ALL THE THINGS Flashcards
(95 cards)
1
Q
What is the strongest type of molecular bond?
A
Covalent
2
Q
What are the other electrostatic bonds seen when analyzing proteins?
A
Ionic bonds, hydrogen bonds, van der Waals
3
Q
What other interactions are commonly seen when looking at proteins?
A
hydrophobic interactions
4
Q
Noncovalent interactions between specific amino acids determine what?
A
the folded shape of the protein
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
6
Q
What does a hydropathy plot measure?
A
hydrophobicity in a protein
7
Q
What determines the chemical properties of the amino acid?
A
the nature of the R group
8
Q
A
A
Alanine, Ala
9
Q
R
A
Arginine, Arg
10
Q
N
A
Asparagine, Asn
11
Q
D
A
Aspartic Acid, Asp
12
Q
C
A
Cysteine, Cys
13
Q
Q
A
Glutamine, Gln
14
Q
E
A
Glutamic Acid, Glu
15
Q
G
A
Glycine, Gly
16
Q
H
A
Histidine, His
17
Q
I
A
Isoleucine, Ile
18
Q
L
A
Leucine, Leu
19
Q
K
A
Lysine, Lys
20
Q
M
A
Methionine, Met
21
Q
F
A
Phenylalanine, Phe
22
Q
S
A
Serine, Ser
23
Q
T
A
Threonine, Thr
24
Q
W
A
Tryptophan, Trp
25
Y
Tyrosine, Tyr
26
V
Valine, Val
27
P
Proline, Pro
28
What are the essential amino acids that are nutrional requirements?
R, H, I, L, T, K, M, F, W, V
29
Which amino acids have nonpolar, aliphatic R groups?
G, A, P, V, L, I, M, C
C behaves like it is hydrophobic despite having a reactive R-SH group
30
What is special about Glycine?
it's small R-H group confers flexibility in proteins
31
What does Proline's unusual ring structure cause in protein structure?
Kinks
32
Which amino acids have aromatic R-groups?
F, Y, W
33
Which of the aromatic R group amino acids is not hydrophobic?
Y
34
Which of the aromatic amino acids absorbs the highest wavelength of UV light?
W with 280nm; F only at 260 nm; nucleic acids at 260 nm
35
At what absorbance level can proteins be quantified using UV light?
280 nm
36
Which amino acids have a polar, uncharged R group?
S, T, C, N, Q
37
Which amino acids have positively charged (basic) R groups?
K, R, H
38
Which amino acid have negatively charged (acidic) R groups?
D, E
39
By what reaction are peptide bonds formed and is it a spontaneous reaction?
condensation (dehydration) and NO!
40
The peptide bonds is ___ , ____ , ____ . There is no rotation at _____ _____ .
rigid, planar, has dipoles.
Peptide Bonds
41
What is the primary structure of an Amino Acid?
the linear sequence of amino acids in the polypeptide chain
42
In secondary protein structure, local regions of amino acids are folded into a limited set of what distinct structures?
alpha helix, beta sheet, and beta turn
43
What does the secondary structure generally involve in terms of bonds?
hydrogen bonds between carbonyl and amide groupsin the peptide bonds
44
Are R groups involved in secondary structure?
NO
45
What do alpha helices look like and how many amino acids per turn?
rigid, right handed helix formin a rod-like structure with 3.6 amino acids per turn
46
How many residues apart are the hydrogen bonds for alpha helices?
4
47
What if proline is present in an alpha helix?
proline is a helix breaker; it destablizes the helix;
also broken by bulky or charge R groups
48
Why is G not present in alpha helices?
confers too much flexibility to the helix
49
How are peptide chains arranged to form beta pleated sheets?
parallel or antiparallel
50
Where are hydrogen bonds formed in beta sheets?
between adjacent peptide chains
51
How are R groups positioned in beat pleated sheets?
alternate above and below the plane
52
What angle and how many amino acids are involved in Beta/Reverse turns?
180 degree turn of the peptide chain. 4 amino acids usually P and G
53
What is the tertiary structure of proteins?
overall 3D arrangement of the entire peptide chain
spatial organization of structures
54
What does the tertiary structure determine?
function of the protein
alterations due to mutations can abolish or alter functions
55
What is the quaternary structure of proteins?
spatial arrangement of polypeptide chains in a multi chain protein complex and the nature of their contacts
56
What does the quaternary structure determine?
function of the protein complex
57
How are tertiary and quarternary structures stabilized?
noncovaelent interations between the peptide bond and R-groups. also done by disulfide bonds
58
What are protein domains?
stable arrangements of several elements of secondary and tertiary structure
59
What do separate domains confer?
separate functions
60
Small proteins/large proteins have how many domains and functions?
Small: one domain, one or few functions
Large: multiple domains, multiple functions
61
How do domains act as evolutionary units?
copying and shuffling of domains led to formation of many protein families
62
What are 3D folds of protein structures associated with?
specific activity; e.g. ATP binding
63
What is used to analyze amino acid sequence alignment?
BLAST algorithm
64
What can the BLAST algorithm be used to identify?
homologous proteins from a sequence database
65
What are Orthologs?
genes in different species, evovled from a common ancestor gene; same function in the different species
66
What are Paralogs?
imperfect copies of genes within species (members of gene families); generally different but likely related functions
67
What is Column Chromatography?
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
How are proteins separated in Column Chromatography?
separates based on some property of the protein
69
How are proteins purified in Column Chromatography?
sequential column chromatographies with different stationary phases
70
What is another name for Size Exclusion Chromatography?
Gel Filtration Chromatography
71
On what basis are proteins separated in Size Exclusion Chromatography?
separation on the basis of size
72
What is the solid phase size exclusion chromatography?
a porous bead
73
Do small or large molecules move fast or slow in Size Exclusion Chromatography?
Small molecules enter the beads and migrate slowly
Large molecules less likely to enter the beads, migrate more quickly
74
Which proteins are the first to elute in Size Exclusion Chromatography?
largest proteins
75
How do proteins separate in Ion Exchange Chromatography?
on the basis of charge
76
Which proteins migrate slowly in ion exchange chromatography?
proteins with opposite charge bind the resin and migrate slowly, unlike proteins that have the same charge as the resin
77
How do proteins separate in affinity chromatography?
on the basis of binding properties
how efficiently they bind a given ligand
78
Which proteins are retained in affinity chromatography?
only proteins that bind the ligand are retained; can elute because of competition with free ligand
79
What is Gel Electrophoresis?
separation of molecules in an electric field through a porous gel
80
What 3 things affect the rate of migration of molecules in Gel Electrophoresis?
size, conformation, and charge
81
How are molecules separated in SDS-PAGE?
on the basis of size
requires proteins to be unfolded without disulfide bonds
82
Which proteins migrate more quickly in SDS-PAGE?
smaller proteins migrate more quickly
opposite to size exclusion chromatography
83
What can be estimated from SDS-PAGE?
estimate the molecular weight of a protein
84
What is the isoelectric point of a protein?
pH at which there is no net charge
85
How are proteins separated in Isoelectric Focusing?
on the basis of their isoelectric points
86
How is the pH gradient established in isoelectric focusing?
by using Ampholytes in a gel
87
How long do proteins migrate in isoelectric focusing?
until they reach their isoelectric points
88
What technique is the best for separating complex protein mixtures?
2D Gel Electrophoresis
89
How are proteins separated in 2D gel electrophoresis?
separated through a gel in 2 perpendicular directions using a different basis of separation in each
90
What are the two binding constants?
Koff = dissociation rate
Kon = association rate
91
What is the equation for dissociation rate?
dissociation rate = koff [AB]
92
What is the equation for association rate?
association rate = kon [A] [B]
93
How do you solve for the equilibrium constant?
[AB]/[A][B} = kon/koff = K = equilibrium constant
94
What is the equilibrium constant (K) usually called and what is it's inverse?
Ka (M^-1) and the inverse is Kd (M)
95
The stronger the binding between ligand and receptor ---
the higher the association constant (Ka)
the lower the dissociation constant (Kd)
