genetics chapter 14 mutations repair
Terms
undefined, object
copy deck
- 2 major proc resp for gen variat?
-
1. mutat
2. recombinat - mutation ______________ playing cards, and ___________________ recombination ____________ playing cards
-
mutat introduces
recombinat shuffles them - mutagens
- cause mutations
- excision repair
- damamged dna strand is cut out, oth strand is used as templ to remake the damaged one
- what is the minimum mutat that can be induced?
- point mutation
-
t or f
its easier to have a loss of funct mutat than a gain of funct mutation - t
- new mutat are categorized as/
-
1. induced
2. spontaneous - what is rate of spont mutat?
- one c in 10^5 to 10^8
- mutagenesis
- prod of mutat thr expos to mutagens
- an organ that has gone thr mutagenesis has been?
- mutagenized
- mutagens have a ______________ dose response
- linear
- there is always a ___________ level of mutations, even when you are inducing mutations on purpose
- background level
- 2 main types of point mutat are?
-
1. base subst
2. base addit or delet - base substit are what 2 kinds?
-
1. transition
2. tranvservion - transition point mutat is?
-
replacement of A with G
or T with C - replacing a purin with a purin in a mutat is?
- transition mut
- replac a pyrimidine w a pyrimidine is a?
- transition mut
- transversion point mutat is?
- replac of purine w a pyrimidine
- purines are?
- A and G
- pyrimidines are?
- C and T
- indel mutat are?
- insertion deletion mutat
- addit or delet mutat are actually?
- addit or mutat of nucleotide pairs
-
mutat at prot level
a mutat that leads to a diff codon that encodes the same original AA is? - a synonymous mutation
- synonymous mutat are also called?
- silent mutat
- missense mutation is?
-
codon for one aa is changed to a codon for another aa
also called nonsynonymous mutat - nonsense mutat are?
- codon for one aa is ch to a stop codon
- synonymous mutat never alter?
- the aa seq of polypeptide chain
- conservative substit (from a missense mutat)
- when an aa is repl wit a chemically similar one
- nonconservative substitution (from a missense mutat) is
- when an aa is repl w a chem non similar other aa
- nonconservat are more likely to prod _______________- in prot struc and funct
- severe changes
- the closer a nonsense mutat is to the ______________ end of open reading frame the _____________
-
3' end
more likely that result prot will stil have some biolog activit - nonsense mutat lead to?
- premat terminat of translat
- indel mutat _________ the reading frame
- changes
- indel mutation leads to a ___________
- frameshift mutation
- frameshift mutat is caused by?
- an indel mutat
-
t or f
you can also have mutations in noncoding an regulatory dna like promoters - t
- you can have mutat in regulatory regions of dna that can change the level?
- of express of a g
- just bec you have a mutat on the genotypic leve does not mean you will have one?
- on the phenotypic lev
- northern blot looks at?
- rna
- western blot looks at
- protein
- mutational specificity
- mutag tend to do a cert kind of mutat and at a certain spot called hot spot
- hot spot
- place where a cert mutag tends to makes its mutations
-
mutagents
3 mech? -
1. replace a base
2. alter a base
3. damage a base - base analogs
- chemic comp that are so similar to normal nitr bases of dna they are accid incorp into dna struct
- tautomers of bases
- the diff forms of dna bases that they can naturally take
-
tautomers of bases
what are the diff forms? -
1. keto
2. imino
3. enol -
keto, imino, enol
which one is the most common? - keto
- what is the change of one tautomer into another called?
- tautomeric shift
- when a dna base bec ionized it can?
- cause a mispair
- if A bec its rare imino form it could accid pair w?
- C instead of T
- name 2 mutagens that alter a base?
- EMS and NG
- EMS is?
- ethylmethanesulfonate
- NG is?
- nitrosoguanidine
- EMS does what to the DnA bases?
- it adds an ethyl gr
- EMS and NG both add?
- alkyl gr to differ positions on the bases
-
base alteration
when is a mutat most likely to occur? - when the alkyl gr is added to the oxy at posit 6 of guanine to make o-6-alkylguanine
- adding an O to posit 6 of guanine leads to what transition?
- G C ---> A T
-
T or F
alkylating agents can ch incoming bases during DNA synth - T
- name 3 types of incalating agents?
-
1. proflavin
2. acridine orange
3. ICR compounds - intercalating agents do what?
- flat planar molecules that mimic base pairs and can slip betw nitrogen bases
-
what caused this to happen - an intercalating agent like acridine orange
- acridine orange, ICR-191, proflavin can cause ___________ in the DNA
- single nucleotide pair insertions or deletions
- if a mutag damages a DNA base it can ___________ DNA synthesis
- block
- E COli uses what system to bypass a damaged DNA base?
- SOS system
-
t or f
SOS is used only as a last resort - t
- DinB , UmuC, and UmuD' are ?
- error prone DNA polymerases
- EP polymerases are also called?
- sloppy copiers or error prone polymerases
- the eukaryote system _____________ is similar to E Coli SOS system
- translesion DNA synthesis
- how do EP polymerases overcome the block in replica?
- they add nucleotides to the strand opposite the damaged bases
-
t or f
error prone polymerases are always present in euk cells - t
- error prone polym in E Coli only appear when?
- they are induced to by UV damage
-
SOS mechan
UV light induces the synth of what protein? - RecA
- REC A is a key player in?
- mechan of DNA repair and recombination
-
e coli
dna damage
DNA polymerase ________ stalls at site of dna damage - III
-
e coli
dna ahead of DNA pol III is unwound and bound by ______, and then ___________- -
SSB
and then RecA - Rec A and SSB join to form?
- protein DNA filament
- nist carcinogens like uv and aflatoxin B1 are ___________ mutagens
- SOS dependent
- name one uv light generated photoproduct?
- cyclobutyl ring that unites adj pyrimidines
- UV light makes what alterations in DNA?
- photoproducts
- what is most freq transition causes by UV light?
- C ---> T
- Aflatoxin B1 comes from?
- a fungus assoc w peanuts
- apurinic site is where?
-
in DNA, where the base and the sugar backbone have been separated..
happens with aflatoxin - aflatoxin B1 causes what kind of mutation?
- G -C --> T-A transversion
- Luria and Delbruck tested?
- e coli to with phage T1 to see if any would bec resistant
-
luria and delbruck
were testing to see if? - the mutations were random or induced by the phage
- who came up with the "fluctuation test"
- luria and delbruck
-
luria and delbruck
their experiment suggested that? - resistant e coli cells are select by environm agent (the phage) but not produced by it
- replica plating reveals mutant colonies on a __________ thr their behavior on __________
-
master plate
selective replica plates - replica plating can be used to screen for mutants that?
- fail to grow under selective regime
- spontaneous lesions are?
- naturally occuring damage to dna
- what are 2 most freq spont lesions?
- depurination and deamination
- which is the more common spont lesion , depurination or deamination?
- depurination
- deamination of cytosine yields?
- uracil.
- deamination of 5-methylcytosine generates?
- thymine. making a C to T transition
- DNA analysis of "hot spots" for mutations freq show what base is there?
- 5-methylcytosine residues
- what is another type of spont lesion?
- oxidatively damaged bases
- name 3 active oxygen species?
- O2-, H2O2, and OH radicals
- errors in dna replicat can cause?
-
base substitut
base insert and deletion - in e coli indel can occur at?
- repeated seq in dna
-
e coli
longer repeats are hot spots for? - deletions
- common mech respons for genetic diseases is?
- expansion of a 3 base pair repeat. called trinucleotide repeat disease.
- what is an ex of a trinucleotide repeat disease?
- fragile X syndrome
- fragile x syndrome results from?
- changes in number of a (CCG)n repeat in a region of the FMR-1 gene
-
(CCG)n repeat in a region of the FMR-1 gene
parents and grandp have increased numb of the repeat so they have? - premutations. cause they dont have the dis yet but they do have increased copy number
-
fragile X syndrome
(CCG)n repeat in a region of the FMR-1 gene
if you have premutations what will happen? - the repeats will increase a lot more in your offspring
-
fragile X syndrome
(CCG)n repeat in a region of the FMR-1 gene
what is proposed mechanism? - slipped mispairing in course of DNA synth
- Huntington disease is assoc with?
- expansion of trinucleotide repeats in a g. huntingtons dis has a repeated seq, often within prot coding regions
- Huntington disease and Kennedy disease result from?
- amplification of a 3 base pair repeat of CAG
-
fragile X syndrome
6-59 number of copies.
phenotype? - normal
-
fragile X syndrome
60-200 number of copies.
phenotype ? - largely normal. this is the premutation stage
-
fragile X syndrome
>200 number of copies.
phenotype IS? - AFFECTED
- FMR-1 g, that are involved in fragile x syndrome, are freq ______ , which is assoc with silenced genes
- hypermethylated
-
dna error free repair
what are 2 ways this happens? -
1. repair the damaged base
2. delete the damaged dna and use complem seq as template -
direct rev of damag dna
which dam can be revers? - a photodimer caused by uv light
- photolyase can repair?
- a photodimer caused by uv light
- light repair or photorepair uses what enzyme?
- photolyase.
- why is photolyase a photorepair enzyme?
- bec you need cert wavelenghts of light for it to work and repair the damag dna
-
t or f
photolyase can not work in the dark - t
- name 2 dna repair enzymes
-
1. photolyase
2. alkyltransferase - alkyltransferase is a ?
- dna repair enzyme. they can remove alkyl gr from damaged dna
- what are 3 types of repair with dam dna?
-
1. direct rev
2. base excision and replac
3. segm removal and replacement - what are 2 types of homology depend repair systems?
-
1. excision repair
2. postreplication repair -
homolog dep repair syst
excision repair occurs? - before replication
-
homolog dep repair systems
depend on _____________ of the DNA - complementarity
- excision is the ____________ of an entire base
- removal and replacement
- what enzyme carries out base excision repair?
- DNA glycosylase
- DNA glycosylase cleaves?
- base-sugar bonds
- DNA glycosylase generates ___________ sites
- apurinic or apyrimidinic
- dna glycosylase works with what enzymes?
-
ap endonuclease
deoxyribophosphodiesterase
dna polymerase
dna ligase - what does ap endonuclease do?
- it cuts the sugar phosphate backbone around the site lacking a base
- base excision repair ends with _____________ sealing the repaired DNA
- dna ligase
- there are more ways to damage a base in dna than?
- there are glycosylases to remove them. so instead you have to use nucleotide excision repair
- nucleotide excision repair system detects?
- distortions in the double helix
-
nucleotide excision repair
e coli
3 enzymes will? - cut the damaged str at 2 sites flanking the lesion
-
nucleotide excision repair
e coli
the uvr exinuclease cuts out? -
8 nucleotides from one side
and 4 from the other -
euk
yeasts
nucleotide excision repair is done by? - repairosome
-
euk
yeasts
repairosome preferentially repairs ? - the template, or transcribed DNA strand
-
euk
yeasts
repairosome has subunits that are also subunits in the? - basal rna transcription apparatus
- name one post replication repair?
- mismatch- repair system
- mismatch repair system has to do what 3 things?
-
1. recog mismatched base pairs
2. determ which base is the wrong one
3. excise the incorr base and carry out repair synth - replication errors produce errors on which strand?
- the new strand
-
t or f
normally bacterial dna is methylated - t
-
post replicat repair
right after replication,
the new bact dna is has not yet been? - methylated
-
post replic repair
e coli
adenine methylase does what? - it methylates the dna strands.
-
post replicat repair
e coli
mismatch repair system can work bec it can dist the old strand from the new one by? - the methylation pattern
-
mismatch repair in hum
it repairs freq errors in what? - short repeat seq (microsatellites)
-
humans
short repeat seq are also called? - microsatellites
- hMutSα and HMutLα fix what kinds of mismatch?
- mispaired regions and loops
-
prok
mismatch repair system corrects errors in replication that are not corrected by? - proofreading function of the replicative dna polymerase.
-
prok
mismatch repair system
it only fixes the? - newly synthesized strand
-
repair of ds breaks
how does this occur? - if both str of double helix break at sites that are close to each other
- making ds breaks is a normal part of what in a human?
- generating antibod diversity
- give 2 examples of normal ds breaks?
-
1. generating antibod divers
2. meiotic recombination - what 2 mech are used to repair ds breaks?
-
1. non homologous end joining
2. homologous recombination - why is ds repair so hard in a non dividing cell?
- bec you dont have anything else to compare it to, like a sister chromatid
-
ds break
if you dont put the ends back together what could happen? - they could initiate chromosomal rearrangements
- non homologous end joining is?
- putting the ends back together of a ds break
-
ds break
what is the proc? -
1. KU70, KU80, DNA dep prot kin bind
2 ends are trimmed
3. ends are joined
3 - what 3 proteins bind ds in a ds break?
-
KU70
KU80
large DNA dependeint Prot kinase - homologous recombination is error free bec?
- it uses the sister chromatid to repair ds breaks
-
homolog recombinat
first step? - trimming of 5' ends
-
homolog recomb
sec step? - broken dna is coated with proteins including RAD51 (a RecA homolog)
- RAD51 is involved in?
- homolog recombination
- RAD51-DNA filament does what after its formed?
- searches for the undamaged sequence in its sister chromatid
-
homol recombin
when RAD51-DNA finds the complementary reg on the sister chrom, what forms? - joint molecule betw the the damaged sister chrom and the undamag sister chromatid
- what proteins are involved in repair by homolog recombinat?
-
1. RAD51
2. DNA Polymerase
3. DNA ligase -
In meiosis you can use
a. nonhomologous endjoining
b. homologous recombination - b. homolog recombination
-
meiosis
crossing over is initiated by? - a ds break
- molec mech of crossing over involves what 2 mech?
-
1. ds break
2. format of heteroduplex DNA - heteroduplex dna is made up of?
- one DNA str from one parent and one from another
- first evidence for heteroduplex dna came from?
-
strange ratios in fungi.
in their ascus.
You should have ratio of A:a of 4:4 but you sometimes got 6:2 2:6 - what were the aberrant ratios seen in the fungi ascus?
-
6:2, 2:6
5:3, 3:5 - when the ascus had extra copies it was said to have undergone?
- gene conversion
-
ds break model of crossing over
what is the holiday structure? - the formation of what looks like 2 single stranded cross overs
-
fungus
ascus
ds model of break crossing over
holiday structure are resolved in what ways? -
1. vetical breakage
2. horizontal breakage -
fungus
ascus
ds break model
if you had no A/a repair you would have a? - 5:3 octad
-
fungus
ascus
ds break model
if you had A/a repair you would have a? - 6:2 octad