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Flashcards in Proteins Deck (43)
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1
Q

Name 3 structures that can occur in tertiary structure of proteins

A

Folds
Loops
Barrels

2
Q

What is quaternary structure

A

Subunits

3
Q

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

A

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

4
Q

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

A

NH2- NH3+
COOH- COO-

NH2 base COOH acid

5
Q

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

A

R group

6
Q

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

A

Chemical

Physical - Aliphatic, aromatic

7
Q

Whats aliphatic

A

Non cyclic - straight

8
Q

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

A

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

9
Q

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

A

Lysine, arginine, histidine

Glutamate, Aspartate

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

10
Q

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?

A

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.

11
Q

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

A

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

12
Q

What does planar mean? Rigid?

A

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

13
Q

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

A

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

14
Q

Amino acid sequence of a protein determines:

A
  • Way in which a polypeptide folds

- Physical characteristics

15
Q

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

A

Conjugate protein - something added. Carb group added.

16
Q

What do the angles in the peptide bond determine?

A

The way in which the protein can fold

17
Q

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

A

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

18
Q

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

A

Small - e.g. Ala, Leu

Large - e.g. Pro

19
Q

Name 4 properties of B sheets

A

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

20
Q

Are beta sheets stronger in parallel or antiparallel?

A

Antiparallel - better angles of H+ bonds

21
Q

Which two amino acids break helices?

A

Gly - supports other confirmations

Pro - no rotation around bond so can’t

22
Q

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

A

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

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

23
Q

Is collagen, myoglobin, carbonic anhydrase globular or fibrous?

A

Fibrous, globular, globular

24
Q

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

A

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

25
Q

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

A

Motifs - folding patterns containing >1 type of secondary structure

Domains - where polypeptide chain forms into distinct regions, with distinct roles.

26
Q

Give an example of a motif

A

Beta barrel

27
Q

What is protein denaturation? How does this occur?

A

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

28
Q

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

A

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

29
Q

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

A
Peptide
H+
Van der Waals
Disulphide*
Ionic
Salt bridges
Hydrophobic effect
30
Q

Where are disulphide bonds formed?

A

Between cys residues

31
Q

Bonds with which kind of bond are mostly secreted proteins?

A

Disulphide e.g. ribonuclease

32
Q

What are salt bridges?

A

Electrostatic interactions between charged groups

33
Q

What is the hydrophobic effect of protein structure?

A

Interaction between hydrophobic side chains- maintains protein structure

34
Q

What are Van der Waals?

A

Dipole dipole interactions

35
Q

Most eukaryotic proteins are D or L?

A

L

36
Q

Which amino acid is does not form stereoisomers?

A

Glycine

37
Q

What is a hydrophilic molecule? Why is it hydrophilic?

A

Polar molecule - makes H+ bonds attracted to water

38
Q

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

A

O N S

39
Q

A protein in the native conformation is what?

A

Functional protein in fully folded structure

40
Q

3 things that denature proteins

A

Heat
pH
Detergents

41
Q

Protein folding is driven by what?

A

Finding the most stable confirmation

42
Q

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

A

Protein misfolding - insoluble protein causes disease

43
Q

With the following will the protein be protonated or deprotonated:

pI 4 < pH 7
pI 10 > pH 7

A

Deprotonated

Protonated