Higher order structure(AA, peptides, proteins)

Question 1

How are beta strands different to alpha strands along the polypeptide backbone?

Answer 1

In beta strands the amino acids zig-zag along the polypeptide backbone whereas AA in alpha helix they sprial.

Question 2

Describe the conformation of the beta conformation in the beta sheet?

Answer 2

• In a b-sheet, carbonyl oxygens and amides form hydrogen bonds.
• These secondary structures can be either antiparallel (as shown) or parallel and need not be planar (like here) but can be twisted.
• The propensity of a peptide for forming b-sheet also depends on its sequence.

Question 3

how do you correct strands in antiparallel sheets?

Answer 3

beta turns

Question 4

How do you connect strands in all parallel sheets?

Answer 4

Loops

Question 5

How does a beta turn work?

Answer 5

It allows the protein backbone to make abrupt turns, the propensity for forming b-turns depends on its sequence.

Question 6

How is an amyloid fibril formed?

Answer 6

Abnormal prion proteins propagate and aggregate to form amyloid fibrils which leads to amyloid disease

Question 7

Give an example of a protein with mostly beta sheet stucture?

Answer 7

Immunoglobin

Question 8

What is the secondary stucture of a protein defined by?

Answer 8

The peptide backbone repeated structure.

It comprises regions of alpha helical structures, beta sheet structures as well as bends and turns in the shape.

Question 9

When a polypeptide chain has a folded conformation and in aqueous environment what can for between the water and polar side chains?

Answer 9

Hydrogen bonds

Question 10

Aqueous vs non aqueous environment for membrane protein hydrophobic and hydrophilic components

Answer 10

non aqueous= hydrophobic components internalised and buried.

Aqueous= folding rules reversed and hydrophobic components face outwards.

Question 11

What are the 3 “special amino acids” that can have “special” influence on tertiary stucture?

Answer 11

Cysteine(Cys, C)
Glycine(Gly, G)
Proline(Pro, P)

Question 12

How does the special AA Glycine affect tertiary structure?

Answer 12

Small side chain- a single H.
Non-chiral
Allows for very tight turns in a polypeptide chain making it looser too.

**PROVIDES HINGE to allow protein stuctures and domains to change orientation relative to each other

Question 13

Which amino acid will be rich in a hinge region of a polypeptide chain?

Answer 13

Gly rich
(glycine)

Question 14

How does the special AA Proline affect tertiary structure?

Answer 14

Very rigid, opposite to the flexibility of glycine.

Side chain is incorporated that is quite bulky.

**LIMITS FLEXIBILITY due to side chain and rigid nature.

Produces a more open helix.

Question 15

How does the special AA Cysteine affect tertiary structure?

Answer 15

Ability to cross-link to other cys residues.
Happens under oxidising conditions.

Cross links INCREASE PROTEIN STABILITY.

Common in extracellular proteins, absent in cytoplasmic proteins.

Question 16

How does a ‘heptad’ 7 residue motif help polypeptide chains in aqueous environments?

Answer 16

Means that the helices wrap around each other to minimise exposure of hydrophobic amino acid side chains to aqueous environment. Increased stability of the coiled coil.

Question 17

What are the characteristics of alpha helix, cross linked by disulfide bonds?

Answer 17

Tough, insoluble protective structures of varying hardness and flexibility.

Question 18

Give an example of an alpha helix structure?

Answer 18

a-keratin of hair and nails.

Question 19

What are the characteristics of beta conformation?

Answer 19

Soft and flexible filaments

Question 20

Give an example of beta conformation?

Answer 20

Silk fibroin

Question 21

Give the characteristics of collagen triple helix?

Answer 21

High tensile strength, without stretch

Question 22

How do vertebrates fight infections with soluble antibodies that specifically bind antigens?

Answer 22

The soluble antibodies are stimulated from antigens.

They coat proteins of bacteria and viruses.
They surface carbohydrates of cells or viruses to help identification of foreign content.

Question 23

Give an example of occurrence for the collagen triple helix?

Answer 23

Collagen of tendons, bone matrix.

Question 24

What is an epitope?

Answer 24

A small region of an antigen.
(Commonly binded to by an antibody)

Question 25

Describe the structure of immunoglobulin G…?

Answer 25

Two heavy chains and two light chains.

Composed of constant domains and variable domains.

Question 26

What is a protein domain?

Answer 26

independently folded units of tertiary structure along a polypetide chain

C= constant
V=Variable

Question 27

How many variable domains does an antigen binding site require?

Answer 27

2 variable domains per antibody, making it hypervariable. Confers antigen specificity.

Question 28

What domains are in a light chain?

Answer 28

One constant and one variable domain

Question 29

What domains are in a heavy chain?

Answer 29

Three constant and 1 variable domain.

Question 30

Give a few factors that help to activate a protein aside from simple folding and assembly of its component polypeptides?

Answer 30

Covalent modification:

• Side chains
• Attachment of macromolecules
• Proteolytic activation
• Crosslinkling

Non-covalent binding of prosthetic groups:

• Functional groups
• Activation signals