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Spring 2015 > Block 4 biochem part 2 > Flashcards

Block 4 biochem part 2 Flashcards

1
Q

in humans, DNA methylation occurs at the C-__ position of cytosine residues

A

5

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2
Q

CpGs (cytosine-phosphate-guanine) in promoter region of DNA is site of 80% of DNA ______

A

methylation

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3
Q

How would DNA hypermethylation cause cancer?

A

silence expression of tumor suppressor genes

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4
Q

How would DNA hypomethylation cause cancer?

A

allow increased transcription of oncogenes

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5
Q

where do most of our methyl groups for DNA methylation come from?`

A

folic acid

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6
Q

genomic imprinting-

A

one copy of a gene is epigenetically silenced

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7
Q

In genomic imprinting, even though the DNA sequence for a given gene is exactly the same in both copies, it is expressed differently based on:

A

whether the expressed gene is maternally or paternally derived

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8
Q

completion of embryogenesis requires both differential maternal and paternal _________

A

genomic expressions

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9
Q

gynogenote-

A

female pronuclei + female pronuclei; diploid zygote that has 2 sets of female chromosomes instead of 1 male 1 female

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10
Q

gynogenotes fail to develop _______, but _______ develops normally

A
  • extraembryonic tissue

- embryo proper

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11
Q

androgenote-

A

male pronuclei + male pronuclei

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12
Q

androgenotes fail to develop ________, but ______ develops normally

A
  • embryo proper

- extraembryonic tissue

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13
Q

ovarian dermoid cyst-

A

all female derived genetic material. Can result from spontaneous ovarian oocyte activation with duplication of maternal genome

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14
Q

hydatidiform mole-

A

all male derived genetic material. An enucleate egg fertilized by haploid sperm, or egg is fertilized by 2 sperm and subsequent loss of maternal pronucleus. A complete mole has little to no fetal tissue and hyperplastic embryonic tissue growth

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15
Q

Histone proteins are _______ charged on lysine rich amino terminal tails that neutralize the charge from DNA

A

positively

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16
Q

How does acetylation make DNA more transcribable?

A

adding acetyl to histone negates positive charge and reduces affinity of DNA for histone

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17
Q

the acetylation enzyme-

A

HAT (histone acetyltransferase)

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18
Q

Trichostatin A-

A

a histone deacetylase inhibitor, activates genes

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19
Q

LYON hypothesis-

A

during embryonic development, one X chromosome in a female embryo is turned off in every cell at random and all progeny from this cell have the same X turned off. Females are mosaics

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20
Q

XIC (X inactivation center)

A

regulates X inactivation

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21
Q

_______ gene makes RNA that inactivates one of the two X chromosomes in a normal female

A

Xist

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22
Q

If extra X chromosomes are inactivated anyways, why are Kleinfelter (XXY) abnormal?

A

there are pseudoautosomal regions on X and Y chromosomes that escape inactivation, so in the case of Kleinfelter, they have normal genetics, but a little extra chromosome input from the pseudoautosomal region of the second X

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23
Q

Prader-Willi syndrome-

A

fat, short, mentally retarded, small hands

caused by loss of paternal 15q11.2-q13.1 expression (due to improper imprinting) and gain of expression of SNRPN

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24
Q

Angelman syndrome-

A

laughing, retardation, motor retardation, no speech, unusual face
caused by loss of paternal 15q11.2-q13.1 expression (due to improper imprinting) and gain of expression of UBE3A

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25
Q

behavior/expression of imprinted genes does not depend on _________. It depends on ______________

A
  • sex of individual in which those genes reside

- the sex of the parent from which the particular allele was inherited

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26
Q

blunt ends of DNA can be rejoined by:

A

T4 DNA ligase

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27
Q

The frequency with which a specific restriction site is cut is directly correlated with:

A

the frequency in which that restriction site appears in DNA

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28
Q

vector-

A

DNA molecule used to clone a piece of foreign DNA

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29
Q

What does a vector need to successfully produce target DNA?

A

restriction site identical to that of the target DNA restriction site, its own origin of rep., and a resistance gene for selection

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30
Q

________ vectors are used to clone DNA in humans

A

retroviral and adenoviral

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31
Q

cosmids-

A

artificial plasmids used to clone small pieces of DNA

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32
Q

cDNA library-

A

a library of DNA fragments that derive solely from expressed genes (retrotranscribed from mRNA)

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33
Q

Genomic DNA library-

A

ideally contain a copy of every nucleotide in an organism’s genome

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34
Q

there is a good chance that the restriction sites used to cleave genes for placement in a genomic library also exist within the genes themselves. To avoid cutting genes in half and compromising the quality of the genomic library, what is done?

A

limit the amount of time that the restriction enzymes have to cleave DNA (called partial digest)

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35
Q

How is a cDNA library made?

A

RNA is extracted from the cell, random primers are added, reverse transcriptase is added to convert it to DNA, alkali treatment destroys RNA, DNA pol, plus ligase is used to convert the ssDNA int dsDNA, then the DNA is ligated into cloning vectors.

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36
Q

cDNA libraries only contain the genes expressed in a given cell, via reverse transcription of its mRNA, so cDNA libraries are specific to ______, and lack ______

A
  • cell types

- promoters, introns, and usually rRNA and tRNA sequences

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37
Q

expression vector-

A

vector that contains promoters for the effective cloning of cDNA, since cDNA doesn’t have it’s own promoters

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38
Q

probe-

A

a short piece of ssDA labeled with a detectable molecule that is complimentary to the DNA sequence of interest

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39
Q

how would you test for allelic specificity of a gene using hybridization?

A

isolate the gene from the Pt., run 2 separate reactions: one with a probe for the dominant allele, one for the recessive allele. If both react, Pt. is heterozygous. If one reacts, they are homozygous for that allele.

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40
Q

southern blot-

A

cleave DNA with restriction enzyme, run on gel, denature to ss, transfer to nitrocellulose, hybridize with probe, detect if DNA of interest is present

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41
Q

Northern blot-

A

same as southern, but with RNA

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42
Q

Western blot-

A

same as southern, but with protein. Differences include using antibodies as probes and using SDS PAGE for separation

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43
Q

polymorphism-

A

infrequent and harmless variation of DNA sequence usually occurring in noncoding regions

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44
Q

RFLP-

A

a genetic variant that alters restriction sites and/or the sizes of restriction fragments and can be observed as differences in mobility by southern blot analysis

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45
Q

SNPs-

A

single base changes in an individual. These can potentially modify or abolish a restriction site, altering restriction fragment lengths. Thus RFLP

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46
Q

Tandem repeats-

A

short sequences of repeating DNA that are different from person to person, so having a different number of tandem repeats in an RF makes that RF different from someone else’s corresponding RF. Thus, a RFLP

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47
Q

What is RT-PCR used for?

A

it is used to determine whether a gene is being expressed in a cell and to what degree.

48
Q

RT-PCR can be used to determine the level of expression of a gene between what 2 states:

A

diseased and normal

49
Q

How do microarrays differ from RT-PCR?

A

they are able to look at thousands of genes at once and compare between 2 sets of genes (either from 2 diff sources or from a single source in 2 diff. states)

50
Q

In case it is asked, in a microarray analysis, Green represents ______, red represents _____ and yellow represents ______

A
  • expressed in diseased state
  • expressed in normal state
  • expressed in both states
51
Q

How is RNA deep sequencing different from microarray?

A

Microarray is limited to the genes placed on the chip. Deep sequencing can examine all the genes in a cell being expressed.

52
Q

the long arm of a chromosome is the ____ arm and the short arm is the ____ arm

A
  • q

- p

53
Q

______ stain is used to visualize chromosome banding patterns

A

giesmsa

54
Q

Chromosome nomenclature example: 13q2.1

A

chromosome 13, long arm, region 2, band 1

55
Q

FISH-

A

flourescence in situ hybridization; flourescent probe denatured and allowed to pair with its complementary sequence of DNA for visualization with microscope. Tells you where gene is located on chromosome.

56
Q

as Down Syndrome children get older, they have increased risk for:

A

heart defects, leukemia, and GI problems

57
Q

What is used to diagnose aneuploidy

A

FISH analysis

58
Q

Trisomy 13-

A

patau syndrome

59
Q

80% of patau syndrome children have

A

cleft lip/palate, heart defects

60
Q

holoprosencephaly-

A

forebrain fails to separate into 2 hemispheres

61
Q

Trisomy 18-

A

Edward’s syndrome

62
Q

Edwards syndrome is usually what gender?

A

female

63
Q

cardinal sign of Edward’s syndrome-

A

clenched hand

64
Q

Turner Syndrom Pt. have congenital lymphedema, leading to what physical characteristic?

A

web-necked

65
Q

Turner syndrome intelligence:

A

normal!

66
Q

Trisomies can occur after conception if a dividing cell of the embryo undergoes nondisjuntion of a chromosome. This is called:

A

mosaicism

67
Q

severity of mosaicism depends on:

A

what tissues and how many cells are affected by the nondisjunction

68
Q

cri-du-chat-

A

deletion o 5p15.2 ; child will have abnormal cry (distinguishing sign); also has big tongue, abnormal larynx, all the other good stuff.

69
Q

unbalanced translocation-

A

exchange of chromosome material is unequal, loss or gain of significant chromosomal material following repair with clinical consequences

70
Q

balanced translocation-

A

even exchange of material, individual is asymptomatic, but has higher risk of child having a chromosomal abnormality

71
Q

Besides classical trisomy Down syndrome, how else may a child be born with down syndrome?

A

translocation 14;21 inheritance

72
Q

a t(21;21) carrier has a _____ chance of having an abnormal child

A

100%

73
Q

although most down syndrome children have the 47, +21 karyotype, a small percentage can have downs from 2 other ways:

A

translocation or mosaic karyotype

74
Q

some cancerous cells have _____ or ______ changes to their chromosomes

A

numerical or structural

75
Q

Double minutes-

A

appear as small, unusually paired dots, no centromere, irregular segregation, variable numbers

76
Q

Homogenously staining regions-

A

material duplicated millions of times and inserted into a chromosome

77
Q

comparative genomic hybridization-

A

variation of FISH for detection of copy number changes

78
Q

Spectral karyotyping-

A

allows simultaneous visualization of multiple chromosome targets in different colors on a single hybridization. Gives each chrom. a unique color and wavelength

79
Q

genetic screening-

A

testing on a population basis to identify individuals at risk of developing or of transmitting a specific disorder

80
Q

genetic testing-

A

testing of INDIVIDUALS based on family history of a disorder. digging deeper and being more precise than screening

81
Q

huntington disease trinucleotide repeat-

A

CAG

82
Q

Fragile X trinuc. repeat-

A

CGG

83
Q

Friedreich ataxia trinuc. repeat-

A

GAA

84
Q

Full penetrance of huntington is >___ repeats

A

40

85
Q

full penetrance of fragile x is >____ repeats

A

200

86
Q

full penetrance of friedreich ataxia is >____ repeats

A

66

87
Q

PCR based genetic testing used to-

A

identify large deletions/insertions that change the size of the products

88
Q

You can discriminate what alleles someone has for genetic testing purposes by running PCR to look at the _____ of the product(s)

A

size

89
Q

sarcoma-

A

cancer of connective and fibrous tissue

90
Q

monoclonal tumor-

A

a tumor that derives from a single cell that receives a series of mutations to produce a cancerous growth

91
Q

polyclonal tumor-

A

a tumor that derives from several individual cells within a similar tissue type all receiving a series of mutations to produce a cancerous growth

92
Q

what does c-Myc do?

A

binds to Max to stimulate the production of cell cycle proteins.

93
Q

how does c-Myc usually cause cancer?

A

it does not mutate, it gets overexpressed

94
Q

Burkitt’s lymphoma-

A

a non-Hodgkin’s B-cell lymphoma- t(8:14) translocation

95
Q

How does the 8:14 translocation of burkitt’s lymphoma cause cancer?

A

c-Myc gene is translocated right next to the IgH chain gene

96
Q

How does chronic myelogenous leukemia occur?

A

9:22 and p34:p11 translocation leads to the fusion of the breakpoint cluster region protein (BCR) to the c-Abl protein. BCR constitutively activates c-Abl so c-Abl constitutively causes cell proliferation

97
Q

Abl is a tyrosine kinase, so researchers had to do a high throughput screen to find something that only specifically inhibited Abl. The drug they formulated is:

A

Gleevec

98
Q

Von Hippel-Lindau Syndrome-

A

spectrum of tumors: hemangioblastomas, pheochromocytomas, etc

99
Q

Familial Adenomatous Polyposis is caused by dominant mutation in the ____ gene

A

APC (tumor suppressor)

100
Q

a mutated oncogene causes cancer, whereas a mutated tumor suppressor gene does what?

A

increases your risk of developing cancer

101
Q

Li-Fraumeni Syndrome is a spectrum of tumors arising from ____ mutations

A

p53

102
Q

E2F stimulates:

A

transition from G1 to S phase.

103
Q

____ normally prevents E2F from progressing the cell cycle by binding to it

A

pRB

104
Q

CDK 4 and 6 hyperphosphorylate ___, releasing ____ and leading to cell proliferation

A

pRB

E2F

105
Q

P16/INK-4 genes inhibit _______, which indirectly inhibits _____ phosphorylation, which indirectly stops cell proliferation

A
  • cyclins

- pRB

106
Q

p53 stimulates production of ____, which keeps cells arrested in G1

A

p21

107
Q

loss or inactivation of both alleles of ___ will remove regulation at G1/S checkpoint

A

pRB

108
Q

_____ inhibits p53 via ubiquitination

A

MDM2

109
Q

amplification of ______ causes big destruction of p53 and causes cancer

A

MDM2

110
Q

which protein can rescue p53 by antagonizing MDM2?

A

ARF

111
Q

mutation of _____ would leave MDM2 to cause cancer

A

ARF

112
Q

the difference between angiogenesis and vasculogenesis-

A

angiogenesis- blood vessels form from pre-existing vessels

Vasculogenesis- de novo formation of vessels from mesoderm precursors

113
Q

the 4 drugs that inhibit angiogenesis

A

the “ib’s” Bevacizumab, Sunitinib, Sorafenib, and Cederaib

114
Q

Anoikis-

A

a form of programmed cell death that is induced when anchorage dependent cells detach from the extracellular matrix. Cancer is resistant to this

115
Q

_______ degrade the ECM and allow invasion and migration

A

Matrix metalloproteinases

116
Q

inhibit the action of MMP’s

A

Tissue inhibitors of MMP’s

Spring 2015 (9 decks)

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