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BIOL 240 > Module 10 > Flashcards

Module 10 Flashcards

1
Q

define: genomics

A

the study of the entire complement of genetic information within an organisms

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2
Q

what does genomics focus on

A
  • genome & its associated genes
  • regulatory sequences
  • noncoding sequences
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3
Q

define: comparative genomics

A

comparing sequenced genomes from many microorganisms

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4
Q

which branch of genomics provides insight into evolutionary histories and relationships among branches of the tree of life

A

comparative genomics

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5
Q

what percentage of sequenced genes from most microorganisms have unknown function

A

~1/3

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6
Q

define: functional genomics

A

discipline that determines the functions of unknown genes

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7
Q

which branch of genomics involves constructing mutants and analyzing the biochemical and physiological effects of the mutations

A

functional genomics

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8
Q

define: proteomics

A

analysis of the structure, function, and regulations of proteins

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9
Q

define: transcriptomics

A

analysis of all of the transcripts in the genome at once

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10
Q

define: metagenomics

A

extraction and analysis of DNA directly from an environmental sample

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11
Q

what are the steps of Sanger/Dideoxy sequencing

A
  1. cloning gene fragments of interest
  2. DNA synthesis
  3. electrophoresis
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12
Q

what does Sanger/Dideoxy sequencing produce

A

an electropherogram

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13
Q

what are dideoxynucleotides (ddNTPs)

A

deoxynucleotides that lack the 3’ hydroxyl groups that allow for continued DNA synthesis

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14
Q

what are terminator nucleotides

A

a way of referring to dideoxynucleotides

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15
Q

what is the use of fluorophores in Sanger sequencing

A

fluorophores are attached to terminators which allows them to be scanned for

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16
Q

what is primer walking used for

A

obtaining longer sequences

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17
Q

how does primer walking work

A

using repeated rounds of sequencing with primers complementary to the end of the last sequenced segment

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18
Q

what are some high-throughput sequencing methods

A
  • pyrosequencing
  • Ion Torrent
  • Illumina
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19
Q

what are the advantages of high-throughput sequencing compared to Sanger sequencing

A
  • provides hundreds of thousands or millions of sequences simultaneously
  • a fraction of the per-second cost
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20
Q

what are the disadvantages of high-throughput sequencing compared to Sanger sequencing

A
  • generates sequences that are a few hundred bases in length
  • has higher error rates
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21
Q

how long are the sequences produced by Sanger sequencing

A

700-1000 bases

22
Q

how are Sanger sequencing and pyrosequencing similar

A

involves monitoring the incorporation of bases by DNA polymerase

23
Q

how does pyrosequencing detect the addition of a nucleotide

A

light is produced

24
Q

what enzymes are involved in pyrosequencing

A
  • polymerase: synthesizes the DNA
  • ATP sulfurylase enzyme: converts pyrophosphate to ATP
  • luciferase enzyme: gives off light using the ATP
25
Q

what does Ion Torrent sequencing track to indicate the incorporation of bases

A
  • the release of protons, like high-throughput pH meter
26
Q

how does Illumina sequencing track the incorporation of bases

A
  • each base is marked with a fluorophore
  • laser scanning identifies base incorporation
  • fluorophore is removed before next base
27
Q

what are the steps of shotgun sequencing

A
  • DNA fragments are sheared
  • fragments are cloned OR fragments are sequenced directly by high-throughput sequencing
  • software aligns/assembles sequences
28
Q

define: bioinformatics

A

use of computational tools to analyze, compare, assemble, and store DNA & protein sequences

29
Q

what are open reading frames (ORFs)

A

likely locations of genes

30
Q

what do ORFs contain

A
  • approximate size of a gene
  • start and stop codons
  • the Shrine-Dalgarno sequence
  • potentially a promoter sequence
31
Q

define: transcriptome

A

collection of transcribed mRNA molecules in a cell

32
Q

define: cDNA

A

DNA version of an mRNA molecule created with reverse transcriptase

33
Q

define: cDNA library

A

collection of cDNA sequences that reflect the mRNA expressed at a particular time under certain conditions

34
Q

what are microarrays used for

A

examining transcriptional activity of all genes in a cell simultaneously

35
Q

what are the steps of a microarray preparation

A
  • place probe DNA fragments on a glass slide in a known pattern
  • convert cell mRNA to cDNA
  • label cDNA with distinct fluorophores depending on condition
  • expose labelled cDNA fragments to the microarray slide
  • cDNA will bind to probes it matched with
  • microarray lights up where more cDNA is present
36
Q

what are microarrays used for

A
  • exploring global gene expression
  • expression of specific gene classes under different conditions
  • expression of genes with unknown functions
37
Q

define: proteome

A

collection of expressed proteins in a cell

38
Q

what are the ways of studying proteomics

A
  • 2D-polyacrylamide get electrophoresis (2D-page)
  • mass spectrometry
  • x-ray crystallography
  • nuclear magnetic resonance (NMR)
39
Q

what are the two dimensions proteins are separated by in 2D-PAGE

A
  • isoelectric point: pH where protein has no charge
  • mass
40
Q

what does mass spectrometry identify

A

mass-to-charge ratio

41
Q

when is mass spectrometry used

A

after proteins have been isolated by 2D-PAGE

42
Q

what does X-ray crystallography identify

A

protein structure

43
Q

what does X-ray crystallography require that makes it a disadvantage

A

a crystal of a purified protein

44
Q

what does nuclear magnetic resonance (NMR) measure

A

measures distances between the atomic nuclei of proteins

45
Q

what is a disadvantage of nuclear magnetic resonance (NMR)

A

doesn’t work well with large proteins that are greater than 30 kDa

46
Q

what is an advantage of nuclear magnetic resonance (NMR)

A

it can measure proteins in a solution, a crystal is unnecessary

47
Q

what are the two strategies metagenomics uses to characterize complex microbial communities

A
  • sequence-driven analysis
  • function-driven analysis
48
Q

what are the two ways of performing sequence-driven analysis for metagenomics

A
  • directly after a shearing step
  • with a cloning step
49
Q

what does sequence-driven analysis with a shearing step involve

A

high-throughput sequencing methods

50
Q

what does sequence-driven analysis with a cloning step involve

A
  • involves Sanger sequencing, with primer targeting the ends of the vector and sequencing into the insert
  • primer walking can provide much longer sequences
51
Q

when is function-driven analysis used

A
  • powerful when completely novel genes are desired for a process of interest
  • can help with gene discovery
52
Q

what are the three cases studies covered in regards to microbial genomics

A
  1. marine vitamin B12 producers
  2. a new view of the tree of life
  3. CRISPR

BIOL 240 (12 decks)

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