Unit 2

Question 1

C-H bonds and Red-Ox

Answer 1

• Increase in C-H bonds = reduction
• Decrease in C-H bonds = oxidation

Question 2

Reduction and Oxidation

Answer 2

• Also applies to partial shift of electrons (formation of polar covalent bonds)
• Oxidation (loss of electrons, dehydrogenation)
• Reduction (gain of electron and H atom, hydrogenation)

Question 3

What is Free Energy Change (delta G)

Answer 3

• Gibbs free energy: amount of energy in a system available to ‘do work’ (energy contained in bonds of molecule)
• Delta G: change in free energy in transition from one molecule to another

Question 4

Exergonic reactions

Answer 4

• -ve Delta G
• Energetically favourable (increase disorder)
• Decrease free energy of system
• Net release of energy
• Reactants contain more energy than products

Question 5

Endergonic reactions

Answer 5

• +ve delta G
• Requires input of energy
• Since cells must carry out anabolic rxns: by coupling (consecutive rxns) to exergonic rxns)
• Products contain more energy than reactants

Question 6

What compounds have high energy bonds?

Answer 6

• Phosphorylated carbon compounds and ATP
• Have large -ve delta G when hydrolyzed

Question 7

Activation of energy carriers

Answer 7

• Transfer of H and an electron (H-, hydride ion) to carrier results in reduction
• High energy electron can now be transferred when needed

Question 8

Activated carrier molecules

Answer 8

• Small molecules that temporarily store energy in form that can be transferred to metabolic rxns
• Readily transferable chemical groups/high energy electrons
• Provide energy for biosynthetic (+ve delta G) rxn
• e.g. ATP, acetyl CoA, NADH

Question 9

Enzymes + activation energy

Answer 9

• Enzymes can greatly accelerate an energetically favourable rxn but cannot force an energetically unfavourable rxn (without coupling)
• Bind reactants (substrates) and accelerate their conversion to products

Question 10

How do cells avoid rxn equilibrium (delta G = 0)

Answer 10

• Exchange of materials w/ environment
• Products of one reaction being substrates in another

Question 11

How do enzymes catalyze a rxn?

Answer 11

• Substrates bind to the active site
• Interactions btw substrates + amino acids at active sites facilitate conversion of substrates to products (AE lowered, enzyme changes shape)
• Products have low affinity at active site so they are released + enzyme returns to original shape

Question 12

Enzyme cofactors

Answer 12

• Help enzymes carry out some chemistry required for cell f(x)
• Inorganic –> metal ions (e.g. zinc, manganese)
• Organic –> coenzymes: shuttling of electrons + protons (NADH) (many vitamins are a part of coenzymes)
• Coenzymes are chemically changed during rxn –> must be regenerated to complete catalytic cycle

Question 13

Regulatory molecules (enzyme)

Answer 13

• Bind to enzyme + change its reactivity
• 2 types of regulation: allosteric + competitive

Question 14

Competitive inhibition

Answer 14

• Inhibitor competes w/ substrate to bind to active site; substrate cannot bind
• Can be overcome by increasing [substrate]

Question 15

Allosteric (non-competitive inhibition)

Answer 15

• Inhibitor may bind to site away from active site, changing enzyme’s conformation so substrate can no longer bind
• Non-competitive inhibitor binds to allosteric site
• Can’t be overcome by excess substrate

Question 16

Covalent modification (enzyme regulation)

Answer 16

• Covalent modification of enzyme by functional groups
• Enzyme changes shape –> changes activity
• Most often phosphorylation at -OH containing side chains

Question 17

What is a hydride ion (H-)?

Answer 17

• Compound transferred to NAD+ in a reduction rxn
• H atom with extra electron
• Anion of hydrogen

Question 18

After TCA cycle and before ETC + oxidative phosphorylation, in what form is most of the energy from glucose?

Answer 18

NADH molecules (“loaded” energy carriers)

Question 19

Substrate level phosphorylation

Answer 19

• Formation of ATP (endergonic) coupled to exergonic rxns
• Immediate production of a few ATP during glycolysis

Question 20

Oxidative phosphorylation

Answer 20

• (aerobic respiration)
• Series of redox rxns leading to transfer of electrons into activated carriers
• energy from activated carriers used to pump H+ across a membrane
• protons allowed back across (diffusing down gradient) and run ATP synthase

Question 21

Where does glycolysis occur?

Answer 21

Cytosol

Question 22

Where does TCA cycle occur?

Answer 22

Mitochondrial matrix

Question 23

Where does oxidative phosphorylation occur?

Answer 23

Mitochondrial matrix/intermembrane space (H+ pumped there)

Question 24

Where does pyruvate oxidation occur?

Answer 24

Mitochondrial matrix

Question 25

Main events of glycolysis

Answer 25

• Energy investment (2 ATP spent to make glucose more reactive)
• Cleavage (doubly phosphorylated sugar is split)
• Energy generation (each 3C sugar joins with free phosphate –> more reactive)
• 2 phosphate groups on each sugar transferred to ATP
• Results in 2 pyruvate per glucose

Question 26

Fermentation

Answer 26

• Goal: to reduce (regenerate) NAD+ for glycolysis to continue
• In absence of oxygen/anaerobic conditions

Question 27

Pyruvate oxidation

Answer 27

• Decarboxylation rxn (taking off a C from pyruvate)
• NAD+ reduced to NADH
• Activating 2-carbon acyl groups using coenzyme A

Question 28

TCA Cycle

Answer 28

• 2 carbon acyl unit (from acetyl CoA) binds to oxaloacetate to form 6 carbon unit (citrate)
• NAD+ and FAD reduced to NADH and FADH2
• Oxaloacetate must be regenerated through cycle to start again

Question 29

ETC

Answer 29

• Series of molecules imbedded in inner mitochondrial membrane (protein complexes)
• NADH reduce protein complexes (hydride ion, H-)
• Protein complexes pump H+ into intermembrane space (forming electrochemical gradient)
• Oxygen is final electron acceptor at last complex, binds with H to form water

Question 30

Proton Motive Force

Answer 30

• Storage of energy as a combo of voltage + proton gradients across membrane

Question 31

ATP Synthase

Answer 31

• Protons pass through to matrix (due to gradient), causing ATP synthase to spin –> catalyze conversion of ADP to ATP
• ATP synthase phosphorylates ADP to form ATP

Question 32

Why regulate phosphofructokinase?

Answer 32

• Conversion of fructose 6-PO4 –> fructose 1,6-bisPO4 is so energetically favourable, it cannot be reversed (commitment to glycolysis)

Question 33

What inhibits phosphofructokinase?

Answer 33

High levels of ATP
- Two ATP binding sites (active site, allosteric site)
- High [ATP] –> binds at regulatory site –> enzyme changes shape (reduced activity)

Question 34

Regulation in TCA cycle

Answer 34

• Feedback inhibition by products of TCA cycle (NADH, ATP, acetyl CoA)

Question 35

Roles of Acetyl CoA

Answer 35

• High [ATP] = oxidative pathway inhibited (cells make fatty acids –> store fat), synthesis of energy storage molecules (carbs, fats)
• Low [ATP] = oxidative pathway predominates (production of ATP)