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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
comparative analysis
identifying sequence similarities to genes found in other organisms
26
most abundant class of genes
metabolic genes and genes coding for protein sequences
27
What makes up a minor fraction of genome?
DNA replication and transcription genes
28
Number of genes with role that can be identified in a given genome is...
70% or less of total ORFs detected
29
Archaea typically devote a high percentage of they genomes to...than bacteria
energy and coenzyme production
30
Archaea contain fewer genes for.... than bacteria
carb metabolism or cytoplasmic membrane function
31
metagenome
total genetic complement of all cells present in a particular environment
32
epigenome
total number of possible epigenetic changes
33
methylome
total number of methylated sites on the DNA
34
mobilome
total number of mobile genetic elements in a cell
35
transcriptome
total RNA produced in an organism under a specific set of conditions
36
proteome
total set of proteins encoded by a genome
37
translatome
total set of proteins present under specific conditions
38
interactome
total set of interactions between proteins or other macromolecules
39
secretome
total set of proteins secreted by a cell
40
metabolome
total complement of small molecules and metabolic intermediates
41
glycome
total complement of sugars and other carbs
42
microbiome
total complement of microorganisms in an environment
43
virome
total complement of viruses in an environment
44
mycobiome
total complement of fungi in a natural environment
45
microarrays
small solid-state supports to which genes or portions of genes are fixed and arrayed spatially in a known pattern
46
metagenome
total gene content of the organisms present in an environment
47
RNA Seq
replacing microarrays for the analysis of gene expression
48
What info can be derived from microarrays?
- 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
homologous
elated sequences that implies common genetic ancestry
50
gene families
groups of gene homologs
51
paralogs
genes within an organism whose similarity to one or more genes in the same organism is the result of gene duplication
52
orthologs
genes found in one organism that are similar to those in another organism, but differ because of speciation
53
Gene analysis in the 3 domains suggests that...
many genes present in all organisms have common evolutionary roots
54
horizontal gene transfer
transfer of genetic info between organisms
55
vertical gene transfer
inheritance from parental organisms
56
core genome
shared by all strains of the species
57
pan genome
includes all the optional extras present in some, but not all strains of the species
58
proteomics
genome wide study of the structure, function, and regulation of an organisms proteins
59
2D polyacrylamide gel electrophoresis
technique for the separation, identification, and measurement of all proteins present in a sample
60
How are proteins separated in a 2D PAGE?
- horizontally, separated by difference in isoelectric points - vertically, by size
61
protein domains
- 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
interactomes
complete set of interactions among molecules and data expressed in form of network diagrams
63
metabolome
complete set of metabolic intermediates and other small molecules produced in an organism
64
What is the primary technique for monitoring metabolites?
mass spectrometry (MALDI and TOF)
65
systems biology
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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