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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
Single Stranded, Segemented RNA
Influenza B virus
26
circular double-stranded DNA
Hepatitus B
27
. Viruses employ both methods of coding for multiple proteins using a single region of the genome.
1. read in same fram but start and stop in different places | 2. read in a different frame
28
Bateria and Archaea
Prokaryotic Genomes
29
Single, circular chromosome – 1 copy | Are exceptions to circular and 1 copy
Prokaryotic Genomes
30
85%-95% protein coding
Prokaryotic Genomes
31
Usually no introns (in rRNA or tRNA) | Few pseudogenes
Prokaryotic Genomes
32
Used to be viruses
Prophages
33
Can vary in different strains
Prophages
34
Can impart virulence to bacteria
Prophages
35
Can no longer replicate, but still work
Prophages
36
Small, nonessential circular DNA
Plasmids
37
Code for additional function – often resistance to antibiotics And their own replication
Plasmids
38
prokaryotes are almost all _____ no____
genes | junk
39
have the smallest geomes
symbionts | -parasites are larger
40
Moving genetic material from one cell to another
HGT
41
phage packages bacterial DNA instead of its own
Transduction (HGT)
42
bacteria takes up free DNA food acquired in DNA repair generate variability
Transformation ( HGT )
43
``` – plasmids pass, some even code for conjugation Sometimes called bacterial sex Not once a generation Not by species Donor does not receive DNA ```
Conjugation (HGT)
44
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
Virulence from HGT
45
May reduce fitness – evolved for other reasons in other places But may increase fitness
HGT
46
Open new evolutionary pathways | Can obtain genes from other species
HGT
47
Enterococcus faecalis not limited to variation within its species Obtained antibiotic resistance genes from soil bacteria
HGT
48
Evolves rapidly | Translocations, inversions, deletions, etc.
Bacterial genome
49
plot one genome against another
Syntenic plots
50
If straight 45° line, no changes | Angles occur for inversions
Syntenic plots
51
compare the gene order of two different strains or species, providing a picture of the genomic reorganization that has occurred.
Syntenic dot plots
52
indicates the relative positions along the chromosome of homologous genes in two genomes
Syntenic dot plot
53
Little is protein coding | Most are transposons and introns
The Eukaryotic Genome
54
move around the genome
Transposable elements
55
excise original DNA and reinsert it elsewhere | jumps and the original is lost
conservative transposons
56
Make a copy and reinsert | -DNA trasposons with DNA intermediate
Nonconservative transposons
57
RNA back to DNA - type of nonconservative transposons - line-1 elements
retrotransposons
58
encode enzymes necessary to catalyze own movement
autononomous transposons (LINE-1)
59
most common transposon at human genome
LINE-1 | long interspersed elements
60
Most are decayed ~100 retain transposon ability Occasional causes of disease
LINE-1 Elements (L1)
61
Can cause nonhomologous regions of DNA to pair
LINE-1 Elements (L1)
62
Short interspersed elements | Nonautonomous
SINE elements
63
Rely on machinery of autonomous trasposons
SINE elements
64
Most inactive | Have to be inserted by chance adjacent to right flanking sequences
SINE elements
65
act for own survival
Selfish genetic elements (SINE)
66
- 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
SINE Elements
67
Can cause problems if inserted in or near critical genes
-SINE Elements
68
Can generate mutation
SINE Elements
69
Cause ectopic recombination – separate chromosomes cross over
SINE Elements
70
May copy adjacent DNA as well – gene duplication
SINE Elements
71
Many, with multiple origins of replication – because of length
chromosome
72
attachment sites for kinetochore proteins
centromere
73
Discreet regions of satellite repeats for 100’s of kb interspersed w/transposons
Chromosome
74
Marked by DNA packaging protein = centromeric histone (CenH3)
Chromosome
75
among fastest evolving DNA | CenH3 and other proteins involved in packaging rapidly evolving
Centromeric DNA
76
Only one of 4 cells becomes egg | Rest are polar bodies
Centromeric Drive
77
Selection favors mutations of centromere that increases chance of chromosome segregating with oocyte
Centromeric Drive
78
Increase repeats to provide targets for microtubules | -Meitotic Drive
Centromeric Drive
79
But might cause problems like nondisjunction
Centromeric Drive
80
Could quickly lead to speciation
Centromeric Drive
81
Extended regions of short repeats at ends of chromosomes
Telomeres
82
DNA polymerase only in 3’ to 5’ direction Would truncate 3’ end of chromosome Ends would truncate by 100 bp per replication
Telomeres
83
extends 3’ end by adding repeat (TTAGGG in vertebrates)
Telomeres
84
encodes a domain (module)
exon
85
Proteins can evolve rapidly by recombining different domains
Exon shuffling
86
problems with this could increase size of genome site for transposons
Exon shuffling
87
– key protein in pathogenesis of Mycoplasma in birds
Sialidase
88
Transcription factors Immune Function Formation of gametes Sensory Function
positive selection, important
89
Structural genes Functional genes Cellular Biosynthesis
purifying selection, not important
90
When there is selection for an allele, nearby genes get moved en mass:
genetic hitchhiking
91
Not enough time to break up the block if recently selected for
Haplotype Blocks
92
Scan genome for these blocks to determine which gene is selected for
Haplotype Blocks
93
Lactose tolerance into adulthood
long blocks
94
no tolerance
short blocks
95
contain promotor at RNA polymerize that can lead to alternative splicing, translation regulation, and there impact is high in stressful conditions
SINE
96
BIOLUMINESING
SINE
97
Genes are moves around on chromosomes because of
transposons

Evolution (15 decks)

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