MCB Lecture 6-7 Protein Structure Flashcards

0
Q

Which groups must form hydrogen bonds?

A

Polar groups must form hydrogen bonds

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1
Q

Describe hydrogen bonding in proteins (h-bonds are between which atoms?)

A

Hydrogen bonding occurs between NH & C=O of two different residues

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2
Q

Compare hydrogen bond length and with that of VDW interactions

A

H-bonds are shorter and allow the protein to pack more closely together than VDW interactions would allow.

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3
Q

What are the three possibilities in terms of hydrogen bonding between different groups?

A
  1. Backbone - Backbone
  2. Backbone - Residue
  3. Residue - Residue
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4
Q

What is a feature of secondary structure of protein?

A

Regular dihedral angles of the residues

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5
Q

Why have secondary structure in proteins?

A

Secondary structure allows close packing of the peptide, and increased stability

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6
Q

What are the dihedral angles in Beta sheets?

A

Phi: -130
Psi: +130

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7
Q

Between which two residues can beta sheets form?

A

Any two within a peptide

i and j

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8
Q

Differentiate between beta sheets and beta strands

A

Individual beta strands make up a beta sheet

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9
Q

How do hydrophobic faces of the beta sheet arise?

A

Side chains point directly up and directly down alternatively.
By having an alternating sequence of hydrophobic and hydrophilic side chains, all the hydrophobic ones will be on one side of the sheet.

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10
Q

Differentiate between anti-parallel and parallel, as well as pure and mixed beta sheets

A

Anti parallel sheets: n termini are at different ends
Parallel: n termini are at the same end

Pure: sheet is made up of only parallel or anti parallel strands
Mixed: there are examples of parallel and anti parallel in the sheet

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11
Q

What is a beta-barrel?

A

A beta barrel is a structure that forms when the beta sheets curve round to form a barrel.
Hydrophobic side chain project into the cavity of the barrel
Hydrophilic side chains project out into the solvent

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12
Q

What are the dihedral angles in alpha helices?

A

Phi: -57
Pi: -47

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13
Q

What are beta-sheet twists? What are the two types?

A

When the plane of the sheet is contorted.
This is really common

The two types are left handed and right handed twists

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14
Q

Describe the handedness of alpha helices

A

Alpha helices are right handed.

Even when turned upside down, the handedness doesn’t change

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15
Q

Between which two residues do alpha helices form

A

NHi and C=O i-4

There are three residues between the two that form hydrogen bonds

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16
Q

Do all residues within a helix form bonds?

A

Yes, apart from four residues at either end

17
Q

How many residues per turn?

A

3.6

18
Q

Where do the side chains point?

A

All side chains point outwards

19
Q

Describe the dipoles in an alpha helix

A

The peptide dipoles add together, making one macro dipole

20
Q

What is an heptad repeat?

A

Repeat uni of seven residues in an alpha helix

21
Q

What does the heptad repeat give rise to?

A

‘a’ and ‘d’ are hydrophobic.

This gives rise to a hydrophobic stripe that curves around the alpha helix structure.

22
Q

One heptad repeat corresponds to how many turns in the alpha helix?

A

Roughly two turns

23
Q

What is a coiled coil?

A

A coiled coil is when two alpha helices coil around each other.
The two hydrophobic stripes interact.
This buries the hydrophobic side chains, sequestering them away from solvent

24
Q

How can beta sheets and alpha helices associate?

A

The hydrophobic stripe along an alpha chain interacts with the hydrophobic face of a beta sheet

25
Q

What are beta-turns?

A

Beta turns is a sequence of residues that changes the direction of the peptide

26
Q

Where are reverse turns normally found?

A

In beta sheets

27
Q

How many residues make up a beta-turn?

A

4

28
Q

Describe the structure of a beta turn

A

Four residues

The first and fourth residue interact with a hydrogen bond to increase the stability.

29
Q

Which amino acids is commonly found in position i+1? Why?

A

Proline. The phi bond of -60 is perfect for the turn required.

30
Q

What is the difference between the two types of beta turns?

A

The difference is the position of the carbonyl of the i+1 residue.

31
Q

How is entropy important in the formation of hydrophobic region?

A

It would seem intuitive that a folded structure of protein is more ordered and thus higher entropy than an unfolded protein.
This would be problematic though, because it would mean that the unfolded state is the naturally occurring one.
Obviously, this isn’t the case.

When a protein folds up, the hydrophobic side chains becomes buried in the core, away from water. This releases water molecules.
The water molecules are more disordered, and thus higher entropy.

32
Q

Formation of a hydrophobic core is driven by…

A

Entropy

33
Q

What are supersecondary structures?

Give three examples

A

Super secondary structures are interactions between beta sheets and alpha helices of one peptide.

aa hairpin
BB hairpin
BaB element

34
Q

What are the features of tertiary structures?

A

Tertiary structures, or domains, represent functional domains

Domains have specific functions, such as catalytic activity, lipid binding etc.

They must show some evidence of independent folding

35
Q

In general, how many residues are there in a domain?

A

40-700

36
Q

Protein domains are an example of … Structure

A

Tertiary

37
Q

What is quaternary structure?

A

Interaction of multiple peptides to form a molecule

38
Q

A single polypeptide can have multiple …

A

Domains

39
Q

In type II beta turns, … often takes position i+2.

Why?

A

Glycine often takes position i+2
Since glycine has no side chain, steric hindrance with the carbonyl of i+1 is reduced, since the two are close in type II Beta turns