Section 4

Question 1

Transitions vs Transversions

Answer 1

-Point mutations
Purines= A,G (single ring) Pyramidines= C,T,U (double ring)
-Transitions= Py–>Py or Pr–>Pr
-Transversions= Py–>Pr or vice versa
-Transitions= more frequent even though transversions= more probable

Question 2

Missense Mutation

Answer 2

• Nonsynonymous mutation
• Diff AA
• Neutral, detrimental, or beneficial

Question 3

Nonsense Mutation

Answer 3

• Stop codon

- Detrimental

Question 4

Silent Mutation

Answer 4

• Synonymous Mutations= same AA

- No effect usually

Question 5

Spontaneous mutations

Answer 5

-Abnormalities by biological process

Question 6

Strand Slippage

Answer 6

-Spontaneous Mutation
-DNA pol temporarily dissociates during replication and stem loop forms
Ex: ALS GGGGCC

Question 7

Germline Mutation

Answer 7

• Occurs in egg or sperm

- Passes to offspring

Question 8

Somatic Mutation

Answer 8

• Occurs in somatic cell

- Passed w/in organism (mosaicism), but not from parent to offspring

Question 9

Mismatch Repair

Answer 9

• Corrects misincorperation of bases after replication

- Detects bulge in helix and fixes based on parent strand’s methylation

Question 10

Base Excision Repair

Answer 10

• Corrects single damages nucleotides

- Ex: AP sites

Question 11

Nucleotide Excision Repair

Answer 11

• Corrects thymine-thymine dimers

- Repair of UV damage

Question 12

Repair in CRISPR

Answer 12

• Homologous Recombination
• –Exonuclease trims back DSB
• –Sister chromatid atcs as template to repair damaged strand
• Non-homologous endjoining
• –Exonuclease trims back DSB
• –Ligase seals back together (deletion results)

Question 13

Depurination

Answer 13

• Removal of purine base from deoxyribose
• -Creates apurinic site
• DNA pol places adenine opposite if not repaired b4 next replication

Question 14

Deamination

Answer 14

• Loss of NH2 GROUP
• Affects mthylated CpG islands
• Changes C-G to A-T

Question 15

Restriction Enzymes

Answer 15

-Nucleases that cut put DNA at specific recognition sequences

Question 16

Transformation and Plasmid Vectors

Answer 16

• T= uptake of exogenous DNA into host cell
• MCS= Location for gene insert
• Ori= enables plasmid to replicate
• LacZ= way to screen for insertion of gene
• —If white, gene inserted (X-gal not converted by B-gal)
• —Blue pig if no gene
• Antibiotic resistance gene= provides selectable marker which plasmids recieved gene
• Prok= shine dalgarno
• Euk= TATA

Question 17

DNA library

Answer 17

• Collection of cloned fragments of DNA

- Single source

Question 18

CRISPR-Cas9

Answer 18

• Guide RNA= engineered to be complimentary to target DNA
• Cas9 nucleade= cuts target DNA bound to guide RNA
• Cut fixed by HDR or NHEJ

Question 19

PCR

Answer 19

• Uses principles of natural DNA replication to artificially synthesize target region of DNA
  1. Denature DNA
  2. Anneal primers
  3. Synthesize new strand
  4. Repeat 1-3 for 20-40
  5. Amount of target DNA doubles each cycle

Question 20

Genetic Maps

Answer 20

• Order and distance of genes based on map units/ cM

- Done using controlled crosses and genetic markers

Question 21

Physicla Maps

Answer 21

• Order and distance of genes from bp units
• Sequencing and assembling genome
• Physical distances SOMETIMES correspond to recombo frequencies

Question 22

Map-Based Sequencing

Answer 22

1. determine map order of clones
   - -using restriction enzymes
2. Assemble clones into contigs
3. Sequence contigs using sanger

Question 23

Whole Genome Shotgun sequencing

Answer 23

• Generates frags of diff sizes from genomic DNA by random sheering
  1. Genomic DNA cut into overlapping frags and cloned in bacteria
  2. Frags sequenced
  3. Overlap is used to order clones and entire genomic sequence is assembled

Question 24

Homologous

Answer 24

Similiar

• Orthologs= arrise from a specification event, 1 ancestral gene
• Paralog= genes that arrise from duplication event

Question 25

Cell Determination

Answer 25

-Process by which cell commits to developing -Totipotent= cell can develop into anything -Pluripotent= cell can become certain type of cell, already has determined cell line Multipotent= cells have capacity to divide into multiple cells

Question 26

Hox genes

Answer 26

-Code for transcription factors that regulate other genes

Question 27

Cancer

Answer 27

- Genetic cuz due to genes, but not always heredetsry cuz can be influenced by environmental factors - Over proliferation of cells

Question 28

Red Flags of cancer

Answer 28

- Early onset - Ashkenazi jewish - Rare types of cancer - Multiple gen. affected by cancer

Question 29

Genes in cancer

Answer 29

- KRAS--> gain of fxn leads to quicker cell proliferation= cancer - BRCA2--> loss of fxn leads to cell proliferation - TP53--> If cell ungergoes stress, no longer works--> cell proliferation

Question 30

Knudson's multistep model of cancer

Answer 30

-1st somatic mutation--> 2nd somatic mutation in same cell---> single tumor (sporadic) OR -Predisposed person inherits 1st mutation-> only 2nd mutation required for cell proliferation (hereditary)

Question 31

Clonal Evolution of Tumors

Answer 31

-Cell predisposed to proliferate at high rate -2nd mutation causes cell to divide rapidly -3rd= structural changes 4th= divide uncontrollably and invade other tissues