Case 2 BIOCHEM - enzymes, micronutrients

Question 1

Define an enzyme

Answer 1

• proteins that catalyse biochemical reactions

Question 2

Enzymes’ role in digestion

Answer 2

• digest food by hydrolysing bonds that link the building blocks of dietary macromolecules

Question 3

Function of digestive enzymes

Answer 3

1. hydrolyse peptide bonds in dietary proteins. Breakdown of proteins into peptides and then into amino acids for absorption
2. hydrolyse glycosidic bonds in dietary carbohydrates. Breakdown of complex carbohydrates into monosaccharides and disaccharides for absorption
3. hydrolyse ester bonds in dietary fats. Breakdown of fat into fatty acids, glycerol, and monoacyglycerol for absorption

Question 4

Enzyme specificity

Answer 4

1. type of reaction (oxidation, hydrolysis or isomerisation)
2. nature of substrates
   - defined by the active site structure

Question 5

Active site

Answer 5

Small area of an enzyme where substrates bind and reaction takes place

Question 6

Roles of amino acid residues at the active site

Answer 6

1. bind substrates in the correct orientation for the reaction to occur
2. take part in catalysis of the reaction

Question 7

Carboxypeptidase

Answer 7

• hydrolyse peptide bond at the amino acid residue at the C terminus

Question 8

Pancreatic Serine Proteases

Answer 8

• chymotrypsin, elastase and trypsin use the same mechanism for catalysis but have different active sites that have different substrate specificities
• chymotrypsin: hydrolyses the peptide bond at the bulky hydrophobic amino acid residue
• elastse: hydrolyses peptide bond at a small amino acid residue
• trypsin: hydrolyses peptide bond at a Lys or Arg (basic) amino acid residue

Question 9

Thermodynamically favourable reactions

Answer 9

free energy change (delta G) is negative

Question 10

Thermodynamically speaking, how does an enzyme catalyse a reaction?

Answer 10

• by lowering the activation energy. This increases the rate and the fraction of molecules reaching the transition stage.
• the lowest the activation energy, the higher the fraction of substrate molecules which attain the transitions state thus the higher the reaction rate.

Question 11

Mechanisms of enzyme catalysis (molecular)

Answer 11

1. straining substrate conformation so it starts to resemble the products
2. covalently binding substrate in order to activate the substrate
3. providing a suitable environment at the active site for the reaction to occur
4. bringing substrates in close proximity and in correct orientation for reaction to occur at the active site
5. acting as a base or acid
   * different enzymes use different combinations of the mechanisms

Question 12

Shapes of enzyme-catalysed reactions

Answer 12

1. Michaelis-Menten = hyperbolic.

2. Allosteric = sigmoid.

Question 13

Define Km

Answer 13

substrate concentration at which v=1/2vmax

Question 14

Significance of Km in the context of enzyme sensitivity

Answer 14

• [s] «_space;km: enzyme will be sensitive to changes in [s]
• [s] = km: enzyme will be half saturated with substrate
• [s]» km: enzyme will be insensitive to changes in [s] and will be operating at Vmax

Question 15

Significance of Km in the context of enzyme sensitivity

Answer 15

• [s] «_space;km: enzyme will be sensitive to changes in [s]
• [s] = km: enzyme will be half saturated with substrate
• [s]» km: enzyme will be insensitive to changes in [s] and will be operating at Vmax

Question 16

Michaelis-Menten equation

Answer 16

v = Vmax[s]/Km+[s]

Question 17

Define enzyme inhibition

Answer 17

• small molecules that decrease the rate of enzyme-catalysed reactions

Question 18

Differentiate between reversible and irreversible inhibitors

Answer 18

• reversible: binds non-covalently

- irreversible: binds covalently

Question 19

Define competitive inhibition

Answer 19

• inhibitors binding at the active site where the substrate binds.
• this prevents the binding of substrate to the enzyme
• binding of I or S to E are mutually exclusive (i.e. EIS complex cannot form)

Question 20

Effect of competitive inhibition on Km

Answer 20

Vmax is attained at a higher [s] as inhibitors have to be competed out. Therefore Km increases.

Question 21

How is the pancreas protected from destruction by proteases

Answer 21

1. pancreatic trypsin inhibitor

2. synthesis of pancreatic proteases as inactive zymogens

Question 22

Define positive cooperativity

Answer 22

binding of substrate at one active site increases the affnity for substrate binding at vacant active sites on remaining subunits.

Question 23

How do the effectors of allosteric enzymes influence its affinity for substrate binding

Answer 23

the binding of substrate at the active site is regulated by the binding of an effector at a regulatory site

Question 24

How do the effectors of allosteric enzymes influence its affinity for substrate binding

Answer 24

the binding of substrate at the active site is regulated by the binding of an effector at a regulatory site

• positive effectors activate the enzyme, thus shifting the sigmoid curve to the left
• negative effectors inhibit the enzyme, shifting the sigmoid curve to the right

Question 25

Two main types of micronutrient

Answer 25

1. vitamins | 2. trace elements/minerals

Question 26

What is a vitamin

Answer 26

Organic compounds needed in minute amounts, obtainable from outside sources.

Question 27

Classification of vitamins

Answer 27

- water soluble (9) vs. fat soluble (4)

Question 28

What is a trace element

Answer 28

a pure chemical element required in minute amounts, essential for normal human development, growth and physiological functioning. Normally obtained through diet and are generally inorganic.

Question 29

Fat-soluble vitamins

Answer 29

1. A- retinol 2. D- calciol 3. E - tocopherol 4. K

Question 30

Water-soluble vitamins

Answer 30

1. B1 - thiamine 2. B2 - riboflavin 3. B3 - niacin 4. B5 - pantothenic acid 5. B6 - pyridoxine 6. B7 - biotin 7. B9 - folic acid 8. B12 - cobalamin 9. C - ascorbic acid

Question 31

Difference between the metabolism of water vs. fat soluble vitamins

Answer 31

- water soluble (B and C) 1. not stored 2. need consistent intake 3. no toxicity associated with excess intake 4. many are synthesised by bacteria - fat soluble 1. absorbed through the GIT 2. capacity for storage 3. excess = toxicity

Question 32

Define a cofactor

Answer 32

- non-protein helper molecules - required for the protein's biological activity - usually function with enzymes, assisting in the chemistry of the reaction - sometimes non-enzyme proteins also require cofactors (Hb) * tightly bound cofactors = prosthetic group * loosely bound cofactors = coenzymes

Question 33

Properties of a coenzyme

Answer 33

- participate in enzymatic reactions - loosely bound and detachable - fn: carry chemical groups or electrons between molecules

Question 34

Properties of a prosthetic group

Answer 34

- required for enzymatic reactions as well as non-enzyme proteins - tightly bound, not detachable

Question 35

The role of Vitamin C (ascorbate) in metabolism

Answer 35

- required for enzymes that make hydroxyproline and hydroxylysine in collagen - act as an antioxidant (reducing agent) - cannot be made by humans * pathology: scurvy, CVD

Question 36

The role of Vitamin B1 (thiamine) in metabolism

Answer 36

- essential to the metabolism of amino acids and sugar - essential to the synthesis of GABA and ACh - synthesised by bacteria, fungi and plants * pathology: peripheral neuropathy

Question 37

The role of Vitamin B3 (niacin) in metabolism

Answer 37

- redox carrier - precursor to NAD and NADP - NB to the catabolism of fat, CHO, protein and alcohol; cell signalling and DNA repair. High energy requiring and turnover rate organs are susceptible to their deficiency * pathology - pellagra

Question 38

The role of Vitamin B12 (cobalamin) in metabolism

Answer 38

- required for the production of succinyl coa and methionine. - without methionine, DNA cannot replicate and result in anaemia-related symptoms - with out succinyl CoA - neurological symptoms * pathology - pernicious anaemia