Protein structure

Question 1

types of side chains

Answer 1

1. Non-polar e.g. glycine - have alkyl group.
2. Uncharged polar e.g. cysteine - has S, N or OH in side chain.
3. Negatively charged polar e.g. aspartic acid - has carboxylic acid group.
4. Positively charged polar e.g. histidine - has amine group

Question 2

peptide bond features

Answer 2

• Joins amino acids.
• 40% double bond character.
• Planar.
• Predominantly trans.
• Display resonance structures

Question 3

peptide

Answer 3

short stretch of amino acids joined by peptide bonds

Question 4

protein

Answer 4

long chain of amino acids joined by peptide bonds

Question 5

primary structure

Answer 5

amino acid sequence of a protein

Question 6

secondary structure

Answer 6

specific coiling or folding of amino acid residues over a short stretch of sequence into beta strand or alpha helix

Question 7

tertiary structure

Answer 7

3D structure of a complete protein chain

Question 8

quaternary structure

Answer 8

3D arrangement and structure of multiple chains within a protein

Question 9

properties of alpha helix

Answer 9

• Interaction between residues that are 4 apart in the protein sequence.
• 3.6 residues/turn; 5.4Å/turn.
• Spiral is “right handed” (turns clockwise as it goes up).
• Side chains point out from the helix.
• stabilised by H bonds
• often have one side polar residues, other side non-polar

Question 10

properties of beta strand/sheet

Answer 10

• Hydrogen-bonding occurs between adjacent chains.
• B-sheet = 2 or more B strands (typically 2-10 strands/sheet).
• Can be parallel or antiparallel.
• Sheets have right-handed twist
• often alternating polar and non-polar residues

Question 11

properties of turns

Answer 11

• Hairpin-like, usually involve 3-4 residues.
• High Gly and Pro content.
• 30% of residues involved in turns.
• Normally have H bond across turn.
• More than 16 types, type I and II are common

Question 12

bond angles limiting protein flexibility

Answer 12

• phi Φ angle = rotation angle around the N–C_a bond
• psi (Ψ) angle = rotation angle around the Ca–C’ bond (C’ = carbonyl carbon)
• omega (ω) angle = rotation angle around peptide bond, not very flexible

These angles take on values from 0 to +/-180 degrees

Phi-Psi angles have restrictions in their values because of steric hinderance

• Phi rotation can lead to O-O collision
• Psi rotation can lead to NH-NH collisions

Question 13

why are most peptide bonds trans

Answer 13

Steric hinderance is increased for cis peptide bonds

Question 14

side chain angles

Answer 14

called chi and usually staggered

Question 15

ramachandran plot of parallel B sheet, antiparallel B sheet, alpha helix and left-handed alpha helix

Answer 15

Question 16

which amino acids are not found in alpha helices

Answer 16

glycine and proline

Question 17

afinsen experiment

Answer 17

denatured and reduced ribonuclease and then it reformed into its original shape - showed that only instructions needed for folding are embedded in the sequence

Question 18

stabilisation of protein folding

Answer 18

• Non-covalent interactions, while individually weak in proteins, collectively make a significant contribution to protein conformational stability
• In some proteins additional covalent bonds (eg. disulfide bonds)
• Hydrophobic core contributes most to protein stability in aqueous solution

Question 19

folding pathway of proteins

Answer 19

1. Formation of short secondary structure segments
2. Nuclei come together, growing cooperatively to form a domain
3. Domains come together (but tertiary structure still partly disordered)
4. Small conformational adjustments to give compact native structure

Question 20

what assists with protein folding

Answer 20

• chaperones help with folding of some proteins
• About 85% of proteins are either chaperone-independent or need a chaperone e.g. Hsp70
• Other 15% need special type of chaperone called chaperonin e.g. GroEL-GroES

Question 21

unfolding of proteins

Answer 21

Weakening of non-covalent interactions can lead to unfolding and loss of biological function (denaturation). Can result from:

• Change in pH
• Heat
• Detergent
• Organic solvents
• Urea

Question 22

misfolding of proteins

Answer 22

• Cause problems e.g. in brain, abnormal form of prion protein PrP causes normal PrP protein to change shape, causing brain damage. Cannot be treated
• Alzheimers disease
• Type 2 diabetes

Question 23

what is phosphorylation, where can it occur and what does it do

Answer 23

• can occur on the side chains of Ser, Thr and Tyr
• catalysed by kinase enzymes and involves ATP
• addition of the larger charged phosphate to a hydroxyl group induces localised conformation changes in the protein
• These changes affect function e.g., the activation of a catalytic activity

Question 24

phosphorylation of insulin receptor

Answer 24

1. Insulin binds to the extracellular protein subunits of the insulin receptor
2. conformation change that is communicated to the intracellular side protein subunits
3. activates tyrosine kinase domains on the b-subunits
4. Specific Tyr residues are then phosphorylated on the b-subunits which then leads to phosphorylation of ‘insulin receptor substrate’ proteins, which act as second messengers in the cell
5. transfer of GLUT4 glucose transporter proteins to the cell membrane to enable uptake of glucose

Question 25

phosphorylation of Na+/K+ pump

Answer 25

• When the ion pump protein complex is phosphorylated a protein conformation change enables three Na+ to bind and be translocated out of the cell
• When the ion pump is dephosphorylated a protein conformation change enables two K+ to bind and be translocated into the cell
• phosphorylation is achieved as a result of the hydrolysis of a high energy phosphate bond in ATP

Question 26

hydroxylation PTM

Answer 26

• addition of hydroxyl groups to Pro at 3’ and 4’, and Lys at 5’
• Present in collagen to hold skin and muscles together, strengthen bones and stabilise joints
• facilitates H bonding
• the more hydroxylation, the stronger the higher order collagen structure
• enzyme required is hydroxylase and cofactors Fe2+ and vit C

Question 27

10 nonpolar amino acids

Answer 27

1. glycine (Gly)
2. Cysteine (Cys)
3. Proline (Pro)
4. Valine (Val)
5. alanine (Ala)
6. phenylalanine (Phe)
7. leucine (Leu)
8. isoleucine (Ile)
9. tryptophan (Trp)
10. Methionine (Met)

Question 28

5 uncharged polar amino acids

Answer 28

1. serine (Ser)
2. Tyrosine (Tyr)
3. Glutamine (Gln)
4. Asparagine (Asn)
5. Threonine (Thr)

Question 29

2 negatively charged acidic amino acids

Answer 29

1. aspartic acid (Asp)
2. Glutamic acid (Glu)

Question 30

3 positively charged basic amino acids

Answer 30

1. lysine (Lys)
2. Arginine (Arg)
3. histidine (His)

Question 31

supersecondary structure

Answer 31

• combinations of secondary structures
• e.g. helix-turn-helix, greek key
• form domains/motifs
• often have hydrophobic core, hydrophilic on outside

Question 32

fibrinogen structure and function

Answer 32

• made up of 2 alpha, 2 beta and 2 gamma subunits linked by disulfide bonds
• thrombin hydrolyses parts of protein to make fibrin which forms mesh to form clot

Question 33

what does warfarin do

Answer 33

has similar structure to vitamin K so interferes with gamma-carboxylation of blood clotting proteins, causing clotting disorders

Question 34

gamma carboxylation

Answer 34

• leads to formation of gamma-carboxy glutamic acid (Gla)
• uses carboxylase enzyme with vitamin K cofactor

Question 35

gamma carboxylation in blood coagulation pathway

Answer 35

• Glu to Gla leads to formation of bidentate Ca2+ binding sites
• allows blood coagulation proteins to interact with platelets as part of blood clot formation process
• e.g. factor IX, factor X and prothrombin

Question 36

amino acid side chains that can form ionic bonds

Answer 36

Arg, Lys, His, Glu, Asp

Question 37

amino acid side chains that can form hydrogen bonds

Answer 37

Arg, His, Glu, Asp, Thr, Ser, Tyr, Asn, Gln