OMICS

Question 1

Term omics refers to

Answer 1

a suite of technologies used in biology and medicine to comprehensively characterize and quantify pools of biological molecules in living systems

Question 2

4 categories of omics

Answer 2

genomics
proteomics
metabolomics
transcriptomics

Question 3

Genomics

Answer 3

study of an organisms entire genome - all DNA

Question 4

Proteomics

Answer 4

large-scale study of proteins in a cell or organism

Question 5

Metabolomics

Answer 5

analysis of small molecules in a system

Question 6

Transcriptomics

Answer 6

study of all RNA transcripts produced by the genome

Question 7

4 categories of genomics

Answer 7

structural
functional
comparitive
epigenomics

Question 8

Structural genomics

Answer 8

mapping and sequencing the genome

Question 9

Functional genomics

Answer 9

understanding gene function and expression

Question 10

Comparative genomics

Answer 10

comparing genomes across species

Question 11

Epigenomics

Answer 11

study of heritable changes beyond DNA sequence

Question 12

Metagenomics

Answer 12

total gene content of microbial community

Question 13

Metagenomics analyzes

Answer 13

pooled DNA or RNA from environmental sample containing organisms which have not been isolated/identified

Question 14

DNA Sequencing Methods

Answer 14

sanger sequencing
next-gen sequencing (NGS/illumina)
nanopore sequencing
PacBio SMRT sequencing

Question 15

Sanger sequencing

Answer 15

chain termination
gold standard for single-gene analysis

Question 16

Next-Gen Sequencing (NGS/Illumina)

Answer 16

massively parallel
high throughput
short reads (about 150bp)

Question 17

Nanopore sequencing

Answer 17

real-time
long reads (>100kb)
portable MinION device

Question 18

PacBio SMRT Sequencing

Answer 18

single-molecule real-time
long reads
low error with CCS

Question 19

Sanger sequencing step 1: dsDNA fragment is

Answer 19

denatured into two ssDNA fragments

Question 20

Sanger sequencing step 2: a fragment of

Answer 20

ssDNA is multiplied into millions of copies

Question 21

Sanger sequencing step 3: a primer that

Answer 21

corresponds to one end of the fragment is attached

Question 22

Sanger sequencing step 4: the fragments are

Answer 22

added to four polymerase solutions

Question 23

Sanger sequencing step 4: each solution contains

Answer 23

four types of bases (dNTP) but only one type of termination nucleotide (ddNTP)

Question 24

Sanger sequencing step 5: the chain grows until

Answer 24

a ddNTP is randomly added and when this is added DNA synthesis stops

Question 25

Sanger sequencing step 6: the resulting dsDNA fragments are

Answer 25

denatured to obtain a series of ssDNA of various lengths

Question 26

Sanger sequencing step 7: the fragments are

Answer 26

separated by electrophoresis and the sequence is read

Question 27

Nanopore sequencing step 1: an enzyme

Answer 27

unzips the DNA helix into two strands

Question 28

Nanopore sequencing step 2: a protein creates a

Answer 28

nanopore in the membrane which holds the adapter molecule

Question 29

Nanopore sequencing step 3: a flow of

Answer 29

ions creates an electric current through the nanopore

Question 30

Nanopore sequencing step 4: the adpater molecule keeps

Answer 30

DNA bases in place long enough to be identified electronically

Question 31

Proteomics ________ and _________ all _________ expressed by a ________ at a ________ ________

Answer 31

identifies quantifies proteins genome given time

Question 32

In proteomics unlike the genome, the proteome is

Answer 32

dynamic - changing with cell type, environment, and disease state

Question 33

Key proteomics workflow

Answer 33

sample preparation protein digestion (trypsin) mass spectrometry (MS/MS) database search protein identification

Question 34

Applications of proteomics

Answer 34

drug target discovery biomarker identification disease mechanisms

Question 35

Transcriptomics captures

Answer 35

when and how much each gene is "turned on", revealing dynamic gene expression patterns

Question 36

Key technologies in transcriptomics

Answer 36

RNA-seq microarrays single-cell RNA-seq (scRNA-seq) spatial transcriptomics

Question 37

RNA seq

Answer 37

deep sequencing of all RNA high resolution and sensitivity

Question 38

Single-cell RNA-seq (scRNA-seq)

Answer 38

gene expression in individual cells

Question 38

Microarrays

Answer 38

hybridisation-based high throughput lower cost

Question 39

Spatial transcriptomics

Answer 39

maps expression to physical tissue location

Question 40

The metabolites measure in metabolomics are the

Answer 40

downstream products of gene expression and protein activity

Question 41

Analytical techniques of metabolomics

Answer 41

NMR spectroscopy Mass spectrometry HPLC/gas chromatography-MS

Question 42

NMR spectroscopy

Answer 42

non-destructive quantitative

Question 43

Mass spectrometry

Answer 43

highly sensitive broad coverage

Question 44

HPLC/gas chromatography-MS

Answer 44

separation + identification

Question 45

Systems biology

Answer 45

takes a holistic approach, integrating data from multiple OMICS platforms to build comprehensive models of biological systems and understand emergent properties

Question 46

3 categories of systems biology

Answer 46

data integration computational modeling predictive medicine

Question 47

Data integration

Answer 47

combining genome, proteome, transcriptome and metabolome data

Question 48

Computational modeling

Answer 48

mathematical models to stimulate biological networks

Question 49

Predictive medicine

Answer 49

forecasting disease and drug response