Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BISC 320 > Protein Structure > Flashcards

Protein Structure Flashcards

1
Q

What is the structure of proteins?

A

polymers of covalently joined amino acids

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

What are the components of amino acids?

A
  1. a central carbon atom
  2. an amino group
  3. a carboxylate group
  4. a side chain, which differs in each of the 20 types of amino acid
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is amphipathic?

A

having both hydrophobic and hydrophilic characteristics

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

What can sulfhydryl (-SH) groups form?

A

on cysteine can form covalent bonds with one another to make disulfide bridges

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

What do all amino acids exist as?

A

two stereoisomers, L and D, depending on the arrangement around Ca

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

What are found naturally in occuring proteins?

A

L-amino acids

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

T or F: glycine exist as two stereoisomers

A

false

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

What is the pKa of histidine?

A

close to the neutral pH of a cell, so it can act as a H+ donor or acceptor during biological reactions

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

What is a peptide bond?

A

results from a condensation reaction between the carboxyl group of one amino acid and the amino group of another amino acid

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

What are incorporated amino acids called?

A

amino acid residues

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

What forms the peptide backbone?

A

a repeating series of C and N atoms form the peptide backbone, with side chains protruding

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

What is the N-terminus?

A

the end of a polypeptide with an exposed amino group

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

What is the C-terminus?

A

the exposed carboxyl at the other end

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

How are residues in a polypeptide numbered?

A

from the N-terminus

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

Why do polypeptide chains have limited conformations?

A

resonance

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

What prevents free rotation of the peptide bond?

A

electrons shared between O, C, and N

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

What is the shape of a peptide bond?

A

planar

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

What are the parts of the polypeptide that can still rotate:

A
  1. the N-Calpha bond has rotation angle
  2. the C-Calpha bond has rotation angle
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What do different angle combinations cause?

A

collisions of side chains or the polypeptide background: these angle combinations do not occur

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

What is the function of a Ramachandran plot?

A

indicates the restricted conformation

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

What does each point on the plot show?

A

a combination of angles

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

What do black regions on the plot show?

A

where clashes do not occur

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

What do gray regions on the plot show?

A

minimal clashes

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

What does the plot depend?

A

the amino acid residues in the polypeptide (e.g. glycine side chain is small (a single -H) so can tolerate many more angles combinations than other residues)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is the primary structure?

A

the amino acid sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

What is the secondary structure?

A

refers to localized regions of repeated regular structures such as beta-strands and alpha-helices

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What are tertiary structures?

A

the final folded structure of a single polypeptide (3D)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What are quaternary structure?

A

the combination of multiple polypeptides in a single protein (many only have one)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What occurs in alpha-helices and beta-sheets?

A

H-bonding between the C=O group of one peptide bond and the N-H group of another

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What are the characteristics of an alpha helix?

A

3.6 amino acids per turn and diameter of 12 A (similar to DNA major groove)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Where are the side chains of an alpha helix?

A

the side chains protrude outward from the alpha helix interact with proteins, nucleic acids, etc.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What disrupts an alpha helix?

A

proline

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What does antiparallel mean?

A

N termini at opposite ends

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What does parallel mean?

A

the same end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

How are beta sheets formed?

A

when peptide backbones (beta strands) hydrogen bond to one another through their carbonyl and amino groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is the shape of beta sheets?

A

slightly twisted, largely planar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Where are side chains located in beta sheets?

A

above and below the plane of the beta sheet

38
Q

Where are amphipathic sheets found?

A

at protein surfaces

39
Q

What determines local secondary structure formation?

A

amino acid composition

40
Q

What amino acids are often found in helices?

A

leucine, methionine, glutamine, and glutamic

41
Q

What amino acids are often found in beta sheets?

A

valine, isoleucine, and phenylalanine

42
Q

What amino groups often found in beta turns?

A

glycine and proline

43
Q

Why does proline have an unusual structure?

A

introduces kinks in the polypeptide chain

44
Q

Why does glycine have an unusual structure?

A

has a very small side chain (-H) and so is very flexible

45
Q

What drives protein folding?

A

hydrophobic interactions

46
Q

How do hydrophobic residues interact?

A

preferentially associate with each other and exclude water molecules; most polar residues are on the exterior of the folded protein

47
Q

How can proteins be unfolded and refolded?

A

by changing conditions (e.g. heat, detergent, solvent), and when restored to native conditions

48
Q

What is an example of a protein that cannot be re-nature?

A

albumin

49
Q

T or F: secondary structures can be fairly reliably predicted

A

true

50
Q

T or F: tertiary structures can be fairly reliably predicted

A

false, very complex and cannot be predicted from primary sequence de novo

51
Q

How are protein structures predicted?

A

conservation of amino acid sequence enables prediction based on known structures

52
Q

How do proteins share similar structures

A

proteins share similar and identical amino acids

53
Q

What percent yields fairly similar structures?

A

25% sequence identity

54
Q

What are similar amino acids?

A

amino acids that have small changes (letter changes) in amino acid sequence

55
Q

How is the function of newly identified genes predicted?

A

based on the amino acid sequence it encodes

56
Q

What percent of similarity indicates similar structure and function?

A

> 25%

57
Q

What is a strong indicator of similar function?

A

conservation of critical amino acids

58
Q

What is a domain?

A

a compact region of a polypeptide than can fold on its own

59
Q

T or F: proteins can have multiple domains?

A

true, domains fold independently and carry out specific functions

60
Q

What are proteins comprised of?

A

domain “modules”

61
Q

What is the structure of proteins?

A

modular

62
Q

What are motifs?

A

stereotypical combinations of 2 degree structures

63
Q

What are motifs associated with?

A

specific amino acid sequences that make specific contacts with each other or ions that coordinate charges

64
Q

What is the structure of secondary amphipathic structures?

A

having a hydrophilic and hydrophobic surface, enabling interactions with other such structures

65
Q

Where is the “recognition” helix located?

A

lies in the major groove of DNA and makes H-bonds with base groups

66
Q

What is the function of other parts of a protein binding to DNA?

A

make non-specific contacts with the DNA backbone that facilitate finding the specific sequence, and stabilize binding

67
Q

What do many proteins bind to DNA as?

A

dimers that interact with DNA sequences separated by approximately one turn of the NA helix

68
Q

What forms a zinc-finger?

A

two cysteines and two histidines coordinate a Zn ion to form a finger

69
Q

What does each finger recognize?

A

~3bp of DNA in a sequence-specific manner

70
Q

Why do chemical groups vary more in the major groove than in the minor groove?

A

because T-A and A-T are the same, and G-C and C-G are the same, so these can’t be distinguished by binding proteins

71
Q

What type of bonds do DNA-binding proteins form?

A

non-covalent interactions with exposed groups

72
Q

What varies in different DNA sequences?

A

different combinations of hydrogen, bond acceptors, hydrogen donors, and methyl groups available

73
Q

What is interaction specificity determined by?

A

specificity between protein and DNA is determined by the DNA sequence and the protein shape/ available binding groups

74
Q

How many bonds can Asparagine form with an A?

A

two hydrogen bonds with an A

75
Q

What covalent modification of amino acid side chains can act as a “switch”?

A

phosphorylation, acetylation, and methylation

76
Q

What happens when covalent modification of amino acid side chains act as a switch?

A

results in allosteric change in the protein. Alternatively, the modification may directly effect ligand binding cooperative interactions

77
Q

What is ubiquitin?

A

small protein (7 kDa) that may be covalently linked to lysine

78
Q

What is the function of mono-Ub?

A

regulates activity

79
Q

What is the function of poly-Ub?

A

targets the protein for rapid degradation

80
Q

What is SUMO?

A

small ubiquitin-like modifier

81
Q

What is the function of glycosylation?

A

adds bulky carbohydrate groups, altering their surface structures. Very common in membrane and secreted proteins

82
Q

Are hydrophobic groups reactive?

A

No, hydrophobic groups are essentially non-reactive

83
Q

What is the function of the sulfhydryl (S-H) group in R group covalent formation?

A

can form disulfide bond with another cysteine (usually in the same protein)

84
Q

What is the function of hydroxyl groups (serine, threonine, tyrosine) in R group covalent formation?

A

react to form O=-linkages, including phosphorylation and glycosylation

85
Q

What process can the amine group of asparagine undergo?

A

glycosylation

86
Q

What process can the amino group of lysine undergo?

A

methylation, acetylation, or ubiquitylation

87
Q

What is phosphorylation?

A

a reversible modification that alters the protein function

88
Q

What is the major donor for phosphorylation?

A

ATP

89
Q

What is the function of protein kinases?

A

catalyze phosphate addition

90
Q

What is the function of protein phosphatases?

A

catalyze phosphate removal

91
Q

What is the role of hydrolysis of the phosphoanhydride bonds of ATP?

A

as pyrophosphate, it provides much of the free energy needed for many enzymatic reactions

92
Q

What are the three characteristics of ATP?

A
  1. major phosphate and adenylate dono in the cell
  2. building block in RNA and the precursor of dATP
  3. major allosteric regulatory of many proteins. May involve binding of ATP only, or binding and hydrolysis of ATP

BISC 320 (20 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions