Chapter 11- Mechanisms of microbial genetics Flashcards
1
Q
Functions of DNA (2)
A
- 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
2
Q
Gene expression
A
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
3
Q
Central dogma
A
The flow of genetic information from DNA to RNA to protein. This describes the mechanism of the “one gene-one enzyme” hypothesis
4
Q
Semiconservative replication
A
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
5
Q
Meselson and Stahl’s experiment
A
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
6
Q
3 types of DNA polymerase (DNA pol) in bacteria
A
- DNA pol 1
- DNA pol 2
- DNA pol 3
7
Q
DNA polymerase function in bacteria
A
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
8
Q
In which direction are deoxyribonucleotides added during DNA replication?
A
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
9
Q
Initiation of replication
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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
10
Q
Supercoiled
A
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
11
Q
Topoisomerase 2/DNA gyrase
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Relax the supercoiled chromosome so that DNA replication to begin
12
Q
Helicase
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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
13
Q
Replication forks
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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
14
Q
Single stranded binding proteins
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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.
15
Q
Primer
A
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
16
Q
RNA primase
A
A polymerase that synthesizes the RNA primer used in DNA replication. These enzymes do not require a free 3’ hydroxyl group
17
Q
Elongation in DNA replication
A
Nucleotides are added at a rate of 1000 nucleotides per second.
18
Q
Leading strand
A
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’
19
Q
Lagging strand
A
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’
20
Q
Okazaki fragments
A
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
21
Q
Sliding clamp
A
A ring shaped protein that binds to DNA and holds the DNA polymerase 3 in place as it adds nucleotides
22
Q
Topoisomerase 2 (DNA gyrase)
A
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
23
Q
Exonuclease
A
DNA polymerase 1 removes the RNA primers during elongation
24
Q
DNA ligase
A
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
25
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
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DNA polymerase 1
Exonuclease activity removes the RNA primer and replaces it with newly synthesized DNA
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DNA polymerase 3
Main enzyme that adds nucleotides in the 5' to 3' direction
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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
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DNA polymerase delta
A eukaryotic polymerase that continuously synthesizes the leading strand during DNA replication
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DNA polymerase epsilon
A eukaryotic polymerase that synthesizes the lagging strand during DNA replication
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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
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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
33
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
34
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
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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
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Transcription
The information encoded in DNA is transcribed into a strand of RNA (an RNA transcript).
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Transcription bubble
The unwound region of the DNA helix that forms in the region of RNA synthesis during transcription.
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Antisense strand
The strand of DNA that acts as a template during transcription
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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
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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
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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.
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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.
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Promoter
A DNA sequences onto which the transcription machinery binds and initiates transcription. They are usually upstream of the genes they regulate.
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What is the initiation site of transcription?
The DNA nucleotide pair that corresponds to the site where the first 5' RNA nucleotide is transcribed
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Upstream vs downstream nucleotides in transcription
Nucleotides preceding the initiation site are designated “upstream,” whereas nucleotides following the initiation site are called “downstream”
nucleotides.
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Initiation of transcription
Begins at a promoter. The transcription machinery binds to the promoter and initiates transcription
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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
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What direction are nucleotides added during transcription?
RNA is synthesized complementary to the template DNA strand in a 5' to 3' direction
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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
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Eukaryotic polymerases used for transcription (3)
RNA polymerase 1, 2, and 3. Each enzyme transcribes a different subset of genes
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Polycistronic
mRNA that codes for multiple polypeptides. The mRNA of bacteria and archaea is polycistronic, but it is monocistronic in eukaryotes
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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
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Primary transcript
The RNA molecules directly synthesized by RNA polymerase
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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
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Exons
Polypeptide coding sequences. After introns are removed, exons are joined together so they can code for a functional polypeptide
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Introns
Intervening polypeptide sequences. Introns are removed from the RNA sequence during processing. Their functions may include gene regulation and mRNA transport
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RNA splicing
The process of removing intron-encoded RNA sequences and reconnection the sequences encoded by exons
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Spliceosome
Facilitates RNA splicing
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Alternative splicing
Introns can be spliced out differently, which results in different exons being included or excluded from the final mRNA product. An advantage of this process is that different types of mRNA transcripts can be generated when they are all derived from the same DNA sequence
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Translation
Protein synthesis, involves decoding an mRNA message into a polypeptide product by a ribosome
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Codon
A triplet of nucleotide that codes for an amino acid
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Genetic code
The relationship between an mRNA codon and its corresponding amino acid
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Degeneracy
The redundancy in the genetic code that occurs because a given amino acid is encoded by more than one codon
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Wobble position
The third position in the codon, which is less critical than the first two positions. In some cases, the same amino acid is still used if the nucleotide in the third position is changed
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Stop/nonsense codons
The 3 codons that stop protein synthesis: UAA, UAG, and UGA
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Start codon
AUG (methionine), the codon that initiates translation
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Reading frame
They way nucleotides in mRNA are grouped into codons. It is set by the AUG start codon near the 5' end of the mRNA
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Ribosomes
Macromolecules made of rRNAs and polypeptides. Prokaryotes, mitochondria, and chloroplasts have 70s ribosomes, while eukaryotes have 80s ribosomes in the cytoplasm.
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Small and large subunits in ribosomes
Ribosomes dissociate into large and small subunits when they are not synthesizing proteins and reassociate during the initiation of translation. The small subunit binds the mRNA template and the large subunit binds tRNAs. Eukaryote ribosomes have a small 40s subunit and a large 60s subunit
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Polyribosome
The complete structure containing an mRNA with multiple associated ribosomes. Each mRNA molecule is simultaneously read by multiple ribosomes reading the mRNA in the 5' to 3' direction
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Why can transcription and translation occur simultaneously in bacteria?
Both processes occur in the same 5' to 3' direction, they both occur in the cytoplasm of the cell, and the RNA transcript does not need to processed once it's transcribed. This means that prokaryotes can adapt to the environment by making new proteins very quickly
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tRNA
Structural TNA molecules. There are many different types of tRNAs in the cytoplasm, bacteria have 60-90 types. tRNA molecules bind to specific codons on the mRNA molecule and adds the corresponding amino acid to the polypeptide chain.
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Mature tRNA structure
tRNA has a 3D structure, because complementary bases in the single stranded RNA molecule bond with each other. The amino acid binding site (CCA amino acid binding end) is located at the 3' end of tRNA. The anticodon is at the other end of the molecule
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Anticodon
A 3 nucleotide sequence on the tRNA molecule that binds to an mRNA codon through complementary base pairing
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How are amino acids added to the end of a tRNA molecule?
They are added to the molecule through tRNA charging. Each tRNA molecule is linked to its correct (cognate) amino acid by a group of enzymes called aminoacyl tRNA synthetases. During this process, the amino acid is first activated by the addition of adenosine monophosphate (AMP) and then transferred to the tRNA
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Charged tRNA
A tRNA molecule that is bound to an amino acid
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N terminus
The beginning of the polypeptide chain
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Initiation of protein synthesis
Begins with the formation of an initiation complex. This includes the small ribosome, the mRNA template, 3 initiation factors that help the ribosome assembly correctly, and GTP which acts as an energy source. The initiator tRNA interacts with the start codon AUG of mRNA and carries a formylated methionine (fMet), which is inserted into the N terminus. The Shine-Dalgarno sequence interacts through complementary base pairing with the rRNA molecules that compose the ribosome. This interacts anchors the small ribosomal subunit at the correct location on the mRNA template. The large ribosomal subunit binds to the initiation complex and forms an intact ribosome
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Shine-Dalgarno sequence
A leader sequence upstream of the first AUG codon in prokaryotic in mRNA
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What is the initiator tRNA in eukaryotes?
A different specialized tRNA carrying methionine called Met-tRNAi
81
Where does the eukaryotic initiation complex bind to the mRNA?
The eukaryotic initiation complex recognizes the 5' cap of the eukaryotic mRNA, and tracks along the mRNA in the 5' to 3' direction until the AUG start codon is recognized. At this point, the 60S subunit binds to the complex of Met-tRNAi, mRNA, and the 40S subunit.
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3 functionally important ribosomal sites
1. A (aminoacyl) site- binds the incoming charged aminoacyl tRNAs
2. P (peptidyl) site- binds charged tRNAs carrying amino acids that have formed peptide bonds with the polypeptide chain but haven't dissociated from their corresponding tRNA
3. E (exit) site- releases dissociated tRNAs so that they can be recharged with free amino acids
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Elongation of translation
Begins with a translocation event. During each one, the charged tRNAs enter at the A site, then shift to the P site, then to the E site where they are removed.
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Translocation event
Single-codon movements of the ribosome during elongation of translation. They are induced by conformational changes that advance the ribosome by 3 bases in the 3' direction. The process requires energy derived from GTP hydrolysis
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Peptidyl transferase
An RNA based ribozyme that catalyzes the formation of the peptide bonds between the amino group of the amino acid attached to the A site tRNA and the carbonyl group of the amino acid attached to the P site tRNA
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Termination of translation
Occurs when a nonsense codon (UAA, UAG, or UGA) is encountered and there is no complementary tRNA. The P site amino acid detaches from its tRNA and releases the new polypeptide
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Post-translational modifications of polypeptides (4)
1. Removal of translated signal sequences, which help with directing a protein to a specific area of the cell
2. Folding of the protein into a 3D structure, directed by chaperone proteins
3. Proteolytic processing of an inactive polypeptide to make it active
4. Chemical modifications like phosphorylation or methylation
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Mutation
A heritable change in the DNA sequence of an organism. The resulting organism is called a mutant. Mutations may lead to an altered phenotype
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Wild type
The phenotype that is most commonly observed in nature
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Point mutation
A mutation where one base is substituted or replaced by another base
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Insertion/deletion mutation
Mutations that result from the addition or removal of one or more bases
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Silent mutation
When a point mutation results in the same amino acid being used in the polypeptide. This occurs due to the degeneracy of the genetic code and has no affect on the protein's structure.
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Missense mutation
When a mutation causes a different amino acid to be used for the protein
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Conditional mutations
When the effects of missense mutations are only apparent under certain environmental conditions.
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Nonsense mutation
Converts a codon that encodes an amino acid into a stop codon. This stops translation and causes proteins that are shorter than normal
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Frameshift mutations
Caused by insertions or deletions of a number of nucleotides that are not a multiple of 3. This is problematic because it causes a shift in the reading frame, and can change every amino acid after the point of mutation. These proteins are usually nonfunctional
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Spontaneous mutations
Mistakes in the process of DNA replication. The error rate of DNA polymerase is one incorrect base per billion base pairs replicated.
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Mutagens
Various types of chemical agents or radiation that cause induced mutations. Mutagens are often also carcinogens
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Nucleoside analogs
Chemical mutagens that are structurally similar to normal nucleotide bases and can be incorporated into DNA during replication. They can induce mutations because they often have different base pairing rules than normal nucleotides
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Intercalating agents
Chemical mutagens that slide between the stacked nitrogenous bases of DNA. They distort the molecule and create atypical spacing between nucleotide base pairs. During DNA replication, DNA polymerase may skip replication several nucleotides or add several extra nucleotides. This can lead to a frameshift mutations. These agents are often also carcinogens
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Ionizing radiation
X-Rays and gamma rays. They cause single and double stranded breaks in the DNA backbone by forming hydroxyl radicals. Ionizing radiation can also modify bases
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Nonionizing radiation
UV light is an example- it is not strong enough to cause chemical changes. It can induce dimer formation between adjacent pyrimidine bases, commonly forming thymine dimers
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Thymine dimers
A mutation caused by UV light. Two adjacent thymines covalently bond. If left unrepaired, DNA replication and transcription are stalled at the point of mutation. DNA polymerase may proceed and then replicate the dimer incorrectly
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Proofreading
Most of the mistakes that occur during DNA replication are promptly corrected by most DNA polymerases through proofreading. The DNA polymerase reads the newly added base and makes sure that it is complementary to the corresponding base in the template strand before it adds the next base. If there is a mistake, the enzyme can cut away the nucleotide and add a new base
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Mismatch repair
This mechanism occurs after the replication machinery has moved. Enzymes recognize the mutation, excise the incorrect nucleotide, and replace it with the correct one
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Nucleotide excision repair
Also called dark repair, this is a mechanism to repair thymine dimers. Enzymes remove the pyrimidine dimer and replace it with the correct nucleotides. The segment of DNA is enzymatically removed and DNA polymerase replaces the missing nucleotides. DNA ligase seals the gap in the sugar-phosphate backbone
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Direct repair
Also called light repair, is a mechanism for repairing thymine dimers. Only occurs in visible light. An enzyme called photolyase recognizes the distortion in the DNA helix and binds to the dimer. In the presence of visible light, photolyase changes conformation and breaks apart the thymine dimer. Then, the thymines can correctly base pair with the adenines on the complementary strand
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Replica plating
A technique used to detect nutritional mutants (auxotrophs). A population of bacterial cells is mutagenized and then plated as individual cells on a complex nutritionally complete plate and grow into colonies. Cells are removed from the master and plate and pressed in the same orientation onto plates of various media. Some plates lack specific nutrients, which allows the researcher to discover the mutants that are unable to produce specific nutrients
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Auxotrophs
Nutritional mutants. They have a mutation in a gene encoding an enzyme in the biosynthesis pathway of a specific nutrient, such as an amino acid. As a result, whereas wild-type cells retain the ability to grow normally on a medium lacking the specific nutrient, auxotrophs are unable to grow on such a medium.
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Ames test
A method that uses bacteria for screening of the carcinogenic potential of new chemical compounds. It measures the mutation rate associated with exposure to the compound. If the mutation rate is elevated, it could indicate that the compound is associated with a greater cancer risk. The Ames test uses as the test organism a strain of
Salmonella typhimurium that is a histidine auxotroph, unable to synthesize its own histidine because of a mutation in an essential gene required for its synthesis. After exposure to a potential mutagen, these bacteria are plated onto a medium lacking histidine, and the number of mutants regaining the ability to synthesize histidine is recorded and compared with the number of such mutants that arise in the absence of the potential mutagen. Chemicals that are more mutagenic will bring about more mutants with restored histidine synthesis in the Ames test.
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Vertical gene transfer
The transmission of genetic information from generation to generation. This is the main mode of transmission in all cells.
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How does genetic diversity develop with sexually reproducing organisms?
Crossing-over events and independent assortment of individual chromosomes during meiosis contribute to genetic diversity in the population. During sexual reproduction, the gametes of the parents combine and produce new combinations of genotypes in the diploid offspring. Mutations also contribute to genetic diversity
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Horizontal gene transfer
The introduction of genetic material from one organism to another organism within the same generation. It allows distantly related species to share genes and influences their phenotypes. It is thought to occur more frequently in prokaryotes, which reproduce asexually
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Mechanisms of horizontal gene transfer (3)
1. Transformation- naked DNA is taken up from the environment
2. Transduction- genes are transferred between cells in a virus
3. Conjugation- use of a hollow tube called a conjugation pilus to transfer genes between cells
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Transformation
The prokaryotes takes up naked DNA from the environment. It is obtained from dead cells that have lysed and released their DNA. Bacteria can bind to DNA and transport it into their cytoplasm to make it single stranded, as double stranded DNA is typically destroyed by the cell as a defense against viral infection. The single strand of DNA can recombine into the bacterial genome
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Recombinant DNA
A molecule of DNA that contains fragments of DNA from different organisms
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How does transformation impact bacterial phenotype?
The bacterial cell can gain new phenotypic properties. For example, if a nonpathogenic bacterium takes up DNA for a toxin gene from a pathogen and then incorporates it into its
chromosome, it can become pathogenic too. However, this process is relatively inefficient
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Why is bacterial transformation important in nature?
It's important for gaining the genes encoding virulence factors and antibiotic resistance. Genes encoding resistance to antimicrobial compounds have been shown to be widespread in nature, even in environments not influenced by humans
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Transduction
When viruses (bacteriophages) infect bacteria and move short pieces of chromosomal DNA between bacteria. It can be generalized or specialized
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Generalized transduction
Any piece of chromosomal DNA may be transferred to a new host cell by accidental packaging of chromosomal DNA into a phage head during phage assembly
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Specialized transduction
A lysogenic prophage is excised from the bacterial chromosome, and it carries a piece of the bacterial chromosome on either side of its site of integration to the new host cell. The host gains different nucleotides and can gain new properties. This is called lysogenic conversion and can involve virulence genes
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Conjugation
DNA is directly transferred from one prokaryote to another by a conjugation pilus. A conjugation pilus brings the organisms into contact with each other
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F plasmid (fertility factor)
An E. coli plasmid that contains the genes encoding the ability to conjugate. The F-plasmid genes encode both the proteins composing the F pilus and those involved in rolling circle replication of the plasmid.
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F+ cells/donor cells
Cells containing the F plasmid that are capable of forming an F pilus
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F- cells/recipient cells
Cells that are lacking an F plasmid
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F pilus
The conjugation pilus of an F plasmid
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Conjugation of the F plasmid
The F pilus of an F+ cell comes into contact with an F- cell and retracts, which brings the envelopes of the 2 cells into contact. A cytoplasmic bridge forms between them at the site of the conjugation pilus. When rolling circle replication occurs in the F+ cell, a single stranded copy of the F plasmid crosses the cytoplasmic bridge into the F- cell. The F- cell synthesizes the complementary strand to make it double stranded. The F- cell becomes an F+ cell that is capable of making its own conjugation pilus
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Conjugation of F' and Hfr cells
The F plasmid can integrate into the bacterial chromosome through recombination between the plasmid and the chromosome. This forms an Hfr cell. The F plasmid can be imprecisely excised from the chromosome, producing an F' plasmid that carries some chromosomal DNA to the integration site. The DNA can be maintained as part of the F' plasmid or be recombined into the recipient cell's bacterial chromosome
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R plasmids
Plasmids with genes that encode proteins that make a bacterial cell resistant to a specific antibiotic. They also contain genes that control conjugation and transfer of the plasmid. R plasmids can transfer between cells of the same species and cells of different species
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Transposons
"Jumping genes"- molecules of DNA that include special inverted repeat sequences at their ends and a gene encoding the enzyme transposase. They allow for transposition. Some are replicative, but most move in a "cut and paste" fashion. They have the ability to introduce genetic diversity because they can move within a DNA molecule, from one DNA molecule to another, or from one cell to another. Movement within the same DNA molecule can alter phenotype by inactivating or activating a gene. They can also carry additional genes, like genes for antibiotic resistance
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Transposition
A process where the entire DNA sequence can be independently excised from one location in a DNA molecule and integrate into the DNA elsewhere. It can occur in prokaryotes or eukaryotes
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Structural vs regulatory genes
Structural genes encode products that serve as cellular structures or enzymes, while regulatory genes encode products that regulate gene expression
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Operon
A block in the genome where structural proteins with related functions are encoded together. They are found in bacteria and archaea. They are transcribed together under the control of a single promoter and form a polycistronic transcript. This is beneficial because all of the enzymes that encode the enzymes needed for a single reaction can be activated/inactivated together. Eukaryotic genes have clusters that are similar to operons, but operons are not found in eukaryotic cells
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Regulatory region
The region of the operon that includes DNA sequences that influence its own transcription. This region contains the promoter and the region surrounding the promoter that transcription factors bind to
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Transcription factors
Proteins encoded by regulatory genes. They influence the binding of RNA polymerase to the promoter and allows it progression to transcribe structural genes. Transcription factors bind to the region surrounding the promoter
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Repressor
A transcription factor that suppresses transcription of a gene in response to an external stimulus. It binds to a DNA sequence in the regulatory region called the operator. Repressor binding physically blocks RNA polymerase from transcribing structural genes.
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Operator
The region of the operon located between the RNA polymerase binding site of the promoter and the transcriptional start site of the first structural gene
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Activator
A transcription factor that increases the transcription of a gene in response to an external stimulus by facilitating RNA polymerase binding to the promoter
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Inducer
A small regulatory molecule that either activates or represses transcription by interacting with a repressor or an activator
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Constitutively expressed
Operons whose gene products are required consistently and whose expression is therefore unregulated. These operons can be transcribed and translated continuously so the cell has constant intermediate levels of protein products. They encode housekeeping functions like DNA replication and repair
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Repressible operons
When operons are controlled by the binding of repressors to operator regions, preventing the transcription of the structural genes. They typically encode the enzymes needed for a biosynthetic pathway, and are repressed when the product of the pathway begins to accumulate in the cell
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Inducible operons
Contain genes encoding enzymes involved in the metabolism of a specific substrate (like lactose). These enzymes are only required when that substrate is available, thus expression of the operons is typically induced only in the presence of the substrate
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Enzyme IIA
Allows bacteria to switch from using glucose to another substrate as an energy source. This is done when glucose is not available. Phosphorylated EIIA activates adenylyl
cyclase, an enzyme that converts some of the remaining ATP to cyclic AMP (cAMP), a cyclic derivative of AMP and important signaling molecule involved in glucose and energy metabolism in E. coli. As a result, cAMP levels begin to rise in the cell
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Catabolite activator protein
Also known as cAMP receptor protein. cAMP binds to CAP when glucose is scarce. The complex binds to the promoter region of the lac operon
