the mechanism of transport of cholesterol around the
body and its uptake into cells:
 Dietary cholesterol is transported from the gut to the liver by
chylomicrons.
 Cholesterol is transported from the liver to the tissues by the low
density lipoproteins (LDLs); these may be taken up by LDL
receptors on cells; the LDL receptors are associated in clathrin
coated pits, and so are frequently endocytosed; if LDL is bound,
this is internalised also. Lysosomes then break up the vesicle
contents into free cholesterol and amino acids (from the LDL
apoproteins).
 HDLs transport cholesterol from the tissues back the liver or to
endocrine glands for steroid synthesis.
50
● Draw a diagram of low density lipoprotein (LDL):
Lipoproteins are used to transport hydrophobic triglycerides in the
bloodstream. The shell’s outside is hydrophilic, and contains
phospholipids, cholesterol and proteins like a normal cell membrane, and
thus its inside is hydrophobic and suitable for fats; the different types of
lipoprotein are classified by their density, which is high with high protein
content and low with high fat content (i.e. high density lipoproteins
(HDLs) have more protein:fat).
● Explain why disturbances in cholesterol homeostasis cause disease:
In familial hypercholesterolaemia (FH) for
example, there is a genetic defect that causes either
an absence of or a mutation of the LDL receptor
(as they do not migrate to clathrin coated pits and
so are not endocytosed); this results in raised
cholesterol levels in the blood, leading to a
predisposition to atherosclerosis. Accelerated
atherosclerosis means that sufferers have high
early MI (myocardial infarction) risk. FH
heterozygotes may be asymptomatic until their
40s, but homozygotes if untreated die in their teens
(due to a complete absence of LDL receptors).
● Give an example of how a selective enzyme inhibitor can be used as
a pharmacological agent in controlling cholesterol metabolism:
 HMG-CoA reductase inhibitors such as Mevastatin inhibit cellular
cholesterol synthesis.
51
Metabolism 8 - Membrane Trafficking
1. Explain the terms ‘endocytosis’ and ‘exocytosis’.
 Exocytosis is the process of secreting macromolecular material from a cell.
 It involves the fusion of a membrane-enclosed intracellular vesicle with the
plasma membrance, followed by the opening of the vesicle and the emptying of its
contenets to the outside.
 Endocytosis is the mechanism of uptake of macromolecular material into a cell
from the outside.
 It typically involves formation of a coated pit on the plasma membrane, which
buds off into the cytoplasm to form a coated vesicle which delivers its contents to
an endosome.
2. Describe the pathway and cellular locations for synthesis, post-translational
modification and exocytosis of a secreted protein.
Secretory or Exocytic Pathway
Endoplasmic reticulum
plasma membrane
golgi apparatus (cis – medial
– trans)
At the Endoplasmic Reticulum







Protein synthesis occurs at the ribosomes.
These are initially free in they cytosol, a common pool of ribosomes is used to
synthesise both those proteins that remain in the cytosol and those that are
transported into the ER.
If a protein is destined for the ER, the ER signal peptide (first piece of the
polypeptide to be synthesised) directs the ngaged ribosome to the ER membrane.
The ribsosmes are then recycled after each round of protein synthesis.
The ER is also the site of some post-translational modifications:
- formation of disulfide bonds
- folding
- glycosylation (makes proteins stronger and more resistant to agressors)
- specific proteolytic cleavages
- assembly of multimeric proteins
- tertiary structure constructed by ER membranes
There is a quality control mechanism, as only proteins properly folded and
glycolated can pass through ER exit.
Unassembled of misfolded proteins are retaine in the ER and exported back to the
cytosol where they are degraded.
The proteins are then transported in vesicles to the golgi apparatus.
At the Golgi Apparatus



More post-translational modifications take place at the golgi apparatus.
At the cis golgi network, the phosphorylation of lysosomal proteins occurs.
in the golgi stack, Man is removed and GlcNAc and Gal are added.
52


At the trans golgi network NANA is added and the proteins are sorted.
The golgi apparatus also returns ER resident proteins – recognised by KOEL
receptors.
Sorting at the Trans Golgi Apparatus and the Plasma Membrane





Here proteins are sorted and packaged into vesicle depending on whether they are
to be released by constitutive or regulated secretion.
Lysosomal emnzymes are also sorted from others.
The mannose in these proteins is phosphorylated in the golgi stack producing
mannose-6-phosphate.
This is then recognised by a M6P receptor and these proteins are taken in a
receptor dependent transport vesicle to a lysosome.
The M6P receptors are recycled by budding from a late endosome.
3. Distinguish ‘constitutive’ and ‘regulated’ secretion.




Constitutive secretion is the secretion of plasma membrane lipids and soluble
proteins.
It is unregulated and so does not require any signals to generate the secretion.
Regulated secretion requires an external signal from a hormone or
neurotransmitter substance before it occurs.
It is used from the secretion of proteins and other substances.
4. Describe the process of receptor-mediated endocytosis and the roles played by
endocytic vesicles, early endosomes, late endosomes and lysosomes.




There are three fates for endocytosed material.
Recycling involves substances entering the cell via the apical plasma membrane,
being transferred to an early endosome and being release back out of the apical
plasma membrane.
The second fate is degradation in which substances are transferred from the apical
plasma membrane, via an early endosome, to a lysosome where they are
destroyed.
The third fate is transcytosis in which substances enter the cell via the apical
plasma membrane and exit via the basolateral plasma membrane, passing through
an early endosome.
Receptor Mediated Endocytosis

Example of this is endocytosis of LDLs.
53




The LDL binds with an LDL receptor at the plasma membrane and is taken into a
coated vesicle via endocytosis.
The vesicle is uncoated in order to fuse with an early endosome.
The LDL receptors bud off the early endosome and it becomes a late endosome.
With the introduction of hydrolytic enzymes a lysosome is formed and free
cholesterol is released into the cytosol.
5. Give a general description of the molecular mechanisms of vesicular transport
within cells.




At the donor membrane, the cargo is sorted and a vesicle forms and buds off the
plasma membrane.
The vesicle then moves through the cytosol – vesicles move along microtubules to
find receptors.
When the vesicle reaches specific receptor molecules on the receptor membrane
recognition occurs between this and specific molecules on the vesicle, resulting in
vesicle tethering or docking to the acceptor membrane.
The vesicle membrane and acceptor membrane then fuse together, opening the
vesicle and releasing the contenets into the lumen of the acceptor organelle.
6. Give examples of diseases resulting from defects in the secretory and endocytic
pathways.


A disease that results from a defect in the secretory pathway is cystic fibrosis.
This results from blocks at the exit of the ER due to misfolding of the proteins.

A disease that results from a defect in the endocytic pathway is familial
hypercholesterolaemia.
Mutations in the LDL receptor mean that receptor mediated endocytosis of LDLs
cannot take place.


Intracellular trafficking is involved in many other diseases including more than 75
genetic diseases of syndromes, cancer and infections.
54
Metabolism 9 – Integration of Metabolism
1. Distinguish the features of metabolic activity in the following tissues: liver, brain,
muscle, adipose tissue.
Liver
 Plays central role in coordinating metabolism throughout the body.
 Immediate recipient of nutrients absorbed at the intestines.
 Wide repertoire of metabolic processes.
 Highly metabolically active and can interconvert nutrient types.
 Central role in maintaining blood glucose at 4.0-5.5 mM.
 Storage organ (glycogen).
 Central role in lipoprotein metabolism.
Brain
 Has continuous high ATP requirement, cannot utilise fats.
 Requires continuous supply of glucose for metabolism.
 Cannot metabolise fatty acids
 Ketone bodies (-hydroxy-butyrate) can partially substitute for glucose.
 Too little glucose (hypo-glycaemia) causes faintness and coma.
 Too much glucose (hyper-glycaemia) can cause irreversible damage.
Muscle
 Can have periods of very high ATP requirement during vigorous contraction.
 During vigorous contraction ATP consumption is faster than supply by oxidative
phosphorylation (O2 diffusion is limiting).
 Energy stores of glycogen (glucose-6-P for glycolysis) and creatine phosphate
(ATP).
 Under anaerobic conditions pyruvate is converted to lactate or alanine which can
leave muscle and reach the liver via the blood.
Adipose tissue
 Is a long-term storage site for fats.
2. Give four examples of extracellular hormones which act as metabolic regulators.
Secreted by pancreatic islets:
 Insulin secreted when glucose levels rise: stimulates uptake and use of glucose
and storage as glycogen and fat.
 Glucagon secreted when glucose levels fall: stimulates production of glucose by
gluconeogenesis and breakdown of glycogen and fat.
Secreted by the adrenal glands:
 Adrenaline (American = epinephrine): strong and fast metabolic effects to
mobilise glucose for “flight of fight”.
 Glucocorticoids: steroid hormones which increase synthesis of metabolic enzymes
concerned with glucose.
3. Describe the changes in metabolic activity while eating and while fasting.
 On having a meal, blood glucose initially rises and is controlled by:
- Increased secretion of insulin (and reduced glucagon) from islets.
- Increased glucose uptake by liver - used for glycolysis and glycogen synthesis.
Acetyl-CoA produced is used for fatty acid synthesis.
55
-
Increased glucose uptake and glycogen synthesis in muscle.
Increased triglyceride synthesis in adipose tissue.
Increased usage of metabolic intermediates throughout the body due to general
stimulatory effect on synthesis and growth.
 After a meal blood glucose starts to fall and is controlled by:
- Increased glucagon secretion (and reduced insulin) from islets.
- Glucose production in liver resulting from gluconeogenesis and glycogen
breakdown.
- Utilisation of fatty acid breakdown as alternative substrate for ATP
production.
- [NB adrenaline has similar effects on liver, but also stimulates skeletal muscle
towards glycogen breakdown and glycolysis, and adipose tissue towards fat
lipolysis to provide other tissues with alternative substrate to glucose]
After prolonged fasting (longer than can be covered by glycogen reserves):
- Glucagon/insulin ratio increases further.
- Adipose tissue begins to hydrolyse triglyceride to provide fatty acids for
metabolism.
- TCA cycle intermediates are reduced in amount to provide substrate for
gluconeogenesis.
- Protein breakdown provides amino acid substrates for gluconeogenesis.
- Ketone bodies are produced from fatty acids and amino acids in liver to
substitute partially the brain’s requirement for glucose.
4. Describe in general terms the relationship to glucose metabolism of: lipid
synthesis and breakdown, amino acid synthesis and breakdown, synthesis of other
components of macromolecules.
56
5. Describe the metabolic processes during vigorous muscular activity and explain
why acidosis can result.
 During vigorous contraction ATP consumption is faster than supply by oxidative
phosphorylation (O2 diffusion is limiting).
 Further ATP by interconversion from creatine phosphate.
 Glycogen stores provide glucose for anaerobic metabolism only (glycolysis).
 Pyruvate is converted to lactate or alanine - otherwise it would build up and the
pathway would be inhibited by excess product.
 Lactate/alanine pass into the blood and the liver uses them to replenish glucose by
gluconeogenesis.
57