13- Chapter 9

Question 1

What is genome and genomics definition?

Answer 1

Genome- entire complement of genetic information (includes genes, regulatory sequences, noncoding DNA)
Genomics- discipline of mapping, sequencing, analyzing, and comparing genomes
Look at slide 5-6 genome sizes

Question 2

What is genome sequencing?

What does generation sequencing mean?

Answer 2

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

First generation sequencing is Sanger method
Most labs use second generation sequencing now
There is also third and fourth generation sequencing
Generation refers to successive major changes in sequencing technology that confer increases in speed and drop in cost of sequencing

Question 3

What is the Sanger sequencing method?

Answer 3

Connecting a deoxynucleotide with another base molecule with the oxygen of phosphate to OH of deoxynucleotide
Slide 8-9

Question 4

What is second generation DNA sequencing?

Answer 4

Generates data 100x faster than sanger method
Massively parallel (large # of samples sequenced side by side)
Uses increased computer power and miniaturization (454 life sciences pyrosequencing)
Slide 11

Question 5

What is 454 sequencing system steps? 7 steps

Answer 5

1. DNA is broken down into 400-600bp
2. DNA adaptor added to both ends of fragment
3. Each fragment is immobilized on a bead and amplified by PCR using primers that anneal to both ends
4. Each bead put in a well with sequencing enzymes
5. dNTPs added which releases pyrophosphate
6. Luciferase enzyme emits light
7. Instrument measures release of light
   (Can only handle short stretches of DNA)
   Slide 11

Question 6

What is genome assembly?

Answer 6

Connects the DNA fragments in the correct order and eliminates overlaps
Done by a computer which examines short fragments sequenced and deduces order from overlaps and generates a genome for annotation
Can have a closed (complete) genome or a draft (small gaps) genome
Slide 14

Question 7

What is annotation and bioinformatics?

Answer 7

Annotation- converting raw sequence data into a list of genes present in the genome (genome sequence is just letters, needs to be annotated by computers)
Bioinformatics- science that applies powerful computational tools to DNA and protein sequences for the purpose of analyzing, storing, and accessing the sequences for comparative reasons

Question 8

What are ORFs?

Answer 8

Open reading frames that encode proteins
Computer algorithms looks for these stop/start codons or shine-dalgarno sequences
Slide 17

Question 9

What are hypothetical proteins?

Answer 9

Uncharacteristized ORFs, proteins the likely exist but whose function is unknown
Likely encode nonessential genes

Question 10

What is the genome size and content of prokaryotic genomes compared to eukaryotic?

Answer 10

Eukaryotic genomes contain a large fraction of noncoding DNA while prokaryotic do not
Prokaryotic genomes range in size from large viruses to eukaryotic microbes
Correlation between genome size and ORFs (slide 18)
As genome size increases, gene content proportionally increases
Genome sizes on slide 20

Question 11

How are genes distributed in prokaryotes?

Answer 11

Metabolic genes are most abundant
DNA replication and transcription genes make up minor fraction of genome

# of genes with role that can be clearly identified in a given genome is 70% or less of total ORFs, others are hypothetical proteins
Graph on slide 23

Question 12

How does gene distribution reflect lifestyle?

Answer 12

Archaea Devote higher percentage of genomes to energy and coenzyme production than bacteria
Archaea contain fewer genes for carb metabolism or cytoplasmic membrane function than bacteria
Look at graph slide 24

Question 13

What does homologous, gene families, paralogs, and orthologs mean?

Answer 13

Homologous- related sequence that implies common genetic ancestry
Gene families- groups of gene homologs
Paralogs- genes within an organism whose similarity to one or more genes in the same organisms is result of gene distribution
Orthologs- genes found in one organism that are similar to those in another organism but differ because of speciation
Diagram showing these on slide 27

Question 14

What are gene duplications or gene deletions?

Answer 14

Gene duplications- mechanism for evolution of most new genes, having 2 genes that do the same thing is a waste so duplicate genes disappear eventually
Gene deletions- eliminate gene no longer needed or it can evolve a new function
Slide 29 example

Question 15

What is vertical and horizontal gene transfer?

Answer 15

Vertical is parents passing down genes generations (genome replication and cell division)
Horizontal is transferring genes across things in real time

Question 16

What are the 3 types of horizontal gene transfer?

Answer 16

Transformation- encountering DNA in environment and picking it up
Transduction- when virus takes genetic info from one host to another host
Conjugation- organism transfers part of genome into another organism
Mobile elements include plasmids, phage, transposons, and insertion sequences
Slides 30-31

Question 17

What is the core genome and the pan genome?

Answer 17

Core genome- shared by all strains of species (all numbers of species)
Pan genome- includes all the optional extras present in some but not all strains of the species
Slides 33-35

Question 18

Study the functional genomics terms and systems biology on slide 36

Answer 18

Okay

Question 19

What is a metagome?

Answer 19

Total gene content of the organisms present in an environment
Microbiome studies
Slide 37

Question 20

What is the transcriptome?

What are the two types? (Hybrid., RNA Seq.)

Answer 20

The entire complement of RNA produced under a given set of conditions
Hybridization can be used in conjunction with genomic sequence data to measure gene expression (microarrays)
RNA sequencing is deep sequencing of cDNAs that allows comprehensive quantitation of all RNAs in a cell
Slide 40

Question 21

How do microarrays work with the transcriptome?

Answer 21

DNA segments/fragments on arrays are hybridized with mRNA from cells grown under specific conditions and analyzed to determine patterns of gene expression
Arrays are large and dense enough that the transcription pattern of an entire genome can be analyzed
Slide 41

Question 22

How is RNA sequencing used in transcriptome?

Answer 22

Replaces microarrays for the analysis of gene expression
All RNA molecules of cell are sequences
Requires high throughput sequencing (2nd or 3rd generation sequencing)
rRNA very abundant and mRNA must be enriched from total RNA pool

Question 23

What are the 5 things that can be derived from microarrays and RNA sequencing?

Answer 23

1. Global gene expression
2. Expression of specific groups of genes under different conditions
3. Expression of genes with unknown function; can yield clues to possible roles
4. Comparison of gene expression in closely related organisms
5. Identification of specific strains

Question 24

What are proteonomics?

What are the two ways to study it?

Answer 24

Genome wide study of structure, function, and regulation of an organisms proteins
1. 2D polyacrylamide gel electrophoresis- separates, identifies, and measures all proteins in first horizontal by isoelectric points and second vertical by size
2. High pressure liquid chromatography (HPLC)
Slide 44

Question 25

What are interactomes?

Answer 25

Complete set of interactions among molecules
Data expressed in the form of network diagrams
Slide 45 picture

Question 26

What is the metabolome?

Answer 26

Complete set of metabolic intermediates and other small molecules produced in an organism
Mass spectrometry is one of primary techniques for monitoring metabolites
Slide 46

Question 27

What is systems biology?

Answer 27

Integration of different fields of “omics” research
Genomics
Proteonomics
Metabolomics
Compares data and builds a computer model of the system being studied
Slide 47-48