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BIOC192 > Lecture 5: ELEMENTS OF PROTEIN STRUCTURE > Flashcards

Lecture 5: ELEMENTS OF PROTEIN STRUCTURE Flashcards

1
Q

What is each protein made of?

A

At least one protein (or polypeptide) chain

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2
Q

How are the amino acid residues in a polypeptide chain numbered?

A

Starting from the amino terminus to the carboxyl terminus (N-terminus to C-terminus)

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3
Q

How many chains may proteins have?

A

Anywhere from one to several

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4
Q

What is the most common variety of proteins?

A

Proteins with one chain

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5
Q

Proteins are mostly…

A

Globular so the main chain has to double back and form a more compact shape

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6
Q

What is the structure of proteins primarily composed of?

A

Alpha helix, beta structure and turns

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7
Q

How many levels of protein structure are there?

A

4

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8
Q

What is the primary structure?

A

Amino acid sequence of a protein

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9
Q

What is the secondary structure?

A

Local three-dimensional (3D) arrangement of a protein chain over a short stretch of adjacent amino acid residues

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10
Q

What is the tertiary structure?

A

Three-dimensional (3D) structure of a complete protein chain

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11
Q

What is the quaternary structure?

A

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

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12
Q

What do the protein main chain and side chain atoms have?

A

Bonds which can rotate and are somewhat flexible

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13
Q

What are the main chain atoms in a protein?

A

Nitrogen, alpha carbon and carbonyl carbon

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14
Q

How are the main chain atoms in a protein connected?

A

By single bonds

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15
Q

What is the bond between N and alpha carbon called?

A

Phi

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16
Q

What is the bond between alpha carbon and carbonyl carbon called?

A

Psi

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17
Q

What is the range of values for phi and psi?

A

0 +/- 180 degrees

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18
Q

What is the bond angle between the carbonyl carbon and N (peptide bond) called?

A

Omega

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19
Q

What is the value of omega usually?

A

Very close to 180 degrees or 0 degrees

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20
Q

What is one way a 3D structure can be described?

A

By listing the rotation angles found around the bonds of each residue of the protein chain

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21
Q

Can phi bonds twist?

A

Yes

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22
Q

Can psi bonds twist?

A

Yes

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23
Q

Can omega bonds twist?

A

No

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24
Q

Why do phi and psi angles have restrictions in their values?

A

Because of steric hinderance

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25
What can phi rotation lead to?
O-O collision
26
What can psi rotation lead to?
NH-NH collisions
27
What may their be steric hinderance between?
The hydrogen on the amide nitrogen and the carbonyl oxygen
28
What are most peptide bonds?
Trans
29
What does omega equal for a trans peptide bond?
About 180 degrees
30
Where are the alpha carbon atoms found in a trans peptide bond?
On opposite sides of the peptide bond
31
What does omega equal for a cis peptide bond?
About 0 degrees
32
Where are the alpha carbon atoms found in a cis peptide bond?
On the same side of the peptide bond
33
When is steric hinderance increased?
For cis peptide bonds
34
Does the peptide bond angle usually rotate?
No, not very much
35
What amino acid tends to have a lot of cis bonds?
Proline
36
What does the combination of all the rotations and twists around all the bonds in a protein lead to?
Its overall 3D structure
37
What does a proteins 3D structure lead to?
The arrangement of all the side chains in the protein
38
What does the arrangement of all the side chains in the protein lead to?
Its function
39
What is secondary protein structure dominated by?
Two structures - alpha helices and beta strands/sheets
40
What does the main chain do in an alpha helix?
Spirals around the central axis like a spiral axis - right handed spiral
41
What type of interaction is there in alpha helices?
A non-covalent interaction called a hydrogen bond between the carbonyl oxygen which is partially negatively charged and the hydrogen attached to the N which is slightly positively charged
42
What symbol is the carbonyl oxygen given?
n
43
What symbol is the nitrogen with hydrogen attached given?
n+4
44
What is the O-N distance?
approximately 2.9 A
45
What do hydrogen bonds do in alpha helices?
Help stabilise the structure, adding 3-7 cal/mol or 12-28kJ/mol of stability
46
How many residues/turn in alpha helices?
3.6
47
What is the rise/turn in alpha helices?
5.4 A
48
What is the d of one amino acid residue?
2.5. A
49
Where are the side chains in alpha helices?
They point outwards to help stabilise the alpha helix
50
What is phi in an alpha helix?
about -57 degrees
51
What is psi in an alpha helix?
About - 47 degrees
52
Which amino acid residues break the alpha helix pattern?
Glycine and proline
53
What exists in the aloha helix?
A dipole, positive at the N terminus
54
What is the beta structure comprised of?
Peptide chains with a more extended structure than the alpha helix. Each is called a beta strand (not stable on own)
55
What occurs between adjacent beta strands?
Hydrogen bonding
56
What can adjacent beta strands form?
A beta sheet with two or more strands
57
How many beta strands per beta Sheed?
Typically 2-10
58
What is the average beta strand length?
About 6 amino acid residues which is typically shorter than alpha helices
59
How many amino acid residues may each strand have?
Up to 15
60
What are the two types of hydrogen bonding interactions between beta sheets?
Parallel and antiparallel
61
Describe parallel strutcure?
The two strands run in the same direction but the hydrogen bonds aren't parallel
62
Describe antiparallel strutcure?
The two strands run in the opposite direction and the hydrogen bonds are parallel
63
How is a beta sheet described?
Extended and pleated, planar with right handed twist
64
Where are the side chains in beta sheets?
Above and below
65
What will commonly form a beta strand?
Any NP-P-NP-p stretch of amino acid residues
66
What are beta structures found in?
Silk
67
What is the model beta sequence in silk?
Gly-Ser-Gly-Ala-Gly-Ala
68
What do the Ala side chains do in silk?
Interlock with the Al side chain from another sheet
69
Is beta sheets in silk parallel or antiparallel?
Antiparallel
70
What do silks from different species have?
Different interlocking groups and differing physical properties
71
What are turns needed for?
To form globules
72
What are turns often like?
Short, hairpin like, involving 3 or 4 residues
73
What amino acids are in high amounts in turns?
Gly (flexibility) and Pro (rigidity)
74
What portion of residues are involve din turns?
Almost 30%
75
What is common across turns?
Hydrogen bonds
76
How many types of turns are there?
More than 16, which are given Roman numeral names
77
What are the common types of turn?
Type I and Type II
78
Where is the oxygen in Type I turns?
Up
79
Where is the oxygen in Type II turns?
Down
80
Why are protein structures challenging to display clearly?
There are lots of atoms, detailed internal cavities and complicated shapes
81
What are all the elements of protein structure?
Alpha helix, beta strands, turns and loops (bigger turns)
82
What are space filling models good for?
Overall shape but you can't really see inside and the elements of structure
83
How are helices shown in the consensus protein structural display?
As spirals (or cylinders)
84
How are strands shown in the consensus protein structural display?
Arrows pointing from N terminus to C terminus
85
How are turns and random coils shown in the consensus protein structural display?
As loops or rope-like structures
86
What is a random coil?
A section of protein structure that does not fit into any of the standard groups
87
What are the advantages of the consensus protein structural display?
- easily visualise the main chain path - identify elements of secondary structure - appreciation of proteins as 3D objects - allows comparison to other proteins

BIOC192 (38 decks)

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