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What is the relationship between DNA, Chromosomes, and Genes?
Chromosomes are made up of DNA. A gene is a segment of DNA
A bacterial cell only has 1 chromosome (may have multiple plasmids) and many genes
Why is a gene so important?
A gene is a blueprint for a protein
-its information is encoded in it's base sequence
How many genes does E.Coli, humans, and HIV have? Who has the most?
E.coli: about 20,000 genes
Human: about 4,400 genes
HIV: 9 genes
*E.coli has the most, but what the gene is coded for can make a big difference in what it does (like HIV)
What is the typical structure of a deoxyribonucleotide?
Contains a sugar (deoxyribose), phosphate, and nitrogenous base (A,T,C,G)
How are the nucleotides in 1 strand of DNA connected to one another?
- They are connected by a sugar/phosphate backbone. There are also covalent bonds between the base pairs
What is the structure of DNA? What are the importance of the double helix and base pairs?
DNA is in a double helix (2 polydeoxyribonucleotide chains)
sugar/phosphate backbone connected by base pairs. These code the gene for it's job
What is a genome and why is it important?
- A genome is an organism's complete set of genes
- *if we know the MO's genome, we know it's capabilities
When is DNA replicated?
- DNA must be replicated before the MO...
How is DNA replicated?
- 1. It begins at the origin (designated spot on the chromosome or plasmid where replication enzymes first attach)
- 2. The helicase unzips the double helix (DNA gyrase goes before to prevent kinking and tangling of DNA)
- 3. A replication fork is created as the DNA polymerase matches each parental strand to its deoxyribosenucelotides. This creates daughter DNA molecules attached to the parental strand
- 4. At the spot of termination the replicated DNA separates
What are the responsibilities of these enzymes: Helicase, DNA polymerase, DNA gyrase?
- Helicase: unzips the DNA
- DNA Polymerase: Matches parental strand with matching base pairs to form a parental/daughter strand match of deoxyribonucleotides
- DNA Gyrase: goes before helicase to prevent kinking and tangling of strands
If translation and transcription are like a factory, what are the products and the parts?
Products: various protein molecules
Parts: amino acids (20 kinds)
If translation and transcription are like a factory, what are the assemblers and the "gofers"?
Assemblers: ribosomes -connect amino acids together in the correct sequence
Gofers: tRNA molecules--transfer amino acids to the ribosomes (10 diff aas means 20 diff tRNAs)
If translation and transcription are like a factory, what are the blueprints and the transcripts?
Blueprints: Genes- 1 gene for each protein the bacteria can make. Genes are the DNA sequences on chromosomes or plasmids
Transcripts: mRNA molecules- cells make mRNAs using genes as templates (mRNAs are "disposable")
What is transcription and what is it's purpose?
Transcription: the phenomenon of using genes as templates to make RNA (RNA nucleotides match up with the DNA template strand nucleotides)
RNA molecules can be tRNA molecules, rRNA molecules, or mRNA molecules (most are mRNA) which are important players in creating proteins
What is the process of transcription?
RNA polymerase attaches at the promotor sequence of the gene (DNA template)
RNA Polymerase matches ribonucleotides to the deoxyribonucelotides according to their base pairing rules
- Termination: When the RNA polymerase reaches this sequence on the gene of the DNA template, it detaches from the gene
What is the purpose of the promoter template strand, RNA polymerase, and the terminator?
Promoter template: where the RNA polymerase attaches and transcription begins
Template Strand: DNA strand used to create RNA
RNA polymerase: matches base pairs of ribonucleotides to the base pairs of the DNA template strand
Terminator: Gene on template strand causing the RNA polymerase to detach and transcription to stop
What is the DNA base pairing rule?
*bonded in a covalent bond
What is the RNA base pairing rule?
*left is base DNA Strand, right is the RNA strand
What is one big difference between RNA and DNA?
RNA have Ribonucleotides containing ribose while DNA have deoxyribonucleotides which contain deoxyribose
What is translation?
- When ribosomes, mRNA molecules, tRNA molecules, and amino acids interact to
- -synthesize proteins!
What is the process of translation?
1. A ribosomal unit attaches to the mRNA at the start codon
2. tRNA carrying the first amino acid enters the ribosome (at the P site) and it's anticodon base pairs are matched the the codon on the mRNA
3. The ribosome moves along the mRNA and another tRNA enters the A site. The amino acid at the top of the tRNA is attached to the previous one with a peptide bond
4. As the ribosome moves along, another tRNA enters and the first tRNA is now in the E site. Pairs are based and amino acids attach
5. The first tRNA is released from the ribosome as another one enters, but the amino acids are attached. As this process continues, a polypeptide chain (protein!) is created.
- 6. Once the ribosome reaches the stop codon, the polypeptide chain is released. The ribosome detaches and the last tRNA is released
What is a codon and an anti-codon?
Codon: base pairs on RNA split into threes where the tRNA will attach the anti-codon
Anti-Codon: base pairs attached to the bottom of a tRNA molecule
How do you know what amino acids go with the codon?
The Genetic code chart
How does a mutation happen? Is it a "rare event"?
- Mutation: any change in a gene's sequence
- *is a random event
- DNA polymerase makes a mistake about one in every billion base pairs replicated
- -doesn't sound like a lot, but when this is done millions of times it leads to a lot of mutations!!
- -not as rare as it seems
What are the two different types of mutations?
- Base substitution: one base is simply replaced with an incorrect one
- -may make the gene work better, worse, or have no effect
- Frame shift: one or more base pairs are either added or deleted from the gene.
- -This can happen anywhere along the gene and completed changes the blueprint
What is a mutagen?
- Mutation generators
- -may increase mutation rate tens of thousands of times
- *gamma radiation, certain chemicals, cigarette smoke
What is the difference between vertical and horizontal gene transfer?
parent to offspring (replication included)
- horizontal: transformation, conjugation, transduction
- -no reproduction needed (no parents/daughter cells)
What is transformation?
When genes on a chromosome or plasmid are taken from a dead cell and utilized by a live cell
How does transformation take place?
1. The recipient cell must have the correct mechanisms to import the DNA from the dead cell
2. Once inside, the new DNA aligns itself with the base pairs on the cells chromosome or plasmid
3. Recombination occurs between new DNA and the original DNA. This creates a new gene sequence
- 4. The unused DNA from the dead cell is degraded
What are some MO that can complete transformation?
Bacillus, Streptococcus, and Staphylococcus can do this naturally
E.coli can be artificially transformed in a lab (useful for producing human insulin!)
What is the significance of transformation?
- transformation allows cells to evolve.
- -Griffith found this with cells that were not encapsulated becoming encapsulated and therefore more pathogenic!
What is conjugation?
- Gene transfer between two live cells
- -required direct cell contact
- -uses conjugation pilus/bridge
* conjugation is considered the most common and efficient mode of gene transfer among gram-negative bacteria
What is the process of conjugation?
1. An E. coli cell with the f factor (F+) forms a conjugal junction with a cell without the f factor (F-)
- 2. The F+ cell replicated and transfers the F factor plasmid to the F- cell, making it an F+ cell
- -F factor only gives the ability to build a conjugal junction
3. Recombination between the cell's chromosome and the F factor occurs in the F+ cell at a specific site where base pairs match. This cell is now called an Hfr cell (high frequency recombination)
4. The Hfr cell functions like an F+ cell and can grow a conjugal junction to an F- cell. This time, a fragment of chromosome is replicated and imported into the F- cell.
- 5. This new DNA is recombined in the F- cell's chromosome creating a recombinant F- cell
What is the significance of conjugation?
The new Recombinant F- cell may now have important capabilities that it did not have before
Happens frequently and can cause fast evolution of the bacteria population
What is the significance of plasmids?
- Plasmids are little rings of DNA that are separate from the chromosome and are not necessary for the cells survival
- -HOWEVER it can give them special traits
- -easy to transfer between cells
How are plasmids categorized?
Plasmids are categorized by the types of genes they carry
What are some different types of plasmids?
Conjugative plasmids: like the F factor, they carry genes coding for protein that carry out the jobs of plasmid replication and transfer via conjugation
R Factors: carry genes for proteins that confer resistance to particular drugs, also carry conjugative genes
Virulence Plasmids: e.g. code for C. tetani neurotoxin, V. cholerae enterotoxin, B. anthracis toxins and capsule, E. coli fimbrae
What factors can lead to rapid evolution of bacterial populations?
- A "low mutation rate" actually leads to millions of mutations
- -some may make the cell work better
- -->those that work better may have a shorter generation time
- *this leads to a large population in a short period of time
- ---->some may have gene transfer mechanisms as mutation continues
- **all of this leads to even more bacterial evolution at a very quick rate