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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

Bloomā€™s syndrome

A

dna helicase is deficient and leads to malignancies

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12
Q

Wernerā€™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
Q

pulsed field gel electrophoresis can

A

separate whole chromosomes

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26
Q

why is southern blotting used?

A
  • detection of trinucelotide repeat expansion detection

- detection of deletions

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27
Q

DNA fingerprinting

A

finding the different RE sites in humansā€”> very variable

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28
Q

FISH

A

chromosome detection

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29
Q

FISH can determine if someone has

A

trisomy or monosomy

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30
Q

DNA band shift

A

determines IF the protein attaches to DNA

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31
Q

DNA footprinting

A

determines WHERE protein and DNA interactions occur

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32
Q

PCR allows detection

A

trinucleotide expansion

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33
Q

PCR process

A
  • Denaturation
  • Annealing
  • Extensionā€“> taq DNA pol (heat stable but no PCNA= low processivity)
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34
Q

RT-PCR allows for

A

to determine cancer reoccurrence

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35
Q

Gene library

A

has all genomic DNA

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36
Q

cDNA library has genes derived from

A

mRNA and made with RT

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37
Q

mRNA is ____to template but ____ to coding strand

A

mRNA is complementary to template but identical to coding strand

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38
Q

difference between a genomic library and a cDNA

A

a genomic library contains fragments of the genome, whereas a cDNA library is derived from the mRNA being expressed in a given tissue

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39
Q

probes hybridyze at

A

lower temperature

40
Q

RFC

A

clamp loader

41
Q

PCNA

A

Clamp

42
Q

MCM complex

A

helicase

43
Q

Polymerase switch

A

RFC
PCNA
Pol epsilon
Pol delta

44
Q

Nucleotide analogues

A

acyclovir, AZT

45
Q

Xeroderma Pigmentosum defect is in the

A

nuclease that cleaves DNA near pyrimidine dimers

46
Q

An additional feature of cloning vectors are

A

origins of replication

47
Q

siRNA uses the

A

RISC complex

48
Q

Cas9 is a

A

programmable nuclease

49
Q

what does Cas9-sgRNA complex does?

A

make a double stranded break in the genomic DNA target

50
Q

what are miRNAs?

A

21 nt long, non-coding that play a role in regulation of translation

51
Q

miRNAs target

A

the 3ā€™ UTR

52
Q

miRNAs role in translation

A

recruit the RISC complex and either cause stalling of the translation complex or degradation of the mRNA

53
Q

How to detect DNA methylation?

A

bisulfite DNA sequencing

54
Q

predominant protein in elastic tissue such as the lungs

A

elastin

55
Q

fibrous protein not dissolved in water

A

elastin, keratin

56
Q

bicarbonate can can absorb

A

H+

57
Q

Exhaling deeply causes

A

pH to rise

58
Q

Aspirin is isoelectric at

A

very low pH

59
Q

hydroxyurea

A

stimulates the production of HbF

60
Q

Bone marrow transplantation

A

replaces HbS with HbA

61
Q

Step 1 in collagen biosynthesis

A

polypeptide chain synthesis

62
Q

Step 2 in collagen biosynthesis

A

Hydroxylation

63
Q

Step 3 in collagen biosynthesis

A

glycosylation

64
Q

Step 4 in collagen biosynthesis

A

Disulfied bond formation at C-terminus

65
Q

Step 5 in collagen biosynthesis

A

triple helix formation

66
Q

Step 6 in collagen biosynthesis

A

secretion from fibroblast

67
Q

Step 7 in collagen biosynthesis

A

hydrolysis of propeptide leading to cleavage of Nā€™/Cā€™ terminal

68
Q

Step 8 in collagen biosynthesis

A

Assembly into fibril

69
Q

Step 9 in collagen biosynthesis

A

assembly into fiber and formation of cross links

70
Q

osteogenesis imperfecta is caused by

A

substitution of a glycine to cysteine in collagen type 1

71
Q

characterized clinically with hyperelastic joints and skin hyper extensibility

A

ehlers danlos

72
Q

Heterezygosity is not Ok in ED

A

gene defects in the collagen genes

73
Q

Heterozygosity is ok

A

improper processing of collagen caused by lack of processing enzyme

74
Q

what does steroid do?

A

they bind to the steroid receptor complex which localizes to the nucleus and binds to enhancer element

75
Q

insulin is

A

cell-specific expression

76
Q

RISC is activated with

A

ATP

77
Q

mRNA therapies focuses on?

A

RNA interference of particular mRNA via hybridization to dsRNA

78
Q

CCA is

A

post-transcriptional modification

79
Q

CCA creates a

A

high energy intermediate

80
Q

in Methemoglobinemia

A

histidine of heme is replaced with tyrosine

81
Q

Methemoglobinemia an be caused by

A

ingesting nitrites and nitrates

82
Q

how to treat thalassemia

A

blood transfusion

83
Q

protein maturation occurs via

A

proteolysis of precursor components

84
Q

what is the importance of the holes in tropocollagen?

A

allows for calcium phosphate deposition during bone formation

85
Q

uracil removal involves

A

a glycosidase that creates an AP site

86
Q

mismatch repair system involves

A

helicase and exonuclease

87
Q

Lines encode a

A

reverse transcriptase

88
Q

processed pseudogenes resemble

A

mRNA

89
Q

hMSH binds to where?

A

mismatched bases

90
Q

SSCP (single strand polymorphism) identifies

A

point mutations

91
Q

remodeling of the nucleosomes

A

SWI-SNF

92
Q

What happens when elF2 gets phosphorolated?

A

it becomes sinactive

93
Q

ways that elF2 can get phosphorolated?

A

aa starvation
dsRNA
unfolded proteins
heme deprivation

94
Q

CRF in termination

A

binds the stop codon and the complex dissociates

95
Q

dideoxy analog

A

sanger method

Biochem (10 decks)

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