6.15 Pathogen Adaptation Flashcards
Features of the Bacterial chromosome
- Usually a single circular dsDNA of 5 million base pairs encoding for about 400 genes.
- Is tightly packaged in central irregular structure called the Nucleoid.
Features of Bacterial Plasmids
- Small usually circular extrachromosomal dsDNA elements
- Replicate independently and are usually dispensable
- Copy number ranges from 1 to 50 per chromosome.
- Can be transferred to same or different species of bacteria
- Can care antibiotic resistance or virulence factors
Do bacteria have a nucleus?
No they have a Nucleoid
Where does bacterial genome replication began?
OriC
How does the genome replicate?
Bidirectional and is semi-conservative
What does semi-conservative mean?
One template strand and one new strand leave replication together.
How many replication forks can occur at a time?
Many because the bacteria can open the ORI multiple times creating many replication forks during log-phase growth.
What does DNA gyrase do?
- It is a type 2-topoisomerase that relives positive super twisting of DNA, by cleaving rotates and anelles ends.
- Some antibiotics target gyrase
Where do sigma factors recognize?
Promoter site TATA boxes
What type of mRNA’s are prokaryotic cells?
Polycistonic (encodes several polypeptides on one mRNA)
What is the first codon for translation?
AUG
What tRNA is the initiator?
Formyl methionine (fMET)
What direction is the mRNA read?
5’ to 3’
What ribosome and subunits do bacteria use?
- 50s catalyzes peptide bond formation
- 30s decodes the mRNA
- 70s ribosome
What do prokaryotic mRNA missing in comparison to eukaryotic cells?
- No 5’ cap
- No poly A tail
- No introns
- No splicing
What does the P or Peptidyl site of the ribosome do?
Contains the growing peptide chain
What does the A or Aminoacyl site of the ribosome do?
Site accepts the incoming tRNA’s
Are prokaryotic transcription and translation separate or coupled?
Coupled
Will the lac operon operate in the presence of glucose?
No glucose is the easier energy molecule to use, thus the lac operon will only work when glucose is absent and lactose is present.
What molecule is produced when glucose is absent?
cAMP
What is negative control?
Negative control of an induce gene via repressor must not be attached for RNA production.
What is positive control?
Positive control of an induce gene via repressor must be attached for RNA productions.
What are regulons useful for?
Global regulation.
How are parental strands id in bacteria?
Mismatch repair id’s the parental strand of DNA as the methylated links.
What are physical agents that can damage DNA?
- Heat may result in deamination of nucleotides
- UV light may cause pyrimidine dimer formation
- Ionizing radiation may produce very reactive hydroxyl radicals that may be responsible for a ring of a base or causing single/double stranded breaks.
What is a Nucleotide based analogues?
lead to misparing and frequent DNA replication mistakes. For example incorporation of 5-bromouracil into DNA instead of thymidine allows base paring with guanine instead of adenine, changing T-A base pair to a G-C base pair.
What is a frameshift mutagen?
Such as polycyclic flat molecules like ethidium bromide or acridine derivatives, inset between the bases as they stake with each other in the double helix. The increase in spacing of successive base pairs cause the addition or deletion of a single base and lead to frequent mistakes during DNA replication
What is DNA-reactive chemicals?
Act directly on the DNA to change the chemical structure of the base. These include nitrous acid (HNO2) and alkylating agents, including nitrosoguanidine and ethyl methane sulfonate, which are known to add methyl or ethyl groups to the rings of the DNA bases. The modified bases may pair abnormally or not at all. The damage may also cause the removal of the base from the DNA backbone.
What is a cause of a frameshift mutation?
They are due to insertions or deli tons.
What are two methods of repair that can occur to DNA?
- Excision repair (cut it out)
- Can be done via recombination repair.
If a mutation occurs in a haploid cell how evident will it be?
It will be immediately evident
What are some examples of mutations in bacteria?
- They can change binding sites
- Can change porens via number size etc, thus antibiotics can not enter cell
- Increase or decrease effectiveness of virulence factor.
- If the mutation is advantageous it will dominate.
What is recombination?
- Occurs when nucleic acid from two different sources are combined to produce a new nucleotide sequence.
- Requires two crossover events.
What are the two types of recombination?
1) Homologous recombination: requires large segments of sequence identity and is controlled by the rec genes in E. coli
2) Site specific recombination: Requires recognition of unique DNA sequences and specific enzymes
What is a Transposon?
- Segments of DNA that may jump within or between chromosomes or plasmids.
- Can carry antibiotic resistance, virulence factors, or metabolism.
Can transposition affect other genes?
Yes, if they insert into a gene they can cause a termination sequence of that gene.
What is conservative transposition?
It is when the transposon is not altered during the move
What is a pathogenicity island?
Blocks of contiguous genes found in a bacterial chromosome or plasmid that encodes for virulence, may contain more than one virulence factor.
What is Programmed rearrangements?
- Moving of DNA segment via homologous recombination in a sequential repeated programed manner; is useful for antigenic variation and phase variation.
- Example of antigenic variation, Neisseria gonorrhoeae uses antigenic variation for its pilin gene to avoid antibodies.
What are two example of phase variation by promoter inversion?
- E. coli uses phase variation to turn on/off expression of type 1 fimbriae
- Samonella uses phase variation to switch between type A/B flagella
What is bacterial conjugation?
Transfer of plasmids or genomic material from one bacteria to another via sex pills.
What are the steps of bacterial conjugation between F+ bacteria and F- bacteria?
- F plasmid in the F+ cell contain genes for sex pills and conjugation tube for transferring the plasmid to an F- cell.
1) F+ cell produces hair like appendages called sex pili, which facilitates cell to cell contact with F- stain by forming a conjugation tube. The formation of the sex pili is governed by genes of F factor.
2) Replication of F Factor
3) Transfer of replicated F plasmid to the recipient cell via sex pili
4) Sex pili dissolved, now both bacterial cells are F+
What is transduction?
Process of DNA transfer via a bacteriophage
-Virulent phages are always lytic
What is generalized transduction?
When random pieces of cellular DNA are packaged into viral particles during a lytic cycle.
What is Specialized transdution?
It is due to the integration of phage into cellular DNA at specific sites, and then when induced, adjacent cellular DNA also gets excised and packaged into viral particles.
What is a Prophage?
A bacteriophage genome inserted into bacterial DNA and then genome is transcribed with bacteriophage genome.
What is transformation?
Uptake of completely pure DNA from external environment?
What does it mean if the bacteria is competent?
It means it can take up DNA/RNA from the environment.
What is an Operon?
One unit of transcription; contains promoter, operator, cisterns and terminator
What is Cistron?
A segment of DNA encoding a polypeptide
What is a promoter?
Site where RNA polymerase binds to initiate transcription
What is a Operator?
Site near the promoter where regulator protein or transcription factor binds.
What is a terminator?
A segment of DNA that signals the end of transcription
What is a repressor?
A protein that binds the operator and blocks transcription; may be enhanced by a co-repressor or inhibited by inducer.
What is a activator?
A protein that binds the operator and is required for transcription; may be activated by an inducer or inhabited by inhibitor.
What is a regulon?
A group of operons under the control of the common regulator.
Define Wild type allele
Normal, usually active, form of the gene.
Define mutant allele
Mutated usually inactive form of a gene
What is a point mutation?
A mutation that involves only a single base
What is a silent mutation
A base substitution that does not affect the resulting proteins amino acid sequence.
What is a missense mutation?
A base substitution that results in a different amino acid to be inserted.
What is a nonsense mutation?
A base substitution that results in a termination codon so protein synthesis stops prematurely.
What is an insertion?
Additional base at a single site
What is a deletion?
Removal of a single base at a single site.
What is a frameshift mutation?
Mutations that result in a change in the reading frame used by the translating ribosome.
