Term
|
Definition
| thymine, cysteine, uracil |
|
|
Term
|
Definition
|
|
Term
|
Definition
| Synthesized chain with termination occurring at specific sites |
|
|
Term
| Maxam-Gilbert Sequencing Method |
|
Definition
| base specific cleavage reactions |
|
|
Term
|
Definition
| temperature at which dsDNA denatures to ssDNA. Greater Tm, greater Stability. |
|
|
Term
| Tm and Solutions Relationship |
|
Definition
| Increase [salt], Increase Tm, Increase stability |
|
|
Term
|
Definition
| G-C pairs are more stable that A-T pairs because G-C pairs have 3 hydrogen bonds (A-T pairs have 2) |
|
|
Term
|
Definition
| Regulate the amount of supercoiling in the DNA inside cells. (regulate superhelical density) |
|
|
Term
|
Definition
| Removes excess negative superhelical turns for DNA |
|
|
Term
| Topoisomerase II (gyrase) |
|
Definition
| adds negative superhelical turns to DNA |
|
|
Term
| Meselson-Stahl Experiment |
|
Definition
| proved replication is semi-conservative (HH,HL,LL) |
|
|
Term
| DNA polymerase reaction requirements |
|
Definition
| dNTPs, template, primer, Mg++ |
|
|
Term
| Polymerase activity: 3' to 5' exonuclease |
|
Definition
| degrade noncomplementary DNA and add complementary DNA ("proof reading") |
|
|
Term
| Polymerase activity: 5' to 3' exonuclease |
|
Definition
| nucleotides are removed one at a time while new ones are being synthesized ("leading strand") |
|
|
Term
| Conditional lethal mutations |
|
Definition
| under some conditions, enzyme is normal, but under other conditions, the enzyme is a phenotypic mutant. (ex: e.coli mutant lacks pol I) |
|
|
Term
| Immediate stop phenotype DNA mutant |
|
Definition
| proteins that code for replication can't start DNA replication at high temperatures and were unable to incorporate 3H thymidine into their DNA |
|
|
Term
| Slow stop phenotype DNA mutant |
|
Definition
| proteins only necessary for replication initiation. (cells that have already started replication will continue, but once round is over, they will not be able to start again) |
|
|
Term
| DNA polymerase III (dnaE) |
|
Definition
| used for replication in E. coli (E.coli doesn't use Pol I). contains the dnaQ gene coding for a seperate editing subunit |
|
|
Term
|
Definition
| unwind helix by use of ATP |
|
|
Term
| single strand binding proteins |
|
Definition
| facilitates synthesize after helicases unwind DNA |
|
|
Term
| Okazaki fragments-primases (dnaG) |
|
Definition
| RNA primer that synthesizes short fragments. When it meets the 5' end of the previous fragment, DNA pol III is replaced by DNA pol I. |
|
|
Term
|
Definition
| 5'-3' exonuclease, replaces pol III at 5' end of previous okazaki fragment. 3' - 5' exonuclease will unpaired base at 3' end of a growing chain (editing) |
|
|
Term
|
Definition
| repairs "nicks", makes lagging strand a continuous DNA strand. Brings together sticky ends |
|
|
Term
|
Definition
| requires gene products of mutH, mutL, and mutS. Scans helix for mismatched bases, nicks on both sides of the mismatch, mismatch is removed, and polymerase and ligase repair the gap. |
|
|
Term
| Methyl-directed mismatch repair |
|
Definition
| DAM methylated adenines of GATC sequences. After replication, DNA is hemimethylated (newly synthesized in not methylated, so the nonmethylated strand is repaired) |
|
|
Term
|
Definition
| DNA replication of the bacterial chromosome begins here |
|
|
Term
|
Definition
| dnaA, dnaB, and dnaC. dnaA is required only for initiation, but dnaB and dnaC are required for primer synthesis once DNA replication is under way. |
|
|
Term
| Bacterial Chromosome Replication Steps (bidirectional) |
|
Definition
| DNA-ATP binds at OriC and opens helix. dnaC-dnaB helicase unwinds strands (dnaC leaves), single stranded binding proteins aid dnaB and the dnaG primerase binds to the ssb proteins to start replication |
|
|
Term
| Bacterial chromosome termination |
|
Definition
| passes either terA or terB halfway around the chromosome. Topoisomerase IV segregates the two daughter chromosomes. |
|
|
Term
| Partitioning (par) proteins |
|
Definition
| ParA, ParB, ParS. ParS binds to DNA, ParB binds to ParS, and ParA interacts with parB (role not clear) |
|
|
Term
|
Definition
| condensins that compact DNA and form sliding filaments like myosin that pull chromosomes apart from the central replication complex |
|
|
Term
|
Definition
| involved in fixing the site of septum formation during cell formation. MinD proteins help localize the MinC and MinE proteins to ensure the septum is formed in the middle of the cell. |
|
|
Term
| Antibiotics and bacterial replication |
|
Definition
| Block precursor synthesis, block polymerization, affect DNA structure, affect gyrase |
|
|
Term
| Restriction endonucleases |
|
Definition
| site specific restriction enzymes that cut DNA at specific sequences often making staggered cuts |
|
|
Term
|
Definition
| endonuclease that recognizes DAM methylation sites |
|
|
Term
|
Definition
| endonuclease that recognizes nonsticky ends (CCC-GGG) |
|
|
Term
| Polymerase Chain Reaction (PCR) |
|
Definition
| 1. DNA denatured at high temp. 2. Primers are annealed to denatured DNA at a lower temp 3. Primers are elongated by DNA polymerase 4. repeat several times |
|
|
Term
| Aminoacyl-tRNA synthetases |
|
Definition
| enzymes that attach the correct AA to the tRNA. Charge the tRNA and ensure fidelity. |
|
|
Term
|
Definition
| more than one gene/protein translation in a mRNA (unique to prokaryotes) |
|
|
Term
|
Definition
| when translation of the upstream gene is required for the translation of the gene immediately downstream. The secondary structure of the RNA blocks translation of the second polypeptide unless it is disrupted by a ribosome translating the first coding sequence. |
|
|
Term
|
Definition
| help proteins fold into the right shape |
|
|
Term
|
Definition
| heat shock protein chaperone (Hsp70) functions in helping proteins fold in E. coli and acts as a cellular thermometer regulating the synthesis of other proteins in response to a heat shock. |
|
|
Term
| negative transcriptional control |
|
Definition
| when protein is bound to cis acting site, gene is turned off. (repressor) |
|
|
Term
| positive transcriptional control |
|
Definition
| when protein is bound to cis acting site, gene is turned on. (activator) |
|
|
Term
|
Definition
| bind trans acting proteins |
|
|
Term
|
Definition
| binding of repressor to DNA (operator) interferes with RNA polymerase binding to promoter |
|
|
Term
| Activators and Activator Sites |
|
Definition
| binding of activator to DNA (activator site) stimulates RNA polymerase binding to promoter |
|
|
Term
|
Definition
| require a supplement to the medium that is not required by WT. cannot utilize a substance that the WT is able to use |
|
|
Term
|
Definition
| Pyridine is replaced with a pyridine. Purine is replaced with a purine. |
|
|
Term
|
Definition
| Pyridine is replaced by purine. Purine is replaced by a pyridine. |
|
|
Term
| Tautomerism base pair change |
|
Definition
| enol form of T can base pair with G, if not repaired, transition mutation |
|
|
Term
|
Definition
| Cytosine is deaminated to thymidine. Repaired by UnG (uracil end glycosilase). Happens often. |
|
|
Term
|
Definition
| base pair change that causes a transversion (GC-TA) |
|
|
Term
|
Definition
| suppressor mutations in the same gene are the original mutation |
|
|
Term
| Extragenic (Intergenic) suppressors |
|
Definition
| suppressor mutations in different genes |
|
|
Term
| Nonsense suppressor mutation |
|
Definition
| mutation in tRNA that changes the anticodon of the tRNA gene product so that it recognizes a stop codon |
|
|
Term
|
Definition
| chromosomal division then chromosome passed down to daughter cell |
|
|
Term
| state of most native plasmid DNA found in a bacterium |
|
Definition
| extrachromosomal, cccDNA, ds, supercoiled |
|
|
Term
|
Definition
| average number of a particular plasmid per one cell under normal growth conditions (phenotypic feature). Directly proportional to the rate at which new rounds of replication begin at oriV. |
|
|
Term
|
Definition
| origin of plasmid replication, plasmid replicon |
|
|
Term
|
Definition
| most common form, gram negative. Bidirectional (2 replication forks, Ex: F plasmid) Unidirectional (1 replication fork, Ex: colE1) |
|
|
Term
|
Definition
| OriV OR oriV + Rep protein OR OriV + RNA molecule |
|
|
Term
|
Definition
| defines all types of bacteria in the plasmid can replicate, determined by oriV |
|
|
Term
| colE1 plasmid copy number mechanism and regulation |
|
Definition
| kills colE1 plasmid negative cells, 10-15 copies of colE1 per cell. Doesn't want too many copies because wasted energy. Involves: RNA II, RNA I, RHase H, Rop |
|
|
Term
|
Definition
| ColE1 plasmid, primer used for new DNA synthesis at oriV. Must be processed by RNaseH first, positive effector |
|
|
Term
|
Definition
| antisense to RNA II. inhibits plasmid replication by binding to 5'end of RNA II, negative effector, mutation of RNA I increases copy number |
|
|
Term
|
Definition
| processes RNA II to form RNA primer for DNA pol to start DNA synthesis. doesn't recognize RNA II when RNA I is bound --> no replication |
|
|
Term
|
Definition
| plasmid encoded protein which enhances RNA I/RNA II binding. Mutation of Rop increases copy number |
|
|
Term
|
Definition
| made from PrepA or PcopB, activator protein which binds to specific sequences at oriV to form a nucleoprotein preinitiation complex, positive effector |
|
|
Term
|
Definition
| low copy number, RepA, RNase III, CopB, CopA |
|
|
Term
|
Definition
| enzyme which cleaves dsRNA |
|
|
Term
|
Definition
| negative regulator protein which blocks repA transcription by binding to promoter of repA |
|
|
Term
|
Definition
| blocks translation of the RepA mRNA by binding with it |
|
|
Term
|
Definition
| F (1-2 copy numbers), pSC101 (5 copies). Iteron and RepA. |
|
|
Term
|
Definition
| direct repeated sequences in the oriV where Rep proteins bind |
|
|
Term
|
Definition
| binds inverted repeats of its own promoter (decrease transcription, - effector). When binds to iterons, + effector |
|
|
Term
| transcriptional autoregulation |
|
Definition
| proteins that bind to their own promoters via inverted repeats |
|
|
Term
| Handcuffing or coupling model |
|
Definition
| pSC101 or F plasmid. At high [plasmid], plasmids will pair via Rep causing steric hinderance and interfering with initiation of replication by RNA polumerase. |
|
|
Term
|
Definition
| gram +, Rep C, Antisense RNA I, medium copy number |
|
|
Term
|
Definition
| positive effector, initiation of replication at OriV |
|
|
Term
|
Definition
| dissimilar replication/ copy number control mechanism |
|
|
Term
|
Definition
| region of DNA which the gene (s) are transcribed as one mRNA, along with the promoter sequence, and any DNA sequence involved with regulating the transcription of those genes. |
|
|
Term
| constitutive gene expression |
|
Definition
| producing a protein/RNA product continually regardless of environmental influences |
|
|
Term
| transcriptionally regulated |
|
Definition
| genes regulated at stage of RNA/ mRNA production. most efficient because synthesis of unneeded mRNA is a waste of energy |
|
|
Term
| posttranscriptional regulation |
|
Definition
| translational regulation, mRNA continuously transcribed, but translation can be inhibited |
|
|
Term
|
Definition
| enzymatic expression only when sugar lactose is present |
|
|
