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BIOC192 > lecture 5 > Flashcards

lecture 5 Flashcards

1
Q

Amino acids are joint together by?

A

Peptide bonds

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2
Q

When amino acids are bonded in a peptide or protein they are called?

A

Amino acid residues

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3
Q

Each protein is made up of at least one type of chain?

A

Polypeptide

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4
Q

How are amino acid residues in a polypeptide chain numbered?

A

Starting from the amino terminus to carboxyl terminus

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5
Q

What causes the main chain to double back on itself forming a compact shape?

A

The globular shape

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6
Q

What does the globular structure mainly comprised of?

A

Alpha helix and beta structure turns

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7
Q

What are the four levels of protein structure?

A

Primary
secondary
tertiary
quaternary

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8
Q

What is the primary structure?

A

amino acid sequence

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9
Q

What is secondary structure?

A

Local 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues

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10
Q

What is tertiary structure?

A

3D structure of a complete protein chain

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11
Q

What is Quaternary structure?

A

interchain packing and structure for a protein that contains multiple protein chains

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12
Q

What are the main chain atoms in a protein?

A

Nitrogen, alpha carbon, Carbon

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13
Q

What is the chain angle between C’ and N?

A

Omega, either 180 or 0 degrees

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14
Q

What is the chain angle between N and alphaC?

A

Phi, 0-180 degrees

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15
Q

What is the chain angle C’ and alphaC?

A

psi, 0-180 degrees

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16
Q

What is the phi angle?

A

Rotation angle around the N-alphaC

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17
Q

What is the psi angle?

A

rotation angle around the alphaC-C’

18
Q

what is the rotation angle around the peptide bond?

A

Omega

19
Q

What degree are all the angles when the polypeptide has its conformation?

A

180 degrees

20
Q

Phi rotation can lead to what kind of collision?

A

O-O collisions

21
Q

Psi rotation can lead to what kind of collision?

A

NH-NH

22
Q

Most peptide bonds are in what formation?

A

Trans formation

23
Q

Why are peptide bonds majority trans?

A

because in the cis peptide bond there is a lot of steric crowding. The alpha carbons are on the same side

24
Q

Protein secondary structures are dominated by which two structures?

A

Alpha helix

Beta strand/sheet

25
Q

What bonds stabilise the alpha helix structures?

A

Hydrogen bonds

26
Q

What is hydrogen bonded in the alpha helix structure?

A

The carbonyl of residue and the N-H of residue, n+4

27
Q

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

A
  1. 6 residues/turn

5. 4 angstrams

28
Q

is alpha helix left or right handed?

A

Right handed

29
Q

Where do side chains point in alpha helix?

A

Out from the alpha helix to stabilise it

30
Q

What is the value of hydrogen bonds?

A

3-7kcal/mol or 12-28kJ/mol

31
Q

What residues are alpha helix breakers?

A

Glycine

Proline

32
Q

What is the alpha helix dipole?

A

~positive at N-terminus

33
Q

What are the two types of hydrogen bonding interactions in a beta sheet?

A

Parallel

Antiparallel

34
Q

Hydrogen bonding occurs between what in beta structures?

A

Adjacent chains

35
Q

What forms a beta sheet?

A

two beta strands, typically 2 to 10 strands

36
Q

what is the average strand length of a beta structure?

A

6 amino acid residues

37
Q

Beta pleated sheets have what kind of twist?

A

right handed

38
Q

Side chains point where in a beta sheet?

A

above and below the sheet

39
Q

NP-P-NP-NP-P stretch of residues commonly forms what?

A

Beta strand

40
Q

What structure exists in silk?

A

beta structure

41
Q

what are the most common turn types in beta structures?

A

Type I

Type II

42
Q

Why are protein structures difficult to display clearly?

A

Lots of atoms
detailed internal cavities
complicated shapes

BIOC192 (4 decks)

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