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MICR 271 > Module 4 > Flashcards

Module 4 Flashcards

1
Q

where does replication begin on the circular bacterial chromosome

A

at the origin oriC (an AT rich region that is easy to separate due to few hydrogen bonds)

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2
Q

how is catenation resolved (decatenation)

A

one of the chromosomes is cleaved by topoisomerase (failure to do this leads to cell death

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3
Q

what is a catenated chromosome

A

interlocked daughter chromosomes
-replication of circular chromosomes result in the daughter chromosomes interlocking

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4
Q

what is the replisome

A

a large protein complex that copies DNA

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5
Q

what is a holoenzyme (ex. DNA pol III)

A

an enzyme and a cofactor

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6
Q

what does the replisome of prokaryotes consist of

A

helicase, primase and DNA pol III

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7
Q

what protein protects single stranded DNA after it is unwound by helicase

A

replication protein A (RPA)

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8
Q

what can optimize replication strategies

A

small genomes, simple genomes (bacteria) - spontaneous mistakes can be beneficial/spread quick

eukaryotes are more complex

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9
Q

compare and contrast replisome components of prokaryotes and eukaryotes

A

Prokaryotes:
Helicase, primase, DNA polymerase III.
DNA pol III synthesizes both leading and lagging strands.
Okazaki fragments joined by DNA pol I and ligase.

Eukaryotes:

Mcm2-7 helicase (activated by proteins like GINS, Cdc45).
DNA pol α synthesizes RNA primer.
DNA pol ε (leading strand) and DNA pol δ (lagging strand).
PCNA (clamp) and RFC (loading factor) involved.
Shorter Okazaki fragments; RNA primers removed by strand displacement.

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10
Q

Briefly explain how the viral mechanisms of genome replication work in DNA, RNA and retroviruses

A

DNA viruses replicate using the host’s DNA polymerase machinery for replication and transcription.

RNA viruses need positive strands to be read as mRNA, and the other strands can be used as templates for the other to be read.

Retroviruses convert their RNA genomes into DNA via reverse transcriptase, and integrate the resulting DNA into the host genome.

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11
Q

what is the main difference of DNA polymerase families in bacteria/archaea and eukaryotes

A

Bacteria and archaea tend to have one specific pol for a very defined function, eukaryotes have several in each family

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12
Q

What are the main groups in the Baltimore Classification?

A

Double-Stranded DNA (dsDNA)

Single-Stranded DNA (ssDNA)

Double-Stranded RNA (dsRNA)

Positive-Sense Single-Stranded RNA (+ssRNA)

Negative-Sense Single-Stranded RNA (-ssRNA)

Retroviruses (Reverse Transcribing ssRNA)

Reverse Transcribing dsDNA

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13
Q

reverse transcribing, for DNA vs retroviruses

A

having a partially ds genome that needs to be filled in-> DNA to RNA

retroviruses start with RNA and have to reverse transcribed into DNA

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14
Q

what is an example of a class I virus

A

T4 phage

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15
Q

how does a T4 phage infect a host

A
  1. T4 injects linear DNA into the host cell.
  2. Host RNA polymerase transcribes early genes (mRNA).
  3. Host DNA is degraded, and phage DNA is replicated.
  4. Once phage DNA is replicated, remaining mRNA is transcribed by host RNA pol
  5. Structural proteins are synthesized and packaged.
  6. Cell is lysed to release new virions.
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16
Q

how does viral replication of dsDNA differ from ssDNA

A

dsDNA: The virus genome is double-stranded, so both strands can be used as templates for transcription and replication.

ssDNA: The virus genome is single-stranded, so it must first be converted into double-stranded DNA before replication can occur.

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17
Q

What is the replication strategy of Class VI (Retroviruses)?

A

Genome type: Positive-sense ssRNA
Reverse transcription: RNA genome is converted to dsDNA by reverse transcriptase.
Integration: The dsDNA is integrated into the host genome by integrase.
mRNA synthesis: Host machinery transcribes proviral DNA into mRNA.

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18
Q

difference in replication between +ssRNA and -ssRNA

A

Positive: Genome directly acts as mRNA for protein synthesis. Negative-sense RNA is synthesized as a template for new positive-sense RNA genomes.

Negative: Genome is transcribed into complementary positive-sense RNA (mRNA). mRNA is translated, and new negative-sense RNA genomes are synthesized.

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19
Q

how does a double stranded RNA virus such as rotavirus replicate in a cell

A
  1. Non enveloped virus enters the host and uncoats, releasing a double-layered particle.
  2. RdRp transcribes the viral genome inside the particle.
  3. mRNA translated for protein synthesis, and genome segments are replicated.
  4. Assembly of viral particles occurs in the viroplasm.
  5. New virions are released via exocytosis or lysis
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20
Q

what is an example of a +ssRNA virus and a -ssRNA virus

A

+: SARS-CoV-2

-: Influenza

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21
Q

how does SARS infect a cell (covid)

A
  1. Enveloped -> Endocytosis.
    • genome is translated
  3. Proteolysis make protein subunits (machinery)
  4. The replicase-transcriptase complex (RTC) synthesizes negative-strand RNA and mRNA.
  5. New genomes are assembled and packaged with structural proteins in the ER
    5.Virions are released via exocytosis.
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22
Q

What are the structural proteins of SARS-CoV-2?

A

Spike (S), Envelope (E), Membrane (M), and Nucleocapsid (N) proteins.

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23
Q

replication strategy of influenza

A

Attachment: HA binds to host receptors, enveloped virus enters via endocytosis.

Uncoating: Acidification releases negative ssRNA into the cytoplasm.

Nucleus: RNA polymerase makes +RNA and mRNA from the - strand.

Replication & Translation: + RNA replicates the genome; mRNA makes viral proteins.

Packaging & Release: New -ssRNA is packaged into virions, which bud off the host cell.

24
Q

what is an example of a retrovirus

A

HIV (enveloped)

25
Q

How does HIV replication proceed after reverse transcription?

A

The dsDNA form of HIV integrates into the host genome.

Proviral DNA is transcribed into mRNA to make viral proteins, and ssRNA replicate

New HIV particles are assembled and released via budding

26
Q

what are the different functions of polymerase

A

replication

repair
-removng RNA primers or damaged bases
-DNA translesion - inserting base across from damaged nucleotide

27
Q

positive sense RNA are in a form that can

A

be recognized by ribosomes to become translated into proteins

28
Q

are RNA or DNA viruses more subject to mutation/harm

A

RNA - repair mechanisms are very important

29
Q

what is a polycistronic mRNA

A

codes for more than one protein, also known as an operon

30
Q

open reading frame

A

An open reading frame has the potential to be translated, it is the portion of the reading frame with no stop codon

31
Q

what do sigma factors do in bacterial transcription

A

help RNA pol bind to the promoter and start initiation

32
Q

what are the stages of translation

A

initiation
elongation
termination/recycling

33
Q

what is an advantage to not having a nucleus

A

transcription and translation can occur at the same time

34
Q

why is the bacterial ribosome a major antibiotic target

A

it is 70S meaning it is different then that of eukaryotes, also prevents the translation of mRNA into bacterial proteins

35
Q

what is a polyribosomal complex

A

when bacterial mRNA are translated by multiple ribosomes, this complex is formed

36
Q

which initiation factor in bacterial translation recognizes the start codon

A

fMet-tRNA

37
Q

what are the initiation factors that make up the bacterial initiation complex for translation

A

fMet-tRNA, GTP, initiation factors 1/2/3, 30S subunit

38
Q

what do release factors do

A

hydrolyze the polypeptide chain from the tRNA and the disassembly of the ribosome

39
Q

steps of bacterial initiation

A
  1. Initiation factors 1/2/3, GTP, fMet-tRNA and the 30S subunit assemble with the mRNA
  2. When the 50S subunit joins the complex, IF2 hydrolyzes GTP and IF3 and 1 are released resulting in the 70S initiation complex
  3. This complex is ready for the next step, elongation
40
Q

stop codons are recognized by ___

A

release factors

41
Q

what are the key elongation factors and what do they do

A

EF-Tu: delivers tRNA with amino acids to the ribosome

EF-G: helps with translocation (moving mRNA and tRNA through the ribosome

42
Q

the terminology for regulation of gene expression

A

Transcriptional regulation: control transcription of gene

Post-transcriptional regulation: control protein production by modifying mRNA. Primarily occurs in eukaryotes

Translational regulation: control translation of mRNA

Post-translational regulation: control activity of protein
after it is produced

43
Q

what is a regulon

A

a group of genes regulated by a specific transcription factor in response to environmental signals

the genes have related functions

44
Q

examples of bacterial transcriptional repressors

A

Repression by steric hindrance
Prevent interaction of RNA pol with the promoter

Repression by looping
Multiple repressors bind and loop DNA so that RNA pol cannot interact with it

Repression by modulation of an activator
Counteract the activator to reduce attraction of RNA pol

45
Q

the 3 types of bacterial transcriptional activators

A

Class I activation
○ Association of an Activator protein upstream of the promoter recruits RNA polymerase to a specific promoter

Class II activation
○ The Activator binds very close to the promoter region where it can interact directly with domain 4 of the sigma factor

Activation by a promoter conformation change
○ Some Activators bind within the promoter region where they act to optimize the alignment of the -35 and -10 elements of the promoter through a conformational change. This facilitates recognition by RNA polymerase.

46
Q

What is the role of microRNAs in translational regulation?

A

MicroRNAs (miRNAs):
Regulate translation by binding to mRNA and blocking its translation or promoting its degradation.
-matching game in eukaryotes presented by RISC

In prokaryotes, Hfq proteins help miRNAs regulate sigma S expression by preventing inhibitory RNA structures.

47
Q

How does post-translational modification (PTM) affect proteins?

A

PTM can:
Alter protein stability, activity, localization, or signaling.

Phosphorylation is a common PTM that regulates protein function, often in response to signaling pathways.
-kinase transfers phosphate from ATP to protein, phosphatease removes it

48
Q

what step in translation do antibiotics like to target

A

elongation

49
Q

mechanisms of preventing elongation by antibiotics

A

Preventing delivery of tRNA to A site

Targeting the peptidyl-transferase center (PTC), blocking
peptide bond formation

Blocking translocation

Causing misreading of mRNA (change protein sequence)

50
Q

how do bacteria resist antibiotics

A

Prevent antibiotic from reaching ribosome
* Efflux, decreased permeability

Target modification
* Change ribosome structure so antibiotic cannot bind

Target protection
* Produce a protein that removes antibiotic from ribosome

Antibiotic modification/degradation

51
Q

what criteria does a spontaneous mutation need to have to be selected for in antibiotic resistance

A

confer resistance to the selecting agent (antibiotic)

not compromise the fitness/normal functioning of the cell

52
Q

what is the best way to treat HIV

A

with a drug cocktail that targets it at different points in its life cycle
protease inhibitor
fusion inhibitor
integrase inhibitors

53
Q

what system do pseudomona infections use to shift between acut and chronic infection

A

GAC system

54
Q

how do pseudomonas infect a cell

A

Detect host signals using membrane protein

Cytoplasmic protein is phosphorylated

Produces microRNAs- control binding of transcriptional regulator to
certain promoters

If microRNA produced, some genes expressed; if no microRNA produced other genes expressed

55
Q

How does quorum sensing regulate Pseudomonas virulence?

A

Bacteria communicate via homoserine lactones (HSLs) produced by LasR and RhlR.

HSL binds to transcription factors and makes more HSL (autoinduction)

Hiercharchal: one HSL controls production of another HSL

Each HSL control a virulence factor ( exotoxin A, pyocyanin) when bacteria reach high density.

56
Q

exotoxin A does what, and pyocyanin does what

A

inhibits protein synthesis, generates reactive oxygen species

57
Q

Tat vs Rev in transcriptional control by HIV

A

Tat binds to viral RNA as it is being synthesized, helping transcription to occur

Rev transports mRNA encoding viral structural proteins out of nucleus, increasing translation

MICR 271 (6 decks)

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