protein structure- week 2

Question 1

What is the secondary structure of a protein?

Answer 1

spatial arrangement of amino acids near to each other in the linear sequence

Question 2

Why are there proteins and hydrogen bonding?

Answer 2

due to polar backbone

Question 3

How can peptides in the backbone rotate and why?

Answer 3

• rotation possible around non-peptide bonds in chain
• because of steric hinderance only 2 angles possible

Question 4

Who and what was proposed 1952?

Answer 4

• pauling and Corey
• idea that proteins could fold into regular repeating units: alpha helix and beta pleated sheet

Question 5

How is the alpha helix formed?

Answer 5

• by H-bonds in same polypeptide chain (backbone not side chains)
• H-bonds formed between peptide bond carbonyl-O and H of N-H every 4th peptide
• regular right-handed helix
• stabilised by H-bonds
• R group on the outside
• rigid cylinder shape, acts as architectural support for protein

Question 6

What is the structure of the alpha helix?

Answer 6

• structure is a regular tight coil
• stabilised by H-bonds between NH and CO groups 4 residues apart in backbone
• 100 degree rotation fo one residue to next
• 3.6 residues per turn
• 1.5 A rise between residues
• coil diameter of ca. 5A

Question 7

What forms can an alpha helix have?

Answer 7

• right and left handed helices possible, RH more energetically favourable

Question 8

Why are RH alpha helices more favourable?

Answer 8

there re fewer steric clashes between the side chains and the main chain

Question 9

In an aloha helix residue which amino acids are very close ?

Answer 9

4 aa apart are spatially very close

Question 10

How much percent of haemoglobin is an alpha helix?

Answer 10

60%

Question 11

What is missing when a peptide linkage includes proline? What’s the consequence?

Answer 11

no H atom bound to nitrogen
- H is not available for hydrogen bond
- structure restricts rotation
- ends alpha helix

Question 12

What stabilises an alpha helix?

Answer 12

hydrogen bonds between NH and CO groups

Question 13

Describe the beta pleated sheet

Answer 13

-consists of 2 or more strands of polypeptide Calle beta strands
- consists of 2 or more strands or polypeptide (beta strands)
- H bonds between adjacent strands stabilise structure

Question 14

What is the difference between alpha helix residues and beta sheets?

Answer 14

in beta sheets the residues are almost fully extended

Question 15

What two forms of beta pleated sheets are there?

Answer 15

antiparallel and parallel

Question 16

What does the antiparallel beta sheet look like?

Answer 16

beta hairpin bend
- widespread in globular proteins

Question 17

What does the parallel beta sheet look like?

Answer 17

arrows point to C terminus

Question 18

What version of the beta pleated sheet is more stable?

Answer 18

anti-parallel, as h bonding is not distorted

Question 19

What is the distance between the adjacent residues in a beta pleated sheet?

Answer 19

around 3.5 A

Question 20

What is the position of the side chains in a beta pleated sheet?

Answer 20

alternate above and below plane of strand

Question 21

Give an example of proteins with beta pleated sheet

Answer 21

transmembrane proteins eg. porin

Question 22

Describe the structure of a beta pleated sheet

Answer 22

• made up of 5 strands, but can also be up to 10
• can be anti-parallel, parallel or a mixture of both

Question 23

Name proteins with a high percentage of beta sheets

Answer 23

-fibrillar proteins - silk fibres
- has high tensile strength but no elasticity

Question 24

What is the tertiary structure of a protein?

Answer 24

spatial arrangement of amino acids, usually far apart form each other in the primary sequence

Question 25

What is myoglobin?

Answer 25

• oxygen and iron binding protein found in muscles
• single polypeptide chain
• exist in unique 3D conformation

Question 26

What happens to the position of residues in 3D structures?

Answer 26

residues that are far apart in amino acid sequence are located close together

Question 27

what is the quaternary structure of a protein?

Answer 27

spatial arrangement in a protein made up form more than one polypeptide chain

Question 28

What is a subunit in the quaternary structure?

Answer 28

a poly peptide chain in a protein
- can be homo or hetero

Question 29

name a protein with a quaternary structure

Answer 29

Haemoglobin
- tetrameric protein with 2 identical alpha subunits and 2 identical beta subunits
alpha2beta2 configuration

Question 30

What is haemoglobin configuration?

Answer 30

alpha2beta2 configuration

Question 31

What does the quaternary structure allow for?

Answer 31

• smaller quantities of generic material to create large proteins and structures
• cooperative regulation of enzymes

Question 32

Describe the structure of the human rhinovirus (causes common cold)

Answer 32

uses 60 repeats of 4 unit structure ti produce its coat

Question 33

what is the allosteric effect?

Answer 33

• causes cooperative regulation of enzymes
• change in one subunit induces a change in another