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BIOC192 2022 > lecture 5 - elements of protein structure > Flashcards

lecture 5 - elements of protein structure Flashcards

1
Q

In what direction are amino acid residues named/numbered?

A

Left to right, from the amino terminus to the carboxyl terminus

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2
Q

What does globular mean, in terms of protein shape?

A

The main chain folds and doubles back to form a compact shape

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3
Q

What are the 4 levels of protein structure?

A

Primary, Secondary, Tertiary, Quaternary

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4
Q

What is the name of the angle between the amino nitrogen and alpha carbon in a polypeptide?

A

Phi - Φ

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5
Q

Phi (Φ) is the angle between which two atoms in a polypeptide chain?

A

Amino nitrogen and alpha carbon

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6
Q

What is the name of the angle between the carboxyl carbon and alpha carbon in a polypeptide?

A

Psi (Ψ)

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7
Q

Psi (Ψ) is the angle between which two atoms in a polypeptide chain?

A

The carboxyl carbon and the alpha carbon

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8
Q

What is the name of the angle between the carboxyl carbon and the Nitrogen of the adjacent amino acid (AKA the peptide bond) in a polypeptide?

A

omega (ω)

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9
Q

Omega (ω) is the angle of which bond in a polypeptide?

A

The peptide bond (between carboxyl carbon and amino nitrogen of adjacent amino acids)

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10
Q

Why are the angles of phi and psi restricted in a polypeptide?

A

Due to steric hindrance experienced by the amino acids which usually sit in a trans configuration.

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11
Q

What collisions can the phi bond rotation lead to?

A

O-O collisions

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12
Q

What collisions can the psi bond rotation lead to?

A

NH-NH collisions

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13
Q

What is the range of phi and psi angles?

A

-180 degrees to +180 degrees

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14
Q

What is the angle of omega in a trans peptide bond?

A

+180 degrees

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15
Q

What is the angle of omega in a cis peptide bond?

A

0 degrees

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16
Q

Why are cis bonds infavourable in peptide bonds?

A

There is steric crowding of the R side chains on one side of the bond, leading to collisions

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17
Q

What are the 2 key structures in secondary protein structure?

A

Beta-strands/sheets and alpha helices

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18
Q

Is an alpha helix a left or right handed ‘spiral’?

A

Right-handed

19
Q

What type of bonds stabilise alpha helices?

A

Hydrogen bonds

20
Q

What atoms are involved in the hydrogen bonds in an alpha helix?

A

The carbonyl oxygen of one peptide bond with the hydrogen attached to the nitrogen of another peptide bond

21
Q

How far apart are the amino acid residues that are involved with hydrogen bonds with each other in alpha helix?

A

4 residues apart (n bonds with n+4)

22
Q

How many residues are there per turn in an alpha helix?

A

3.6

23
Q

Do the side chains point outwards or inwards in an alpha helix?

A

Out wards

24
Q

What types of amino acids will break an alpha helix?

A

Glycine and proline (non-polar side chains)

25
Q

What is the direction on an alpha helix dipole?

A

positive at N terminus and negative at C terminus

26
Q

What is the degree of separation of the side chains in an alpha helix, and why?

A

100 degrees - There are 3.6 residues per 360 degrees.

27
Q

How many Beta strands are in a typical Beta sheet?

A

2-10

28
Q

How is hydrogen bonding involved in Beta strands/sheets?

A

Hydrogen bonds link adjacent strands to form a sheet

29
Q

What is the typical number of residues in a Beta strand?

A

6 resides long, can have up to 15

30
Q

What are the 2 types of Beta sheet?

A

Parallel and anti-parallel

31
Q

What are parallel Beta sheets?

A

Sheets where the individual beta strands are in the same direction (N and C termini are at the same end)

32
Q

What are anti-parallel Beta sheets?

A

Sheets where the individual beta strands are in the opposite direction (N and C termini are at opposite alternating ends)

33
Q

What is the shape of hydrogen bonds in a parallel beta sheet?

A

V-shaped

34
Q

What is the shape of hydrogen bonds in an anti-parallel beta sheet?

A

Linear

35
Q

What is the overall shape of an extended Beta sheet?

A

Pleated

36
Q

Do pleated Beta sheets have a left or right handed twist?

A

Right handed

37
Q

Where do side chains point in a pleated Beta sheet?

A

Above and below the sheet

38
Q

What pattern/sequence of amino acid residues commonly form Beta strands?

A

Alternating polar and non-polar residues

39
Q

What is the most stable type of Beta sheet?

A

Antiparallel, due to its linear hydrogen bonds

40
Q

What are turns required to form?

A

Globules

41
Q

How many residues are typically involved in a hair pin-like turn?

A

3 or 4

42
Q

What amino acids are commonly involved in turns?

A

Glycine and proline (non-polar side chains)

43
Q

What type of bonds stabilise turns?

A

Hydrogen bonds

44
Q

What type of diagram represents protein structure as ‘ribbon-like’?

A

Richardson diagram

BIOC192 2022 (37 decks)

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