Genomes

Question 1

Long repeated sequence

Answer 1

several thousand nucleotides long

Question 2

Tandem LRS

Answer 2

next to each other

Question 3

Dispersed LRS

Answer 3

spread throughout genome

Question 4

Short repeating sequences

Answer 4

difficult to sequence b/c can can fold back on itself to form double stranded structure
can make secondary structure

Question 5

human genome similarity

Answer 5

99.7-99.9%`

Question 6

Individual’s genome can indicate

Answer 6

susceptible to disease
drug sensitivity
personalized medicine

Question 7

Genomes contain sequence types:

Answer 7

• protein coding regions
• noncoding regions
• regions that are transcribed into RNA but never translated into protein

Question 8

Genome annotation

Answer 8

process by which researches ID various types of sequence present in genome and where they are located

Question 9

Sequence Motiff

Answer 9

signurature of protein coding gene.

looking for very long strands of reading frames that make open reading frames

Question 10

Protein coding region

Answer 10

contains open reading frame

Question 11

Open reading frame motif

Answer 11

long stretch of codons for amino acids with no stop codons

Question 12

transfer RNAs

Answer 12

forms hairpin structure, can fold back on itself

Question 13

Transcription factor motifs

Answer 13

hard b/c short
6-8 nucleotide long sequences
close to each other, upstream of long ORF

Question 14

Notes about Genome annotation

Answer 14

imperfect
hypothetical protein
analyzes differences and similiarities in protein coding genes in genomes of different species

Question 15

Hypotehtical protein

Answer 15

Common annotation,
found in large ORF, but dont know what it is
conserved regions

Question 16

Comparative Genomics

Answer 16

analyzes differences and similiarities in protein coding genes in genomes of different species

Question 17

conserved regions

Answer 17

sequences that are similar in different organisms

Question 18

Genome size (number of bases)

Answer 18

does not correlate with complexity

Question 19

Polyploidy

Answer 19

having more than 2 sets of chromosomes in genome

Part of reason for genome size not being relative to complexity

Question 20

Allopolyploidy

Answer 20

• Species A X Species B= new species AB
• 2 genomes, A and B
o Mom and dads genomes stayed diploid, didn’t go haploid

Question 21

Autoploidy

Answer 21

Same genome, doubling
• Species A produces unreduced gamets: new species AA
Unreduced gametes

Question 22

Repetitive elements

Answer 22

Highly repeptitive: .100,000 copies
o	moderately repetitive DNA 100-10,000 copies
o	Human genome examples
•	Alpha satellite
Transposable elements:

Question 23

Alphasatelile DNA

Answer 23

repetitive DNA in microtubule attachmment to centromeres, really important for cell division

Question 24

Transposible Elements

Answer 24

replicates and inserts itself into new positions in genome

DNA all the time

Question 25

Genome Organization of Mitochondria and Chloroplasts

Answer 25

Circular genomes o organized kinda like nucleoid o different than others because living symbiotically with the rest of the cell for quite a while

Question 26

Viral genomes and their organization

Answer 26

Virus consists of: • nucleic acid • DNA or RNA, single or double strands • protein coat called capsid • sometimes a lipid envelope/membrane o viruses can reproduce only by infecting living cells and sucerting cellular metabolism and protein synthesis to produce more viruses o most viruses tiny, harly larger than ribosome, 25-30 nm in diameter

Question 27

Repetitive DNA problems

Answer 27

hard to assemble correctly don't know how many times it should be repeated sequencing technical problem

Question 28

Exons and introns

Answer 28

whole genome sequencing or RNA SEEK

Question 29

RNA Seek

Answer 29

all expressed RNAs (mRNAs) and sequence just these. | compare back to genomic RNA to find where introns are (b/c not present in mRNA)

Question 30

LTR, LINE, and SINE

Answer 30

``` Other class RNA intermediate transpose it: o Start as DNA, go to RNA, then back • LTR (long terminal repeats), LINE (long interspered nuclear elements), SINE (short interspersed nuclear elements). can replicate and move around. But DNA transcribed into RNA, then reverese transcribed back to DNA and put back into genome ```

Question 31

Underwinding

Answer 31

``` counterclockwise winding of DNA strand, get higher order elements forming supercoiling, Topoisomerase II Cuts and winds to get underwinding due to no histones Prokaryotes ```

Question 32

Supercoiling

Answer 32

doesnt always allow easy access for transcription | may have to cleave to relax for transcriptional elements to access it

Question 33

scaffolding proteins

Answer 33

to organize/hold DNA in nucleus

Question 34

Chromosome painting

Answer 34

fluorecesnt dyes lable probes of chromosomes hybridize probes to another set of chromosomes can see where select chromosomes are

Question 35

Giemsa Dyes

Answer 35

Banding patterns

Question 36

Host range

Answer 36

rabies: broad range | tobacco mossiac: also broad

Question 37

Host specificity

Answer 37

composition can allow for jump from host to host | specificity in getting in and out

Question 38

Bacteriophages

Answer 38

head capisd tail insertion of double stranded DNA of host through tail

Question 39

Helical shape

Answer 39

Tobacco Mosaic

Question 40

Globular

Answer 40

largely affect us plasma membrane proteins or glycoproteins

Question 41

Tobacco Mosaic

Answer 41

o Self assembly: • assemble and then excrete, then infect genome encodes parts to make new virus