PL 4, 5, 6

Question 1

what is the basic structure of an amino acid

Answer 1

• central carbon
• COOH
• H2N
• H
• R group

Question 1

amino acids are bi functional, what are the two functional groups

Answer 1

• H2N amino group
• COOH carboxylic acid group

Question 2

what happens when an amino acid is in aqueous solution

Answer 2

• a zwitterion is formed
• The -COOH donates a proton to the NH2
• NH2 —> NH3+
• COOH —> COO-

Question 3

are amino acids soluble in water? why?

Answer 3

• they are very soluble in water because they are ionic

Question 4

what is the effect do the following have on amino acids
- acid solutions
- alkaline solutions
- neutral solutions

Answer 4

they have very little effect because amino acids act as a buffer
- acid: H3N+- CHR -COOH
- alkaline: H2N- CHR -COO-
- neutral: H3N+- CHR -COO-

Question 5

what are enantiomers

Answer 5

• mirror images of the isomers of amino acids
• shown in carbon groups that have four different groups around a central atom - chiral molecules

Question 6

how are peptides formed (and what are they)

Answer 6

• when an NH2 group reacts with a COOH group in a carboxylic acid and a secondary amide is formed
• CONH group formed
• secondary amides

Question 7

how do you name amino acids

Answer 7

the amino acid with the free NH2 group is written first, then the one with the free carboxylic acid group is written

Question 8

describe the hydrolysis of proteins

Answer 8

• the peptide link is hydrolysed to release the individual amino acids
• done by boiling with moderately concentrated hydrochloric acids under reflux

Question 9

define the following:
- primary structure
- secondary structure
- tertiary structure

Answer 9

1. the order of amino acid residues
2. the coiling parts of the chain int a helix or the formation of a region of sheet
3. the folding of the secondary structure

Question 10

describe the secondary structure of a protein

Answer 10

• helices and sheets are held together by hydrogen bods between NH groups on one peptide link (CONH) and the C=O groups on another peptide link

Question 11

describe the tertiary structure of a protein

Answer 11

• held together by intermolecular bonds, ionic and covalent bonds
• ID-ID bonds between non polar side chains, tend to be at the centre of protein molecules
• Hydrogen bonds between polar side chains, and form with water if polar groups are on the outside
• covalent bonds between -SH groups on neighbouring cysteine residues

Question 12

which proteins are fibrous and which are globular

Answer 12

• fibrous are muscles and hairs, long and thin and consist of main helices
• globular proteins control the metabolism, e.g. enzymes and hormones, they have sheets and helices

Question 13

describe the active site of an enzyme

Answer 13

• they have a precise tertiary structure that results in a cleft in the enzyme surface
• R groups from amino acid residues bind to substrate molecules and react with them
• this is where catalysis takes place

Question 14

describe the bonding that occurs in the active site of an enzyme

Answer 14

• the bonds that bind to the substrate are usually weak so the binding can be readily reversed when the products are form
• bonds usually consist of hydrogen bonds or interactions between ionic groups

Question 15

describe when the reaction when it is zero order with respect to the substrate

Answer 15

• if the substrate concentration is high enough where as all the enzymes active sites will be taken up by substrate molecules
• no more ES complexes can form at the rate which molecules pass through reaction pathway
• reaction does NOT depend on substrate conc.
• RDS EP —-> E+P

Question 16

what are competitive inhibitor

Answer 16

• molecules that fit into the active site of an enzyme but cannot be catalysed
• bind reversibly

Question 17

how does pH affect enzyme performance

Answer 17

• reduces it because active site contains ionisable groups e.g. COOH or NH2
• affected by change in pH
• e.g. COOH –> COO-
• or tertiary structure loses shape and side chains aren’t held close together and enzyme denatures

Question 18

how does temperature affect enzyme performance

Answer 18

• when temp. increases, activity rises because molecules gain enough energy to collide and their combined energy succeeds the activation enthalpy
• some bonds holding tertiary structure are weak D-D bonds and H bonds, bond sbreak, enzyme denatures