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BMSC 210 > Chapter 9 > Flashcards

Chapter 9 Flashcards

1
Q

genome

A

entire complement of genetic info including genes, regulatory sequences, and noncoding DNA

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2
Q

genomics

A

discipline of mapping, sequencing, analyzing, and comparing genomes

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3
Q

First genome sequenced in 1976

A

RNA virus MS2; 5386 bp

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4
Q

First cellular genome sequenced in 1995

A

Haemophilus influenzae

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5
Q

The human genome contains…

A

3 billion bp and 25000 protein coding regions

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6
Q

sequencing

A

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

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7
Q

generation

A

successive major changes in sequencing technology that confer
-increase in speed, drop in cost of sequencing

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8
Q

Sanger method

A

first generation sequencing

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9
Q

Presently, most labs access ______ generation sequencing

A

second

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10
Q

shotgun sequencing

A

entire genome is cloned, and resultant clones are sequenced

-sequencing is redundant

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11
Q

genome assembly

A

connecting the DNA fragments in the correct order and eliminating overlaps

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12
Q

annotation

A

converting raw sequence data into a list of genes present in the genome

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13
Q

bioinformatics

A

science that applies powerful computational tools to DNA and protein sequences for the purpose of analyzing, storing, and accessing the sequences for comparative purposes

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14
Q

Majority of genes encode…

A

proteins

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15
Q

functional open reading frame (ORF)

A

encodes a protein

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16
Q

How do computer algorithms search for ORFs?

A

look for start/stop codons and Shine-Dalgarno sequences

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17
Q

hypothetical proteins

A

proteins that likely exists, but whose function is currently unknown and encode nonessential genes

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18
Q

noncoding RNA

A

RNA that does not code for protein; lack start codons and have multiple stop codons (tRNA, rRNA)

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19
Q

Unlike prokaryotes, eukaryotic genomes contain…

A

a large fraction of noncoding DNA

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20
Q

On average, a prokaryotic gene is ______ bp long

A

1000

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21
Q

As genome size increases, gene content…

A

proportionally increases

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22
Q

smallest cellular genomes belong to..

A

parasitic or endosymbiotic prokaryotes

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23
Q

estimates suggest minimum # of genes for a viable cell is…

A

250-300 genes

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24
Q

Many genes can be identified by..

A

comparative analysis

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25
Q

comparative analysis

A

identifying sequence similarities to genes found in other organisms

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26
Q

most abundant class of genes

A

metabolic genes and genes coding for protein sequences

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27
Q

What makes up a minor fraction of genome?

A

DNA replication and transcription genes

28
Q

Number of genes with role that can be identified in a given genome is…

A

70% or less of total ORFs detected

29
Q

Archaea typically devote a high percentage of they genomes to…than bacteria

A

energy and coenzyme production

30
Q

Archaea contain fewer genes for…. than bacteria

A

carb metabolism or cytoplasmic membrane function

31
Q

metagenome

A

total genetic complement of all cells present in a particular environment

32
Q

epigenome

A

total number of possible epigenetic changes

33
Q

methylome

A

total number of methylated sites on the DNA

34
Q

mobilome

A

total number of mobile genetic elements in a cell

35
Q

transcriptome

A

total RNA produced in an organism under a specific set of conditions

36
Q

proteome

A

total set of proteins encoded by a genome

37
Q

translatome

A

total set of proteins present under specific conditions

38
Q

interactome

A

total set of interactions between proteins or other macromolecules

39
Q

secretome

A

total set of proteins secreted by a cell

40
Q

metabolome

A

total complement of small molecules and metabolic intermediates

41
Q

glycome

A

total complement of sugars and other carbs

42
Q

microbiome

A

total complement of microorganisms in an environment

43
Q

virome

A

total complement of viruses in an environment

44
Q

mycobiome

A

total complement of fungi in a natural environment

45
Q

microarrays

A

small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern

46
Q

metagenome

A

total gene content of the organisms present in an environment

47
Q

RNA Seq

A

replacing microarrays for the analysis of gene expression

48
Q

What info can be derived from microarrays?

A
  • global gene expression
  • expression of specific groups of genes under different conditions
  • expression of genes with unknown function
  • comparison of gene content in closely related organisms
  • identification of specific organisms
49
Q

homologous

A

elated sequences that implies common genetic ancestry

50
Q

gene families

A

groups of gene homologs

51
Q

paralogs

A

genes within an organism whose similarity to one or more genes in the same organism is the result of gene duplication

52
Q

orthologs

A

genes found in one organism that are similar to those in another organism, but differ because of speciation

53
Q

Gene analysis in the 3 domains suggests that…

A

many genes present in all organisms have common evolutionary roots

54
Q

horizontal gene transfer

A

transfer of genetic info between organisms

55
Q

vertical gene transfer

A

inheritance from parental organisms

56
Q

core genome

A

shared by all strains of the species

57
Q

pan genome

A

includes all the optional extras present in some, but not all strains of the species

58
Q

proteomics

A

genome wide study of the structure, function, and regulation of an organisms proteins

59
Q

2D polyacrylamide gel electrophoresis

A

technique for the separation, identification, and measurement of all proteins present in a sample

60
Q

How are proteins separated in a 2D PAGE?

A
  • horizontally, separated by difference in isoelectric points
  • vertically, by size
61
Q

protein domains

A
  • distinct structural modules within proteins
  • have characteristic functions that can reveal much about a protein’s role, even in absence of complete sequence homology
62
Q

interactomes

A

complete set of interactions among molecules and data expressed in form of network diagrams

63
Q

metabolome

A

complete set of metabolic intermediates and other small molecules produced in an organism

64
Q

What is the primary technique for monitoring metabolites?

A

mass spectrometry (MALDI and TOF)

65
Q

systems biology

A

integration of different fields of “comics” research

0compares data and builds a computer model of system being studied

BMSC 210 (15 decks)

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