module 4

Question 1

Peptide bond Mainchain

Answer 1

• Discard charges between amino and carboxyl groups
• Loss of a H2O molecule
• Mainchain will always be in NCCNCC

Question 2

Partial Double Bonds
hint: cis or trans

Answer 2

• Resonance in partial double bonds
• Most likely trans
  Cis causes steric interference (Can’t occupy same space at same time)

Question 3

What are polypeptides?

Answer 3

The long chain of amino acids

Question 4

Primary Protein structure

Answer 4

Linear sequence of amino acids (polypeptide)

Question 5

Secondary Protein Structure

Answer 5

Localized interactions within a polypeptide
- Formation of H bonds
- Lonic interactions
- Vander wal Interactions

Question 6

Tertiary Protein Structure

Answer 6

The final folding pattern of a polypeptide

Question 7

Quaternary Protein Structure

Answer 7

Multiple foldings of polypeptides involved

Question 8

How is Primary Structure presented hint: n-c

Answer 8

It starts from the amino side and ends at the carboxyl

Question 9

2 Forms of Secondary Sturcture

Answer 9

alpha helix and beta sheets

Question 10

Secondary Structure doner acceptor

Answer 10

Polypeptides in the secondary structure must have equal amounts of donor and acceptor

Question 11

Degree of Rotation In Polypeptide

Answer 11

Phi Ca-N
Psi Ca-C

Question 12

Alpha Helix

Answer 12

• Right-handed turn with 3.6 residues/ turn
• Stabilized by hydrogen bonds

Question 13

Amino acid restrictions that won’t allow it to form a helix

Answer 13

Proline - too rigid
Glycine - too flexiblele
Side chain Val, Thr, Ile
Ser, Asp, Asn
Charged residues tend to be positioned to form favourable ion pairs

Question 14

A helix dipole

Answer 14

N terminus has positive dipole
stabilized by (Asp, Glu) negative dipole

C terminus has negative dipole
stabilized by (Lys, Arg, His) at positive dipole

Question 15

Amphipathic Helices

Answer 15

Page 19
one side polar
other side non-polar

Question 16

Beta Sheets

Answer 16

Beta sheets involve multiple beta strands side by side
- made up of 4-5 strands

Question 17

Parallel and Anti Parallel beta-sheets

Answer 17

Parallel goes the same direction
Anti-parallel goes the opposite direction
antiparallel is better for geometry

Question 18

Tertiary Structure keys

Answer 18

Natural shape for polypeptides
arrangement of amino acids determines the function
different amounts of ahelix and bsheets
amino acids in a polypeptide that are far may be close when folded

Question 19

Protein folding
hint: funnel

Answer 19

big funnel that a large number of unstable conformations collapse into a single stable folding pattern

Question 20

Protein facts
Joined by which type of forces?

Answer 20

Non-covalent forces are the most important forces stabilizing protein structure

Question 21

Keratin

Answer 21

7 letters repeating
abcdefg
a and d are hydrophobic so they will latch on to their hydrophobic parts form coiled coils
Forms alpha helix

Question 22

Keratin Post-translational stabilization

Answer 22

Linked by disulfide bonds (covalent linkages)

Question 23

Collagen

Answer 23

Collagen repeats Gly-Pro-Y
Forms left-handed helix that has 3 residues per turn
3 helices come together to form coiled coiled (proline outside)
Glycine inside)

Question 24

Collagen Post-translational Modifications

Answer 24

Linkages undergo hydroxyproline and hydroxylysine
as they age they get stronger
needs vitamin C

Question 25

Vitamin C and Cancer

Answer 25

your body produces a free radicle which goes and kills cancer if too much vitamin C is consumed your body will stop producing those free radicles

Question 26

Slik structure and strength

Answer 26

Primary structure of GSGAGA

Fully extended polypeptides

Hydrogen bonding strands

hydrophobic and van der waals

Question 27

Prions

Answer 27

When a protein misfolds a new region is exposed for antibody binding
Antibodies target these misfolded parts