Lecture 6 - Metabolism I

Carbohydrate metabolism

• highly conserved

• Mutations are often lethal-evolutionary disadvantage

• regulated by allosteric regulators and kinases

Monosaccharides

simplest form of carbohydrates

• ends in the suffix “ose”

• 3-9 carbons (ex. 5 are pentose, 6 are hexose)

• Carbonyl group

Ketoses vs. aldoses

Both are monosaccharides

• Ketoses: has ketone group on Carbon 2 (good rule: the carbonyl group in ketose is usually NOT at the end of the chain)

• Aldoses: has aldehyde group on Carbon 1

Anomeric carbon

• Feature of a monosaccharide

• carbon with a carbonyl

Penultimate carbon

• Feature of a monosaccharide

• the farthest chiral carbon from the anomeric carbonyl (C=O)

  • usually right next to the achiral carbon

Achiral carbon

• Feature of a monosaccharide

• The farthest carbon away with two hydrogens

D vs L

Penultimate carbon → if the OH group is on the right, its D.

if the OH group is on the left, its L.

• most carbohydrates are D

Beta isomer vs alpha isomer

beta - OH on anomeric carbon points up

alpha - OH on anomeric carbon points down

Confirmations of monosaccharide rings

Chair form - monosaccharide zig-zags, and the ends of the backbone point in opposite direction

Boat form - ends of backbone point in same direction

How can monosaccharides be modified?

By attaching side chain groups

Nomenclature of polysaccharide linkages

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Overview of metabolism

Metabolism = total of all chemical rxns carried out by an organism (anabolism + catabolism)

Anabolic

Processes that build up molecules

• reductive (gain of electrons), requires energy

Catabolic

The process of breaking down molecules

• Yields energy (product is energy), oxidative (loss of electrons)

Metabolites + list examples

molecules made or used when living things break down stuff during metabolism

• carbs

• lipids

• amino acids

• nucleotides

What is glycolysis (generally), and its inputs/outputs

When glucose is broken down to pyruvate

• inputs: 1 glucose, 2 NAD+, 2 ADP, 2Pi

• outputs: 2 pyruvate, 2 NADH, 2 H+, 2ATP, 2 water

Note: glycolysis generates 4 ATP, but it uses 2 ATP, so net +2 ATP

Schiff base (main idea)

When an amine (NH2-R) reacts with the carbonyl carbon of a ketone or aldehyde

1. Amine + carbonyl carbon → Schiff base + water

2. Schiff base attracts and stabilizes the charge as an electron sink for the active site → makes difficult chemical rxns easier for the enzyme to perform

TIM mechanism

TIM converts DHAP to GAP

1. Glu removes H from C1 of DHAP

• (Glu acts like a base)

2. Electrons at C1 move to C1-C2 bond. at the same time, C2=O electrons move to oxygen → C2 oxygen becomes negatively charged (alkoxide), making it unstable

3. His donates H to C2 oxygen → negatively charged oxygen becomes OH → intermediate stabilizes, and DHAP temporarily becomes enediol

• (His acts like an acid)

4. His takes H from OH at C2 → electrons from OH move back to oxygen → C2=O reforms (His acts like a base)

5. Glu donates H to C1 → becomes aldehyde carbon

6. GAP is produced

This process is reversible

NAD/NADH

Redox coenzyme that shuttles protons and electrons

• NAD → NADH

  • picks up 2 electrons and 1 proton

GAPDH mechanism

1. Cysteine sulfur (S) attacks the carbonyl carbon of GAP. At the same time, the C=O electrons move onto oxygen → thiohemiacetal intermediate forms.

2. NAD⁺ accepts 2 electrons and an H from thiohemiacetal → NAD+ becomes NADH → thioester intermediate forms

3. Pi attacks the carbonyl carbon of the thioester → the cysteine is released → 1,3-BPG forms.

4. NADH leaves → another NAD⁺ binds

1,3-BPG is high energy because there is repulision between phosphates at a short distance

Phosphoglycerate mutase mechanism

1. 3PG binds to the active site

2. The phosphate group on phosphohistidine is transferred to the OH on C2 of 3PG
   → This forms 2,3-BPG

3. The phosphate that was originally on C3 of 3PG is transferred to His
   → 2PG forms and the His becomes phosphorylated again

4. 2PG is released

explain what this means - Due to cellular metabolite concentrations, free energies become almost entirely favorable during glycolysis

Inside a real cell, the concentrations of metabolites can make many biochemical reactions energetically favorable, even if their standard free energies aren't favorable

How is step 1 of glycolysis regulated (hexokinase)?

• HK is regulated by G6P, its product, via allosteric inhibition → slows glucose phosphorylation

Inhibitors of PFK: ATP

Allosteric inhibitor for PFK

• if the cell already has a lot of ATP, it signals that it doesn’t need to make more → PFK slows down and glycolysis slows down

PFK and AMP

High AMP levels → allosteric activator for PFK

• When there is high AMP, it signals there is low ATP → AMP binds to and activates PFK → glycolysis happens and more ATP is produced

How is PFK affected by pH levels?

Low pH inhibits PFK

• high rates of glycolysis → increased production of lactate (low pH, very acidic) → if it’s too acidic, there is low pH, and PFK is inhibited, slowing down glycolysis

How is PFK affected by citrate?

Citrate is an allosteric inhibitor

• citrate is part of the TCA cycle, so if citrate levels are too high, it signals that the TCA cyle has enough fuel → that means that no more material has to be sent via glycolysis → glycolysis slows down

Explain feed forward activation in PFK

1. Cell needs energy (signaled by low ATP and high AMP)

2. AMPK (energy sensor) is activated → promotes PFK-2 activity

3. PFK-2 makes F2,6BP → F2,6BP activates PFK-1 → glycolysis increases → more ATP generated

• If insulin increases → F2,6BP activated → glycolysis increases

• If glucagon increases → F2,6BP is decreased → glycolysis decreases

How is pyruvate kinase (PK) regulated?

Activators of PK:

• AMP

• F1,6BP

• Insulin

Inhibitors of PK:

• Alanine

• ATP

• Acetyl-coA