Macromolecules (proteins)

Question 1

mode of action of enzyme

Answer 1

• enzymes speed up the rate of a chemical reaction by lowering the activation energy
• in order to do so, enzymes and substrates must collide in the correct orientation
• thus forming ES complex
• the active site then provides a microenvironment to make or break covalent bonds in a controlled way
• product is then released from the active site, and enzyme is reused to take up another substrate

Question 2

structure of enzyme

Answer 2

• active site has a specific 3d conformation that must be maintained for an enzyme to remain functional
• contains binding amino acid residues, the R grps of which hold the substrates in position
  through non-covalent bonds (such as ionic bonds or H bonds)
• also contains catalytic amino acid residues, the R groups of which are involved in the making or breaking of chemical bonds

Question 3

the 2 hypothesis for the mode of action of enzymes

Answer 3

1. lock and key hypothesis
   - enzyme has a rigid structure, and only substrates that are exactly complementary are able to bind to active site
2. induced fit hypothesis
   - active site of enzyme is not in exact complementary conformation to substrate before binding
   - change in 3d conformation of active site being induced upon binding,
   -> thus moulding the active site into a more precise / better fit for substrate
   -> enzyme can perform its catalytic function more effectively
   - this explains group specificity, where an enzyme is able to catalyse reactions from a variety of structurally or chemically similar substrates

Question 4

how enzyme activity can be regulated

Answer 4

• competitive inhibitor, resembling the substrate in structure
• is complementary and able to bind to active site of enzyme
• non-competitive inhibitor, not resembling the substrate in structure
• binds to a site other than the active site
  to cause a change in the 3d conformation of the active site
  => thus inhibitors reduce the frequency of effective collisions
  -> reduce the no of ES complexes formed per unit time
• apoenzyme associates with cofactor, which facilitates the binding of the substrate to the enzymes
  
  • e.g. inorganic metal ions which bind reversible to enzyme and alters enzyme’s active and allosteric sites to facilitate catalysis
  • e.g. coenzymes which loosely associates with the enzyme and acts as transient carriers of specific functional groups
• post-translational modification
  
  • e.g. phosphorylation of kinases to change enzyme from active to inactive conformation or vice versa
• end-pdt inhibition, in which end-pdt inhibits enzyme(s) controlling the preceding step(s) of the metabolic pathway

Question 5

Description of how a protein structure is maintained

Answer 5

Determine the highest level of protein structure and describe all protein structures (with the highest level one being the most crucial for marks)

Question 6

1º structure of proteins

Answer 6

• each polypeptide has a specific sequence of amino acids
• joined by peptide bonds

Question 7

2º structure of proteins

Answer 7

• which is then folded/coiled into a-helix and B-pleated sheets
• via H bonds bet amine (-NH) group and carbonyl (C=O) group of pp chains

Question 8

3º structure of proteins

Answer 8

• each polypeptide is then further **bended/twisted/folded ** to give a specific 3d conformation
• via R groups interactions (H bonds, ionic bonds, HI)

Question 9

4º structure of proteins

Answer 9

• 2/3/4/… polypeptide chains with R grps interacting
• (elaboration may be needed) to form a dimer

Question 10

general definition of polymer

Answer 10

a macromolecules that is made up of many monomers

Question 11

effect of increasing temp on enzyme activity

Answer 11

1. as temperature increases
   - KE increases
   - frequency of effective collisions increases
   - no of ES complexes formed per unit time increases
2. up till optimum temp
   - where max no of ES complexes formed per unit time
3. as temperature increases beyond optimum temp
   - enzyme undergoes denaturation
   - loss of 3d conformation of active site
   - no longer complementary to substrate
   - no of ES complexes formed per unit time decreases

Question 12

effect of substrate concentrations on enzyme activity

Answer 12

1. at low substrate concentrations,
   - active sites are readily available
   and substrate concentration limiting
   - as [substrate] increases,
   freq of effective collisions bet enzyme an substrate molecules increases,
   rate of ES complex formation increases
   an ROR increases
2. at high substrate concentrations,
   - (all available) active sites occupied/saturated
   - max no of ES complexes formed per unit time / rate of ES complexes formation will remain constant
   - substrate concentration no longer limiting,
   and enzyme concentration limiting

Question 13

why addition of non-competitive inhibitor causes rxn to become constant at a lower rate

Answer 13

• (definition) inhibitor binds to site other than active site and changes 3D conformation of active site
• thus effectively decreasing availability of enzymes to form ES complex
• effects of inhibition cannot be overcome by increasing substrate conc

Question 14

why protein only binds to certain parts of DNA molecule

Answer 14

• binding site of protein has a specific 3D conformation that is complementary to major and minor grooves on the doubles stranded DNA, allowing it to be positioned on the DNA
• binding site of protein has a specific 3D conformation that is complementary to the conformation formed by a specific sequence on the DNA molecule
• thus protein can only bind to regions that is complementary to both the conformation …,
  resulting in specificity of binding