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Microbiology > Week 3 > Flashcards

Week 3 Flashcards

1
Q

What is the difference between nucleoside and nucleotide?

A
  • Nucleoside: base + sugar

- Nucleotide: base + sugar + phosphate

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2
Q

What direction is DNA replication in bacteria?

A
  • Synthesised from 5’ to 3’ which forms phosphodiester bond (linked at 3’ hydroxyl).
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3
Q

What is the role of RNA primer in bacterial DNA replication?

A
  • Provides free 3’ hydroxyl group that DNA polymerase can extend from.
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4
Q

What specific DNA polymerase is used in bacterial DNA replication and what does it do?

A
  • Polymerase III holoenzyme has 3 core polymerase in each holoenzyme which binds to DNA and proof reads it.
  • Its beta clap tethers core enzyme to DNA while clamp loader loads beta clamp.
  • Can only add 5’ to 3’.
  • DNA polymerase I is for lagging strand.
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5
Q

What is the role of replisome?

A
  • Creates 2 replication forks.
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6
Q

What is a gene?

A
  • a polynucleotide sequence that codes for a functional product.
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7
Q

What makes up a bacterial gene structure?

A
  • promotor, leader, coding region, trailer and terminator
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8
Q

What role does the promotor region carry out?

A
  • Recognition/binding site of RNA polymerase.
  • It is not transcribed/translated
  • 2 binding regions, one at -35 (recognition site) and another at -10 (binding site, Pribnow box)
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9
Q

What does the leader region contain and what is its function?

A
  • Region between promoter and coding
  • Transcribed but not translated
  • Directs ribosome to bind here
  • Contains transcription start site (shine-dalgarno sequence- important in initiation of translation)
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10
Q

Where is the coding region?

A
  • Bounded by start and stop codon

- Transcribed and translated

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11
Q

Where is the trailer region and what is its role?

A
  • Region after stop codon

- Transcribed and stops ribosome translation

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12
Q

What does the terminator region do?

A
  • Signals RNA polymerase to stop transcription.
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13
Q

What is spontaneous mutation?

A
  • From error in DNA replication

- Rare due to proof reading mechanisms

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14
Q

What is induced mutation and name a few examples?

A
  • Exposure to mutagen

- Examples include base analogues, DNA-modifying agents, intercalating agents, UV radiation/ionising radiation

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15
Q

What are 4 types of mutations?

A
  • Silent: no change
  • Missense: changes codon
  • Nonsense: change codon to STOP
  • Frameshift: changes reading frame of gene
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16
Q

What does polycistronic mean in terms of RNA?

A
  • Can encode for more than one gene
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17
Q

What is an operon?

A
  • Genes that can be transcribed together
18
Q

What does a sigma factor do?

A
  • Separate protein part of enzyme complex that assist RNA polymerase to bind to particular promoters.
  • Different sigma factors recognise different -10 and -35 promoters.
19
Q

What are the 3 stages of transcription?

A
  • Initiation, elongation and termination
20
Q

What are some differences between prokaryotes and eukaryotes in terms of transcription?

A
  • Prokaryotes have 1 type of RNA polymerase whilst eukaryotes have 3.
  • Eukaryotes have 5’ caps on mRNA and poly A tail whilst prokaryotes have none.
  • Prokaryotes have sigma factors whilst eukaryotes have several transcription factors.
  • Eukaryotes have exons and introns whilst prokaryotes don’t.
21
Q

What are 2 ways genes are regulated?

A
  • Regulation of gene expression (transcription initiation, elongation, translation)
  • Alter activity of enzymes and proteins (post-translational)
22
Q

What are inducible genes?

A
  • Expression (transcription) turned on by stimulus. eg.metabolism
  • B-galactosidase is an inducible protein
23
Q

What are repressible genes?

A
  • Expression (transcription) turned off by stimulus. eg. bio synthetic pathway
  • lac operon or trp operon
24
Q

What regulation mechanisms are used at level of translation?

A
  • Regulation by riboswitch where mRNA directly binds to metabolite causing it to fold differently (impedes access to ribosome binding sites)
  • Small RNA regulation where antisense RNAs bind to mRNA leader sequence and inhibit ribosome attachment and translation.
25
Q

What are some mechanisms used for global regulation?

A
  • regulatory proteins
  • alternative sigma factors
  • two component signal transduction system where 2 proteins govern the pathway. (sensor kinase: extracellular recpetor for metabolite, response-regulator protein: activated by sensor kinase and can enhance transcription (activator) or inhibit transcription (repressor).
26
Q

Describe the structure of plasmids.

A
  • usually double stranded circular DNA (some are linear)
  • usually supercoiled by DNA gyrase
  • can have more than one type of plasmid per cell
27
Q

What is the function of plasmid?

A
  • Contain non-essential genes for bacterial growth
28
Q

What is the function of plasmid in B.anthracis?

A

Produce toxins for mammalian cells

29
Q

What is the function of plasmid in B.thuringiensis?

A

Produce toxin used in GM crops

30
Q

What is the function of plasmid in B.cereus?

A

Produce toxins that cause food poisoning

31
Q

What are 3 types of plasmid replication?

A
  • Theta replication: unidirectional and bidirectional

- Rolling circle replication

32
Q

What is theta replication?

A
  • Most common plasmid replication.

- Same mechanism as chromosomal replication

33
Q

What is rolling circle replication?

A
  • When one strand is nicked, the 3’ end serves as primer and DNA polymerase synthesise complementary strand from here.
  • Intact strands serve as template and displaces original second strand. Displaced ssDNA is then converted to dsDNA circle.
34
Q

What is host range? Name the two types.

A
  • The species of bacteria in which the plasmid can replicate.
  • Broad host range replicate in many species (often encode own replication proteins).
  • Narrow host range restricted to single species (often rely on host proteins for replication).
35
Q

What is the copy number?

A
  • Avg number of a single plasmid tpye per cell
36
Q

What do incompatibility group mean?

A
  • Plasmids with similar mechanisms of replication are incompatible.
37
Q

What is a transconjugant?

A
  • recipient cell that has received DNA as a result of conjugation.
38
Q

Describe the mechanism for DNA transfer in bacteria.

A
  • Donor cell produce pilus (encoded by plasmid tra genes)
  • Pilus contacts potential recipient
  • Retraction of pilus brings cells into close contact and a pore forms in adjoining cell membranes
  • In rolling cricle replication, new complementary DNA strand is synthesised in the donor
39
Q

When is bacteria considered transformed?

A
  • When uptake of naked DNA is successful (transformant).

- Bacteria that are able to do this are called competent.

40
Q

What does PCR require?

A
  • primers, DNA polymerase, dNTPs, template strand, some co-factors
41
Q

What is a primer and describe 2 types?

A
  • short DNA or RNA strands that primes DNA synthesis
  • can incorporate restriction enzyme sites
  • PCR requires both forward (analogous to target sequence) and backward (complementary to target sequence) primers.

Microbiology (8 decks)

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