Chapter 18 Lecture 12

Question 1

The Tinman gene

Answer 1

aka NKX2.5
studies in flies in 1980s
- mutations in a gene prevented heart development
- fail to form the muscle of the midgut and heart

Question 2

Somatic mutations

Answer 2

arise in tissues other than those that produce gametes

• impact is restricted to the individual
• not in germline so won’t be passed

Question 3

germ-line mutations

Answer 3

arise in tissues that produce gamets

- can be passed to offspring

Question 4

Are gene mutations always harmful?

Answer 4

no, source of all genetic variation

source of organisms ability to adapt to environment

Question 5

De novo mutation

Answer 5

an alteration in a gene that is present for the first time in one family member as a result of a mutation in a germ cell (egg or sperm) of one of the parents or in the fertilized egg itself

• can be germ-line or somatic
• NOT INHERITED FROM PREVIOUS GENERATIONS

Question 6

Frame shift mutations: insertion and deletions

Answer 6

addition or removal of one or more nucleotide pairs
- changes the reading frame
common way of inactivating a protein

Question 7

in-frame deletion

Answer 7

deletion or insertion of a multiple of 3 nucleotides that does not alter the reading frame

Question 8

expanding nucleotide repeats

Answer 8

repeated sequence of a set of nucleotides in which the number of copies of the sequence increases

Question 9

missense mutation

Answer 9

base substitution that results in a different amino acid

Question 10

nonsense mutation

Answer 10

mutation that changes a sense codon into a termination codon

Question 11

forward muation

Answer 11

mutation that alters the wild-type phenotype

Question 12

backward mutation

Answer 12

mutation that changes the mutant phenotype back into the wild-type

Question 13

silent mutation

Answer 13

mutation changes the codon sequence but not the amino acid

Question 14

neutral mutation

Answer 14

missense mutation that alters the amino acid sequence but does not change the function of the protein

Question 15

loss of function mutation

Answer 15

causes the complete or partial absence of a normal protein function
- usually recessive

Question 16

lethal mutation

Answer 16

causes premature death

Question 17

is a nucleotide change does not change the amino acid, doe it have no effect?

Answer 17

not always; can have phenotypic changes

• could change the rate of protein synthesis
• also can change if mRNA translated or not

Question 18

gain of function mutation

Answer 18

produces an entirely new trait or causes it to appear in an inappropriate tissue or at an inappropriate time

Question 19

suppressor mutation

Answer 19

genetic change that hides or suppresses the effect of another mutation

• intragenic- same gene of mutation
• intergenic - in another gene

Question 20

How is a suppressor mutation different from a reverse mutation?

Answer 20

reverse restores original phenotype by returning to wild-type and a suppressor restores the phenotype by causing an addition change in the DNA at a site different than mutation

Question 21

gain or loss of a nucleotide in the coding sequence is very likely to be devastating to protein function. why?

Answer 21

alters the reading frame and may change many codons

Question 22

expanding nucleotide repeats

Answer 22

mutations in which the number of opies of a set of nucleotides increases

• ex. fragile x and huntingtons
• number of repeats often leads to severity of disease

Question 23

what 3 factors affect mutation rates?

Answer 23

1. freq with which the changes arise in DNA
2. how often changes are repaired by DNA-repair mechanisms
3. ability to detect a mutation

Question 24

tautomeric shifts

Answer 24

proton position shifts, allowing mispairing

Question 25

Indels

Answer 25

small insertion or deletions that result from unequal crossing over

Question 26

strand slippage

Answer 26

newly synthesized strand forms a loop

can result in insertion or deletion

Question 27

depurination

Answer 27

loss of a purine

• result NT can’t pais
• cause presence of endogenous metabiline undergoing chemical reactions

Question 28

deamination

Answer 28

loss of an amino groups

• can result from nitrous acid
• corrected by enzyme thymine-DNA glycolase

Question 29

intercalating agents

Answer 29

proflavin, acridine orange, ethidium bromide

- disrupt rotation of pairing and assumes carcinogenic

Question 30

Base analogs are mutagenic because of which characteristic

a. they produce changes in DNA polymerase that cause it to malfunction
b. the distort the structure of DNA
c. they are similar in structure to the normal bases
d. they chemically modify the normal bases

Answer 30

c. they are similar in structure to the normal bases

base analogs are incorportated into DNA and frequently pair with the wrong base thus altering their pairing properties

Question 31

ionizing radiation

Answer 31

dislodges electrons n tissue causing free radicals which often damages DNA

Question 32

UV light induces the formation of pyrimidine dimer

Answer 32

two thymine bases that block replication

Question 33

sos system in bacteria

Answer 33

sos system allows bacteria cells to bypass the replication block with a mutation-prone pathway

Question 34

spontaneous mutation vs induced mutation

Answer 34

spontaneous occur under normal condition and happen naturally
- induced cause by environmental chemicals or radiation

Question 35

explain how some types of induces mutation occir, such as the effects of base analogs, intercalating agents, oxidative reactions, and UV light

Answer 35

base analogs are incorportated into DNA and frequently pair with the wrong base thus altering their pairing properties

• intercalating agents - wedge between the bases and cause single-base insertions and deletions in replication
• oxidative - change the structure of DNA bases
• UV light induces the formation of pyrimidine dimer two thymine bases that block replication

Question 36

what kind of mutations are most often created by UV radiation

Answer 36

formation of pyrimidine dimers that disrupt replication and transcription

Question 37

Mismatch repair

Answer 37

corrects incorrectly inserted nucleotides that escape proofreading
- enzymes cut out a section of the newly synthesized strand and replace with new NTs

Question 38

direct repair

Answer 38

change altered nucleotides back into their correct structures

Question 39

base-excision repair

Answer 39

glycosylase enzymes recognize and remove specific types of modified bases; entire NT removed and a section of the polynucleotide strand is replaces

Question 40

nucleotide-excision repair

Answer 40

removes and replaces many types of damaged DNA that distort the structure. two strands separated, a section containing distortion removed, DNA polymerase fills in the gap and DNA ligase seals the filled in gap

Question 41

how do direct-repair mechanisms differ from mismatch repair and base-excision repair?

Answer 41

direct return an altered base to its correct structure without removing and replaces NT
the other removes and replace NTs

Question 42

double strand repair breaks

Answer 42

homologous recombination
or
nonhomologous end joining

Question 43

transposons

Answer 43

mobile DNA sequences found the the genome

• most able to reinsert at many different locations
• often cause mutations

Question 44

common features of ransposons

Answer 44

short flanking repeats (3-12 bp) on both sides
-no not travel with
-regenerated at pt of insertion
staggered cuts in target DNA, leaving short, single stranded pieces on either side of transposable element
- replication of ssDNA create flanking direct repeats
- terminal inverted repeats at ends of many elements

Question 45

mechanism of transposition

Answer 45

• staggered breaks made in target DNA
• transposable element is joined to single stranded ends of target DNA
• dNA is replicated at the single-strand gaps

Question 46

replicative transposition

Answer 46

“copy and paste”

• copy made, jumps to new, leave old there
• increases # of copies of element
• can be between two different DNA molecules or between 2 parts of the same DNA molecule

Question 47

nonreplicative transposition

Answer 47

“cut and paste”

• excised from old and inserted to new
• no increase in copies
• cleavage require transposable enzyme
• joining carried out by normal replication and repair enzymes
• old site typically repairs using homologous sister chromatid

Question 48

retrotransposons

Answer 48

elements that transpose through RNA intermetiate
RNA transcribes, copied back to another DNA site using reverse transcriptase,
- only through replicative transposition
- more common thanDNA transposons in eukaryotes

Question 49

how are flanking direct repeats created in transposition?

Answer 49

staggered cuts are made in DNA and the transposable element inserts into the cut. later replication of the single-stranded pices of DNA creates short flanking direct repeats on either side of the inserted transposable element

Question 50

briefly explain how transposition causes mutationand chromosome rearrangements

Answer 50

becaus it inserts into a gene, destroying its function,
-chromosome rearrangements arise becuase transposition includes the breaking and exchange of DNA sequences.
additionally multiple copies of a transposable element may undergo homologous recombination, producing chromosome rearrangements

Question 51

which type of transposable element possesses terminal inverted repeats?

a. insertion sequence
b. composite transposons
c. noncomposite transposon Tn3
d. all the above

Answer 51

d. all the above

Question 52

what are the two groups of eukaryotic transposons

Answer 52

• structurally similar to transposable elements in bacteria
• -typically end in short inverted repeats
• -transpose DNA
• maize and fly
• retrotransposons
• -similar to retroviruses
• -include alu elements in humans, Ty in yeast, Copia in flies

Question 53

SINES

Answer 53

short interspersed nuclear elements
-11% of genome
include Alu

Question 54

LINES

Answer 54

long interspersed nuclear elements
-approx 9000,000 copes in human genome
-most can’t jump
21% of total human genome

Question 55

Barbara McClintock

Answer 55

40/50s discovered transposition in maize

• 1983 nobel prize
• only women to receive unshared prize
• showed genes are responsible for turning physical characteristics on and off

Question 56

first known active human transposon

Answer 56

L1 element

• causing a de novo case of hemophilia
• result of retrotransposition into the factor VIII gene