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Bioinformatics > quiz 1 > Flashcards

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
Q

RNA processing

A

5’ cap
poly A tail
splicing

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26
Q

5’ cap functions

A

ribosome binding
translation initiation
stability
splicing

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27
Q

poly a tail functions

A

stability
ribosomal attachment
passage into cytoplasm

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28
Q

sequences required to splice

A

5’ splice site
3’ splice site
branch point

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29
Q

two major phases of cell cycle

A

interphase
m phase

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30
Q

primary nucleotide structure

A

nucleotide sequence of single stranded

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31
Q

secondary nucleotide structure

A

base pairing between strands

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32
Q

tertiary nucleotide structure

A

three dimentional shape of paired strands
double helix

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33
Q

quaternary nucleotide structure

A

higher order folding facilitated via polynucleotide-polynucleotide and polynucleotide-protein interactions

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34
Q

nucleosome

A

DNA double helix bound to histone core

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35
Q

chromatosome

A

adding h1 histone to the nucleosome
beads on a string
10nm

36
Q

30nm solenoid

A

coiled chromatosome

37
Q

chromatin

A

solenoid is looped and attatched to non-histone scafold proteins

38
Q

centromere

A

region of chromosome where spindle fibers attatch

39
Q

telomeres

A

protect ends of linear chromosomes
g rich repeats
form a g loop
proteins bind to form

40
Q

euchromatin

A

loose
dispered throughout nucleus
weak binding of h1 histones
non-uniformly compacted
may or may not be actively expressed

41
Q

heterochromatin

A

tight
remains highly compacted
not usually expressed
telomers, centromere, barr body, y chromosome

42
Q

cytogenetics

A

obtain non-dividing cells and induce them to divide in culture
adult white blood cells or skin bibroblasts
fetal cells

43
Q

how are non dividing cells induced to divide

A

phytohemagglutinin

44
Q

q banding

A

stained with quinacrine dye that binds to AT rich regions

45
Q

g banding

A

partial digestion with trypsin
stained with Giemsa
binds heterochromatic AT rich regions
most commonly used method

46
Q

r banding

A

heat and stain with Giemsa
staines GC rich regions

47
Q

t banding

A

stains telomeres

48
Q

c banding

A

stains centromeres

49
Q

how is banding resolution increased

A

by elongating chromosomes

50
Q

long arm

A

q for quite large

51
Q

short arm

A

p for petite

52
Q

proximal

A

towards centromere

53
Q

distal

A

towards telomere

54
Q

linkage mapping

A

crossing over events
recombination frequencies
map units or centimorgans
roughly additive

55
Q

in situ hybridization

A

labeled probe with flourecent label

56
Q

what is the probe in in situ hybridization

A

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
Q

metaphase FISH

A

hybridize labeled probe to metaphase spread
resolution of sevral megabases

58
Q

Fiber FISH

A

hybridize labeled insert to stretched chromatin
kilobase resolution

59
Q

interphase FISH

A

hybridize labeled insert to interphase cells

60
Q

chromosome painting

A

label a series of different probes from the same chromosome

61
Q

molecular karyotyping

A

chromosomes separated by flow cytometry

62
Q

single nucleotide polymorphism (SNP)

A

1/300 nucleotides are polymorphic
frequency of rare allele is greater than 0.01

63
Q

single nucleotide varient (SNV)

A

not polymorphic

64
Q

restriction fragment length polymorphism (RFLP)

A

SNP within a palindromic sequence
results in the creation or destruction of a restriction endonuclease site

65
Q

short interspersed nuclear elements (SINE)

A

mobile element
transposon derived
100-700 bp in length
13% of human genome

66
Q

long intersperced nuclear elements (LINE)

A

mobile DNA element
transposon derived
7kb in length
21.1% of human genome

67
Q

copy number variation (CNV)

A

number of copies of a genetic sequence varies from one individual to another

68
Q

tandem repeats

A

minisatellites- 10-60 nucleotides
microsatellites - short tandem repeats (STR) 1-6 nucleotides

69
Q

why is copy number variation more informative than SNPs

A

more alleles
increased variation in genotype in different individuals

70
Q

origin of tandem repeat polymorphism

A

meiotic recombination within repeats
polymerase stuttering during replication

71
Q

large copy number variants

A

tandem repeats with a large copy number
1447 regions with variable repeats > 1kb
12% of genome
average size is 250 kb

72
Q

fragile sites

A

regions where chromatin is uncoiled

73
Q

are there more SNPs or CNVs in genome

A

SNPs

74
Q

what is responsible for the greatest number of nucleotides that vary between individual genomes

A

copy number varients

75
Q

TGAC- database of genomic varients

A

varients observed in healthy individuals

76
Q

decipher

A

pathogenic varients data base

77
Q

complete linkage

A

markers are located so close to eachother that recombination is so so so so rare
0 cM

78
Q

linkage disequilibrium

A

a chromosomal segment exists as a block that is rarely broken by recombination
haplotypes and haplotype blocks

79
Q

haplotype

A

a set of alleles linked together on the same chromosome segment that are transmitted as a block

80
Q

HapMap

A

first attempt to look at human variation
2 million SNP
269 healthy individuals
11 populations
SNPs grouped into haplotypes

81
Q

1000 genomes project

A

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
Q

model free linkage analysis

A

usually affected sib pairs
low sample size and statistical power
limited to broad regions of the genome based on linkage analysis

83
Q

candidate gene association

A

choose genomic regions based on previous research
usually limited to protein encoding genes
poor reproducability

84
Q

quantitative trait loci (QTL)

A

broad regions of the genome associated with quantitative traits
usually use hundreds or thousands of markers

85
Q

Genome-Wide Association Study (GWAS)

A

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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