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CBE 2290 > Module 10 > Flashcards

Module 10 Flashcards

Microbial Genetics

1
Q

What is a genome?

A

All DNA present in a cell or virus

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2
Q

How many sets of genomes do bacteria and archaea typically have?

A

One set (haploid - 1N)

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3
Q

What is the difference between the genotype and phenotype?

A

Genotype is the specific set of genes an organism possesses, while phenotype is the collection of observable characteristics

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4
Q

What are the two main steps in gene expression?

A
  1. Transcription: produces an RNA copy of specific genes
  2. Translation: uses mRNA to synthesize a polypeptide
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5
Q

What is the central dogma of molecular biology?

A

The flow of genetic info from DNA to RNA to protein

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6
Q

What are nucleotides linked by in nucleic acids?

A

Phosphodiester bonds

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7
Q

How do DNA and RNA differ?

A

In their nitrogenous bases, sugars, and whether they are single or double-stranded

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8
Q

Which bases pair in DNA and how many hydrogen bonds link them?

A
  • Adenine (A) pairs with Thymine (T) by 2 H-bonds
  • Guanine (G) pairs with Cytosine (C) by 3 H-bonds
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9
Q

What is the sugar in DNA?

A

Deoxyribose

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10
Q

How many base pairs are there per helical spiral of DNA?

A

10 base pairs

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11
Q

Which base is unique to RNA and what does it pair with?

A

Uracil (U), which pairs with Adenine (A) by 2 H-bonds

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12
Q

What are the three types of RNA?

A
  1. Messenger RNA (mRNA)
  2. Ribosomal RNA (rRNA)
  3. Transfer RNA (tRNA)
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13
Q

How is most prokaryotic DNA organized?

A

Circular, double helix, often supercoiled

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14
Q

What helps organize bacterial DNA?

A

Basic proteins help organize DNA into a coiled chromatin-like structure

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15
Q

What is a nucleosome?

A

A combination of DNA and histone proteins

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16
Q

How is DNA in eukaryotes organized compared to prokaryotes?

A

More highly organized into chromatin and associated with histones

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17
Q

What does “semiconservative” DNA replication mean?

A

Each daughter cell receives one old strand and one newly synthesized strand

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18
Q

How fast does DNA replication occur in E. coli vs. eukaryotes?

A

E. coli: 750-1000 bp/sec
Eukaryotes: 50-100 bp/sec

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19
Q

In which direction does DNA synthesis occur?

A

5’ to 3’ direction

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20
Q

What three things does DNA polymerase require for DNA synthesis?

A
  1. A template strand
  2. A primer (DNA or RNA)
  3. dNTPs (deoxynucleotide triphosphates)
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21
Q

What role does DNA polymerase III play in E. coli replication?

A

It is the major enzyme replication, responsible for synthesis and proofreading

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22
Q

How many proteins are in the DNA polymerase III complex, and what do the core enzymes do?

A

The complex has 10 proteins, including 2 core enzymes that catalyze synthesis, proofread, and bind both strands of DNA simultaneously

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23
Q

What is the role of DnaA and DnaB proteins in template preparation?

A

DnaA binds to the origin of replication and directs DnaB to break hydrogen bonds between strands

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24
Q

What is the role of topoisomerases during DNA unwinding?

A

They relieve tension caused by unwinding by transiently breaking DNA strands to prevent supercoiling

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25
Q

What is DNA gyrase, and where is it found?

A

DNA gyrase is a topoisomerase in E. coli that helps relieve tension during DNA replication

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26
Q

What is the function of primase in DNA replication?

A

Primase is an RNA polymerase that synthesizes short RNA primers complementary to the DNA strand

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27
Q

What is a primosome?

A

A complex of primase and other proteins involved in primer synthesis

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28
Q

How is the leading strand synthesized during DNA replication?

A

It is synthesized continuously in the 5’-3’ direction with a single RNA primer by DNA polymerase III

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29
Q

What are Okazaki fragments, and how are they formed?

A

Short DNA fragments synthesized on the lagging strand; each fragment requires a new RNA primer

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30
Q

What happens to RNA primers on the lagging strand?

A

They are removed, and DNA fragments are joined by DNA ligase

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31
Q

What is the role of DNA ligase in replication?

A

It forms a phosphodiester bond between the 3’ hydroxyl of the growing strand and the 5’ phosphate of an Okazaki fragment

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32
Q

How does DNA polymerase III proofread?

A

It removes mismatched bases at the 3’ end of the growing strand using its exonuclease activity

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33
Q

How do eukaryotic chromosomes solve the problem of replicating telomeres?

A

Telomerase synthesizes DNA at the ends of chromosomes using an internal RNA template

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34
Q

Why is a telomerase needed in eukaryotes but not in prokaryotes?

A

Eukaryotic chromosomes are linear, so the 3’ end of the lagging strand cannot be fully replicated without a telomerase

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35
Q

What is a gene?

A

A unit of genetic information that codes for a polypeptide, tRNA, or rRNA

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36
Q

What is a promoter, and what is its function?

A

A sequence at the start of a gene that acts as a recognition/binding site for RNA polymerase, orienting it for transcription

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37
Q

What is the Shine-Dalgarno sequence?

A

A leader sequence in mRNA important for initiating translation in prokaryotes

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38
Q

What is the template strand in transcription?

A

The strand of DNA read in the 3’ to 5’ direction to direct RNA synthesis

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39
Q

What codon initiates translation in bacteria, and what does it code for?

A

The codon AUG, which codes for N-formylmethionine

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40
Q

What are the three types of RNA produced in transcription?

A

mRNA, tRNA, and rRNA

41
Q

What is polycistronic mRNA and where is it found?

A

mRNA containing instructions for multiple polypeptides, found in bacteria and archaea

42
Q

What is the core enzyme in bacterial RNA polymerase responsible for?

A

Catalyzing RNA synthesis

43
Q

What is the role of the sigma factor in bacterial RNA polymerase?

A

It helps the core enzyme recognize the start of genes but has no catalytic activity

44
Q

What is the holoenzyme in bacterial transcription?

A

The combination of the core enzyme and the sigma factor, which is necessary to begin transcription

45
Q

What is a promoter in bacterial transcription?

A

A DNA site where RNA polymerase binds to initiate transcription. It contains a specific sequence and a Pribnow box

46
Q

Is the promoter transcribed during transcription?

A

No

47
Q

What is the transcription bubble?

A

A region where DNA is unwound, moving with RNA polymerase as it transcribes mRNA, forming a temporary RNA:DNA hybrid

48
Q

What marks the end of a gene in bacterial transcription?

A

DNA sequences in the trailer and terminator regions

49
Q

What is the role of the rho factor in termination?

A

It aids in the termination of transcription for certain terminators

50
Q

How does eukaryotic transcription differ from bacterial transcription?

A

Eukaryotes have three RNA polymerases, complex promoters with multiple elements, and RNA polymerase II, which produces hnRNA

51
Q

What post-transcriptional modifications occur in eukaryotic mRNA?

A

Addition of a 5’ cap, removal of introns, splicing of exons, and addition of a 3’ poly-A tail

52
Q

What are the functions of the 5’ cap and 3’ poly-A tail in eukaryotic mRNA?

A

They protect the mRNA from degradation, signal readiness for transport, and aid in ribosome recognition

53
Q

What are introns and exons?

A

Introns are non-coding sequences removed during splicing, while exons are expressed sequence that remain in the mRNA

54
Q

What is alternative splicing?

A

A process where different patterns of exons are spliced, allowing one gene to produce multiple proteins

55
Q

How is archaeal transcription similar to eukaryotic transcription?

A

It has similar gene promoters, RNA polymerase binding, and the presence of introns in some genes

56
Q

How is archaeal transcription similar to bacterial transcription?

A

Archaeal mRNA is polycistronic like bacterial mRNA

57
Q

What is a codon?

A

A genetic code “word” consisting of three nucleotides that specify an amino acid

58
Q

What is code degenracy?

A

Up to 6 different codons can code for the same amino acid

59
Q

What are the stop codons?

A

Codons that terminate translation; they do not encode amino acids

60
Q

What is the direction of polypeptide synthesis?

A

From the N-terminal (amino end) to the C-terminal (carboxyl end)

61
Q

What is a polyribosome?

A

A complex of mRNA with several ribosomes

62
Q

What enzyme attaches an amino acid to tRNA?

A

Aminoacyl-tRNA synthetase

63
Q

What does aminoacyl-tRNA synthetase require to activate amino acids?

A

ATP, amino acids, and tRNA

64
Q

What is the reaction catalyzed by aminoacyl-tRNA synthetase?

A

AA + tRNA + ATP —> aminoacyl-tRNA + AMP + PPi

65
Q

What is the bacterial initiator tRNA?

A

N-formylmethionine-tRNA (fMet-tRNA)

66
Q

What do Archaea and eukaryotes use as their initiator tRNA?

A

Methionine-tRNA

67
Q

What is the role of the Shine-Dalgarno sequence in mRNA?

A

It aligns mRNA with complementary bases on the 16S rRNA, ensuring the fMet-tRNA codon is translated first

68
Q

What happens after the 30S ribosomal subunit binds to the mRNA?

A

the 50S subunit binds, forming the complete ribosome-mRNA complex

69
Q

What are the three phases of the elongation cycle in translation?

A
  1. Aminoacyl-tRNA binding
  2. Transpeptidation reaction
  3. Translocation
70
Q

What are the tRNA binding sites in the ribosome?

A
  • A (aminoacyl) site: Where aminoacyl-tRNA binds
  • P (peptidyl) site: Where the growing polypeptide is held
  • E (exit) site: Where empty tRNA exits the ribosome
71
Q

What enzyme catalyzes the transpeptidation reaction?

A

Peptidyl transferase

72
Q

What are the three stop codons in translation?

A
  1. UAA
  2. UAG
  3. UGA
73
Q

What is the role of release factors (RFs) in protein synthesis?

A

They recognize stop codons and facilitate the release of the completed polypeptide

74
Q

What are molecular chaperones?

A

Proteins that aid in the folding of nascent polypeptides, protect against thermal damage, and assist in protein transport

75
Q

What are domains in protein structure?

A

Structurally independent regions of a polypeptide, separated by less structured portions

76
Q

What are introns and extrons?

A

Introns: portions of a polypeptide that are removed during splicing
Extrons: portions that remain in the protein

77
Q

At what levels can gene expression be regulated?

A
  • transcription initiation
  • transcription elongation
  • translation
  • post-translational modifications
78
Q

What are constitutive genes?

A

Housekeeping genes expressed continuously

79
Q

What are inducible genes?

A

Genes that produce enzymes only when needed, such as β-galactosidase.

80
Q

What does β-galactosidase do?

A

Catalyzes the hydrolysis of lactose into galactose and glucose

81
Q

What happens to β-galactosidase production in the presence of lactose?

A

Its levels increase significantly due to the presence of the inducer (ex. allolactose)

82
Q

What are effector proteins, and how do they regulate transcription?

A

Small molecules that bind regulatory proteins non-covalently, altering their activity and influencing transcription

83
Q

What do repressor proteins do in transcription?

A
  • Inhibit transcription by binding to the operator region
  • Prevent RNA polymerase binding or movement
84
Q

What do activator proteins do in transcription?

A
  • Promote transcription by binding upstream of the promoter
  • Enhance RNA polymerase binding (ex. CAP and cAMP in the lac operon)
85
Q

What is an operon?

A

A sequence of DNA that codes for one or more polypeptides, along with its promoter and operator or activator binding sites

86
Q

Which operon is an example of negative transcriptional control of inducible genes?

A

The lac operon, regulated by the lac repressor

87
Q

What type of control does the lac operon involve?

A
  • negative control by lac repressor
  • positive control by the catabolite activator protein (CAP)
88
Q

What happens when the lac repressor is bound to DNA?

A

CAP cannot activate transcription

89
Q

What happens when lactose is present in the cell?

A
  • lactose permease imports lactose
  • low levels of β-galactosidase convert lactose into allolactose (inducer)
  • allolactose binds and inactivates the lac repressor, enabling transcription
90
Q

What is CAP, and how does it regulate the lac operon?

A

CAP (catabolite activator protein) enhances transcription when bound to cAMP

91
Q

What happens to CAP when glucose is present?

A

CAP remains inactive because adenyl cyclase is inhibited, leading to low cAMP levels

92
Q

How does catabolite repression affect bacterial growth?

A

It results in diauxic growth, where glucose is used first, followed by a lag phase, then growth resumes using other carbon sources

93
Q

What is the role of adenyl cyclase in CAP activity?

A

It synthesizes cAMP from ATP; active only when glucose is absent

94
Q

What are the combined roles of the lac repressor and CAP in lac operon regulation?

A
  • Allolactose inactivates the lac repressor
  • Low glucose increases cAMP, activating CAP, which binds to the CAP site and promotes RNA polymerase binding
95
Q

What does the trp operon encode?

A

5 structural genes that synthesize tryptophan

96
Q

How is the trp operon regulated?

A

By negative transcriptional control. The trp repressor binds the operator only when tryptophan (co-repressor) is present

97
Q

What is attenuation in the trp operon?

A

A regulatory mechanism where transcription is initiated but terminated early in the leader region, depending on tryptophan levels

98
Q

What happens during attenuation when tryptophan levels are low?

A
  • low tRNA(trp) causes ribosomes to stall at the trp codon
  • region 2 of the mRNA pairs with region 3, preventing the formation of the terminator loop (regions 3 and 4)
  • transcription proceeds
    ​
99
Q

What happens during attenuation when tryptophan levels are high?

A
  • translation progresses, blocking region 2
  • region 3 pairs with region 4 for form a terminator loop, stopping transcription

CBE 2290 (12 decks)

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