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General Biology II Lecture > Lesson 9 > Flashcards

Lesson 9 Flashcards

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1
Q

Genome

A

the complete set of genes or genetic material present in a cell or organism

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2
Q

Evolution

A

change in the heritable characteristics of biological populations over successive generations.

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3
Q

Genomics

A
  • key challenge of modern evolutionary biology
  • comparing genomes of different species
  • genomes also contain the history of life or evolutionary lineage
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4
Q

Doug langur

A

Gene duplication allowing it to ferment and digest leaves

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5
Q

Link DNA changes to phenotype

A
  • the key challenge of modern evolutionary biologists- link DNA sequences with the evolution of the complex morphological characters used to construct a traditional phylogeny
  • pine trees have~6 times more DNA than humans?!! single-celled amoeba can up to 400 times more!
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6
Q

Most traits are polygenic

A

As we sequence more genomes, we can compare genomic level differences and
- understand the workings of evolution
- improve crops
- identify the genetic basis of disease

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7
Q

sequenced genomes

A
  • the size of its genome, measured either by DNA content or the number of genes
  • Multi-cellular organisms with multiple tissues generally have more genes than eukaryotes without distinct tissues.
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8
Q

Phylogenetic trees

A
  • displays relationships among modern life forms
  • ## the relationship between similar organisms, better to focus on more neutral mutations
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9
Q

Human and pufferfish genomes comparison

A
  • common ancestor 450 MYA
  • 25% human genes have no counterparts in fugu
  • genome rearrangements since mammal lineage and fish diverged
  • human genome 50% repetitive DNA but less than 1/6 of fugu sequence repetitive
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10
Q

comparison between human and mouse genome

A
  • diverged about 75 MYA
  • a human has 400 million more nucleotides than the mouse
  • both have 20,00 genes and they share 99%
  • 300 genes unique to either organism(1%)
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11
Q

comparison between human and chimpanzee genomes

A
  • diverged 4.1 MYA
  • 1.5% difference in insertions and deletions
  • 53 of human-specific indwells lead to loss of function changes- may be loss of hair or larger cranium
  • 2.7% of the two genomes have consistent differences in single nucleotides
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12
Q

genomes evolve at different rates

A
  • bacterial evolve in a matter of days
  • insects evolve more rapidly than mammalian
  • Plants change more rapidly than animal genomes, especially in noncoding DNA
  • transposable elements frequently remodel plant genomes.
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13
Q

5% of the human genome contains………….

A

highly conserved regions of the genome but not ask of the genome, but not all of this is coding

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14
Q

compare plants with animals and fungi

A
  • 1/3 of arabidopsis and Oryza(rice) are plant genes- not found in fungi or animals
    genes for photosynthesis and photosynthetic anatomy
  • the rest are more universal
    genes for basic metabolism, genome replication and repair, protein synthesis
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15
Q

how do genes/genomes evolve

A
  • both genome size and gene number vary greatly among the eukaryotes species- contributing factor is whole genome duplication, which results in polyploidy
  • occurs commonly in plants
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16
Q

whole genome duplication

A
  • polyploidy(three or more chromosome sets) common in plants:
  • autopolyploids- genome duplication within a single lineage(same species)
  • allopolyploids- of two lineage followed by genome duplication
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17
Q

-measuring allopolyploidy
Two avenues of research into genome alterations following polyploidization
- Paleopolyploids: studies ancient polyploids to reconstruct history

A
  • Sequence divergence between homologues
  • Presence or absence of duplicated gene pairs from hybridization
18
Q
  1. Synthetic polyploids (another way to study genome structure)
A
  • Crossing plants most closely related to ancestral species and chemically (colchicine) inducing chromosome doubling
  • Without doubling the plant will be sterile because it lacks homologous chromosomes needed to pair during metaphase
  • Commercial bananas are 3n and sterile – seedless – aborted ovules appear as brown dots in center of cross section
19
Q

Polyploidy in plants

A
  • Occurred numerous times in flowering plants
  • Polyploidy may provide increased variation and genes for selection to work for
20
Q

Polyploidy in plants

A

Expect genomes to continue growing in size after duplication
* But this is not always the case

21
Q

Polyploidy in plants

A
  • Comparison of soybean, forage legume, and garden pea shows a huge difference in genome size
  • Some genomes increased in size through polyploidization
  • Some decreased in size through loss of genes or whole chromosomes
22
Q

Polyploidy in plants

A

Often, many genes are immediately lost after polyploid event maybe to reduce redundancy
* This may explain the disconnect between genome size and number of genes, and complex

23
Q

Transposons mobilized by polyploidization

A

Transposable (mobile) genetic elements Barbara McClintock (Nobel Prize)
* Hypothesized that they are controlling elements, move around the genome, disrupting genes, or rearranging exons
* Respond to genome shock (polyploidization) and jump into a new position
* New phenotypes could emerge
* Transposable element activity increases after polyploidization event

24
Q

Polyploidy alone doesn’t explain variation in genome size

A

All genome size variation is not due to polyploidy
* Humans have 9x the amount of DNA found in the pufferfish genome, but around the same number of genes
* Plants can have a 200-fold difference in genome sizes, but all have between 24,000- 60,000 genes
- Tulips have 170 times more DNA than Arabidopsis

25
Q

Noncoding DNA inflates genome size

A

Much of the extra DNA in humans compared with pufferfish is in introns
* Large expanses of retrotransposon DNA contribute to difference in genome size
* Both rice and maize have 40,000 protein-coding genes; Rice genome is 370 Mb, maize genome is 2 Gb
– Maize contains lots of repetitive DNA

26
Q

Polyploidy is change in

A

the whole set of chromosomes

27
Q

Aneuploidy is

A

numerical change in part of the chromosome set

28
Q

Evolution within genomes

A

Duplication within parts of the genome can also lead to evolution
* Aneuploidy
– Duplication or loss of an individual chromosome
* Duplication of segments of DNA is one of the greatest sources of novel traits
– Paralogues – two genes within an organism that have arisen from a gene duplication event
– Orthologues – reflects conservation of a single gene from a common ancestor

29
Q

DNA sequences can be duplicated

A

Gene families grow through gene duplication Fates of duplicate gene:
– Losing function through subsequent mutation * Fate of most duplicated genes
– Gaining a novel function through subsequent mutation
– Having total function partitioned into the two duplicates

30
Q

Segment duplication

A

5% of human genome consists of segmental duplications
Gene duplication in humans
– Most likely to occur in three most gene-rich chromosomes
– Least amount of duplication in seven chromosomes with the least genes
Certain types of human genes more likely to be duplicated
– Growth and development genes, immune system genes, and cell-surface receptors

31
Q

DNA segments can be rearranged

A

Humans have 1 fewer chromosome than chimpanzees, gorillas, and orangutans
* Fusion of two chromosomes into one chromosome; chromosome 2 in humans
- phylogenies from the rearrangements
– But how do we re-construct past genome
structural changes
35 Copyright © 2017 McGraw-Hill Education. All rights reserved. No reproduction or distr

32
Q

Conservation of synteny (conservation of large blocks of DNA)

A

Preservation over evolutionary time of arrangements of DNA segments in related species
* But rearrangements can occur at different rates between species, adding to the complexity of genome size and gene number
– Allows researchers to locate a gene in a different species using information about synteny (Identify markers traveling together)

33
Q

Rearranged DNA can acquire new functions or lose it

A
  • Loss of Olfactory Receptor genes (pseudogenes)
    – Olfactory receptor (OR) genes
  • Inactivation best explanation for our reduced sense of smell
  • 63% of human OR genes are pseudogenes
    – Genes that do not produce a functional product due to premature stop codons, missense mutations, or deletions
34
Q

Rearranged DNA can acquire new functions or lose it

A

Icefish survive in Antarctic waters due to antifreeze protein
- 9 bp of a gene coding for a digestive enzyme evolved to encode part of an antifreeze protein
- Series of errors persisted only because it coincided with massive cooling of Antarctic water
- Natural selection worked on the chance mutation

35
Q

Gene swapping and genome
evolution

A

Horizontal Gene Transfer (HGT)
– Genes hitch hike from other species Contrast to Vertical Gene Transfer (VGT)
– Genes Pass from generation to generation Base of the tree of life is a web rather than a branch

36
Q

Noncoding DNA

A

All these rearrangements lead to noncoding-DNA (ncDNA), which makes up much of the genome
* There is also retrotransposon DNA
– 30%ofanimaland40–80%ofplantgenomes
* Much of noncoding DNA is involved with gene regulation – Mayexplainmanydifferencesbetweenspecies

37
Q

Gene Function and Expression
Patterns

A

Inferred by comparing genes in different species at different times
– Genes are expressed at different times
– In different tissues
– In different amounts
– In different combinations
* Humans and chimps diverged from a common ancestor only about 4.1 MYA
Chimp DNA is 98.7% identical to human
– Comparing only protein encoding genes it is 99.2% identical
* Differences may be explained by different patterns of gene transcription activity – brain cells

38
Q

Complex gene expression

A
  • Speech is uniquely human
    – Single point mutation in FOXP2 gene means impaired speech and grammar but not in language comprehension
    – FOXP2 found in chimps, gorillas, orangutans, rhesus macaques, and mice, yet they don’t speak
  • Gene expressed in areas of brain that affect motor function
    – FOXP2 protein in mice and humans differs by only 3 AA; 2 AA in other primates
39
Q

Applying Comparative Genomics

A

Comparative genomics reveals genetic basis for disease
Genome comparisons between pathogen and host aid drug development
Comparative genomics helps conservation biologists

40
Q

Pathogen-host genome differences reveal drug targets

A

Malaria caused by protist Plasmodium falciparum with the mosquito Anopheles gambiae as a vector; ~ 1.7– 2.5 million deaths/year
* Plasmodium has apicoplast (non-photosynthetic plastid) where 12% of all its proteins act to produce fatty acids
* Drugs targeted at fatty acid pathway may be effective against malaria

41
Q

Pathogen-host genome differences reveal drug targets

A

Amino acids critical to protein function tend to be preserved over the course of evolution, and changes at such sites within genes are more likely to cause disease

42
Q

Genome comparisons inform conservation biology

A

Conservation biology
– Tasmanian devil facial tumor disease
– Sequencing of devil genomes showed low genetic diversity, explaining high spread of disease
Comparisons of mitochondrial genomes reveal genetic diversity in organisms
* Polar bears evolved about 150,000 years ago. Geneticists were shocked to find that the entire maternal line of polar bears can be traced back to a brown bear living in Ireland between 20,000 and 50,000 years ago.
*

General Biology II Lecture (25 decks)

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