BCMB

Phosphorylation

The addition of a phosphoryl (PO₃) group to a substrate.

Dephosphorylation

The removing of a phosphoryl (PO₃) group from a substrate

Phosphorolysis

A reversible reaction that breaks down compounds using inorganic phosphate.

Thermodynamically Unfavourable Reactions

Sometimes reactions will not occur on their own usually because the activation energy is too high. These reactions are normally coupled with ATP hydrolysis to make them thermodynamically favourable.

ATP Hydrolysis

ATP hydrolysis is the reaction that removes phosphate groups from ATP to turn it into ADP or AMP (releasing energy).

Types of Work

• Chemical - building molecules

• Transport - pushing molecules against a concentration gradient

• Mechanical - muscle movement

Energy Charge

A measurement of the energy level in a cell. It's a dimensionless number that ranges from 0 to 1. A higher energy charge indicates more high-energy stores (ATP, ADP).

Kinases

Catalyse phosphorylation reactions.

Phosphatases

Catalyse dephosphorylation reactions

Phosphorylases

Catalyse phosphorolysis reactions

Synthases

Catalyse condensation reactions in which no nucleotide triphosphate (ATP, GTP) is required

Synthetases

Catalyse condensation reactions that require a nucleotide triphosphate (ex. ATP, GTP)

Dehydrogenases

Catalyse oxidation-reduction reactions. They usually involve NAD⁺/FAD as cofactors.

NAD⁺/NADH

NAD = nicotinamide adenine dinucleotide

Tend to be in reactions with dehydrogenases.

Likes to oxidise -CH₂-CHOH-

FAD/FADH₂

FAD = flavin adenine dinucleotide

Tend to be in reactions with dehydrogenases.

Likes to oxidise -CH₂-CH₂- to -CH=CH-

Coenzyme A

Carrier of acyl groups and is great at trapping metabolites within the cell because it’s very polar.

Fatty Acids

• Long carbon chains with a polar head group

• Stored as a triglyceride in adipose tissue

• Very energy dense

Glucose

• Stored as glycogen in the body

• Hydrophilic

• Not very energy dense

• Low stores in the body - because it’s very hydrophilic so it carries a lot of water with it as glycogen

7 Big Concepts/Rules

1. The H/e^- carriers are in short supply

2. ADP is in short supply

3. ATP is really stable

4. The inner mitochondrial membrane is impermeable to protons

5. Protons only flow into the matrix if ATP is being made

6. The proton pumps don’t work if the proton gradient is very high

7. No proton pumping, no H/e^- movement down the ET chain

Type 1 Muscle

• Contracts relatively slowly

• Many mitochondria

• Good blood supply

• Called “red muscle”

Type 2B Muscle

• Contracts relatively rapidly

• Few mitochondria

• Poor blood supply

• Packed full of contractile filaments

• Called “white muscle”

ATP Concentration in Cells

• ATP concentration in cells is 5 mM. If it goes < 3 mM then cells die.

• Sprinting muscle cells use ATP at 5 mM per second.

Gentle Exercise

Glucose is the first source of ATP production because it is readily available from the bloodstream. Fatty acids will then come along to inhibit glycolysis.

Moderate Exercise

A mixture of fatty acid oxidation and glucose oxidation. Glucose comes from the liver and any further increase in pace is met by an increase in glucose oxidation.

Strenuous Exercise

Rate of supply and transport of glucose from blood can’t keep up so muscle endogenous glycogen is broken down and undergoes full oxidation.

Very Strenuous Exercise

Now the rate of ATP production can’t be met by oxidative phosphorylation alone. Glycogen then also goes through glycolysis to make those 2 ATP and then the pyruvate made from that is made into lactate.

Sprinting

• Uses Type IIb muscles which have poor blood supply and few mitochondria. Because of this they can’t use fatty acids really or blood glucose.

• Creatine phosphate (CP) is an instant store of ATP (but there is less than 5 seconds supply). Creatine phosphate + ADP → ATP + creatine

• The glycogen through glycolysis is used after the few seconds it takes for this to kick in

Beta-Oxidation

• The process where fatty acids are oxidised in the mitochondria to produce acetyl-CoA

• It’s called beta oxidation because the action occurs on the beta-carbon atom.

Albumin

A protein that transports fatty acids through the blood.

Fatty Acid Binding Protein

Transport fatty acids through cell membranes by passive diffusion.

Carnitine Acyl-Transferase (CAT-1)

An enzyme that transfers the acyl group from a fatty acid to carnitine. This is so that the FA can be transported into the mitochondria.

Carnitine Acyl-Transferase (CAT-2)

Transfers the fatty acid back to CoA after transport into the mitochondria.

Glycolysis

• Occurs in the cytoplasm of all tissues 

• Very fast but very inefficient

• No requirement of oxygen

• Only generates 2 ATP

GLUT-1

Glucose transporter that is present in all cells all the time.

GLUT-4

Glucose transporter that is present in muscle and adipose tissue (insulin sensitive tissues).

GLUT-2

Glucose transporter that is present in the liver and pancrease (blood glucose regulating tissues)

Link Reaction

Pyruvate is broken down into carbon dioxide and acetyl before the start of the Krebs cycle.

Krebs Cycle

• The cycle that completely oxidises acetate carbons to CO₂ and produce lots of NADH, FADH₂, and ATP.

• The cycle produces 3 NADH, 1 reduced FADH₂ plus a GTP

What would happen if there was a hole in the mitochondrial membrane?

• This would lead to uncoupling

• The proton gradient would dissipate and no ATP would be made

• Massive fuel oxidation rate and oxygen consumption as ATP tries to get made but doesn’t

Dinitrophenol (DNP)

• An uncoupling drug

• It’s hydrophobic and so is able to pass across a cell membrane 

• It picks up an H⁺ from outside the mitochondrial membrane then moves in and loses the H⁺ and continuously does that

Uncoupling Protein-1 (UCP-1)

• Found only in adipose tissue

• This is a protein that sits in the mitochondrial membrane and allows protons to move through it when needed

• It is a thermogenin - it’s job is to generate heat

• Noradrenaline binds to β₃-receptors on cell surface which stimulates fatty acid release and opens the UCP-1 channel

Electron Transport Chain

Contains 4 complexes which are embedded in the inner mitochondrial membrane. Functions to generate a proton gradient which is then used to produce ATP via oxidative phosphorylation.

Electron Transport Chain Complexes

Labelled complex I, II, III, and IV. They consist of many proteins that either maintain the shape of the complex or form the prosthetic group (bits that transport H⁺/e^-)

Composition of Complexes in ETC

• H⁺ expelling reactions are on the outside

• H⁺ consuming reactions are on the matrix side

NADH in the Electron Transport Chain

• 10 H⁺ are pumped out for each NADH

• NADH passes on Hs that go through complex I (4 H⁺), then Q, then 3 (4 H⁺), then 4 (2 H⁺)

FADH₂ in the Electron Transport Chain

• 6 H⁺ are pumped out for each FADH₂

• FADH₂ passes on Hs that go through complex II , then Q, then 3 (4 H⁺), then 4 (2 H⁺)

• Present inside complex II - stuck there so any step of beta-oxidation, glycolysis, or the Krebs cycle that involves FADH₂ is happening right next to complex II

UQ (

• Electrons move around in complex I from one prosthetics group to another until they reach the Q pool - a.k.a. UQ, coenzyme Q, Q10, etc.

• UQ is very hydrophobic and lives in the inner mitochondrial membrane

• UQ also picks up Hs from Complex II

• Reduced UQ is UQH₂

• UQH₂ transfers Hs to Complex III

Cytochrome C

• Cyt C picks up e^- from Complex III and gives the e^- to Complex IV

• Cyt C has a prosthetic groups which contains an iron atom

Iron in Cyt C

• It changes from ferrous to ferric acid as it loses and, vice versa, as it accepts the electrons

• Iron does not carry hydrogens!

• The iron atoms are held in place either in the middle of porphyrin rings or in Iron-Sulphur complexes

Two Mechanisms that Transport NADH into the Inner Mitochondrial Membrane

Glycerol 3-phosphate shuttle and malate aspartate shuttle

4 Routes to Q in the ETC

1. From Complex I

2. From Complex II

3. From the first step of beta-oxidation

4. From the Glycerol 3-P shuttle

Free Radicals from the ETC

• Electrons in the UQ pool can react with molecular oxygen to produce free radicals

• They are less likely to form if Complex III is vacant - more likely to form if there are issues with the electron transport chain

ATP Synthase

• Uses the H⁺ gradient to make ATP

• Movement of 3 protons → generation of 1 ATP

• Consists of two functional domains: F₁ and F₀

The H⁺ Gradient is Also Used in Transport

The swapping of ATP/ADP takes negative charge outside the matrix so to counteract this H⁺ ions need to flow back from the cytoplasm into the matrix. Therefore some H⁺ generated from the electron transport chain is lost and not used to make ATP.

What organs and cells have obligatory requirements for glucose?

The brain, kidney, skin, and red blood cells.

Early Stages of Starvation

Begins at the start of the postabsorptive period when all food is digested and there are no substrates coming in from the gut.

Glycogenolysis

The process of converting glycogen into glucose triggered by glucagon.

Why is the phosphorylation cascade of glycogenolysis so complicated?

• It allows for amplification of the signal - 1 glucagon allows 10,000x molecules of glucose to be released

• There is more control over the whole process - each enzyme can be further  influenced by other factors

Why doesn’t muscle breakdown glycogen much in starvation?

• It has no glucagon receptors

• It has no G6Pase and therefore cannot convert G6P into glucose

After a Few Hours of Starvation

• After a few hours of blood glucose being lower than 5 mM, insulin secretion stops. 

• Hypoinsulinemia leads to stimulation of lipolysis and widespread proteolysis mainly from muscles (not very selective though).

• Proteins are broken into amino acids and the skeletons (carbon chains) are used for gluconeogenesis.

Proteolysis

• In the liver, amine groups are taken off amino acids and transferred to keto acids by amino-transferase. 

What amino acid skeletons can be used to make glucose?

• If an AA backbone can only be made into ac-CoA, it cannot be made into glucose.

• If it can be made into pyruvate or a Krebs Cycle intermediate, it can be made into glucose.

Why is making amino acids into glucose unproductive?