61 Questions
What is the typical length of a bacterial gene?
1 kb
Which type of DNA transfer is mediated by a virus that targets bacteria?
Transduction
What is the main function of plasmids in prokaryotic genomes?
Contain genes for antibiotic resistance
What phenomenon can introduce new functions to prokaryotic genomes?
Horizontal gene transfer
What term is used for regions of the genome with signs of horizontal transfer?
Genomic islands
What is the primary method by which genetic information can be transferred from the environment to bacteria?
Natural transformation
In which type of genomes have microbial genomes undergone extensive gene loss and gain?
Prokaryotic genomes
What is the number of loops into which the nucleoid forms chromosomes called?
~50 loops
What is the primary factor contributing to the malleability of prokaryotic genomes?
Gene transfer processes
What is the range of bacterial and archaeal chromosome size in kilobase pairs (kb)?
490 to 9,400 kb
What is the nature of all microbial genomes, as revealed by bioinformatic studies?
Mosaic
When was the first bacterial genome sequenced?
1995
What is the term for the entire genetic complement of DNA in a cell?
Genome
What is the range of genome size (in Mb) for bacteria?
0.12-9.4 Mb
What is the number of genes in bacterial and archaeal chromosomes?
120-8000
When comparing eukaryotic and bacterial genomes, what is a significant difference in chromosome size range?
Bacterial and archaeal chromosomes are smaller than eukaryotic chromosomes
What was the publication where the microbial genome variability is mentioned?
Welch, et al. 2002, PNAS, 99:17020
What experiment led to the discovery of transformation?
$\alpha$-hemolysis experiment
'Genes and operons' were distinguished based on what criteria?
Function and location
'Monophyletic vs polyphyletic ancestries for bacteria' refers to what aspect of bacterial evolution?
'Monophyletic' represents single ancestral lineage while 'polyphyletic' represents multiple ancestral lineages
Which process involves the uptake of DNA directly from the environment?
Natural transformation
What is the process called when bacteriophages carry host DNA from one cell that has been infected to another cell?
Transduction
Which protein complex at the cell surface takes up foreign DNA during natural transformation?
Competence protein complexes
What physiological state of cells greatly affects competence during natural transformation?
Early log phase growth
What is the process called that involves the transfer of DNA from one bacterium to another following cell-to-cell contact?
Conjugation
What process allows some bacteria to transfer genes across biological domains, such as Agrobacterium tumefaciens transferring genes to plant cells?
Conjugation
Which type of recombination requires a short 10-20bp sequence recognized by a recombination enzyme (recombinase)?
Site-specific recombination
What is the fate of plasmids entering the cell?
They coexist and replicate in the cell as extrachromosomal DNA
What protein machine unwinds donor DNA during recombination?
RecBCD
Which process involves viruses that attack bacteria and carry host DNA from an infected cell to another cell?
Transduction
What is the function of restriction endonucleases in the restriction and modification system?
Cut foreign DNA at specific sequences
In the restriction/modification system, what is the role of protective methylation?
Destroy foreign DNA without native DNA methylation pattern
What is the function of CRISPR in bacterial defense against viral DNA?
Cuts up invading viral DNA and inserts pieces into the bacterial genome
What happens to spacers in the CRISPR system after they are transcribed?
They are used by the Cas9 enzyme to monitor complementary DNA sequences
What is the main function of restriction and modification system in bacteria?
Defend against transferred DNA
How does the restriction/modification system protect host DNA from alien DNA?
By adding methyl groups to host DNA
What is the role of Cas9 enzyme in the CRISPR system?
Uses transcribed spacers to monitor and degrade matching sequences
How do bacteria defend against transferred DNA using CRISPR?
By cutting up invading viral DNA and inserting pieces into their own genome
What is the protective role of restriction endonucleases in bacteria?
Cut foreign DNA at specific sequences (restriction sites)
In the CRISPR system, what happens after spacers are transcribed?
They are used by Cas9 enzyme to monitor and degrade matching viral sequences
What is the function of RNase H in DNA replication?
Recognizes DNA/RNA heteroduplexes and removes the RNA primers
What is the primary role of DNA ligase in DNA replication?
Seals the junctions between Okazaki fragments
What is the function of topoisomerase IV in DNA replication?
Passes the chromosomes through one another at defined termination sites
What is the origin of replication in plasmids known as?
oriT (Origin of transfer)
In plasmids, what is a replicon dependent on?
Chromosomal genes, such as DNA polymerases
What is the term for the loss of plasmids if they no longer confer a benefit to the host cell?
Plasmid curing
Which system in plasmids pushes plasmids to opposite ends of the dividing cell?
Segregation system
What is the function of a toxin-antitoxin module in plasmids?
Self-maintenance of plasmids
What type of replication does rolling circle replication involve?
"Unidirectional" replication
'ParMRC' system is associated with which function in plasmids?
"Segregation"
What process allows some bacteria to transfer genes across biological domains?
Transformation
What is the role of Cas9 enzyme in the CRISPR system?
Targets and cleaves foreign DNA during bacterial defense mechanisms
What is the function of DNA helicase in bacterial DNA replication?
It unwinds the two strands of DNA
What is the role of DNA polymerase III in bacterial DNA replication?
It synthesizes new DNA strands
Why are RNA primers required for DNA replication?
To provide the 3’-OH group for DNA polymerase III to synthesize new DNA strands
What is the function of SSBs (single-stranded DNA binding proteins) in bacterial DNA replication?
To keep the single DNA strands apart during DNA synthesis
Which enzyme is responsible for producing RNA primers in bacterial DNA replication?
DNA primase
What evolutionary remnant is suggested by the fact that RNA was the first genetic material?
RNA primers
Which component recruits DNA polymerase III and tethers it to the DNA during bacterial DNA replication?
Clamp loader and sliding clamps
What is the main role of clamp loader and sliding clamps in bacterial DNA replication?
To recruit DNA polymerase III and tether it to the DNA
What is the function of clamp loader in bacterial DNA replication?
Recruits DNA polymerase III and tethers it to the DNA
Study Notes
Bacterial Genomes
- The typical length of a bacterial gene is not specified, but bacterial and archaeal chromosome sizes range from 0.5-12.2 megabase pairs (Mb).
- Bacterial genomes have undergone extensive gene loss and gain in microbial genomes.
DNA Transfer
- The primary method of genetic information transfer from the environment to bacteria is through natural transformation.
- Horizontal gene transfer can introduce new functions to prokaryotic genomes.
- Regions of the genome with signs of horizontal transfer are referred to as genomic islands.
- Transduction, mediated by a virus that targets bacteria, is a type of DNA transfer.
- Conjugation, which involves the transfer of DNA from one bacterium to another following cell-to-cell contact, is another type of DNA transfer.
- Some bacteria, such as Agrobacterium tumefaciens, can transfer genes across biological domains, such as to plant cells.
Genome Structure
- The nucleoid forms chromosomes into 4-10 loops.
- The genetic complement of DNA in a cell is referred to as the genome.
Plasmids
- The main function of plasmids in prokaryotic genomes is to provide additional genetic information.
- Plasmids can enter the cell through natural transformation.
- The fate of plasmids entering the cell is to replicate and be maintained.
- Some plasmids can transfer genes across biological domains.
Restriction and Modification System
- The restriction and modification system protects host DNA from alien DNA through the action of restriction endonucleases and protective methylation.
- The function of restriction endonucleases is to cleave foreign DNA.
- Protective methylation prevents the host DNA from being cleaved by restriction endonucleases.
CRISPR System
- The CRISPR system is a defense mechanism against viral DNA.
- CRISPR involves the transfer of spacers from the host genome to the CRISPR array, which are then transcribed and used to target viral DNA.
- The role of Cas9 enzyme is to cleave targeted viral DNA.
- The main function of the CRISPR system is to defend against viral DNA.
DNA Replication
- The function of RNase H is to remove RNA primers during DNA replication.
- The primary role of DNA ligase is to seal gaps between Okazaki fragments.
- The function of topoisomerase IV is to relax DNA supercoiling.
- The origin of replication in plasmids is known as the replicon.
- The function of DNA helicase is to unwind DNA during replication.
- The role of DNA polymerase III is to synthesize new DNA strands.
- RNA primers are required for DNA replication because DNA polymerase cannot initiate synthesis de novo.
- The function of SSBs is to protect single-stranded DNA during replication.
- The enzyme responsible for producing RNA primers is primase.
- The clamp loader and sliding clamps play a crucial role in recruiting DNA polymerase III and tethering it to the DNA during replication.
Test your knowledge of DNA replication with a focus on the lagging strand and Okazaki fragments. Explore the roles of DNA primase, DNA Polymerase III, RNase H, and DNA polymerase I in the process of completing DNA replication.
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