Genomics And Evolution

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Virus genome size

Back 1

1-350 kb

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HIV genome size

Back 2

8.5 kb

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Largest virus genome size

Back 3

1 Mb

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Bacterial genome size

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5 kb - 13 Mb

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Cyanobacteria genome size

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13 Mb

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E. coli genome size

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4 Mb

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Chloroplast genome size

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0.1 Mb

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Bacterial genomes vary is size across what range

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22-fold

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Largest currently sequence bacteria

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8.7 Mb

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Eukaryotic genome size

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8 Mb - 686 Gb

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Fungi genome size

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8 Mb

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Amoebae genome size

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686 Gb

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Algae genome size

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300 Gb

Front 14

Algae genomes vary across what range

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2,000-fold

Front 15

Human genome size

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4 Gb

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Human Chr 21/22 genome size

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15 Mb

Front 17

Human mitochondrial genome size

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10 kb

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Drosophila genome size

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250 Mb

Front 19

Nematode genome size

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100 Mb

Front 20

Yeast genome size

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15 Mb

Front 21

Eukaryote genomes vary across what range

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75,000-fold

Front 22

Haploid cell genomes are equal to what

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the total amount of DNA

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Diploid/polyploid genomes are equal to what

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the amount of DNA in the unreplicated haploid genome (e.g., equal to sperm genome)

Front 24

Ernst Haeckel

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molecules to plants and animals; "moner" (monera)

Front 25

Edouard Chatton

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prokaryotes and eukaryotes

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Carl Woese

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archaea

Front 27

Johann Friedrich Miescher

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discovered NAs

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Frederick Sanger

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dideoxynucleotide chain termination

Front 29

What taxa undergo enormous numbers of DNA changes

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viruses

Front 30

Approximately how much of the human genome is noncoding

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98%

Front 31

2 traits of the human genome

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Approximately 98% of genome is noncoding

Large regions of repetitive DNA

30,000-40,000 protein coding genes

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2 traits of eukaryote genomes

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35-45% G-C

contain both genes and large amounts of noncoding DNA

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What is noncoding DNA (3)

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Repetitive DNA

Genes that have regulatory functions

Introns

Front 34

2 traits of bacterial genome

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Much greater range of G-C compared to eukaryotes

have genes and additional, relatively small intergenic regions

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1 trait of archaea genome

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have genes and additional, relatively small intergenic regions

Front 36

What organism was first sequenced and when

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bacteriophage MS2 (1976)

Front 37

When was the first bacteriophage sequenced

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1976

Front 38

When was the first eukaryotic structure sequenced and what was it

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human mitochondria (1981)

Front 39

When was the first chloroplast sequenced

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1986

Front 40

When was the first eukaryotic chr sequenced

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1992

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When was the first free living organism sequenced and what was it

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H. influenzae (1995)

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When was the first eukaryotic organism sequenced and what was it

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yeast (1996)

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When was the first archaea

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1996

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When was E. coli first sequenced

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1997

Front 45

When was the first complete multicellular organism sequenced and what was it

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nematode (1998)

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When was the first human chr sequenced and which chr was it

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chr 22 (1999)

Front 47

when was human chr 21 sequenced

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2000

Front 48

Approximate total genomes complete as of 2008

Back 48

eukaryotes ~ 500

archaea ~ 96

bacteria ~ 2000

Front 49

What do the first sequenced genomes have in common (2)

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All circular

Little to no noncoding DNA

Front 50

Isochores

Back 50

is a large region of DNA (greater than 3 KB) with a high degree uniformity in G-C and C-G (collectively GC) which tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Overall, isochores are largely homogeneous in GC content in contrast to the heterogeneity of the entire genome.

Front 51

Orthologs

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sequences of genes that evolved from a common ancestor and can be traced evolutionarily through different species. By comparing the ortholog sequences of a specific gene between many species, the amino acid sequences which are conserved can be determined. These highly conserved sequences are important, because they provide information on which amino acids are essential to the protein structure and function.

Front 52

PCR polymerase name and origin

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Taq and T. aquatacus

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What taxa is typically associated with repetitive DNA

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eukaryotes

Front 54

Last common ancestor of modern bacteria and archaea was likely

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hyperthermophile

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Genome analysis projects (4)

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de novo sequencing ~ sequencing an organism

resequencing ~ human variation

transcriptome ~ RNA transcripts

epigenetics ~ heritable changes

Front 56

how are genomes identified (3)

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gene-specific codon bias

absence of repetitive DNA sequences

Presence of signals like promoter region specific motifs

Front 57

c-value

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variation in genome size

Front 58

which genomes are typically bigger: prokaryotes or eukaryotes

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eukaryotes

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c-paradox

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genome size doesn't correspond w/ complexity or phylogenetic position

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genome size variation is due to

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non-coding DNA (not gene number)

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cot curves

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corresponds with DNA reassociation

DNA is sheared into small fragments; Denatured at high temperatures; Placed at a set temperature; Re-association is measured using a spectophotometer; Measures kinetics

Fast reassociation occurs w/ sequences that occur often since the probability of finding a match is higher

Slow reassociation …

Front 62

name the types of repetitive DNA (4)

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microsatelilites (STRs)

transposons

minisatellites (VNTRs)

Telomeres

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microsatellites

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shot tandom repeats (STRs)
nonmobile
2-10 bp motifs
High mutation rate
Highly polymorphic
Good markers for mapping

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Transposons

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Mobile

Some encode their own genes

Transpose throughout RNA intermediates

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minisatellites

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Longer tandem repeats

Nonmobile

High mutation rate

Highly polymorphic

Good markers for mapping and genotyping (e.g., DNA fingerprinting)

Front 66

history of genetics and genomics

Back 66

sutton (1902)
morgan (1910)
bridges

griffith (1928)
gel electrophoresis (1930s)
avery (1948)
hershey (1952)

Watson/crick/franklin/wilikins (1953)
messelson (1958)
brenner (1961)
crick (1961)
nirenberg (1966)

thomas (1971)
maxam-gilbert (1973)
sanger (1975)
mullis (1983)
hood (1986)
dupont (1986)

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Central dogma

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deals with the detailed residue-by-residue transfer of sequential information. It states that information cannot be transferred back from protein to either RNA or nucleic acid

exceptions (i.e., reverse transcriptase)

DNA -> RNA -> protein

Genotype -> phenotype

Crick

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Hood contributions

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automated DNA sequencing

laser DNA fragment detection

flourescent primers

automated base calling

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year ~ sutton

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1902

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year ~ morgan

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1910

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year ~ griffith

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1928

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year (approx.) ~ gel electrophoresis

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1930s

Front 73

year ~ avery

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1948

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year ~ hershey

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1952

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year ~ watson/crick

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1953

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year ~ messelson

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1958

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year ~ brenner

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1961

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year ~ crick

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1961

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year ~ nirenberg

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1966

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year ~ thomas

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1971

Front 81

year ~ sanger

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1975

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year ~ mullis

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1983

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year ~ hood

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1986

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year ~ dupont

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1986

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sutton ~

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chromosomal theory of heredity

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Thomas Hunt Morgan ~

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found inheritance of red and white eye phenotype (controlled by alleles of the same gene) mimicked inheritance of X chromosome (males are hemizygous)

Front 87

Calvin Bridge ~

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primary non-disjunction of homologous chromosomes in Drosophila

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Frederick Griffith ~

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transforming principle

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Avery ~

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transformation cannot occur in the absence of DNA thus DNA is the substance that causes bacterial transformation

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Hershey ~

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viral DNA enters the cell, not protein thus more evidence that DNA is the genetic material

Front 91

Watson/crick ~

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Double helix comprised of NTs
Sugar-phosphate backbone
Bases point inward
Antiparallel
H-bonding between bases holds strands together
A-T; G-C

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Messelson ~

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demonstrate DNA replication is semiconservative

Front 93

Brenner ~

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demonstrate mRNA ferries information between DNA and protein

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Crick ~

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demonstrate that the genetic code consists of 3 BP codons

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Nirenberg ~

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decipher genetic code

Front 96

Thomas ~

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C-value paradox

Front 97

Maxam-Gilbert

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DNA sequencing

Front 98

Sanger

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Chain termination method

Front 99

Kary Mullis

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PCR

Front 100

Dupont

Back 100

labeled ddNTPs

Front 101

automated base calling

Back 101

Detection of a fluorophore (e.g. red)
reveals which dideoxy nucleotide the
fragment ends with (ddTTP)

Data are stored in a computer

Eliminated need for gels

Front 102

Laser detection of DNA fragments

Back 102

Argon ion laser

Detects fragments & fluorescence as
they pass a certain point in the gel

Since each of the 4 separate reactions (i.e. ddATP, ddTTP, ddGTP, ddCTP) received a primer with a different fluorophore, one can tell what nucleotide a fragment of a given size ends with based on the wavelength it fluoresces at

Front 103

Fluorescent primers

Back 103

Fluorescence instead of radioactivity

Label each primer with a different
fluorophore

Run different primers in different
reactions (e.g. primer 1 with ddTTP)

Load all 4 reactions into one lane of
an acrylamide gel & electrophorese

Front 104

Sanger method is visually represented via

Back 104

chromatograms

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usher ~ year

Back 105

1650

Front 106

steno ~ year

Back 106

1687

Front 107

linnaeus ~ year

Back 107

1735

Front 108

Hutton ~ year

Back 108

1795

Front 109

malthus ~ year

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1798

Front 110

lamarck ~ year

Back 110

1809

Front 111

curvier ~

Back 111

paleontology

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lyell ~ year

Back 112

1830

Front 113

darwin ~ year

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1859

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owen ~

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dinosauria

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name of intermediate fish/terapod and where was it found

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Tiktaalik found in Nunavut, Northern Canada in the Artic Circle

Front 116

Essentialism

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horses (or any other species) have an immutable essence, but each individual horse has imperfections. In this philosophy of essentialism, variation is accidental imperfection

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fixity of species (3)

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species were created in their present form

extinction was impossible

fossils were thought to have been created in the rock

Front 118

ockham's razor

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parsimony

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tongue stones

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glossopetrae

Front 120

what was believed to have formed "fossils" (note they were considered rocks)

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spontaneous generation

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three basic laws of geology

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steno

1. law of superposition: sedimentary layers are deposited in a time sequence, with the oldest on the bottom and the youngest on the top

2. law of lateral continuity: layers of sediment initially extend laterally in all directions; in other words, they are laterally continuous. As a result, rocks that are otherwise similar, but are now separated by a valley or other erosional feature, can be assumed to be originally continuous. Changes are a function of erosion.

3. law of original horizontality: rock layers form in the horizontal position, and any deviations from this horizontal position are due to the rocks being disturbed later

Front 122

uniformitarianism replaced what

Back 122

catastrophism

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uniformitarianism

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hutton

assumes that the same natural laws and processes that operate in the universe now, have always operated in the universe in the past and apply everywhere in the universe. It is frequently summarized as "the present is the key to the past," because it holds that all things continue as they were from the beginning of the world.

Front 124

where did hutton develop unconformity based model

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siccar point, scotland

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malthus's essay

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principle of population

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lamarck's book

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philosophie zoologique

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lamarck's theory

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theory of evolution through the inheritance of acquired traites

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lyell's book

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principles of geology

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mendel ~ year

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1865

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origin of species was published when

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1859

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who proposed theory of gradualism

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hutton

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teleology

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The use of ultimate purpose or design as a means of explaining phenomena

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geocentric

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earth is center of solar system

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heliocentric

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sun is center of solar system

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lithification

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formation of rock via compaction of sedimentary layers

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year ~ nirenberg

Back 136

1966

Front 137

Edouard Chatton

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prokaryotes and eukaryotes

Front 138

Thomas ~

Back 138

c-value paradox

Front 139

When was e. coli first sequenced

Back 139

1997

Front 140

E. coli genome size

Back 140

4 Mb

Front 141

Fungi genome size

Back 141

8 Mb

Front 142

Crick ~ year

Back 142

1961

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hershey ~ year

Back 143

1952

Front 144

Human Chr 21/22 genome size

Back 144

15 Mb

Front 145

HIV genome size

Back 145

8.5 kb

Front 146

uniformitarianism replaced what

Back 146

catastrophism

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year ~ sanger

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1975

Front 148

Drosophila genome size

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250 Mb

Front 149

Algae genomes vary across what range

Back 149

2,000-fold

Front 150

Yeast genome size

Back 150

15 Mb

Front 151

steno ~ year

Back 151

1687

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year ~ brenner

Back 152

1961

Front 153

Bacterial genome size

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5 kb to 13 Mb

Front 154

Who developed the geocentric model

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Ptolemy

Front 155

Cyanobacteria genome size

Back 155

13 Mb

Front 156

lamarck ~ year

Back 156

1809

Front 157

Largest currently sequence bacteria

Back 157

8.7 Mb

Front 158

how are genomes identified (3)

Back 158

gene-specific codon bias<br /><br />absence of repetitive DNA sequences<br /><br />Presence of signals like promoter region specific motifs

Front 159

Johann Friedrich Miescher

Back 159

discovered NAs

Front 160

Where was tiktaalik found

Back 160

Nunavut

Front 161

year ~ mullis

Back 161

1983

Front 162

When was the first complete multicellular organism sequenced and what was it

Back 162

nematod 1998

Front 163

lyell ~ year

Back 163

1830

Front 164

Bacterial genomes vary is size across what range

Back 164

22-fold

Front 165

"dinosauria"

Back 165

owen

Front 166

malthus ~ year

Back 166

1798

Front 167

When was the first chloroplast sequenced

Back 167

1986

Front 168

Ernst Haeckel

Back 168

molecules to plants and animals; "moner" (monera)

Front 169

linnaeus ~ year

Back 169

1735

Front 170

Hutton ~ year

Back 170

1795

Front 171

Paneontology ~

Back 171

corvier

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year ~ thomas

Back 172

1971

Front 173

Nematode genome size

Back 173

100 Mb

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What is the modern synthesis

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Mendel + Darwin and Wallace

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repetitive DNA is primarily what

Back 175

non-coding

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one interesting feature of Dictyostelium

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over 90% of mRNA are transcribed from non-repetitive sequences

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who invented pcr

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mullis

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what was so special about dupont's innovations

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allowed for 1 reaction instead of 4<br /><br />so you mix all ddNTPs w/ the dNTPs, primers, polymerase, buffers and templates<br /><br />reaction is then loaded into one lane where laser excitation leads to emission of fluorescence for detection

Front 179

owen ~ year

Back 179

1842

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darwin's 5 theories

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1.Characteristics of groups of organisms change over time (Darwin borrowed this idea from his predecessors.)<br />2.Decent with modificationfrom ancestral forms. All life can be portrayed as one great family tree. (The opposite of Lamarck)<br />3.Gradualism: organisms evolve incrementally (Influenced by Hutton and Lyell)<br />4.Evolution occurs by the changes in proportions of individuals within a population. (Influenced by Malthus)<br />5.Natural Selection–changes in the proportions of different types of individuals are caused by differences in their ability to survive and reproduce.