Lecture 21

Question 1

the complete set of DNA within a single cell of an organism

Answer 1

genomes

Question 2

is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes

Answer 2

genomics

Question 3

Human genome project sequenced human genome, model system genomes, and –

Answer 3

EST (expressed sequence tags) = cDNAs

Question 4

map the fragments, sequence the fragments, and piece it together = slow and careful (public)

Answer 4

clone-by-clone sequencing approach

Question 5

Take a lot of copies of the genome
Break it up into little fragments
Sequenced all the little fragments
Computer puts it all together

Answer 5

shotgun sequencing

Question 6

next generation sequencing: after each nucleotide is added, its identity is determined by –

Answer 6

fluorescence

Question 7

Once a sequence is obtained, it must be –

Answer 7

annotated

Question 8

annotating a sequence includes – the genes, promoters, exons/introns, and function of genes

Answer 8

locating

Question 9

process of attaching biological functions to DNA sequences

• describes both structural and functional features of a gene
• goal = identify known genes, regulatory sequences, etc as well as to identify sequences that are likely to be genes through their function

Answer 9

annotation

Question 10

– cDNAs allow designation of all introns and exons

Answer 10

complete

Question 11

– cDNAs (referred to as expressed sequence tags (EST)) allow expressed genes to be identified

Answer 11

incomplete

Question 12

same info from all cell types from the same individual
includes: cis-elements (promoter, enhancer, etc.)
introns, repetitive sequences, etc.

Answer 12

genomic DNA

Question 13

– is expressed genes that is derived from mRNA contains coding regions (no introns or regulatory sequences)

Answer 13

cDNA

Question 14

What type of library do you need to piece the genome together?

Answer 14

genomic

Question 15

What type of library do you need to determine the exon/intron complete sequence and structure of a gene?

Answer 15

genomic and cDNA

Question 16

expression levels are based on frequency of –

Answer 16

cDNA clones

Question 17

exon/intron structure are based on

Answer 17

cDNA clones

Question 18

alternative splicing are based on –

Answer 18

cDNA clones

Question 19

databases contain info on function which is based on –

Answer 19

homology to known genes

Question 20

Where experimental data is not available, – is used to predict gene structure from ORFs, splice sites, promoter sequences

Answer 20

bioinformatics

Question 21

Bioinformatics: the use of – approaches to decipher DNA-sequence information

Answer 21

computational

Question 22

sequences without a stop codon, appear to possibly code for polypeptides

Answer 22

open reading frames

Question 23

DNA – analysis can analyze mRNA concentrations – a cheaper alternative to sequencing.

Answer 23

microarray

Question 24

Sequence analysis of all living organisms in an environment

Answer 24

metagenomics

Question 25

in metagenomics -- are over represented

Answer 25

most common species

Question 26

Addition of foreign DNA into the genome.

Answer 26

transgenic

Question 27

Removal of a specific piece of DNA from the genome.

Answer 27

knock-out

Question 28

Replacement of a specific piece of DNA from the genome with a different piece of DNA.

Answer 28

gene replacement

Question 29

transgenes from different species

Answer 29

heterologous

Question 30

human cells can properly translate bacterial genes because the genetic code is --

Answer 30

universal

Question 31

-- sequences are not universal: promoters, enhancers are species specific so need to use sequences specific for host

Answer 31

regulatory

Question 32

-- vectors are vectors that have been furnished with sequences capable of directing efficient transcription and translation of transgenes

Answer 32

expression

Question 33

All vectors need | -- and Selectable marker so that you can transform it and select for things

Answer 33

Origin of replication

Question 34

Series of restriction sites into which the gene to be expressed is inserted in recombinant clones

Answer 34

MCS (multi-cloning site)

Question 35

You can put a human gene in the MCS If you have the bacterial promoter and transcription terminator you can express a human gene But need to get rid of human introns since bacteria cannot splice introns therefore you need to use --

Answer 35

cDNA

Question 36

Eukaryotic expression vector must contain --, polyadenylation signal, adn MCS

Answer 36

TATA box

Question 37

different species may prefer different codons, reflected in levels of particular tRNA

Answer 37

codon bias

Question 38

factors that affect heterologous protein synthesis: | codon bias, -- and high levels of synthesis can lead to aggregation and precipitation of inactive protein

Answer 38

post-translational modifications (rarely occur in bacterial cells)

Question 39

some proteins produced in E. coli for humans include insulin human growth hormone erythropoietin (induces red blood cell formation) --

Answer 39

proteases used in detergents

Question 40

-- is also commonly used to express heterologous genes

Answer 40

Yeast

Question 41

replicates in both bacteria and yeast

Answer 41

shuttle vector

Question 42

With this shuttle vector, DNA sequences can be manipulated in -- where manipulation is easier, after which the modified plasmids can be shuttled into yeast for heterologous protein expression

Answer 42

E. coli (bacteria)

Question 43

an advantage of using S. cerevisiae as a protein factory is that it has the ability to splice introns and -- modify proteins

Answer 43

post-translationally

Question 44

S. cerevisiae can -- proteins out of the cell

Answer 44

secrete

Question 45

stable transgenic yeast can be made by integration of a plasmids without --

Answer 45

an origin of replication

Question 46

stable transgenic yeast can be made by double crossover through -

Answer 46

circular or linear plasmid with homology to genome

Question 47

integrates introduced DNA at a random, nonhomologous location

Answer 47

illegitimate recombination

Question 48

integration of entire plasmid is useful for -- or making transgenic yeast

Answer 48

gene disruption

Question 49

double crossover is useful for gene disruption or --

Answer 49

gene replacement

Question 50

In homologous recombination with circular DNA, a single crossover results in integration of introduced DNA without the -- of target gene

Answer 50

replacement

Question 51

In homologous recombination with circular DNA, a double crossover results in the -- of target gene

Answer 51

replacement

Question 52

In homologous recombination with linear DNA, a single crossover results in integration of introduced DNA and --

Answer 52

terminal deletion

Question 53

In homologous recombination with linear DNA, a double crossover results in the -- of target gene

Answer 53

replacement (or knockout)

Question 54

linearized DNA molecules recombine at a -- frequency than circular ones so in yeast a double crossover at linearized plasmid is the best choice

Answer 54

higher

Question 55

Common technique used to determine the function of a gene is to disrupt it and examine the phenotype

Answer 55

gene knockout

Question 56

Using a --, it is a simple process in yeast to disrupt any gene

Answer 56

selectable marker

Question 57

Drosophila genome contains a predicted POU-domain gene, pdm-3 but nothing is known about its function. How can you figure out where in the body pdm-3 is functioning?

Answer 57

transgenic fly

Question 58

Advantages of transgenic animals: can examine the -- of a gene of interest

Answer 58

expression pattern

Question 59

Advantages of transgenic animals: can -- particular cells or cell types with a reporter

Answer 59

label

Question 60

Advantages of transgenic animals: can -- a normal or mutant allele of a gene to look for associated phenotypes

Answer 60

overexpress

Question 61

Disadvantages of transgenic animals: integration site is -- so expression can vary depending on where the foreign DNA integrates

Answer 61

random

Question 62

Disadvantages of transgenic animals: Random integration can sometimes disrupt genes and cause --.

Answer 62

unrelated mutant phenotypes

Question 63

Disadvantages of transgenic animals: Often, multiple copies of the transgene are integrated, so the expression level cannot be controlled and is often much -- than normal.

Answer 63

higher