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Biochemistry and molecular science > Module 2 > Flashcards

Module 2 Flashcards

protein structures

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1
Q

What forces drive protein folding

A

Electrostatic forces, van der Walls interactions, hydrogen bonds, hydrophobic interactions

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2
Q

How do you help protein refold properly

A

adding a trace of beta ME. beta-mercaptoethanol to reduce srcambled disulfides

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3
Q

Does disulfide bonds direct folding

A

No, folding directs disulphide bond formation

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4
Q

What do disulfide bonds do

A

increase relative stability of the folded state over the unfolded states

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5
Q

Why does the condition in the call make the folding slow or impossible

A

Molecular crowding

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6
Q

What does chaperones do

A

they help to avoid misfolding but does not fold proteins

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7
Q

what does Ionic interactions between oppositely charged groups in proteins are called

A

salt bridges, Charges tend to be distributed over several atoms, component due to electrostatic interactions and hydrgen bonding

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8
Q

Arrange N,C,S,H,O from most electronegative to leave electronegative

A

O>N>C>S>H

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9
Q

What is the optimal distance between two particle

A

~3 angstrom

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10
Q

What is the distance for 1 Å

A

0.1 nm

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11
Q

What drives protein folding

A

Negative gibbs free energy, G = H-TS

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12
Q

Why are some phi and psi combination unfavourable

A

steric crowding

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13
Q

Why are some phi and psi combination favourable

A

because of the chance to form favorable H-bonding interactions along the backbone

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14
Q

what are the region of the ramachandran plot

A

beta L

alpha D

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15
Q

What are the distance for VDW and hydrogen bonding

A

2.7 angstrom and 1.9 angstrom

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16
Q

Beta sheets hydrogen bonding sequence

A

NH residue i to C=O residue j

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17
Q

alpha-helix hydrogen bonding sequence and its angle

A

NH residue i to C=O residue i-4 (phi, psi, -57, -47

18
Q

Reverse turns hydrogen bonding sequence

A

NH residue i+3 to C=O residue i

19
Q

Where are the non-polar aa placed in a alpha helix

A

heptad repeat, 1st - 4th, a-d

20
Q

Which hydrophobic residues are strong helix formers

A

Ala and Leu

21
Q

Which aa are helix breakers and why?

A

Pro because it lacks NH hydrogen bond donor, Gly because the tiny R group don’t contribute to stability of helix

22
Q

phi and psi angles of beta sheets

A

-130, +130

23
Q

What are the reverse turns position for proline and glycine

A

Pro in position 2(i+1), Gly in position 3(i+2)

24
Q

what are tertiary structures

A

Fold, modules, domains and arrangement of domains(in a single subunit)

25
Q

What are quarternary structures?

A

arrangement of two or more protein subunits

26
Q

What is a domain

A

an existence independant of the rest of the protein( fold independantly)

27
Q

`What is a fold?

A

arrangement of secondary stucture elements relative to each other in space

28
Q

What is a module?

A

Have one or more repeating fold within the overall structure

29
Q

What is intragenic mutation

A

point mutations, insertions and deletions

30
Q

What is gene duplication

A

whole or part of a genome is duplicated

31
Q

what is DNA segment shuffle

A

two or more existing genes can be broken and recombined

32
Q

What is gene lateral transfer

A

one organism acquires parts of the genome of another

33
Q

Why are domain defined as an evolutionary unit

A

New proteins are evolved by gene duplication annd domain shuffing, no new domains are created

34
Q

What does identical mean

A

exactly the same residue

35
Q

What does similar mean

A

residues with similar physical chemical properties

36
Q

What are honologues

A

2 sequence that shows >25% identity

37
Q

What are orthologue

A

Homologous proteins that perform the same function in different species

38
Q

What are paralogue

A

Homologous protein that perform different but related functions within one organism (eg. human trypsin, compared with human thrombin)

39
Q

Does structure change slower than sequence?

A

yes

40
Q

Does different parts of the protein mutate at different rates

A

yes

41
Q

What are chymotrypsin(digestion) and thrombin(blood clotting)?

A

Paralogues

Biochemistry and molecular science (12 decks)

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