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Biochem > Review exam 1 > Flashcards

Review exam 1 Flashcards

Exam 1 review

1
Q

Major groove is accessible to

A

proteins

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2
Q

DNA bending (2) ways

A

(1) intrinsic bending via adenine repeats

(2) protein-induced bending

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3
Q

only _______ proteins are encoded by the genome

A

25,000

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4
Q

Junk DNA (8)

A

(1) pseudogenes
(2) processed pseudogenes
(3) proviruses
(4) SINES
(5) LINES
(6) microsatellites
(7) minisatellites
(8) SNPs

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5
Q

microsatellites occur in

A

non-coding areas

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6
Q

minisatellites occur in

A

non-coding areas

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7
Q

Single Nucleotide Polymorphisms (SNPs) occurs in

A

coding, non-coding or intergenic areas

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8
Q

what allows cancer cell to be immortal

A

telomerase is turned on

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9
Q

DNA methylation occurs in which residues

A

cytosine and adenine

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10
Q

Histone acetylation occurs in which residue

A

lysine

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11
Q

Bloom’s syndrome

A

dna helicase is deficient and leads to malignancies

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12
Q

Werner’s syndrome

A

dna helicase is deficient leading to premature aging

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13
Q

PCNA increases?

A

processivity

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14
Q

Li-Fraumeni Syndrome

A

p53 malignancy

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15
Q

defects in hMSH and hMLH are associated with

A

HNPCC

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16
Q

mismatch repair dx

A

trinucleotide expansion

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17
Q

(3) trinucleotide repeats

A

(1) fragile x syndrome
(2) myotonic dystrophy
(3) Hnt disease

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18
Q

Dx in excision repair

A

Xeroderma Pigmentosum

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19
Q

What causes Deamination

A

nitrous Acid (HNO2)

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20
Q

Cytosine deaminates into

A

uracil

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21
Q

Adenine deaminates into

A

hypoxanthine

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22
Q

intercalators (2)

A

proflavin

ethidium bromide

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23
Q

what do intercalators do?

A

gives rise to insertions/ deletions

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24
Q

restriction endonucleases look for

A

palindromic sequences and cut

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25
pulsed field gel electrophoresis can
separate whole chromosomes
26
why is southern blotting used?
- detection of trinucelotide repeat expansion detection | - detection of deletions
27
DNA fingerprinting
finding the different RE sites in humans---> very variable
28
FISH
chromosome detection
29
FISH can determine if someone has
trisomy or monosomy
30
DNA band shift
determines IF the protein attaches to DNA
31
DNA footprinting
determines WHERE protein and DNA interactions occur
32
PCR allows detection
trinucleotide expansion
33
PCR process
- Denaturation - Annealing - Extension--> taq DNA pol (heat stable but no PCNA= low processivity)
34
RT-PCR allows for
to determine cancer reoccurrence
35
Gene library
has all genomic DNA
36
cDNA library has genes derived from
mRNA and made with RT
37
mRNA is ____to template but ____ to coding strand
mRNA is complementary to template but identical to coding strand
38
difference between a genomic library and a cDNA
a genomic library contains fragments of the genome, whereas a cDNA library is derived from the mRNA being expressed in a given tissue
39
probes hybridyze at
lower temperature
40
RFC
clamp loader
41
PCNA
Clamp
42
MCM complex
helicase
43
Polymerase switch
RFC PCNA Pol epsilon Pol delta
44
Nucleotide analogues
acyclovir, AZT
45
Xeroderma Pigmentosum defect is in the
nuclease that cleaves DNA near pyrimidine dimers
46
An additional feature of cloning vectors are
origins of replication
47
siRNA uses the
RISC complex
48
Cas9 is a
programmable nuclease
49
what does Cas9-sgRNA complex does?
make a double stranded break in the genomic DNA target
50
what are miRNAs?
21 nt long, non-coding that play a role in regulation of translation
51
miRNAs target
the 3' UTR
52
miRNAs role in translation
recruit the RISC complex and either cause stalling of the translation complex or degradation of the mRNA
53
How to detect DNA methylation?
bisulfite DNA sequencing
54
predominant protein in elastic tissue such as the lungs
elastin
55
fibrous protein not dissolved in water
elastin, keratin
56
bicarbonate can can absorb
H+
57
Exhaling deeply causes
pH to rise
58
Aspirin is isoelectric at
very low pH
59
hydroxyurea
stimulates the production of HbF
60
Bone marrow transplantation
replaces HbS with HbA
61
Step 1 in collagen biosynthesis
polypeptide chain synthesis
62
Step 2 in collagen biosynthesis
Hydroxylation
63
Step 3 in collagen biosynthesis
glycosylation
64
Step 4 in collagen biosynthesis
Disulfied bond formation at C-terminus
65
Step 5 in collagen biosynthesis
triple helix formation
66
Step 6 in collagen biosynthesis
secretion from fibroblast
67
Step 7 in collagen biosynthesis
hydrolysis of propeptide leading to cleavage of N'/C' terminal
68
Step 8 in collagen biosynthesis
Assembly into fibril
69
Step 9 in collagen biosynthesis
assembly into fiber and formation of cross links
70
osteogenesis imperfecta is caused by
substitution of a glycine to cysteine in collagen type 1
71
characterized clinically with hyperelastic joints and skin hyper extensibility
ehlers danlos
72
Heterezygosity is not Ok in ED
gene defects in the collagen genes
73
Heterozygosity is ok
improper processing of collagen caused by lack of processing enzyme
74
what does steroid do?
they bind to the steroid receptor complex which localizes to the nucleus and binds to enhancer element
75
insulin is
cell-specific expression
76
RISC is activated with
ATP
77
mRNA therapies focuses on?
RNA interference of particular mRNA via hybridization to dsRNA
78
CCA is
post-transcriptional modification
79
CCA creates a
high energy intermediate
80
in Methemoglobinemia
histidine of heme is replaced with tyrosine
81
Methemoglobinemia an be caused by
ingesting nitrites and nitrates
82
how to treat thalassemia
blood transfusion
83
protein maturation occurs via
proteolysis of precursor components
84
what is the importance of the holes in tropocollagen?
allows for calcium phosphate deposition during bone formation
85
uracil removal involves
a glycosidase that creates an AP site
86
mismatch repair system involves
helicase and exonuclease
87
Lines encode a
reverse transcriptase
88
processed pseudogenes resemble
mRNA
89
hMSH binds to where?
mismatched bases
90
SSCP (single strand polymorphism) identifies
point mutations
91
remodeling of the nucleosomes
SWI-SNF
92
What happens when elF2 gets phosphorolated?
it becomes sinactive
93
ways that elF2 can get phosphorolated?
aa starvation dsRNA unfolded proteins heme deprivation
94
CRF in termination
binds the stop codon and the complex dissociates
95
dideoxy analog
sanger method

Biochem (10 decks)

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