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quiz 1 Flashcards

1
Q

at what levels is gene expression regulated

A

chromatin structure
transcription
mRNA processing
mRNA stability
translation
posttranslational modification

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2
Q

central dogma

A

dna rna protein

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3
Q

messenger RNA

A

carries genetic information from DNA to ribosome
coding RNA

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4
Q

transfer RNA

A

noncoding RNA
small RNA that contains a binding site for an amino acid

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5
Q

ribosomal RNA

A

noncoding RNA
part of ribosomal structure

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6
Q

transcription unit

A

stretch of DNA that encodes for an RNA molecule and sequences needed for transcription

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7
Q

template strand

A

nucleotide strand used for transcription

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8
Q

non template strand

A

strand which is not used for transcrition

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9
Q

template strand names

A

antisense strand
minus strand
non-coding strand
3’ to 5’

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10
Q

nontemplate strand names

A

sense strand
plus strand
coding strand
5’ to 3’
“same as RNA”

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11
Q

which strand is usually shown on databases

A

nontemplete strand

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12
Q

promotor

A

a dna sequence that the transcrition apparatus recognizes and binds

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13
Q

RNA coding region

A

sequence of DNA nucleotides that is copied to an RNA molecule

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14
Q

consensus sequence

A

sequences that show considerable similarity between genes

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15
Q

prokaryotic promotor elements

A

-35 consensus sequence
-10 consensus sequence

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16
Q

terminator

A

a DNA sequence that signals where transcription should end

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17
Q

upstream

A

towards promotor

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18
Q

downstram

A

towards terminator

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19
Q

what does prokaryotic RNA polymerase bind to

A

consensus sequences

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20
Q

what does prokaryotic transcription not require

A

a primer

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21
Q

kinds of promotors in eukaryotic transcritption

A

cis-acting
core promotor
regulatory promotor

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22
Q

promotor elements in eukaryotes

A

TATA box
GC box
CAAT box

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23
Q

transcription factors in eukaryotes

A

trans acting
are attracted to promotor elements
attracts RNA polymerase to transcription start site
TFIIA,B,D,E,F,H

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24
Q

enhancers and silencers

A

sequences that interact with transcription regulatory proteins and stimulate or repress transcription

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25
RNA processing
5' cap poly A tail splicing
26
5' cap functions
ribosome binding translation initiation stability splicing
27
poly a tail functions
stability ribosomal attachment passage into cytoplasm
28
sequences required to splice
5' splice site 3' splice site branch point
29
two major phases of cell cycle
interphase m phase
30
primary nucleotide structure
nucleotide sequence of single stranded
31
secondary nucleotide structure
base pairing between strands
32
tertiary nucleotide structure
three dimentional shape of paired strands double helix
33
quaternary nucleotide structure
higher order folding facilitated via polynucleotide-polynucleotide and polynucleotide-protein interactions
34
nucleosome
DNA double helix bound to histone core
35
chromatosome
adding h1 histone to the nucleosome beads on a string 10nm
36
30nm solenoid
coiled chromatosome
37
chromatin
solenoid is looped and attatched to non-histone scafold proteins
38
centromere
region of chromosome where spindle fibers attatch
39
telomeres
protect ends of linear chromosomes g rich repeats form a g loop proteins bind to form
40
euchromatin
loose dispered throughout nucleus weak binding of h1 histones non-uniformly compacted may or may not be actively expressed
41
heterochromatin
tight remains highly compacted not usually expressed telomers, centromere, barr body, y chromosome
42
cytogenetics
obtain non-dividing cells and induce them to divide in culture adult white blood cells or skin bibroblasts fetal cells
43
how are non dividing cells induced to divide
phytohemagglutinin
44
q banding
stained with quinacrine dye that binds to AT rich regions
45
g banding
partial digestion with trypsin stained with Giemsa binds heterochromatic AT rich regions most commonly used method
46
r banding
heat and stain with Giemsa staines GC rich regions
47
t banding
stains telomeres
48
c banding
stains centromeres
49
how is banding resolution increased
by elongating chromosomes
50
long arm
q for quite large
51
short arm
p for petite
52
proximal
towards centromere
53
distal
towards telomere
54
linkage mapping
crossing over events recombination frequencies map units or centimorgans roughly additive
55
in situ hybridization
labeled probe with flourecent label
56
what is the probe in in situ hybridization
a single stranded DNA fragment complementary to a region of interest synthesized or isolated from genomic DNA DNA copies of RNA longer probes are more specific
57
metaphase FISH
hybridize labeled probe to metaphase spread resolution of sevral megabases
58
Fiber FISH
hybridize labeled insert to stretched chromatin kilobase resolution
59
interphase FISH
hybridize labeled insert to interphase cells
60
chromosome painting
label a series of different probes from the same chromosome
61
molecular karyotyping
chromosomes separated by flow cytometry
62
single nucleotide polymorphism (SNP)
1/300 nucleotides are polymorphic frequency of rare allele is greater than 0.01
63
single nucleotide varient (SNV)
not polymorphic
64
restriction fragment length polymorphism (RFLP)
SNP within a palindromic sequence results in the creation or destruction of a restriction endonuclease site
65
short interspersed nuclear elements (SINE)
mobile element transposon derived 100-700 bp in length 13% of human genome
66
long intersperced nuclear elements (LINE)
mobile DNA element transposon derived 7kb in length 21.1% of human genome
67
copy number variation (CNV)
number of copies of a genetic sequence varies from one individual to another
68
tandem repeats
minisatellites- 10-60 nucleotides microsatellites - short tandem repeats (STR) 1-6 nucleotides
69
why is copy number variation more informative than SNPs
more alleles increased variation in genotype in different individuals
70
origin of tandem repeat polymorphism
meiotic recombination within repeats polymerase stuttering during replication
71
large copy number variants
tandem repeats with a large copy number 1447 regions with variable repeats > 1kb 12% of genome average size is 250 kb
72
fragile sites
regions where chromatin is uncoiled
73
are there more SNPs or CNVs in genome
SNPs
74
what is responsible for the greatest number of nucleotides that vary between individual genomes
copy number varients
75
TGAC- database of genomic varients
varients observed in healthy individuals
76
decipher
pathogenic varients data base
77
complete linkage
markers are located so close to eachother that recombination is so so so so rare 0 cM
78
linkage disequilibrium
a chromosomal segment exists as a block that is rarely broken by recombination haplotypes and haplotype blocks
79
haplotype
a set of alleles linked together on the same chromosome segment that are transmitted as a block
80
HapMap
first attempt to look at human variation 2 million SNP 269 healthy individuals 11 populations SNPs grouped into haplotypes
81
1000 genomes project
more through look at variation 2504 individuals 26 populations low coverage whole genome sequancing targeted deep exome sequencing dense SNP data 88.3 million variants
82
model free linkage analysis
usually affected sib pairs low sample size and statistical power limited to broad regions of the genome based on linkage analysis
83
candidate gene association
choose genomic regions based on previous research usually limited to protein encoding genes poor reproducability
84
quantitative trait loci (QTL)
broad regions of the genome associated with quantitative traits usually use hundreds or thousands of markers
85
Genome-Wide Association Study (GWAS)
uses SNP analysis to find specific nucleotides and haplotypes associated with traits most multifactorial traits are influenced by a large number of genomic regions

Bioinformatics (1 decks)

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