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MCB 2020 > 1.2 Protein structure > Flashcards

1.2 Protein structure Flashcards

1
Q

Considering lysozyme where are different residues found?

A
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2
Q

Comparing glycine and proline amino acids where are these residues likely to be found in a folded polypeptide?

A
  • Glycine tend to be at the top of the turns
  • Its flexible as it has no side chains so it accomodates where the backbone needs to turn
  • The proline backbone is fixed on the side chain with restricted geometry, but also found in turns less frequently than glycine though
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3
Q

Fill in the blanks

A
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4
Q

Name the four forces that drive protein folding

A

Electrostatic forces

Van der Waals interactions

Hydrogen bonds

Hydrophobic interactions

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5
Q

What are the terms for the folded and unfolded state?

A

Folded state is called the native state

Unfolded state is said to be denatured

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6
Q

What is meant by the term protein folding is ‘co-operative’?

A

If any part of a protein fold is disrupted then interactions with the rest of the protein structure are disrupted and the remainder of the structure will be lost.

Half the molecules are folded and half are unfolded, no such thing as a protein that is half isolated

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7
Q

Explain the experiment that shows protein folding

A
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8
Q

In the protein refolding experiment what showed the role of disulfide bridges in dictating protein structure?

A

If you had the denatured reduced ribonuclease and you removed B-mercaptoethanol first then urea, you would get disulfide bonds reformed but not the right ones so the rest of the protein could not refold.

  • Disulfide bonds increase the relative stability of the folded state over the unfolded state
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9
Q

How can conditions within the cell hinder protein folding?

A
  • Cells are highly concentration solutiosn of proteins/nucleid acids/sugar/lipids
  • Inappropriate interactions may occur with other molecules before the protein can fold
  • Nascent polypeptide may misfold as it comes off the ribosome
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10
Q

What is the role of chaperones in protein folding?

A
  • Chaperones help avoid misfolding by binding to unfolded/partially folded polypeptides and protecting them from misfolding
  • Especially exposed hydrophobic regions so they do not have inappropriate interactions
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11
Q

Fill in the blanks about these protein interactions

A
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12
Q

Explain the graph of van der waals interactions

A
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13
Q

What is the geometry of a hydrogen bond?

A

THe most favourable geometry has D-H …. A collinear

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14
Q

Why do proteins fold if all these interactions are not favourable as comparable competing interactions are possible with water?

A
  • Proteins also contain nonpolar groups
  • Water is a poor solvent for non polar groups compared with organic solvents
  • Non polar groups cannot form hydrogen bond networks
  • Non polar groups prefer to interact with other non polar groups

This process is driven by entropy

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15
Q

What is the hydrophobic effect?

A

Removal of hydrophobic side chains from water which releases ordered water from hydrophobic side chains.

More favourable, higher entropy

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16
Q

Name axis of ramachandran plot

A
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17
Q

Why are some phi and psi combinations more or less favourable?

A
  • Some unfavourable because of steric crowding of backbone atoms with other atoms in the backbone or side chains
  • Some more favourable because of the chance to form H bonding interactions along the backbone
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18
Q

Label the regions of the ramachandran plot

A
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19
Q

Label these general regions on the ramachandran plot

A
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20
Q

What is the secondary structure defined as?

A

Secondary structure refers to a local spatial arrangement of the polypeptide backbone

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21
Q

What is the alpha helix structure defined by?

A
  • Multiple consecuitive residues in the alpha region
  • Stabilised by hydrogen bonds between residues nearby in the sequence
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22
Q

What is the beta pleated sheet defined by?

A
  • Multiple consecutive residues in the beta region
  • Stabilised by hydrogen bonds between adjacent segments that may not be nearby in the sequence
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23
Q

What is the size of hydrogen bonds in a protein compared to a random O and H elsewhere?

A

The atoms of a hydrogen bond can approach much closer that a VDW interaction (2.7 A compared to 1.9) due to the covalent character of the hydrogen bond

  • This increases the compactness and stability of the protein
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24
Q

Label these locations of where hydrogen bonds can be found

A
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25
Q

Which residues bind to which ones in alpha helix and beta sheet?

A
  1. Beta-sheet (NH residue i to C=O residue j)
  2. Alpha-helix (NH residue i to C=O residue i-4)
  3. Reverse turns (NH residue i+3 to C=O residue i) L/R-handed
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26
Q

How many residues per turn of alpha helix?

What is the distance between turns?

A
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27
Q

Which side is the alpha helix turned?

A

Right handed becuase of the chirality of the alpha carbon so R groups point outwards, better for packing

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28
Q

What is the phi psi angle inside the alpha helix?

A
29
Q

How many of the residues in an alpha helix form favourable internal hydrogen bonds?

A

All NH and C=O within the helix except four at each end form favourable H bonds

30
Q

What direction is the macrodipole in an alpha helix?

A
31
Q

Fill in the blanks about the alpha helix interior

A
32
Q

Which two residues are strpng helix formers?

A

Small hydrophobic residues such as Ala and Leu

33
Q

Why does pro act as a helix breaker?

A

Because it lacks the NH hydrogen bond donor

34
Q

Why does Gly act as a helix breaker?

A

Because the tiny R group doesn’t contribute to the stability of the helix

35
Q

What two factors contribute to the pleated beta structure?

A

The planarity of the peptide bond and the tetrahedral geometry of the alpha carbon

36
Q

What is the sheet like arrangement of the beta sheets backbone held together by?

A

Hydrogen bonds between the backbone amides in different strands

37
Q

Which directions do the side chains appear in beta sheets?

A

Side chains protrude from the sheet alternating in an up and down direction

38
Q

What are the approximate phi and psi angles of the beta sheets?

A
39
Q

Difference between parallel and antiparallel H bonds in terms of beta sheets?

A
40
Q

Fill in blanks about parallel beta sheets

A
41
Q

Fill in the blanks about antiparallel beta sheets

A
42
Q

What are the characteristics of the Beta barrel?

A
43
Q

When do reverse turn occur?

A

Whenever strands in Beta sheets change their direction

44
Q

Over how many amino acids does the reverse turn take place?

A

The 180o turn is accomplished over four amino acids

45
Q

How is the reverse turn stabilised?

A

The turn is stabilised by a hydrogen bond from a carbonyl oxygen of position 1 to amide hydrogen of position 4 in the turn (i and i+3)

46
Q

What amino acids are common to be found in a reverse turn?

A

Proline in position 2 (i+1) or glycine in position 3 (i+2)

47
Q

What is the difference between a type 1 turn and a type 2 turn?

A

The carbonyl group at position 2 is pointing away from the page in a type I turn but out of the page in type II

48
Q

Why is proline found in position i+1 in a beta reverse turn?

A

The phi = -60 matches requirement of most beta turns

49
Q

Where is glycine found in a beta turn?

A

Type II turns often have glycine in position i+2 because the lack of side chain lessens steric hindrance (c=O clash with R group)

It has positive phi at position i+2

50
Q

What defines regular protein structure?

A
  • Residues that have repeating phi psi angles in consecutive residues
  • Stabilised by repeating pattern of hydrogen bonds, they present side chains in a predictable fashion and pack them together in limited ways
51
Q

Label these supersecondary structural elements

A
52
Q

What does tertiary structure refer to in a protein?

A

The overall spatial arrangement of atoms in a protein

53
Q

What interactions stabilise the tertiary structure?

A
  • Stabilized by numerous weak interactions between amino acid side chains
  • Largely hydrophobic and polar interactions
  • Can be stabilised by disulfide bonds
54
Q

What is the quaternary structure of a protein?

A

Formed by the assemby of individual polypeptides into a larger functional cluster

55
Q

What is a domain in protein tertiary structure?

A

A domain is a region within the native tertiary structure for which evidence can be provided of an existence independent of the rest of the protein (fold independently)

56
Q

What is a protein fold defined as?

A

The arrangement of secondary structure elements relative to each other in space

57
Q

What is a module?

A

They have one or more repeating fold within their overall structure

58
Q

Fill in the blanks about the four ways that new proteins with new properties can be generated by

A
59
Q

Label these genetic mutations

A
60
Q

How have new proteins evolved and what does this imply?

A
  • New proteins have evolved by gene duplication and domain shuffling. This implies domains can have a common protein ancestor
  • Individual domains subject to mutations
  • No new domains are being creating only modified
61
Q

Fill in the blanks about gene mutations

A
62
Q

What does identity and similar mean in the context of protein domains?

A
  • Identity means exactly the same residue (invariant)
  • Similar means a change to a residue that is observed frequently or with similar physical-chemical properties
63
Q

How do the structures of proteins that are related by such evolutionary events such as gene duplication, but have different sequences, compare?

A
  • Each sequence “change” results in a small change to structure.
  • Structure, however, changes much more slowly than sequence. This means that for two proteins whose sequences show >25% identity they will have a similar structure.
  • In general they will have similar secondary and tertiary structures. Gaps between two sequences will result in a loop insertion within the general structural fold.
64
Q

When aligning amino acids sequences of a domain what does homologues mean?

A

If the two sequences show >25% identity the protein domains are considered to be homologues - implies they arose from an event such as gene duplciation (sharing common protein domain ancestor) and they have same fold

65
Q

What is an orthologue in protein domains?

A

Homologues proteins that perform the same function in different species eg horse and tuna trypsin

66
Q

What is paralogue in protein domains?

A

Homologous proteins that perform different but related functions within one organism eg human trypsin vs human thrombin

67
Q

How can we tell whether domains are homologues?

A

If sequence identity is low <<25% and proteins are functionally diferent then it is hard to draw conclusions. If we find the fold to be similar then they are likely to be homologues

68
Q
A

MCB 2020 (38 decks)

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