LS-MCRB 121 1nd Edition Lecture 12Microbial GeneticsI. Terminologya. Genetics: The study of what genes are, how they carry information, how information is expressed, and how genes are replicatedb. Gene: A segment of DNA that encodes a functional product, usually a proteinc. Chromosome: Structure containing DNA that physically carries hereditary information; the chromosomes contain the genesd. Genome: All genetic information in a celle. Genomics: The molecular study of genomesf. Genotype: The genes of an organism. “Blueprint of cell”i. DNAii. Obtained from a parent cell or from another cellg. Phenotype: Expression of genes. “how blueprint is expressed or how the finishedproduct appearsh. DNA Gyrase: relaxes supercoiling ahead of the replication forki. DNA ligase: makes covalent bonds to join DNA strands; joins Okazaki fragments and new segmentsj. DNA polymerase: Synthesizes DNA; proofreads and repairs DNAk. Endonucleases: Cut DNA backbone in a strand of DNA; facilitate repair and insertionsl. Exonucleases: Cut DNA from an exposed end of DNA; facilitate repairm. Helicase: Unwinds double-stranded DNAn. Methylase: adds methyl group to selected bases in newly made DNAo. Photolyase: uses visible light energy to separate UV-induced pyrimidine dimersp. Primase: makes RNA primers from a DNA templateq. Ribozyme: RNA enzyme that removes introns and splices exons togetherr. RNA Polymerase: copies RNA from a DNA templates. snRNP: RNA-protein complex that removes introns and splices exons togetherThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.t. Topoisomerase: relaxes supercoiling ahead of the replication fork; separates DNAcircles at the end of DNA replicationu. Transposase: Cuts DNA backbone leaving single-stranded “sticky ends”II. E. colia. Single chromosomeb. 4.5 million basesc. 4.6 Mbd. 1mm in lengthe. Cell = 1 umf. CircularIII. The Flow of Genetic Informationa. A cell uses genetic info contained in DNA to make its proteins, including enzymesb. Expression: genetic information is used within a cell to produce the proteins needed for the cell to functionc. Recombination: genetic information can be transferred between cells of the same generationd. Replication: genetic information can be transferred between generations of cellsIV. DNA structurea. Polymer of nucleotidesi. Adenine, thymine, cytosine, and guanineb. Double helix associated with proteinsc. Backbone: deoxyribse-phosphated. Strands held together by hydrogen bonds between AT and CGi. Organic molecules are pointed towards interior, vs outer ones are covalent bonds so they can be separated during replicatione. Strands are antiparallelV. Semiconservative Replicationa. Step 1: The double helix of the parental DNA separates as weak hydrogen bonds between the nucleotides on opposite strands break in response to the action of replication enzymesb. Step 2: Hydrogen bonds form between new complementary nucleotides and each strand of the parental template to form new base pairsc. Step 3: Enzymes catalyze the formation of sugar-phosphate bonds between sequential nucleotides on each resulting daughter strandVI. DNA Synthesisa. DNA is copied by DNA polymerasei. In the 5’  3’ directionii. Initiated by an RNA primer (MUST)iii. Leading strand is synthesized continuouslyiv. Lagging strand is synthesized discontinuouslyv. Okazaki fragmentsvi. RNA primers are removed and Okazaki fragments joined by a DNA polymerase and DNA ligasevii. Process is very accurate (high fidelity)viii. Error rate contributes to spontaneous mutation frequencyb. Primingi. DNA polymerases cannot synthesize DNA strand: de novoii. Requires a free 3’ –OHiii. RNA polymerases can synthesize RNA polymer: de novoiv. Needs the involvement of RNA polymerase laying down RNA primerVII. Transcription: Gene Expressiona. DNA is transcribed to make RNA (mRNA, tRNA, rRNA)b. Transcription begins when RNA polymerase binds to the promoter sequencec. Transcription proceeds in the 5’  3’ directiond. Transcription stops when it reaches the terminator sequencee. Processi. RNA polymerase binds to the promotor, DNA unwinds at the beginning of the geneii. RNA is synthesized by complementary base pairing of free nucleotides with the nucleotide bases on the template strand of DNAiii. The site of synthesis moves along DNA; DNA that has been transcribed rewindsiv. Transcription reaches the terminatorv. RNA and RNA polymerase are released and the DNA helix re-formsf. When RNA is transcribed, it is translated at the same timei. This does not occur in a eukaryotic cellVIII. Translationa. mRNA is translated in codons (three nucleotides)b. Translation of mRNA begins at the start codon: AUGc. Translation ends at the nonsense codons: UAA, UAG, UGAd. Genetic Codei. 64 sense codons (61 sense, 3 nonsense) on mRNA encode the 20 amino acidsii. The genetic code is degenerateiii. tRNA carries the complementary anticodoniv. Located in the nucleuse. 6 possible reading chains for each strand of DNA (3 on each side with the starting/ending codons)f. Rates of translation depends on RNALecture 2I. Gene Regulationa. Constitutive genes: expressed at a fixed ratei. Other genes are expressed as needed1. Repressible genes: transcribed until they are turned ofa. Usually in response to the abundance of an end-product2. Inducible genes: transcribed only in presence of inducera. Lactose operonb. Not made until needed or signaled to be made3. Catabolite repression: regulation of carbon source utilization based on environmental and/or metabolic signalsII. Mutationa. A change in the genetic materialb. May be neutral, beneficial, or harmfulc. Spontaneous mutations: Occur in the absence of a mutagend. Base substitution (point mutation)i. May be silent (degeneracy of code)e. Missense mutationi. Change in one baseii. Result in change in amino acidf. Nonsense mutationi. Results in a nonsense codong. Frameshift mutationi. Insertion or deletion of one or more nucleotide pairsIII. The Frequency of Mutation i. Spontaneous mutation rate = 1 in 10^9 replicated base pairs or1 in 10^6 replicated genesb. Population Frequency: Given a mutation frequency of 10^-7, a population of 10^8 bacterial cells will likely harbor ~10 mutations in any 1 genec. Mutagens: Substance that increases the spontaneous mutation frequencyi. Increase to 10^-5 or 10^-3 per replicated geneIV. Selection of Mutationsa. Positive (direct)