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Microbiology > Lecture 5: Bacterial Genome Replication And Regulation 1 > Flashcards

Lecture 5: Bacterial Genome Replication And Regulation 1 Flashcards

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1
Q

What is a nucleoside?

A

-the base, the sugar, and no phosphate group are present

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2
Q

What is a nucleotide?

A

-the base, the sugar, phosphate group are present

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3
Q

What amino acids base pair together?

A
  • A=T
  • GC with triple bond
    The combination of this leads to formation of a major and minor groove in the helix
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4
Q

What nucleotides are present in RNA, and what does the strand look like?

A
  • A,G,C,U

- mostly single stranded, but can be double stranded

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5
Q

These RNA subtypes are produced after the transcription of DNA.

A
  • tRNA
  • mRNA
  • rRNA
  • snRNA
  • miRNA
  • siRNA
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6
Q

What is unique about bacterial DNA when compared to that of eukaryotic?

A
  • mostly circular, with a bidirectional replication fork

- begins at the replicon, which is also copied.

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7
Q

What is DNAa?

A

-component of E.Coli replication that initiates replication, and binds the origin of replication (oriC)

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8
Q

What is DnaB?

A

Helicase. Involved with primosome assembly and DNA primase activity

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9
Q

DNA Gyrase?

A

Acts like topoisomerases to relieve supercoiling.

- separates daughter molecules in final stage of replication

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10
Q

SSB protiens have what function?

A

They bind to the free ends of DNA to prevent reformation of the double strand

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11
Q

DnaC has what function?

A
  • helicase loader; helps direct the helicase to the DNA template
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12
Q

DNA Primase has what function?

A

Synthesizes the RNA primer; is a component of primosomes

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13
Q

DNA Polymerase III holoenzyme does what?

A

Catalyzes the DNA synthesis during replication. Contains 3’—>5’ proofreading mechanism

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14
Q

DNA Polymerase I does what?

A
  • removes RNA primers, and fills in the spaces that are left by removing the primer
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15
Q

Ribonuclease H does what?

A
  • helps to remove RNA primers
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16
Q

Tus has what function?

A

-signals termination of replication

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17
Q

What does topoisomerase IV perform?

A

-separation of chromosomes upon completion of DNA replication

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18
Q

What materials does DNA Polymerase require in order to properly perform replication?

A
  1. Template strand in order to make a complementary strand
  2. DNA or RNA primer
  3. dNTPs
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19
Q

What 3 proteins form the core enzyme of DNA polymerase III

A
  • alpha
  • epsilon
  • theta
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20
Q

The beta clamp has what function and is formed how?

A
  • holds polymerase III to the template strand DNA
  • formed by the gamma subunit and ATP hydrolysis. After the ring is formed by the two subunits, they generate an affinity for the alpha and epsilon subunits
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21
Q

The gamma complex of DNA polymerase III does what?

A

-catalyze ATP to chaperone two beta subunits to bind to DNA,

This is also referred to as the clamp loader

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22
Q

What is unique about the alpha complex of DNA pol III?

A

-has DNA polymerase activity

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23
Q

What is unique about the epsilon subunit of DNA pol III?

A
  • this subunit acts as a 3’-5’ exonuclease; therefore has proofreading activity
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24
Q

What does the subunit tao do in DNA pol III?

A
  • this subunit is flexible and helps maintain the two core enzyme and sliding clamps within a certain distance to the clamp loader, which will sit behind the helicase at the replication fork
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25
Q

What happens with DnaA at the replication fork?

A
  • Dna A binds to oriC which bends and separates the two strands
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26
Q

After DnaA binds at oriC, what proteins bind to help separate the two strands of DNA even more?

A
  • DnaB and helicase bind followed by SSB proteins to prevent reformation
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27
Q

What is the function of DNA Pol. I?

A

-removes the RNA primers and fills in the gap with DNA

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28
Q

Replication process ends when reaching the ter site. Catenated chromosomes are what, and how are they fixed?

A
  • two chromosomes that have not separated.
  • a double stranded break is introduced in one circle, the other passed out, and the nick is ligated. Successful separation of teh two strands
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29
Q

How do dimerized chromosomes form and how are they fixed?

A
  • they form at ter sites where crossing over has occured, and prevents separation.
  • XerCD recombinase is required to fix the dimerized chromosomes
30
Q

Eukaryotes solve the ‘end replication’ problem by using telomerase to prevent chromosome shortening. What do bacteria do?

A
  • the ends of the chromosome are disguised as hairpins, which appears as a pseudocircular strand of DNA.
  • LEading strand synthesis occurs, and produces a dimerized chromosome.
  • dimerized chromosomes are repaired with the use of XerCD recombinase
31
Q

What is the best way to describe a gene?

A
  • nucleic acid sequence that codes for a polypeptide, tRNA or rRNA
32
Q

What is a promoter and what does it do?

A
  • the recognition/binding site of RNA polymerase

- functions to orient the polymerase

33
Q

Is the leader sequence every translated?

A

-no, it will be transcribed into mRNA, but will not be translated into amino acids.

34
Q

What sequence on mRNA is important for initiating the translation?

A

Shine Dalgarno sequence

35
Q

What amino acid initiates protein synthesis in bacteria?

A

> N-formylmethionine

36
Q

What is the difference between polycistronic and monocistronic mRNA?

A
  • poly: is an mRNA sequence that will encode for 2 or more proteins.
  • mono: an mRNA sequence that will encode for only 1 protein
37
Q

When is the sigma factor used in bacterial transcription?

A
  • sigma factor directs the RNA polym. to the promoter

- 1st step of transcription initiation.

38
Q

When does transcription leave the initiation stage and enter into the elongation stage?

A
  • after 12 nucleotides have been linked together

- when sigma factor dissociates.

39
Q

What function can rho do during transcription?

A
  • can help the terminator sequence elicit termination at the end of a gene
40
Q

What are the two types of termination processes that can occur for transcription?

A
  1. Rho-dependent

2. Factor independent

41
Q

Describe factor independent termination of transcription.

A
  • the RNA polymerase will encounter an ‘A’ rich region at which it will begin to pause. The pause allows enough time for mRNA to form a loop, straining the DNA:RNA hybrid and falls away.
42
Q

Describe rho factor dependent termination.

A
  1. The rho protein binds to the rot site on mRNA moving towards the RNA polym.
  2. RNA reaches rho dependent region on DNA, causing a pause.
  3. Rho catches and inserts itself into the new rho region in the bubble and separates the DNA:RNA hybrid like helicase would.
43
Q

What is a codon?

A
  1. Genetic code word 3 bp long
  2. Specifies and amino acid
  3. The anticodon on tRNA is complementary
44
Q

What are nonsense codons?

A

These consist of three codons, that are mostly used at translation termination sites. They do not code for an amino acid, and cause termination of a sequence.

45
Q

What is the wobble effect and what are the benefits of it?

A
  1. Provides loose bp that is less specific for the 3rd position of codons.
  2. The benefit is eliminating the need for unique tRNA for each codon
46
Q

Whic part of the tRNA is responsible for binding the amino acid?

A

-3’ end

47
Q

What is aminoacyl-tRNA synthetase?

A
  • an enzyme that catalyzes the attachment of amino acids to tRNA.
  • each one is specific for all tRNAs that may properly attach
48
Q

What does the 30S subunit of RNA contain?

A

Contains the 16S rRNA ribosomal binding site.

  • which binds to the shine dalgarno sequence.
  • binds proteins needed to initiate translation and amino-acyl-tRNA
49
Q

What specific unit is contained in the 50S RNA subunit?

A
  • 5S rRNA and 23S rRNA
50
Q

What is the 23S rRNA region responsible for?

A
  • ribozyme that catalyzes peptide bond formation
51
Q

What phases are required during elongation of a polypeptide chain during translation?

A
  1. Aminoacyl-tRNA binding
  2. Transpeptidation reaction
  3. Translocation
52
Q

What are the different sites located in the ribosome for tRNA?

A

P site: binds the tRNA attached to the growing peptide chain
A site: binds the incoming aminoacyl-tRNA
E site: does not truly have a position, but briefly binds the tRNA before it leaves the ribosome.

53
Q

What takes place in order to terminate protein synthesis in prokaryotes?

A
  1. A stop codon must be encountered
  2. Release factors aid in recognition of a stop codon
  3. The 3 RFs use GTP hydrolysis to release the ribosome
    - eukaryotes only have 1 RF
54
Q

What is the function of a molecular chaperone?

A
  1. Help fold nascent proteins
  2. Protect cells from thermal damage
  3. Transport proteins across membranes
55
Q

What is a genome?

A

All DNA that is present in a cell or virus

56
Q

What is the transpeptidation reaction important for?

A
  • catalyzed by peptidyl transferase 23S rRNA

- interaction of amino acid in the “A” site and the polypeptide chain in the “P” site that adds the new amino acid

57
Q

What events occur simultaneously during translocation?

A
  1. peptidyl-tRNA moves from A to P site
  2. ribosome moves down one codon
  3. empty tRNA leaves the P site
    - -is GTP dependent
58
Q

What portion remains in the polypeptide after splicing?

A
  • exteins
59
Q

What is the Sec-dependent pathway?

A
  • major pathway for bacteria to transport proteins across the PM, and is energy requiring
60
Q

What pathways do gram- negative bacteria use for material secretion?

A
  • Sec pathway

- outer membrane passage requires Type I,II,III,IV,V systems

61
Q

The Sec pathway consists of multiple proteins that all perform different functions. What are these proteins and their function?

A
  1. Y, E, G: form a channel in the PM for protein travels
  2. A: uses ATP to translocate the preprotein through the PM
  3. B: chaperone protein that maintains the translocation state of protein
62
Q

What are type I secretion systems similar to?

A

-ABC transport systems

63
Q

What are the primary secretions of type I secretion systems?

A
  • endotoxins, proteases, and other proteins
64
Q

Who primarily uses the Type I secretion systems?

A
  • gram positive
  • gram negative
  • archaea
65
Q

What is the Tat system?

A

-protein translocation system that moves FOLDED proteins across PM

66
Q

What system works in conjunction with the Type II secretion system?

A
  • Tat system
67
Q

What is the type IV secretion system best at secreting?

A
  • proteins

- secretes DNA from donor to recipient bacteria DURING conjugation

68
Q

Where can Type IV secretion system be found?

A
  • gram positive and negative systems
69
Q

What secretion systems are unique to Gram negative bacteria that secrete virulence factors?

A

-Type II, III, V

70
Q

What type of transport is type V?

A

-sec dependent autotransporter

71
Q

Which gram negative secretion system form injectisomes?

A

Type III

72
Q

In what ways can gene expression be regulated?

A
  • transcription initiation
  • transcription elongation
  • translation
  • -all can be affected in some way to alter what genes will be expressed or repressed.

Microbiology (14 decks)

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