Lecture 18

Question 1

Genome

Answer 1

all genes in an organism

Question 2

does bigger genome mean more complex

Answer 2

No!

Question 3

genomics

Answer 3

The study of an organism’s complete set of DNA (genome), including its structure, function, evolution, and mapping.

Question 4

a cell’s “recipe book”

Answer 4

genome

contains coding and non-coding DNA

Question 5

the language of cell’s genome

Answer 5

nucleotides

Question 6

genome size range

Answer 6

viruses : tiny - small
prokaryotes : small
eukaryotes : small - gigantic

Question 7

dinoflagellates genome

Answer 7

(single celled algae)

1-80 x larger than the human genome

Question 8

complexity of genome

Answer 8

not directly correlated to size

Question 9

Prokaryote and Viruses genomes (small)

Answer 9

huge collective metabolic diversity despite small individual genomes

genomes have high coding density (little to no “wasted space”)

Question 10

eukaryotes genomes (small - huge)

Answer 10

high morphological diversity, but low metabolic diversity

huge euk genomes have low coding density (more DNA, but gene content does not increase proportionally)

Question 11

DNA sequencing

Answer 11

reading the specific order of genes

Question 12

PCR

Answer 12

polymerase chain reaction

(“photocopies” genes)

Question 13

applications of DNA sequencing

Answer 13

enviro : study natural microbiomes
evolutionary : infer evolutionary relationships
applied : seek out biomolecules of interest (antibiotics, drugs, nutrition)

Question 14

microbiome

Answer 14

community of microorganisms that inhabit a particular environment

Question 15

NGS

Answer 15

next generation sequencing

Question 16

first generation in the age of genomics

Answer 16

“sanger sequencing”

labour intensive but highly accurate

Question 17

“next generation” sequencing technologies

Answer 17

no need for purified molecules - can now sequence directly

highly accurate - used for liquid biopsies

Question 18

liquid biopsies

Answer 18

lab test that samples bodily fluid

Question 19

3rd generation sequencing technologies

Answer 19

lower accuracy
immediate results possible

Question 20

meta- prefix

Answer 20

when working with communities

Question 21

The two main strategies for DNA sequencing

Answer 21

targeted approaches and untargeted approaches

Question 22

targeted approaches examples

Answer 22

amplicon sequencing and barcoding

Question 23

untargeted approach

Answer 23

shotgun genome sequencing

Question 24

targeted approaches

Answer 24

use PCR to amplify a genetically conserved marker gene (e.g. rRNA)
- read DNA ‘barcodes’
- compare to database to classify
- cheap, reliable, simple but limited info

Question 25

untargeted approaches

Answer 25

fragment and sequence DNA directly (whole genomes) - need to put pieces back together - then compare to db more complex info (whole book) but more expensive and complicated

Question 26

amplicons

Answer 26

aka metabarcodes DNA (often rRNA) fragments amplified (via PCR)

Question 27

census

Answer 27

community profile "who and how many"

Question 28

metabarcoding

Answer 28

PCR + sequencing of rRNA from enviro samples allows census of enviro without cultivation

Question 29

steps to rRNA metabarcoding

Answer 29

1. sampling 2. dna extraction 3. PCR 4. Sequencing

Question 30

language of life

Answer 30

nucleotides