Brainscape's Knowledge GenomeTM

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


See full index

bisc 330 > CHEN EXAM 1 > Flashcards

CHEN EXAM 1 Flashcards

1
Q

C-C single bond length

A

1.5 A

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

C=C double bond length

A

1.3-1.4 A

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

hydrogen bond length in biosystem

A

2-4 A

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

optimum van der waals distance

A

4.5 A

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

hydrophobic interactions

A

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

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

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

down syndrome

A

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

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

TATA-box Binding Protein (TBP)

A

molecular structure conserved among archebaterium, plants, and humans

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

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

hydrophobic amino acids

A

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

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

polar amino acids

A

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

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

basic amino acids

A

KRH
lysine, argenine, histidine

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

acidic amino acids

A

DE
aspartic acid, glutamic acid

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

histidine

A

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

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

cysteine cross-linking

A

oxidation can induce disulfide bonds between two cysteines
occurs in insulin

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

sickle cell

A

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

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

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

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

C-N peptide bond length

A

1.32 A

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

C=N bond length

A

1.27 A

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

C-N single bond length

A

1.49 A

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

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

ramachandran plot

A

illustrates favorable and possible torsion angles

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

torsion angles

A

phi and psi angles in amino acids

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

how many DIFFERENT proteins are there in 1 human cell?

A

10,000 - 30,000

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

levels of protein structure

A

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

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

alpha helix characteristics

A

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)

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

beta sheets

A

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

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

how can primary structures predict secondary structures?

A

identifying amphipathic helix (alpha helix has both polar and non polar)
beta strands have hydrophilic and hydrophobic faces

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

chameleon sequences

A

can adopt alpha helix or beta strand in different contexts

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

reserve/beta/hairpin turn

A

C-O group of residue i is H-bonded to the N-H group of residue i+3

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

polypeptide loops

A

part of antibody molecule
lie on protein surfaces
participate in interactions between proteins

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

protein motifs

A

common combinations of secondary structure present in many proteins, usually similar function
ex. helix turn helix in DNA binding proteins

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

coiled-coils

A

two right-handed alpha helices intertwine and form a left-handed super helix
stabilized by ionic and VDWs

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

heptad repeat & leucine zipper

A

3.5 residues per turn
allows side chain pattern to repeat every 7 AAs
2 helices interact through leucine side chain

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

collagen

A

rich in gly and pro
3 helical polypeptide chains form a superhelical cable
substitution mutation of Gly –> osteogenesis imperfecta

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

hemoglobin structure

A

2 alpha-globin, 2 B-globin subunits = heterotetramer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

icosahedron

A

example of quarternary structure, 4 subunits of 60 each
many viruses: rhinovirus, coronavirus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

denaturing proteins

A

urea & B-mercaptoethanol

40
Q

bring a denatured protein back to its native form

A

remove agents, dialysis, oxidation

41
Q

amyloidoses

A

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
Q

green fluorescent protein (GFP)

A

from jellyfish, can be attached to a protein to determine cellular location
oxidation of SYG polypeptide chain = modification for fluorescence

43
Q

proteome

A

entire set of proteins expressed and modified by a cell under a particular set of biochemical conditions

44
Q

gradient centrifugation

A

separate molecules based density

44
Q

protein purification

A

homogenate supernatants undergo a series of centrifuges, the final supernatant is the cytoplasm of soluble proteins

45
Q

salting out

A

solubility of proteins vary with salt concentration
when salt conc increases, different proteins precipitate out

46
Q

dialysis

A

removes salt from protein solution
dialysis bag holes let salt equilibrate but do not let protein through

47
Q

gel-filtration chromatography

A

separates protein by size
smaller proteins enter beads
larger proteins exit first

48
Q

ion-exchange chromatography

A

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
Q

affinity chromatography

A

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
Q

high-performance liquid chromatography

A

very fine beads + high pressure pumps move liquid through column, increased interaction sites (surface area) > higher resolving power

51
Q

SDS PAGE

A

coat proteins in negative charge, separate in gel electrophoresis by size
stain proteins to visualize

52
Q

isoelectric focusing

A

separates protein by pI value
protein is put through a pH gradient and goes to the pH where it has no charge

53
Q

2D gel electrophoresis

A

1) isoelectric focusing and 2) SDS electrophoresis
separates by charge (pH) then size, each unique

54
Q

antibody diversification

A

hypermutation of antigen binding site

55
Q

monoclonal antibody

A

binds to 1 epitope

56
Q

polyclonal antibody

A

binds to different epitopes on the same antigen

57
Q

hybridoma technology

A

beta cells and cancer cells form immortalized B cells and can induce tumors

58
Q

ELISA (enzyme-linked immunosorbent assay)

A

quantifies amount of protein present based on color
indirect: antigen, antibody, then second antibody linked to fluorophore
sandwich: antibody, antigen, antibody

59
Q

western blotting / immunoblotting

A

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
Q

co-immunoprecipitation

A

antibody incubation + antibody binding protein –> complex can be separated and analyzed

61
Q

mass spectrometry

A

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
Q

edman degradation

A

protein exposed to PTH which reacts with N-terminus, last AA can be released without cleavage, identify the AA at N-terminas

63
Q

X-Ray crystallography

A

detects x-ray diffraction
only 1 formation (limitation)
determines exact atomic location

64
Q

NMR

A

detects nuclear spin states
nuclei of atoms absorb different frequencies called chemical shifts
smaller proteins only, approximate (not super accurate)

65
Q

nuclear overhauser effect

A

identifies pairs of protons in close proximity (adjacent hydrogens)

66
Q

cyro-electron microscopy

A

detects electron density
larger proteins, exact atomic location

67
Q

RNA viruses

A

RNA genome, mRNA to make protein

68
Q

retrovirus

A

RNA > DNA > RNA > protein

69
Q

nucleoside

A

base and sugar

70
Q

nucleotide

A

base, sugar, phosphate

71
Q

2 ‘OH

A

2 ‘OH in RNA can be deprotonated in basic conditions (auto-hydrolysis), unstable

72
Q

B DNA structure

A

R-handed, 3.4 A rise, 10.4 bp/turn, 20 A diameter, 35.4 pitch, C2’ endo sugar pucker

73
Q

chargaff’s rule

A

A=T and C=G but A+T does not equal C+G

74
Q

hammerhead ribozyme

A

first discovery of enzyme made of RNA
catalytic RNA that can catalyze bond hydrolysis

75
Q

tyrosine pKa

A

10

76
Q

cysteine pKa

A

8.3

77
Q

lysine pKa

A

10.4

78
Q

argenine pKa

A

12.5

78
Q

aspartic and glutamic acid pka

A

4.1

79
Q

pitch

A

height of a turn, rise * (residues/turn)

80
Q

rise

A

height of a residue, A/residue

81
Q

pKa of N terminal

A

8

82
Q

pKa of C terminal

A

3.1

83
Q

structure of A DNA

A

R-handed, 2.3 A rise, 11 bp/turn, 26 A diameter, 25.3 pitch, C3’ endo sugar pucker

84
Q

structure of Z DNA

A

L-handed, 3.8 A rise, 12 bp/turn, 18 A diameter, 45.6 pitch

85
Q

major and minor grooves length

A

13 and 9 A

86
Q

how many base pairs in human genome?

A

6.4 B

87
Q

how long is DNA per cell?

A

2 m

88
Q

DNA base length

A

1.2 nm

89
Q

Angstrom to nm

A

10 A = 1nm

90
Q

A N1 pKa

A

4.5

91
Q

C N3 pKa

A

4.2

92
Q

what % of DNA codes for proteins?

A

1

93
Q

cell nucleus diameter

A

10 μm

94
Q
A

bisc 330 (3 decks)

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