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microbio unit 2 > week 5- microbial genetics > Flashcards

week 5- microbial genetics Flashcards

1
Q

Eukaryotic DNA
shape?
Present in?
telomeres present or no?
introns present or no?
# of chromosomes?
Strands?

A

Linear
Present in nucleus
Telomeres
Introns
Multiple chromosomes
Strands twist

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2
Q

prokaryotic DNA
shape?
Present in?
telomeres present or no?
introns present or no?
# of chromosomes?
Strands?

A

Circular structure
Present in cytoplasm
No telomeres
No introns
Only one chromosome
Bidirectional replication (single orgin)

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3
Q

what is the replication fork? replicon?

A
  • is where DNA is unwound
  • Replicon- portion of the genome that contains an origin and is replicated as a unit
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4
Q

why is synthesis semiconservative ?

A

each daughter cell obtains one old and one new strand.

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5
Q

helicase

A

disrupts H-bonds and helps move the replisome

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6
Q

SS DNA binding protein

A

protects DNA from damage

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7
Q

Topoisomerase

A

relives twisting of unwound DNA

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8
Q

primase

A

synthesizes short RNA primers (~10bp) for DNA polymerase

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9
Q

clamp loader complex

A

holds DNA polymerase at the DNA strand

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10
Q

Tau

A

binds and organizes R coli replication proteins

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11
Q

leading strand?

A

Leading - once opened, DNA polymerase adds complementary strands 5 to 3

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12
Q

lagging? process?

A
  • Lagging - once opened, primase adds RNA primers for DNA polymerase3 to use
  • primers create a lagging strand and synthesize the shirt fragments
  • helicase will separate strands SSB will attach, and DNA polymerase 1 removes primers and fill the gaps with DNA
  • ## Okazaki fragments joined by DNA ligase
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13
Q

How does proofreading happen?

A
  • DNA pol I can make errors
  • If an error occurs, the exonuclease activity enzyme from DNA polymerase will remove the incorrect nucleotide.
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14
Q

Central dogma? how is that different in porkaryotes?

A
  • DNA to mRNA (transcription) to protein (Translation)
  • In prokaryotes, transcription and translation are coupled and not separated. This allows the cell to make proteins very quickly (polyribosome)
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15
Q

what is transcription and its three steps?

A
  • Transcription is the synthesis of mRNA from DNA, and the RNA is a complementary sequence to the template DNA
  • Initiation -> elongation -> termination
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16
Q

what is the core enzyme made out of? what is missing from it? and combined togther what can be made?

A
  • The core enzyme is made of 5 polypeptides (enzyme without the sigma factor)
  • sigma: a protein that helps bacterial RNAP core enzymes recognize the promoter at teh start of the gene
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17
Q

what is a halo-enzyme made up of? when does it start?

A
  • RNA polymerase holoenzymes= core enzyme + sigma factor
  • Only the holoenzyme can initiate transcription
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18
Q

what direction does RNA pol go in after doing what?

A
  • After binding, RNA polymerase unwinds DNA and proceeds in 5 to 3 direction
19
Q

What does RNA pol use in prokaryotes? Eukaryotes? for initation of trasncription?

A
  • RNA polymerase uses the TATA box in eukaryotes and the Pribnow box in prokaryotes (both located in promoter) for the initiation of transcription
20
Q

What is a bacterial promoter?

A
  • is the non-transcribed region of the DNA to which RNA polymerase binds to initiate transcription
21
Q

What does the bacterial promoter region contain? What does it mean?

A
  • The promoter contains the region of DNA where sigma factors recognize -35 bps upstream and a Pribnow box that is -10 bps upstream where DNA strands start to separate, and transcription starts at +1
  • Signs tell you teh position of the nucleotide sites in relation to the transcription start site
  • (-) tells if its upstream and is before transcription start sites
    + indicates downstream
22
Q

Where do teh repressor and activator bind?

A
  • Repressor proteins bind to the operator region
  • Activator protein vines to the DNA site called the enhancer region
23
Q

What is elongation in transcription?

A
  • after binding, RNA polymerase unwinds DNA and proceeds in 5 to 3 directions using the template DNA strand to add nucleotides to make RNA
24
Q

what is termination in transcription? whart are the two ways that it can happen?

A
  • core RNA polymerase dissociates from template DNA
  • intrinsic termination (stem-loop formation) and factor-dependent Rho protein (helicase)
25
Q

What is stem-loop formation also referred to as?

A
  • rho independent: Transcription is terminated without the involvement of Rho protein
26
Q

What is the stem-loop process?

A
  • As RNA polymerase transcribes DNA, part of the RNA can fold into a hairpin loop (due to complementary base pairing in the RNA).
  • After this loop, there is a stretch of U nucleotides in the RNA, which pairs weakly with a stretch of A nucleotides in the DNA (because U-A bonds are weak).
  • This weak bond and the hairpin cause RNA polymerase to pause, making it easier for the polymerase to detach from the DNA, which ends transcription and releases the RNA strand.
27
Q

How does Rho-dependent termination work?

A
  • Rho protein attaches to a specific spot on the RNA called the rut site.
  • Once bound, Rho moves along the RNA toward the RNA polymerase, unwinding the RNA from the DNA.
  • When RNA polymerase reaches a stop signal in the DNA, it pauses, allowing the Rho protein to catch up and separate the RNA from the DNA, ending transcription.
    This process helps ensure the RNA is released at the right time.
28
Q

What does translation do? what is teh direction for synthesis?

A
  • synthesis of proteins from mRNA
  • n to c terminal
29
Q

What is an initiation in translation?

A
  • ribosome (rRNA) assembles around mRNA, and the first tRNA binds to start the codon of mRNA
30
Q

What is the initiator for tRNA for bacteria, archaea, and eukaryotes?

A
  • In bacteria, the initiator tRNA in N-formylmethionine binds to teh start codon of the mRNA; this tRNA carries a formulated version of methionine (amino acid)
  • In archaea and eukaryotes, the initiator tRNA used is methionine-tRNA, which installs methionine at the AUG start codon
31
Q

What is elongation in translation?

A

Elongation: The ribosome moves along mRNA and reads each codon, and then tRNA brings the corresponding amino acid, elongating the polypeptide chain. tRNA moves from A to P to E site on teh ribosome

32
Q

what are the two exceptions in organelles with a reduced genome?

A
  • Mycoplasm uses stop codon (UGA) to code for glutamine
  • Some microbes use 2 rare amino acids: selenocysteine and pyrrolysine
  • These are both encoded by codons that typically function as stop codons but are repurposed in microbes through specific mechanisms
33
Q

What is termination in translation?

A

Termination: when a stop codon is encountered, ribosomes disassemble, and the polypeptide chain is released

34
Q

What is protein translocation?

A

movement of proteins from cytoplasm or across the plasma membrane - epends on where made and where folding needed

35
Q

what is the sec system? and tat system?

A
  • Sec system: generalized secretion pathway - Recognizes signal sequences within the protein to help
    translocate a protein from the cytoplasm to the periplasm or external environment
  • Tat system: specialized secretion pathway for folded proteins
  • Recognizes “twin” arginine residues in the protein signal sequence to direct a protein across the cytoplasmic (inner) membrane.
36
Q

What is secretion? signal peptide?

A

movement of proteins from the cytoplasm to teh external environment
- N-terminal sequence that directs peptide-specific route -removed after maturation

37
Q

What is DNA? Why do A and T bind together? Sugar? sugar-phosphate backbone?

A
  • Double-stranded
  • A (purine) - T (pyrimidine) - 2 H bonds
  • Sugar = deoxyribose
  • Sugar phosphate backbone - phosphodiester bond
38
Q

what is DNA supercoiling?

A

DNA supercoiling - DNA is helical, forming a coil that will ‘“loosen” up the DNA, making it easier to separate the two strands for replication/transcription

39
Q

What is DNA replication?

A
  • The two strands separate, each serving as a template for synthesizing a complementary strand.
40
Q

What does polymerase require? how many DNA pols is in E. coli?

A
  • A template
    A primer - DNA or RNA strand
    dNTPs (dATP, dTTP, dCTP, dGTP) - raw materials
  • , there are 5 DNA polymerases, with polymerase 3 playing a significant role in replication.
41
Q

How does termination occur in E. coli?

A
  • Replication stops when the replisome reaches the termination site on DNA
  • Catenases form when epimerase breaks and rejoins the DNA strand to ease supercoiling
  • Recombinase enzymes will catalyze an intramolecular crossover that separates the 2 chromosome
    (think of the magician analogy)
42
Q

What is the function of aminoacyl-tRNA synthetases?

A
  • are enzymes that attach amino acids to the correct tRNA (transfer RNA)
  • There are at least 20 different synthetases, each specific to one amino acid.
  • This ensures that the right amino acid is paired with the correct tRNA, allowing for accurate protein synthesis during translation.
43
Q

what is the third position wobble?

A

the base at the third position of the codon can often pair with more than one base in the anticodon. This allows for a single tRNA to recognize multiple codons that code for the same amino acid, contributing to the redundancy of the genetic code.

44
Q

how is protein secreted in gram-negative bacteria? two steps vs one step?

A
  • Reviews crossing two membranes
    Some proteins cross in two steps
  • First translocation to the periplasm by the sec or tat system
  • Second secretion across the outer membrane
  • One-step processes involve multiple polypeptides that completely span the periplasm

microbio unit 2 (6 decks)

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