Part 1 espyr1 S6a

Cellular Metabolism I

Metabolism

Catabolism Anabolism

Metabolic Process Breakdown of large  small molecules small  large molecules Energy consumption Produces Energy Requires Energy

Metabolism – Sum of all chemical processes of biomolecules in a cell or an organism

Thermodynamics

- Spontaneous process

o Takes place with no intervention o Cannot determine the rate of reaction - Free energy change ∆G

o Change in free energy before and after reaction

o Most useful criterion for predicting spontaneity of a process

∆G < 0 ∆G = 0 ∆G > 0

Type of reaction & Spontaneity ^Exergonic

Spontaneous At equilibrium Endergonic Not spontaneous Energy consumption Energy released No net energy consumption Energy required

- Standard free energy change (∆G^o) o Under stp

o T=298K; p^gas =1 atm=101 kPa; Pure substance; Solution concentration = 1 M - _{If [H}⁺]=1 M, pH=0, but pH in our cells are most in the neutral range

- With this limitation, the standard transformed free energy change (∆G^′o) is introduced o For biochemical reactions

o Standard state, [H^+]=10-7 M, pH=7.0 o _{[H2O]=55.5 M}

Metabolic Pathways

Catabolism Anabolism

Convergent, converges to 1 particular compound

E.g. Acetyl CoA ^Divergent

- Metabolic pathways are irreversible

- At least one reaction ( and one enzyme) far from equilibrium - Committed step is in the early pathway

- Regulated at several levels o Availability of substrates

o Allosteric Control of enzymes by products or coenzymes o Covalent modification

o Extracellular growth factor and hormones o Genetic Control

High Energy Bonds

Adenosine Triphosphate (ATP) - ATPADP+Pⁱ releases energy - _ADP+PiATP requires energy - ATP has high energy bonds

o Phosphoanhydride bond

o When these bonds break, they realesed large amount of energy (∆G^{′o <}−25 �/ � ) o ATP=AR-P~P~P

Activation

- Coenzyme A (CoA) is an important compound in metabolism

- Often written as CoASH too to emphasize the thiol group is the reactive portion of the molecule - CoA consist of

o Adenosine 3’-phosphate o Panthothenic Acid

o 2-Mercaptoethlamine group - Formation of Acetyl CoA will

activate the metabolism

- The Acetyl (-COCH³) group is replacing the hydrogen at the thiol group via thioester bond - Thioester bond is also a high energy bond

- Hydrolysis of Acetyl CoA results in large free energy change (-31.4 kJ/mol)

Acetyl_{− CoA + H2}O^hydrolysis CH3^{COO−+ CoA + H+}

Redox Reactions

- Oxidation (loss of electron OR loss of H) - Reduction (Gain of electron OR gain of H)

- In aerobes, the ultimate electron acceptor is Oxygen

o Electrons transferred via series of redox reactions through electron carriers o _O2 reduced to H2O

- Biochemical electron carriers

o _NAD⁺ _{and NADP}⁺ (Oxidising agent) o _FAD

High energy bonds

NAD⁺ and NADP⁺

Nicotinamide adenine dinucleotide (NAD⁺) Coenzymes of dehydrogenases

- Association with enzymes are relatively loose - Two-electron oxidizing agent

o Release 2 H atoms o Accepts hydride ion (:H^-)

o Second proton released to solvent - Redox reaction is reversible

FAD

Flavin adenine dinucleotide (FAD)

- Tightly bound conenzymes of flavoproteins

- Prosthetic groups – do not diffuse from one enzyme to another - Participates in several types of redox reactions

o Fused ring can accept one or two electrons (in H atoms) from reducing agent o One electron accepted - FADH•

o Two electrons accepted – FADH² - Reduction is reversible

Glucose Metabolism

- Glucose occupies the central position in metabolism

- In higher plants/animals, there are 3 major pathways of glucose metabolism o Synthesis of storage polysaccharides (Glycogen, starch, sucrose, etc) o Oxidised to pentoses and pyruvate

Glycolysis – Breakdown of sugar

- Main functions:

o Provides significant portion of free energy

o Prepare glucose for further oxidative degradation - 10 enzyme-catalysed reactions

o Net ATP Production= 2

o Glucose oxidized to pyruvate (C3) o 3 IRREVERSIBLE reactions

- Occurs in cytosol (cytoplasm, not in any organelles)

- Preparatory stage

o Phosphorylation of glucose (Uses 1 ATP)

o Phosphorylation of Fructose 6- phosphate to fructose 6- bisphosphate (Uses 1 ATP)

- Payoff stage

o Conversion of dihydroxyacetone phosphate to glyceraldehydes 3- phosphate o Substrate-level

phosphorylation (Produce 4 ATPs) - Net yield

o _{2 NADH} o _{2 ATP} o 2 Pyruvate

Regulation of Glycolysis

- The three irreversible reactions provide great decrease in overall standard transformed free energy - Enzymes which catalyses the irreversible reactions

are allosteric enzymes - Irreversible reactions: 1,3, 10

- To control glycolysis, it is the best to regulate the enzymes in these 3 steps

Reaction (1)

Reaction (3) Reaction (10)

- Reaction 3 is more effective in regulating the glycolysis

o Fructose 1,6-bisphosphate has no other pathway of reaction except continuing carry on the glycolysis

o The enzyme phosphofructosekinase is an allosteric tetramer.

o It can bind 2 ATPs, one is the substrate site while another is a allosteric site

- At high ATP, excess ATP will bind to the enzyme to produce low reaction rate, a sigmoid curve on the graph - While ATP is the inhibitor for the reaction, AMP and ADP can hence be the activator for the synthesis of

Fructose 1,6-bisphosphate

Fate of Pyruvate

- The pyruvate produced after the glycolysis will undergo three processes depends on the type of cell and presence/absence of O2

- Reduction to lactate

o Homolactic fermentation (Enzyme: lactate dehydrogenase) o In muscle

o Regeneration of NAD⁺ under anaerobic conditions in vertebrates - Alcoholic fermentation

o Two step pathway for regeneration of NAD⁺ under anaerobic conditions in yeast Anaerobes in plants Anaerobic conditions in

vertebrates

- Oxidation and decarboxylation to acetyl CoA o Under aerobic conditions

o Acetyl CoA completely oxidized to CO^{2 and H2}O via citric acid cycle and electron transport chain

Non-glucose Hexoses

- They will enter glycolytic patway after conversion of phosphorylated derivatives - Fructose

o Two separate pathways depend on tissues( muscle, liver) - Galactose

o Some individuals with galactosaemia unable to convert galactose to glucose o Result in cataract formation, mental retardation, death from liver damage

- Most non-glucose hexoses will converge to fructose 6-phosphate, so it is a good point to regulate (Reaction 3)

Glycogen

- Three main enzymes involved in hydrolysis of glycogen to enter glycolytic pathway o Glycogen phosphorylase

 Produce G1P from the non-reducing ends of Glycogen o Debranching enzyme

 Remove branches o Glycogen phosphoglucomutase

 Converts G1P  G6P