Protein Structure

Question 1

what is a polyamide

Answer 1

the functional unit of a protein

–CONH–

Question 2

what is an amide group

Answer 2

RCON-

Question 3

properties of a peptide bond

Answer 3

• ability to be polar
• can form H bonds
• can contribute to the proteins ability to fold

Question 4

why/how are proteins highly flexible

Answer 4

bcs each bond is flexible therefore the whole protein is flexible

Question 5

why do proteins fold

Answer 5

the thermodynamics of hydrophobic AA interactions forces them to the core of the protein, away from water -> which gives structural stability

Question 6

3D structure of protein

Answer 6

hydrophobic core and salvation shell
(scotch egg)

Question 7

protein structure hierarchy

Answer 7

primary structure -> amino acid sequence and motifs
secondary -> 3D elements formed from folding of discrete peptide
tertiary -> the overall protein fold and shape

Question 8

what % fold types make up secondary protein structure

Answer 8

alpha helix - 31%
beta sheet - 28%
turns - 30%

Question 9

alpha helix

Answer 9

• most commonly occurring protein secondary structure
• energetically favourable for AA sequence bcs it involved peptide backbone interaction > R groups
• helix is right handed

Question 10

alpha helix hydrogen bonds

Answer 10

H bonds between peptide backbone parts of residues
- R groups not involved
- H bond between backbend carbonyl and every 4th amino acid nitrogen
-3.6 AA per complete turn of the helix

Question 11

beta strand

Answer 11

relys on association with other beta strands for stability
- multiple beta strands form beta sheets
- discovered in the major protein of silk, fibroin

Question 12

parallel and anti parallel beta sheets

Answer 12

inter molecular H bonds between beta strands give beta sheets

Question 13

protein turns and loops

Answer 13

the bits that join helixes and strands together

• defined as not H bonding
• often as few as 3-5 AA linking

Question 14

what is a super secondary structure + example

Answer 14

a small beta sheet that lied across the DNA major groove
- beta strands are hydrogen nodded to one another by peptide backbone interactions
- leaves R groups free to interact w backbone and bases

Question 15

what is a domain

Answer 15

autonomously folding polypeptide chain which provides specific functionality to the structure or function of a protein

Question 16

are domains part of the same or different polypeptides

Answer 16

same

Question 17

what is RecA

Answer 17

DNA repair protein

Question 18

what are protein motifs based on

Answer 18

conserved amino acid sequences that have the same specific function

Question 19

what is a protein motif

Answer 19

a sequence that can be picked out in proteins from diverse organisms
- a part of a folded single domain

Question 20

what does lysine from a salt bridge to

Answer 20

gamma ATP

Question 21

what is a structural motif

Answer 21

an energetically favourable way that proteins fold to do their job

Question 22

what is protein quaternary structure

Answer 22

when proteins come together non covalently

Question 23

what is a dimer

Answer 23

A molecule made of two monomers joined together

Question 24

what is a homo/heterodimer

Answer 24

Homodimer – two of the same molecule join
Heterodimer – two different molecules join