Genomics

Question 1

what is high throughput sequencing

Answer 1

technology that quickly generates large volumes of sequence data
quantitative and qualitative

Question 2

what are sequence census assays

Answer 2

use quantitative data from high throughput sequencing to understand genome function

• RNA-seq for transcriptome
• PCR- seq for metagenomics

Question 3

define genomics

Answer 3

the study of whole sets of genes, their products and their interactions
encompasses a bunch of -omics

Question 4

define bioinformatics

Answer 4

application of computational methods of storage and analysis of bio data

Question 5

define gene annotation

Answer 5

identifying protein encoding genes and their functions

Question 6

T/F: majority of our DNA consists of repetative DNA

Answer 6

T

Question 7

what % of human genes are conserved in other organisms

Answer 7

50%

Question 8

what do genomes vary in

Answer 8

size, density, and number of genes

Question 9

diff between euk and prok genomes

Answer 9

1) prok genomes have higher density

2) euk larger, more genes

Question 10

what are the 3 kinds of variation

Answer 10

1) SNPs
2) Various types of chormosomal structural rearrangements
3) CNVs

Question 11

explain SNPs

Answer 11

a single bp substitution at a particular site, must occur in pop at least > 1%
most do not have ptypes or cause disease
can be used as bio markers associated with disease causing genes
some directly causes disease
-ex FGFR3 gene in achondroplasia
can vary in freq
minor allele freq- freq at which least common allele occurs in a pop
common/freq variants >5%
rare variants < 1%

Question 12

various chromosomal structural rearrangements

Answer 12

genetic rearranement between diff chromosome or same one
balanced translocation are harmless
unbalanced translocations have lots of health affects

Question 13

CNVs

Answer 13

due to segmental duplication and deletion
loci w/ diff numbers of copies between indiv in pop; some indiv have >=1 copies of a particular gene rather than standard 2 copies
can be 50 bp to whole chromosome
may or may not cause phenotype or disease
cover large part of genome

Question 14

4 types of repetitive DNA?

Answer 14

1) STR
2) TR
3) Interspersed repeats (DNA transposons and retretransposons)
4) segmental duplications (large blocks of 10,000-300,000 bp that have been copied to another region of genome)

Question 15

STR

Answer 15

duplications of simple sets of 1-5 bp

directly involved in ptype variation

Question 16

TR

Answer 16

normally found at centromeres and telomeres
duplications of more complex, 100-200 bp
variation in number of TR in FLO1 gene in yeast can make cells stick to each other or be loose in liquid culture

Question 17

when was TE first observed/experimented on

Answer 17

color of corn kernels

Question 18

how do DNA transposons work

Answer 18

transposon in DNA is copied and moves to region of insertion
moves through DNA intermediate
BOTH cut-paste and copy-paste mechanism

Question 19

how do retrotransposons work

Answer 19

ss RNA intermediate synthesized from retrotransposon in DNA, reverse transcriptase uses RNA intermediate to synthesize ss DNA which is copied and moved to insertion region
RNA intermediate
ONLY copy-paste
most abundant

Question 20

T/F: TE content is relatively the same between species

Answer 20

false

Question 21

T/F: TE have not contributed to human proteins

Answer 21

F

Question 22

T/F: TE are a source of ptypic variation

Answer 22

T

Question 23

an ex of TE being a source of ptypic variation

Answer 23

carbernet has no retrotransposon
retrotransposon inserted leads to color loss–> chardonay
rearrangment of retrotransposon leads to red color

Question 24

diversity through gene duplication

Answer 24

duplication of ancestral gene–> mutation in both copies–> transposition to diff chromosomes-> further duplications and muts
ex. fetal hgb

Question 25

diversity through changes in gene regulation

Answer 25

Ubx Hox gene 7 suppressed legs in crustacean ancestor but are expressed in present day insects

Question 26

diversity through gene loss

Answer 26

humans have 3 pseudogenes for yolk, so no yolk
chickens have all 3 genes for yolk
monotremes have 1 yolk gene, 2 pseudos