Proteins

Question 1

Name 3 structures that can occur in tertiary structure of proteins

Answer 1

Folds
Loops
Barrels

Question 2

What is quaternary structure

Answer 2

Subunits

Question 3

What is a zwitterion? What is an example of this?

Answer 3

Overall no net charge, has internal transfer of H+ ion so one end is + charged (NH3+) and one end is - charged (COO-)

Question 4

What happens to an ionised form of amino acid. Which is the acid/base?

Answer 4

NH2- NH3+
COOH- COO-

NH2 base COOH acid

Question 5

What does the properties of proteins mostly depend on in terms of structure of amino acid?

Answer 5

R group

Question 6

How can you characterise R groups of amino acid? Give the two physical properties

Answer 6

Chemical

Physical - Aliphatic, aromatic

Question 7

Whats aliphatic

Answer 7

Non cyclic - straight

Question 8

what does pK value mean, what does a low pK mean

Answer 8

pH at which there is no net overall charge. Low pK=acidic

Question 9

Name 3 basic amino acid residues, name 2 acidic. What makes them basic/acidic a physiological pH?

Answer 9

Lysine, arginine, histidine

Glutamate, Aspartate

The basic ones have + charge, the acidic ones have - charge.

Question 10

What kind of reaction is peptide bond formation? What does the bond form between? Which atoms is the bond between? What is special about the peptide bond?

Answer 10

Condensation reaction - produces H20.

Between amine group NH3+ of one amino acid and carboxyl group COO- of another amino group. Peptide bond forms between C and N. It has resonance so partial double bond characteristics - unable to rotate.

Question 11

Are peptide bonds trans or cis? What does this mean? Why isn’t it the other way?

Answer 11

Trans - alpha carbons are on opposite sides of the chain. Other way can cause steric clashes - repel.

Question 12

What does planar mean? Rigid?

Answer 12

Alpha carbon, C O N H and alpha carbon all lie in same plane. Doesn’t really rotate

Question 13

Whats the Psi Phi exception to rigidity of a peptide bond? Why is there restricted bond angles in proteins?

Answer 13

They can rotate freely. They are the C-N and C-C bonds. Restricted as would get clashes - steric hindrance.

Question 14

Amino acid sequence of a protein determines:

Answer 14

• Way in which a polypeptide folds

- Physical characteristics

Question 15

What is a glycoprotein an example of? What does it contain?

Answer 15

Conjugate protein - something added. Carb group added.

Question 16

What do the angles in the peptide bond determine?

Answer 16

The way in which the protein can fold

Question 17

What does 3.6aa/turn mean? What has this? What is the pitch of alpha helix? How are alpha helices stabilised?

Answer 17

alpha helix has this - means 3.6 residues per turn. Pitch is 0.54nm. Stabilised with H+ bonds

Question 18

Are alpha helices more likely to have small or large R groups? Compared to beta sheets?

Answer 18

Small - e.g. Ala, Leu

Large - e.g. Pro

Question 19

Name 4 properties of B sheets

Answer 19

Fully extended
0.35nm between each amino acid
Stabilised by H+ ions
R groups alternate between sides of the beta sheet.

Question 20

Are beta sheets stronger in parallel or antiparallel?

Answer 20

Antiparallel - better angles of H+ bonds

Question 21

Which two amino acids break helices?

Answer 21

Gly - supports other confirmations

Pro - no rotation around bond so can’t

Question 22

Name 2 things about fibrous protein shape and 2 things about globular protein shape, and their roles in the body

Answer 22

Fibrous -
Single repeating secondary structure
Sheets/strands
Role: protection, shape, support

Globular -
Different types of secondary structure
Compact shape
Role: catalysis, regulation

Question 23

Is collagen, myoglobin, carbonic anhydrase globular or fibrous?

Answer 23

Fibrous, globular, globular

Question 24

Name 4 things about the protein structure of collagen & how they’re arranged

Answer 24

Triple helical arrangement of collagen chains
Gly - X - Y repeating sequence
H+ bond stabilise chains
Fibrils formed from covalently cross-linked collagen molecules

Question 25

What kind of tertiary structures do globular proteins have? Explain them

Answer 25

Motifs - folding patterns containing >1 type of secondary structure Domains - where polypeptide chain forms into distinct regions, with distinct roles.

Question 26

Give an example of a motif

Answer 26

Beta barrel

Question 27

What is protein denaturation? How does this occur?

Answer 27

Loss of quaternary, tertiary, secondary structure - loss of function. By breaking bonds

Question 28

Why would different quaternary structures of proteins be hydrophobic/hydrophillic on outside?

Answer 28

Depending if they need to cross membrane (want to be hydrophobic out outside) Or need to interact with water - hydrophilic outside needed

Question 29

6 bonds/forces/effects involved up to and including tertiary structure?

Answer 29

``` Peptide H+ Van der Waals Disulphide* Ionic Salt bridges Hydrophobic effect ```

Question 30

Where are disulphide bonds formed?

Answer 30

Between cys residues

Question 31

Bonds with which kind of bond are mostly secreted proteins?

Answer 31

Disulphide e.g. ribonuclease

Question 32

What are salt bridges?

Answer 32

Electrostatic interactions between charged groups

Question 33

What is the hydrophobic effect of protein structure?

Answer 33

Interaction between hydrophobic side chains- maintains protein structure

Question 34

What are Van der Waals?

Answer 34

Dipole dipole interactions

Question 35

Most eukaryotic proteins are D or L?

Answer 35

L

Question 36

Which amino acid is does not form stereoisomers?

Answer 36

Glycine

Question 37

What is a hydrophilic molecule? Why is it hydrophilic?

Answer 37

Polar molecule - makes H+ bonds attracted to water

Question 38

Which atoms tend to make H+ bonds and make a molecule hydrophilic?

Answer 38

O N S

Question 39

A protein in the native conformation is what?

Answer 39

Functional protein in fully folded structure

Question 40

3 things that denature proteins

Answer 40

Heat pH Detergents

Question 41

Protein folding is driven by what?

Answer 41

Finding the most stable confirmation

Question 42

What is amyloidosis a form of? How does it happen?

Answer 42

Protein misfolding - insoluble protein causes disease

Question 43

With the following will the protein be protonated or deprotonated: pI 4 < pH 7 pI 10 > pH 7

Answer 43

Deprotonated Protonated