Term
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Definition
| specific sequence on DNA where transcription begins. it is always upstream of the unit of DNA to be transcribed. it may also be called the CONSENSUS SEQUENCE in bacteria. |
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Term
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Definition
| TTGACA-----------------TATAAT-------A. the "G" of TTGACA is roughly -35, while between the "T" and "A" in the middle of TATAAT lies -10. "A" at the end of this strand is the +1 transcription region. |
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Term
| factors determining promoter strength |
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Definition
| DISTANCE. the closer the consensus sequence, the stronger the promoter. farther away, the promoter is weaker. strength of promoter determines how often a gene is expressed. |
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Term
| RNA polymerase holoenzyme is made up of what 2 things? |
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Definition
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Term
| 2 types of termination in DNA replication |
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Definition
| rho-dependent and rho-independent |
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Term
| rho-dependent termination |
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Definition
| occurs when the rho factor binds to the mRNA, moving along just ahead of the RNA polymerase. when rho reaches the stem loop in the mRNA, rho's helicase unwinds the DNA-RNA complex and RNA polymerase is disassociated. TRANSCRIPTION ENDS. |
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Term
| rho-independent termination |
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Definition
| a stem loop structure forms in the RNA due to the structure of the basepairs. essentially, the bp are able to pair to one another on the same strand, forming a hairpin loop formation. just ahead of the stem loop is a large amount of uracil bases in the RNA strand. the RNA polymerase is destabilised by the uracil concentration and stem loop combination, and will fall off the RNA. TRANSCRIPTION ENDS. |
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Term
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Definition
| the message encoded by mRNA is translated into a protein |
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Term
| mRNA is translated 5' to 3', but the protein chain is translated... |
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Definition
| amino terminus (NH2) to carboxyl terminus (COOH). remember, mRNA is made up of nucleotides, but the protein is made up of amino acids! therefore, the 5' and 3' terminology does not apply to proteins. |
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Term
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Definition
| 1+ ribosomes binding to the (same) mRNA to begin translation. this way, several copies of the same protein can be made from the same mRNA strand more or less simultaneously. |
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Term
| 3 major requirements of translation |
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Definition
| 1) energy. 2) ribosomes. 3) "charged" tRNAs |
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Term
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Definition
| 70S ribosome composed of 50S and 30S subunits. |
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Term
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Definition
| composed of 23S rRNA, 5S rRNA, and about 34 proteins |
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Term
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Definition
| composed of 16S rRNA and about 16 proteins. |
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Term
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Definition
| 2 states: "charged" and "uncharged." charged tRNAs have amino acid bound to their 3' end, while uncharged tRNAs do not. charged tRNAs enter the ribosome complex, bringing amino acids to form the protein chains. |
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Term
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Definition
| AUG. first AUG in the sequence encodes for fmet (formyl-methionine). note that subsequent AUGs in the same strand encode for methionine. |
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Term
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Definition
| ribosome binding sequence. consensus sequence AGGAGG, 7-10 bp upstream of AUG on the mRNA. the 16S rRNA of 30S subunit binds to this sequence. in gram+, this sequence must be very strong. |
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Term
| initiation complex (translation) |
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Definition
| 30S + 50S subunits, mRNA, fmet, and tRNA |
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Term
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Definition
| 3 are recruited by 30S + 50S to the ribosome during translation |
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Term
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Definition
| the process by which proteins are made once initiation is complete. the ribosome attaches to the mRNA and tRNAs are recruited to it, pass through it, and deposit their amino acids along the growing protein chain. |
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Term
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Definition
- A site (aminoacyl): acceptor region, where charged tRNAs pass through first.
- P site (peptidyl): donor region, where amino acids from the tRNAs are added to the protein.
- E site (exit): uncharged tRNAs leave the ribosome.
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Term
| termination (translation) |
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Definition
| ribosome reaches the stop codon (UAG, UGA, or UAA). tRNAs leave the ribosome. 30S and 50S subunits disassociate from one another. the polypeptide (protein) detaches from the ribosome and mRNA. |
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Term
| what happens to a protein after synthesis? |
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Definition
| the protein can be folded into secondary, etc, shapes, either spontaneously (without help from other molecules) or with help from chaperone molecules. fmet is typically removed at this stage, and sugars or lipids can be added to the protein to form glycoproteins and lipoproteins, respectively. if the protein is needed outside of the cell (e.g., toxin or extracellular enzyme), it can enter the secretion pathway. |
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Term
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Definition
| a gene is always "on" (expressed). EXAMPLE: housekeeping genes |
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Term
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Definition
| the genes are only on when needed. EXAMPLE: genes that allow E. coli to process lactose when there is no glucose available; formation of spores. |
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Term
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Definition
| sequences upstream of genes and promoter regions, which can be bound by receptor proteins so they know to turn on the genes they control. |
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Term
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Definition
| a regulatory region (1) controlling 2 or more genes and their promoter region. operons are valuable in initiating swift responses to changing environments. instead of switching on several different promoters and their genes, an operon can switch on an entire suite of genes controlling many different trait expressions (e.g., in response to heat shock or when spore formation is required) |
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Term
| diauxic growth in E. coli |
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Definition
| an example of transcription initiation control. E. coli will naturally utilise glucose in the environment, and only switch on lactose utilisation after all the glucose in the environment as been used up. the glucose genes are constitutive, while the lactose genes are inducible. |
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Term
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Definition
| use of regulatory (activator) protein to bind to activation site in promoter region. promoter region is turned ON. |
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Term
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Definition
| a repressor protein binds to the operator sequence just downstream of the promoter region. transcription fails because RNA polymerase cannot pass the operator region; it will "fall off" the DNA strand once it reaches the operator + repressor. |
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Term
| 2 component phosphorelay system |
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Definition
| when a stimulus binds to the receptor on the cell surface (e.g., temperature), the sensor component inside the cell picks up the signal and becomes phosphorylated. the phosphorylated sensor transfers the signal into the cytoplasm, where the phosphate transfers to a response regulator. once phosphorylated, the response regulator becomes an active transcriptional regulator unit. it will bind to the appropriate gene(s)/operons and initiate translation of the protein(s) required for the response to the outside stimulus. |
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Term
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Definition
| a series of operons all controlled by the same regulatory proteins. example of regulatory proteins: sigma factors. |
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Term
| control of gene expression at enzyme level (3) |
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Definition
| affinity of enzyme for product; allosteric; covalent |
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Term
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Definition
| this is expressed as velocity over substrate concentration. as the substrate is increased, the velocity of the enzyme turning substrate into product is increased (up to a certain point). beyond a certain point, the product rate will plateau, because the enzyme is working as fast as it can regardless of how much substrate is present. |
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Term
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Definition
| the end product inhibits its own production by binding to the enzyme responsible and changing its 3D structure (thus inhibiting its ability to make the end product). end products bind to the allosteric site of the enzyme during allosteric regulation (NOT the active site). feedback inhibition refers to the end product binding to precursor enzymes earlier in the loop, while self inhibition refers to the end product binding to the intermediate enzyme directly responsible for its production. end products can also inhibit just themselves (in the case of 2 or more products being made) so that other products from the same enzyme loop can be made. |
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Term
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Definition
| the breakdown of larger molecules to create precursor metabolites (polymers > monomers > end products) |
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Term
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Definition
| use light and CO2 to create energy (photosynthesis). EXAMPLE: cyanobacteria |
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Term
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Definition
| require preformed organic compounds from other organisms (carbs, lipids, proteins, etc) |
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Term
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Definition
| use organic compounds as energy (carbon, electrons, protons). EXAMPLE: pathogens |
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Term
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Definition
| loss of electrons; energy is released. EXAMPLE: glycolysis |
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Term
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Definition
| gain of electrons; energy is used. EXAMPLE: photosynthesis |
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Term
| oxidant (oxidation agent) |
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Definition
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Term
| reductant (reducing agent) |
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Definition
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Term
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Definition
| sum total of all chemical reactions in an organism |
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Term
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Definition
| synthesis of large molecules from precursor metabolites (complex from simple); requires energy |
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Term
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Definition
| identified "transforming principle" (later known DNA) in S. pneumoniae through his experiments in live mice. he found that mice infected with heat-killed strains of S. pneumoniae did not die; but mice infected with heat-killed strains AND nonfatal strains would die. this was later revealed that the nonfatal strains were picking up genes needed for capsule formation from the remnants of the heat-killed strains. |
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Term
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Definition
| using griffith's data, they discovered that DNA carries genetic information. they found that, if DNA is degraded or damaged, it cannot be traded between bacteria and so virulence factors (like capsules) cannot be passed from one fatal strain to a nonfatal strain. |
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Term
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Definition
| tagged bacteriophages with 32p tags (for DNA) and 35s tags (for protein). following exposure and infection by these tagged phages, bacteria were found to have only the 32p tags inside of them. thus, they were able to deduce that DNA was passed between virus and bacteria, NOT protein. (s = sulfur, p = phosphate) |
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Term
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Definition
| discovered the helix structure of DNA in 1953 |
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Term
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Definition
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Term
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Definition
| supercoiled compact DNA, usually circular in bacteria |
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Term
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Definition
| extrachromosomal (not on chromosome) DNA in the cytoplasm |
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Term
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Definition
| deoxy/ribose + purine/pyramidine |
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Term
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Definition
| deoxy/ribose + purine/pyramidine + phosphate |
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Term
| how many H bonds between G-C? |
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Definition
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Term
| how many H bonds between A-T? |
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Definition
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Term
| what holds DNA strands together? |
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Definition
| phosphodiester backbone (with sugars) |
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Term
| 3 stages of DNA replication |
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Definition
| initiation, elongation, termination |
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Term
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Definition
- begins at oriC, a region on the DNA that is rich in A-T bonds.
- DnaA binds to oriC in order for replication to begin (replication WILL NOT BEGIN without DnaA).
- DnaB (helicase) attaches next, and begins to unwind the DNA at the DnaA-oriC complex.
- small single-stranded binding proteins keep the 2 DNA strands from re-annealing to one another.
- a topoisomerase called gyrase binds up- and downstream of the DnaA-oriC complex and begins making single stranded cuts along the DNA to relieve tension as the DNA is unwound.
- from gyrase to gyrase, the rapidly "unzipping" DNA forms the repliosome (replication bubble).
- after initiation has begun, oriC is methylated to prevent DnaA from binding again; this methylation is carried out by DAM methylase (DNA adenosin methylase).
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Term
| what controls initiation of DNA replication? |
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Definition
| intracellular concentration of DNA and how much ATP is readily available in the cell |
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Term
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Definition
| the replication bubble created during the initiation of replication |
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Term
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Definition
this is the period where new copies of DNA are created from the original chromosome.
- DNA polymerase I and III control elongation by adding nucleotides to the growing replication chains.
- RNA primase adds primers to the 3' end, which allows DNA pol 3 to begin laying down new nucleotides.
- all of this creates 2 strands in the repliosome (leading and lagging).
- the RNA primers are laid down 5'-3' and have okazaki fragments in between them.
- DNA pol 1 will remove the primers and fill in the gaps. this is done by using DNA ligase to link the okazaki fragments together to form a whole strand.
- just prior to termination, near the end of elongation, the newly synthesised strand(s) are proofed to remove and reduce errors in the genetic code.
- proofing is done in two ways: 1) highly specific base paring; 2) exonuclease activity by DNA pol 1 and 3 allows them to "back up" on the strand if they make a mistake and correct it immediately. if these 2 methods fail, then another DNA polymerase entirely will enter the scene and engage the mismatch repair system to fix replication errors in the DNA.
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Term
| rate of replication of DNA |
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Definition
| 1000 nucleotides per second |
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Term
| time it takes E. coli to replicate ____ base pairs |
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Definition
| ~40 minutes; 4.5 million bp |
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Term
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Definition
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Term
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Definition
| the continuous strand. DNA pol 3 extends the strand 5'-3' |
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Term
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Definition
| the discontinuous strand. RNA primers are laid down on this strand in the 5'-3' configuration, with okazaki fragments laid down in between. these primers are later removed by DNA pol 1 and ligase is used to add phosphodiester bonds and fill in the blanks between okazaki fragments. |
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Term
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Definition
| small fragments of nucleotides added in between RNA primers on the lagging strand of the repliosome |
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Term
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Definition
- 180 degrees from oriC, the two ends of the repliosome meet at the ter region of the chromosome.
- tus proteins combine at ter and halt replication.
- topoisomerase enters the scene, and makes double stranded cuts in the DNA to separate the 2 chromosomes. once separated, the topoisomerase repairs the cuts it made in each of the chromosomes.
- DAM methylase methylates the parent strand to protect it from restriction endonucleases and to signal to the cell that it should not proofread that chromosome.
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Term
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Definition
| repair new DNA strands; protect DNA from endonucleases so that the parent DNA will not be repaired. |
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Term
| restriction endonucleases (major functions) |
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Definition
| repair/digestion proteins that will digest and break down non-methylated DNA. they are useful to bacteria for DNA repair and as protection against viral DNA. |
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Term
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Definition
| "jumping genes". discovered in 1940s by barbara mcclintock during her work with multicoloured corn. transposons are able to transpose -- move from 1 location to another on the chromosome with help from transposase. they contribute to genetic diversity and may contain genes for antibiotic resistance in bacteria. |
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Term
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Definition
| breakdown of glucose for energy. glucose + 2 ADP + 2 Pi + 2 NAD -> 2 pyruvate + 2 NADH + 2 ATP |
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Term
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Definition
| replaces the first half of glycolysis for many anaerobic bacteria (pseudomonias spp.). glucose + 2 NADP + 2 ADP + Pi -> 2 pyruvate + 2 NADPH + ATP |
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Term
| pentose phosphate pathway |
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Definition
| generates ribose, NADPH for biosynthesis, and erythrose-4-phosphate for reducing power |
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Term
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Definition
| generates precursor metabolites: NADH, FADH, ATP, CO2. major source of macromolecules for the cell. some bugs perform partial krebs just to get those precursor metabolites. |
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Term
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Definition
| substrate level phosphorylation; fermentation; oxidative phosphorylation; respiration |
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Term
| substrate level phosphorylation |
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Definition
| an organic substrate is oxidised. the energy released by this oxidation is trapped to form a high-energy phosphate, P~. P~ is used to create ATP from ADP. |
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Term
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Definition
| anaerobic catabolism. glucose + 2 ADP + 2 Pi + 2 NAD [glycolysis] -> 2 pyruvate + 2 ATP + 2 NADH -> 2 lactic acid + 2 NAD [fermentation]. organic molecules are used as final e- acceptors in fermentation (e.g., pyruvate accepts e- from NADH). |
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Term
| oxidative phosphorylation |
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Definition
| ATP is made by electrochemical energy gradient (proton motive force). when H+ flow from high concentration to low, energy is produced (1 ATP/3-4 H+). as H+ enter the cell, they pass through the ATP synthase protein embedded in the cell membrane, and produce ATP via phosphorylation of ADP. |
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Term
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Definition
| primary means of generating transmembrane protein gradient. e- from NADH or FADH2 are passed through a serie of membrane bound e- carriers to regenerate NAD. the terminal e- acceptors are inorganic compounds, for example O2 (aerobic) or NO3- and SO42- (anaerobic). NADH/FADH2 carry e- to the electron transport chain; from there the e- flow from carriers with more negative reduction potential to ones with more positive reduction potential. for each jump of e- to the next acceptor, H+ is released. when H+ concentration is high enough outside the cell membrane, H+ flows back down the gradient and can be used for cell functions (ATP synthesis, flagellar motor movement, etc). |
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Term
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Definition
| alpha-ketoglutaric acid [from krebs] + NADPH + NH3 [simple compounds] -> glutamate dehydrogenase [monomer] -> glutamic acid + NADP + H2O |
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Term
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Definition
| protein synthesis. amino acid sequence is determined by DNA (DNA -> mRNA -> protein). |
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Term
| what direction is mRNA synthesised in? |
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Definition
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Term
| mRNA (major characteristics) |
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Definition
| single stranded. 5'-3' synthesis. uses uracil in place of adenine. |
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Term
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Definition
| the "words" that translate DNA into mRNA into proteins. each triplet consists of 3 nucleotides (e.g., AUG, AGG, UGA). |
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Term
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Definition
| mRNA; rRNA; tRNA; small regulatory RNAs |
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Term
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Definition
| forms ribosome (e.g., 16S rRNA on the 30S subunit) |
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Term
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Definition
| brings amino acids to mRNA and ribosome during translation |
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Term
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Definition
| noncoding regulatory factors in the cell |
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Term
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Definition
| initiation, elongation, termination |
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Term
| transcription: initiation |
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Definition
| RNA pol synthesises RNA and forms the core enzyme. RNA pol joins with sigma to form the holoenzyme. the holoenzyme binds to the promoter region (-35, -10, +1) |
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Term
| 3 things required for initiation of transcription |
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Definition
| RNA polymerase, sigma, promoters |
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Term
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Definition
| enhances affinity of RNA pol for specific DNA promoters and makes sure transcription begins at the right place. |
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Term
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Definition
| housekeeping genes (basic cell functions) |
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Term
| how many different types of sigma factors does E. coli have? |
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Definition
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Term
| how many different types of sigma factors does B. subtilis have? |
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Definition
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Term
| maximum speed of transcription of DNA |
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Definition
| 2000 copies per cell (during log phase) |
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Term
| RNA pol core enzyme is composed of what? |
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Definition
| 5 subunits: alpha, beta, beta-prime, and "w" (omega?) |
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Term
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Definition
| tRNAs are charged with an amino acid at their 3' end by amino acyl tRNA synthethase, which attaches the amino acid to the tRNA. |
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Term
| what does "wobble base pair" refer to? |
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Definition
| the "wobble" bp is the last nucleotide in the tRNA codon that can differ (i.e., be a different base) but still function as required and be incorporated into the correct amino acid during translation. |
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Term
| how does the ribosome know that the first AUG encodes for fmet? |
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Definition
| the first AUG has the ribosome binding site directly before it on the mRNA strand. therefore, the ribosome binding site signals to the ribosome that this AUG alone should encode for fmet. subsequent AUGs in the same strand do not have a ribosome binding site (shine-delgarno sequence), so they only encode for methionine. |
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Term
| what protein catalyses the addition of amino acids during elongation? where does this protein come from? |
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Definition
| the protein peptidyl transferase is released by the 23s rRNA in the 50S subunit of the 70S ribosome. |
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Term
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Definition
| occurs between the A and P sites of the ribosome during translation. this term describes the transfer of the amino acid from the charged tRNA onto the growing polypeptide chain (protein) being made from the mRNA. |
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Term
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Definition
| the movement of the newly uncharged tRNA from the ribosome via the E site. |
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