Midterm 2

Question 1

What is classical genetics and who started it?

Answer 1

Gregor mendel in 1865 – the science of solvingg biological questions by examining the offspring of living organisms

Question 2

What is molecular genetics, how did it start and when?

Answer 2

the science of solving biological questions using DNA, RNA and proteins isolated from organisms – began in 1970 with the discovery of restriction enzymes

Question 3

What are falcon tubes used for?

Answer 3

made by falcon for centrifuges

Question 4

What are epp tubes used for?

Answer 4

made by eppendorf for microcentrifuges

Question 5

What do restriction enzymes do?

Answer 5

they’re used by bacteria to cut virus DNA in vivo (inject their chromosome into host cell, takes it over and kills it) or by scientists to cut DNA in vitro

Question 6

What do restriction enzymes target?

Answer 6

4-8 bp sequences

Question 7

What does endonuclease EcoRI do?

Answer 7

it finds the cut site from a restriction enzyme in foreign DNA and cuts it

Question 8

Whatt does methyltransferase M-EcoRI do?

Answer 8

finds the same site as EcoRI and methylates it (protects it)

Question 9

What is the name of most cut sites?

Answer 9

palindromes (same forwards as backwards)

Question 10

What is the online resource for cut sites?

Answer 10

NEB (new england biolabs)

Question 11

What is electrophoresis?

Answer 11

the separation of charged molecules using an electric field

Question 12

What gel materials are used and when?

Answer 12

agarose: dsDNA over 100bp (cheap and edible)
acrylamide: dsDNA under 1 kb and ssDNA (expensive and poisonous)

Question 13

What are the speeds of linear DNA?

Answer 13

short moves fast, long moves slow

Question 14

How are recombinant chromosomes vs DNA made?

Answer 14

CHR: in vivo by crossovers from each parents alleles
DNA: in vitro by geneticists (from 2 organisms)

Question 15

How do you do gene cloning?

Answer 15

you instert DNA into a vector DNA and ligate it to form a recombinant DNA. Then you transform it into a bacterial cell and voila

Question 16

What is subcloning?

Answer 16

moving an insert from one vector to another

Question 17

Whats the best vector to work with and why?

Answer 17

pBluescript because its easy (pEZ BAC is harder to work with)

Question 18

What is indexing?

Answer 18

finds out what DNA is in which clone

Question 19

What is a BAC clone?

Answer 19

bacterial artificial chromosome – an engineered DNA molcule used to clone DNA sequences in bacterial cells (ex. ecoli) (used with DNA sequencing)

Question 20

What is a cDNA and what does it contain?

Answer 20

copy/complementary DNA: only has coding sequences (DNA of genes without introns)
- has no introns
- exons are spliced together for mRNA
- has reverse transcriptase

Question 21

Where do most reagents, cells, DNA molecules and machines in molecular genetics come from?

Answer 21

made and sold by biotech companies

Question 22

What are oligonucleotides (oligos)?

Answer 22

• synthetic ssDNA
• 20nt long
• can bind to complementary ssDNA
• work as primers for in vitro DNA replication

Question 23

What is a PCR test?

Answer 23

amplifies small segments of DNA (less than 5kb)
- in vitro exponentially
- uses a thermocycler machine

Question 24

What are the 4 results of a PCR test?

Answer 24

1. original template DNA
2. some unused dNTPs and primers
3. some variable length DNA
4. lots of constant length DNA (only one visible on a gel)

Question 25

Where do the primers end up on on a PCR test?

Answer 25

at the beginning of the 5' end

Question 26

When did manual and auto sanger sequencing first come out?

Answer 26

1977, then automated in 1986

Question 27

When did next gen dna sequencing come out?

Answer 27

2008 (use this and manual sanger today)

Question 28

What do ddNTPs do?

Answer 28

stop dna replication

Question 29

Cy3 vs Cy5

Answer 29

3: emits greenish yellow light 5: emits red light

Question 30

What does yellow fluorescence come up as?

Answer 30

black ink

Question 31

Where is PCR done?

Answer 31

in vitro -- presents a chromatogram with about 5kb of data (dsDNA of equal lengths)

Question 32

What does auto sanger do with what?

Answer 32

produces 700nt of useful data from ssDNA of unequal lengths

Question 32

What does auto sanger do with what?

Answer 32

produces 700nt of useful data from ssDNA of unequal lengths

Question 33

What was the first genome sequences

Answer 33

phage phiX174 (took 1 year) -- 1977

Question 34

How long would it take to sequence a human?

Answer 34

2 days with next gen - about $1000

Question 35

How many encoding genes do humans have?

Answer 35

about 20K - most noncoding

Question 36

What is metagenomics?

Answer 36

the sequencing of all DNA from an environment to find out which species are present

Question 37

When were human genomes first sequenced?

Answer 37

in the 1990s

Question 38

What did Barbara mcclintock do?

Answer 38

- discovered transposable elements - proved that meiotic crossovers involved dsDNA breaks

Question 39

What are TEs?

Answer 39

genes that can move to a new location through insertion - found in prokaryotes and eukaryotes - make one unique protein, most steps are done by host proteins - these insertions can disrupt genes (mutates and can render non functional) - rare in humans, common in pea plants and fruit flies (1/2 in FF are due to TEs) - 45% in human chromosomes - found in introns and the space between genes - can be polymorphic

Question 40

What are 5 ways to make a crop plant?

Answer 40

1. hybridization 2. spontaneous mutations and artificial selection 3. induced mutations and artificial selection 4. transgenic plants 5. targeted mutations with CRISPR

Question 41

How and why is transgenic insulin and factor 8 blood clotting factor made?

Answer 41

to treat hemophilia A

Question 42

What did golden rice do?

Answer 42

treats vitamin A deficient children and pregnant women mostly in africa and india

Question 43

What is a genetic cross?

Answer 43

an experiment in which males and females of a model organism are mated to produce offspring

Question 44

What is a reciprocal cross?

Answer 44

genetic crosses in which males of genotype A are crossed to females of genotype B and vice versa

Question 45

What 3 things make a good model?

Answer 45

1. simple 2. explains most if not all of the data 3. testable

Question 46

If the results aren't the same on crosses of 2 strains from a reciprocal cross, what does this indicate?

Answer 46

that the gene is on a sex chromosome

Question 47

What is the multiplication rule?

Answer 47

the probability that 2 events both occur is equal to the probability that one event occurs times the probability that the other event occurs (probability x probability)

Question 48

What is the addition rule?

Answer 48

the probability that either of 2 events occur is = to the probability that one event occurs plus the probability that the other event occurs (probability + probability)

Question 49

What is the subtraction rule?

Answer 49

either something will happen or it won't (probability occurring + probability doesn't occur = 1)

Question 50

What is gamblers fallacy?

Answer 50

that past events influence future possibilities (more/less likely an event will occur)

Question 51

What is pleiotropy?

Answer 51

when one gene influences several phenotypic traits

Question 52

What is codominance?

Answer 52

VERY RARE - when heterozygotes show the phenotypes of both homozygotes (ex. roan cattle)

Question 53

What are the 3 antigens?

Answer 53

a, b, h

Question 54

What combo makes A?

Answer 54

a and h

Question 55

What combo makes B?

Answer 55

b and h

Question 56

What combo makes AB?

Answer 56

a, b, h

Question 57

What combo makes O?

Answer 57

h

Question 58

Who can donate to A?

Answer 58

a or o

Question 59

Who can donate to B?

Answer 59

b or o

Question 60

Who can donate to AB?

Answer 60

ab, a, b or o

Question 61

Who can donate to O?

Answer 61

o

Question 62

What is a test cross?

Answer 62

Breeding of the dominant phenotype with the homozygous recessive phenotype (parent)

Question 63

What is a self cross?

Answer 63

The process of fusion of male and female gametes of the same organism

Question 64

What is an intercross?

Answer 64

A mating between two members of the F1 generation or between two animals that are heterozygous at the same locus

Question 65

Who proved that genes were on chromosomes?

Answer 65

thomas morgans lab

Question 66

Who figured out how genes fit onto chromosomes?

Answer 66

alfred sturtevant

Question 67

Where can genes be located?

Answer 67

autosomal: on an autosome sex-linked: on an X or Z chromosome

Question 68

What happens if RF is below or above 50%

Answer 68

below: genes are linked and on same chromosome above: genes are not linked and are far apart on the same or different chromosomes

Question 69

RF won't go above what?

Answer 69

50% (but could be more mu's than that)

Question 70

What is the old and new method for mapping genes?

Answer 70

old: RFLP new: GWAS

Question 71

What does GWAS do?

Answer 71

maps genes responsible for. phenotype to 700,000 SNPs in a single step - analyzes it with a DNA microarray reader - graphs the probability that the mutation is less than 10mu from each SNP (when it peaks = close to the gene of interest) - can have one peak or multiple - can work with just about any organism, model or not

Question 72

What are GWAS graphs called?

Answer 72

manhattan plots