Chapter 11: Microbial Genetics

Question 1

What are Homologs

Answer 1

evolutionarily linked genes or genes derived from the same ancestral gene

Question 2

What are Paralogs

Answer 2

A homolog that has risen from a duplication event. Paralogs often differ in biochemical function in contrast with orthologs.

Question 3

What are Orthologs

Answer 3

A homolog that has risen from a duplication event. Orthologs have the same function in
contrast with orthologs. In different genomes in contrast with paralogs

Question 4

How does G+C content between microbes affect horizontal gene transfer

Answer 4

The more equivalent the G+C content, the higher likelihood of successful horizontal gene transfer

Question 5

What is metagenomic or environmental genomics

Answer 5

DNA is extracted directly from microbial communities and analyzed as a composite mixture. Or Study of genomes isolated from environmental samples using cultivation-independent methods

Question 6

genomics

Answer 6

Determination and study of complete genome sequences

Question 7

automated sequencing

Answer 7

Technique based on Sanger sequencing that yields sequences of up to 1,000 nucleotides; see also cycle sequencing

Question 8

cycle sequencing

Answer 8

Technique based on Sanger sequencing that yields sequence of up to 1,000 nucleotides within hours; see also automated sequencing

Question 9

pyrosequencing

Answer 9

Next generation sequencing method in which incorporation of a pyrophosphate (PPi) drives a luciferase reaction, producing light that can be detected with a charge-coupled device (CCD) camera; see also 454 DNA sequencing

Question 10

Sanger sequencing

Answer 10

Technique to determine DNA sequence that relies on incorporation of chain-terminating dideoxy nucleotides and includes cloning of the fragment to be sequenced, DNA synthesis, and gel electrophoresis; see also dideoxy sequencing

Question 11

dideoxy sequencing

Answer 11

Technique to determine DNA sequence that relies on incorporation of chain-terminating dideoxy nucleotides and includes cloning of the fragment to be sequenced, DNA synthesis, and gel electrophoresis; see also Sanger sequencing

Question 12

primer walking

Answer 12

Technique in which a DNA sequence obtained from an early sequencing run is used to design a new primer that will anneal farther along the fragment to be sequenced; consecutive runs allow sequencing of the entire DNA segment

Question 13

high-throughput sequencing
or
next-generation sequencing

Answer 13

Use of post-Sanger-sequencing platforms to sequence many DNA fragments simultaneously and at a fraction of the cost of previous electrophoresis-based approaches; see also next-generation sequencing

Question 14

454 pyrosequencing

Answer 14

High-throughput sequencing method in which incorporation of a pyrophosphate (PPi) drives a luciferase reaction, producing light that can be detected with a charge-coupled device (CCD) camera

Question 15

Ion Torrent

Answer 15

A high-throughput sequencing method that measures a pH change with successive nucleotide additions to a growing DNA chain to identify many target DNA molecules simultaneously

Question 16

Illumina sequencing

Answer 16

High-throughput sequencing approach that uses massively parallel synthesis of DNA fragments on a glass surface, with light emission, in order to sequence large numbers of DNA fragments simultaneously

Question 17

PacBio

Answer 17

High-throughput sequencing method for sequencing relatively large DNA fragments of interest

Question 18

shotgun sequencing

Answer 18

Technique for sequencing DNA that shears DNA into short fragments that are sequenced, after which computer programs are used to identify regions of sequence overlap; allows researchers to sequence complete genomes, starting with individual genome fragments.

Question 19

bioinformatics

Answer 19

Field that uses computers to analyze large quantities of biological data, such as DNA or protein sequences; facilitates the analysis of genome sequences and the prediction of gene function

Question 20

annotation

Answer 20

Use of computer programs to predict the beginning and end of protein-encoding sequences of DNA; helps identify ORFs

Question 21

genomic library

Answer 21

Collection of cloned DNA fragments that comprise the entire genome of an organism

Question 22

Northern blot

Answer 22

Use of nucleic acid probes specific to a gene of interest to identify the size of targeted RNA templates of interest

Question 23

Southern blot

Answer 23

Technique for detecting specific DNA sequences by hybridization using labeled probes of complementary sequence

Question 24

transcriptome

Answer 24

Set of transcripts encoded by each of the genes within a genome

Question 25

microarray

Answer 25

Solid support on which single-stranded DNA molecules within a genome are fixed in position; can be used to study the transcriptional activity of all genes in the genome simultaneously; opposite of northern blot

Question 26

RNA-seq

Answer 26

Methodology involving high-throughput sequencing of cDNA fragments derived from extracted RNA from an organism or sample of interest; involves direct sequencing of a cell’s transcriptome by using high-throughput sequencing of RNA-derived cDNA.

Question 27

proteome

Answer 27

Collection of proteins within a cell under specific conditions

Question 28

2D-PAGE

Answer 28

Two-dimensional polyacrylamide electrophoresis in which molecules are separated based on both isoelectric point and mass

Question 29

mass spectrometry (MS)

Answer 29

Technique that involves ionization of target chemicals to characterize ions based on their corresponding mass to charge ratio

Question 30

Individual polypeptides can be identified by

Answer 30

mass spectrometry (MS)

Question 31

liquid chromatography-mass spectrometry (LC-MS)

Answer 31

An analytical chemistry approach using liquid chromatography for physical separation alongside mass analysis for measuring the mass of targeted molecules; can be combined to separate and identify individual proteins from a protein mixture.

Question 32

X-ray crystallography and nuclear magnetic resonance (NMR)

Answer 32

can be used to determine the three-dimensional structure of proteins.

Question 33

comparative genomics

Answer 33

Field of study that determines evolutionary relationships among organisms based upon DNA sequence data

Question 34

genomic island

Answer 34

DNA sequence transferred from one species to another; result of horizontal gene transfer

Question 35

pan-genome

Answer 35

Collection of all genes from multiple representatives from a single species or clade within specific bacteria or archaea pf interest

Question 36

3 steps of Sanger Sequencing

Answer 36

1. Cloning of the gene fragment to be sequenced
2. DNA synthesis
3. Electrophoresis