Proteins

Question 1

Describe the basic process of protein synthesis

Answer 1

DNA transcribes to RNA (by transcription)

RNA translates to form a protein (by translation)

Question 2

What is a triplet code (codon)?

Answer 2

The initial nucleotide from which translation starts

Question 3

Give examples of stop codons

Answer 3

UAA
UAG
UGA

Question 4

Describe what the amino acid structure contains

Answer 4

Amino group (NH2)
Side chain (R1)
Carboxylic acid group (COOH)

Question 5

Give examples of amino acids, under the aliphatic amino acid class

Answer 5

Aliphatic - glycine, leucine, alanine, valine, isoleucine (H, CH2, CH3)

Question 6

How is a peptide bond formed?

Answer 6

Formation of covalent bond with the loss of one molecules of water

Reaction occurs within a ribosome in a process called translation

Dipeptide - two amino acids joined
Tripeptide - three amino acids joined

Question 7

Define primary structure

Answer 7

The sequence of amino acids in a polypeptide chain

Polypeptide of 100 monomers (20 possible occupants to power of 100)

1.27x10 (power of 130) sequences are possible

Source of versatility in protein structure and function

Question 8

Define secondary structure

Answer 8

The spatial arrangement of amino acid residues that are near each other in the linear sequence

Question 9

Describe the alpha helix and the types of proteins that have this structure

Answer 9

The telephone cord shape (old fashioned telephone) of a-helix is held in place by H-bonds between every N-H and the oxygen of every CO (double bond) in the next turn of the helix (4aa residues apart)

Examples:
Troponin
Myoglobin
Ferritin

Question 10

Describe what the beta sheet structure is and give examples

Answer 10

The pleated sheet structure is held together by H bonds between amide groups of linear polypeptide chains

Examples:
Porin
Fatty acid binding protein

Question 11

What types of interactions occur in tertiary structures?

Answer 11

Van Der Waals
Ironic interactions 
Hydrogen bonds 
Disulphide bridges 
Hydrophobic interactions

Question 12

Describe tertiary structure of ionic interactions

Answer 12

Occur between 2 close, oppositely charged R groups. These are strong, but few in most proteins

Question 13

Give examples of amino acids, under the aromatic amino acid class

Answer 13

Tyrosine, tryptophan, phenylalanine (aromatic ring)

Question 14

Give examples of amino acids, under the sulphur- containing amino acid class

Answer 14

Cysteine, methionine (SH, S)

Question 15

Give examples of amino acids, under the basic amino acid class

Answer 15

Lysine, arginine, histidine (CH2NH)

Question 16

Give examples of amino acids, under the acidic amino acid class

Answer 16

Aspartate, glutamate (COOH)

Question 17

Give examples of amino acids, under the uncharged polar amino acid class

Answer 17

Serine, threonine, asparagine, glutamine (OH, CONH2)

Question 18

Give examples of amino acids, under the ‘other’ amino acid class

Answer 18

Proline (CHCOOHNH)

Question 19

Describe tertiary structure of Van der waals

Answer 19

Non-specific, weak attractions between atoms 0.3-0.4nm apart.
Individually weak but, in a folded protein structure, a large number exist - thereby stabilising the structure

Question 20

Describe tertiary structure of hydrogen bonds

Answer 20

Similar to van der waals but are stronger and permanent.
1/20 the strength of a covalent bond.
Occur when H is bonded to either O, N or F, and a lone pair of electrons are present.
Examples:
Water
Ammonia

Question 21

Describe tertiary structure of hydrophobic interactions

Answer 21

These are intra-polypeptide interactions which occur in an environment within proteins from which water is excluded.

So in globular water-soluble proteins hydrophobic R groups tend to be on the inside of the protein, hydrophilic R groups tend to be on the outside H-bonding to water, and making the protein water-soluble

Question 22

Describe tertiary structure of disulphide bridges

Answer 22

There are strong covalent bonds between 2 cysteine residues

They are common in extra-cellular proteins

They can occur between, as well as within a polypeptide

Question 23

Give examples of tertiary structures

Answer 23

Chmotrypsin
Transferrin
Caeruloplasmin

Question 24

What is a quaternary structure?

Answer 24

Refers to spatial arrangement of of individual polypeptide chains in a multi-subunit protein

Question 25

What does protein denaturation involve?

Answer 25

Disruption and possible destruction of both the secondary and tertiary structures

These reactions are not strong enough to break the peptide bonds, so the primary structure remains the same after a denaturation process

Question 26

List the different causes of denaturation

Answer 26

Acids 
Heat 
Solvents- ethanol, methanol 
Cross-linking reagents - formaldehyde 
Chaotropic agents  urea 
Disulphide bond reducers 2 mercaptoethanol

Question 27

What are the effects of denaturation?

Answer 27

Decreased solubility
Altered water binding capacity
Loss of biological activity
Improved digestibility

Question 28

Peptidases are a group of proteins involved in digestion, that cleave peptide bonds. Give the names and functions of the two subgroups of the peptidases.

Answer 28

Endopeptidase - cleavage of internal bonds

Exopeptidase - cleavage of one amino acid at a time

Question 29

Exopeptidases, are a group of proteins involved in digestion. Provide the names and functions of the two subgroups of the exopeptidases.

Answer 29

Carboxypeptidases - cleavage at -COOH terminal

Aminopeptidases - cleavage at -NH2 terminal

Question 30

What is the structure of a protein dependent on?

Answer 30

DNA sequence coding for amino acids

Question 31

What ultimately controls the final structure of a protein?

Answer 31

The interactions of amino acids (that are coded for by DNA sequence)

Question 32

What terms describe the configuration of proteins?

Answer 32

Primary
Secondary
Tertiary
Quaternary

Question 33

How is the structure and function of a protein lost?

Answer 33

Denaturation