Proteins 3

Question 1

primary protein structure

Answer 1

sequence of a chain of amino acids

Question 2

secondary protein structure

Answer 2

regular, local arrangement of polypeptide chain

Question 3

tertiary protein structure

Answer 3

complete folding of a single chain

Question 4

quaternary protein structure

Answer 4

association of multiple chains into multi-subunit structures

Question 5

residue

Answer 5

an amino acid in a polypeptide chain

Question 6

no. of peptide bonds in a polypeptide chain

Answer 6

no. of residues - 1

Question 7

features of polypeptides in 3D

Answer 7

• flexible yet conformationally restricted
• peptide bond is essentially planar
• peptide bond is uncharged

Question 8

2 configurations for a planar peptide bond

Answer 8

Trans, Cis

Cis causes steric clashes to arise, so Trans is strongly favoured

Question 9

Alpha helix

Answer 9

This conformation is formed when the polypeptide chain is twisted by the same amount about phi and psi rotation

a helix may be characterized by the number, n, of peptide units per helical turn, by its pitch, p, the distance the helix rises along its axis per turn and by helical rise per repeating unit, d=p/n

Question 10

define a repeat unit

Answer 10

a single turn of the helix

Question 11

what is an alpha helix stabilised by?

Answer 11

hydrogen bonds between the NH and CO groups of the main chain

Question 12

if the helix has a positive value for n

Answer 12

Right-handed helix, anticlockwise

Question 13

if the helix has a negative value for n

Answer 13

Left-handed helix, clockwise

Question 14

helical structures

Answer 14

only one helical polypeptide conformation has simultaneously allowed conformation angles and a favourable hydrogen bonding patter –> the alpha helix

Question 15

the polypeptide made from L-alpha amino acid residues is …

Answer 15

right handed

torsion angles  (phi)= -57
(psi) = -47
n=3.6 residues per turn
p=5.4 Å
d=1.5 Å

Question 16

the polypeptide made from D-alpha amino acids residues is …

Answer 16

left handed

torsion angles
phi = 57
psi = 47
n= -3.6 residues per turn
p=5.4 Å
d=1.5 Å

Question 17

are essentially all alpha helices in proteins right or left-handed?

Answer 17

right handed

Question 18

are alpha helices common in fibrous or globular proteins?

Answer 18

both

the combination of multiple alpha helices by loop and turn can construct large proteins such as Ferrin

Question 19

Beta pleated sheet

Answer 19

composed of two or more polypeptide chains called β strands.

• common structural motifs in proteins
• β strand is almost fully extended. A range of extended structures are sterically allowed

Question 20

antiparallel β sheet

Answer 20

neighbouring hydrogen bonded polypeptide chains run in opposite directions

Question 21

parallel β sheet

Answer 21

hydrogen bonded chains extend in the same direction

Question 22

how do β sheets compare with alpha helices

Answer 22

β sheets are structurally diverse more than α helices

Question 23

what is a dipole moment

Answer 23

the product of magnitude of electronic charge of the molecule and the internuclear distance between the atoms in a molecule

Question 24

which type of secondary structure has dipole moments?

Answer 24

alpha helices have a dipole moment, beta sheets have no dipole moment

Question 25

Types of β turns

Answer 25

two types of β turn:

• Type 1 contains proline residues, occurs more frequently
• Type 2 always have Glycine as 3rd residues

Question 26

features of loops and turns

Answer 26

connect segments of an alpha helix and beta strands

loop structures are often rigid and well-defined

Turns and loops invariably lie on the surfaces of proteins and often participate in interactions between proteins and other molecules

Question 27

techniques used for tertiary structure analysis

Answer 27

• X-ray crystallography
• nuclear magnetic resonance
• cryo-electron microscopic studies

Question 28

how does the properties of amino acids affect where they are found in the tertiary structures if proteins?

Answer 28

hydrophobic amino acids are found on the inside of the the structure

charged (polar) amino acids are found on the protein surface

Question 29

how does the structure of globular proteins compare to fibrous proteins?

Answer 29

Insoluble fibrous proteins, such as those that make up keratin, collagen, and silk, have simple repeating elements of secondary structure

Globular proteins have more complicated tertiary structures, often containing several types of secondary structure in the same polypeptide chain

Question 30

what is the ramachandran plot

Answer 30

a map of sterically allowed values of phi and psi rotations - only 3 regions are physically accessible to a polypeptide chain due to local steric clashes

Question 31

C-N bond

Answer 31

Phi

Question 32

C-C bond

Answer 32

Psi