Exam 2: Genomics

Question 1

define genomics

Answer 1

branch of molecular biology concerned with the structure, function, evolution, and mapping of genomes

Question 2

what are the key findings from the human genome sequence project (3)

Answer 2

1. less than 25,000 protein coding genes in humans (same range as in other mammals)
2. human genome has significantly more segmental duplications than was suspected
3. fewer than 7% of protein families appeared to be specific to vertebrates

Question 3

take away from the key findings of human genome project

Answer 3

7% of proteins that were categorized are unique to vertebrates, ie only a small part of our genome has evolved to make us who we are (special to us). evolution has created functional motifs/domains in proteins that are used over years because the function was worthwhile then and is still now.

Question 4

social consequences of the human genome project

Answer 4

• first large scientific undertaking to dedicate a portion of its budget for research into social, legal, and ethical implications
• ethical board (training judges)

Question 5

tools and machines were being mass produced: the con and a pro for this in HGP

Answer 5

tools and machines were expensive but genes were being completely sequenced; number of euk genomes sequenced today is incredible (learning tool and spin offs)

Question 6

what does the number of protein domains encoded by some eukaryotic genomes delineate?

Answer 6

many proteins use similar subunits found w/in proteins; domains are intact all the way back to yeast so we share domains with yeast but w/ incr complexity we see incr in amount of protein domains

Question 7

is this in absolute: the bigger the genome, the more comlexity?

Answer 7

no compare humans to barley and barley has bigger genome

Question 8

repeated sequences in a genome is a puzzle why?

Answer 8

we are not too sure of its significance, in corn, 85% of genome is due to jumping genes whereas humans it is 44%

Question 9

most genes have about _ exons

Answer 9

8 and is fairly small compared to introns which are larger

Question 10

typical size of a protein is

Answer 10

about 1300 bp; the biggest ones are over 5000 bp and prone to mutations (ex DMD)

Question 11

giant introns are common to what euk genome?

Answer 11

humans

Question 12

genetic maps

Answer 12

provide rough approx of the locations of genes relative to locations of other known genes; based on the genetic function of recombination

Question 13

cons of a genetic map

Answer 13

• resolution/detail is very limited
• do not accurately correspond to physical distances btwn genes
• based off rates of crossing over, which vary from one part of the chromosome to another; so distances are only approx

Question 14

physical maps

Answer 14

are based on the direct analysis of DNA, and they place genes in relation to distances measured in base pairs, kilobases, or megabases

Question 15

physical maps and how they complete the sequence and produce a contiguous sequence

Answer 15

connects isolated pieces of genomic dna that have been cloned in bacteria/yeast

Question 16

restriction mapping determines

Answer 16

the position of restriction sites on DNA; piece of DNA is cut w/ a restriction enzyme and the fragments are separated to by gel electrophoresis = # of restriction sites in DNA and the distances btwn them can be determined by the # and positions of bands on the gel

Question 17

con of restriction mapping

Answer 17

does not tell us the order or the precise location of the restriction sites

Question 18

what is a restriction endonuclease

Answer 18

an enzyme that cleaves DNA into fragments at or near specific recognition sites

Question 19

two cut DNA, all restriction enzymes make 2 incision once through

Answer 19

once through each sugar-phosphate backbone (ie each strand) of the DNA double helix

Question 20

restriction enzyme origin

Answer 20

found in bacteria and archaea and provide a defense mechanism against invading viruses; cuts up foreign DNA but leaves host DNA alone since protected by methylation

Question 21

what protects DNA against DNA cleavage from most restriction enzymes

Answer 21

methylated DNA

Question 22

a set of two or more overlapping DNA fragments that form a contiguous stretch of DNA is called a _

Answer 22

contig

Question 23

the order of clones/artificial chromosomes can be determined w/o use of preexisting genetic maps via

Answer 23

(YACs) each clone can be cut w/ a series of restriction enzymes which creates a unique set of restriction fragments akin to fingerprint for each clone; areas of overlap is used to arrange the clones in order

Question 24

restriction enzymes that produce sticky ends

Answer 24

(EcoRI) cuts in a staggered fashion and creates sticky ends so easy to recombine to sequences that used the same restriction enzyme bc of the overlap is a compliment

Question 25

restriction enzymes that produce blunt ends

Answer 25

(Smal) blunt cut = cuts btwn both strands and blunt end but difficult to ligate back together (advantage is that the sequence does not need to match up/do not have to be compliments

Question 26

what was an unexpected finding that came from HGP and the amount of genetic variation?

Answer 26

amount of genetic variation each indiv has, we predicted that it would be more than the avg 3 million nucleotides that represent the physical diff btwn indivs that creates diversity. Our haplotype reflects the 3 million SNPs that are unique to my genome vs others

Question 27

how many SNPs would we expect to find between 2 siblings

Answer 27

1.5 million

Question 28

what is a transcriptome

Answer 28

all of the transcripts that get made thought of as just coding sequences, however also includes miRNA and snoRNAs (noncoding), and lncRNAs which contribute to the bulk of transcriptomic seqs (portion of the 2%)

Question 29

sequencing tools do not work well with RNA, so what must you do?

Answer 29

reverse transcriptase (RNA into DNA) so we can seq DNA

Question 30

it is hard to seq an entire message so what must we do

Answer 30

break them up into smaller fragments and overlap fragments (tools are constantly evolving)

Question 31

transcriptome analysis starts with

Answer 31

RNA

Question 32

whole genome mutagenesis can identify

Answer 32

genes associated w/ specific traits (impact of genetic variation on phenotypic outputs/conseq of mutations)