exam 4

Question 1

loss of function approaches (reverse genetics)

Answer 1

1. RNAi
2. homologous recombination to create mutations
3. P-elements/transposons (insertional mutagenesis)
4. CRISPR-Cas9

Question 2

gain of function approaches (reverse genetics)

Answer 2

1. transgenes to over-express or mis-express genes (forced gene expression)

Question 3

reverse genetics

Answer 3

DNA sequencing - mutant allele - phenotype

Question 4

homologous recombination (reverse genetics)

Answer 4

loss of function method, creates mutations, changes genetic sequence by replacing target gene with heterologous or exogenous DNA

Question 5

p-elements

Answer 5

common way to mutate genes through the use of transposons (transposons)

Question 6

p-elements in reverse genetics

Answer 6

used to introduce mutations to study the effects on the phenotype

Question 7

p-elements in forward genetics

Answer 7

causing mutations to identify the genes responsible for specific phenotypes

Question 8

next generation sequencing (NGS)

Answer 8

technology used for DNA and RNA sequencing and mutation detection, can determine nucleotide sequence. forward genetics

Question 9

complementation assay

Answer 9

(P1) M1M1 x (P2) M2M2 = (F1) M1M2

Question 10

enhancer + mutation =

Answer 10

inhibit

Question 11

suppressor + mutation =

Answer 11

promote

Question 12

without enhancement, mutations occur in:

Answer 12

different genes

Question 13

if a gene has the same phenotype as the mutation genes it means

Answer 13

the gene carries that mutation

Question 14

forward genetics

Answer 14

phenotype - mutant allele - DNA sequencing

Question 15

forward genetics, mutagenic strategies

Answer 15

1. X-ray (physical)
2. p-elements (insertional)
3. EMS (chemical)
4. RNAi

Question 16

3 types of cancer genes

Answer 16

1. tumor suppressors
2. proto-oncogenes
3. caretaker

Question 17

tumor suppressors

Answer 17

• inhibit cell survival/proliferation
• loss of function
• keywords: apoptosis, DNA/chromosomal damage
• recessive

Question 18

proto-oncogenes

Answer 18

• promote cell survival/proliferation
• gain of function
• keywords: signaling, transcription factors
• dominant

Question 19

caretaker

Answer 19

• repair/prevent DNA damage
• loss of function
• keywords: DNA repair enzymes
• recessive

Question 20

multiple genetic hit hypothesis

Answer 20

each mutation is a progression towards a cancer cell
- 1st mutation inactivates negative cell cycle regulator
- 2nd mutation inactivates positive cell cycle regulator
- 3rd mutation inactivates genome stability factor, cancer cells develop after the 3rd mutation

Question 21

four characteristics of cancer cells

Answer 21

1. higher rate of proliferation: evades normal controls on cell growth
2. dedifferentiated: cancer cells behave more like stem cells
3. structural abnormalities: larger structures than normal cells
4. poorly organized: abnormally interacts with body/tissue, overgrown normal confines

Question 22

satellite DNA

Answer 22

highly repetitive sequences

Question 23

unique sequences in the genome

Answer 23

introns

Question 24

a component of moderately repetitive sequences

Answer 24

transposons

Question 25

repetitive sequences used in forensics

Answer 25

variable number of tandem repeats - VNTR

Question 26

genes arising from a duplication event

Answer 26

paralogs

Question 27

the basis for structural prediction of genes

Answer 27

open reading frame

Question 28

bulk RNA-seq

Answer 28

captures all mRNA in a sample-snapshot of gene expression

Question 29

HI-C

Answer 29

captures chromatin conformation, revealing long-range DNA interactions such as enhancer-promoter contacts

Question 30

metagenomics

Answer 30

sequences mixed microbal communities directly from their environment

Question 31

whole genome shotgun WGS sequences

Answer 31

sequences the entire genome (all DNA), including mutations and structural variants. critical for tumor profiling

Question 32

ATAC-seq

Answer 32

identifies regions of open chromatin, accessible euchromatin

Question 33

single cell RNA-seq

Answer 33

captures the transcriptomes of individual cells

Question 34

chIP-seq

Answer 34

identifies DNA-binding sites for transcription factors

Question 35

new gene (gene evolution) mechanisms

Answer 35

1. gene duplication 2. exon shuffling 3. gene fusion 4. reverse transcription 5. de novo derivation 6. horizontal gene transfer

Question 36

hyperplasia

Answer 36

extra cell growth

Question 37

dysplasia

Answer 37

disorganized growth

Question 38

neoplasia

Answer 38

highly disorganized, malignant tumors

Question 39

metastasis

Answer 39

spreading to other tissues

Question 40

5 steps for a forward genetic screen

Answer 40

1. identify trait or assay 2. mutagenesis 3. screening (select hits) 4. initial analysis of hits 5. identify DNA sequence changes

Question 41

balancer chromosomes

Answer 41

- used to track visible markers - engineered to suppress recombination

Question 42

3 types of cancer mutations

Answer 42

gatekeeping, driver, passenger

Question 43

gatekeeping mutation

Answer 43

first mutation, confers selective growth advantage to normal cell

Question 44

driver mutation

Answer 44

confers selective growth advantage to tumor cell

Question 45

passenger mutation

Answer 45

confers no selective growth advantage to tumor cell

Question 46

potential consequence of using EMS (chemical mutagen)

Answer 46

point mutations

Question 47

molecular approach to detect point mutation

Answer 47

PCR to amplify and map the DNA change

Question 48

if phenotype is alone/not enhanced

Answer 48

mutations are on different genes

Question 49

tandem repeats

Answer 49

one repeat after another, in moderate repetitive sequences

Question 50

interspaced repeats

Answer 50

gaps in between repeats, has transposons, in moderate repetitive sequences