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Spring 2015 > Block 4 biochem part 2 > Flashcards

Block 4 biochem part 2 Flashcards

(116 cards)

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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
behavior/expression of imprinted genes does not depend on _________. It depends on ______________
- sex of individual in which those genes reside | - the sex of the parent from which the particular allele was inherited
26
blunt ends of DNA can be rejoined by:
T4 DNA ligase
27
The frequency with which a specific restriction site is cut is directly correlated with:
the frequency in which that restriction site appears in DNA
28
vector-
DNA molecule used to clone a piece of foreign DNA
29
What does a vector need to successfully produce target DNA?
restriction site identical to that of the target DNA restriction site, its own origin of rep., and a resistance gene for selection
30
________ vectors are used to clone DNA in humans
retroviral and adenoviral
31
cosmids-
artificial plasmids used to clone small pieces of DNA
32
cDNA library-
a library of DNA fragments that derive solely from expressed genes (retrotranscribed from mRNA)
33
Genomic DNA library-
ideally contain a copy of every nucleotide in an organism's genome
34
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?
limit the amount of time that the restriction enzymes have to cleave DNA (called partial digest)
35
How is a cDNA library made?
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.
36
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 ______
- cell types | - promoters, introns, and usually rRNA and tRNA sequences
37
expression vector-
vector that contains promoters for the effective cloning of cDNA, since cDNA doesn't have it's own promoters
38
probe-
a short piece of ssDA labeled with a detectable molecule that is complimentary to the DNA sequence of interest
39
how would you test for allelic specificity of a gene using hybridization?
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.
40
southern blot-
cleave DNA with restriction enzyme, run on gel, denature to ss, transfer to nitrocellulose, hybridize with probe, detect if DNA of interest is present
41
Northern blot-
same as southern, but with RNA
42
Western blot-
same as southern, but with protein. Differences include using antibodies as probes and using SDS PAGE for separation
43
polymorphism-
infrequent and harmless variation of DNA sequence usually occurring in noncoding regions
44
RFLP-
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
45
SNPs-
single base changes in an individual. These can potentially modify or abolish a restriction site, altering restriction fragment lengths. Thus RFLP
46
Tandem repeats-
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
47
What is RT-PCR used for?
it is used to determine whether a gene is being expressed in a cell and to what degree.
48
RT-PCR can be used to determine the level of expression of a gene between what 2 states:
diseased and normal
49
How do microarrays differ from RT-PCR?
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
In case it is asked, in a microarray analysis, Green represents ______, red represents _____ and yellow represents ______
- expressed in diseased state - expressed in normal state - expressed in both states
51
How is RNA deep sequencing different from microarray?
Microarray is limited to the genes placed on the chip. Deep sequencing can examine all the genes in a cell being expressed.
52
the long arm of a chromosome is the ____ arm and the short arm is the ____ arm
- q | - p
53
______ stain is used to visualize chromosome banding patterns
giesmsa
54
Chromosome nomenclature example: 13q2.1
chromosome 13, long arm, region 2, band 1
55
FISH-
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
as Down Syndrome children get older, they have increased risk for:
heart defects, leukemia, and GI problems
57
What is used to diagnose aneuploidy
FISH analysis
58
Trisomy 13-
patau syndrome
59
80% of patau syndrome children have
cleft lip/palate, heart defects
60
holoprosencephaly-
forebrain fails to separate into 2 hemispheres
61
Trisomy 18-
Edward's syndrome
62
Edwards syndrome is usually what gender?
female
63
cardinal sign of Edward's syndrome-
clenched hand
64
Turner Syndrom Pt. have congenital lymphedema, leading to what physical characteristic?
web-necked
65
Turner syndrome intelligence:
normal!
66
Trisomies can occur after conception if a dividing cell of the embryo undergoes nondisjuntion of a chromosome. This is called:
mosaicism
67
severity of mosaicism depends on:
what tissues and how many cells are affected by the nondisjunction
68
cri-du-chat-
deletion o 5p15.2 ; child will have abnormal cry (distinguishing sign); also has big tongue, abnormal larynx, all the other good stuff.
69
unbalanced translocation-
exchange of chromosome material is unequal, loss or gain of significant chromosomal material following repair with clinical consequences
70
balanced translocation-
even exchange of material, individual is asymptomatic, but has higher risk of child having a chromosomal abnormality
71
Besides classical trisomy Down syndrome, how else may a child be born with down syndrome?
translocation 14;21 inheritance
72
a t(21;21) carrier has a _____ chance of having an abnormal child
100%
73
although most down syndrome children have the 47, +21 karyotype, a small percentage can have downs from 2 other ways:
translocation or mosaic karyotype
74
some cancerous cells have _____ or ______ changes to their chromosomes
numerical or structural
75
Double minutes-
appear as small, unusually paired dots, no centromere, irregular segregation, variable numbers
76
Homogenously staining regions-
material duplicated millions of times and inserted into a chromosome
77
comparative genomic hybridization-
variation of FISH for detection of copy number changes
78
Spectral karyotyping-
allows simultaneous visualization of multiple chromosome targets in different colors on a single hybridization. Gives each chrom. a unique color and wavelength
79
genetic screening-
testing on a population basis to identify individuals at risk of developing or of transmitting a specific disorder
80
genetic testing-
testing of INDIVIDUALS based on family history of a disorder. digging deeper and being more precise than screening
81
huntington disease trinucleotide repeat-
CAG
82
Fragile X trinuc. repeat-
CGG
83
Friedreich ataxia trinuc. repeat-
GAA
84
Full penetrance of huntington is >___ repeats
40
85
full penetrance of fragile x is >____ repeats
200
86
full penetrance of friedreich ataxia is >____ repeats
66
87
PCR based genetic testing used to-
identify large deletions/insertions that change the size of the products
88
You can discriminate what alleles someone has for genetic testing purposes by running PCR to look at the _____ of the product(s)
size
89
sarcoma-
cancer of connective and fibrous tissue
90
monoclonal tumor-
a tumor that derives from a single cell that receives a series of mutations to produce a cancerous growth
91
polyclonal tumor-
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
what does c-Myc do?
binds to Max to stimulate the production of cell cycle proteins.
93
how does c-Myc usually cause cancer?
it does not mutate, it gets overexpressed
94
Burkitt's lymphoma-
a non-Hodgkin's B-cell lymphoma- t(8:14) translocation
95
How does the 8:14 translocation of burkitt's lymphoma cause cancer?
c-Myc gene is translocated right next to the IgH chain gene
96
How does chronic myelogenous leukemia occur?
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
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:
Gleevec
98
Von Hippel-Lindau Syndrome-
spectrum of tumors: hemangioblastomas, pheochromocytomas, etc
99
Familial Adenomatous Polyposis is caused by dominant mutation in the ____ gene
APC (tumor suppressor)
100
a mutated oncogene causes cancer, whereas a mutated tumor suppressor gene does what?
increases your risk of developing cancer
101
Li-Fraumeni Syndrome is a spectrum of tumors arising from ____ mutations
p53
102
E2F stimulates:
transition from G1 to S phase.
103
____ normally prevents E2F from progressing the cell cycle by binding to it
pRB
104
CDK 4 and 6 hyperphosphorylate ___, releasing ____ and leading to cell proliferation
pRB | E2F
105
P16/INK-4 genes inhibit _______, which indirectly inhibits _____ phosphorylation, which indirectly stops cell proliferation
- cyclins | - pRB
106
p53 stimulates production of ____, which keeps cells arrested in G1
p21
107
loss or inactivation of both alleles of ___ will remove regulation at G1/S checkpoint
pRB
108
_____ inhibits p53 via ubiquitination
MDM2
109
amplification of ______ causes big destruction of p53 and causes cancer
MDM2
110
which protein can rescue p53 by antagonizing MDM2?
ARF
111
mutation of _____ would leave MDM2 to cause cancer
ARF
112
the difference between angiogenesis and vasculogenesis-
angiogenesis- blood vessels form from pre-existing vessels | Vasculogenesis- de novo formation of vessels from mesoderm precursors
113
the 4 drugs that inhibit angiogenesis
the "ib's" Bevacizumab, Sunitinib, Sorafenib, and Cederaib
114
Anoikis-
a form of programmed cell death that is induced when anchorage dependent cells detach from the extracellular matrix. Cancer is resistant to this
115
_______ degrade the ECM and allow invasion and migration
Matrix metalloproteinases
116
inhibit the action of MMP's
Tissue inhibitors of MMP's

Spring 2015 (9 decks)

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