TEST 4 Flashcards
(116 cards)
1
Q
mutation
A
heritable alterations in DNA sequence
2
Q
somatic mutation
A
body cell, mutation wont be passed on
3
Q
germline mutation definintion
A
gamete, mutation will be passed on
4
Q
spontaneous mutations definition
A
nonavoidable
occurs under normal conditions
5
Q
induced mutation
A
caused by environmental conditions
can be chemical or physical
6
Q
are mutations directed or random? experiment?
A
random.
Experiment: cells are cultured then placed in virus agar plate. Some cultures lived and died. Meaning it was random mutation not mutation after engagement of problem
7
Q
spontaneous mutuation
A
misparing due to wobble
tautomeric shift
strand slippage
depurination
deamination
unequal crossing over
8
Q
tautomeric shift
A
paring T-G A-C
every base has 2 tautomeric forms
causes damage
9
Q
strand slippage
A
can be cause due to insertion/deletion
c
c-c^c-c
g-g-g-g
10
Q
depurination/deamination
A
cutting off the puring/pyrimidine from the nucleotide leaving the 5’ sugar and phosphates only
11
Q
induced mutation
A
chemical mutagens-
base modifiers
intercalating agents
base analogs
physical mutagens-
radiation
12
Q
base modifiers
A
creates point mutations
13
Q
intercalating agents
A
insert in between the bases affects the structure ofDNA,
creates frameshift mutations
14
Q
base analogs
A
chemicals similar to nucleotides that insert themsleves in DNA
more likely to create tautomeric shifts
15
Q
direct damage of radiation
A
destroys the backbone of DNA causing cell death
16
Q
indirect damage of radiation
A
creates radicals/mutagens/reactive oxygen species that destroy the sugar phosphate backbone causing cell death
17
Q
deletion mutation
A
causes a framshift
deletion of a base
18
Q
insertion mutation
A
causes a frameshift
insertion of a base
19
Q
loss of function mutation
A
A mutation that results in reduced or abolished protein function.
20
Q
missense mutation
A
a single nucleotide change results in a codon that codes for a different amino acid
21
Q
nonsense mutation
A
where a codon that codes for an amino acids is changed to a chain-terminating codon
22
Q
silent mutation
A
mutation where a single nucleotide changes but the codon codes for the same product as before
23
Q
forward mutation
A
mutation that changes a functional gene to a nonfunctional or mutant gene
24
Q
neutral mutation
A
alterations in the DNA that are non-detrimental and non-beneficial for the survival and reproduction of the organism. also dont result in any phenotypic changes
25
lethal mutation
mutation in which the effect can result in death or reduce significantly the expected longevity
26
reverse mutation
this is the correction of a previous mutation to the correct state
27
conditional mutation
mutation that is only expressed under certain environmental conditions can be good or bad
28
transposable elements
mobile genetic codes, that add copies in new locations
29
transposon structure
flanking direct repeats
terminal inverted repeats
internal sequence
30
flanking direct repeats
repeats that are identical at the ends of transposons. these are left behind when it leaves
31
steps in transposition
1) staggered breaks in target DNA
2)TE joined to single stranded ends of target DNA
3) DNA replication fills in gaps
32
transposon forms
DNA transposon
retrotransposons
33
DNA transposons
moves in form of DNA intermediate
34
retrotransposons
moves an an RNA transcript of TE
35
replicative transposition
original plus new TE (increases TE's)
36
nonreplicative transposons
original is excied and moved to new target location
37
transition mutation
A-->G
C-->T
Base substitution in which a purine replaces a purine or a pyrimidine replaces a pyrimidine
38
transversion mutation
A/G-->C/T
base substitution in which a purine replaces a pyrimidine or a pyrimidine replaces a purine
39
intragenic suppressor muation
suppresses the effect of an earlier mutation within the same gene
40
intergenic suppressor muation
suppresses the effect of an earlier muation in another gene
41
mutagenic effects of transposons
gene disruption
unequal crossing over
42
expanding nucleotide repeats
type of insertion that increases the number of copies of a set of nucleotides
one strand hairpins itself, DNA pol re-synthesizes the same part again in after the hair pin
43
SOS system
occurs when many breaks are in the backbone
2 main proteins
LexA:keeps responce switched off when healthy
RecA:turns on repair when DNA is damaged
44
LexA
in a healthy cell, the LEXA protein binds to the DNA called the SOS box. Codes for over 50 genes
45
RecA
If RecA finds it, it will bind and stimulate the cleavage of LEXA from the SOS box letting the genes in the SOS box express
46
base excision repair
recognizes damaged bases not causing a significant distortion to the DNA helix such as oxidizing agents
occurs similar to nucleotide exsision repair
47
mutations rates comparing prokaryote to eukaryote
lower in prokaryotes
higher in eukaryotes
48
mismatch repair
MLH MSH MUT
finds incorrect part, continues down strand until methylated section is found which indicates which strand is parental, then it cuts from the methylated group to the incorrect part. Once peice leaves it resynthesizes section of dna cut out
1/100->1/1000 mistakes
49
direct repair
MGMT
repairs modified base to original structure
ex
methylated base to non methylated base
thymine dimers to thymine
50
excision repair
cuts out mismatch reopening the remaining complementary strand of DNA for resynthesis
cut-exsision
copy-DNA pol 1
paste- ligase
most common
51
nucleotide excision repair
3 part complex UvRABC
A moves down DNA
B attaches to problem sequence
C cuts out area around incorrect sequence
DNA pol 1 re sythesizes dna
52
loss of function genetic disorder example
cistic fibrosis
53
what does transposase do
binds to ends of transposon and cuts it out from its inverse repeat DNA sequence
54
photoreactivation
repairs thymine dimers using DNA photolyase 1
direct repair
55
translesion synthesis
last resort for DNA repair
DNA polymerase shifts from template directed to random incorperation of nucleotides
3/4 are mutations
56
Epigenetic modification of histones
acetylation
methylation
phosphorylation
ubiquitination
sumoylation
57
Where does acetylation occur
occurs on lysines
58
acetylation
occurs on lysines
neutralizes positive charge on histone, loosening its grip on DNA
accelerates transcription
HATs do this
HDAC undo this
59
methylation
occurs on lysines/ arginines
can be mono, di or tri methylated
can accelerate/decelerate transcription rates
60
HATs
acetylates histones
61
HDACs
deacetylates histones
62
lysine abbreviation and methylation enzyme
K
PKMTs
63
arginine abbreviation and methylation enzyme
R
PRMTs
64
Ubiquitination
attaches ubiquitin to lysines
accelerate/decelerate transcription rates depending on his tone
H2A histone- repressive
H2B histone- activating/repressing
DUBs do this
65
Phosphorylation
occurs on serine threonine and tyrosine
decondenses and activates genes
66
Sumoylation
small ubiquitin related modifer SUMO
stabilizes proteins
can repress transcription
67
Insulators
block effects of enhancers when they are between enhancers and promoters
68
ground state of bacterial and eukaryotic transcription
bacterial-on negative regulation (repressor)
eukaryotic-off positive regulation (activator)
69
remodeling proteins
all use ATP
can move DNA from under nucleosomes grip
can expose promoters to regulatory factors
70
histones
H1-clamp
H2A H2B H3 H4-inside of nucleosome
71
epigenome effects
changes gene expression
leads to changes in traits
are remembered during mitosis
reversible
not cause by DNA sequence
72
epigenetic effects
cell to cell
must persist 3 generations
parts of epigenome are heritable
73
regulatory mechanisms unique to eukaryotes
alterations of DNA structure
assembly of transcription complexes
RNA processing
74
EMSA
identifies sequence specific binding proteins
look for changes in ability of proteins to bind to DNA as you remove sequences from DNA sequence
final step is gel electrophoresis, if there are proteins on the DNA it will move less than non bound DNA sequences
75
Construction & Analysis of 5' deletion series
locates transcription control sequences in DNA up stream of gene
take a plasmid, reproduce a lot, place in exonuclease enzymes, place the same plasmid in these enzymes for different lengths, allowing for smaller and smaller plasmid DNA sequences
reassimalate into new plasmid, with gene
if gene is expressed our regulatory sequence from the inserted peice was enough to allow normal expression
76
nutrition and epigenetics
bees
worker bees stop eating royal jelly early and dont develop
queen bees eat royal jelly theyre whole life developing differently
77
temperature and epigenetics
plants
plants developing in cold climates inhibit flowering
plants developing in warm climates dont inhibit flowering
78
horomones and epigenetics
rats and licking
rats that get licked as a child pass on that behavior to theyre offspring as well
helps them regulate stress
79
detecting genome wide methylation
immunoprecipitate
methyl sensitive restriction enzyme
bisulphite treatement
80
immunoprecipitate
antibodies bond to methylated sites then you call pull them out of solution using methy binding proteins
81
methyl sensitive restriction enzyme
restriction enzymes that only cut DNA sequences when methylated
82
bisulphite treatment
converts unmethylated C's to U's
find ratios between ATs and CGs at specific sites, doing that can find methylated groups
83
lytic cycle
attachment & DNA insertion
biosynthesis of phage dna
cell lysis
84
lysogenic cycle
-viral DNA inserts itself into bacterial genome
-this is replicated and passed onto daughter cells
-eventually viral DNA leave bacterial genome and recreates itself entering the lytic cycle killing the bacterium
85
Crispr acronym
Clustered
Regularly
Interspaced
Short
Palindromic
Repeats
86
Cas9
gene that encodes cas proteins before the cripsr DNA sequence
these genes encode proteins to find foreign DNA
then they transcribe the foreign DNA into RNA, so that it can be transcribed back into DNA into the crispr to fight the pathogen for later
87
Crispr
bacterial memory of previous foreign pathogens DNA it has encountered so that if encountered again it can identify and destroy the DNA
88
palindromic part of crispr serves what function
these palindromes form hairpins when transcribed into RNA
these hairpins are recognized by crispr proteins to form crispr complexes to fight foreign pathogens
89
3 stages of CRISPR associated adaptive immunity
1) acquisition
2)CRISPR RNA biogeneis
3)Foreign DNA interference
90
PAM
small number of bases next to complementary DNA sequence found on foreign DNA sequence
NOT found on native DNA
91
PAM acronym
Protospacer Adjacent Motif
92
Class 1 crispr systems
multisubunit
93
Class 2 crispr systems
single subunit
94
Crispr cas9 system
Class 2
single subunit
95
nobel prize for crispr
the development of a method for genome editing
96
study of immune systems for beneficial microbes
food
biomining
pharmaceuticals
Bioremediation
97
study of immune systems for pathogenic microbes
destroy: human, animal, and plant, pathogens
98
tracrRNA
encoded by Cas9
base pairs with CRISPR RNA
when this RNA base pairs with crRNA, it hair pins with the CRISPRs repeat region
this hair pin signals to an RNAse to cut up CRISPR rna bonded to tracr RNA
once cut up, each of these segments encode for a different pathogen and are taken up by the CRISPR associated proteins to fight foreign pathogen reinfection
the crRNA is the guide rna
99
what stage of infection is precrRNA produced
preinfection
100
where does the Cas9-gRNA bind to the phage genome?
it looks for the PAM's, once found it breaks hydrogen bonds in the DNA and probes along the whole DNA piece for the complementary piece of DNA in the CRISPR and on the foreign DNA piece.
once the complementary piece is found it breaks the DNA
101
how does Cas9 get into the nucleus
it contains the nuclear localization signal
it allows it to get into the nucleus
102
what break does the Cas9 make?
blunt clean cuts
nonsticky
103
double strand break fixes
non homologous end joining
homology directed repair
104
non homologous end joining
glues together the two ends, usually loses or adds extra bases ending up w a framshift mutation which can cause gene knockout
105
homology directed repair
donor DNA with homology on the ends is added to the breaks, rejoining the two strands
this can allow for gene knock out through frameshift mutuation or gene knock ins by adding a gene with the donor homologous DNA
106
gene knockout examples
nonbrowning mushrooms
hornless cows
107
assumptions of HW equation
large population
random mating
no migration
no natural selection
overall no mutation
108
natural selection
process acting on individuals explaining the pattern of decent w modification
individuals with certain alleles produce the most
surviving offspring in a population
109
adaption
heritable trait increases fitness of an individual in a particular environment relative to other individuals without that trait
110
HW equation
p2+2pq+q2
111
df of hw
of genotype classes - # of alleles
112
how to find expected values for chisquaredtest of HW equation
find allele frequency- (homozygotic frequency + .5(heterozygotic frequency))
insert allele frequencies into HW equation
take the value for P^2, 2PQ, and Q^2. Multiply each of those numbers by the total population
that is the expected value
113
selection coefficient
1-W
W=fitness
114
W11W22
overdominance
both allele frequencies are maintained
115
W11>W12
underdominance
unstable equilibrium
116
speciation occurs when and how
when two populations become reproductively isolated and evolve independently
allopatrically- in different areas
sympatrically- in same area
