lecture 5 - elements of protein structure

Question 1

In what direction are amino acid residues named/numbered?

Answer 1

Left to right, from the amino terminus to the carboxyl terminus

Question 2

What does globular mean, in terms of protein shape?

Answer 2

The main chain folds and doubles back to form a compact shape

Question 3

What are the 4 levels of protein structure?

Answer 3

Primary, Secondary, Tertiary, Quaternary

Question 4

What is the name of the angle between the amino nitrogen and alpha carbon in a polypeptide?

Answer 4

Phi - Φ

Question 5

Phi (Φ) is the angle between which two atoms in a polypeptide chain?

Answer 5

Amino nitrogen and alpha carbon

Question 6

What is the name of the angle between the carboxyl carbon and alpha carbon in a polypeptide?

Answer 6

Psi (Ψ)

Question 7

Psi (Ψ) is the angle between which two atoms in a polypeptide chain?

Answer 7

The carboxyl carbon and the alpha carbon

Question 8

What is the name of the angle between the carboxyl carbon and the Nitrogen of the adjacent amino acid (AKA the peptide bond) in a polypeptide?

Answer 8

omega (ω)

Question 9

Omega (ω) is the angle of which bond in a polypeptide?

Answer 9

The peptide bond (between carboxyl carbon and amino nitrogen of adjacent amino acids)

Question 10

Why are the angles of phi and psi restricted in a polypeptide?

Answer 10

Due to steric hindrance experienced by the amino acids which usually sit in a trans configuration.

Question 11

What collisions can the phi bond rotation lead to?

Answer 11

O-O collisions

Question 12

What collisions can the psi bond rotation lead to?

Answer 12

NH-NH collisions

Question 13

What is the range of phi and psi angles?

Answer 13

-180 degrees to +180 degrees

Question 14

What is the angle of omega in a trans peptide bond?

Answer 14

+180 degrees

Question 15

What is the angle of omega in a cis peptide bond?

Answer 15

0 degrees

Question 16

Why are cis bonds infavourable in peptide bonds?

Answer 16

There is steric crowding of the R side chains on one side of the bond, leading to collisions

Question 17

What are the 2 key structures in secondary protein structure?

Answer 17

Beta-strands/sheets and alpha helices

Question 18

Is an alpha helix a left or right handed ‘spiral’?

Answer 18

Right-handed

Question 19

What type of bonds stabilise alpha helices?

Answer 19

Hydrogen bonds

Question 20

What atoms are involved in the hydrogen bonds in an alpha helix?

Answer 20

The carbonyl oxygen of one peptide bond with the hydrogen attached to the nitrogen of another peptide bond

Question 21

How far apart are the amino acid residues that are involved with hydrogen bonds with each other in alpha helix?

Answer 21

4 residues apart (n bonds with n+4)

Question 22

How many residues are there per turn in an alpha helix?

Answer 22

3.6

Question 23

Do the side chains point outwards or inwards in an alpha helix?

Answer 23

Out wards

Question 24

What types of amino acids will break an alpha helix?

Answer 24

Glycine and proline (non-polar side chains)

Question 25

What is the direction on an alpha helix dipole?

Answer 25

positive at N terminus and negative at C terminus

Question 26

What is the degree of separation of the side chains in an alpha helix, and why?

Answer 26

100 degrees - There are 3.6 residues per 360 degrees.

Question 27

How many Beta strands are in a typical Beta sheet?

Answer 27

2-10

Question 28

How is hydrogen bonding involved in Beta strands/sheets?

Answer 28

Hydrogen bonds link adjacent strands to form a sheet

Question 29

What is the typical number of residues in a Beta strand?

Answer 29

6 resides long, can have up to 15

Question 30

What are the 2 types of Beta sheet?

Answer 30

Parallel and anti-parallel

Question 31

What are parallel Beta sheets?

Answer 31

Sheets where the individual beta strands are in the same direction (N and C termini are at the same end)

Question 32

What are anti-parallel Beta sheets?

Answer 32

Sheets where the individual beta strands are in the opposite direction (N and C termini are at opposite alternating ends)

Question 33

What is the shape of hydrogen bonds in a parallel beta sheet?

Answer 33

V-shaped

Question 34

What is the shape of hydrogen bonds in an anti-parallel beta sheet?

Answer 34

Linear

Question 35

What is the overall shape of an extended Beta sheet?

Answer 35

Pleated

Question 36

Do pleated Beta sheets have a left or right handed twist?

Answer 36

Right handed

Question 37

Where do side chains point in a pleated Beta sheet?

Answer 37

Above and below the sheet

Question 38

What pattern/sequence of amino acid residues commonly form Beta strands?

Answer 38

Alternating polar and non-polar residues

Question 39

What is the most stable type of Beta sheet?

Answer 39

Antiparallel, due to its linear hydrogen bonds

Question 40

What are turns required to form?

Answer 40

Globules

Question 41

How many residues are typically involved in a hair pin-like turn?

Answer 41

3 or 4

Question 42

What amino acids are commonly involved in turns?

Answer 42

Glycine and proline (non-polar side chains)

Question 43

What type of bonds stabilise turns?

Answer 43

Hydrogen bonds

Question 44

What type of diagram represents protein structure as ‘ribbon-like’?

Answer 44

Richardson diagram