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BISC 330 > CHEN EXAM 1 > Flashcards

CHEN EXAM 1 Flashcards

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1
Q

C-C single bond length

A

1.5 A

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2
Q

C=C double bond length

A

1.3-1.4 A

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3
Q

hydrogen bond length in biosystem

A

2-4 A

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4
Q

optimum van der waals distance

A

4.5 A

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5
Q

hydrophobic interactions

A

powered by the increase of entropy in water (favors increase in entropy)

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6
Q

how can you deprotonate dsDNA?

A

heat or increase pH, pH 9.9 most strands denatured (thymine), at 9.7 about half (guanine)

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7
Q

down syndrome

A

trisomy 21, 3 copies of chromosome 21 due to chromosome segregation error

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8
Q

TATA-box Binding Protein (TBP)

A

molecular structure conserved among archebaterium, plants, and humans

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9
Q

amino acid ionization states

A

both protonated (in acidic conditions): NH3+ and COOH
zwitterionic: NH3+ and COO-
both deprotonated (in basic conditions): NH2 and COO-

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10
Q

hydrophobic amino acids

A

GAPLIVYMWF
guanine, alanine, proline, leucine, isoleucine, valine, tyrosine, methionine, tryptophan, phenylalanine

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11
Q

polar amino acids

A

STYNQC
serine, threonine, tyrosine, asparagine, glutamine, cysteine

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12
Q

basic amino acids

A

KRH
lysine, argenine, histidine

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13
Q

acidic amino acids

A

DE
aspartic acid, glutamic acid

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14
Q

histidine

A

acts like a physiological pH sensor, pKa=6
can accept or donate protons at this pH

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15
Q

cysteine cross-linking

A

oxidation can induce disulfide bonds between two cysteines
occurs in insulin

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16
Q

sickle cell

A

substitution of valine for glutamic acid
change in primary structure affects function
survived due to malaria advantage

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17
Q

cis/trans configurations of amino acids

A

based on if the alpha carbons are on the same side (split by peptide bond)
trans is lower energy and favored

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18
Q

proline configurations

A

cis and trans have similar steric clashes so both isomers exist, isomerase can convert the proline from one configuration to another

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19
Q

C-N peptide bond length

A

1.32 A

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20
Q

C=N bond length

A

1.27 A

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21
Q

C-N single bond length

A

1.49 A

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22
Q

which angles in amino acids can be rotated and which are fixed?

A

peptide bond (C-N) is fixed due to partial double bond character/resonance
alpha C and NH3 (phi) can rotate, -80
alpha C and COO (psi) can rotate, 85

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23
Q

ramachandran plot

A

illustrates favorable and possible torsion angles

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24
Q

torsion angles

A

phi and psi angles in amino acids

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25
how many DIFFERENT proteins are there in 1 human cell?
10,000 - 30,000
26
levels of protein structure
1: AA N to C sequence 2: a helix or beta sheet via hydrogen bonding 3: 3D folding via side chain interactions (noncovalent bonds, Cys disulfide bonds) 4: interaction of tertiary structures of 2+ polypeptide chains
27
alpha helix characteristics
right handed coil with protruding R groups CO and NH groups H bond 3.6 residues/turn (3.6 AA/turn) 1.5 A/residues-rise (height of one AA) 5.4 A/turn-pitch (height of one turn)
28
beta sheets
distance between adjacent AAs: 3.5 A antiparallel or parallel or mixed antiparallel arises by hairpin folding of a single strand twisted sheets, hydrophobic/hydrophilic faces
29
how can primary structures predict secondary structures?
identifying amphipathic helix (alpha helix has both polar and non polar) beta strands have hydrophilic and hydrophobic faces
30
chameleon sequences
can adopt alpha helix or beta strand in different contexts
31
reserve/beta/hairpin turn
C-O group of residue i is H-bonded to the N-H group of residue i+3
32
polypeptide loops
part of antibody molecule lie on protein surfaces participate in interactions between proteins
33
protein motifs
common combinations of secondary structure present in many proteins, usually similar function ex. helix turn helix in DNA binding proteins
34
coiled-coils
two right-handed alpha helices intertwine and form a left-handed super helix stabilized by ionic and VDWs
35
heptad repeat & leucine zipper
3.5 residues per turn allows side chain pattern to repeat every 7 AAs 2 helices interact through leucine side chain
36
collagen
rich in gly and pro 3 helical polypeptide chains form a superhelical cable substitution mutation of Gly --> osteogenesis imperfecta
37
hemoglobin structure
2 alpha-globin, 2 B-globin subunits = heterotetramer
38
icosahedron
example of quarternary structure, 4 subunits of 60 each many viruses: rhinovirus, coronavirus
39
denaturing proteins
urea & B-mercaptoethanol
40
bring a denatured protein back to its native form
remove agents, dialysis, oxidation
41
amyloidoses
diseases resulting from protein aggregates (amyloid fibrils) Alzheimer's, Mad Cow Disease beta sheets are prone to aggregate one aggregate is a nucleus to recruit more
42
green fluorescent protein (GFP)
from jellyfish, can be attached to a protein to determine cellular location oxidation of SYG polypeptide chain = modification for fluorescence
43
proteome
entire set of proteins expressed and modified by a cell under a particular set of biochemical conditions
44
gradient centrifugation
separate molecules based density
44
protein purification
homogenate supernatants undergo a series of centrifuges, the final supernatant is the cytoplasm of soluble proteins
45
salting out
solubility of proteins vary with salt concentration when salt conc increases, different proteins precipitate out
46
dialysis
removes salt from protein solution dialysis bag holes let salt equilibrate but do not let protein through
47
gel-filtration chromatography
separates protein by size smaller proteins enter beads larger proteins exit first
48
ion-exchange chromatography
separation of proteins by charge beads are charged, same charged proteins will leave and opposite charged will bind bound proteins released by increasing salt conc. or adjusting buffer pH
49
affinity chromatography
beads with attached target chemicals will bind proteins with high affinity to chemical bound proteins are released by passing the target chemical through the solution
50
high-performance liquid chromatography
very fine beads + high pressure pumps move liquid through column, increased interaction sites (surface area) > higher resolving power
51
SDS PAGE
coat proteins in negative charge, separate in gel electrophoresis by size stain proteins to visualize
52
isoelectric focusing
separates protein by pI value protein is put through a pH gradient and goes to the pH where it has no charge
53
2D gel electrophoresis
1) isoelectric focusing and 2) SDS electrophoresis separates by charge (pH) then size, each unique
54
antibody diversification
hypermutation of antigen binding site
55
monoclonal antibody
binds to 1 epitope
56
polyclonal antibody
binds to different epitopes on the same antigen
57
hybridoma technology
beta cells and cancer cells form immortalized B cells and can induce tumors
58
ELISA (enzyme-linked immunosorbent assay)
quantifies amount of protein present based on color indirect: antigen, antibody, then second antibody linked to fluorophore sandwich: antibody, antigen, antibody
59
western blotting / immunoblotting
SDS PAGE transfer to polymer stain with primary antibody specific to protein stain with 2nd antibody specific to primary antibody 2nd antibody attached to fluorescence
60
co-immunoprecipitation
antibody incubation + antibody binding protein --> complex can be separated and analyzed
61
mass spectrometry
protein sample is ionized by a laser electrical field accelerates ions toward detector lightest ions arrive first, time of flight for ions is measured
62
edman degradation
protein exposed to PTH which reacts with N-terminus, last AA can be released without cleavage, identify the AA at N-terminas
63
X-Ray crystallography
detects x-ray diffraction only 1 formation (limitation) determines exact atomic location
64
NMR
detects nuclear spin states nuclei of atoms absorb different frequencies called chemical shifts smaller proteins only, approximate (not super accurate)
65
nuclear overhauser effect
identifies pairs of protons in close proximity (adjacent hydrogens)
66
cyro-electron microscopy
detects electron density larger proteins, exact atomic location
67
RNA viruses
RNA genome, mRNA to make protein
68
retrovirus
RNA > DNA > RNA > protein
69
nucleoside
base and sugar
70
nucleotide
base, sugar, phosphate
71
2 'OH
2 'OH in RNA can be deprotonated in basic conditions (auto-hydrolysis), unstable
72
B DNA structure
R-handed, 3.4 A rise, 10.4 bp/turn, 20 A diameter, 35.4 pitch, C2' endo sugar pucker
73
chargaff's rule
A=T and C=G but A+T does not equal C+G
74
hammerhead ribozyme
first discovery of enzyme made of RNA catalytic RNA that can catalyze bond hydrolysis
75
tyrosine pKa
10
76
cysteine pKa
8.3
77
lysine pKa
10.4
78
argenine pKa
12.5
78
aspartic and glutamic acid pka
4.1
79
pitch
height of a turn, rise * (residues/turn)
80
rise
height of a residue, A/residue
81
pKa of N terminal
8
82
pKa of C terminal
3.1
83
structure of A DNA
R-handed, 2.3 A rise, 11 bp/turn, 26 A diameter, 25.3 pitch, C3' endo sugar pucker
84
structure of Z DNA
L-handed, 3.8 A rise, 12 bp/turn, 18 A diameter, 45.6 pitch
85
major and minor grooves length
13 and 9 A
86
how many base pairs in human genome?
6.4 B
87
how long is DNA per cell?
2 m
88
DNA base length
1.2 nm
89
Angstrom to nm
10 A = 1nm
90
A N1 pKa
4.5
91
C N3 pKa
4.2
92
what % of DNA codes for proteins?
1
93
cell nucleus diameter
10 μm
94

BISC 330 (3 decks)

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