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AMINO ACIDS & PROTEINS > ALL THE THINGS > Flashcards

ALL THE THINGS Flashcards

1
Q

What is the strongest type of molecular bond?

A

Covalent

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2
Q

What are the other electrostatic bonds seen when analyzing proteins?

A

Ionic bonds, hydrogen bonds, van der Waals

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3
Q

What other interactions are commonly seen when looking at proteins?

A

hydrophobic interactions

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4
Q

Noncovalent interactions between specific amino acids determine what?

A

the folded shape of the protein

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5
Q

How do nonpolar groups hide from water? What does this due?

A

cluster together; decreases the disruption of H-bonds with water solvent; more energetically stable

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6
Q

What does a hydropathy plot measure?

A

hydrophobicity in a protein

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7
Q

What determines the chemical properties of the amino acid?

A

the nature of the R group

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8
Q

A

A

Alanine, Ala

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9
Q

R

A

Arginine, Arg

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10
Q

N

A

Asparagine, Asn

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11
Q

D

A

Aspartic Acid, Asp

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12
Q

C

A

Cysteine, Cys

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13
Q

Q

A

Glutamine, Gln

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14
Q

E

A

Glutamic Acid, Glu

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15
Q

G

A

Glycine, Gly

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16
Q

H

A

Histidine, His

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17
Q

I

A

Isoleucine, Ile

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18
Q

L

A

Leucine, Leu

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19
Q

K

A

Lysine, Lys

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20
Q

M

A

Methionine, Met

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21
Q

F

A

Phenylalanine, Phe

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22
Q

S

A

Serine, Ser

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23
Q

T

A

Threonine, Thr

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24
Q

W

A

Tryptophan, Trp

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25
Q

Y

A

Tyrosine, Tyr

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26
Q

V

A

Valine, Val

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27
Q

P

A

Proline, Pro

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28
Q

What are the essential amino acids that are nutrional requirements?

A

R, H, I, L, T, K, M, F, W, V

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29
Q

Which amino acids have nonpolar, aliphatic R groups?

A

G, A, P, V, L, I, M, C

C behaves like it is hydrophobic despite having a reactive R-SH group

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30
Q

What is special about Glycine?

A

it’s small R-H group confers flexibility in proteins

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31
Q

What does Proline’s unusual ring structure cause in protein structure?

A

Kinks

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32
Q

Which amino acids have aromatic R-groups?

A

F, Y, W

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33
Q

Which of the aromatic R group amino acids is not hydrophobic?

A

Y

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34
Q

Which of the aromatic amino acids absorbs the highest wavelength of UV light?

A

W with 280nm; F only at 260 nm; nucleic acids at 260 nm

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35
Q

At what absorbance level can proteins be quantified using UV light?

A

280 nm

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36
Q

Which amino acids have a polar, uncharged R group?

A

S, T, C, N, Q

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37
Q

Which amino acids have positively charged (basic) R groups?

A

K, R, H

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38
Q

Which amino acid have negatively charged (acidic) R groups?

A

D, E

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39
Q

By what reaction are peptide bonds formed and is it a spontaneous reaction?

A

condensation (dehydration) and NO!

40
Q

The peptide bonds is ___ , ____ , ____ . There is no rotation at _____ _____ .

A

rigid, planar, has dipoles.

Peptide Bonds

41
Q

What is the primary structure of an Amino Acid?

A

the linear sequence of amino acids in the polypeptide chain

42
Q

In secondary protein structure, local regions of amino acids are folded into a limited set of what distinct structures?

A

alpha helix, beta sheet, and beta turn

43
Q

What does the secondary structure generally involve in terms of bonds?

A

hydrogen bonds between carbonyl and amide groupsin the peptide bonds

44
Q

Are R groups involved in secondary structure?

A

NO

45
Q

What do alpha helices look like and how many amino acids per turn?

A

rigid, right handed helix formin a rod-like structure with 3.6 amino acids per turn

46
Q

How many residues apart are the hydrogen bonds for alpha helices?

A

4

47
Q

What if proline is present in an alpha helix?

A

proline is a helix breaker; it destablizes the helix;

also broken by bulky or charge R groups

48
Q

Why is G not present in alpha helices?

A

confers too much flexibility to the helix

49
Q

How are peptide chains arranged to form beta pleated sheets?

A

parallel or antiparallel

50
Q

Where are hydrogen bonds formed in beta sheets?

A

between adjacent peptide chains

51
Q

How are R groups positioned in beat pleated sheets?

A

alternate above and below the plane

52
Q

What angle and how many amino acids are involved in Beta/Reverse turns?

A

180 degree turn of the peptide chain. 4 amino acids usually P and G

53
Q

What is the tertiary structure of proteins?

A

overall 3D arrangement of the entire peptide chain

spatial organization of structures

54
Q

What does the tertiary structure determine?

A

function of the protein

alterations due to mutations can abolish or alter functions

55
Q

What is the quaternary structure of proteins?

A

spatial arrangement of polypeptide chains in a multi chain protein complex and the nature of their contacts

56
Q

What does the quaternary structure determine?

A

function of the protein complex

57
Q

How are tertiary and quarternary structures stabilized?

A

noncovaelent interations between the peptide bond and R-groups. also done by disulfide bonds

58
Q

What are protein domains?

A

stable arrangements of several elements of secondary and tertiary structure

59
Q

What do separate domains confer?

A

separate functions

60
Q

Small proteins/large proteins have how many domains and functions?

A

Small: one domain, one or few functions

Large: multiple domains, multiple functions

61
Q

How do domains act as evolutionary units?

A

copying and shuffling of domains led to formation of many protein families

62
Q

What are 3D folds of protein structures associated with?

A

specific activity; e.g. ATP binding

63
Q

What is used to analyze amino acid sequence alignment?

A

BLAST algorithm

64
Q

What can the BLAST algorithm be used to identify?

A

homologous proteins from a sequence database

65
Q

What are Orthologs?

A

genes in different species, evovled from a common ancestor gene; same function in the different species

66
Q

What are Paralogs?

A

imperfect copies of genes within species (members of gene families); generally different but likely related functions

67
Q

What is Column Chromatography?

A

separation of a crude protein sample in a buffer (mobile phase) through a stationary porous matrix

stationary phase properties and it’s interaction with the proteins form the basis of the separation

68
Q

How are proteins separated in Column Chromatography?

A

separates based on some property of the protein

69
Q

How are proteins purified in Column Chromatography?

A

sequential column chromatographies with different stationary phases

70
Q

What is another name for Size Exclusion Chromatography?

A

Gel Filtration Chromatography

71
Q

On what basis are proteins separated in Size Exclusion Chromatography?

A

separation on the basis of size

72
Q

What is the solid phase size exclusion chromatography?

A

a porous bead

73
Q

Do small or large molecules move fast or slow in Size Exclusion Chromatography?

A

Small molecules enter the beads and migrate slowly

Large molecules less likely to enter the beads, migrate more quickly

74
Q

Which proteins are the first to elute in Size Exclusion Chromatography?

A

largest proteins

75
Q

How do proteins separate in Ion Exchange Chromatography?

A

on the basis of charge

76
Q

Which proteins migrate slowly in ion exchange chromatography?

A

proteins with opposite charge bind the resin and migrate slowly, unlike proteins that have the same charge as the resin

77
Q

How do proteins separate in affinity chromatography?

A

on the basis of binding properties

how efficiently they bind a given ligand

78
Q

Which proteins are retained in affinity chromatography?

A

only proteins that bind the ligand are retained; can elute because of competition with free ligand

79
Q

What is Gel Electrophoresis?

A

separation of molecules in an electric field through a porous gel

80
Q

What 3 things affect the rate of migration of molecules in Gel Electrophoresis?

A

size, conformation, and charge

81
Q

How are molecules separated in SDS-PAGE?

A

on the basis of size

requires proteins to be unfolded without disulfide bonds

82
Q

Which proteins migrate more quickly in SDS-PAGE?

A

smaller proteins migrate more quickly

opposite to size exclusion chromatography

83
Q

What can be estimated from SDS-PAGE?

A

estimate the molecular weight of a protein

84
Q

What is the isoelectric point of a protein?

A

pH at which there is no net charge

85
Q

How are proteins separated in Isoelectric Focusing?

A

on the basis of their isoelectric points

86
Q

How is the pH gradient established in isoelectric focusing?

A

by using Ampholytes in a gel

87
Q

How long do proteins migrate in isoelectric focusing?

A

until they reach their isoelectric points

88
Q

What technique is the best for separating complex protein mixtures?

A

2D Gel Electrophoresis

89
Q

How are proteins separated in 2D gel electrophoresis?

A

separated through a gel in 2 perpendicular directions using a different basis of separation in each

90
Q

What are the two binding constants?

A

Koff = dissociation rate

Kon = association rate

91
Q

What is the equation for dissociation rate?

A

dissociation rate = koff [AB]

92
Q

What is the equation for association rate?

A

association rate = kon [A] [B]

93
Q

How do you solve for the equilibrium constant?

A

[AB]/[A][B} = kon/koff = K = equilibrium constant

94
Q

What is the equilibrium constant (K) usually called and what is it’s inverse?

A

Ka (M^-1) and the inverse is Kd (M)

95
Q

The stronger the binding between ligand and receptor —

A

the higher the association constant (Ka)

the lower the dissociation constant (Kd)

AMINO ACIDS & PROTEINS (1 decks)

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