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Genetics > chromosomes- rnai (unit 2) > Flashcards

chromosomes- rnai (unit 2) Flashcards

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1
Q

karyotype

A

spread illustrates the human 46 chromosomes

-taken during metaphase

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2
Q

geimsa staining

A

gives characteristic bands on each chromosome and allows for chromosome identification

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3
Q

chromosome painting

A

repetitive DNA sequences that have been identified on each chromosome- DNA complementary to these sequences are synthesized and labeled with a specific color probe (allowed to hybridize a prep of metaphase chroms)

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4
Q

dosage compensation

A

adjusts for differences in the numbers of sex chromosomes- accomplished by X inactivation in females

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5
Q

Xist

A

gene still expressed on Barr body- acts to keep the X chromosome in its inactive state
-tips of the X chromosome escape inactivation and these contain genes that Are also on Y chromosome

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6
Q

pseudoautosomal regions

A

regions of X-Y homology; patterns of inheritance of genes in pseudo auto regions are indistinguishable from autosomal inheritance patterns

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7
Q

SRY

A

master sex determination gene- presence of SRY gene determines male development- encodes for transcription factor called testis- determining factor (TDF)

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8
Q

turner syndrome

A

individuals are missing one X chromosome- affects growth and sexual development
-girls with this disorder are short, stocky, delayed puberty, and infertile

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9
Q

kleinfelter syndrome

A

XXY affects sexual development- males with this disorder have a variety of symptoms including little body hair, breasts, and infertility

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10
Q

haplotype

A

set of alleles at 2+ loci in a particular chrom= a chromosome type defined by multiple alleles= combination of alleles at multiple loci that are transmitted together on the same chromosome

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11
Q

trisomy

A

third copy of one of the chromosomes

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12
Q

aneuploidy

A

not having the same number of each chromosome

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13
Q

polyploidy

A

an extraset (or 2) of all of the chromosomes

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14
Q

monosomy

A

only one of a particular chromosome

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15
Q

down syndrome

A

result of trisomy 21- usually result of chromosome 21 nondisjunction
-in 3% of cases, trisomy is caused by chromosome translocation that has attached chromosomes 21 onto another chromosome

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16
Q

trivalent

A

two chroms try to pair up with the one chrom

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17
Q

univalent

A

one chrom is unpaired at metaphase

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18
Q

chromosome deletion

A

missing genes- can be mapped via recessive phenotypes that show up

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19
Q

chrom duplication

A

caused by unequal crossover

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20
Q

inversions

A

DNA breaks can result in this- fine in mitosis, problematic in meiosis
*inverted regions form loops during gene pairing (synapsis) in meiosis- crossing over in the inversion loop leads to acentric and dicentric chromatids

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21
Q

acentric

A

chroms without centromeres= genetically unstable

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22
Q

dicentric

A

chroms with two centromeres= 2 centromeres can then attach and separate to opposite poles= breaking chrom= very unstable

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23
Q

translocations

A

chrom abnormalities which occur when chroms break and the fragments rejoin other chroms

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24
Q

reciprocal translocation

A

2 non-hom chroms break and exchange fragments

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25
Q

robertsonian translocation

A

type of centric fusion translocation caused by fusions of acrocentric chroms

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26
Q

types of chromosomes abnorms

A 
monosomy and trisomy
aneuploidy
deletions
translocations
duplications
inversions
accentric and dicentric
polyploidy (OK for plants)
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27
Q

DNA composition

A

sugar deoxyribose
phosphoric acid
4 nitrogen-containing bases

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28
Q

hydrogen bonds

A

FON share H atom

  • AT base pairs have 2 H bonds
  • CG base pairs have 3
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29
Q

semi-conservative replication

A

each DNA strand is used as a template for the new strand

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30
Q

template

A

older strands that are used to make a copy (parental strands)

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31
Q

replication origin

A

DNA sequence where replication begins

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32
Q

replication fork

A

region where parental strands are separated and new strands are synthesized

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33
Q

exonuclease

A

activity of DNA polymerase to remove mismatches- decreases the rate of mutations

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34
Q

PCR (polymerase chain reaction)

A

technique for amplifying DNA- DNA polymerase (that takes high temps best) extends the DNA by adding base pairing nucleotides

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35
Q

growth media

A

contains amino acids and sugars that support bacterial growth
-bacterial growth is exponential until nutrients run out

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36
Q

petroff-hauser slide counter

A
  • similar to hemocytometer but with less depth in field of view (10 microns vs 100 microns)
    1) dilute cells
    2) pipet 1 microliter diluted cells
    3) count average cells per square area
    4) multiply by dilution factor to get cells/ mL in OG
  • **doesn’t tell if cells are viable or not
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37
Q

3 principle types of mutants

A

1) antibiotic resistant mutants
2) nutritional mutants
3) carbon-source mutants

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38
Q

antibiotic resistant mutants

A

mutation allows growth in presence of an antibiotic (ampR cells)

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39
Q

nutritional mutants

A

(auxotrophs) cells that cannot grow without a nutrient supplied by a researcher (Met-)

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40
Q

carbon-source mutants

A

cells can only metabolize certain sugars (Lac-)

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41
Q

persister

A

dormant cells that are not killed by most antibiotics that target dividing cells
-NOT mutant (resisters)- they are regular cells that remain dormant and return once antibiotics are removed

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42
Q

bacterial acquisition of resistance

A

1) transformation (transfer of free DNA), 2) conjugation (plasmid transfer), 3) transduction (transfer via virus)

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43
Q

bacterial chromosomes

A

haploid, reproduces asexually, plasmids

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44
Q

transformation

A

process by which bacteria pick up DNA from environment= most likely from remnants of DNA from dead bacteria
-can be used in lab to take up plasmids

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45
Q

conjugation

A

joining of bacterial cells in order to transfer DNA

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46
Q

conjugative plasmid

A

plasmids that can be transferred this way- mostly small ones use larger recombinants to get into conj plasmids

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47
Q

F factor

A

conjugative plasmids= encodes many genes that ensure its maintenance in cell and transfer cell to cell

  • directs formation of the F plus
  • transfer of F factor works by rolling circle replication
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48
Q

F factor conjugation

A

transfer of F factor results in both cells containing the F factor- quickly transfers (only in 10% of EColi in nature

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49
Q

transposable elements

A

DNA sequences that can jump from one position to another or from one DNA molecule to another

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50
Q

insertion sequences

A

simplest and smallest and encode transposase

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51
Q

transposase

A

enzyme that excises transposable elements and integrates them back in somewhere
-recombination between transposable elements allows non-conj plasmids and pieces of genomic DNA to be transferred

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52
Q

cointegrate

A

the recombined plasmid

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53
Q

recombinase

A

enzyme that catalyzes recombination of DNA

54
Q

transduction

A

a phage (virus that infects bacteria) transfers DNA from bacteria by mistake instead of phage DNA genome

55
Q

lytic cycle

A

reproductive cycle of a phage including lysing and release of new phages

56
Q

lysogenic cycle

A

no progeny particles produced- phage DNA hangs out in bacterial DNA

57
Q

temperate phages

A

lysogenic phage

58
Q

virulent phages

A

lytic phage

59
Q

transposable elements

A

DNA sequences that can jump from one position to another

60
Q

gene expression

A

using the info in DNA to produce RNA and protein molecules that determine the phenotype of organisms

61
Q

transcriptioon

A

synthesis of RNA mcl from DNA template

62
Q

RNA vs DNA

A

ribose// deoxyribose

uracil// thymine

63
Q

transcription

A

1) promoter recognition
2) chain initiation
3) chain elongation
4) chain termination

64
Q

promoter recognition

A

RNA identifies promoter by binding consensus sequences at -10 and -35 bp
-euk promoter regions are longer and more complex

65
Q

transcription initiation

A

1) RNA polymerase binds the promoter
2) DNA separates
3) 1st RNA nucleotide base pairs with DNA
4) cont RNA building (5’ of 2nd and 3’ of 1st join in RNA to elongate)

66
Q

RNA polymerase

A

forms bond between 3’ OH group at end of the chain and the next 5’ phosphate group of the next nucleotide

67
Q

termination regions

A

reverse inverts that undergo self-pairing and form hairpin structure that signals a cessation of transcription

68
Q

intron

A

interrupt- removed by RNA splicing

69
Q

exon

A

expressed- coding region

70
Q

5- end cap

A

modified by addition of guanosine residue cap

71
Q

poly A tail

A

up to 200 A residues long, regulates RNA stability, useful to identify and isolate RNA from eukaryotes

72
Q

splicing

A

1) the 2’ OH group of adenine forms bond with phosphate group to 5’ splice site creating a loop in RNA
2) the released free 3’ POH group at end of exon then reacts with the start of the next exon sequence, joining the two eons together
3) the intron lariat (lasso) is released and exons are joined
- controlled by spliceosome

73
Q

self-splicing introns

A

fold into structures that bring the 2 nucleotides that engage in splicing reaction into proximity

74
Q

ribozymes

A

RNAs that fold up and have enzymatic activity on their own (catalyze)

75
Q

helicase

A

unwinds DNA at replication fork

76
Q

gyrase

A

cleaves and swivels duplex to release supercoiling

77
Q

single strand binding protein (SSB)

A

binds and stabilizes single stranded DNA at fork

78
Q

sliding clamp

A

protein fold that promotes DNA replication and prevents DNA polymerase from dissociation from template DNA

79
Q

DNA polymerase

A 
I= 5' to 3' exonuclease, repair enzyme, adds new DNA and removes primers
II= 3' to 5' exonuclease, 5' to 3' polymerase, proofreads DNA
80
Q

ligase

A

joins Okazaki fragments on lagging strand

81
Q

primase

A

initiates how strand synthesizes- this is an RNA polymerase

82
Q

peptide bond

A

formed between carboxyl and amino group and releases H2O

83
Q

N terminus (of amino acid)

A

amino end

84
Q

C terminus

A

carboxyl end (of amino acid)

85
Q

colinear

A

amino acids are added to the polypeptide chain in the same order as RNA bases

86
Q

translation

A

using info in mRNA to produce a protein

-coupled with transcription in proks

87
Q

translation steps

A

1) initiation= initiation factor binds the mRNA, ribosome assembles and factors help start transcription at the start codon
2) elongation= charged tRNA enters A site of ribosome and peptide bond forms between amino acid on tRNA and growing polypep chain
3) termination= when the stop codon is reached, release factors help the ribosome dissociate

88
Q

mRNA

A

provides coding sequence of bases that determines the amino acid sequence and brings ribosomal subunits together

89
Q

ribosome

A

protein and RNA machine that directs protein synthesis

90
Q

tRNA

A

transfer RNA molecules bring in amino acids to ribosome and put them in correct order by binding to codons in mRNA

91
Q

aminoacyl-tRNA sythetase

A

catalyzes the attachment of a particular amino acid to its corresponding tRNA

92
Q

Shine-Dalgarno sequence

A

helps proks recruit the ribosome to mRNA to initiate protein synthesis by aligning the ribosome with the start codon

93
Q

Kozak sequence

A

helps elk’s ribosome identify start codon

-ribo binds to 5’ cap and then scans to find the Kodak sequence near the AUG

94
Q

elongation

A

1) new charged tRNA enters A site and binds to codon by

95
Q

CRP and adenyl cyclase

A

required for transcription of lac operon

  • CRP= cyclic AMP receptor protein
  • adenyl cyclase= enzyme that makes cAMP
    1) CRP binds cAMP
    2) CRP binds lac promoter and positively regulates (turns on) transcription of lac operon
  • ** lac operon is on only when cAMP CRP is present (low glucose) and the repressor is absent (high lactose)
96
Q

tryptophan operon

A

quickly responds to trp amount in cell by dialing up or down the transcription of enzymes needed to make trp
-gene expression must be repressed when trp is adequate in concentration

97
Q

repressible transcription

A

gene transcription is on until active repressor binds

98
Q

aporepressor

A

a protein that has no DNA binding activity on its own, but which requires the presence of a co-repressor to turn transcription off

99
Q

leader sequence (trpL)

A

acts like dimmer switch to tune trp operon expression

-trpL transcript (mRNA) can sense level pf trp

100
Q

attenuation

A

controlling transcription in proks by coupling translator effects with transcription effects

101
Q

TrpL

A

codes for a short 14 amino acid peptide

-measures amount of trp via translation coupling

102
Q

antiterminate

A

low trp levels- transcription continues

103
Q

terminate

A

resembles transcription terminator sequence and the trp transcription is halted= attenuator

104
Q

basal transcription factors

A

proteins in the complex that are used in the transcription of many different genes

105
Q

transcriptional activation

A

occurs by mechanism called recruitment- the interaction of transcription factors with promoters and enhancers

106
Q

enhancers

A

usually in vicinity of gene they regulate, but can be on either side (5’ or 3’ or in intron)

107
Q

transcription factors (TFs)

A

can activate or repress transcription by binding to DNA

  • general (basal TFs
  • transcriptional activators or repressors
108
Q

general (basal) TFs

A

bind DNA near promoter and associate with RNA polymerase- required for low level basal transcription

109
Q

transcriptional activators/ repressors

A

bind enhancer DNA sequences- activate or repress transcription of genes- required for the cell to change gene expression levels in response to changing conditions (not needed for basal levels)

110
Q

DNA binding domain

A

binds specific sequences of DNA (enhancer or promoter) adjacent to regulated genes- DNA seqs which bind TFs= response elements

111
Q

activation domains (AD)

A

regulates transcription by interacting with other proteins (RNA polymerase or basal TFs)

112
Q

helix-turn-helix form

A

protein fold found in TFs that binds DNA- fits into DNA grooves

113
Q

zinc-finger motif

A

found in TFs- folded structure with zinc ion

-GAL4 binds DNA using this; preferentially binds specific DNA seqs

114
Q

inducible

A

able to be turned on

115
Q

non-inducible

A

always off

116
Q

constitutive

A

always on

117
Q

chromatin remodeling complexes

A

make hidden binding sites (enhancers/ promoters) accessible to transcription factors- prepare the DNA for transcription- reposition nucleosomes/ chemically modify histones to unwind the DNA

118
Q

DNA methylation

A

turns off genes bc methyl groups- “disguise” the enhancers/ promoters- preventing transcription factor binding and activation of transcription

119
Q

DNA methylase

A

adds the methyl (CH3) group to cytosine

120
Q

epigenetic silencing

A

methylation to turn genes off (Barr body)

121
Q

genomic imprinting

A

epigenetic phenomenon by which certain genes can be expressed in a parent-of origin specific manner- diffs due to diffs in methylation patterns

122
Q

prader-willi syndrome

A

deletion of chromosome 15 genes inherited from the father- heterozygotes are affected
-hunger, obesity, decreased mental capacity

123
Q

angel man syndrome

A

deletion of chromosome 15 genes from the mother and heterozygotes are affected- intellect/ neuroscience development delays, happy/ laugh, seizures

124
Q

RNA stability

A

mRNAs vary in stability- balance between degradation and transcription of new messages determines the level of individual mRNAs in cell

  • 5’ caps and poly A tails contribute
  • AU rich sequences in UTR can contribute to easily degraded mRNA
125
Q

nonsense mediated mRNA decay

A

targets incorrect mRNAs that have premature stop codons

*poly A tail and 5’ cap help to stabilize mRNA= euks

126
Q

RNA functions

A 
mRNA
snRNP (splicing)
tRNA
rRNA (ribosome)
ribozymes= RNA enzymes
miRNAs and RNAi= regulate gene expression
127
Q

RNAi (RNA interference)

A

method by which intro of a dsRNA triggers destruction of any matching mRNAs by nucleases
-used to decrease expression of ANY gene

128
Q

dsRNA (double stranded)

A

triggers RNA

=siRNA (small interfering RNA) in mammals

129
Q

siRNA

A

trigger the RNAi mechanism in mammals, but not the anti-viral (suicide) response

130
Q

miRNA (microRNAs)

A

might regulate most genes

  • needed for normal development
  • conserved throughout evolution
  • control tumor development (miR31)
  • usually regulate gene expression by blocking translation
131
Q

B-gal

A

monitors gene expression- cleaves X gal which causes blue precipitate

Genetics (5 decks)

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