Microbial Genetics Flashcards
(134 cards)
1
Q
What is the main problem faced by bacteria and archaea regarding genetic variability?
A
They need new genes for survival, such as breaking down unusual nutrients or degrading antibiotics.
2
Q
What is Horizontal Gene Transfer (HGT)?
A
The process by which bacteria acquire new genes from other organisms.
3
Q
Define conjugation in bacteria.
A
The process by which a donor bacterium transfers a copy of a plasmid to a recipient bacterium through a pilus.
4
Q
What is a pilus?
A
A threadlike filament used by donor bacteria to bind to recipient bacteria during conjugation.
5
Q
What type of DNA does a conjugative plasmid contain?
A
Extrachromosomal dsDNA that codes for proteins necessary for pilus formation.
6
Q
What is transformation in bacteria?
A
The process by which a bacterial cell acquires new genes directly from the environment.
7
Q
What is required for a cell to be competent in transformation?
A
The cell must be capable of taking up DNA from the environment and incorporating it into its genome.
8
Q
What factors typically promote transformation in bacteria?
A
High cell density and limited nutrients.
9
Q
What is transduction?
A
The process of transferring bacterial genes from one cell to another using a virus (bacteriophage).
10
Q
Differentiate between generalized and specialized transduction.
A
Generalized transduction involves random packaging of bacterial DNA by a phage, while specialized transduction involves excision of adjacent bacterial genes along with viral DNA.
11
Q
What occurs during generalized transduction?
A
A bacteriophage mistakenly packages bacterial DNA into its viral particles, which can then infect other bacterial cells.
12
Q
What is the role of RecA in molecular recombination?
A
RecA facilitates the pairing of DNA from two sources based on similar nucleotide sequences.
13
Q
What is homologous recombination?
A
A mechanism where DNA from two sources pair based on similarity, involving RecA and an endonuclease.
14
Q
What are transposable elements?
A
DNA segments that can move from one location to another within a DNA molecule.
15
Q
Who is Barbara McClintock and what did she demonstrate?
A
A scientist who showed that transposable elements can activate or inactivate genes within an organism.
16
Q
What is the simplest form of a transposable element?
A
An insertion sequence (IS), which contains transposase and inverted repeats.
17
Q
What is conservative transposition?
A
A process where a transposon is removed from one location and relocated to another.
18
Q
What is replicative transposition?
A
A process where a transposon is copied and the copy is inserted at a second site.
19
Q
Fill in the blank: The process of acquiring new genes from the environment without cell-to-cell contact is called _______.
A
Transformation
20
Q
True or False: Specialized transduction can occur with virulent bacteriophages.
A
False
21
Q
How are genes/proteins named?
A
With a three-letter prefix and one-letter suffix
22
Q
What is a gene?
A
The basic unit of genetic information and the nucleic acid sequence that encodes information necessary to make a product
23
Q
What do genes produce?
A
tRNA, mRNA, and rRNA
24
Q
What does a simple gene create?
A
Monocistronic RNA
25
26
What does an operon create?
Polycistronic RNA
27
Define Template Strand
The strand of DNA that binds RNA polymerase and guides transcription (a.k.a complementary strand or antisense strand)
28
Define Coding Strand
The DNA strand is identical to the produced RNA but with T's
29
Define Promoter
The sequence on the DNA strands where transcription is initiated
30
Define UP elements
The section at the start of the transcribing area on the DNA strands that stabilizes the binding of RNA polymerase
31
Define Leader
This section of DNA on the strands initiates translation with Trx start site
32
Define Coding Region
The section of the DNA strands that hold the code for creating tRNA, rRNA, and mRNA
33
Define Trailer
This section of the DNA strands codes for the termination of translation
34
Define Terminator
This section of the DNA strand is for the termination of transcription
35
True or False:
Transcription is conducted on both the template strand and the coding strand
False
36
What are the five parts of a gene?
Promoter, Leader, Coding Region, Trailer, and Terminator
37
The promoter has a -35 site that is important to the transcription process. Why is it important?
The -35 is the RNA polymerase recognition site. It recognizes the RNAP to prep for binding
38
The promoter has a -10 site that is important to the transcription process. Why is it important?
The -10 site in the promoter is the RNA polymerase binding site. It is also called the Pribnow box, and it makes sure that RNAP binds to the strand for transcription
39
Which strand does the RNA polymerase bind to?
The coding strand
40
True or False: The RNA has a promotor section
False, the RNA starts with the leader section
41
Define Shine-Dalgarno sequence
It is a sequence in the mRNA within the Leader region of the strand. It is the ribosomal binding site.
42
Describe the rrn operon
It is the operon that encodes for the creation of ribosomal RNAs or rRNAs.
43
What genes does the rrn operon have?
16S rRNA
tRNA
23S rRNA
5S rRNA
tRNA
44
What is the product of rrn operon's transcription?
The 30S pre-rRNA
45
What happens to the pre-rRNA after transcription?
It undergoes cleavage and trimming, which will leave the rRNAs and the tRNAs separated and free
46
What is the first process of transcription?
Initiation (Promotor Binding)
47
What is the second process of transcription?
Elongation (Escaping the promotor)
48
What is the third process of transcription?
Termination
49
What are RNA secondary structures?
They are the stems and loops that RNA can form and are responsible for much of the RNA function
50
True or False
The sigma binds to RNA polymerase before the DNA recognizes the RNAP
True
51
When does the sigma escape the RNA polymerase?
It escapes the RNAP at the last step of initiation, where the DNA has been unfurled, and the RNAP is ready to hit the START codon sequence on the template strand
52
When the sigma binds to the RNA polymerase, what does it create?
A Holoenzyme
53
What is the sigma responsible for in transcription?
specificity, it determines which promoters RNA polymerase binds to
54
What does the "core" of RNA polymerase consist of?
alpha, alpha, beta, and beta-prime proteins
55
What is the difference between a closed complex and an open complex?
An open complex promoter looks like it has something enclosing the transcription start site, while a closed complex does not
56
What is the "housekeeping" sigma?
It directs the transcription of "housekeeping" genes with essential or routine function
57
True or False
The "housekeeping" sigma consensus sequence is made up of one promoter
False; the consensus sequence is an average of all the promotor sequences that "housekeeping" sigma recognizes.
58
True or False
The closer the site is to consensus, the stronger the transcription initiation
True
59
What does the term regulon stand for?
It refers to prokaryotes regulating hundreds of genes with similar functions by the sigma
60
True or False
Different sigma factors recognize different promoter sequences
True; there are sigma factors that are meant to specify for different functions
61
What does the term isomerization refer to?
It refers to the process of the holoenzyme opening the DNA strands in the initiation phase of transcription
62
True or False
The process to get from initiation to elongation requires ATP or GTP
True
63
What happens to the NTP nucleotides in Elongation?
They are added to the growing RNA chain
64
True or False
The sigma factor dissociates after initiation
True
65
How does elongation start?
It starts with RNA polymerase melting a bubble of dsDNA into single strands
66
What are the two known transcription termination mechanisms?
Rho-dependent and Rho-independent
67
68
True or False
Rho-dependent and Rho-independent utilize specific sequences in the DNA/RNA
True
69
What is the Rho protein?
It is a protein in an RNA translocase that recognizes a GC-rich region of the elongating mRNA. It will cleave the RNA polymerase, ending transcription
70
How does Rho end transcription?
It hydrolyzes ATP to wrap RNA around the Rho hexamer, pulling it toward the RNA polymerase. Contact between Rho and RNA polymerase causes termination
71
How does Rho-independent termination work?
The nRNA forms a key shape that will cleave the RNA polymerase once it reaches the RNAP
72
True or False
In termination, the polymerase and RNA product dissociate from the DNA template
True
73
Define Translation
The process where RNA is decoded to produce protein
74
True or False
The phases of translation are the same as translation
True, but what happens during each phase is different
75
What happens during the initiation phase of translation
The ribosome binds to its binding site, the START codon is identified by tRNA, and the placement of initiating amino acid
76
What happens during the elongation phase of translation?
More amino acids are added to the growing peptide chain as directed by complementarity of tRNA to the mRNA sequence
77
What is the key molecule that decodes mRNA
Transfer RNA (tRNA)
78
Why is the tRNA remarkably stable?
The unusual bases (Y, T, P, D, and M) help explain the stability of tRNAs. Most of them make up the loops present on the tRNA
79
True or False
Amino acids are attached to the appropriate tRNA by proteins
False; The amino acids are attached by enzymes called aminoacyl-tRNA synthetases, which require ATP
80
True or False
Each tRNA matches a specific amino acid with the appropriate codon
True
81
Describe the ribosome
It is an RNA-protein enzyme complex that polymerizes activated amino acids
82
How many different rRNAs and proteins are there?
There are 3 different rRNAs and 52 different proteins
83
True or False
rRNA makes up the majority of the ribosome structure
True
84
What are the three binding sites for tRNAs on the Ribosome?
1. A-site ("Acceptor site")
2. P-site ("Peptidyl-tRNA site")
3. E-site ("Exit site")
85
What does the A-site do?
It binds incoming aminoacyl-tRNA
86
What does the P-site do?
It harbors tRNA attached to the growing peptide
87
What does the E-site do?
It harbors tRNA recently stripped of the polypeptide
88
How does the ribosome find the start codon?
The 3' end of the ribosomal 16S rRNA base pairs matches with the complementary ribosome binding site (RBS) within the message
89
True or False
The START codons can be AUG, GUG, UUG, or CUG in prokaryotes
True
90
How is the START codon chosen?
It is based on the distance from the ribosome-binding site
91
True or False
The "strength" of the ribosomal binding site and how it matches the 16S rRNA can not significantly influence the efficiency of translation
False; the strength of it does significantly influence the efficiency of translation
92
How is the placement of initial amino acids done during the initiating phase
1. mRNA binds to a small subunit of the ribosome via complementary sequences
2. f-Met tRNA binds to the mRNA with the fMet attached to its end
3. The large subunit binds the DNA where the ribosome is, and is ready to start elongation
93
What is fMet?
It is the first amino acid in a protein chain for bacteria. It is a modified methionine called N-formyl-methionine
94
True or False
Often, the N-formyl group of fMet is removed after translation, or the entire fMet residue may be removed
True
95
Why have the N-formyl group during translation?
It protects the N-terminus of the growing protein, preventing it from forming spurious peptide bonds
96
What catalyzes the process of forming a peptide bond between amino acids during elongation?
The 23S rRNA of the large ribosomal subunit catalyzes the process. It is a ribozyme, in this case
97
Describe translocation
The tRNA that had the previous amino acid attached to it moves to ribosomal compartment "E." That lets the next aminoacyl tRNA come into the peptidyl site to bind and release the next amino acid in the sequence
98
True or False
There is only one STOP codon for the termination of translation
False; there are three STOP codons (UAA, UAG, and UGA)
99
True or False
Each gene (cistron) has its own ribosome-binding site, start codon, and stop codon
True
100
Describe the differences between bacteria translation and eukaryotic translation for transcript recognition
Ribosome recognizes the ribosome-binding site in bacteria, while eukaryotic ribosomes recognize 5' cap modification
101
Describe the differences between bacterial and eukaryotic translation for the initiating codon
Bacteria have multiple initiating codons (AUG, UUG, GUG, and CUG), while eukaryotes only have one (AUG)
102
Describe the differences between bacterial and eukaryotic translation for initiating the formation of the amino acid chain
In bacteria, N-Formylmethionine is used to initiate the sequence, while eukaryotes only use methionine
103
Describe the differences between bacterial and eukaryotic translation location
In bacteria, translation takes place in the same space as translation simultaneously, while eukaryotes require transcription and translation to occur separately
104
Describe the differences between bacterial and eukaryotic translation ribosome structures
Bacteria have 70S ribosomes, and eukaryotes have 80S ribosomes
105
What happens if the ribosome gets stuck on an mRNA?
The tmRNA (trans-Translation) recognizes the stalled RNA and goes into the stalled ribosome to "unlock" it and target the polypeptide for proteolysis
106
Describe Transpeptidation during trans-Translation
The tmRNA moves and replaces the aminoacyl tRNA after the tRNA adds the last acid.
107
What does it Message Switching mean for trans-Translation?
It is when the mRNA is targeted for degradation by RNases to control stability
108
True or False
The translation of the tmRNA peptide tag will free the ribosomal units and mark the created protein for degradation
True
109
True or False
tmRNA is not a cross between tRNA and mRNA
False; It is a cross between tRNA and mRNA
110
What comes after translation?
Protein folding
111
True or False
Correct protein folding is encoded in the mRNA sequence
False; The code is in the primary amino acid sequence for the protein
112
True or False
Most proteins can fold spontaneously
True
113
What happens when proteins require assistance to fold?
They use chaperones
114
True or False
Protein chaperones do not dictate the final three-dimensional structure
True
115
What does a protein chaperon do?
A protein chaperon protects the unfolded or partially folded protein from aggregation, which gives it more time to fold
116
What if protein folding fails?
The chaperone-protease complexes destroy the misfolded proteins and recycle the amino acids in the peptidase chamber on the chaperon
117
True or False
The protein chaperons need energy from ATP hydrolysis to fully unfold the protein prior to snaking it into the peptidase chamber to destroy it
True
118
True or False
Perfectly folded and functional proteins can be degraded
True; This is called Regulated Proteolysis
119
Define Secretion
The movement of a protein out of the cytoplasm
120
Describe the SecYEG proteins from the General Secretion Pathway
It is an integral membrane protein that forms a pore on the inner membrane of the gram-negative bacteria.
121
Describe the SecA protein in the General Secretion Pathway
It is a peripheral membrane protein that binds proteins to be exported into the periplasm and provides export power
122
Describe the SRP protein in the General Secretion Pathway
It is a signal recognition particle that binds proteins that are able to be inserted in the membrane
123
True or False
The General Secretion Pathway (Sec-Dependent) secretes a wide variety of unfolded proteins to the membrane or the periplasm
True
124
How does unfolded protein get exported in the General Secretion Pathway?
The proteins have a signal sequence that the machines recognize for export. That signal sequence enters the SecYEG secretion machinery. Then, the SecA hydrolyzes ATP to pump protein out of the cell, and the signal sequence is inserted into the membrane. Proteins fold after secretion.
125
True or False
Some proteins are cleaved by signal peptidase to be released, while others remain in the membrane in the General Secretion Pathway
True
126
How are unfolded proteins delivered to the SecYEG?
Chaperones (not the same as folding ones) such as SecB help ensure that proteins remain unfolded prior to secretion
127
Describe the TatA protein in the Twin Arginine Translocase (TAT)
It is a protein that forms a large pore in the membrane for secretion
128
Describe the TatB proteins in the Twin Arginine Translocase (TAT)
The proteins provide energy for the secretion
129
Describe the TatC protein in the Twin Arginine Translocase (TAT)
It is the gate mechanism for TatA
130
True or False
Protein to be secreted folds inside the cell
True
131
132
What is the signal sequence for Twin Arginine Translocase (TAT)?
It is two conserved arginine residues (RR) near the N-terminus
133
What is secretion powered by in the Twin Arginine Translocase?
It is powered by PMF
134
