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130 Cards in this Set
- Front
- Back
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How does bacterial RNA polymerase differ from eukaryotic RNA polymerase? |
There is only one type of bacterial RNA polymerase, while eukaryotes have multiple types |
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What are the subunits of the bacterial RNA polymerase core? |
β β' α (2 copies) omega |
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Many ____ target RNA polymerase |
Antibiotics |
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How do bacteria develop resistance to antibiotics that target RNA polymerase? |
Mutations in genes encoding RNA polymerase subunits |
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What is the function of the sigma component of bacterial RNA polymerase? |
Guides RNA polymerase to the appropriate section of DNA to begin transcription |
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What is the function of the rho component of bacterial RNA polymerase? |
Aids termination of transcription |
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What are the components of a bacterial ribosome? |
3 small rRNA molecules
Approximately 52 proteins |
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Many ____ target bacterial ribosomes through interactions with ribosomal proteins |
Antibiotics |
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How do bacteria develop resistance to antibiotics that target ribosomes? |
Mutations in genes encoding ribosomal proteins |
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Why is the ribosome-targeting antibiotic chloramphenicol only used as a last resort? |
It affects mitochondrial ribosomes |
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Do bacteria use the same genetic code as humans? |
Essentially, yes |
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What nucleotide sequences are "stop" codons? |
TAA, TGA, and TAG |
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What nucleotide sequence is the "start" codon? |
ATG |
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The start codon codes for which amino acid? |
Methionine |
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Open reading frame (ORF) (Definition) |
A region of DNA between a start and a stop codon that codes for a protein |
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Gene (Definition) |
Usually synonymous with open reading frame, but also DNA sequences that encode structural RNAs (rRNA, tRNA, etc.) |
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Promoter (Definition) |
A sequence of DNA recognized by RNA polymerase as the starting point of transcription |
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Which component of RNA polymerase facilitates promoter recognition? |
Sigma |
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How can bacteria manipulate RNA polymerase to control gene transcription? |
They make several different sigmas (>20 in some cases), each of which recognizes a different DNA sequence |
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Operator (Definition) |
A DNA sequence, generally located near the promoter, that binds a specific protein that affects interactions between RNA polymerase and the promoter DNA |
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How can bacteria manipulate operators to control gene transcription? |
By making or not making the operator-binding protein
Altering the protein's affinity for the operator |
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Operon (Definition) |
The basic unit of transcription, including the gene(s), promotor, and operators |
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Cistron (Definition) |
Synonym for "gene" |
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Monocistronic operon (Definition) |
Operon containing one gene |
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Polycistronic operon (Definition) |
Operon containing multiple genes |
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Genomics (Definition) |
Identification of all of the genes in an organisms DNA (the genome) |
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What is the goal of bacterial genomics? |
To identify ORFs and compare predicted amino acid sequence with previously identified proteins of known function |
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How long is a typical ORF? |
>100 amino acids |
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Which bacterium causes Lyme disease? |
Borrelia burgdorferi |
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Proteomics (Definition) |
Identification of all proteins produced by an organism (the proteome) |
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Transcriptomics (Definition) |
Identification of all RNAs produced by an organism (the transcriptome) |
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Why do bacteria need to regulate protein synthesis? |
1) Adaptation to different environments (e.g. changing glucose levels)
2) Adaptation to being in a host (parasitize nutrients, change surface proteins)
3)Efficiency (don't wast energy on unneeded proteins)
4) Development (e.g. spore formation in stressful conditions) |
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What are some aspects of the environment that can be sensed by bacteria? |
Temperature
Availability of carbon sources, amino acids, nucleic acids, etc.
Presence of iron, nitrogen, phosphorus, etc. |
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What happens to iron-sensing bacteria in humans? |
They sense that iron is low, triggering the release of toxins |
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How is bacterial adaptation most frequently accomplished? Why |
By regulating gene expression
Why:
Transcription and translation are tightly coupled (no nucleus)
mRNAs generally have short half-lives
Fast generation time quickly dilutes out old proteins
It's fuel efficient (avoids production of unnecessary mRNA and proteins) |
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How is bacterial gene regulation accomplished? |
Alternate sigma proteins
Chemical modification of DNA (methylation, etc.)
Structural modification of DNA (histone-like proteins)
Protein binding to operators |
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How do operator-binding proteins affect gene transcription? |
The protein may physically prevent RNA polymerase from interacting with the promoter
OR
The protein may interact with RNA polymerase to increase or decrease its adherence to the promoter |
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Inducer (Definition, Examples) |
A substance that increases the level of transcription from an operon (e.g. lactose in the lac operon, arabinose in the ara operon) |
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Repressor protein (Definition, Example) |
A protein that reduces the level of transcription from an operon (e.g. LacI in the lac operon) |
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Activator protein (Definition, Example) |
A protein that increases the level of transcription from an operon (e.g. AraC in the ara operon) |
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Anti-repressor (Definition) |
A molecule that blocks repressor binding |
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Anti-activator (Definition) |
A molecule that blocks activator binding |
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Genes for catabolic enzymes are generally ____ by the presence of the catabolite |
Induced |
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Genes for anabolic enzymes are generally ____ by the presence of the end product |
Repressed |
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What three genes contribute to the E. coli lac operon, and what do they encode? |
lacZ - a protein that degrades lactose
lacY - a lactose-transporter
lacA - a protein that acetylates lactose (not sure why this happens) |
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In the absence of lactose, what happens to LacI? |
It binds the lac operator, preventing transcription of the lac operon |
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In the presence of lactose, what happens to LacI? |
It is bound by lactose, preventing it from binding to the lac operator and allowing transcription of the lac operon |
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In the absence of arabinose, what happens to AraC? |
It does not bind the ara operator, and RNA polymerase does not bind the ara promoter |
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In the presence of arabinose, what happens to AraC? |
It binds arabinose, allowing it to bind the ara operator; binding of AraC to the ara operator stimulates RNA polymerase binding to the ara promoter |
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Regulon (Definition, Example) |
A control system that regulates several different operons (e.g. cyclic AMP and CRP) |
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What is the relationship between cellular glucose levels and cAMP levels? |
↓ Glc = ↑ cAMP (and vice versa) |
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Describe the cAMP and CRP regulon |
Glucose starvation → ↑ cAMP → cAMP binds cAMP-receptor protein (CRP) → CRP-cAMP binds to specific sites on DNA → Transcription of operons encoding enzymes that catabolize "alternative" carbon sources (lactose, arabinose, etc.) |
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What does the ppGpp regulon regulate? |
Amino acid starvation response (activates Met operon, halts translation) |
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What is the role of the SOS system regulon? |
It senses DNA damage and halts replication |
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E. coli is sensitive to both lactose and ____ |
Glucose |
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What role does glucose play in the lac operon? |
RNA polymerase cannot effectively transcribe the lac operon without CRP-cAMP bound to the operator (thus, cellular Glc must be low) |
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What are the components of a two-component regulator system? |
A sensor and a response regulator |
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What kinds of signals are sensed in two-component regulator systems? |
Proteins, carbohydrates, light, etc. |
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What is the role of the sensor in a two-component regulatory system? |
It detects a stimulus and autophosphorylates a histidine residue; the phosphate is then transferred to the response regulator |
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What is the role of the response regulator in a two-component regulator system? |
It is activated by the sensor (via phosphorylation) and goes on to regulate transcription |
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What signal is sensed by Enterococcus faecium, and how does the bacterium respond? |
Sense vancomycin
Response = vancomycin resistance |
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Quorom sensing (Definition) |
Signaling used to coordinate gene expression according to the density of the local bacterial population |
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What are some quorum signaling molecules? |
Homoserine lactones
Polypeptides
Autoinducer-2 (AI-2) |
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Why do bacteria use quorum sensing? |
To determine if there are enough bacteria present to overcome the host immune response |
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Pathogens may specifically ____ an organ, tissue, or cell |
Target |
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Are pathogenic bacteria usually passive or aggressive? |
Aggressive |
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Chemotaxis (Definition) |
Directed movement along a chemical gradient |
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What direction must E. coli flagella rotate for smooth swimming? |
Counterclockwise |
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What direction must E. coli flagella rotate for a tumbling motion? |
Clockwise |
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How does E. coli regulate the direction of its flagellar rotation? |
A two-component regulatory system |
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Describe the process of E. coli chemotaxis |
Repeated cycles of smooth swimming and tumbling with an overall movement in the direction of increasing chemical concentration |
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How do changes in bacterial DNA occur? |
Mutations or acquisition of new DNA sequences |
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Are mutations usually advantageous or deleterious for bacteria? |
Deleterious |
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Transition (Definition) |
Purine to purine (A to G) or pyrimidine to pyrimidine (T to C) mutation |
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Transversion (Definition) |
Purine to pyrimidine (or vice versa) mutation |
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Insertion (Definition) |
Mutation via addition of new nucleotide bases; DNA sequence may encode a useful protein |
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Deletion (Definition) |
Mutation via loss of nucleotide bases |
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Duplication (Definition, Example) |
The creation of additional copies of a DNA sequence without transfer from another organism (e.g. β and β' RNA polymerase genes) |
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Inversion (Definition, Example) |
Reversal of DNA sequence (e.g. regulation of fimbriae synthesis in E. coli via inversion of promoter DNA) |
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How do bacteria develop resistance to streptomycin? |
A single base change (K to R) in the rpsL gene, producing an S12 ribosome subunit that cannot bind streptomycin |
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(Long or short?) stretches of repeated DNA sequences are prone to insertion and deletion mutations? |
Long |
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Why are long stretches of repeated DNA sequences prone to insertion and deletion mutations? |
The DNA polymerase/DNA complex occasionally dissociates very briefly during replication, and the newly aligned strand may not become correctly aligned with the template strand |
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How does Neisseria gonorrhoeae utilize a DNA replication error for gene regulation? |
A specific gene is turned on (17 copes of G) or off (16 or 18 copies of G) by spontaneous deletion of bases within the protein coding region |
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Homologous recombination (Definition) |
Nucleotide sequences are randomly exchanged between two nearly homologous sections of DNA |
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Site-specific recombination (Definition) |
Enzyme-mediated recombination between specific short segments of DNA with only a short region of homology |
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Non-homologous ("illegitimate") recombination (Definition) |
Random recombination between segments of DNA with no sequence homology via an unknown mechanism |
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Why does Borrelia hermsii cause a relapsing fever? |
It expresses different VMP proteins (via homologous recombination) to avoid destruction by the host immune system |
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Competence (Definition) |
The ability to take up naked DNA from the environment |
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Examples of naturally competent bacteria |
Haemophilus influenzae
Streptococcus pneumoniae
Neisseria gonorrhoeae |
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DNA-uptake sequence (DUS) (Definition) |
DNA segments containing a specific sequence found frequently throughout the bacterium's genome, but rarely in other organisms |
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Examples of bacteria that only take up DNA-uptake sequences |
Neisseria gonorrhoeae
Haemophilus influenzae |
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Example of a bacterium that develops competence in response to quorum singaling |
Streptococcus pneumoniae |
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Example of a bacterium that can be induced to a state of artificial competence by chemical treatment |
E. coli |
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What are the implications of natural competence in bacteria? |
Spread of antibiotic resistance
Increased genetic variation
Increased virulence
Acquisition of beneficial genes
Increase in host range |
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Plasmid (Defintion) |
Extrachromosomal DNA or episomes |
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What is the structure of a plasmid? |
Circular or linear |
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Plasmids are generally a metabolic ____ on bacteria (Why?) |
Drain
The bacterium has to spend energy to replicate the plasmid |
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How do plasmids confer selective advantage to bacteria? |
By encoding:
Essential proteins
R-factors (confer antibiotic resistance)
Antibiotics (kills off competing bacteria)
Specialized catabolic enzymes (allows use of nutrients that cannot be used by other bacteria)
Virulence determinants (allows survival in hosts) |
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Conjugation (Definition) |
Plasmid transfer from donor ("male") cell into recipient ("female") cell |
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What is the origin of the conjugative bridge used to transfer plasmids between bacteria? |
It is encoded by the plasmid itself |
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Conjugation can occur between... |
Bacteria of the same species
Bacteria of different species
Bacteria and eukaryotic cells |
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How is a plasmid transferred from one cell to another? |
A single strand of plasmid DNA is replicated in the donor and crosses over to the recipient, where the complementary strand is synthesized |
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Once a plasmid has been transferred to the recipient bacterium, where does it end up? |
It may remain separate or be integrated into the bacterial genome |
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Once integrated into a bacterial chromosome, is a plasmid stuck there? |
No, it may later be excised from the chromosome, and it might even carry some adjacent chromosomal sequences (Hfr = high frequency recombination) with it |
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Bacteriophage (Definition) |
A bacterial virus |
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How does a bacteriophage recognize the appropriate host? |
By interacting with a specific bacterial surface component |
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What are the two types of bacteriophages? |
Lytic phage
Lysogenic phage |
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Lytic phage (Definition) |
A bacteriophage that produces multiple copies of itself, then lyses the bacterial cell |
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Lysogenic (temperate) phage (Definition) |
A bacteriophage that replicates along with the host cell, but does not kill the cell |
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What are the two types of lysogenic bacteriophages? |
Integrant
Episome (plasmid-like) |
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Example of a bacteriophage and its host |
Bacteriophage: λ
Host: E. coli |
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Is λ a lytic phage or a lysogenic phage? |
It can be either |
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For λ, what triggers a transition from lysogenic to lytic? |
Stress |
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What is a prophage? |
A bacteriophage genome inserted into the circular bacterial DNA chromosome |
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Examples of genes encoding for virulence properties that are carried by bacteriophages |
Cholera toxin of Vibrio cholerae
Shiga-like toxins of E. coli
Erythrogenic toxin of Group A Streptococci (GAS) |
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Shiga-like toxins of E. coli cause... |
Hemorrhagic colitis
Infant diarrhea |
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Transduction (Definition) |
The exchange of DNA between bacteria via bacteriophage particles |
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Transposable elements (Definition) |
Sequences of DNA that move from one location in the genome to another |
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Features of bacterial transposable elements: |
1) Defined ends with inverted terminal repeats
2) Encode an element-specific transposase (an enzyme that mediates transposition)
3) Can cause mutations and mediate genetic rearrangements
4) Generate a direct repeat in target DNA |
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Difference between an insertion sequence (IS) and a transposon |
An insertion sequence contains only genes for transposition, while a transposon also contains other genes (e.g. for resistance to antimicrobial agents) |
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Where might a bacterial transposon end up after it removes itself from the bacterial chromosome? |
Another location within the chromosome, within a plasmid, etc. |
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What is unique about Mu? |
It is both a bacteriophage and a transposon |
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What bacterium does Mu infect? |
E. coli |
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Is Mu lytic or lysogenic? |
Can be either |
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How and where is the Mu DNA integrated into the E. coli chromosome? |
Integrates via transposition mechanism at random sites (not site-specific) |
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How is a conjugative transposon like a "normal" transposon? |
Inverted repeats at both ends
Encodes enzymes needed for transposition
Can carry antibody resistance genes |
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How is a conjugative transposon unlike a "normal" transposon? |
Can transfer itself between cells
Utilizes a different mechanism of transposition
Does not generate direct repeat upon integration |
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What often promotes transposition? |
Stresses to bacteria |
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Example of a stressor that may cause transposition |
Antibiotics |
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How can antibiotic use promote spread of antibiotic resistance? |
By stressing bacteria, leading to transposition of antibiotic resistance genes |
