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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 sequences in 1976

A

RNA citrus MS2; 5386 bp

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4
Q

first cellular genome sequenced in 1995

A

haemophilus influenzae

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5
Q

human genome contains..

A

3 billion pb and 25000 protein coding regions

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6
Q

sequencing

A

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

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7
Q

generation

A

succesive 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 overlap

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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 of 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

looks for start/stop codon and Shine-Dalgarno sequences

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17
Q

hypothetical proteins

A

proteins that 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 proteins; lack start codon and have multiple stop codons (tRNA, rRNA)

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19
Q

unlike prokaryotes, eukaryotes genome contains….

A

large fraction of non coding DNA

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20
Q

on average a prokaryotic genome is ____ bp long

A

1000

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21
Q

as genome size increases, gene content….

A

proportionally increases

22
Q

smallest cellular genomes belong to…

A

parasitic or endosymbiotic prokaryotes

23
Q

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

A

250-300 genes

24
Q

many genes can be identifies by….

A

comparative analysis

25
Q

comparative analysis

A

identifying sequence similarities to genes found in other organisms

26
Q

most abundant class of genes

A

metabolic genes and gene coding for protein sequences

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% > total ORFs detected

29
Q

archaea typically devote a high percentage of their genomes to ___ than bacteria

A

higher

30
Q

archaea contain fewer genes for ___ than bacteria

A

carbohydrate metabolism or cytoplasmic membrane functions

31
Q

metagenome

A

total gene content of the organism present in an enviro

32
Q

transcriptome

A

entire complement of RNA produced under a given set of conditions

33
Q

interactome

A
  • complete set of interactions among molecules

- data expressed in the form of network diagrams

34
Q

metabolome

A

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

35
Q

microbiome

A
  • lyses and extract DNA
  • sequence DNA
  • assemble genomes
36
Q

microarrays

A

hybridization techniques can be used in conjunction with genomic sequence data to measure gene expression

37
Q

RNA sequence

A

deep sequencing of cDNAs allowing comprehensive quantitation of all RNAs in a cell

38
Q

what info can be derived from microarray

A
  • global gene expression
  • expression of specific group of genes under different conditions
  • expression of genes with unknown function
  • comparison of gene expression
  • identification of specific strains
39
Q

homologous

A

related sequence that implies common genetic ancestry

40
Q

gene families

A

group of gene homologs

41
Q

paralogs

A

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

42
Q

orthologs

A

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

43
Q

gene analysis in the 3 domains suggests that…

A

many genes present in all organisms have common evolutionary roots

44
Q

horizontal gene transfer

A
  1. transformation
  2. transduction
  3. conjugation
    elements: plasmids, phage, transposons and insertion sequences (isoelectric points)
45
Q

vertical gene transfer

A

gene replication and cell division (size)

46
Q

core genome

A

shared by all strains of the species

47
Q

pan genome

A

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

48
Q

polyacrylamide gel electrophoresis

A

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

49
Q

how are proteins separated in a 2D page?

A
  1. horizontal–> isoelectric points

2. vertical–> size

50
Q

interactomes

A
  • complete set of interaction among molecules

- data expressed in the form of network diagrams

51
Q

what is the primary technique for monitoring metabolites?

A

mass spectrometry

52
Q

systems biology

A

integration of different field of “ohms” research

  • genomics
  • proteomics
  • transcriptomics
  • metabolomics

BMSC 210 (4 decks)

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