LECTURE 1

INTRODUCTION, LIFE’S BEGINNINGS FROM SPACE GREASE

Key Concepts
• Life requires macromolecules
• Polymers form

Life
• Life started off as an RNA/DNA world
• RNA can fold up into ribosomes
• Nucleic acids are made from sugars etc.
• Life must’ve started off with metabolism that can construct sugar
• Life start off with big bang and matter started forming etc.
o Matter coalesce and create to stars/solar systems etc.
• We’re made of common stuff and most abundant elements (H, C, O, P)
o A lot of hydrogen and oxygen as we are made up of 80% water (water is very abundant in
the universe)

H2O
• H2O has the 2nd highest specific heat capacity
• This buffers earth’s climate by buffering large fluctuations in temperature
• Powerful solvent
• Polarity attracts positive and negative ions
• Form barriers with hydrophobic molecules (lipids – membranes)
• Allows/drives structure and shape of molecules – proteins, base paring of DNA
• Transport substrates

The building blocks of life are not very rare

• Methyl amine and ethyl amine and glycine on comet out in space

Stanley Miller 1952

Evolution from metabolism

• Nucleotides and adenosine
LECTURE 2
Lipids
• A simple compound acetate (vinegar), is an initial building block of many compounds, including
lipids
• Lipids can grow to form hydrophobic fatty acid (acyl) chains
• Addition of phosphate (and often other bits) makes fatty acids amphipathic (hydrophobic and
hydrophilic parts)
• Phospholipids form membranes
• Membranes form vesicles – the first cell or protocell
• Acyl chains can be saturated or unsaturated

Acetate
• Life came from central parts of metabolism
• Acetyl CoA – has acetate on it
• Take molecules of acetate and add them together (determined by how many carbons are in them)
o Short chain of carbon, acetate molecule is added by dehydration (take away H2O)

Lipids:
• Hydrophobic: water insoluble
• Functions:
o Energy storage (for mass, 6x energy stored sugar – e.g. glycogen)
§ Don’t attract water, so they can be packed in the body
§ Lighter than water
o Structural molecules e.g. membranes
o Steroid hormones
• Structure of Triglyceride
o Glycerol molecule across top
o 3 acyl chains attached to the glycerol molecule through ester linkage

Saturated and Unsaturated Fatty Acid

• Saturated fats
o Single bond between each carbon to carbon – zigzag
o Straight legs on triglyceride
o Fat can go hard as they are saturated with straight chains
• Unsaturated fat
o Desaturate bonds
o Have a bend with a carbon-carbon double bond
o Stop lipid rotating and can’t stack properly
o More fluid at cold temp.
• Why the difference?
o Saturated stack cleanly
o When they have a double bond it’s harder to chill and demobilise them/take up more space
(vegetable oils)

Phospholipids
• Glycerol, ester linkage, 2 acyl chains, 1 phosphate group
• Charges
o Phosphate group carries negative charge
LECTURE 2
o Molecules attached to phosphate groups can have a charge as
well (e.g. choline – positive charge) - hydrophilic
o Phosphate also attached to something hydrophobic
o Hydrophilic head and hydrophobic tail
• Can form a micelle – round with hydrophobic tails on the inside and
hydrophilic head on the outside
• Can form a phospholipid bilayer

Mitochondria
• Many lipid membranes
• Partitions ions such as sodium, potassium and hydrogen (protons)

Phospholipids form self-organising vesicles

• Put things into water and they start to for globular vesicles – must have specific salts which are
found in cells
• No genetic information required
• Physical laws of stability of vesicle size
• Become too big and unstable to synthesize and form new vesicles
• Vesicles form barriers and barriers can form reactions

Sugars
Key Concepts
• Sugars forms from central pathways (trioses)
• Monosaccharides are single sugars and there are different types
• Disaccharide – oligosaccharides form from several mixed sugar types (e.g. sucrose)
• Polysaccharides form from many repeated units connected by glycosidic bonds
• Polysaccharides are useful for energy storage
• Plants and animals use polysaccharides to form structures (e.g. cellulose and chitin) and specific
glycosidic bonds determine flexibility

Monosaccharides: 1 sugar molecule (glucose, fructose, ribose)

Disaccharides: 2 sugar molecules (sucrose, lactose)
Polysaccharides: many sugar molecules linked by glycosidic bonds

Monosaccharides and Disaccharides

• Bonds occur by dehydration – removal of H2O
• Glycosidic bond
o 1, 4 linkage
o 1, 2 linkage
o Numbers refer to carbon numbers which are bonded
• Different bonds between sugars
• These change properties of polymers

Polysaccharides
• Functions:
o Energy storage (fuel)
§ Glycogen is stored in animal tissues (e.g. liver and muscles)
o Starch is stored in plants
• Structural molecules
o Cellulose in plants (polymer of glucose)
LECTURE 2
o Chitin in exoskeletons in arthropods and fungi cell walls
• Carbohydrate residues can be joined to proteins or lipids (glycoproteins or glycolipids)

Starch – sugar storage in plants

• Glucose molecules are attached to each other
• Bond is bendy and it has branches
• Starch has fewer branches than glycogen and is less dense
o Plants don’t really move anywhere and don’t require much space in the cell
• Space becomes a problem for muscles as it gets in the way of the machinery that allows the
muscles to contract
• Starch is stored as granules

Glycogen – sugar storage in animals

• Stain with iodine to identify it
• Similar to starch, but it has more branches in it
• More extensively branched than starch
• Animals move, therefore need to pack more energy stores into liver and muscle
• Alpha 1, 4 linked glucose ring
o Alpha is done with how the glucose is shaped
o Important bond as it’s flexible, can be crumpled up and packed

Cellulose – structural polysaccharides in plants

• Few animals can break down cellulose
o Eat cellulose for fibre (bacteria break it down for us)
• Polymer of glucose (not branched)
• Stored in the cell wall
• Beta 1,4 linkage – can’t rotate

Chitin – structural polysaccharides in animals

• Polymer of glucose
• Glucose monomer has nitrogen containing appendage (amine groups)
o Amine group can attach to other molecules (i.e. chitin) and form exoskeleton
• Beta 1,4 linkage – can’t rotate

Nucleic Acids
• Functions
o All information processes in the cell involve DNA and RNA
o Storage of chemical energy ATP
o Intracellular signalling cAMP

• DNA in a way like an energy store

o Has ribose (sugar) – stores energy in form of ATP
o ATP makes your feel sleepy/alive
• Pentose phosphate pathway to make sugar – ribose
• 5, 3 carbons important
o 5’ end has phosphate group with phosphodiester bonds
• Bonds form through dehydration

Components of nucleic acids

• DNA more stable than RNA as it has one less oxygen
LECTURE 2
• Nitrogenous bases
o 2 rings – A, G
o 1 ring – C, T, U

Proteins
Key Concepts
• Proteins are formed from amino acids
• Peptide bonds are formed through dehydration, are broken through hydrolysis
• There are a range of amino acids (23 used in eukaryotes, some more recently discovered in
bacteria)
• Properties determine protein structure and function

Peptide bond
• Formed through dehydration
o Carboxy terminus, amine terminus
• Broken by hydrolysis
• Different proteins have different charges, properties etc.
Lecture 3
Key Concepts
• Energy is captured and stored into reduced bonds (C=O C-C and C-H)
• This is ultimately transferred to ATP following their oxidation
• The phosphate bond of ATP is an ancient energy store, that now acts as a short term energy
source for biological work
• Thermodynamic laws govern life!
• The free energy (ΔGo‘) released on ATP hydrolysis is used for biological work (e.g. muscle
contraction, ion transfer)
• ΔGo‘ can be calculated from thermodynamic laws
• The more negative the ΔGo‘ the greater the likelihood a reaction occurs
• The hydrolysis of ATP to ADP and inorganic phosphate releases most of the ΔG in ATP

Energy and its transfer

• Most energy is powered by the sun
• Absorbed by plants, plants gain blue and red parts of light – turning electromagnetic energy into
chemical energy
• Absorb light into organic matter
• Energy from sun captured from plants plays into Einstein’s e=mc2

Energy flow at a big scale

• Anabolic process – organic molecules + O2

• Catabolic process – CO2 + H2O

Energy flow at animal scale

• Specific dynamic action – sweat when digesting food,
releasing heat and energy (i.e., pump acids, exchange salts
and ions in gut, move gut to move food)
• Can’t break down some food (i.e. cellulose)
• Some of the nutrients we can digest pass through body
• Break down to get rid of nitrogen
• Biosynthesis: build ourselves up (proteins, fats to build more
muscle etc.), generate a lot of heat
• Heat is the common thing
o Releasing energy
o Form of combustion
Lecture 3
Different food sources release different amount of
energy when combusted (kJ/g)
• Least to most
o Carbohydrate, protein, alcohol, fat
• Calorimeter
o Calorie: the amount of energy required to
heat a gram of water by one degree
o Have sample in a can and ignite the sample to burn (explosive)
o Release of heat from sample heats water
o Measure water before and after – calculate since we know specific heat energy of water

Fuel consumptions of the average 70kg male after an

overnight fast (in kilograms and as a percentage of total
calories)

Overview of fuels and energy extraction

• Macronutrient fuel sources that supply substrates
for regenerating ATP
o Deaminated glucose (carbon), glucose, free
fatty acids are the three main fuel sources
Lecture 3
Three Stages of Catabolism Acetyl-CoA is a hub molecule
1. Hydrolysis of complex molecules to their building blocks
2. Conversion of Acetyl CoA
3. Oxidation of acetyl CoA – occurs by oxidative phosphorylation

ATP – life’s universal currency

• GTP also used for energy (protein synthesis)
• Three phosphates have negative charges – important for how it works

The ATP-ADP Cycle

ATP is hydrolysed. The hydrolysis of ATP
to yield ADP and inorganic phosphate. In
the cell, the most hydroxyl groups of
phosphates are ionised (-O-)

There is a release of energy when the ATP

is hydrolysed

ATP used to make myosin relax

Lecture 3
ATP
• ATP is not quite universal, cells use GTP, UTP and also creatinine phosphate (CrP)
• But ATP is the most abundant, likely ancestral
• Phosphoanhydride bond of ATP relatively stable in water at physiological pH
• Overall release of energy on hydrolysis is exothermic reaction (outwards flow of energy)
• Other bonds can yield more energy, but less water stable
• While ATP can be hydrolysed twice to ADP and AMP, most of the power is in the 3rd P

• Some bacteria use ATP and can also use polyphosphate

• Polyphosphates are strings of phosphates and can wrap around metal ions
• When humans get sick we increase polyphosphates in blood to bind to iron etc.

• Resonance, charge delocalisation (only on linear ATP)

o Electrons constantly moving around phosphate and evenly spread when just one phosphate
molecule
o Two phosphate molecules joined – repulsion where they are constantly moving but away
from joining of phosphate
o Three phosphates add more repulsion (1 and 2)
o Put a ‘starting block’ at the end to finish the ATP molecule which add the same amount of
repulsion to the first and second phosphate group making the third have less repulsion and
easier to break off
• In reality, ATP is curved
o Magnesium or calcium sit in the middle of curve
o Helps shape the phosphate group
• Pi in ATP carries charge
o ATP binds to protein
o Donates charge to protein, which changes protein shape/conformation
o ATP dephosphorylates and loses charge, straightens out
o Leaves and goes back to it’s native shape

ATP is special
• The energy released from the terminal phosphate (Pi) of anhydride bond hydrolysis is high
• The free energy of formation of ATP is greater than the sum of the products of formation of ADP
and Pi
o Need a lot more energy to bond last phosphate to form ATP than ADP or Pi
o Therefore ATP can drive reactions that would otherwise go too slowly or not at all

What is ∆G
• Willard Gibbs
• ∆H - T∆S = ∆G
• Laws of thermodynamic
1. Energy cannot be created or destroyed, it changes form
2. The universe is becoming increasingly disordered
• The 1st law
o ∆H = q + w
o The change in enthalpy = heat + work done
o Energy cannot be created or destroyed but transformed
§ Energy is released as heat and work done
Lecture 3
• The 2nd law of thermodynamics
o Universe tends towards disorder
o Non-equilibrium = ordered (low entropy)
o Equilibrium = less order (high entropy)
o When reactions reach equilibrium they go no further
o Life fights equilibrium/entropy
o Entropy is S
§ Means turning in
§ Measure of disorder

• ∆H – change in energy work and heat

• T∆S – change in order
• ∆G – change in energy for a given reaction

Burning match
• ∆H - Heat from flame, expansion of hot air = work
• T∆S – Entropy comes from breakdown of cellulose/carbohydrate; one stick of the wood becomes
water/CO2 molecules
becoming disordered (from
one thing to trillions)

∆G
• This predicts whether
reaction will occur
• It predicts the maximum
possible change in
concentrations between
reactants and products
• The more negative (-∆G) the
more work can be done
• But not it does not predict the rate at which reactions
will occur
o Tells you whether reactions will occur and
how far it will g

• Using free energy gradient to power metabolism

• (a) Short life (anaerobic metabolism works like this)
• (b) Life
• (c) A more productive life. Although somewhat more
complicated (mitochondria)
Lecture 3
How does ∆G relate to ATP?
• Terminal phosphate has the most power
• Arrows indicate that this process is theoretically reversible, but more easily towards one direction
when the arrows differ in size
o Easier going to ‘ADP + Pi’ than ‘ATP’
• Higher ATP in the heart than ADP
o Must have lots of ATP to drive the
reaction
o Laws of mass action

How does the second law of dynamics help to explain

how a membrane may partition charged ions to
generate membrane potential?
• We increase entropy (messiness)

Cellular respiration uses glucose and oxygen, which

both have very -ΔGo', and it releases CO2 and H2O,
which have lower (less negative) ΔGo'.
• Is respiration energetically favourable?
o Yes
• Is respiration exergonic or endergonic?
o Exergonic
• What happens to the energy released from
the glucose?
o Energy is conserved in ATP, does work,
lost as heat. Ultimately it all forms heat
Lecture 4
Key Concepts
• Make sure you understand how enzymes and pathways contribute to metabolism

Random Facts
• 70 kg of ATP required each day at rest
• 6-7 kg of ATP just for the heart
• A marathoners efforts (42,200m) run for 2 hours
• 47-40 kg of ATP used for marathon runners
o These people weigh 52 kg so ATP is 70% - 80% of their body mass

REDOX
• Oxidation – loss of electron
• Reduction – gain of electron
• LEOGER

Oxidation reactions extract energy from bonds

• Energy from C-C bonds = C-H bonds, but C-Cs aren’t oxidised directly
• Molecules must be rearranged to C-H, C=O or C-OH for oxidation
• The electrons from these bonds ultimately flow to oxygen (or other compounds in odd critters)

Leaving hydrogens take electrons

• Malate à Oxaloacetate
• REDOX reactions use dehydrogenases – removing hydrogen with enzyme; can also add in a
hydrogen

Why only oxidise certain bonds?

• To control energy release
o C6H12O6 + 6O2 à GCO2 + 6H20 + Energy
o Metabolism is controlled
o When uncontrolled, there is an explosive release of heat and light energy
• Only C-H, C=O, O-H can be used
• Fundamental restriction

Cellular respiration is
controlled captured in
ATP
Lecture 4
The Pathways

Glycolysis
• Sugar splitting (glycol-lysis) requires a pathway
• Glycolysis is universal – ancient
• Other sugars can be used – stick with glucose
• Steps
1. Glucose – 6 carbon (6C) molecule is trapped using phosphate
2. Rearranged and split into 2x 3C molecules
• 2 ATP are first invested, and 4 ATP harvested
• Net 2 ATP are made
• Electrons are stripped (there is oxidation)
o Used to make NADH
• Substrate level phosphorylation
• 10 enzymes, one oxidation reaction, it rearranges and prepares for respiration

Step 1: Phosphorylation (ATP)

Glucose Transporter
• Glucose transporters on the
outside of the cell
o Different affinities for the
transporters
o Can go back out through the
transporter
• Glucose fits into channel, it goes in
and channel rearranges, now inside
the cell
• Must have Na+ for glucose uptake
• If no Na+, you feed bacteria in gut
and get diarrhoea
Lecture 4
Conversion of glucose to glucose-6-phosphater
• Hexokinase/glucokinase attach phosphate to ATP
o Hexokinase – in most tissues and works at low conc. of glucose
o Glucokinase – only adds phosphate when reach high conc. of glucose in cell (found in liver,
pancreas and little bit of the kidneys); faster than hexokinase
• Phosphates are charged and change property of glucose, therefore no longer recognised as glucose
and won’t go out of glucose transporter
• KM and Vmax
o Increasing concentration of
glucose, increases velocity of
enzyme
o Half of maximal velocity (50%) can
work out conc. of glucose that will
half saturate the enzyme
o Hexokinase
§ Accelerates quickly and
saturates quickly
o Glucokinase
§ KM is around 4.5-5mM –
same as blood glucose
level

The KM and Affinity

• A high KM = a low affinity
• If glucokinase has a higher KM than hexokinase, does this mean GK binds glucose better than HK at a
low glucose concentration?
o No

Glucose is trapped
• The added phosphate is negatively charged and changes the glucose’s shape and charge so GLUT
can’t recognise it
• Glocose-6-phsophate is now tagged for other things

Step 2: Phosphogluco-isomerase (Rearrangement)

• Glucose not ready to go into metabolism yet
• Goes from glucose to a fructose
o Rearrangement to change the shape
o 6C ring to 5C ring
o Still has 6C in the molecule

Step 3: Phosphofructokinase (ATP)

• Takes ATP and adds another phosphate onto the fructose
• Glucose is now fully committed – symmetrical

Step 4: Aldolase (The Cut)

• Gets cut into two 3C molecules
• End up with dihydroxyacetone phosphate and glyceraldehyde-3-phosphate
Lecture 4
Step 5: Triose phosphate isomerase (Rearrangement)
• Rearrangement still occurs to turn dihydroxyacetone phosphate to get it to glyceraldehyde-3-
phosphate
• Triose phosphate isomerase is the enzyme to make this rearrangement possible

Step 6: Glyceraldehyde-3-phosphate dehydrogenase

• Takes molecule NAD to make NADH
• Add inorganic phosphate
• Only oxidation step in glycolysis as it moves the H
• Glyceraldehyde-3-phosphate oxidised to 1,3-bisphosphoglycerate
• No ATP

GADPH
• It’s a dehydrogenase
• Hydrogens are removed
• Alongside the leaving hydrogen goes and electron
• The intermediate is oxidised
• The NADH is reduced

NADH
• Accepts one H+ and two e-
• NAD+ acts as an electron
shuttle
• Water-soluble
• In glycolysis NADH + H+ is
formed by glyceraldehyde-3-
phsophate dehydrogenase
(GAPDH)

Step 7: Phosphoglycero-kinase
• Only kinase in glycolysis
• This kinase removes a phosphate (usually adds phosphate)
• Removes a phosphate, sticks it onto ADP to make ATP
• End up with 3-phosphoglycerate

Step 8: Phosphoglycero-mutase
• Moves the phosphate in the molecule

Step 9: Enolase
• Removes the water - dehydration
• End up with phosphoenolpyruvate

Step 10: Pyruvate kinase

• Removes two phosphates to add to
Lecture 4

Where ATP is injected

How we get extra phosphate in there through GAPDH
Where we extract ATP

Substrate level phosphorylation

• substrate goes into enzyme, loses phosphate, phosphate given to ADP to make ATP
• Phosphoglycerate kinase and pyruvate kinase are the enzymes that help with substrate level
phosphorylation

Highly regulated and irreversible

• Hexokinase or glucokinase
• Phosphofructokinase
• Pyruvate kinase

PFK
• Glucose is now committed
• Highly regulated point in pathway
• Another ATP invested

Phosphofructokinase (PFK)
Most important regulator
PFK is regulated by:
• High ATP (making a lot of ATP means that there doesn’t need to be any more)
• AMP activates PFK (i.e. not very much ATP, make more!)
• Citrate inhibits PFK from the CAC
• Acidification inhibits PFK (save fuel, demands too high on metabolism?)
PFK is the first committed step, there is no going back, PFK is not reversible

• Put phosphofructokinase at the beginning of the cycle as we can control it better

o So there isn’t a big balloon effect with a lot of different intermediates
• In glycolysis phosphofructokinase (PFK) is a highly regulated step and is allosterically regulated by
ATP.
• What do you think very high concentrations of ATP will do to the activity of PFK? Go slower
• Be careful in your interpretation, as ATP is also a substrate of PFK.

Two fates of glucose (anaerobic vs aerobic)

• NAD+ all used up to make NADH
• Usually free up NADH through respiration but no O2
• Lactate dehydrogenase (LDH)
o Take hydrogens off and out them onto pyruvate to
produce lactate
o Lactate triggers pain receptors and make muscles burn
o Produce NAD+ which can keep glycolysis going
• Lactate builds up, when at very high conc. it breaks down
• Reductions step

Blood lactate as an energy source: the Cori cycle

• Lactate still has energy in it and is recycled
Lecture 4
Recycle lactate by the Cori cycle
Lactate is taken up by the blood,
transported to the liver and made back into
pyruvate (lactate dehydrogenase works
backwards)
Most of the reactions occurring here is
glycolysis in reverse.
3 reactions can’t go back, so we use 6 ATP

Alternatives to lactate

• Yeasts ferment glucose to ethanol

• Ethanol
o Two carbon molecule
o Water-soluble so can be kicked out of the cell and get rid of it
o Toxic – build-up of ethanol will kill the plant
• Gold fish can also make alcohol
o No oxygen in winter
o Highest glycogen stores in liver to form lactate
o Lactate goes to muscle and produces ethanol

Energy yield of anaerobic glycolysis

• ATP releases 30-70 kJ/mol
• At 2 mole ATP – 60 – 140 kJ
• Glucose molecule contains 2870 kJ/mole
• 60 or 140/2870 x 100
• Only 2-4.5% efficiency

Energy yield of aerobic glycolysis

• 31-37% efficiency
Lecture 4
Lecture 5
Key Concepts
1. Pyruvate produced in the glycolytic pathway is converted to acetyl CoA and then further oxidised
by the CAC cycle to CO2.
2. Fats and proteins are also degraded by the CAC cycle.
3. Most reactions of the CAC cycle occur in mitochondria (cytosol of bacteria).
4. During oxidation of each molecule of acetyl CoA only one molecule of high- energy phosphate
(GTP/ATP) is produced.
5. Most of the energy released from the oxidation of acetyl CoA is conserved as reduced NAD+ and
FAD i.e. NADH and FADH2.
6. The energy from NADH and FADH2 is released in the process of oxidative phosphorylation.

Learning Objectives
• be familiar with the CAC
• know the four oxidation reactions which transfer electrons to NAD+ and FAD and the substrate
level phosphorylation reaction.
• understand the importance of the coenzymes Coenzyme A, NAD+ and FAD in the CAC cycle
• understand how the rates of key enzymes are regulated to control the CAC.

Citric Acid Cycle

• Start with pyruvate and extract CO2 from it, bind
Coenzyme A to it.
• This produces and NADH.
• The CoA is released and the acetate is bound to
oxalacetate to form citrate.
• As citrate goes around, we add 2 C and then
extract 2 C.
• The molecules go around and we extract NADH
which are used to produce ATP.

• Pyruvate produced by glycolysis can be converted

to acetyl CoA as can fats and some amino acids
(releases NADH and CO2)
• Acetyl CoA is oxidised in the CAC to 2CO2, FADH2
& 3NADH
• Othewr amino acids can also be degraded by the
CAC at different points
• Oxidation of one acetyl CoA also makes GTP or
ATP
• The energy from NADH and FADH2 is released in
the process of oxidative phosphorylation

• CAC occurs in the matrix of the mitochondria

• Link reaction links glycolysis to CAC

Lecture 5
Endosymbiosis
• mitochondria first came from bacteria as its DNA was circular
• taken up to get digested, but didn’t get digested and had a double membrane
• kept because it gave advantage to host
• as time progressed mitochondria lost some of its genome and the only genes that remain have to
do with oxidative phosphorylation
• what was the point of endosymbiosis?
o Mitochondria permit an existence
with oxygen (it is quite toxic and in
effect ages us).
o Mitochondria allowed larger cells. The
cristae increase the efficiency of ATP
synthesis (to come), and this increases
a cells capacity to make ATP.
o Increased ATP production led to more
complex genomes (DNA is effectively
made of ATP, more ATP, more DNA, more complexity)
o More complex genomes allow for increased gene copy numbers, this possibly drove rapid
diversification of genes, cell structures, types and body plans

Krebs observed that specific metabolites/intermediates increased respiration, or accumulated when

poisons were added
• Radio labelled acetate (2C) went into the cycle, yet different 2Cs came out as 2 x CO2 (indicated C
incorporation, rearrangement and oxidation) – CO2 come
out in molecules that didn’t come in a set order and
found out that there was a cycle – urea cycle
• The same processes occurred in all organisms
Highly conserved ancient pathways
Krebs then solved a major key to the puzzle...
• Pyruvate wasn’t used directly in the CAC and saw a 2C
molecule being used
• There was a loss of a C (as CO2) from pyruvate (3C) makes acetate (2C)
• Now acetate could then be linked to citrate formation
• The junction between glycolysis and the CAC, this step is irreversible! (very large –ΔG, and
regulated)
• This also means fatty acids cannot be turned into glucose

• Pyruvate is decarboxylated, oxidised and CoA attached

Lecture 5

Vitamin B1 (Thiamine)
• TPP is within E1, and acts to remove CO2
• Two circled groups react with pyruvate coming in
• Attached to enzyme – pyruvate dehydrogenase
Lecture 5

1. Pyruvate bunds the thiamine and CO2 is ripped off (breathe out in lungs) ends up with acetate
2. Acetate transferred to lysin lipoamide and Coenzyme A and the sulphur groups exchange the
acetate on the Coenzyme A (goes to CAC)
3. Sulphur groups are reduced (must be oxidised to carry on the cycle for the next round of
pyruvate/acetate)
4. E3 moves around and within it is a molecule of FAD in the oxidised state
5. FAD takes the electrons and becomes reduced (bound within protein and cannot move around so
how do the electrons move)
6. NAD+ comes and collects the electrons from he FADH and becomes NADH

So,
• We now have acetyl CoA, and NADH + H+
• We also released a CO2 (you breathe this out)

1. oxaloacetate goes from 4C to 6C to citrate

catalysed by enzyme citrate synthase
2. water is removed, twisted around and put
back in by the enzyme aconitase – enables
oxidation of OH group
a. targeted by fluoroacetate (1080)
poison for killing pests and found in
some plants
3. isocitrate dehydrogenase – extracts CO2
which comes out in breath to make NADH,
release of hydrogen to NADH
4. a-ketoglutarate dehydrogenase – used like
pyruvate dehydrogenase. Just like PDH, a-
KDH removes CO2 and another NAD
reduction (actually uses FAD as well) and CoA-SH added
a. poisoned by arsenic – arsenic binds against sulphur groups and blocks it; kills you
5. succinyl CoA synthetase – CoA-SH released, P, bound & substrate level phosphorylation where GDP
is turned to GTP, either GTP or ATP is formed. Liver will make GTP, muscle will make ATP (GTP and
ATP can be interchanged easily)
6. succinate dehydrogenase – Complex II of the electron transport system where it oxidates succinate
taking 2 H+ and reducing FAD to FADH2
a. SDH is part of the electron transport system and sits in the inner mitochondrial membrane,
directly connects to electron transfer
b. FAD sits in SDH/CII
7. Fumarase – water added to fumarate and rearrangement
8. Malate dehydrogenase – last oxidation step and oxalacetate formed

Summary
• Glycolysis makes 2 pyruvates
• For 2 pyruvates – 6CO2, 8NADH, 2FADH2, 2GTP or 2ATP
Lecture 5
The CAC makes things
• Amphibolic (cata- or anabolic)
• CAC cycle intermediates are used for biosynthesis of important molecules

How to control CAC

• ATP/ADP and NADH are powerful regulators of metabolism
• The NADH/NAD ratio is often referred to as the REDOX state
o ADP/ATP ratio regulated IDK activity
o 10/2 goes faster
o 2/10 goes slower
o Ca2+ also regulates PDH, aKDH AND IDH
• High NADH = a lot of reducing power (too many electrons will
compromise cell)
• PDH is regulated allosterically
o Allosteric: different ligand bind to enzyme change its
shape slightly and change how it works
o Pyruvate, NAD, AMP and Ca2+ drive PDH
• If there is too much Succinyl-CoA or Acetyl-CoA, CoA becomes
limiting and the CAC slows
Lecture 6
Key Concepts
1. The location and number of mitochondria correlates with the energy demands of different tissues
2. Oxidative phosphorylation takes place in mitochondria.
3. The energy from the oxidation of fuels is converted to ATP by the process of oxidative
phosphorylation.
4. Some electron carriers are fixed within respiratory complexes and others are mobile within and next
to the mitochondrial membrane.
5. Oxidative phosphorylation involves the transfer of electrons to oxygen and energy is used to transfer
H+ and to develop a proton gradient and the synthesis of ATP.

The sites of the ETS in eukaryotes are the mitochondrial

inner membrane
Black sports are glycogen
Mitochondria lined up in cardiac muscle always used
because our hearts always beating compared to
skeletal muscles that are voluntarily used

Honeybees
• Aerobic turnover is massive
• V02 – Volume of oxygen per kg per min
o Humans – 100
o Honeybees – 2000
• Cristae is incredibly dense

Electron Transport System

• Complex 1, 2, 3 and 4 aren’t arranged in a
straight line
• Found in inner mebrane of mitochondria
• Electrons flow through electron carriers and
respiratory proteins and end up flowing to
O2
• Respiratory complexes pumps protons from
matrix to outside into intermembrane
space
• Generate gradient
• Protons go through ATP Synthase

• Electrons are injected to Complex I and II

• NADH taken by CI and FADH is in CII
• Super complex
o Blue – CI
o Purple – CIII
o Green – CIV
o Makes it more efficient
Lecture 6
How do electrons flow and drive metabolism?
• As NADH lose electrons, they flow down through chain to O2
• NADH starts in CI – different voltage form where its put in, higher
potential difference
• FADH starts in CII – lower potential difference
• FADH2 has less bang

Complex I (NADH oxidase)

• Large and complicated
• Work as proton pump
• Pumps 4 protons per NADH
• Top part sticks out in matrix where NADH is
floating, bottom horizontal part is where the
pumping occurs
• Iron sulphur complex are in a line and act like
wires
o Electrons pass quickly through them
o If the gap between them are too big
then electrons can’t pass through
• NADH oxidised to NAD and electrons passed
flavin mononucleotide
o Similar structure to FAD but doesn’t
hold electrons for long
• Electrons passed through iron sulphur
complexes
• As they’re passed on, they transfer an
electrical charge which does some work
• Black pocket is ubiquinone and accepts
electrons
• Electrical charge can change the conformation of proteins
o Makes channels open up allowing protons bind to them
o When electron leaves ubiquinone, they go back to shape and makes protons cross
membrane through conformational change of channels
• Ubiquinone
o Electrons flow down to ubiquinone to turn into alcohol group to become ubiquinol
o Intermediate state is semiquinone (half reduced)

Complex II
• Succinate feeds directly into this and oxidised to fumarate
• Electrons transported through iron sulphur groups to haem group
• Electrons then passed to ubiquinone which is made to ubiquinol
• Passed onto CIII
Lecture 6
Complex III
• CI and CII both use ubiquinone
• Electrons flow from CI to CIII or CII to CIII – not in a straight line but they converge
• Ubiquinol comes in and releases 2 protons into intermembrane space
• Four protons make their way to the membrane space and the electrons flow one at a time to the
molecules cytochrome C
o 2 molecules of cytochrome C are used to carry electrons away from complex III
• Overall
o 4 x protons are transferred (not technically pumped!)
o 2 x from reduced QH2, 2 x from the matrix
o 2 x Cytochrome c then carry away 1 e- each to CIV (aka, cytochrome c oxidase)

Cytochrome C
• Found in all anaerobic organisms
• Unlike Q it carries single electrons at one time
• Can change colour whether they’re reduced or oxidised
• Complex II, III, IV and cytochrome c have metals bound
within them (Fe and Cu)
• Use change in colour to see how mitochondria are
working and different diseases
• Shine light on it and some light is absorbed where we can make chart
to have a spectra – analyse to see what is occurring in the
mitochondria

Complex IV
• Works as a pump
• Cytochrome C enters one at a time with their electrons
• O2 comes in and broken down to one O by an enzyme
• Protons attach to the oxygen and produce water
• Protein changes shape
• Overall, 2 proton are pumped and the electrons flow to O2 to form H2O
Lecture 6

How do we learn how thee complexes work?

• Drugs and poison
• Rotenone added to CI
o Lose electrons and become
oxidised
• Antimycin blocks CIII
o CI still gains electrons and will be
reduced
o Electrons depleted at CIII and fine
before
o ETS oxidated
• Cyanide
o ETS reduced as electrons build up
throughout all of it (same with no
oxygen – hypoxia/anoxia)

Different electron transport systems pump different numbers of protons

• CI, II, and III transfer protons across the IMM
• So for 1NADH + H, 10 protons are shifter
• Complex II doesn’t have the capacity to pump
• Only 6 protons are pumped
• NADH moves 4 more hydrogens than FADH2 Why?
o Voltage difference
Lecture 7
Learning Objectives
• understand how the energy from the transport of electrons to O2 is transformed into the high
energy phosphate bonds of ATP.
• understand why the net yield of oxidative phosphorylation is about 2.5 moles of ATP per mole of
NADH oxidized or 1.5 moles of ATP per mole of FADH2 oxidized.
• understand the chemiosmotic coupling hypothesis and the role and mechanisms of ATP synthase

Discovery of a molecular machine

• There was a problem with aerobic ATP synthesis!
• Glycolysis produced exact amounts of ATP (1 glucose à 2 ATP)
• So Substrate level phosphorylation gives exact amounts of ATP
• But 80-95% of a cells’ ATP comes from aerobic metabolism 1 glucose à 28-38 ATP why so variable?
• Was it an error in method, or was ATP synthesised by some other process?

How was the energy from NADH or FADH2 linked to ATP?

• Sir Peter Mitchell had another idea
• Mitchell’s opponents believed ATP formed by substrate level phosphorylation, i.e. the reactions
were all biochemical
• The link was unknown, how did hydrogen/e- carriers get to ATP?
• The “link” was called the ... SQUIGGLY

• So what happens with all those protons from lecture

4?A chemiosmotic gradient
• Oxidation and ATP synthesis are coupled by
transmembrane proton fluxes
• Believe that protons pumped out of the cell were
used to make ATP
o Knew they were used to make ATP because of
H+ powered bacterial flagella
o Similarities of the motors to the ATP synthase H+ powered rotation of flagella and the ATP
synthase

EXPERIMENT
• Purified membranes from bacteria – ones that he knew could consume ATP
• Reconstruct it in lipid vesicle and make it up in a buffer
• Added acid so it was pH 4
• Centrifuge it down
• Vesicles get squished to bottom of tube making a pellet
• Pour off liquid and add a higher pH to make pH gradient
• Added ADP and inorganic phosphate which was radio-labelled to make radioactive ATP
• How pH grad. could drive this

EXPERIEMENT – bacterial rhodopsin

• Purple bacteria have protein in it which makes it purple – absorb light and when it does the protein
changes shape then pumps proton
• They had proton pump they could regulate by turning the light on
Lecture 7
Proton Motive Force
• Protons are transported across the
membrane through the different complexes
– shifts away from equilibrium
• Two components (in mitochondria)
o Concentration gradient ∆pH
o Electric charge (mV)
o Both have an effect and can provide
power
o Electro-chemical gradient
o Moved it away from equilibrium
• Let protons flow back in, capture it and
make ATP
• Similar to a hydro dam
o Capture water, let it flow through,
turn the turbine
• 30 million Volts/m2

Structure is important for mitochondria

• ATP Synthases are on cristae ridges
• Electron transport system are on the flat parts
of the cristae
• ATP Synthase gives the membrane structure

• How do H+ flow?
o If you just pump H+ across the
membrane they just float around.
Must tighten mitochondria to make it
more concentrated
• What shapes cristae folds?
o ATP synthase does this but also a protein and special lipids
• The pH difference across mito membranes may not be enough to drive the ATP synthase?
o Works like conducting rod forcing protons to flow through region of negative charge
Lecture 7
How does ATP Synthase work
• ADP go into little clefts at the top
• Rotor spinning around in the middle
• Phosphate goes in and ATP gets mushed together as
rotor turns
• Rod goes up into catalytic knob – not evenly shaped
• For each turn you make 3 ATP
o 6 subunits at the top
o 3 alpha and 3 beta
o Paired together to help form ATP from ADP and
phosphate

• The internal rod isn’t straight

o Bumps subunits as it goes around
o Moves around with catalytic knob, exerts
pressure on the subunits and changes their
conformation
• The more subunits in the motor the more ATP produced
• Helicases split DNA, they hydrolyse ATP and physically move strands of DNA
• F
• NADH can’t get across mitochondria by itself
• Two system effectively transfer electrons
o Malate aspartate shuttle – 2.5 ATP
§ Complicated but efficient
§ Oxalacetate turned into malate which is transported into mitochondria
§ Turned back to oxaloacetate and get NADH
o G3DPH shuttle – 1.5 ATP
§ Makes less ATP as like CII it uses FADH2
§ Loss of one ATP but fast
§ Bees use this t warm up during winter

SUMMARY
• Net glycolysis makes 2 ATP and 2 NADH
• 2 x Pyruvate à acetyl-CoA makes 2 x NADH
• 2 CAC cycles makes 2 GTP (2ATP), 6 NADH, and 2 FADH2
• OXPHOS converts 1 NADH into à about* 2.5 ATP , 1 FADH2 à about * 1.5 ATP

• Net ATP Glycolysis 2

• Glycolysis 2 x NADH ( x 2.5 or 1.5) 5 or 3
• PDH 2 x NADH (x 2.5) 5
• CAC 2 x GTP 2
• CAC 2 x 3 x NADH (x 2.5) ~15
• FADH2 (x 1.5) ~3
• Total 28-38

Why is the yield vague? (28-38 ATP)

1. Temperature, membranes can be leaky when hot, in the early days experiments were done at 25oC
(mammals are ~ 37oC, cows 39 oC, Birds often 40-42 oC)
2. NADH from glycolysis has 2 fates!
a. The malate aspartate shuttle gives ~2.5 ATP/NADH,
Lecture 7
b. The glycero-3-phosphate dehydrogenase shuttle gives 1.5 ATP/NADH.
3. Protons are also used for other processes (e.g. ADP/ATP exchange, substrate uptake, ion exchange,
conversion of NADH to NADPH...)

Relevance to medicine
• Relevance-Leigh’s disease
o Mutations in the C-ring of the ATP synthase results in proton slippage – cerebral problems

• CI (10) pumps more protons than CII (6)

• Many disease states mitochondria are impacted especially at Complex I (e.g. oxidative stress, heart
attack...)
• What consequence would this have? (good test question)
o Less efficient at making ATP because your losing efficiency of 10 vs 6
• Membrane issues
o damaged inner mitochondrial membranes (oxidative stress, age, diabetes) increases the
leakiness to proton, also structure changes
o occurs when we get older

Global Warming
• more heart attacks in warmer weather
• cristae start to lose their shape – protons transported out of mitochondria
• membrane becomes more leaky
• mitochondrial efficiency drops with increased heat – can’t make enough ATP

Uncoupling ATP Synthesis can also be useful, making heat

• mitochondria in brown adipose deliberately leak protons and inefficient

o special channel in it called uncoupling protein I which allows proton to flow through
• as electrons flow through ETS they make heat
• if they flow faster they make more heat. Like electrons flowing through a wire
• this occurs to make heat in neonates cold exposed lean people and thawing hibernators
Lecture 7

Get skinny fast

• Some chemical (ionophores) shuttle H+ and “un-couple” respiration
• Dinitrophenol (an ingredient in TNT) is an uncoupler, causes overheating
Lecture 8
Key Concepts
• Photosynthesis takes place in the chloroplasts (and many bacteria).
• Photoreceptive compounds (eg. Chlorophyll(s)) within the chloroplast are grouped together with
other compounds, to form photosystems, and it is these complexes which absorb light.
• The processes within photosystems are called the light reactions. These reactions include:
o splitting of water to produce O2 and H+
o NADP+ reduction to produce NADPH
o H+ gradient generation to power ATP synthesis (yes chloroplasts undertake oxidative

Learning Objectives
• describe the two photosynthetic stages and the overall reaction of photosynthesis
• explain the structure of the chloroplast and the molecules involved in light absorption
• understand the reactions taking place during the light reactions
• discuss how the absorption of light if coupled to ATP synthesis

Bulk Capture of Carbon

• Conservation of energy into matter
• Jean Baptist van Helmont 1579-1644
• Noted the mysterious generation of mass by plants
• He grew 2.5 kg tree in 91 kg soil. Five years later, 76.5 kg
• Only water was added, the soil was only 56 g lighter

Where did the tree’s mass come from?

• Cornelius van Niel (1897-1985)
• Showed that H2O was split not CO2
• Using labelled oxygen isotopes 18O incorporated into either CO2 or H2O van Neil showed that….
• CO2 + H2 18O à (CH2O) + 18O2
• 6CO2 + 6H2O à (C6H12O6 ) + 6O2

• 6CO2 + 6H2O à (C6H12O6 6CO2 ) + 6O2

• This is the opposite reaction to respiration overall i.e. oxidation of oxygen and fixing/capture of carbon
• 6CO2+ 6H2O à (C6H12O6 ) + 6O2
• The incorporation of H means there has been a reduction

Serious equity issues

The site of photosynthesis in a plant (bacteria and

algae do well)
• Vein transports moisture/water around
plant
• The thylakoid membrane is impermeable
to most ions and molecules (not Mg2+ and
Cl- however)
Lecture 8
Photosynthesis
• Starts with the absorption of light
• H2O + CO2 à (CH2O) + O2
• Chloroplast thylakoid membrane have chlorophyll a and b
• Chlorophyll – most abundant compound on earth
• Porphyrin ring
o Light hits this and energy/wavelength is absorbed
o Think of it as vibration in molecule
• Chlorophyll doesn’t use all the light that hits it
• Green light reflected and not absorbed
o Blue and red light is used
o If plants or algae use green wavelength they may overload
o When light hits chlorophyll molecule they excite electrons
§ Release energy – some comes off as heat (don’t release the
same colour à
§ Release light
• Where there are peaks show where light is being absorbed

Having a photosystem harvests light

• Z scheme
• Light hits chlorophyll molecules and there is an energy
transfer from on chlorophyll to another and another etc.
• When plants are stressed some of the energy is lost in
fluorescence
• Finds its way to special chlorophyll molecules (i.e. chlorophyll
a)
• Electrons flow to reaction centre in the middle
• Reaction centre don’t just lose energy but lose an electron
which then jumps up to an electron acceptor
o Creates high energy electron

Quantum tunnelling
• Light harvesting system/antennae
• Channel energy through quantum tunnelling
• Photon hits chlorophyll and energy is transferred –
tunnelling its way through the chloroplast
• It’s not electrons tunnelling
• Finds path of least resistance to acceptor molecule
Lecture 8
• Electrons are pumped up and then transferred
• Energy is transferred to the plastoquinone (can
also use ubiquinone)
• Plastoquinone transfers energy to cytochrome
complex (CIII in plants)
• Electrons then make their way through
plastocyanin

• Photosystem II is the first in the chain of linear

electron flow
• Photosystem I was just discovered first

• Light hits PSII and electrons are excited

• Electrons pop up and are rapidly transferred by quinone molecules
• Two electrons bind to plastoquinone and attract two protons from stroma
• Quinone goes to cytochrome Bf
• Unloads protons into the thylakoid lumen
• One at a time electrons go to plastocyanin and jump to PSI
• Water is split and end up with electrons from water is transferred to the electron holes

• Cytochrome C complex does not directly make ATP

• It does so indirectly, it transfers 4H+ by a Q-cycle

Photosystem I
• Absorbs light and has slightly different absorption spectra
• Electrons don’t flow down to plastoquinone but to ferredoxin and then transfer to NADP reductase
• Electrons then transferred to NAD
• There are electron holes and the electrons from plastocyanin bring electrons to photosystem I
Lecture 8
• End up with increase of protons in thylakoid space creating a gradient and therefore making ATP
• Produce membrane potential

There is another difference in the ATP synthesis capacities when comparing mitochondria and chloroplasts
There are differences in membrane permeability

• Mitochondria has three places

where it can pump proton
• Chloroplast transfers protons at
cytochrome complex and splits
water so only has two places to get
protons
• Big difference in pH
o Thylakoid membrane is
permeable to Cl- and Mg2+
o These are used to equilibrate
the charges on the sides, so
there needs to be more
protons to create a gradient
o Chloroplast only use proton
gradient

Is there function in the structure

• Photosystems are distributed in a certain way
• Cytochrome complexes are on the joins
• Due to cyclic electron flow
o Some organisms don’t have photosystem II but only photosystem I
o Electrons are recycled
• Cyclic electron flow is not going to NADP reductase so can’t make NADH
1

8.0: Conversion of Light Energy to

Chemical Energy – Light there be life!

Key Concepts (the big picture):

• Photosynthesis takes place in the chloroplasts

(and many bacteria).
•Photoreceptive compounds (eg. Chlorophyll(s))
within the chloroplast are grouped together with
other compounds, to form photosystems, and it
is these complexes which absorb light.

1
 Key Concepts (the big picture) cont:

The processes within photosystems are called the

light reactions. These reactions include:
- splitting of water to produce O2 and H+
- NADP+ reduction to produce NADPH
- H+ gradient generation to power ATP synthesis
(yes chloroplasts undertake oxidative
phosphorylation!)

WHAT YOU NEED TO KNOW!! You should:

• describe the two photosynthetic stages and the

overall reaction of photosynthesis
• explain the structure of the chloroplast and the
molecules involved in light absorption
• understand the reactions taking place during the
light reactions
• discuss how the absorption of light is coupled to ATP
synthesis

2
5

Photosynthetic light harvesting can achieve a

quantum efficiency that approaches 100% (that is,
the conversion of 100 photons of light into 100
chemically available electrons), and yet it displays
notable robustness in the face of ever-changing
external light conditions.

But a bigger question is why are plants green!

3
 https://www.quantamagazine.org/why-are-plants-
green-to-reduce-the-noise-in-photosynthesis-
20200730/

4
9

Mathematical model predicted that the absorption peaks of

chlorophyll a and b, which green plants use to harvest red
and blue light. It appears that the photosynthesis
machinery evolved not for maximum efficiency but
rather for an optimally smooth and reliable output.

10

5
 A tentative model for the organization of the thylakoid membrane
This is a good summary so learn this

STROMA
(low H+ concentration) Cytochrome
Photosystem II Photosystem I
complex
4 H+ Light NADP+
Light reductase
Fd 3
NADP+ + H+

Pq NADPH

e– Pc
e– 2
H2O
THYLAKOID SPACE 1 1/
2 O2
(high H+ concentration) +2 H+ 4 H+

To
Calvin
Cycle

Thylakoid
membrane ATP
STROMA synthase
ADP
(low H+ concentration)
+ ATP
Pi
H+

11

The site of photosynthesis in a plant

(bacteria and algae do this as well)

The thylakoid membrane is impermeable to most ions and

molecules (not Mg2+ and Cl- however)
12

6
13

b has -CHO

Photosynthesis
• H20 + CO2 (CH2O) + O2
• Chloroplast thylakoid
membranes have chlorophyll
a and b

14

7
 Absorbance of
Chlorophyll a & b
note lack of absorbance 500-600 nm

So photosynthesis
uses mostly blue

!
and red light!

15

Fig. 9.2

Excited
e– state
Energy of electron

Heat

Photon
(fluorescence)
Photon Ground
Chlorophyll state
molecule

(a) Excitation of isolated chlorophyll molecule (b) Fluorescence

16

8
17

Light energy has

now been turned
into chemical
energy!!!!!

Light harvesting systems / antennae

Channel energy through quantum tunnelling
Note: it is not electron tunnelling

18

9
 How a photosystem harvests light

Robert Hill
1899-1991

19

Note that there are two photosystems II and I

20

10
 Photosystem 2

Electron transfer and proton translocation

Pheophytin
chlorophyll minus Mg2+

e e e
Qa Qb
Qb Plastoquinone/ol
Q QH2
e e

Stroma
PC e
Qb
PC e
Cyt
bf
complex
e e
2 x P680

4H+ in to thylakoid space adds to proton gradient Thylakoid lumen

21

Splitting of water and

O2 release at PSII
H2O Stroma

O There are now

electron “holes”,
Mn Mn Electron “holes”,
i.e. they are
E-
E-
Mn Mn filled
missing

E- E-

2xH Thylakoid lumen

P680

H+ in Thylakoid space - Adds to proton gradient

22

11
 How linear electron flow during the light reactions
generates ATP and NADPH
Please note that the cytochrome complex does not directly
make ATP,
This cartoon is highly misleading!
It does so indirectly, it transfers 4 H+ just like Complex III of
the mitochondria
These then drive ATP synthesis as in the mitochondria

23

Photosystem 1 (P700) Stroma

Acceptor chlorophylls and phyloquinones

e-
Ae- A1Fe-S
-- --0
Fe-S
Fe-S
Ferredoxin
NADP
e- reductase
PC --
NADP+ NADPH
PC e-
--

Cyt
bf
comple e- e-
x -- --
Thylakoid lumen
P700

24

12
 Photosystem 1 (P700) Stroma

e-
Ae- A1Fe-S
-- --0
Fe-S
Fe-S
Ferredoxin
Now there restored
Electrons are NADP
again electron reductase
PC e-
-- holes NADP+ NADPH
PC e-
--

Cyt
bf
complex e- e-
-- --
Thylakoid lumen
P700

25

A tentative model for the organization of the thylakoid membrane

STROMA
(low H+ concentration) Cytochrome
Photosystem II Photosystem I
complex
4 H+ Light NADP+
Light reductase
Fd 3
NADP+ + H+

Pq NADPH

e– Pc
e– 2
H2O
THYLAKOID SPACE 1 1/
2 O2
(high H+ concentration) +2 H+ 4 H+

To
Calvin
Cycle

Thylakoid
membrane ATP
STROMA synthase
ADP
(low H+ concentration)
+ ATP
Pi
H+

26

13
 There is a proton gradient developed by:
1) The splitting of water H+ released in thylakoid space
2) Cytochrome complex transfers 4 H+ to in thylakoid space
H+
H+
H+ H+ H+ H+
H++ H+ H+
H
2H + O
H+
H2O

NADPH
H+
ATP H+
H+ H
+

Chloroplast

27

Chloroplast ATPase

Is very similar across species, but there are 14 c-ring subunits in plants chloroplasts, only
8 subunits in animal and plant mitochondria
As it turns each subunit binds a proton.
Potential exam question!
What does this mean for ATP synthesis efficiency (ATP/H)?

28

14
 Mitochondrion Chloroplast

MITOCHONDRION CHLOROPLAST
STRUCTURE STRUCTURE
H+ Diffusion
Intermembrane Thylakoid
space space
Electron
Inner Thylakoid
transport
membrane chain membrane

ATP
synthase
Matrix Stroma
Key
ADP + P i
ATP
Higher [H+] H+
Lower [H+]

29

H+
H+
H+ H+
H+ H+
H+ H+
H+ H+
H+
H+

+
-150 m V

CI CIII CIV -
H+
H+

There is another difference in the ATP synthesis capacities

when comparing mitochondria and chloroplasts
There are differences in membrane permeability
Mitochondria uses the proton gradient and electrical charge

30

15
 In chloroplasts the thylakoid membrane is permeable to Cl-
and Mg2+
H +
H+
H+ H+ H+ H +
H+ H+
H + H+
H + H+ H +
H+
H+
H+ H+ H+
Mg2+

Mg2+ H + Mg 2+

H+ H+
H+

Cl- Cl- H+
Cl- H+
H+ H
+

Chloroplast proton gradient only, very low pH

31

Differences between mitochondria and

chloroplasts
Chloroplast inner membranes are permeable to Cl- and Mg2+

Chloroplasts are therefore reliant on pH (H+ gradient)

Mitochondria can use net charge potential and H+ gradient

Larger pH difference required in chloroplasts as only H+

gradient is used.

32

16
 Photosystem II and I separated?
Possibly to do with ….
Cyclic Electron Flow
33

Cyclic electron flow

34

17
 Photosystem 1 P700

A0
A1
Fe-S
Ferredoxin

PQ

Cyt
bf
comple
PC
x PC
ee
ee
P700
H+
Cyclic electron flow
35

Why have cyclic electron

flow?
-This produces ATP only (no NADPH)
-Some bacteria only have PSI
36

18
 The plant may simply want more ATP!

ATP is required in C4 plants

What are C4 plants?

….

37

Part 2 Melvin Calvin, a man with mean parents?

Key Concepts (the big picture):

•The light reactions produce O2, H+, ATP and NADPH.

•The Calvin cycle uses NADPH and ATP to fix atmospheric
CO2 to form glyceraldehyde 3-phosphate (G3P).
•Ribulose bisphosphate (RuBP) is used to bind/fix CO2 by the
enzyme RUBISCO (ribulose bisphosphate carboxylase)
•The consumption of ATP and NADPH by the Calvin Cycle is
sustained by the light reactions.

38

19
 WHAT YOU NEED TO KNOW!! You should:

• describe the processes taking place in the Calvin

cycle
• discuss how the absorption of light is coupled to
the synthesis of glucose

39

A simple Calvin Benson cycle

40

20
 The Calvin Cycle is confined to the Stroma

This partitioning stops intermediates and products

(e.g. glyceraldehyde 3 phosphate) being
metabolized, as some of the intermediates feed
directly into glycolysis.

Plants also have mitochondria and glycolytic

enzymes!

41

The Calvin Cycle

This is the level you

need to understand

42

21
 Three Phases of the Calvin
Cycle

1. CO2 fixation
3. Regeneration

2. Reduction

43

Three Phases of Calvin Cycle

1. CO2 fixation

44

22
 Input 3 (Entering one
at a time)
CO2
6C 3C
Phase 1: Carbon fixation
5C Rubisco

3 P P
Short-lived
intermediate
3P P 6 P
Ribulose bisphosphate 3-Phosphoglycerate
(RuBP)

3 x 5C 3 x 6C 6 x 3C

45

Ribulose Bisphosphate Carboxylase (RuBisCo)

carboxylates ribulose-1,5-bisphosphate, (5-C
compound) with CO2

x 2!!!

A 2-step reaction gives extremely unstable 6-C

intermediate. This splits in half to form 3-
phosphoglycerate (3PGA), a 3-carbon compound.

46

23
 Fig. 10-18-2
Input 3 (Entering one
at a time)
CO2

Phase 1: Carbon fixation

Rubisco

3 P P
Short-lived
intermediate
3P P 6 P
Ribulose bisphosphate 3-Phosphoglycerate
(RuBP) 6 ATP

6 ADP

Calvin
Cycle
Again note multiple 6 P P
1,3-Bisphosphoglycerate

molecules pass 6 NADPH

through the 6 NADP+

6 Pi

reactions 6 P
Glyceraldehyde-3-phosphate Phase 2:
(G3P) Reduction

1 P Glucose and
Output G3P other organic
(a sugar) compounds

47

Enzymes similar to glycolysis!

Again note multiple molecules pass through the

reactions and therefore 6 x ATP and NADPH
Reduction (gain of electron) and de-
phosphorylation of carbon

48

24
 As a very rough rule NADP/NADPH is involved in reducing
reactions NAD/NADH in oxidation!

NADPH tends to be used for biosynthesis / regeneration

49

Input 3 (Entering one

at a time)
CO2

Phase 1: Carbon fixation

Rubisco

3 P P
Short-lived
intermediate
3P P 6 P
Ribulose bisphosphate 3-Phosphoglycerate
(RuBP) 6 ATP

6 ADP

3 ADP Calvin
Cycle
6 P P
3 ATP
1,3-Bisphosphoglycerate
6 NADPH
Phase 3:
Regeneration of 6 NADP+
the CO2 acceptor 6 Pi
(RuBP)
5 P
G3P
6 P
Glyceraldehyde-3-phosphate Phase 2:
(G3P) Reduction

1 P Glucose and
Output G3P other organic
(a sugar) compounds

50

25
 We will settle with “the regeneration
phase”

After the loss of 1 x C3

5 x C3 are left,
Then these are rearranged to 3 x
C5 (ribulose bisphosphate)
& RuBP is regenerated!

51

The Calvin Cycle takes…

3CO2 6NADPH 9ATP → 6G3P

1G3P is removed/cycle!
So 2 cycles required to make 1 glucose
(The Calvin cycle releases 1 three-carbon sugar phosphate/turn,
A triose phosphate = glyceraldehyde-3-phosphate (G3P)
Hexoses (e.g. glucose) are made using enzymes of gluconeogenesis (coming))
Hexose sugars are not products of Calvin Cycle, C6H12O6, is convenient as it balances
with glycolysis.

52

26
 Thus, only 1 G3P available for subsequent
conversion to ½ a hexose
This required 9 ATPs and 6 NADPH
per 3 CO2 fixed
Energetically $$$$$!
Lucky sunlight is cheap

53

Photorespiration and Issues with Carbon Fixation and Water

The Calvin Cycle is regulated by light in several ways

(The Dark Reactions are a misnomer)

1) pH! The more alkaline the Stroma, the faster the CC

works, the stromal pH rises when the light reactions
are working.
2) Ferrethio reductase (an antioxidant enzyme of sorts)
needs NADPH to reduce/stabilse RuBisCo.
3) Explains why RUBISCO doesn’t work well in isolation
and it needs light

54

27
 RuBisCo has major issues (-or not?)
Rubisco is slow!
It also binds O2 in the process photorespiration
This makes a useless/toxic product (2-phosphoglycolate) and wastes
water!
Also the faster RuBisCo works it makes more errors (high
temperature increases reaction rates & errors!)
When O2 is high (& low CO2) up to 20-30% of photosynthesis
is wasteful! Not so good for farmers!

55

In the Cambrian 33% Oxygen and very

low CO2,
Maybe photorespiration may remove
reactive O2 and this leaves CO2
Still, this must slow growth and requires
more water?

Some plants have evolved a solution

56

28
 C4 plants: Evolution of a solution for photorespiration

Corn is a C4 plant it needs

much less water

oxaloacetate

Rice is a C3 plant
Requires much water

Some plants (hot climates) can concentrate CO2 into

oxaloacetate (4C)

They are called C4 plants (sugarcane and corn).

There is partitioning of specific cycles into different leaf

cells. 4-Carbon oxaloacetate is used as a “CO2” shuttle.

57

C4 plants have different structures in leaves

58

29
 Shuttle enzymes we associate with the
CAC and gluconeogenesis concentrate
CO2 for the CC

Malate and Oxaloacetate have 4 Cs

This acts like a chemical pump, which collects CO2 and concentrates it
This vastly decreases competition with O2 at Rubisco!

59

But why?
If C3 plants photosynthesise at a high rate, O2
accumulates and results in photorespiration.

This is a wasteful use of H2O and the carbon already in the

CC.

The C4 system concentrates CO2 and decreasing for

photorespiration.

But C4 plants uses more ATP!

This extra ATP comes from cyclic electron flow and

sunlight is cheap, especially in the tropics.

Ultimately C4 plants use water more efficiently and

function better in warm climates.

60

30
Lecture 10
Learning Objectives
• understand glycogen’s structure
• understand different roles of liver and muscle glycogen stores
• understand glycogen synthesis and degradation
• understand roles of glycogen synthase and glycogen phosphorylase
• be familiar with enzyme defects associated with glycogen storage diseases
• understand how the liver synthesizes glucose

Glycogen
• Liver
o Big glycogen stores in liver
• Muscle (cardiac)
o Smaller stores to allow room for
muscle to move and contract

• Stored in cytosol, in most tissues (driven

by insulin)
• Insoluble & rapidly accessed.
• Synthesis driven by insulin
• Breakdown driven by glucagon
• Large glycogen polymers do not attract as
much water as glucose.
• Protects osmotic pressure of the cell.
o Must use glycogen instead of glucose
o Glucose attract water and will make cell swell/burst
• Only glycogen in liver (and a little bit in kidney) can release glucose to other tissues
• Liver can store 8-10% of wet mass as glycogen
• Muscles 1-2% (space limits in muscle)?

Fish store a lot of glucose in liver and can produce alcohol to survive horrendous conditions - anaerobic
Turtle survive extended periods with no oxygen and produce lactate
• Lactate breaks down the shell forming calcium lactate
• Some turtles suck water up bum which is like gills and absorb oxygen in rectum

• Glycogen has protein in middle –

glycogenin
• Attach glucose molecule to the
ends of the glycogenin and keep
adding
• Enzymes will chop off glycogen at
the tips for quick access when it’s
needed
Lecture 10

Glycogen Synthesis (glycogenesis)

• Glucose goes into blood and through wall

• Carried to the liver through the hepatic portal vein
• Becomes phosphorylated through two enzymes to
get glucose-6-phsophate
o Hexokinase – operates at low
concentration and high affinity
o Glucokinase – operates at high
concentration and low affinity
• Wont form glycogen immediately
• shuffle the phosphate around from glucose-6-
phosphate to glucose-1-phosphate
o ensure that it doesn’t go the wrong way
• pyrophospharylase gets rid of enzyme adds UTP to
a UDPG
o prepares it for the next enzyme
• glycogen synthase which adds it to a growing chain of glycogen
• this is an energy intensive process (using phosphate and an equivalent of ATP)
Lecture 10

• Glucose added on the non-reducing end

• Glucose opened up into linear molecule
• The end is the reducing – reactive end

• Two types of bond

o a 1-4 glycosidic bonds: make it flexible
o a 1-6 glycosidic bonds: branches
• add glycosyl units
• don’t want chain to get longer so branching units comes and shifts glycosyl units up 4 glycosyl units
in towards the core
o limited by the enzyme
• branches are created by the transfer of
glycosyl residues
• each branch must grow to 11 residues before
transfer
• new branches are exactly 4 residues away
and move towards the core, this keeps the
overall granule dense

Glycogen Breakdown (glycogenolysis)

• One powerful driver of glucose release is adrenaline
• Adrenaline stimulates heart to beat faster
and liver to breakdown glycogen to glucose
• Prolonged stress response stimulates
cortisone – makes glucose from amino
acids etc.

• There are 3 (4) enzymes used

1. Glycogen Phosphorylase
2. Glycogen de-branching enzyme
(actually 2 enzymes)
3. Phosphoglucomutase
• Cut it from non-reducing ends from the
outside
Lecture 10
Glycogen phosphorylase cuts non-reducing ends by process of phosphorylysis
• Doesn’t use ATP but an inorganic phosphate
• Phosphate group comes and adds to the glucose to have a glucose 1 phosphate
• Glycogen phosphorylates only work until the 5th glycosyl residue leaving 4 left on the chain

Phosphorolysis why not hydrolysis?

• Hydrolysis will leave an un-phosphorylated glucose
• Ensures released glucose is charged and trapped in cells (important in muscles)
• It saves an ATP each time! Pi is used directly, i.e. hexokinase isn’t used

• The last 3 glycosyl units have been transferred to

the end of the chain and can be ‘muched’ by
phosphorylase
• The last bond is broken by a 1-6 glucosidase and is
hydrolysed

• Have glucose-1-phosphate but now must get glucose-

6-phosphate to be used in the cell
o Done by the enzyme phosphoglucomutase
• This goes into metabolism of the cell

• Glucose makes 2 ATP in glycolysis

• Because G6P is formed by phosphorolysis, therefore the first step in glycolysis is
bypassed.
• Glycolysis of G6P will yield 3 ATP (If we forget the original investment)
Lecture 10
The kidney/liver use the phosphate group elsewhere – take it off

SUMMARY

Regulation
• Don’t want both pathways working at the same
time
• This is a cascade and amplifies the reaction
Lecture 10
Diseases
Glycogen Storiage Disease
• 11 known types of GSD
• Incidence ~ 2.5 children / 100,000 births
• 7 result in muscle weakness or wastage
• 5 result in enlarged livers
• von Gierke’s Disease- (type I GSD) glucose 6-phosphatase mutation (can’t release glucose from
liver)

von Gierke’s disease

• Hypoglycaemia
• Can result from glucose 6 phosphatase deficiency – can’t release it
• Excess G6P shunted to triglycerides, hyperlipidaemia
• Elevated lactate during fasting
• Gout (hyperuricaemia)
• Enlarged liver and kidneys
• Treatment fructose and other carbohydrates

Mc Ardle’s disease
• Glycogen in muscle, but severe muscle cramps?
• Lack of glucose release, little glycogen phosphorylase
activity in muscle (isoform called
“myophosphorylase”)

What to do in depletion of glucose

In average resting male
• Brain uses 120g/day glucose
• Entire body 160g/day glucose
• Glucose stores 20g blood glucose, 190g in
glycogen
• 90% glucose used/day, 57% by brain
• Only 10% left at the end of the day
• We don’t rest all day
• Must make glucose (gluconeogenesis)

Sources of building blocks for gluconeogenesis

• Lactate → pyruvate (Cori Cycle)
• Amino acids (except leucine and lysine)
• Glycerol (remainder of fats cannot be used in animals to make glucose)
• TCA intermediates (conversion to citrate/oxaloacetate/malate)
Lecture 10
Overall gluconeogenesis:
2Pyr + 4ATP +2GTP+2NADH + 6H2O →Glucose +4ADP
+2GDP +2NAD+ + 2H+ + 6Pi

If glycolysis is simply reversed ΔG = + 83.7 kJ/mol

Using gluconeogenesis
ΔG = -15.6 kJ/mol
But it uses 11-12 ATP equivalents** Assumes 2.5-3 ATP /
NADH

Three bypasses are required

for the kinases as they do not reverse
• Pyruvate Kinase (PK)
• Phosphofructokinase (PFK)
• Hexo/Glucokinase (HK, GK

Important gluconeogenic enzymes

• Pyruvate carboxylase (bypass I)
• Phosphoenolpyruvate carboxykinase (PEPCK)
(bypass I)
• Fructose 1,6-bisphosphatase (bypass II)
• Glucose 6-phosphatase (bypass III)

Control of gluconeogensis and glycolysis

• Gluconeogenesis consumes ~ 12 ATP
• Glycolysis makes + 2 ATP (or + 3 from glycogen)
• mis-match of ~ 10 ATP
• The 2 pathways must not run at the same time!
Lecture 10
 Blood glucose,
insulin and glucagon
levels after a high
carbohydrate meal.

Human endocrine glands

Secretes
hormones into
the bloodstream

The endocrine
organ that
maintains blood THE PANCREAS
glucose level
(BGL) is…….

3
 The pancreas is neuroendocrine in origin

Exocrine (secretes digestive enzymes)

Endocrine Islet of
Langerhans
(secretes
hormones)

The pancreas has neuroendocrine origins, parts of the gut are considered
an enteric brain!
8

4
 Mouse pancreatic
islet, a spherical
group of hormone-
producing cells.

Insulin is labelled
here in green,
glucagon in red,
nuclei in blue.

Heller R.S. (2015) The Comparative Anatomy of Islets. In: Islam M. (eds) Islets of
Langerhans. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-6686-0_2

10

5
 Glucagon
Glucagon is a 29aa polypeptide

α-cells produce glucagon in response to LOW

BGL

RAISES blood glucose levels by:

- stimulating glycogen break down (&
stopping glycogen synthesis)
- signaling the liver cells to hydrolyse glycogen
releasing glucose into the blood

11

Insulin
Insulin is a 51aa polypeptide

β-cells produce insulin in response to HIGH

blood glucose levels
Insulin LOWERS BGL levels by:
- Stimulating all body cells (except brain cells) to
take up glucose

Has numerous other effects such as:

- Stimulating glycogen synthesis
- Promoting storage of fuel e.g. glycogen, muscle
growth and fat

12

6
 Fig. 8.2 Maintenance of glucose homeostasis by insulin
Glucose homeostasis
and glucagon

High blood
glucose
Insulin

Insulin
decreases Low blood
glucagon glucose
secretion Glucagon

13

Constant glucose management

Insulin Insulin Insulin Insulin

9
7
Glucose mM

5
3
1

Glucagon Glucagon Glucagon

Glucagon
0

Time
14

7
15

Post high carbohydrate glucose management

Glucose 10 mM

5 mM

Insulin 120 uU/ml

40 uU/ml

Glucagon 120 pg/ml

80 pg/ml

0 20 40 60 80 100 120 mins

16

8
 So what does insulin do?
• Many things
• In the case for the exam, it drives
glucose uptake in tissues, importantly
into the skeletal muscle and the liver!
• But insulin also promotes fat deposition,
glycogen storage, growth
• Insulin is part of a broad hormone family
that are generally anabolic

17

Insulin history, discovery and

mechanisms

18

9
 51 aa protein when cleaved

19

Insulin is a growth factor

It drives biosynthesis and storage

20

10
 GLUT1 is ubiquitous, highly conserved, but GLUT2 is
found in the pancreas beta-cells, liver and gut
GLUT2

Pancreatic islet b-cell

GLUT2 has high Km (low affinity) glucose enters when the concentration is
high (GLUT1 Km = 1 mM, GLUT2 Km = 15-20 mM)

21

Glucose uptake stimulates cell metabolism in

the pancreas b-cells

GLUT2

22

11
Glucose uptake stimulates cell metabolism in
the pancreas b-cells

ATP
ATP ATP
ATP
ATP

23

Glucose uptake stimulates cell metabolism in

the pancreas b-cells

Insulin
containing
vesicles move to KATP sensitive channel
membrane

ATP
ATP ATP
ATP
ATP

24

12
Glucose uptake stimulates cell metabolism in
the pancreas b-cells

ATP ATP
ATP
ATP
ATP

So high glucose (which = high energy) uses metabolic flow/flux

to signal a global regulator of energy levels (glucose)
25

Metformin
Is a sulfonylurea

It is actually a tad more complicated

Not just glucose triggers insulin release,
Back to the brain thing, β-cell works like a neuron
Diabetes Res Clin Pract. 2011 Aug;93 Suppl 1:S27-31. doi: 10.1016/S0168-8227(11)70010-9.

26

13
 Back to insulin

27

Insulin mediated
glycogenesis
many tissues Glucose

Stimulation of Insulin
receptor
glycogen
synthesis Insulin

Fats

Mitochondria

Glucose
transporter

PI-3K & IRS1

28

14
 DIABETES MELLITUS.

Diabetes -to straddle legs apart- -siphon

Mellitus -sweet (honey) tasting

Hyperglycaemic- excess glucose in blood

appears in urine.

29
16 (mmol/l)

Normal fasted blood

glucose = 4.5-5 mM
12

Diabetic > 11 mM
(or frequent fasted levels
of > 7 mM)
8
4
0

0 1 2 3 4
Hours following glucose bolus

30

15
 Diabetic complications
Cardiomyopathy
~80% of diabetics die from heart failure
Nephropathy –kidney failure
Retinopathy –visual issues
Neuropathy –peripheral nerve damage
Peripheral circulation issues-gangrene ulcers
Glycation of hemoglobin

31

DIABETES
Two main types:

Insulin dependent, common in juveniles,

Sometimes in adults viral infection triggers
Type 1:
loss of b cells.
Loss of Insulin production.

Non – Insulin dependent, common in older people

Type 2: (90%), obesity, stress, variable insulin levels, it starts
high then drops
Insulin insensitivity no insulin

32

16
 Type I diabetes

Type I diabetes mellitus (insulin-dependent diabetes)

- Autoimmune disorder

- Usually appears in childhood

- Treatment: insulin injections

Normal pancreas Diabetic pancreas

33

Type 1

Pancreas beta cells

destroyed

34

17
 A closer look

Pancreas

35

Type 1 DM
No insulin

No insulin, no
glucose uptake
Must inject insulin

Complicated

Insulin is not the only

hormone involved
and it is a growth
hormone

36

18
 Type II diabetes

Type II diabetes mellitus (non-insulin dependent)

- Usually due to target cells having a decreased

responsiveness to insulin

- Usually occurs after age 40 – risk increases with age

- Accounts for over 90% of diabetes cases

37

Type 2 Diabetes
Generally mediated by obesity

Bodies cells Beta cells also work

desensitised to harder to supply
insulin, blood larger body mass
glucose levels rise with insulin, cells fail
Note this is grossly simplified, there
Glucose uptake and are many things occurring and
disposal impaired T2DM can occur through extreme
stress, genetic mutation and
evolutionary background….

38

19
Type 2 Diabetes
Generally mediated by obesity

39

Insulin insensitivity

High fat content of the

blood may alter
signalling, and or
glucose metabolism

40

20
 Type II
Reactive oxygen
species, and Too much fuel
Maternally inherited Too few mitochondria
DM Free radicals
released by mitos

The cell responds

and protects the cell
by decreasing GLUT

Blood glucose rises

Mitochondrial DNA
mutations can also
impair glucose uptake

It is thought that this process may be the cell protecting

itself from elevated glucose and holding it outside the cell

41

Fit Unfit

In almost all cases exercise improves if not eradicates type II diabetes

(also extends life marginally, improves life quality, mental capacity,
requires no drugs).

42

21
 Minnesota Starvation Experiment 1944-1945

Figure 8.3b
The five (i.e. in the blood)
phases of
glucose
homeostasis
in humans

1
Fuel choice during starvation

Fuel switching with starvation

The brain requires glucose
However, it can use ketone bodies
(smell of acetone)

Note this occurs in the liver

Fats are hydrlysed to ketones
Fats
Acetyl-CoA

2
Ketone Bodies

• Brain cannot use fat

• After 3 days starvation, 30% of brain’s energy
is from ketone bodies (mostly from liver,
astrocytes maybe a little).
• After ~ 40 days, ~70% ketones & glucose
use drops from ~120 to ~40g/day.
• The ketones acetoacetate and β-
hydroxybutyrate are acidic, pH of the blood
drops, resulting in ketoacidosis.

Ketoacidosis

• In untreated Type I diabetes and binge

drinking alcoholics (alcohol-induced
impairment of liver gluconeogenesis),
acidosis is an issue

3
 The ketogenic diet

What is the ketogenic diet?

• Note the keto diet is not starvation.
• Seafood. Fish and shellfish are very keto-friendly
foods. ...Low-carb vegetables. ...Cheese.
...Avocados. ...Meat and poultry. ...Eggs. ...Coconut
oil. ...Plain Greek yogurt and cottage cheese.
• Low carbohydrate!

4
 Pros and Cons?

CON: FEWER CARBS ISN’T NECESSARILY A GOOD THING.

You may or may not live longer, but you may feel like you are living longer and
miserable for a while

PRO: IT MIGHT BE HELPFUL FOR THE DAYS SPENT AT YOUR DESK JOB.
Low carbs less risk of diabetes etc.

CON: YOU MAY NOT BE GETTING ENOUGH SUGAR.

You may feel flat, brain fade

PRO: IT MAY HELP PREVENT CANCER

Some studies have shown that there may be a link between very low carb diets
and cancer prevention.

CON: IT COULD HAVE A NEGATIVE IMPACT ON HEART HEALTH.

Many of the foods that make up the Keto diet are high in saturated fats and meats.

Exercise

10

5
 Exercise & glucose regulation

11

Classification of physical
activity on the basis of
duration and intensity of
exercise and the
corresponding intracellular
energy pathways

From: Exercise Physiology

5th Edition.. McArdle et al

12

6
 Human variation

Kenyan Jamaican, West African Descent

Endurance
Evolution at over 1500m

13

Muscle variation in humans

Muscle varies
considerably across
humans (one of the
most genetically
uniform species on
earth)

14

7
Creatine phosphate (CrP)

• With exercise ATP levels remain relatively

stable.
• If ATP stores decline cells die by necrosis!
• While ATP is used, it is replaced, through CrP
almost immediately.

15

25

20

15
mM

10

0
phospho-creatine ATP pre exercise phospho-creatine ATP post-exercise
pre-exercise post-exercise

16

8
 Creatine phosphate stores
CP
CP CK = creatine kinase
CP
CP CP CP
ATP
ATPase
CK s

C ADP
ADP

ATP = 518 g/mole

CP = 211 g/mole
ATP is bulky and more charged (binds metals e.g. Ca2+)
Contractile machinery

17

In heart and aerobic muscles

mtCK = creatine kinase

ATP ATP
CP CP CP
ATPase
mtCK MCK s

C C C
ADP ADP

CP = 211 g/mole
ATP = 518 g/mole

ATP is bulky and more charged (binds metals e.g. Ca2+)

18

9
19

Sled dogs VO2MAX ~200 l/min/kg

Maximal elite human athlete 97 l/min/kg
Mere mortal ~30-50l/min/kg
(humans are still good athletes)
Dogs fueled on 60% fat
20

10
 Husky sled dogs in Iditarod
9-day sled event
• Run at 50% of VO2max, ~160km/day
(~1400km)
• Sub 4 min miles for 112 km
• Heart mass increases by 50%
• Fueled on high fat food
• Recovery from stomach ulcers during
event with minimal rest

21

Fig. 4. Transmission electron

micrographs of dog adductor
magnus of (A,B) in summer
condition and (C,D) in winter
condition. A and C
are samples of dogs from
Qeqertarsuaq, B and D
are samples from Qaanaaq.
Mitochondria (mt)
are located next to lipid droplets
(ld) between the
myofibrils (mf). Scale bars, 1 μm.
Transmission
electron micrographs are average
representations
of muscle ultrastructure taken
from different dogs.

Note that similar patterns occur in

diabetic and obese patients, but
minus the mitochondria

22

11
 Fuel use during exercise

Marathon record ~ 2 hrs

23

Fuel sources for muscle contraction

Note how slow liver glycogen derived ATP delivery is!

Fats are slow as well, but the ATP potential is huge!
Note this is adipose fat. Athletes also store intramuscular
fat, more quickly accessed
24

12
 Why use anaerobic
pathways?
• Creatine phosphate and glycogen
(glucose) are within cells, and are very
rapid
• Oxygen dependent pathways
(respiration) dependent on transport of
oxygen, this takes time, organ
coordination and many more reactions
• Oddly lactate forms even with oxygen??

25

Why not to use anaerobic

pathways

Mostly use glucose to fly

Wings move at 200-250 Hz

Honeybee gets the equivalent of 2,015,301 km/l petrol

(50 x around the world)
Can not form lactate in flight muscles
Why would this be a bad thing?
26

13