ML3: Metabolism and bioenergetics

Question 1

What is metabolism?

Answer 1

A linked series of chemical reactions, whereby one molecule is converted to another molecule(s) in a defined way

Question 2

What are the different types of reaction? Give their general formulae and an example of each.

Answer 2

• Substitution
  
  • A + B–X → B + A–X
  • e.g. glucose + ATP → glucose 6-phosphate + ADP + H⁺
• Addition
  
  • ​A + B → AB
  • e.g. DHAP + GAP → F-1,6-BP
• Elimitation
  
  • ​AB → A + B
  • e.g. F-1,6-BP → DHAP + GAP
• Condensation
  
  • ​AX + BY → AB + XY
  • e.g. amino acid 1 + amino acid 2 → dipeptide + H₂O

Question 3

What are the two types of metabolic pathway? Define them and give their general forumlae.

Answer 3

• Catabolic
  
  • ​Breakdown of complex molecule to produce energy; usually oxidative
  • fuel → CO₂ + H₂O + useful energy
• Anabolic
  
  • ​Formation of complex moleules from simple ones, utilising energy; usually reductive
  • energy + simple precursors → complex molecules

Question 4

Define ‘exergonic’ and ‘endergonic’ reactions.

Answer 4

Exergonic reactions are spontaneous and release energy

Endergonic reactions are non-spontaneous and need energy to occur

Question 5

Define the energy of a reaction (equation). Give the meaning of each component.

Answer 5

ΔG = ΔH – TΔS

ΔG = Gibbs free energy change of a reaction = energy available to do work

ΔH = enthalpy change = heat exchange with surroundings

ΔS = entropy change = measure of the order/disorder

T = temperature measured in K

Question 6

What is the Gibbs value for exergonic and endergonic reactions?

Answer 6

Exergonic reactions occur spontaneously and release energy so ΔG < 0

Endergonic reactions are non-spontaneous and need energy to occur so ΔG > 0

Question 7

What are the standard conditions under which free energy change is normally expressed?

How do you write standard free energy change?

Answer 7

1M concentrations of reactants and products, 25°C, pH 7

Standard free enrgy change = ΔG°’

Question 8

Give the equations which show that a thermodynamically unfavourable reaction can be driven by a favourable one.

Answer 8

A ⇌ B + C (ΔG = +21 kJmol^–1)

B ⇌ D (ΔG = –34 kJmol^–1)

A ⇌ C + D (ΔG = –13 kJmol^–1)

Question 9

What is energy used for in organisms?

Answer 9

• Energy is supplied to organsims as food. Food is broken down (catabolism) to produce energy.
• Used for:
  
  • Synthetic processes (anabolism) for growth and renewal
  • Mechanical work (cell movement, muscle contraction)
  • Active transport of molecules and ions

Question 10

What are the dietary requirements and which are sources of energy?

Answer 10

Carbohydrate

Lipid

Protein

Water

Source of elements (Mg, Ca, Fe, etc.)

Vitamins (fat- and water-soluble)

Essential amino acids and fatty acids (biosynthesis)

Question 11

What is ATP?

Answer 11

Adenosine triphosphate (ATP) is a mononucelotide containing an adenine base, a ribose sugar, and three phosphate groups. It is the ‘energy currency’ in organisms

Question 12

Why is ATP used as an energy currency?

Answer 12

Hydrolysis of phosphoanhydride bonds releases lots of energy because of:

1. Resonance stabilisation
   Resonance stabilisation of orthophosphate favours ATP hydrolysis
2. Electrostatic repulsion
   4 negative charges results in electrostatic repulsion which is reduced when ATP is hydrolysed
3. Stabilisation due to hydration
   Water binds more effectively to ADP and Pi than ATP, thus stabilising ADP/Pi ⇌ ATP

Question 13

What are the two processes by which ATP is produced?

Answer 13

• Substrate-level phosphorylation (some)
• Oxidative phosphorylation using reduced coenzymes (NADH, FADH₂) generated by catabolic pathways (most)

Question 14

What is redox?

Answer 14

• Reduction and oxidation
• Whenever something gets oxidised, something else gets reduced, hence the use of the term redox
• e.g. when fuel molecules (A-2H) are oxidised, hydrogen atoms and electrons are transferred to another molecule (B)
• During catabolic processes, intermediates are oxidised and coenzyme (NAD⁺) is reduced in redox reactions
  
  • AH₂ + NAD⁺ → A + NADH + H⁺

Question 15

What are carrier molecules? Give some major examples.

Answer 15

• Molecules that pass electrons and protons
  e. g.
• NAD^{<strong>+</strong>} (nicotinamide adenine dinucleotide)
• NADP^{<strong>+</strong>} (nicotinamide adenine dinucleotide phosphate)
• FAD (flavin adenine dinucleotide)
• FMN (flavin mononucleotide)

Question 16

What is the structure of NAD and what is its role in redox?

Answer 16

It is a dinucleotide with 1 nicotinamide base, 1 adenine base, 2 ribose sugars, and 2 phosphate groups. Its R group is a hydrogen

During catabolic processes, intermediates are oxidised and coenzyme (NAD⁺) is reduced in redox reactions

Question 17

What is the structure of NADP and what is its role in redox?

Answer 17

Same structure as NAD (dinucleotide, 1 nicotinamide base, 1 adenine base, 2 ribose sugars, 2 phosphate groups) but with a phosphate R group

During anabolic processes, intermediates are reduced and coenzyme (often NADPH) is oxidised in redox reactions

Question 18

Give an overview of Stage I catabolism.

Answer 18

• Extracellular (GI tract)
• Complex molecules → building block molecules (BBM)
• BBM absorbed into circulation
• No energy produced

Question 19

Give an overview of Stage II catabolism.

Answer 19

• Intracellular (cytoplasmic and mitochondrial)
• Many pathways (not all in all tissues)
• BBM → even simpler molecules
• Oxidative (require NAD⁺, NADP⁺, FAD)
• Some energy (as ATP) produced

Question 20

Give an overview of Stage III catabolism.

Answer 20

• Mitochondria
• A single pathway (citric acid cycle)
  
  • Oxidative
  • Acetyl converted to 2CO₂
  • Produces precursors for biosynthesis
• Oxidative phosphorylation (electron transport and ATP synthesis)
  
  • NADH and FAD₂H re-oxidised
  • O₂ required (reduced to H₂O)
  • Lots of ATP produced