Chapter 6- Genomics

Question 1

Genome

Answer 1

Entire complement of genetic information

- includes genes, regulatory sequences, and noncoding DNA

Question 2

Genomics

Answer 2

Discipline of mapping, sequencing, analyzing and comparing genomes

Question 3

Sequencing

Answer 3

determining the precise order of nucleotides in a DNA or RNA molecule

Question 4

generation

Answer 4

refers to successive major changes in sequrncing technology that confer:

• significant increases in speed
• drop in the cost of sequencing

Question 5

Sanger Dideoxy Method

Answer 5

• first generation sequencing
• Dideoxy analogs of dNTPs used in conjuction with dNTPs
• Analog prevents further extension of DNA chain
• Bases are labeled with radioactivity
• Gel electrophoresis is them performed on products

Question 6

Second Generation DNA sequencing

Answer 6

• DNA is broken into small segments
• DNA is amplified using PCR
• Light is released each time a base is added to DNA strand
• instrument actually measured release of light
• can handle only short stretched of DNA
• 454 sequencing system

Question 7

Shotgun Sequencing

Answer 7

Entire genome is clines and resultant clines are sequenced

• much of the sequencing is redundant (to reduce/catch errors)
• generally 7 - to 10-fold coverage of genome
• computer algorithms are used to look for replicate sequences and assemble them

Question 8

Genome assembly

Answer 8

consists of connecting the DNA fragments in the correct order and eliminating overlaps
(usually done by computer)

Question 9

closed genome vs draft genome

Answer 9

closed= entire gene sequence obtained
draft= some small gaps

Question 10

Annotation

Answer 10

converting raw sequence data into a list of genes present in the genome

Question 11

Bioinformatics

Answer 11

science that applies powerful computational tools to DNA and protein sequences for the purposes of analyzing, storing, and accessing the sequences for comparative purposes

Question 12

Functional ORF

Answer 12

an open reading frame that encodes a protein

Question 13

Hypothetical proteins

Answer 13

uncharacterized ORF’s; proteins that likely exist but whose function is currently unknown; likely encode nonessential genes

Question 14

Noncoding RNA

Answer 14

RNA that does not code for protein; lack star codons and have multiple stop codons

Question 15

Steps to finding probable ORFs

Answer 15

1. computer finds possible start codons
2. Computer finds possible stop codons
3. Computer counts codons between start and stop
4. Computer finds possible RBS
5. Computer calculates codon bias in ORF
6. Computer decides if ORF is likely to be genuine
7. List of probable ORF

Question 16

As genome size increases, gene content…

Answer 16

proportionally increases

Question 17

eukaryotic genomes conatain

Answer 17

a large fraction of noncoding DNA

Question 18

Smallest genomes belong to

Answer 18

parasitic or endosymbiotic prokaryotes

Question 19

Minimum number of genes for a viable cell is

Answer 19

250-300 genes

Question 20

comparative analysis

Answer 20

many genes can be identified by sequence similarity to genes found in other organisms

Question 21

most abundant class of genes

Answer 21

metabolic genes

genes for protein coding are also abundant

Question 22

Gene distribution in Archaea

Answer 22

typically devote a higher percentage of their genomes to energy and coenzyme production than bacteria

contain fewer genes for carbohydrate metabolism or cytoplasmic membrane functions than Bacteria

Question 23

Transciptome

Answer 23

the entire complement of RNA produced under a given set of conditions

Question 24

Microarrays

Answer 24

small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern
(sophisticated northern blot)
- can have high background (cross hybridization)
- requires/relies on known information on the gene

Question 25

RNA-Seq

Answer 25

• replacing microarrays for the analysis of gene expression
• All RNA molecules of the cell are sequenced
• Requires 2nd or 3rd gen.
• rRNA are very abundant and mRNA must be enriched from total RNA pool

Question 26

What can be learned from microarray experiments

Answer 26

• global gene expression
• expression of specific groups of genes under different conditions
• Expression of genes with unknown function; can yield clues to possible roles
• comparison of gene content in closely related organisms
• Identification of specific organisms

Question 27

Proteomics

Answer 27

Genome-wide study of the structure, function, and regulation of an organism’s proteins

Question 28

2-D polyacrylamide gel electrophoresis

Answer 28

technique for the separation, identification, and measurement of all proteins present in a sample

• In first (horizontal) dimension, proteins separated by differences in isoelectric point
• In second (vertical) dimension, proteins separated by size

Question 29

Proteins with ____ sequence similarity typically have similar finctions

Answer 29

> 50%

Question 30

Proteins with ___ sequence similarity almost certainly have similar functions

Answer 30

> 70%

Question 31

Interactomes

Answer 31

Complete set of interactions among molecules

- Data expressed in the form of network diagrams

Question 32

Metabolome

Answer 32

The complete set of metabolic intermediated and other small molecules produced in an organism
Mass spec is one of the primary techniques for monitoring metabolites

Question 33

Systems Biology

Answer 33

Integration of different fields of “omics” research

• Genomics
• Protoeomics
• Transcriptomics
• Metabolomics

Question 34

metagenome

Answer 34

total gene content of the organisms present in “an” envoronement