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BIOC192 > Elements of Protein Structure > Flashcards

Elements of Protein Structure Flashcards

1
Q

This is when amino acids are bonded together in a peptide or a protein

A

Amino acid residues

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2
Q

How are amino acids numbered?

A

From the N (amino terminus) to C (carboxy terminus)

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3
Q

Globular proteins are comprised of:

A

a-helix, B-structure, and turns

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4
Q

What are the 4 levels of protein structure?

A

Primary, secondary, tertiary, quaternary

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5
Q

This is the linear sequence of amino acids that make up the polypeptide

A

Primary structure

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6
Q

This is the 3-dimensional arrangement of a protein chain over a short stretch of adjacent amino acid residues. Includes a-helices and B-sheets

A

Secondary structure

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7
Q

This is the 3-dimensional structure of a complete protein chain

A

Tertiary structure

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8
Q

This is the interchain packing and structure for a protein that contains multiple polypeptide chains (eg., haemoglobin)

A

Quaternary structure

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9
Q

What is the bond angle between N and Ca?

A

phi bond angles

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10
Q

What is the bond angle between Ca and C’?

A

psi bond angles

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11
Q

What is the chain angle between C’ and N (peptide bond)? These bond angles can only be 180 degrees or 0.

A

Omega bond angles

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12
Q

What is the specific bond angle of a polypeptide when it’s in its final structure?

A

180 degrees

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13
Q

Why are there restrictions on phi and psi angles? Describe these restrictions.

A

Because of steric hindrance.

  • Phi rotations can lead to O-O collision
    -Psi rotations can lead to NH-NH collision
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14
Q

For a trans peptide bond, what is the bond angle?

A

180 degrees

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15
Q

Where are the alpha carbon atoms found on trans peptide bond?

A

Opposite sides of the peptide bond.

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16
Q

What is increased for cis peptide bonds?

A

Steric crowding because both alpha carbon atoms are on the same side of the peptide bond.

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17
Q

Does the peptide bond angle rotate very much once formed? Why/why not?

A

Because the peptide bond is a double bond. There will always be limited rotation when it comes to double bonds because there’s that sp1 structure that covers the whole molecule.

18
Q

What are the 2 main secondary structures?

A

a helix and B structures: B sheet and strand

19
Q

These are main chain spirals around the central axis. They participate in non-covalent interaction (hydrogen bonding).

A

alpha helix

20
Q

What stabilises the secondary structures?

A

Hydrogen bonds

21
Q

How do sidechains stabilise the alpha helix?

A

Hydrophilic side chains point out, hydrophobic sidechains fold towards the middle

22
Q

These are stretches of residue with a more extended structure than an a-helix.

A

B structure

23
Q

Each section of a B structure is called a…

A

B-strand

24
Q

What kind of bonding occurs between adjacent B-strands?

A

Hydrogen bonding

25
Q

What do adjacent B strand chains form?

A

Beta sheets

26
Q

What are the 2 types of hydrogen bonding interaction in a B-sheet?

A

Parallel and antiparallel

27
Q

Beta sheets are not planar they are:

A

pleated

28
Q

How are sidechains orientated in the B sheet?

A

Side chains either point above or below.

29
Q

These are needed to form globular proteins. Often short, hairpin like and involves 3/4 residues. Has a high Gly/Pro content and often have H-bond across width.

A

Turns

30
Q

This side chain is very flexible and has a lot of conformational freedom.

A

Glycine

31
Q

This is too rigid but has a built in turn because of the bonding between R-group and amino group.

A

Proline

32
Q

How many residues per turn in alpha helices?

A

3.6 residues per turn

33
Q

How many rises per turn in alpha helices?

A

5.4 rices

34
Q

Is the spiral of an alpha helix left or right handed?

A

Right handed

35
Q

What two residues are helix breaker and therefore would not be used to form helices?

A

Proline and glycine

36
Q

The dipole of the alpha helix is positive/negative in the N terminus?

A

Positive

37
Q

In an alpha helix, each amino acid side chain is separated by how much degrees? (in a helix wheel)

A

100 degrees

38
Q

Approximately how many strands are there in each beta sheet?

A

2-10 strans

39
Q

The average strand of a B strand is about how many amino acid residues?

A

6 amino acid residues, but the maximum would be around 15

40
Q

Which level of protein structure determines the overall shape of a protein?

A

Primary structure => because it contains the instructions for protein folding hence, protein shape

41
Q

This is the process of forming alpha helices and beta sheets early in the folding process.

A

Nucleation

BIOC192 (15 decks)

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