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Evolution > Chapter 10 > Flashcards

Chapter 10 Flashcards

1
Q

amount of DNA in a haploid cell

A

C-value

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2
Q

amount of DNA not correlated with complexity

A

C- value Paradox

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3
Q

Lungfish have how many time the DNA of humans

A

40x

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4
Q

the first genome sequencing

A

bacteriophage MS2 ( RNA virus)

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5
Q
  • 1.8 terabases of data — 16 human genomes’ worth — per three-day run
  • 18,000 human genomes per year. Each genome 30x
  • Machine is $1,000,000, –but genome ~$1,000
A

Illumina HiSeqX

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6
Q
  • Connects to a computer through USB
  • Uses Nanopore technology - draw DNA through a small hole
  • Each chip would be about $1000
  • Can’t handle big genomes yet
A

Oxford Nanopore MinION

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7
Q

C-value paradox

A
  • Even though about the same number of genes in organisms

- Larger % noncoding in Eukaryotes

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8
Q

move sections of DNA around, - may drive and increase in genome size over time

A

transposons

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9
Q

selection for replication speed, small cell size, and energetic efficiency may favor reductions in size over time

A

transposons

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10
Q
  • Evolutionary history
  • Drosophila has lots of active transposons
  • Humans had them in past, but few active now
A

balance of these forces leads to C-value paradox

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11
Q

Increase in DNA leads to increase in…

A

cell size

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12
Q

number of protien -coding genes

A

G-values

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13
Q

does not appear correlated with complexity

A

G-value Paradox

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14
Q

it is all about the regulatory genes

A

G-value Paradox

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15
Q

Bind to specific regions of DNA in order to regulate when where and to what degree specific genes are expressed

A

-Transcription factors

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16
Q

often act upon another

A

Transcription factors

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17
Q

Degree of regulatory control of non-coding regions
Increase # regulatory elements with C-value
One protein-coding gene ≠ one protein

A

G-value Paradox

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18
Q

put the exons together in different ways

- can increase the diversity of an organisms functional proteins

A

alternative splicing

-humans: more alternative spliced genes and more introns than nematodes

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19
Q

changes to newly transcribed RNA

A

Posttranscriptional modification

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20
Q
  • pre-mRNA
  • Alternatively spliced mRNA
  • Different protein isoforms
A

steps of alternative splicing

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21
Q

RNA or DNA

Single linear, set of linear, or circular chromosomes

A

The Viral Genome

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22
Q

Compact – RNA up to 30kb
Few proteins
DNA to 1mb

A

The Viral Genome

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23
Q

May have overlapping, but same reading frame genes

Or different reading frames

A

The Viral Genome

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24
Q

is a single-stranded positive-sense RNA virus with a genome composed of a single linear chromosome

A

SARS Coronavirus Single Stranded RNA

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25
Q

Single Stranded, Segemented RNA

A

Influenza B virus

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26
Q

circular double-stranded DNA

A

Hepatitus B

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27
Q

. Viruses employ both methods of coding for multiple proteins using a single region of the genome.

A
  1. read in same fram but start and stop in different places

2. read in a different frame

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28
Q

Bateria and Archaea

A

Prokaryotic Genomes

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29
Q

Single, circular chromosome – 1 copy

Are exceptions to circular and 1 copy

A

Prokaryotic Genomes

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30
Q

85%-95% protein coding

A

Prokaryotic Genomes

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31
Q

Usually no introns (in rRNA or tRNA)

Few pseudogenes

A

Prokaryotic Genomes

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32
Q

Used to be viruses

A

Prophages

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33
Q

Can vary in different strains

A

Prophages

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34
Q

Can impart virulence to bacteria

A

Prophages

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35
Q

Can no longer replicate, but still work

A

Prophages

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36
Q

Small, nonessential circular DNA

A

Plasmids

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37
Q

Code for additional function – often resistance to antibiotics
And their own replication

A

Plasmids

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38
Q

prokaryotes are almost all _____ no____

A

genes

junk

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39
Q

have the smallest geomes

A

symbionts

-parasites are larger

40
Q

Moving genetic material from one cell to another

A

HGT

41
Q

phage packages bacterial DNA instead of its own

A

Transduction (HGT)

42
Q

bacteria takes up free DNA
food
acquired in DNA repair
generate variability

A

Transformation ( HGT )

43
Q 
– plasmids pass, some even code for conjugation
Sometimes called bacterial sex
Not once a generation
Not by species
Donor does not receive DNA
A

Conjugation (HGT)

44
Q

E. coli K-12 harmless enteric strain
E. coli O157:H7 a pathogen that causes bloody diarrhea and (in some) hemolytic uremic syndrome which causes kidney failure

A

Virulence from HGT

45
Q

May reduce fitness – evolved for other reasons in other places
But may increase fitness

A

HGT

46
Q

Open new evolutionary pathways

Can obtain genes from other species

A

HGT

47
Q

Enterococcus faecalis not limited to variation within its species
Obtained antibiotic resistance genes from soil bacteria

A

HGT

48
Q

Evolves rapidly

Translocations, inversions, deletions, etc.

A

Bacterial genome

49
Q

plot one genome against another

A

Syntenic plots

50
Q

If straight 45° line, no changes

Angles occur for inversions

A

Syntenic plots

51
Q

compare the gene order of two different strains or species, providing a picture of the genomic reorganization that has occurred.

A

Syntenic dot plots

52
Q

indicates the relative positions along the chromosome of homologous genes in two genomes

A

Syntenic dot plot

53
Q

Little is protein coding

Most are transposons and introns

A

The Eukaryotic Genome

54
Q

move around the genome

A

Transposable elements

55
Q

excise original DNA and reinsert it elsewhere

jumps and the original is lost

A

conservative transposons

56
Q

Make a copy and reinsert

-DNA trasposons with DNA intermediate

A

Nonconservative transposons

57
Q

RNA back to DNA

  • type of nonconservative transposons
  • line-1 elements
A

retrotransposons

58
Q

encode enzymes necessary to catalyze own movement

A

autononomous transposons (LINE-1)

59
Q

most common transposon at human genome

A

LINE-1

long interspersed elements

60
Q

Most are decayed
~100 retain transposon ability
Occasional causes of disease

A

LINE-1 Elements (L1)

61
Q

Can cause nonhomologous regions of DNA to pair

A

LINE-1 Elements (L1)

62
Q

Short interspersed elements

Nonautonomous

A

SINE elements

63
Q

Rely on machinery of autonomous trasposons

A

SINE elements

64
Q

Most inactive

Have to be inserted by chance adjacent to right flanking sequences

A

SINE elements

65
Q

act for own survival

A

Selfish genetic elements (SINE)

66
Q
  • In bacteria, can get to other cells via plasmids
  • In eukaryotes, can move to other chromosomes to ensure survival
  • May have evolved from retroviruses that lost the ability to form a protein coat
A

SINE Elements

67
Q

Can cause problems if inserted in or near critical genes

A

-SINE Elements

68
Q

Can generate mutation

A

SINE Elements

69
Q

Cause ectopic recombination – separate chromosomes cross over

A

SINE Elements

70
Q

May copy adjacent DNA as well – gene duplication

A

SINE Elements

71
Q

Many, with multiple origins of replication – because of length

A

chromosome

72
Q

attachment sites for kinetochore proteins

A

centromere

73
Q

Discreet regions of satellite repeats for 100’s of kb interspersed w/transposons

A

Chromosome

74
Q

Marked by DNA packaging protein = centromeric histone (CenH3)

A

Chromosome

75
Q

among fastest evolving DNA

CenH3 and other proteins involved in packaging rapidly evolving

A

Centromeric DNA

76
Q

Only one of 4 cells becomes egg

Rest are polar bodies

A

Centromeric Drive

77
Q

Selection favors mutations of centromere that increases chance of chromosome segregating with oocyte

A

Centromeric Drive

78
Q

Increase repeats to provide targets for microtubules

-Meitotic Drive

A

Centromeric Drive

79
Q

But might cause problems like nondisjunction

A

Centromeric Drive

80
Q

Could quickly lead to speciation

A

Centromeric Drive

81
Q

Extended regions of short repeats at ends of chromosomes

A

Telomeres

82
Q

DNA polymerase only in 3’ to 5’ direction
Would truncate 3’ end of chromosome
Ends would truncate by 100 bp per replication

A

Telomeres

83
Q

extends 3’ end by adding repeat (TTAGGG in vertebrates)

A

Telomeres

84
Q

encodes a domain (module)

A

exon

85
Q

Proteins can evolve rapidly by recombining different domains

A

Exon shuffling

86
Q

problems with this could increase size of genome site for transposons

A

Exon shuffling

87
Q

– key protein in pathogenesis of Mycoplasma in birds

A

Sialidase

88
Q

Transcription factors
Immune Function
Formation of gametes
Sensory Function

A

positive selection, important

89
Q

Structural genes
Functional genes
Cellular
Biosynthesis

A

purifying selection, not important

90
Q

When there is selection for an allele, nearby genes get moved en mass:

A

genetic hitchhiking

91
Q

Not enough time to break up the block if recently selected for

A

Haplotype Blocks

92
Q

Scan genome for these blocks to determine which gene is selected for

A

Haplotype Blocks

93
Q

Lactose tolerance into adulthood

A

long blocks

94
Q

no tolerance

A

short blocks

95
Q

contain promotor at RNA polymerize that can lead to alternative splicing, translation regulation, and there impact is high in stressful conditions

A

SINE

96
Q

BIOLUMINESING

A

SINE

97
Q

Genes are moves around on chromosomes because of

A

transposons

Evolution (15 decks)

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