Module 10 Flashcards
Microbial Genetics (99 cards)
1
Q
What is a genome?
A
All DNA present in a cell or virus
2
Q
How many sets of genomes do bacteria and archaea typically have?
A
One set (haploid - 1N)
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
4
Q
What are the two main steps in gene expression?
A
- Transcription: produces an RNA copy of specific genes
- Translation: uses mRNA to synthesize a polypeptide
5
Q
What is the central dogma of molecular biology?
A
The flow of genetic info from DNA to RNA to protein
6
Q
What are nucleotides linked by in nucleic acids?
A
Phosphodiester bonds
7
Q
How do DNA and RNA differ?
A
In their nitrogenous bases, sugars, and whether they are single or double-stranded
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
9
Q
What is the sugar in DNA?
A
Deoxyribose
10
Q
How many base pairs are there per helical spiral of DNA?
A
10 base pairs
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
12
Q
What are the three types of RNA?
A
- Messenger RNA (mRNA)
- Ribosomal RNA (rRNA)
- Transfer RNA (tRNA)
13
Q
How is most prokaryotic DNA organized?
A
Circular, double helix, often supercoiled
14
Q
What helps organize bacterial DNA?
A
Basic proteins help organize DNA into a coiled chromatin-like structure
15
Q
What is a nucleosome?
A
A combination of DNA and histone proteins
16
Q
How is DNA in eukaryotes organized compared to prokaryotes?
A
More highly organized into chromatin and associated with histones
17
Q
What does “semiconservative” DNA replication mean?
A
Each daughter cell receives one old strand and one newly synthesized strand
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
19
Q
In which direction does DNA synthesis occur?
A
5’ to 3’ direction
20
Q
What three things does DNA polymerase require for DNA synthesis?
A
- A template strand
- A primer (DNA or RNA)
- dNTPs (deoxynucleotide triphosphates)
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
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
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
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
25
What is DNA gyrase, and where is it found?
DNA gyrase is a topoisomerase in E. coli that helps relieve tension during DNA replication
26
What is the function of primase in DNA replication?
Primase is an RNA polymerase that synthesizes short RNA primers complementary to the DNA strand
27
What is a primosome?
A complex of primase and other proteins involved in primer synthesis
28
How is the leading strand synthesized during DNA replication?
It is synthesized continuously in the 5'-3' direction with a single RNA primer by DNA polymerase III
29
What are Okazaki fragments, and how are they formed?
Short DNA fragments synthesized on the lagging strand; each fragment requires a new RNA primer
30
What happens to RNA primers on the lagging strand?
They are removed, and DNA fragments are joined by DNA ligase
31
What is the role of DNA ligase in replication?
It forms a phosphodiester bond between the 3' hydroxyl of the growing strand and the 5' phosphate of an Okazaki fragment
32
How does DNA polymerase III proofread?
It removes mismatched bases at the 3' end of the growing strand using its exonuclease activity
33
How do eukaryotic chromosomes solve the problem of replicating telomeres?
Telomerase synthesizes DNA at the ends of chromosomes using an internal RNA template
34
Why is a telomerase needed in eukaryotes but not in prokaryotes?
Eukaryotic chromosomes are linear, so the 3' end of the lagging strand cannot be fully replicated without a telomerase
35
What is a gene?
A unit of genetic information that codes for a polypeptide, tRNA, or rRNA
36
What is a promoter, and what is its function?
A sequence at the start of a gene that acts as a recognition/binding site for RNA polymerase, orienting it for transcription
37
What is the Shine-Dalgarno sequence?
A leader sequence in mRNA important for initiating translation in prokaryotes
38
What is the template strand in transcription?
The strand of DNA read in the 3' to 5' direction to direct RNA synthesis
39
What codon initiates translation in bacteria, and what does it code for?
The codon AUG, which codes for N-formylmethionine
40
What are the three types of RNA produced in transcription?
mRNA, tRNA, and rRNA
41
What is polycistronic mRNA and where is it found?
mRNA containing instructions for multiple polypeptides, found in bacteria and archaea
42
What is the core enzyme in bacterial RNA polymerase responsible for?
Catalyzing RNA synthesis
43
What is the role of the sigma factor in bacterial RNA polymerase?
It helps the core enzyme recognize the start of genes but has no catalytic activity
44
What is the holoenzyme in bacterial transcription?
The combination of the core enzyme and the sigma factor, which is necessary to begin transcription
45
What is a promoter in bacterial transcription?
A DNA site where RNA polymerase binds to initiate transcription. It contains a specific sequence and a Pribnow box
46
Is the promoter transcribed during transcription?
No
47
What is the transcription bubble?
A region where DNA is unwound, moving with RNA polymerase as it transcribes mRNA, forming a temporary RNA:DNA hybrid
48
What marks the end of a gene in bacterial transcription?
DNA sequences in the trailer and terminator regions
49
What is the role of the rho factor in termination?
It aids in the termination of transcription for certain terminators
50
How does eukaryotic transcription differ from bacterial transcription?
Eukaryotes have three RNA polymerases, complex promoters with multiple elements, and RNA polymerase II, which produces hnRNA
51
What post-transcriptional modifications occur in eukaryotic mRNA?
Addition of a 5' cap, removal of introns, splicing of exons, and addition of a 3' poly-A tail
52
What are the functions of the 5' cap and 3' poly-A tail in eukaryotic mRNA?
They protect the mRNA from degradation, signal readiness for transport, and aid in ribosome recognition
53
What are introns and exons?
Introns are non-coding sequences removed during splicing, while exons are expressed sequence that remain in the mRNA
54
What is alternative splicing?
A process where different patterns of exons are spliced, allowing one gene to produce multiple proteins
55
How is archaeal transcription similar to eukaryotic transcription?
It has similar gene promoters, RNA polymerase binding, and the presence of introns in some genes
56
How is archaeal transcription similar to bacterial transcription?
Archaeal mRNA is polycistronic like bacterial mRNA
57
What is a codon?
A genetic code "word" consisting of three nucleotides that specify an amino acid
58
What is code degenracy?
Up to 6 different codons can code for the same amino acid
59
What are the stop codons?
Codons that terminate translation; they do not encode amino acids
60
What is the direction of polypeptide synthesis?
From the N-terminal (amino end) to the C-terminal (carboxyl end)
61
What is a polyribosome?
A complex of mRNA with several ribosomes
62
What enzyme attaches an amino acid to tRNA?
Aminoacyl-tRNA synthetase
63
What does aminoacyl-tRNA synthetase require to activate amino acids?
ATP, amino acids, and tRNA
64
What is the reaction catalyzed by aminoacyl-tRNA synthetase?
AA + tRNA + ATP ---> aminoacyl-tRNA + AMP + PPi
65
What is the bacterial initiator tRNA?
N-formylmethionine-tRNA (fMet-tRNA)
66
What do Archaea and eukaryotes use as their initiator tRNA?
Methionine-tRNA
67
What is the role of the Shine-Dalgarno sequence in mRNA?
It aligns mRNA with complementary bases on the 16S rRNA, ensuring the fMet-tRNA codon is translated first
68
What happens after the 30S ribosomal subunit binds to the mRNA?
the 50S subunit binds, forming the complete ribosome-mRNA complex
69
What are the three phases of the elongation cycle in translation?
1. Aminoacyl-tRNA binding
2. Transpeptidation reaction
3. Translocation
70
What are the tRNA binding sites in the ribosome?
- 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
What enzyme catalyzes the transpeptidation reaction?
Peptidyl transferase
72
What are the three stop codons in translation?
1. UAA
2. UAG
3. UGA
73
What is the role of release factors (RFs) in protein synthesis?
They recognize stop codons and facilitate the release of the completed polypeptide
74
What are molecular chaperones?
Proteins that aid in the folding of nascent polypeptides, protect against thermal damage, and assist in protein transport
75
What are domains in protein structure?
Structurally independent regions of a polypeptide, separated by less structured portions
76
What are introns and extrons?
Introns: portions of a polypeptide that are removed during splicing
Extrons: portions that remain in the protein
77
At what levels can gene expression be regulated?
- transcription initiation
- transcription elongation
- translation
- post-translational modifications
78
What are constitutive genes?
Housekeeping genes expressed continuously
79
What are inducible genes?
Genes that produce enzymes only when needed, such as β-galactosidase.
80
What does β-galactosidase do?
Catalyzes the hydrolysis of lactose into galactose and glucose
81
What happens to β-galactosidase production in the presence of lactose?
Its levels increase significantly due to the presence of the inducer (ex. allolactose)
82
What are effector proteins, and how do they regulate transcription?
Small molecules that bind regulatory proteins non-covalently, altering their activity and influencing transcription
83
What do repressor proteins do in transcription?
- Inhibit transcription by binding to the operator region
- Prevent RNA polymerase binding or movement
84
What do activator proteins do in transcription?
- Promote transcription by binding upstream of the promoter
- Enhance RNA polymerase binding (ex. CAP and cAMP in the lac operon)
85
What is an operon?
A sequence of DNA that codes for one or more polypeptides, along with its promoter and operator or activator binding sites
86
Which operon is an example of negative transcriptional control of inducible genes?
The lac operon, regulated by the lac repressor
87
What type of control does the lac operon involve?
- negative control by lac repressor
- positive control by the catabolite activator protein (CAP)
88
What happens when the lac repressor is bound to DNA?
CAP cannot activate transcription
89
What happens when lactose is present in the cell?
- lactose permease imports lactose
- low levels of β-galactosidase convert lactose into allolactose (inducer)
- allolactose binds and inactivates the lac repressor, enabling transcription
90
What is CAP, and how does it regulate the lac operon?
CAP (catabolite activator protein) enhances transcription when bound to cAMP
91
What happens to CAP when glucose is present?
CAP remains inactive because adenyl cyclase is inhibited, leading to low cAMP levels
92
How does catabolite repression affect bacterial growth?
It results in diauxic growth, where glucose is used first, followed by a lag phase, then growth resumes using other carbon sources
93
What is the role of adenyl cyclase in CAP activity?
It synthesizes cAMP from ATP; active only when glucose is absent
94
What are the combined roles of the lac repressor and CAP in lac operon regulation?
- Allolactose inactivates the lac repressor
- Low glucose increases cAMP, activating CAP, which binds to the CAP site and promotes RNA polymerase binding
95
What does the trp operon encode?
5 structural genes that synthesize tryptophan
96
How is the trp operon regulated?
By negative transcriptional control. The trp repressor binds the operator only when tryptophan (co-repressor) is present
97
What is attenuation in the trp operon?
A regulatory mechanism where transcription is initiated but terminated early in the leader region, depending on tryptophan levels
98
What happens during attenuation when tryptophan levels are low?
- 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
What happens during attenuation when tryptophan levels are high?
- translation progresses, blocking region 2
- region 3 pairs with region 4 for form a terminator loop, stopping transcription
