Lecture 7 DA

Question 1

What determines the function of a protein?

Answer 1

Its structure.

Question 2

What determines the conformation of a protein’s active site?

Answer 2

The conformation of the side chains of the protein’s non-active site regions.

Question 3

Are non-active site region residues crucial to a protein’s function?

Answer 3

Yes, because they help correctly form the active site.

Question 4

What are the aliphatic/polar amino acids?

Answer 4

Glycine
Alanine
Valine
Leucine
Methionine
Isoleucine

Question 5

Where are aliphatic/polar amino acids generally found, and why?

Answer 5

Typically inside the protein, usually not on the surface. Stabilises the protein’s structure by hydrophobic interactions, reducing free energy.

Question 6

What are the aromatic amino acids? Which are hydrophobic/polar/non-polar?

Answer 6

Tyrosine - polar
Tryptophan - non-polar
Phenylalanine - very hydrophobic

Question 7

Which amino acids strongly absorb UV light?

Answer 7

Aromatic

Question 8

What are the polar/hydrophilic amino acids?

Answer 8

Serine
Threonine
Cysteine
Proline
Asparagine
Glutamine

Question 9

Where are polar/hydrophilic amino acids typically found?

Answer 9

On the surface.

Question 10

Which amino acid is the only one able to form disulphide bridges?

Answer 10

Cysteine

Question 11

What are the acidic amino acids? What charge do they have?

Answer 11

Aspartate
Glutamate
Both negative

Question 12

What are the basic amino acids? What charge do they have?

Answer 12

Lysine
Asparagine
Histidine
All positive

Question 13

Do peptide bonds have any degrees of freedom, or are they rigid? Do they contribute to 3D structure?

Answer 13

They are planar, with no degrees of freedom. Doesnt contribute to 3D structure, the phi and psi angles do.

Question 14

Do all proteins form secondary structures?

Answer 14

Most, but not all.

Question 15

What bonds are responsible for hydrogen bonds?

Answer 15

Hydrogen

Question 16

Can the secondary structure of proteins be predicted by the primary structure?

Answer 16

Some regions, but not all.

Question 17

What is the central paradigm?

Answer 17

Amino acid sequence of a protein determines its structure and function.

Question 18

How can we tell if the primary sequence determines structure?

Answer 18

Protein can be denatured in urea, then allowed to renature. Some, but not all of the proteins will fold to its native state again.

Question 19

What are three approaches to determining the structure-function relationship of a protein?

Answer 19

Predictive
Experimental
Protein peptide arrays - synthetic/expressed

Question 20

What are two methods in the predictive approach to determining the structure-function relationship of a protein?

Answer 20

Sequence analysis

Modelling

Question 21

What are two methods in the experimental approach to determining the structure-function relationship of a protein?

Answer 21

Site directed mutagenesis

Synthetic peptide analogues

Question 22

What is looked for in a new protein sequence when determining function?

Answer 22

• Similar sequences (ie. BLAST)
• Distinctive patterns or domains with associated functions
• Secondary/tertiary structure predictions
• Motifs/residues important for function
• Physical properties - MW, pI, solubility etc

Question 23

Describe the levels of protein structure/function relationship (6).

Answer 23

Superfamily
Family
Domain
Motif
Site
Residue

Question 24

Which levels of the protein structure/function relationship is associated with the secondary structure (3)?

Answer 24

Superfamily, family, and domain

Question 25

What are some examples of protein structure from motifs or regions (3+)?

Answer 25

• Active sites
• Loops
• Interior of the protein
• Others include hydrophobicity, transmembrane regiosn, glycosylation sites, localisation signals, GPI anchors etc

Question 26

What are the limitations of predicting protein structure/function by sequence analysis (2)?

Answer 26

• Doesn’t account for post-translational modifications such as glycosylation.
• pI calculations - assumes all side chains are accessible, but theyre not.

Question 27

What are predictions of secondary structures based on (3)?

Answer 27

Statistical analysis
Physical properties
Amino acid distribution in known structures

Question 28

How accurate are predictions of secondary structures?

Answer 28

Not very accurate, 55-65%

Newer methods are 70% accurate, still not enough.

Question 29

How can predictions of secondary structures be improved?

Answer 29

Can incorporate information from multiple sequence alignments.

Question 30

What is the best approach to predicting secondary structures?

Answer 30

Use a number of algorithms, and develop a consensus analysis.

Question 31

Describe hydropathy analysis, and its use.

Answer 31

Sliding window analysis of a protein structure, to determine hydrophobic/philic regions.
Used to identify transmembrane sequences.

Question 32

What do antigenicity algorithms predict, and what do they use to do so (4)?

Answer 32

Algorithms predict antibody epitopes, using hydrophilicity, side chain flexibility, surface probability, and predicted B-turns.

Question 33

When determining domains and motifs, what can be detected (5+)?

Answer 33

• Post-translational modifications
• Domains
• Repeats
• DNA/RNA associated proteins
• Proteolytic cleavage sites
• Enzymes/transport/receptor proteins etc

Question 34

What is a motif?

Answer 34

Small, highly conserved regions, shown as regular expressions.

Question 35

Give an example of motif nomenclature.

Answer 35

[AG] x V x(2) {YW}
[] - means any amino acids in the bracket
x means any amino acid
V means only valine
x() means any amino acid by the number in the bracket
{} any amino acid except whats in the bracket

Question 36

What do most proteins require for secretion? What happens to it? What is this entire process called?

Answer 36

Most have a signal peptide of 30-50 amino acids long. Cleaved off during secretion. Process called classical secretion.

Question 37

Can classical secretion be predicted?

Answer 37

Yes.

Question 38

Regarding chemical synthesis of proteins, what can be made (4)?

Answer 38

Proteins/peptides, which can be novel, toxic, or ones difficult to secrete, as well as hybrids.

Question 39

What can chemically synthesised proteins be used for?

Answer 39

Epitope mapping.

Question 40

Describe epitope mapping.

Answer 40

b