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Genetics > Smith for Midterm > Flashcards

Smith for Midterm Flashcards

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Biology 101 flashcards
1
Q

Which domain represents the most ubiquitous form of life?

A

archaea

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2
Q

If one organism is eaten by another, not digested and loses a gene allowing it to be free-living, what is this called?

A

endosymbiotic gene loss

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3
Q

What is endosymbiotic gene transfer?

A

endosymbiont genes are transferred to the host

host gains more control, endosymbiont loses autonomy

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4
Q

What was eukaryotic life the result of?

A

an endosymbiotic event between bacteria and archaea 1.8bya

resulted in mitochondria

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5
Q

What is believed to be the endosymbiont that was the start of eukaryotic life?

A

alpha-proteobacterium

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6
Q

How much of the nuclear genome of eukaryotic cells came from the endosymbiont? What is this called? Is this still going on?

A

35-75%, called the “endosymbiotic footprint”

still ongoing

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7
Q

What was involved in the genetic merger that gave rise to chloroplasts?

A

cyanobacteria and a eukaryotic host

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8
Q

List the 6 steps for a genetic merger

A

1) Feeding (engulfs it)
2) Endosymbiosis (stays, isn’t digested)
3) Sharing (i.e. benefit)
4) Entrapment (gene loss)
5) Transfer of control (gene transfer)
6) Genetic integration

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9
Q

What are genetic mosaics? What are 2 examples?

A

the result of genetic mergers between 3 things

plants and algae are examples

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10
Q

Who is Lynn Margulis?

A

the endosymbiosis to make mitochondria and chloroplasts was her idea

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11
Q

When did the endosymbiosis event occur between a cyanobacterium and a eukaryotic host?

A

1.5 bya

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12
Q

Give examples of eukaryotic organisms with 2 genomes. What genomes are they?

A

nuclear and mitochondrial

humans, jellyfish, dogs, mushrooms etc

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13
Q

How many genomes do RBCs have?

A

only have one (mitochondrial) because they don’t have a nucleus

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14
Q

Give examples of eukaryotic organisms that have 3 genomes. What genomes are they?

A

nuclear, mitochondrial and chloroplast

i.e. plants and algae

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15
Q

What is an example of a eukaryote with only one genome? Describe it

A

Microsporidian parasites
intracellular parasites that infect fish, humans, rodents etc
they are closely related to mushrooms and yeast, are actually fungi
They have lost their mitochondrial genome and have a reduced nuclear genome

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16
Q

What organism has one of the smallest genomes we’ve ever seen?

A

microsporidian parasites

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17
Q

What is a mitosome?

A

a mitochondria that has lost all of its DNA through gene loss or transfer
it still has electron transport but does not perform oxidative phosphorylation

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18
Q

What is unique about Polytomella?

A

it is a unicellular alga that has lost its chloroplast genome
has chloroplasts still but does not perform photosynthesis
(i.e. it only has 2 genomes)

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19
Q

What is unique about Rafflesia?

A

it is a parasitic flower that has lost its chloroplast genome and therefore only has 2 genomes
it doesn’t perform photosynthesis, it sucks nutrients and water out of Tetrastigma

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20
Q

Give an example of a eukaryotic organism that has 4 genomes. How is this possible?

A

Chlorarachniophyte algae, Bigelowiella
(are actually as far from algae as us)
the 4 genomes come from a non-photosynthetic eukaryote engulfing a photosynthetic eukaryote
nuclear, mitochondrial, chloroplast and nucleomorph genomes

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21
Q

What is a nucleomorph?

A

it is what is left of the nuclear genome that was from the endosymbiont (when a eukaryotic organism is engulfed by another)

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22
Q

How many genomes can each domain of life have? Viruses?

A

bacteria, archaea and viruses - 1

eukaryotes - 1-4

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23
Q

What is horizontal gene transfer?

A

bacteria and archaeans swap genes even between VERY different species
results in a mosaic and genomes that are always changing

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24
Q

Does horizontal gene transfer occur in eukaryotes? Viruses?

A

there is probably actually a lot go HGT in eukaryotes (except for land plants and animals) and viruses

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25
Q

What is 1pg of DNA equal to?

A

1pg = 1 000 000 000bp (1Gb)

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26
Q

How big is the haploid human genome?

A

3Gb (3 billion base pairs), 3pg

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27
Q

How do you measure genomes? Why is this not good for large genomes?

A 
sequence it (make contigs and assemble)
not good for large genomes because repeats confuse the computer, there can be gaps, too much data, not enough reads, not enough computer power or low coverage
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28
Q

What is Feulgen Image Analysis Denstometry? What is it good for?

A

Stain the DNA using Sciff Reagent
Use a high-powered microscope hooked up to a computer to look at the pixel intensity which the computer can use (stain intensity) to estimate the genome size
good for larger genomes, usually used for nuclear genomes

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29
Q

Give 2 other techniques for measuring the amount of DNA in a genome and what they are good for

A

Gel electrophoresis, good for small pieces of DNA

DNA flow cytometry, good for larger pieces of DNA

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30
Q

What is DNA flow cytometry?

A

Use a molecule that binds to DNA that emits fluorescence and measure the amount of fluorescence
Better for larger pieces of DNA

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31
Q

What is the C-value paradox?

A

that increasing genome size does not mean increasing complexity

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32
Q

What organism has the smallest nuclear genome? How big is it?

A

Microsporidia

2Mb

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33
Q

Are all genomes highly variable in size? i.e. chloroplast, nuclear etc

A

yes

34
Q

What do big genomes have that little ones don’t?

A

non-coding DNA

35
Q

Give a chronological list of whole-genome sequencing that we covered

A 
bacteriophage
human mitochondrial 
tobacco chloroplast
Haemophilius influenzae (first living)
yeast (first eukaryotic)
C elegans (first multicellular)
human nuclear
36
Q

What is non-coding DNA?

A

DNA that does not code functional proteins OR functional RNA

37
Q

What are the 2 types of non-coding DNA?

A

intergenic and intronic

38
Q

What is intergenic DNA?

A

non-coding DNA found between genes

39
Q

What is intronic DNA?

A

non-coding DNA found between exons

40
Q

How large is the lungfish’s genome? How much of it is non-coding?

A

130 billion bp

99.9% is non-coding

41
Q

How much of microsporidian parasites’ genomes are coding?

A

90%

42
Q

Describe Polytomella’s mitochondrial genome

A 
10 000bp
7 protein coding genes
1 tRNA and a few rRNA
linear chromosome that has telemeters that are loops
(i.e. its densely packed)
43
Q

Describe a cucumber’s mitochondrial genome

A

over 1 million bp
lots of non-coding DNA
many repeats and foreign sequences (junk) that are coming from the nucleus, chloroplast, viruses etc
NOTE: this is NOT gene transfer because its all non-coding

44
Q

Does non-coding DNA have a function?

A

sometimes but usually not

45
Q

Explain the skeletal DNA hypothesis

A

There is a correlation between nuclear volume and cell size for eukaryotes, bacteria and archaea
More DNA=bigger cell
Select the amount of DNA you have based on the cell size you want
i.e. may want a big cell for a greater lifespan, greater control of development etc

46
Q

Explain the “selfish” DNA hypothesis

A

Lots of non-coding elements can replicate and reinsert themselves in other places in the genome (mobile elements)
“parasitic”
once you have one its hard to get rid of
some genomes have many

47
Q

Explain the “Race to Replication” hypothesis

A

There is a selective premium on high replication rates because of the metabolic costs of DNA
If your genome is smaller, you can replicate faster and use less energy

48
Q

What is the difference between intact and fragmented chromosomes?

A

same info but fragmented have it spread out between more than one piece

49
Q

Describe the human nuclear genome

A

fragmented
linear
diploid

50
Q

Describe the human mitochondrial genome

A

intact
circular
polyploid

51
Q

Can a genome be made of both linear and circular chromosomes? What are some other unique genomes like

A

Very rare, but can be both

Can also be branched or linked circles

52
Q

Give an example of a bacterium and archaea that are monoploid and circular

A 
E coli (bacteria)
Methanothermobacter (archea found in sewage)
53
Q

What is the most common genome type for archaea and bacteria?

A

polyploid, circular

54
Q

Give an example of a bacterium and archaea that are polyploid and circular

A 
Deinococcus radiodurans (B)
Halobacterium (A)
55
Q

Are plasmids considered essential?

A

no

56
Q

What is Epulopiscium fishelsoni? Explain its genome

A

It is a bacteria that is a symbiont of the surgeonfish
It has thousands of copies of a 3.8Mb circular chromosome
3.8Mb x 200 000 =760Gb in a cell
It is also one of the largest known bacteria…skeletal DNA hypothesis..?

57
Q

Describe Borrelia burgdorferi’s genome

A

It has one single linear chromosome (unique for bacteria!)
Its chromosome ends are closed single-stranded loops (this deals with the shortening of telomeres bc it is now continuous and has no end)

58
Q

How does Polytomella deal with telomere shortening?

A

the same way as Borrelia burgdorferi does…single-stranded loops connecting the ends of the chromosome

59
Q

How do we deal with shortening telomeres?

A

Telomerase (enzyme), part protein, part RNA
Has its own RNA template that it can use as a primer to extend the end
A DNA polymerase then comes in a fills in the other strand

60
Q

Do bacteria and archaea have telomerase?

A

No it is unique to eukaryotes

61
Q

Give 2 examples of organisms that have lost telomerase

A

jellyfish, damsel flies

62
Q

List the characteristics of mitochondrial and chloroplast genomes

A

Linear or circular
Intact or fragmented
No telomerase
Always polyploid

63
Q

List the characteristics of eukaryotic nuclear chromosomes

A

Linear
Fragmented
Haploid, diploid or polyploid

64
Q

How can genomes in a single eukaryotic cell differ?

A

chromosome architecture
ploidy levels
telomere maintenance

65
Q

Describe Adder’s tongue (Ophioglossum) genome

A

Diploid
Has over 1200 nuclear chromosomes (600 x 2)
i.e. the highest number in a eukaryotic organism

66
Q

How did Adder’s tongue’s genome become the way it is?

A

duplication and divergence

duplicate whole chromosome, become polyploid, diverge, now diploid with multiple chromosomes over and over

67
Q

Describe how the mitochondrial genomes of Cnidaria (corals and jellyfish) are unique

A

Most animal mitochondrial genomes are circular however the Cndarians have lots of variety (circular, linear, linear fragmented) even though its basically the same info
They also don’t have telomerase (have proteins that bind etc)

68
Q

What explains the variety in Cnidarians mtDNA?

A

Genetic ratchet, got fragmented and survived and now you can’t go back

69
Q

How large are most chloroplast genomes?

A

150kB, a few dozen genes

70
Q

Describe Dinoflagellates symbiodinium’s chloroplast genome

A

(algae that causes fluorescence)
Its chloroplast genome has been shattered and it has dozens of 2-3 kB circular chromosomes that each have one gene
(probably a “genetic ratchet”)

71
Q

Describe the mitochondrial genomes of Trypanosomes (blood parasites)

A

Their mitochondrial genomes are kinetoplasts
which means they have thousands of mini circular molecules 500-1000bp long all wrapped around each other like chain mail
There are also a few maxi circles
Genes are usually found on the maxi circles (one each), while the mini circles help express the gene i.e. by editing etc
Note: this is very time and energy consuming!!

72
Q

How much DNA has to fit in the human nucleus?

A

2m (nucleus is 10um)

73
Q

How is DNA packaged in the nucleus?

A

wrapped into nucleosomes, the into chromatin fibres etc

74
Q

Descrive a nucleosome

A

160bp of DNA

Has 2 copies of each histone: H2A, H2B, H3 and H4

75
Q

Do archaea have histones?

A

yes this is where eukaryotes got them from

76
Q

How large is Protopterus aethiopicus’s genome?

A

(marble lungfish)
130 billion bp
99.9% non-coding

77
Q

How large is Pratylenchus coffeae’s genome?

A

(nematode that affects coffee plantations)

20 million bp

78
Q

How large is Paris japonica’s genome?

A

(slow growing mountain flower)

150 million bp

79
Q

How large is Genlisea margaretae’s genome?

A

(photosynthetic and carnivorous plant)

60 million bp

80
Q

How large is Polychaos dublium’s genome?

A

(unicellular amoeba)

600 billion bp

Genetics (5 decks)

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