Chapter 11- Mechanisms of microbial genetics Flashcards
Functions of DNA (2)
- Passed from parent to offspring in the inheritance of genetic information
- Directs and regulates the construction of proteins necessary to a cell for growth and reproduction in a particular cellular environment
Gene expression
The processes of transcription and translation, which allow for the synthesis of a specific protein with the sequence of amino acids that is encoded in the gene
Central dogma
The flow of genetic information from DNA to RNA to protein. This describes the mechanism of the “one gene-one enzyme” hypothesis
Semiconservative replication
The two strands of the DNA double helix separate during replication. Each strand acts as a template to make a new complementary strand. Therefore, each double stranded DNA molecule includes one old strand and one new strand
Meselson and Stahl’s experiment
Demonstrated that the semiconservative model of DNA replication is correct. They cultured E. coli bacteria in one medium containing denser nitrogen 15 and another medium containing nitrogen 14. They then determined the density of the DNA containing each nitrogen isotope through centrifugation. After one generation of growth in N14, the density band of DNA was intermediate in position in between the DNA of cells grown exclusively in N15 or N14, suggesting a semiconservative model of replication
3 types of DNA polymerase (DNA pol) in bacteria
- DNA pol 1
- DNA pol 2
- DNA pol 3
DNA polymerase function in bacteria
DNA pol 3 is the enzyme required for DNA synthesis. DNA pol 1 and DNA pol 2 are primarily required for repair. DNA 3 adds deoxyribonucleotides that complementary to a nucleotide on the template strand. These enzymes require the hydrolysis of ATP by breaking the phosphate bonds in the molecule, so that they can get energy
In which direction are deoxyribonucleotides added during DNA replication?
Added to the 3’ hydroxyl group of the growing DNA chain, meaning that nucleotides are added in the 5’ to 3’ direction by DNA pol 3
Initiation of replication
Occurs at a specific nucleotide sequence called the origin of replication. This is where various proteins bind to begin the replication process. oriC is the origin of replication of E. coli
Supercoiled
DNA is wrapped and twisted around histones in eukaryotes and archaea, or histone-like proteins in bacteria. Enzymes called topoimerases change the shape and reduce the supercoiling of the chromosome for DNA replication to occur
Topoisomerase 2/DNA gyrase
Relax the supercoiled chromosome so that DNA replication to begin
Helicase
Separates the DNA strands by breaking the hydrogen bonds between the nitrogenous base pairs. AT sequences have fewer bonds and therefore have a weaker interaction
Replication forks
The Y shaped structures that are formed as DNA opens up. Two replication forks are formed at the origin of replication, which allows for bidirectional replication. This also forms a structure called a replication bubble
Single stranded binding proteins
Proteins that coat the DNA near each replication fork, preventing the single stranded DNA from rewinding into a double helix. It prevents hydrogen bonds from forming between the strands.
Primer
An RNA sequence that provides the free 3’ hydroxyl group that is needed for DNA pol 3 function. It is complementary to the parental DNA
RNA primase
A polymerase that synthesizes the RNA primer used in DNA replication. These enzymes do not require a free 3’ hydroxyl group
Elongation in DNA replication
Nucleotides are added at a rate of 1000 nucleotides per second.
Leading strand
The continuously synthesized strand of DNA. It is complementary to the 3’ to 5’ parental strand. It is synthesized toward the replication fork because polymerase can add nucleotides in this direction. The overall direction will be 5’ to 3’
Lagging strand
The strand that is complementary to the 5’ to 3’ parental DNA. It grows away from the replication fork. The polymerase must move back toward the replication fork to add the bases to a new primer, and then move away from the replication fork. This creates Okazaki fragments. The overall direction is 3’ to 5’
Okazaki fragments
Form in the lagging strand. The polymerase must move back toward the replication fork to add the bases to a new primer, and then move away from the replication fork. It moves away from the replication fork until it bumps into the previously synthesized strand and then it moves back again. This creates the Okazaki fragments, which are small DNA fragments that are separated by an RNA primer
Sliding clamp
A ring shaped protein that binds to DNA and holds the DNA polymerase 3 in place as it adds nucleotides
Topoisomerase 2 (DNA gyrase)
Proteins that reduce the supercoiling of DNA for replication to occur. They help relieve the stress on DNA when unwinding by causing breaks and then resealing them
Exonuclease
DNA polymerase 1 removes the RNA primers during elongation
DNA ligase
Seals the gaps that exist in the newly synthesized DNA due to removal of the RNA primer. It catalyzes the formation of covalent phosphodiester bonds between the 3’ hydroxyl end of one DNA Okazaki fragment and the 5’ phosphate end of the other fragment
Topoisomerase 4
Introduces single stranded breaks into chromosomes to release them from each other, then reseals the DNA. This prevents overwinding of the helix during replication
DNA polymerase 1
Exonuclease activity removes the RNA primer and replaces it with newly synthesized DNA
DNA polymerase 3
Main enzyme that adds nucleotides in the 5’ to 3’ direction
Prereplication complex
A complex composed of several proteins that forms at the origin of DNA replication in eukaryotic cells. It includes helicase, topoisomerase, single stranded binding protein, RNA primase, and DNA polymerase
DNA polymerase delta
A eukaryotic polymerase that continuously synthesizes the leading strand during DNA replication
DNA polymerase epsilon
A eukaryotic polymerase that synthesizes the lagging strand during DNA replication
Ribonuclease H
A eukaryotic enzyme that removes the RNA primer and replaces it with DNA nucleotides. This is not done by DNA polymerase in eukaryotes like it is in bacteria
Telomeres
The ends of linear chromosomes. In eukaryotic DNA replication, the replication fork reaches the end of the chromosome and there is nowhere to make a primer for the DNA fragment to be copies at the end of the chromosome. The ends will be unpaired and can become progressively shorter as the cells divide. Telomerases consist of noncoding repetitive sequences and protect coding sequences from being lost as the cell keep dividing
Telomerase
A eukaryotic enzyme that replicates the ends of chromosomes (telomeres). It attaches to the end of the chromosome and complementary bases to the RNA template are added to the 3’ end of the DNA strand. DNA polymerase is able to add nucleotides that are complementary to the telomeres once the 3’ end of the lagging strand is long enough
In humans, where are telomeres typically active?
They are usually active in germ cells and adult stem cells, but not active in adult somatic cells. They may be associated with the aging of somatic cells
Rolling circle replication
The replication process that is used to copy the bacterial chromosome and some plasmids, bacteriophages, and eukaryotic viruses. An enzyme nicks one strand of the chromosome at the double stranded origin site. In bacteria, DNA polymerase 3 binds to the 3’ hydroxyl group of the nicked strand and begins to replicate using the other strand as a template. It displaces the nicked strand during this process, and the strand is fully displaced by the time replication is completed. It can recircularize into a single stranded DNA molecule. Then, RNA primase synthesizes a primer to start DNA replication of this strand and make a double stranded DNA molecule
Transcription
The information encoded in DNA is transcribed into a strand of RNA (an RNA transcript).
Transcription bubble
The unwound region of the DNA helix that forms in the region of RNA synthesis during transcription.
Antisense strand
The strand of DNA that acts as a template during transcription
Sense strand
The DNA strand that is not used as a template during transcription. The new RNA strand is almost identical to this strand, except T is replaced with U nucleotides
RNA polymerase
Adds nucleotides to the 3’ hydroxyl group of the nucleotide chain being synthesized during transcription. RNA polymerase does not require a 3’ hydroxyl group and therefore does not require a primer
Sigma factor
The sixth polypeptide subunit of RNA polymerase in E. coli. It enables RNA polymerase to bind to a specific promoter that allows for the transcription of various genes.
How are nucleotides added without a primer during transcription?
During transcription, a ribonucleotide complementary to the DNA template strand is added to the growing RNA strand and a covalent phosphodiester bond is formed by dehydration synthesis between the new nucleotide and the last one added.
Promoter
A DNA sequences onto which the transcription machinery binds and initiates transcription. They are usually upstream of the genes they regulate.
What is the initiation site of transcription?
The DNA nucleotide pair that corresponds to the site where the first 5’ RNA nucleotide is transcribed
Upstream vs downstream nucleotides in transcription
Nucleotides preceding the initiation site are designated “upstream,” whereas nucleotides following the initiation site are called “downstream”
nucleotides.
Initiation of transcription
Begins at a promoter. The transcription machinery binds to the promoter and initiates transcription
Elongation in transcription
Begins when the sigma subunit dissociates from the polymerase. This means that the core polymerase enzyme can start synthesizing RNA complementary to the DNA template strand. DNA is unwound ahead of the enzyme and rewound behind it
What direction are nucleotides added during transcription?
RNA is synthesized complementary to the template DNA strand in a 5’ to 3’ direction
Termination of transcription
The polymerase dissociates from the DNA template and releases the new RNA. This occurs because the DNA template strand contains termination nucleotide sequences
Eukaryotic polymerases used for transcription (3)
RNA polymerase 1, 2, and 3. Each enzyme transcribes a different subset of genes
Polycistronic
mRNA that codes for multiple polypeptides. The mRNA of bacteria and archaea is polycistronic, but it is monocistronic in eukaryotes
What is the main difference between eukaryotes and prokaryotes in transcription?
Eukaryotes have a membrane bound nucleus, so it’s more difficult to use RNA for translation. mRNA has to leave the nucleus and be transported through the cytoplasm to get to the necessary organelles
Primary transcript
The RNA molecules directly synthesized by RNA polymerase
How is mRNA modified before it leaves the nucleus?
A special nucleotide called a 5’ cap is added to the 5’ end of the developing RNA molecule. It prevents degradation and helps the ribosomes to initiate translation. Then, 200 nucleotides are added to the 3’ end at the end of transcription, which is called the poly-A tail. It prevents degradation and signals to the cell that the transcript needs to enter the cytoplasm
Exons
Polypeptide coding sequences. After introns are removed, exons are joined together so they can code for a functional polypeptide
Introns
Intervening polypeptide sequences. Introns are removed from the RNA sequence during processing. Their functions may include gene regulation and mRNA transport
RNA splicing
The process of removing intron-encoded RNA sequences and reconnection the sequences encoded by exons