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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
what does Ion Torrent sequencing track to indicate the incorporation of bases
- the release of protons, like high-throughput pH meter
26
how does Illumina sequencing track the incorporation of bases
- each base is marked with a fluorophore - laser scanning identifies base incorporation - fluorophore is removed before next base
27
what are the steps of shotgun sequencing
- DNA fragments are sheared - fragments are cloned OR fragments are sequenced directly by high-throughput sequencing - software aligns/assembles sequences
28
define: bioinformatics
use of computational tools to analyze, compare, assemble, and store DNA & protein sequences
29
what are open reading frames (ORFs)
likely locations of genes
30
what do ORFs contain
- approximate size of a gene - start and stop codons - the Shrine-Dalgarno sequence - potentially a promoter sequence
31
define: transcriptome
collection of transcribed mRNA molecules in a cell
32
define: cDNA
DNA version of an mRNA molecule created with reverse transcriptase
33
define: cDNA library
collection of cDNA sequences that reflect the mRNA expressed at a particular time under certain conditions
34
what are microarrays used for
examining transcriptional activity of all genes in a cell simultaneously
35
what are the steps of a microarray preparation
- 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
what are microarrays used for
- exploring global gene expression - expression of specific gene classes under different conditions - expression of genes with unknown functions
37
define: proteome
collection of expressed proteins in a cell
38
what are the ways of studying proteomics
- 2D-polyacrylamide get electrophoresis (2D-page) - mass spectrometry - x-ray crystallography - nuclear magnetic resonance (NMR)
39
what are the two dimensions proteins are separated by in 2D-PAGE
- isoelectric point: pH where protein has no charge - mass
40
what does mass spectrometry identify
mass-to-charge ratio
41
when is mass spectrometry used
after proteins have been isolated by 2D-PAGE
42
what does X-ray crystallography identify
protein structure
43
what does X-ray crystallography require that makes it a disadvantage
a crystal of a purified protein
44
what does nuclear magnetic resonance (NMR) measure
measures distances between the atomic nuclei of proteins
45
what is a disadvantage of nuclear magnetic resonance (NMR)
doesn't work well with large proteins that are greater than 30 kDa
46
what is an advantage of nuclear magnetic resonance (NMR)
it can measure proteins in a solution, a crystal is unnecessary
47
what are the two strategies metagenomics uses to characterize complex microbial communities
- sequence-driven analysis - function-driven analysis
48
what are the two ways of performing sequence-driven analysis for metagenomics
- directly after a shearing step - with a cloning step
49
what does sequence-driven analysis with a shearing step involve
high-throughput sequencing methods
50
what does sequence-driven analysis with a cloning step involve
- involves Sanger sequencing, with primer targeting the ends of the vector and sequencing into the insert - primer walking can provide much longer sequences
51
when is function-driven analysis used
- powerful when completely novel genes are desired for a process of interest - can help with gene discovery
52
what are the three cases studies covered in regards to microbial genomics
1. marine vitamin B12 producers 2. a new view of the tree of life 3. CRISPR

BIOL 240 (12 decks)

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