Chapter 12

Question 1

What is a genome

Answer 1

The entire complement of genetic information. Includes genes, regulatory sequences, and noncoding DNA

Question 2

What is genomics

Answer 2

Discipline of mapping, sequencing, analyzing, and comparing genomes

Question 3

What is shotgun sequencing

Answer 3

A technique used by virtually all genomic sequencing projects. Random fragments of entire genome are cloned or amplified and sequenced to produce millions of sequence “reads”

Question 4

How can you sequence with shotgun sequencing

Answer 4

The organisms genome is broken up into random fragments, there will be so many fragments that every part of the genome will be sequenced. Computer algorithms assemble the overlapping reads into contiguous regions in order to produce the entire genome

Question 5

What are some difficulties with shotgun sequencing

Answer 5

Assembly of complete circular chromosome

Question 6

When sequencing a circular chromosome how are gaps between contigs filled

Answer 6

They can be filled using PCR or cloning techniques or by sequencing methods that will produce very long reads

Question 7

What is a closed genome

Answer 7

A genome that is complete

Question 8

What is a draft genome

Answer 8

A fast and cheap method of sequencing but will contain gaps

Question 9

What is annotation

Answer 9

Converting raw sequence data into a list of genes present in the genome. The majority of genes encode proteins

Question 10

What is a functional ORF

Answer 10

An open reading frame that encodes a protein. The ORFs are bounded by start/stop codons, Shine-Dalgarno sequences upstream of ATG start site.

Question 11

How are ORFs used in genomics

Answer 11

You can compare new ORFs that have been identified by a computer to those previously found in other genomes, finding homologs suggests the gene is real

Question 12

What is bioinformatics

Answer 12

Science that applies computational tools to DNA and protein sequences. Analyze, annotate, and compare homologs. And identify genes for metabolic pathways by comparison to those well-studied model organisms

Question 13

What is comparative analysis and what is it used for

Answer 13

Identifying genes by comparing similarities between sequences with previously identified genes in other organisms. Allows for predictions of metabolic pathways and transport systems. Can be used to determine how to grown an organism in a lab

Question 14

What are homologous genes

Answer 14

Genes that may have a common evolutionary ancestor

Question 15

What are hypothetical genes and proteins

Answer 15

Only about 70% or less of total ORFs are detected and these are the uncharacterized ORFs. They encode for proteins that likely exist but whose function is unknown (nonessential genes). All essential genes have been identified

Question 16

Describe a metagenome

Answer 16

The total gene content of all organisms present in an environment. Allow a variety of bioinformatic analyses to identify organisms, types of metabolisms, etc. Can be obtained by shotgun sequencing of total DNA from an environmental sample. Goal is to determine DNA sequences of organisms in a population and identify all of them. Sequencing the rRNA is primarily used.

Question 17

Describe a transcriptome

Answer 17

Provides data on expressed genes by measuring RNA. The entire complement of RNA produced under a given set of growth conditions (temperature, nutrients, other organisms)

Question 18

What are microarrays

Answer 18

Hybridization technique based on genomic sequence data for target organism. Thousands of gene probes are arrayed in a known pattern on solid-state chips or glass slides

Question 19

What is RNA-seq

Answer 19

Direct shotgun sequencing of total RNA samples

Question 20

What can be learned from transcriptomes

Answer 20

Gene expression patterns for every gene in genome under different conditions and in different mutants. And expression of specific groups of genes under different conditions can yield clues to possible roles of unknown genes.

Question 21

What is proteomics

Answer 21

The study of all proteins present in cells/tissues under different conditions (proteins produce phenotypes). It combines genomic info with quantitative data on protein amounts

Question 22

What are the techniques used in proteomics to obtain data of all the proteins present

Answer 22

2D gel electrophoresis, liquid chromatography, and mass spectrometry

Question 23

Describe the 2D gel electrophoresis

Answer 23

On the horizontal acis they have been separated by their isoelectric point (the point where they have no charge) and on the vertical axis they have been separated by size.

Question 24

Describe mass spectrometry

Answer 24

Can be used to cut out individual spots and determine what protein is in there

Question 25

What are proteins with >50% sequence similarity

Answer 25

Typically have similar functions, and are probably homologs

Question 26

What are proteins with >70% sequence similarity

Answer 26

Almost certainly have similar functions and are LIKELY homologs

Question 27

What are protein domains

Answer 27

Distinct structural regions or functional modules within proteins (transcription repressor protein would have a DNA-binding domain and a co-repressor binding domain). Have characteristic functions that can reveal a protein's role/function, even in the absence of complete sequence homology

Question 28

What is an interactome

Answer 28

Complete set of interactions among proteins. Proteins that physically interact are likely to be involved in the same process or pathway. Is the combination of genome info and experimental data on protein-protein interactions.

Question 29

What is a metabolome

Answer 29

The complete set of metabolic substrates, products, and intermediates, and other small molecules in an organism

Question 30

What is used to identify and measure metabolites

Answer 30

Mass spectrometry

Question 31

What are homologous chromosomes

Answer 31

They are related in sequence to an extent that implies common genetic ancestry

Question 32

What are gene families

Answer 32

Groups of gene homologs. The whole gene or part of a gene is homologous and related to other genes. They can all transport molecules but they use different molecules for transporting.

Question 33

What are paralogs

Answer 33

Homologous genes within an organism, often the result of gene duplication. Ex. Cyanobacteria contain multiple psbA gnes: psbAI, psbAII, psbAIII. Often they all have the same function in a single species of bacteria but one gene may function better in the light while another gene may function better in the darkness

Question 34

What are orthologs

Answer 34

Homologous genes found in different organisms. They are found in different organisms but will have the same function

Question 35

What are gene duplications

Answer 35

They are the mechanism for the evolution of new genes.

Question 36

Describe the mechanism of gene duplication in evolution

Answer 36

Two gene copies can evolve independently: One copy keeps the original function and the other copy can evolve to acquire a new function.

Question 37

What is deletion

Answer 37

Deletions can eliminate genes no longer needed, genes that do not provide a selective advantage

Question 38

Where are housekeeping genes found and what does that tell us

Answer 38

Many housekeeping genes are found in all three domains of life showing that all organisms have common evolutionary roots (these housekeeping genes were originally found in LUCA)

Question 39

What is horizontal gene transfer

Answer 39

The transfer of genetic information between organisms, as opposed to vertical inheritance (from parental organisms). Can also occur between different species and different genera

Question 40

What does crossing phylogenetic boundaries mean

Answer 40

Bacteria can pick up genetic material from something that is very different as long as the codon usage is not so different that the gene is not expressed

Question 41

How do you detect horizontal gene flow

Answer 41

Presence of genes typically found only in distantly related species (finding a gene normally in G+ bacteria in just one strain of a G- bacteria). Presence of a DNA region with GC content or codon bias that differes significantly from remainder of genome. or presence of DNA sequence signatures that indicate mobile DNA element such as a transposon or virus

Question 42

What are transposons and insertion sequences

Answer 42

Transposons can trasfer DNA between different organisms. Transposons and insertion sequences (IS) may also mediate large-scale chromosomal changes within a single organism. Multiple ISs are often found in a genome. Recombination between related IS elements can result in large-scale chromosomal rearrangements

Question 43

What are chromosomal islands

Answer 43

Region of bacterial chromosome of foreign origin (HGT) that contains clustered genes. They usually contribute specialized functions not essential for growth

Question 44

What are pathogenicity islands

Answer 44

Chromosomal islands containing genes for virulence

Question 45

What are some specialized functions that are not essential for growth that chromosomal islands are responsible for

Answer 45

Virulence, biodegradation of unusual compounds and symbiosis