Molecular genetics exam 2 Flashcards
(132 cards)
1
Q
2 categories of mutations
A
somatic vs germline
2
Q
somatic mutation
A
cannot be passed to offspring
3
Q
Germline mutation
A
can be passed to offspring bc mutation occurs in oocyte and sperm
4
Q
Point mutations
A
change of a single base
5
Q
Silent or synonymous mutation
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when the change results in the same AA
6
Q
Missense mutation
A
when the change results in a different AA
7
Q
Conservative mutation
A
when the change is still the same type of aa such as polar or np
8
Q
Nonconservative mutation
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when the change results in a different type of AA such that it results in a differently folded protein
9
Q
Nonsense mutation
A
Leads to a premature stop codon and degradation of protein occurs
10
Q
Transitions
A
changing to the same type of base
11
Q
transversions
A
changing to a different type of base
12
Q
Frameshift mutation
A
when the insertion or deletion of a nucleotide changes the reading Frame and the sequence of aa
13
Q
What does a single nucleotide change in hemoglobin result in?
A
A sickle shaped red blood cell that is sticky
14
Q
Normal individuals may have fewer than __ nucleotide repeats
A
30
15
Q
Over 20 disorders exhibit over __ nucleotide repeats
A
200
16
Q
Examples of disorders with over 200 nucleotide repeats
A
Fragile X syndrome, Huntington’s diseases and myotonic dystrophy
17
Q
isoallele impact on phenotype
A
none or small that can only detected by special techniques
18
Q
Null allele impact on phenotype
A
No gene product or nonfunctional gene product
19
Q
Recessive allele impact on phenotype
A
Alter only when homozygous
20
Q
Gain of function impact on phenotype
A
produce new
21
Q
neutral impact on phenotype
A
no effect due to degeneracy and order in genetic code
22
Q
induced mutation
A
result from the influence of an extraneous factor, either natural or artificial
23
Q
4 examples of induced mutations
A
radiation, UV, natural and synthetic chemical
24
Q
spontaneous mutations
A
usually linked to normal biological or chemical processes in the organism
25
During DNA replication, DNA polymerase occasionally inserts incorrect nucleotides due to misfiring and predominantly leads to
point mutations through addition or deletion of nucleotides
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Replication slippage
If a DNA strand loops out and becomes displaced or if DNA polymerase slips, small insertions and deletions can occur
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where is replication slippage common
in repeat sequences
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Deamination
Amino group in cytosine or adenine is converted to uracil, and adenine is converted to hypoxanthine
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what does Deamination result in?
base pair change during replication mispairing
30
Depurination
loss of one of the nitrogenous bases (usually a purine) in an intact double helical DNA molecule
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what does deportation result in?
Frameshift because pairing cannot occur during replication
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Oxidative damage
induced by the by products of normal cellular processes and exposure to high energy radiation
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examples of things that cause oxidative damage
superoxides, hydroxyl radicals, and hydrogen peroxide
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what does oxidative damage result in?
DNA breaks
35
Mutagens
natural or artificial agents that induce mutations
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examples of mutagens
fungal toxins, cosmic rays, UV, industrial pollutants, medical x rays, and chemicals in smoke
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Base analogs
mutagenic chemicals that substitute for purines or pyrimidines during nucleic acid replication
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Specific mispairing
alter base such that it will mispair
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alkylating agents
donate an alkyl group to amino or keto groups in nucleotides to alter base pairing affinity
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what mutations result from alkylating agents?
transition mutations result
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Intercalating agents
Chemicals that have dimensions and shapes that allow them to wedge between DNA base pairs, causing base pair distortions and unwinding
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examples of intercalating agents
ethidium bromide and chemotherapeutic agents
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Pyrimidine dimers
distort the DNA conformation in such a way that errors tend to be introduced during DNA replication
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what causes pyrimidine dimers?
UV radiation
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Transposable elements
Sequences that can move about the genome and when they leave it results in DNA damage
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what is an example of something that acts as a transposable element?
Virus which is why hpv leads to cancer
47
Ionizing radiation causes __ damage
base
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What causes ionizing radiation
x rays, gamma rays and cosmic rays
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what happens during ionizing radiation?
stable molecules and atoms are transformed into free radicals
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what 3 things does ionizing radiation do?
alter purines/pyrimidines, break phosphodiaster bonds, and produce deletions, translocations, and fragmentation
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mismatch repair
responds after damaged DNA has escaped repair and failed to be completely replicated.
52
Base excision repair
corrects DNA containing a damaged DNA base
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3 steps of Base excision repair
Exonuclease cuts base, DNA polymerase inserts complementary nucleotides into gap and DNA ligase seals the nick
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2 steps of mismatch repair
excision of segment of DNA that contains a base mismatch followed by repair synthesis. Through a process of recombination
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Nucleotide excision repair
Repairs bulky lesions that alter/distort the double helix
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3 steps of NER
Exonuclease cuts distortion, DNA polymerase inserts nucleotides and DNA ligase seals nick
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NER may repair
pyrimidine dimers
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Double strand breaks are caused by
ionizing radiation
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DSB have 2 options for repair
homologous recombination and non nonhomologous end joining
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what us the preferred option of repairing DSB
homologous recombindation
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what does non homologous end joining involve?
bringing the 2 ends together but it may result in the deletion of some bases
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steps of homologous recombination
Damaged chromosome finds its homologous chromosome (same genes but not exactly the same sequence)
One strand of the damaged chromosome inserts itself into the homologous chromosome between the strands on DNA. It copies the sequence until it has copied all the DNA that was deleted
The damaged chromosome (blue one) will leave the homologous chromosome
The overlap area will match up
The gaps in the DNA will be filled in by DNA polymerase
63
Chromatin modifications can occur in 3 different ways
Histone modifications, nucleosomal remodeling, and dna methylation
64
Nucleosome organization
DNA molecule is wound 1 and 3/4 turns around a histone October called core particles
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what are histones made of
4 different subunits
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chromatin remodeling must occur to
allow the DNA to be accessed by DNA binding proteins to allow replication and gene expression
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Histone tails are potential targets along the chromatin fiber for chemical modifications that may include
acetylation, methylation, ubiquitination, and phosphorylation
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Regulating genes via nucleosomes
addition or removal of certain groups to the tails of histone proteins disrupts chromatin structure allowing transcription to take place
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Epigenetic inheritance
involves the copying of the histone modifications after the DNA has been replicated
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how does DNA methylation inhibit transcription?
the addition or removal of methyl groups from the bases of DNA can repress transcription by binding to transcription factors in DNA
71
Cis acting elements
postion regulator proteins in regions where those proteins can act to stimulate or repress transcription of the associated gene
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Promotors
nucleotide sequences that serve as recognition sites for transcription machinery that are critical for the initiation of transcription and are located adjacent to the genes regulated
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Examples of cis acting elements
enhancers or activators and silencers or repressors
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activators ___ transcription intitiation whereas repressors ___ TI
increase, decrease
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What do transcription factors do?
bind to cis-acting elements
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2 parts of the transcription factors
DNA binding domain and trans activating domain
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what is the DNA binding domain?
Binds to specific DNA sequences in the cis-acting regulatory site
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what is the trans activating domain
Activates or represses transcription by biding to other transcription factors or RNA polymerase
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What is DNA looping?
bending of the DNA such that the transcription factors interact wit the DNA of the transcription complex
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Enhancer
DNA sequence stimulating transcription a distance away from the promotor
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insulator
dna sequence that blocks or insulates the effect of enhancers
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2 types of post transcriptional processing
alternative splicing and RNAinterference
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Alternative splicing
generate different forms of mRNA from identical pre-mRNA giving rise to a number of proteins from one gene
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Steady state level of mRNA
amount in cell
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The steady state level of mRNA can be regulated by
in response to cell needs, through removing cap and tail, and through rna interference
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How does RNAi occur?
Short interfering RNA (siRNA) and microRNA (miRNA) represses mRNA translation ad triggers degradation
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Explain the process of miRNAs
miRNAs are transcribed from DNA to form a hairpin loop which targets them to degradation because they are double stranded. Dicer cleaves the miRNA into smaller pieces where it is packed up by RISC and the short strands target any other mRNA with that sequence
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Translational control
regulates the rate of protein synthesis
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Posttranslational modifications
Stability of a protein can be modulated. protein can change its structure and its activity
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translation can be regulated to
produce the correct quantity of a protein
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Recombinant DNA technology (genetic engineering)
Techniques for locating, isolating, altering, and studying DNA segments
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Molecular genetics
Biotechnology, the use of these techniques to develop new products
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What do restriction enzymes do?
Recognize and cut DNA at specific nucleotide sequences
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2 ends made by restriction enzymes
Blunt and cohesive ends
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cohesive ends
fragments with short, single stranded overhanging ends
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blunt ends
even length ends from both single strands
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sticky ends allow for
2 strands of DNA to come together due to base pairing
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CRISPR-Cas genome editing
makes a double stranded cut at a specific sequence and the dna repair mechanism in the cell repairs the break. Repaired by non homologous end joining or homologous recombination
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where is CRISPR-Cas found?
bacteria and archaea
100
Gel electrophoresis
Separates molecules such as DNA or protein based on size and electrical change
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Southern blotting
detect DNA
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Northern blotting
detect RNA
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western blotting
to detect protein
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Probe
dna or rna with a base sequence complementary to a sequence in the gene of interest
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Purpose of southern blotting
determine the presence of a specific gene sequence
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Purpose of western blot
to determine if a protein is being expressed
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cloning vector
a replicating DNA molecule attached with a foreign DNA fragment to be introduced in cell
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3 things a cloning vector must have
origin of replication, selectable markers-traits, and a cleavage site
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why is an OOR needed in a cloning vector?
So that it is replicated along with the DNA that it carries
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Why are selectable markers needed in a cloning vector?
Enables cells containing the vector to be identified or selected
111
why is a cleavage site needed on a cloning vector?
it needs a site for each of one or more restriction enzymes used
112
what are plasmids?
circular DNA molecules from bacteria
113
what are linkers?
synthetic DNA fragments containing restriction sites
114
how does foreign DNA get inserted into plasmids?
restriction enzymes
115
what are selectable markers used for in recombinant plasmids?
to confirm whether the cells have been transfromed
116
DNA markers
short segments of DNA whose sequence and location are known and they represent landmarks along chromosome
117
Name the different types of molecular markers
Single nucleotide polymorphisms, restriction fragment length polymorphisms, and microsatellites
118
what are the molecular markers used for?
Crime scene investigation, parental disputes, disease diagnosis, determining the type of species in cases of poaching
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what are micro satellites?
short tandem repeats (STR) variable number of copies of repeat sequences possessed by many organisms
120
what are micro satellites detected by?
PCR
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Homozygotes show a
single tail peak
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heterozygotes show
2 shorter peaks
123
Forward genetics
begins with a phenotype to a gene that encodes the phenotype
124
reverse genetics
begins with a gene of unknown function, first inducing mutations and then checking the effect of the mutation on the phenotype
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transgenic techniques
an organism permanently altered by the addition of a DNA sequence to its genome
126
Knockout mice
a normal gene of a mouse has been fully disabled
127
transgene
the foreign DNA that a transgenic organism carries
128
How are GMOs produced?
alteration of an organisms genome using recombinant DNA technologies to add or remove a gene from the genome
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what is biotechnology?
use of living organisms to create a product or a process that helps improve the life of humans or other organisms
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Biopharming
production of proteins in genetically modified plants and animals
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Bi transgenic crops
have built in insecticide protection from insect pests
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where are bi transgenic crops found
in many plants including corn, cotton, tomatoes, and tobacco
