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Proteins > Protein Structural Elements > Flashcards

Protein Structural Elements Flashcards

1
Q

What are the 9 hydrophobic amino acids?

A 
glycine (Gly)
alanine (Ala)
valine (Val)
leucine (Leu)
isoleucine (Ile)
proline (Pro)
phenylalanine (Phe) methionine (Met)
tryptophan (Trp)
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2
Q

How many residues needed to get around a turn of a right handed alpha helix?

A

3.6 residues

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3
Q

How do you draw a helical wheel?

A
  • every 100 degrees place a residue
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4
Q

What is an EF hand?

A

helix-loop-helix structural domain or motif found in a large family of calcium-binding proteins

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5
Q

What is calmodulin?

A

is a calcium-binding protein found in the cytoplasm of all eukaryotic cells

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6
Q

What is the structure of calmodulin?

A

2 EF hands that interact

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7
Q

What happens when calcium binds to Calmodulin?

A
  • EF hands change conformation
  • one EF hand has a higher affinity for Ca than the other so one has a stronger affinity and once that has bound, it increases the other ones affinity like in O2 in haem
  • Hydrophobic residues are exposed on the surface rather than in the middle like usual
  • Protein changes conformation
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8
Q

What variations of signalling can be done with the binding of Ca2+ to CaM.

A
  1. Ca2+ binding modulates conformation and either activates or inhibits target protein
  2. Ca2+ binding dissociates the protein to free active site for phosphorylation or associates the protein, inhibiting it
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9
Q

What are β pleated sheets?

A
  • patterns in the primary structure
  • Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet
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10
Q

What are the differences between parallel and anti parallel beta sheets?

A 
parallel:
hydrogen bonds are slightly straight 
hydrogen bonds are not parallel but at an angle
anti parallel:
H bonds are completely straight
H bonds are parallel
Twists more than the parallel
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11
Q

What are some common β strand motifs?

A

Hairpin
- hairpin is β strands antiparallel to each other
β meander / Beta barrel (which is a repetition of hairpin motif)
- makes a pore in the membrane allowing things to go in and out
β Propeller
β-α-β
- active site in loop 1
- right handed is dominant
α/β barrels (TIM barrels)
- alpha helix sits on the outside, beta sheets in the middle
- e.g. pyruvate kinase
- >10% of enzymes contain α8β8 barrels

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12
Q

What is the structure of pyruvate kinase?

A
  • made of 4 domains

- each domain made of repeated alpha/beta barrels

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13
Q

What is divergent evolution? Inc example

A

Divergent evolution occurs when two separate species evolve differently from a common ancestor
- TIM barrels and Beta barrels diverged from a common ancestor

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14
Q

What is convergent evolution?

A

Convergent evolution occurs when species have different ancestral origins but have developed similar features.

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15
Q

Describe the immunoglobulin fold.

A

The immunoglobulin fold consists of a pair of β sheets, each built of antiparallel β strands, that surround a central hydrophobic core. A single disulfide bond bridges the two sheets.

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16
Q

Compare the constant and variable domains of immunoglobulins.

A

three loops present at one end of the structure form a potential binding surface. These loops contain the hypervariable sequences present in antibodies and in T-cell receptors. Variation of the amino acid sequences of these loops provides the major mechanism for the generation of the vastly diverse set of antibodies and T-cell receptors expressed by the immune system.

17
Q

What other polypeptide helices occur other than right handed α helices?

A 
3(10) helix:
- 3 residues/turn
- pitch = 6.0A
- short, distorted segments
- H bonds every 3 amino acids
- thinner + longer than right handed α helices
π helix:
- 4.4 residues/turn
- pitch = 5.2A
- lack of van der Waals
- H bonds every 5 amino acids
- shorter + fatter than right handed α helices
18
Q

Why don’t L-amino acids form left handed helices?

A
  • the side chains and CO groups do not fit in the space
19
Q

How do amino acids sequences affect the stability of α helices?

A

side chains 3 or 4 residues apart in the a.a. seq will interact so:
- bulky residues 3/4 residues apart in seq destabilise α helix formation
- residues of the same charge will repel and also destabilise α helix formation
proline breaks/ kinks α helix

20
Q

Why does proline create kinks in α helices?

A
  • doesn’t have free backbone rotation
  • steric hindrance
  • N doesn’t form H-bonds
21
Q

What conformation are all non-proline amino acids usually in?

A

Trans configuration

22
Q

Why is there a steric clash when proline is in the a configuration?

A

It can exists in both configurations as clashes in both

  • if in trans configuration backbone clashes with N
  • restriction around phi angle
  • if in cis, clash between 2 Cα’s
23
Q

What sort of helices does Poly-Proline form?

A

PPII (seen more in nature) and PPI

24
Q

What sort of helices are present in Collagen?

A
  • 3 PPII helices come together
  • glycine, proline and hydroxy proline make 45% of the amino acids
  • mediate protein interactions
25
Q

What is the difference between PPII and PPI helices?

A 
PPII - 3.1A rise per residue
- left handed
- 9.3 pitch/turn
PPI - 1.7A rise per residue
- right handed
- 5.6 pitch/turn
26
Q

How many types of helices are there?

A

PPI, PPII, collagen helix, 310 helix, alpha helix, Pi helix, beta helix, DNA double helix, coiled coil

27
Q

What is a Coiled coil?

A
  • type of helix
  • 7 residue repeat
  • 4th residue is leucine
  • 1st residue is hydrophobic
  • 3.5 residues per turn
28
Q

Name a specialised coiled coil.

A

The leucine “zipper”

  • 2 amphipathic α helices
  • helices dimerise and bind DNA
  • control DNA binding by controlling dimerisation
29
Q

What are the different ways to determine tertiary structure?

A
  1. experimental determination

2. Structure prediction

30
Q

What experimental techniques can be used to determine tertiary structure?

A
  • x-ray
  • NMR
  • Cryo Electron Microscopy
31
Q

What structure prediction techniques can be used to determine tertiary structure?

A

Ab initio folding
identification of a.a. sequences
Comparative modelling

32
Q

What is comparative modelling?

A
  1. Take protein sequence and put through a database
    - Compares sequences
    - Shows anything that is the same
  2. Align sequences and compare them to see if the same a.a is present, or similar ones (e.g. if they are both amines or both similar hydrophilic a.a’s)
33
Q

What is Ab initio modelling modelling?

A
  • using simplified physics to simulate the folding process
  • only possible for small proteins and peptides
  • Coulombs Law
34
Q

What does Coulombs Law show?

A

Relationship between opposite and like chargers and their electrostatic attractions

Proteins (5 decks)

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