chromosomes- rnai (unit 2) Flashcards
1
Q
karyotype
A
spread illustrates the human 46 chromosomes
-taken during metaphase
2
Q
geimsa staining
A
gives characteristic bands on each chromosome and allows for chromosome identification
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)
4
Q
dosage compensation
A
adjusts for differences in the numbers of sex chromosomes- accomplished by X inactivation in females
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
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
7
Q
SRY
A
master sex determination gene- presence of SRY gene determines male development- encodes for transcription factor called testis- determining factor (TDF)
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
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
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
11
Q
trisomy
A
third copy of one of the chromosomes
12
Q
aneuploidy
A
not having the same number of each chromosome
13
Q
polyploidy
A
an extraset (or 2) of all of the chromosomes
14
Q
monosomy
A
only one of a particular chromosome
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
16
Q
trivalent
A
two chroms try to pair up with the one chrom
17
Q
univalent
A
one chrom is unpaired at metaphase
18
Q
chromosome deletion
A
missing genes- can be mapped via recessive phenotypes that show up
19
Q
chrom duplication
A
caused by unequal crossover
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
21
Q
acentric
A
chroms without centromeres= genetically unstable
22
Q
dicentric
A
chroms with two centromeres= 2 centromeres can then attach and separate to opposite poles= breaking chrom= very unstable
23
Q
translocations
A
chrom abnormalities which occur when chroms break and the fragments rejoin other chroms
24
Q
reciprocal translocation
A
2 non-hom chroms break and exchange fragments
25
robertsonian translocation
type of centric fusion translocation caused by fusions of acrocentric chroms
26
types of chromosomes abnorms
```
monosomy and trisomy
aneuploidy
deletions
translocations
duplications
inversions
accentric and dicentric
polyploidy (OK for plants)
```
27
DNA composition
sugar deoxyribose
phosphoric acid
4 nitrogen-containing bases
28
hydrogen bonds
FON share H atom
- AT base pairs have 2 H bonds
- CG base pairs have 3
29
semi-conservative replication
each DNA strand is used as a template for the new strand
30
template
older strands that are used to make a copy (parental strands)
31
replication origin
DNA sequence where replication begins
32
replication fork
region where parental strands are separated and new strands are synthesized
33
exonuclease
activity of DNA polymerase to remove mismatches- decreases the rate of mutations
34
PCR (polymerase chain reaction)
technique for amplifying DNA- DNA polymerase (that takes high temps best) extends the DNA by adding base pairing nucleotides
35
growth media
contains amino acids and sugars that support bacterial growth
-bacterial growth is exponential until nutrients run out
36
petroff-hauser slide counter
- 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
37
3 principle types of mutants
1) antibiotic resistant mutants
2) nutritional mutants
3) carbon-source mutants
38
antibiotic resistant mutants
mutation allows growth in presence of an antibiotic (ampR cells)
39
nutritional mutants
(auxotrophs) cells that cannot grow without a nutrient supplied by a researcher (Met-)
40
carbon-source mutants
cells can only metabolize certain sugars (Lac-)
41
persister
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
42
bacterial acquisition of resistance
1) transformation (transfer of free DNA), 2) conjugation (plasmid transfer), 3) transduction (transfer via virus)
43
bacterial chromosomes
haploid, reproduces asexually, plasmids
44
transformation
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
45
conjugation
joining of bacterial cells in order to transfer DNA
46
conjugative plasmid
plasmids that can be transferred this way- mostly small ones use larger recombinants to get into conj plasmids
47
F factor
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
48
F factor conjugation
transfer of F factor results in both cells containing the F factor- quickly transfers (only in 10% of EColi in nature
49
transposable elements
DNA sequences that can jump from one position to another or from one DNA molecule to another
50
insertion sequences
simplest and smallest and encode transposase
51
transposase
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
52
cointegrate
the recombined plasmid
53
recombinase
enzyme that catalyzes recombination of DNA
54
transduction
a phage (virus that infects bacteria) transfers DNA from bacteria by mistake instead of phage DNA genome
55
lytic cycle
reproductive cycle of a phage including lysing and release of new phages
56
lysogenic cycle
no progeny particles produced- phage DNA hangs out in bacterial DNA
57
temperate phages
lysogenic phage
58
virulent phages
lytic phage
59
transposable elements
DNA sequences that can jump from one position to another
60
gene expression
using the info in DNA to produce RNA and protein molecules that determine the phenotype of organisms
61
transcriptioon
synthesis of RNA mcl from DNA template
62
RNA vs DNA
ribose// deoxyribose
| uracil// thymine
63
transcription
1) promoter recognition
2) chain initiation
3) chain elongation
4) chain termination
64
promoter recognition
RNA identifies promoter by binding consensus sequences at -10 and -35 bp
-euk promoter regions are longer and more complex
65
transcription initiation
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
RNA polymerase
forms bond between 3' OH group at end of the chain and the next 5' phosphate group of the next nucleotide
67
termination regions
reverse inverts that undergo self-pairing and form hairpin structure that signals a cessation of transcription
68
intron
interrupt- removed by RNA splicing
69
exon
expressed- coding region
70
5- end cap
modified by addition of guanosine residue cap
71
poly A tail
up to 200 A residues long, regulates RNA stability, useful to identify and isolate RNA from eukaryotes
72
splicing
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
self-splicing introns
fold into structures that bring the 2 nucleotides that engage in splicing reaction into proximity
74
ribozymes
RNAs that fold up and have enzymatic activity on their own (catalyze)
75
helicase
unwinds DNA at replication fork
76
gyrase
cleaves and swivels duplex to release supercoiling
77
single strand binding protein (SSB)
binds and stabilizes single stranded DNA at fork
78
sliding clamp
protein fold that promotes DNA replication and prevents DNA polymerase from dissociation from template DNA
79
DNA polymerase
```
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
ligase
joins Okazaki fragments on lagging strand
81
primase
initiates how strand synthesizes- this is an RNA polymerase
82
peptide bond
formed between carboxyl and amino group and releases H2O
83
N terminus (of amino acid)
amino end
84
C terminus
carboxyl end (of amino acid)
85
colinear
amino acids are added to the polypeptide chain in the same order as RNA bases
86
translation
using info in mRNA to produce a protein
| -coupled with transcription in proks
87
translation steps
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
mRNA
provides coding sequence of bases that determines the amino acid sequence and brings ribosomal subunits together
89
ribosome
protein and RNA machine that directs protein synthesis
90
tRNA
transfer RNA molecules bring in amino acids to ribosome and put them in correct order by binding to codons in mRNA
91
aminoacyl-tRNA sythetase
catalyzes the attachment of a particular amino acid to its corresponding tRNA
92
Shine-Dalgarno sequence
helps proks recruit the ribosome to mRNA to initiate protein synthesis by aligning the ribosome with the start codon
93
Kozak sequence
helps elk's ribosome identify start codon
| -ribo binds to 5' cap and then scans to find the Kodak sequence near the AUG
94
elongation
1) new charged tRNA enters A site and binds to codon by
95
CRP and adenyl cyclase
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
tryptophan operon
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
repressible transcription
gene transcription is on until active repressor binds
98
aporepressor
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
leader sequence (trpL)
acts like dimmer switch to tune trp operon expression
| -trpL transcript (mRNA) can sense level pf trp
100
attenuation
controlling transcription in proks by coupling translator effects with transcription effects
101
TrpL
codes for a short 14 amino acid peptide
| -measures amount of trp via translation coupling
102
antiterminate
low trp levels- transcription continues
103
terminate
resembles transcription terminator sequence and the trp transcription is halted= attenuator
104
basal transcription factors
proteins in the complex that are used in the transcription of many different genes
105
transcriptional activation
occurs by mechanism called recruitment- the interaction of transcription factors with promoters and enhancers
106
enhancers
usually in vicinity of gene they regulate, but can be on either side (5' or 3' or in intron)
107
transcription factors (TFs)
can activate or repress transcription by binding to DNA
- general (basal TFs
- transcriptional activators or repressors
108
general (basal) TFs
bind DNA near promoter and associate with RNA polymerase- required for low level basal transcription
109
transcriptional activators/ repressors
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
DNA binding domain
binds specific sequences of DNA (enhancer or promoter) adjacent to regulated genes- DNA seqs which bind TFs= response elements
111
activation domains (AD)
regulates transcription by interacting with other proteins (RNA polymerase or basal TFs)
112
helix-turn-helix form
protein fold found in TFs that binds DNA- fits into DNA grooves
113
zinc-finger motif
found in TFs- folded structure with zinc ion
| -GAL4 binds DNA using this; preferentially binds specific DNA seqs
114
inducible
able to be turned on
115
non-inducible
always off
116
constitutive
always on
117
chromatin remodeling complexes
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
DNA methylation
turns off genes bc methyl groups- "disguise" the enhancers/ promoters- preventing transcription factor binding and activation of transcription
119
DNA methylase
adds the methyl (CH3) group to cytosine
120
epigenetic silencing
methylation to turn genes off (Barr body)
121
genomic imprinting
epigenetic phenomenon by which certain genes can be expressed in a parent-of origin specific manner- diffs due to diffs in methylation patterns
122
prader-willi syndrome
deletion of chromosome 15 genes inherited from the father- heterozygotes are affected
-hunger, obesity, decreased mental capacity
123
angel man syndrome
deletion of chromosome 15 genes from the mother and heterozygotes are affected- intellect/ neuroscience development delays, happy/ laugh, seizures
124
RNA stability
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
nonsense mediated mRNA decay
targets incorrect mRNAs that have premature stop codons
| *poly A tail and 5' cap help to stabilize mRNA= euks
126
RNA functions
```
mRNA
snRNP (splicing)
tRNA
rRNA (ribosome)
ribozymes= RNA enzymes
miRNAs and RNAi= regulate gene expression
```
127
RNAi (RNA interference)
method by which intro of a dsRNA triggers destruction of any matching mRNAs by nucleases
-used to decrease expression of ANY gene
128
dsRNA (double stranded)
triggers RNA
| =siRNA (small interfering RNA) in mammals
129
siRNA
trigger the RNAi mechanism in mammals, but not the anti-viral (suicide) response
130
miRNA (microRNAs)
might regulate most genes
- needed for normal development
- conserved throughout evolution
- control tumor development (miR31)
- usually regulate gene expression by blocking translation
131
B-gal
monitors gene expression- cleaves X gal which causes blue precipitate
