Amino acids and Protein structure

Question 1

Why is the primary structure of the a protein important ?

Answer 1

It defines the structure of a protein which is influential in determining the function of the protein- ie. globular protein or fibrous protein

Question 2

Name 11 functions of proteins.

Answer 2

Structural, Movement, Enzymes & Catalysts , Transport, Membrane Transport, Hormones, Receptors, Defence, Gene Regulation, Chromosome Sorting

Question 3

Comment on direction of polypeptide sequence .

Answer 3

1st aa - NH3 +
last aa - COO- group
There is alternation of R groups up and down the plane with each residue in the polypeptide chain

Question 4

What is meant by a peptide bond?

Answer 4

The C — N bonds between the carboxyl group of one amino acid and amino group of another amino acid.
It is shorter than expected:
Rigid
No rotation
Nearly always has trans arrangements of groups

Question 5

Name other covenant linkages between polypeptides

Answer 5

Disulfide Bridges
Glycosylation
Phosphorylation
Methylation

Question 6

Describe what is meant by Disulifide bridges

Answer 6

Covelant bonds derived by two thiol groups ( in Cys subunits)
Can be intramolecular and intermolecular

Question 7

Describe what is meant by Glycosylation

Answer 7

Adding a sugar element to a protein- can either be 
O linked ( OH of thr and ser) OR N linked ( NH2 of asn)

Question 8

Describe what is meant by Methylation?

Answer 8

Adding on of a methyl group via the NH2 group of lys or arg eg. histones affecting gene expression

Question 9

Explain what is meant by primary structure?

Answer 9

The specific sequence of amino acid in a polypeptide chain

Question 10

Explain what is meant by secondary structure?

Answer 10

The folding of polypeptide chain- eg. alpha helix and beta pleated sheet

Question 11

Explain what is meant by tertiary structure?

Answer 11

Relating to the 3D structure of the protein

How the whole polypeptide folds upon itself

Question 12

Explain what is meant by quaternary structure?

Answer 12

How the folded polypeptides chains interact and join together- hoe the whole functional protein is formed in 3D

Question 13

Describe the structure alpha helix

Answer 13

Formed due to H bonds forming between the peptide bond carbonyl O and the H of the N - H of every 4th peptide bond- INTRAMOLECULAR

Said to be the max stabilisation energy due to 3-6 turns

Has rigid cylindrical shape- is said to act as a support for the protein.

R groups are on the outside and Right handed helix

Question 14

Describe the structure of beta pleated sheet

Answer 14

H bonds hold strands together in a Beta sheet
R groups can be up/down the plane

Proteins with high % of beta sheet are fibrillar proteins
and high tensile strength.

Question 15

What are the two types of beta pleated sheet?

Answer 15

antiparalel or paralel

Question 16

Describe the collagen triple structure

Answer 16

Ideal for structural proteins-
three chains- with hydrogen bonds every 3 residues which form intermolecularly between the chains-

optimal state- Gly - X - Y - Gly - X - Y
X= proline mainly
Y=mainly hydroxyproline

Question 17

What is a super-secondary structure?

Answer 17

when alpha helix and beta pleated sheets form common domains found in domains.
e.g. Beta barrel
Beta sandwich
Rossman fold

Question 18

What is meant by phosphorylation?

Answer 18

The adding of phosphate ( big negative group) to a molecule. The structure of the molecule changes which means that the function changes.

e.g cell signal transduction- phosphorylation of Tyr in insulin receptor
changes activity of enzyme - phosphorylation of GP in response to glucagon- activating the enzyme- increasing production of glucose. - glycogenolysis

Question 19

What are the forces that stabilise protein structure?

Answer 19

Covalent (DBS) and Non covalent ( H bonds, electrostatic interactions, VdW forces and hydrophobic interactions)

Question 20

Explain what is meant by Hydrogen Bonding?

Answer 20

2 d- atoms compete for the same H atom- A hydrogen bond is a partially electrostatic attraction between a hydrogen (H) which is bound to a more electronegative atom such as nitrogen (N), oxygen (O), or fluorine (F), and another adjacent atom bearing a lone pair of electrons.

H-Bond Donators:

O eg O-H
N eg N-H

H-Bond Acceptor”

O eg carbonyl c=O

Question 21

Explain what is meant by Electrostatic interactions

Answer 21

The interactions present between charged side chains

eg. physiological pH

Asp, Glu COOH —> COO- (ionised)
Lys, Arg NH2 —> NH3+ (ionised)

Question 22

Explain what is meant by VdW forces?

Answer 22

The sum of attractive forces between molecules

This is due to the fact there is dipole effect from the momentary unequal distribution of electrons

Question 23

Explain what is meant by Hydrophobic effect

Answer 23

when proteins are in aqueous environment- hydrophobic regions of the protein fold in such a way that they minimise contact with aqueous environment- these regions do not form H bonds

Question 24

What conditions are proteins sensitive to?

Answer 24

pH- due to fact that electrostatic and H bonding is affected- changing the structure.
Temperature- breaks the non-covenant bonds which changes the structure
Ionic strength

Question 25

Comment on protein pathway

Answer 25

there are one thousand possible structures - only one functional - the amino acid sequence codes for the final structure AND the pathway

Question 26

When can there be misfiled proteins?

Answer 26

Mutations can cause a proteintofoldincorrectly – Sickle cell disease Glu→Val (charged to hydrophobic)
stablising the polymerization of HbS

Formation of stable aggregations of protiens
– amyloid proteins forming plaques in Alzheimer’s Disease – prion protein polymerisation in Creutzfeldt-Jakob Disease