Topic 5: Mutations Flashcards by Megan Ganley

Mutations are the source of…

Genetic variation, providing the raw material for evolution
Diseases and disorders

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Mutations are useful for…

Probing fundamental biological processes

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What is a mutation

A permanent change in the genetic material ie DNA seq
does not need to result in phenotypic change

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Spontaneous vs induced mutation

Spont = in nature (UV)
Induced = in lab

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Genetic variation is the result of…

Mutations combined with processes of recombination, independent segregation, fertilization of gametes

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What are somatic mutations

Arise in somatic tissues (non-heritable mutations)

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What are germ-line mutations

Arise in germline tissues/cells (sexual tissues; make gametes (eggs/sperm) -> are heritable
Mutation affects one allele or one homolog

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Gene vs chromosomal mutations

Gene = alter genes - relatively small
Chromosomal = altering order or presence of genes on a chromosome - relatively large

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Slide 7

Somatic vs germ-line mutations

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Mutations that usually cause phenotypic changes

Mutations in protein coding genes, non-coding genes (fxnal RNA), regulatory elements

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Types of mutations (based on molecular nature)

Base substitutions
Insertions and deletions

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Types of base substitution mutations

Transitions
Transversions

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Insertions and deletions can cause.. Why wouldn’t they

frame-shift mutations
Unless the indel occurs in a unit of 3

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What is a transition

Base substitution
Substitution of a purine for a purine or of a pyrimidine for a pyrimidine

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What is a transversion

Base substitution
Substitution of a pyrimidine for a purine or a purine for a pyrimidine

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What are expanding nucleotide repeats

Type of in-frame indel mutation
Increases the number of copies of a set of repeated nucleotides

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What is the fragile site

Associated with characteristic constriction on X chromosome

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Forward vs reverse mutation

Forward = wild type -> mutant type
Reverse = mutant type -> WT

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What are missense, nonsense, silent and neutral mutations

Missense = aa -> diff aa
Nonsense = sense codon -> nonsense codon (stop)
Silent = codon -> synonymous codon
Neutral = no change in fxn

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Slide 13

Missense, nonsense, silent mutations

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Two phenotypic effects of mutations

Loss-of-function mutation
Gain-of-function mutation

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What is a loss-of-function mutation

DNA that is mutated stops its normal fxn
Straight forward relationship between genotype and phenotype

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What is gain-of-function mutation

More of the same fxn or totally new fxn
Not straight forward

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What can mutations be caused by

Study These Flashcards

spontaneous replication errors
spontaneous chemical changes
chemically induced mutations
radiation

Types of spontaneous replication errors

- tautomeric shifts - non-standard base pairing - causes of deletions and insertions (strand slippage, unequal crossing over)

What are tautomeric shifts

H moves to different N on base, causes it to bond to diff base

Examples of non-standard base pairing

Wobble pairing

What is wobble pairing

Non-standard base pairing where thymine binds with guanine or cytosine binds with adenine

How are DNA lesions usually repaired

DNA polymerase proofreading mismatch repair direct and excision repair mechanisms

What happens if lesions are not reparied

become replicated errors in subsequent round of DNA synthesis

Slides 18-22***

Wobble, strand slippage, unequal crossing over

Examples of spontaneous chemical changes

Depurination: loss of purine Deamination: loss of amino group

Slide 24, 25**

Depurination, deamination

Mutagens of chemically induced mutations

Base analogs Alkylating agents Oxidative reaction

E.g. of base analog, what does it do

5-bromouracil is an analog of thymine If present, can be incorporated into DNA during replication in place of T

Slide 28**

Base analog 5-bromouracil

What is an intercalating agent? Causes...

Inserts themselves between adjacent bases in DNA, distorting the 3D structure of the helix Causes single-nucleotide indels during DNA replication

Examples of ionizing radiation, what does it do?

X-rays, gamma rays and cosmic rays Penetrate tissue and damage DNA - dislodge electrons - break phosphodiester backbone (DS break-> if error in repair = mutation)

Energy level of UV radiation vs ionizing

UV has less energy

UV radiation can cause...

Pyrimidine dimer; two thymines block replication

Pyrimidine dimers block...

Cell division - block DNA polymerase from continuing replication - cells get stuck in G2 = death

How do pyrimidine dimers cause mutations

Specific repair mechanisms deal with them, but if mistake is made = mutation

Slide 32***

The Ames Test

What is forward genetics

Begins with a phenotype we try to find the genes encoding that phenotype

What is reverse genetics

Begins with a gene of unknown function, induce mutations, check the effect of the mutation on the phenotype

Slide 34

Forward and reverse genetics

Steps of creating random mutations

1. Apply mutagens (e.g. radiation) to model species 2. Screen for interesting phenotypes in the F2 generation

Slide 36

P0, F1 and F2 generations

Forms of targeted mutagenesis

Insertion mutants RNAi mutants CRISPR-Cas9 system

What is transgenic insertion mutant

Piece of DNA is inserted into your gene of interest using transgenic technology Insertion acts like large insertion mutation (frameshifts if in coding region = "kockout" mutant = LOF)

Transgenic insertion mutants mice

neo/tk system is often used to introduce insertion into a target gene

Slides 39, 40**

Transgenic insertion mutants in arabidopsis

What is RNAi (functions)

RNA interference, has two functions: 1. controls gene expr at post-transcriptional level by destroying target mRNAs 2. Protect against invading viruses by destroying viral RNAs

Two proteins in RNAi

Dicer: finds and cuts dsRNA into small interfering RNAs or micro RNAs RISC: RNA-induced silencing complex: uses RNAs as template for search and destroy (of other ssRNAs that complement with it)

How do we silence genes with RNAi

Engineer transgenic organisms that produce siRNA (small interfering RNA) that will complement our gene of interest, triggers RNAi process to destroy all mRNA produced from our gene of interest

What are knock-downs

In RNAi, mutant b/c some mRNAs will always escape the RISC

What does the CRISPR/Cas9 system do

Combines single guide RNA with a nuclease, together they attach to specific DNA sequences and make double-stranded cuts Repair these cuts by nonhomologous end joining or homology-directed repair, providing the means to introduce alterations to the genome

What does the single guide RNA do in CRISPR/Cas9

Provides specificity through complementation

Topic 5: Mutations Flashcards

(58 cards)