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Genomics > Chapter 5 > Flashcards

Chapter 5 Flashcards

1
Q

What are some properties of prokaryotes?

A
  • They cause infectious diseases
  • can be studied as simple cells to understand fundamental principles
  • represents the earlist form of life
  • important mediators of ecological processes and geological cycles
  • shows a variety of metabolic processes
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2
Q

Where are the major habitats of prokaryotes?

A
  • Open ocean
  • surface soils
  • subsurface sediments beneath oceans and soils
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3
Q

What are some effects of prokaryotic cells dividing actively?

A
  • gives promaryotes the opportunity to evolve quickly
  • colonizes inhospitable habitats such as hot springs and salty lakes
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4
Q

What 2 groups are prokaryotes divided into?

A
  • archaea
  • bacteria
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5
Q

What are some differences between archaea and bacteria?

A
  • bacteria don’t contain introns but some protein-coding genes in archaea do
  • there are differences between tRNA sequences of bacteria and archaea
  • enzymes involved in DNA replication differ between the two
  • members of all cells contain phospholipids but bacteria and euloyotes build well membranes from phospholipids containing d-glycerol while archaea use l-glycerol
  • the organic chains in bacteria and eukaryotes are fatty acids while archaea use polyisoprenes
  • bacteria and eukaryotes link the organic side chains to glycerol useing ester linkage while archaea prefer an ether linkage
  • bacterial cell walls contain peptidoglycon
  • archaea and bacteria differ in their complements of metabolic pathways
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6
Q

What is the earliest evidence of life?

A

Microfossils called stromatolites that arose from Cyanobacteria (related to modern prokaryotes)

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7
Q

Why can’t wo assign Luca - the last common ancestor of all known life forms - to either archaeal or bacterial branch of the evolutionary tree?

A

There has been extensive gene transfer between archaea and bacteria (even though it is likely archaea are closest to LUCA)

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8
Q

What’s the form of a typical probargotic genome?

A

Single circular molecule of double-stranded DNA between 0.6 and 10 million bp long

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9
Q

What’s the structural form of E. coli?

A
  • Single molecule of double stranded DNA closed into a circle
  • DNA is supercoiled and associated with histone-like proteins called the nucleoid
  • some E. colincells may contain plasmids (short double-stranded DNA molecules)
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10
Q

Although circular genomes are common in archaea and factories there are exceptions, what are they?

A
  • many prokaryotic cells contain plasmids
  • some prokaryotic cells have linear DNA (ex. Borrelia burgdorferi, organism that causes lyme disease)
  • some prokaryotes content more than one chromosome (ex. Vibrio cholero, the organism that causes cholera)
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11
Q

Some prokaryote genomes contain insertion sequences which are what?

A

Mobile genetic elements, similar to eukaryotic transposons

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12
Q

Why are enzymes unique to prokaryotes studied?

A

Can be used to manufacture drugs against infection

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13
Q

In E. coli where does replication begin, end, and which direction does it proceed in?

A
  • Starts at oriC
  • ends at terC
  • proceeds in both directions
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14
Q

How many sites of replication does bacteria have and how many does archaea have?

A

Bacteria has one while archaea generally have multiple

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15
Q

In prokaryotes, many mRNA transcripts contain several tandem genes which requires what?

A

Separate initiation of translation ( unlike viral polyproteins which are translated in one piece and then cleaved )

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16
Q

Bacteria ( sometimes archaea) co-transcribed genes have a related function forming what?

A

An operon

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17
Q

What are the 3 methods of transfer of DNA between prokaryotic cells?

A
  • transformation: the uptake of ‘naked’ DNA
  • conjugation: insertion of some or all of the DNA from one cell to another
  • transduction: transfer of DNA from one all to another via a bacteriophage (virus)
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18
Q

What are the major groupings of archaea?

A
  • crenarchaeota
  • euryarchaeota
  • korarchaeota
  • nanoarchaeota
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19
Q

What was the first archaeal genome sequenced?

A

M. jannaschii

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20
Q

Why is greenhouse gas production so high in New Zealand?

A

The sheep and cattle host methonogenic orchaca in their stomachs

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21
Q

In which ways are archaea more closely related to eukaryotes than bacteria and vice versa?

A
  • archaeal proteins involved in metabolism are more similar to those of bacteria
  • archaeal proteins involved in transcription, translation, and regulation are more similar to those of eukaryotes
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22
Q

To survive at elevated temperatures, what must thermophiles and hyperthermophiles do?

A

Synthesize molecules that are stable to heat denaturation

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23
Q

For double stranded DNA and RNA what does thermal stability increase linearly with?

A

G + C content

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24
Q

Codon preference pattern tends to be preserved in closely-related species but diverges as what?

A

Species diverge

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25
Q

Highly expressed proteins show stronger bias in what?

A

Codon usage

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26
Q

How do thermophiles and hyperthermophiles strabilice their DNA structures?

A

Tight binding of special ligands

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27
Q

The G + C content of what is correlated with the growth temperature and what is not?

A
  • Protein-coding RNAs are
  • codon usage patterns are
  • DNA are not
28
Q

Singer and Hickey’s study showed association of thermostability with what?

A
  • DNA
  • RNA
  • proteins
29
Q

What do hyperthermophiles’ special chaperone’ proteins do?

A

Assist in protein folding

30
Q

What are inteins?

A

Proteins that catalyze the excision and splicing of intervening sequences after translation (protein itself contains the self-splicing activity)

31
Q

A bacterial pathogen is a bacterium than can cause diseases because it has virulence factors which may include what?

A

Toxins, surface proteins that mediate attachment to cells, defensive shields, and secreted enzymes

32
Q

What would knowledge of virulence factors permit?

A

Testing of foods for pathogenic strains, choosing suitable drug targets, and designing vaccines

33
Q

What type of gene transfer is a common theme in development of virulence and antibiotic resistance?

A

Horizontal

34
Q

How have genomics and recombinant technology made possible a new generation of approaches to vaccine design?

A
  • antibodies raised against the detoxified form protect against the native protein
  • comparing genome sequences of pathogenic and non-pathogenic strains identify virulence factors that may act as the basis of vaccines
35
Q

What are viruses?

A

Nucleoprotein particles with a nuclei acid genome encapsulated with a protein or glycol protein coat or viral capsids

36
Q

How do viruses infect cells?

A
  • Using specialized proteins on cell surfaces that affect attachment and invasion viral nucleic acid enters the host cell
  • once inside, the invading molecules must make multiple copies of the viral genome, synthesize viral proteins to be assembled into the progeny virions, “pack up and leave”
37
Q

How are the burst sizes in virus in eukaryotic and prokaryotic culls different?

A

Burst size in eukaryotes can range from thousands to tens of thousands but they are much smaller in prokaryotes

38
Q

Why do some virus integrate their genome into the genome of their host cells?

A

Sometimes it is mandatory for replication and sometimes it makes the host cell and its descendants a reservoir

39
Q

Relatively how short are viruses genome?

A

Short, bacteriophage for example was 5386 bp long

40
Q

Why did the discovery of giant viruses bring about a new problem in the scientific community?

A

Scientists used to filter viruses because the particles were small enough to pass through a filter of diatomaceous earth or porcelain which retain bacteria, giant viruses are not

41
Q

What are some properties of giant viruses?

A
  • they have large double-stranded DNA genomes
  • large particle size
  • their proteomes include more proteins than regular virus
  • they synthesize enzymes involved in protein biosynthesis
42
Q

What are some large viruses parasitized by?

A

Small DNA virophages

43
Q

What do some mimiviruses have as a defence system?

A

CRISPR / Cas-like defence system

44
Q

What amount of nucleic acids do viral genomes contain?

A

Relatively small amounts

45
Q

What situation permits genetic recombination to produce recombinant viruses?

A

Mixed infections of a cell by different viruses (sort of like a natural Hershey-Chase experiment)

46
Q

Why have HIV-1 and influenza viruses become major threats to human health after jumping from animal hosts?

A

They have high mutation rates which also reflects that their genomes are RNA

47
Q

What are single-stranded DNA viral genomes generally converted to once inside the host?

A

Double-stranded DNA

48
Q

Why is replication of RNA viruses prove to mutation?

A

It helps viruses to evade host human immune systems and facilitates their jumping between host species

49
Q

What are the 3 types of viral genome consisting of single-stranded RNA?

A
  • (+) sense : same sequence as protein translatable mRNA
  • (-) sense : complementary sequence to mRNA
  • ambisense : mixture of both
50
Q

What happens to (+) sense viral RNAs inside the cell?

A

They present themselves as mRNA and are translated

51
Q

What happens to (-) sense viral RNAs and double-stranded viral RNAs inside the cell?

A

They require specialized polymerases for conversion to mRNA

52
Q

What happens to retroviral genomes that contain (+) sense RNA?

A

They are reverse transcribed into host DNA

53
Q

In the laboratory, a virus can be constructed as a vector to produce foreign proteins inside a cell. What are 2 applications of this technique?

A

1- to produce a vaccine, insert a DNA sequence coding for an immunogen into the vaccinia virus genome. Infection by recombinant virus leads to expression of immunogen giving the host protective immunity. (intracellular exposure to the immunogen is more powerful)
2- a recombinant virus carrying a normal human genome can be useful in gene therapy because the retroviral. Vector can reintroduce the normal variant into the patient’s genome

54
Q

Why are there more viruses than cellular life forms?

A

Viruses pates of mutation are a million times faster, they have short generation times, and large numbers of progeny

55
Q

Cellular DNA-replication systems are equipped with high error-correction mechanisms, does RNA have the same system in place?

A

No, the error rate of RNA replication is very high and because viral genomes doesn’t contain much “junk”, a mutation is more likely to have a phenotypic effect

56
Q

What is “mutational meltdown”?

A

When a too high mutation rate tips the population into an instability

57
Q

How are viruses agents of gene transfer?

A

By insertion into crucial sites in the genome, they can affect gene expression patterns

58
Q

What are some properties of influenza?

A
  • it is a contagious disease caused by a virus that infects the respiratory tract
  • it can survive outside the host, greatky facilitating transmission
59
Q

Which characteristics of the host population are contagion and mortality of influenza dependent on?

A

Density and general health levels

60
Q

Why was avian flue considered a particular threat to humans and how does it spread?

A
  • it has a high mortality rate and recombines readily
  • it first infects birds which then infects pigs and then humans (human to human transfer is unlikely)
61
Q

What has DNA sequencing made possible?

A
  • clarifying evolutionary relationships
  • using high-throughput sequencing methods to study a coss-section of the life in a natural sample
  • study the majority of strains that are difficult to grow in culture
  • appreciate the relationships and interactions among different species that share an ecosystem
62
Q

What can metagenomics explore?

A

Microflora of every niche in the world (includes exterior and interior of human body)

63
Q

What are some disadvantages of characterizing an organism by its rRNA?

A
  • rRNA is not prone to horizontal gene transfer so it preserves the distinctions between taxa which means that this may disguise the mixing that has taken place by gene exchange
  • rRNA does not reveal any details of the metabolism or other adaptations of the species
64
Q

The “topology” of evolutionary space depends on complicated interactions of which variables?

A

Physical and geographical variables such as landscape, climate, and interspecies cooperation or competition

65
Q

How do cells respond to the threat of mutation that ultraviolet light can cause by damaging DNA?

A

Cells contain repair enzymes, including photolyase, which recovers thymines from dimers

Genomics (4 decks)

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