BIOL 111 > L7 + 8: Protein Structure + Function > Flashcards

L7 + 8: Protein Structure + Function Flashcards

(97 cards)

Study These Flashcards
1
Q

What is the primary structure?

A

Sequence of amino acids, N-terminal to C-terminal

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Write Met-Ala-Ala-Glu-Cys-His-Gly as a single letter code

A

MAAECHG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is secondary structure?

A
  • Folding of parts of primary sequence into particular structures
  • Involve several amino acids that are contiguous (right next to each other in primary sequence) or different parts in primary sequence
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are the 2 important types of secondary structures?

A
  • Alpha helix
  • Beta sheet
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the typical length of amino acid stretches that form an alpha helix?

A

Usually formed from stretches of 5-40 amino acids.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How are the main chain N-H and C=O groups arranged in an alpha helix?

A

They are hydrogen bonded to one another along the axis of the helix.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the stability characteristic of an alpha helix?

A

Very stable

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How many degrees does each amino acid turn the helix in an alpha helix?

A

Each amino acid turns the helix through 100 degrees.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the vertical distance between consecutive amino acids in an alpha helix?

A

0.15 nm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the pitch of the alpha helix?

A

The pitch (turn length) of the helix is 0.54 nm.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Which amino acid groups are hydrogen bonded in an alpha helix?

A

The C=O group of amino acid n is hydrogen bonded to the N-H group of amino acid n+4.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What do amino acid side chains do in a helix?

A

They project out from the edge of the helix.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How can the sequence of amino acids in a helix be represented visually?

A

It can be plotted on a helical wheel diagram.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the angle at which each amino acid residue is plotted on a helical wheel diagram?

A

Each residue is plotted 100 degrees around a circle/spiral.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are beta sheets formed from?

A

Non-continuous regions of the polypeptide chain called beta strands

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How do beta strands interact in a beta sheet?

A

Line up + form hydrogen bonds between the C=O groups of one strand and the N-H groups of another

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What characterises parallel beta sheets?

A

All strands run in the same direction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What characterises anti-parallel beta sheets?

A

Strands run in opposite directions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What type of bonding is characteristic of parallel beta sheets?

A

Hydrogen bonds are evenly spaced within the beta sheet.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is the conformation of beta strands in a parallel beta sheet?

A

Beta strands are in an almost fully extended conformation (not packed)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How do beta strands differ in packing compared to alpha helices?

A

Beta strands are not packed like alpha helices

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What characterizes the hydrogen bonds in anti-parallel beta sheets?

A

Narrowly spaced hydrogen bond pairs are separated by a larger gap.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is the conformation of beta strands in anti-parallel beta sheets?

A

Beta strands are in an almost fully extended conformation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Why are beta-sheets described as pleated?

A

Carbons lie successively above and below the plane of the sheet

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
What connects secondary structures in proteins?
Loop regions link secondary structures
26
How do loop regions vary in proteins?
Loops vary in length
27
What are long loops in proteins called?
Long loops are referred to as random coils
28
What connects anti-parallel beta strands?
Short loop regions connect anti-parallel beta strands called hairpin loops or beta turns.
29
What part a of protein is the most flexible?
Loop region
30
Which 2 amino acids ares found in looped regions?
- Proline - Glycine
31
Why is proline found in looped regions?
Its locked ringed structure introduces a 'kink' into polypeptide chain
32
Why is glycine found in looped regions?
Its small side chain enables it to form turns when other amino acids couldn't
33
How are parallel beta strands typically connected?
By an alpha helix
34
What structural feature crosses the beta sheet in a β-α-β motif?
The helix crosses the beta sheet from one edge to another
35
What does a hairpin loop connect?
Anti-parallel beta strands
36
What are post-translational modifications?
Modifications made to proteins after translation, which can alter their function and properties.
37
What are some examples of 'rare' amino acids produced by post-translational modifications?
Hydroxyproline and hydroxylysine
38
What is glycosylation?
The addition of sugars/carbohydrates/glycans to amino acids resulting in glycoproteins.
39
What 2 types of glycosylation are there?
N-linked and O-linked glycosylation
40
What is the role of lipids in post-translational modifications?
Lipids can be added to proteins, resulting in lipoproteins
41
How do post-translational modifications affect protein structure?
They can contribute to the protein's secondary structure.
42
What is a tertiary structure of a protein?
3D structure of a protein by association of secondary structures into compact domains
43
Name 3 non-covalent bonds which are important in correct tertiary structure
- Ionic bonds - Hydrogen bonds - Van der Waals forces
44
What forms a disulphide bridge?
A side chain of one cysteine forms a disulphide bridge with the side chain of another cysteine
45
What type of bond is a disulphide bridge?
Covalent bond
46
What is the function of disulphide bridges in proteins?
Make proteins more resistant to degradation + denaturation
47
Difference between cysteine + cystine
2 individual molecules = cysteine Bonded together = cystine
48
What part on diagrammatic representation of a protein usually show? Why?
Polypeptide backbone of the protein Too many atoms so diagram looks too complex
49
How is the alpha helix represented in the diagram?
By a spiral or cylinder shape
50
What indicates the beta strands in the protein diagram?
Thick arrows pointing from the N-terminal to the C-terminal
51
What structural feature is emphasised in the diagram of a protein? Why?
Polypeptide backbone of the protein, without side chains Too many atoms so diagram looks too complex
52
What does triosephosphate isomerase contain?
Contains a beta-barrel formed from a twisted parallel beta sheet
53
How can myoglobin be represented? (2)
Alpha helices shown as: - Spirals - Cylinders
54
What is cytochrome b composed of?
Composed entirely of alpha helices
55
What has cytochrome b bound to it? Function?
Iron atom bound that functions as electron transporter
56
What is a quaternary structure of a protein?
Formed form more than 1 polypeptide chain
57
What type of complex is associated with chains/subunits in a quaternary protein?
Multimeric complex
58
What does thioredoxin contain?
Contains a mixed beta sheet that is twisted
59
Difference between homodimer + heterodimer?
Homodimer - formed by the joining of 2 identical subunits Heterodimer - formed by the joining of 2 non-identical subunits
60
Name an example of a homodimer
Superoxide dimutase
61
Name an example of a heterodimer
Cyclin A
62
What is haemoglobin composed of?
4 polypeptides: - 2 identical alpha chains - 2 identical beta chains
63
What is Immunoglobulin G?
A type of antibody
64
How many polypeptide chains compose Immunoglobulin G?
Four polypeptide chains.
65
What types of disulphide bridges are present in Immunoglobulin G?
Intramolecular and intermolecular disulphide bridges.
66
What are the 2 major classes of proteins?
- Globular - Fibrous
67
What are globular proteins arranged into?
Compact domains
68
What are fibrous proteins arranged into?
Fibres
69
What are the 3 main groups of fibrous proteins defines by secondary structure? Examples of these groups?
Coiled-coil - keratin + myosin Beta-sheets - amyloid fibres + silks Triple helix - the collagens
70
What is alpha keratin?
A family of mechanically durable proteins found in hair, nails, feathers, etc.
71
What is the primary structure of alpha keratin composed of?
7 amino acid repeats (a-b-c-d-e-f-g) forming an alpha helix.
72
Which residues in this alpha keratin helix are hydrophobic? a-b-c-d-e-f-g
Residues a and d, which lie on the same side of the alpha helix
73
How do two alpha keratin helices associate?
They twist around each other, associating via the hydrophobic faces to form a coiled-coil
74
What structure is formed by the alignment of coiled-coil dimers?
A staggered antiparallel tetramer.
75
What are the building blocks of protofilaments in alpha keratin?
Tetramers
76
What do protofilaments form in the structure of alpha keratin?
Protofibrils, which then form microfibrils
77
What organism produces fibroin?
Silkworms
78
What is the repeating amino acid sequence in fibroin?
6 amino acid repeat (-Gly-Ser-Gly-Ala-Gly-Ala-)n
79
What type of secondary structure does fibroin form?
Antiparallel beta sheet
80
How do glycine, serine, and alanine side chains orient in the beta sheet structure of fibroin?
Glycine side chains project from one side, while serine + alanine side chains project from the other side
81
What contributes to the strength of fibroin?
Stretching requires the breaking of covalent bonds
82
What allows fibroin to be flexible despite its strength?
Due to beta sheets interacting through weak Van der Waals bonds.
83
How do fibroin layers stack together?
Layers stack with glycine inside chains alternating with layers of serine + alanine side chains.
84
What is collagen?
An abundant vertebrate protein that forms strong fibres present in skin, bone, teeth, + cartilage.
85
What percentage of collagen's amino acids are glycine?
1/3 of the amino acids in collagen are glycine.
86
What are the other major amino acids found in collagen?
15-30% of the amino acids are proline or hydroxyproline (Hyp)
87
What is the primary amino acid sequence of collagen?
It consists of a repeating tripeptide of Gly-X-Y, where X is often proline and Y is hydroxyproline
88
Why can't collagen form an alpha helix?
Due to the presence of proline and hydroxyproline residues
89
What type of helix does collagen form?
Collagen forms a 'loose' helix with approximately 3 residues per turn
90
What is the unique feature of collagen's triple helix regarding amino acids?
Every third amino acid passes through the center of the triple helix, which is so crowded that only Glycine (Gly) can fit.
91
Which amino acid residues contribute to the rigidity of collagen?
Proline (Pro) and Hydroxyproline (Hyp) residues confer rigidity
92
What type of bonds do polypeptide chains in collagen form?
Polypeptide chains form inter-chain hydrogen bonds
93
What do triple-helical trimers in collagen often associate to form?
Form large, strong fibres
94
In a globular protein, a leucine residue would most likely be found?
On the interior
95
A parallel beta strands are usually connected by what?
Alpha helix
96
A 2.7nm long alpha helix contains how many amino acids?
18 2.7/0.15 (length of amino acid)
97
Which type of proteins usually have disulphide bridges + which do not?
Extracellular usually do - Intercellular usually don't due to reductuve environment
BIOL 111
flashcards
Decks in class (10)
# Cards
Brainscape helps you reach your goals faster, through stronger study habits.
© 2026 Bold Learning Solutions. Terms and Conditions