DNA Repair

Transcription Differences Between RNA & DNA 1.) RNA has 2’ OH 2.) RNA has uracil instead of thymine 3.) RNA is single stranded (but can fold to self base-pair) RNA Polymerases --- catalyze the polymerization of RNA using a DNA template --- in prokaryotes RNA polymerases require a sigma factor to bind DNA and initiate transcription Sigma Factors --- a protein that binds a specific nucleotide sequence, called a promoter --- a bacterium will generally have multiple sigma factors (allows for better gene regulation) --- one sigma factor usually controls most of the central metabolic and biosynthesis genes (  70 in E. coli)

Transcription

Regulation of Transcription 1.) Sigma factors 2.) Other DNA binding proteins A.) Negative, block RNA polymerase’s access to DNA --- lac repressor B.) Positive, enhance recruitment of RNA polymerase --- catabolite activation --- sometimes both negative and positive systems compete to operate on the same set of genes --- genes in bacteria are often grouped into regulatory elements called operons (groups of genes controlled by the same operator), this saves time and energy for the cell

Lactose Operon in E. coli

Tryptophan Operon

Positive Regulation: The Maltose Operon

Catabolite Activation, dual regulation: (positive & negative) in the lac operon

Two Component Systems

Translation Requires: 1.) Ribosomes 2.) charged tRNAs 3.) mRNA 4.) accessory factors (initiation factor, elongation factor, etc.) 5.) ATP & GTP Based on Genetic Code --- need at least 20 “words” so must have 3 nucleotide codons --- code is degenerate, multiple codons specify the same amino acid, effects: A.) reduces likelyhood of mutational damage B.) codon useage can vary between different organisms

Translation

Other Tidbits: RNA interference: --- Use non-coding (ncRNA) to block translation or trigger destruction of mRNA Quorum Sensing: --- Small rapidly diffusing molecules are used to measure cell density --- Often used by pathogens to time toxin release for maximum effect

Mutation --- a change in the genetic information (DNA sequence) of an organism --- cells spend considerable energy fixing mutations --- preventing all mutation would actually be a bad idea, WHY? Types of Mutation: A.) Base Substitution: swap one base for another 1.) Transition: change from one purine or pyrimidine base to another (A  G or T  C) 2.) Transversion: change from a purine to a pyrimidine or a pyrimidine to a purine --- only possibility of change to AA sequence of protein, WHY?

Types of Mutations (Continued): B.) Insertion/ Deletion: add or remove one or more base pairs --- these types of mutations can cause a frameshift, changing the reading frame of the rest of the gene (often results in a premature stop codon). --- What is one case where there would be almost no effect of a frameshift mutation?

Mutagens and Mutagenesis Mutagen: something that causes DNA damage 1.) Chemicals, chemical modification of DNA bases can easily result in mutation 2.) DNA intercalators, aromatic compounds that can form  stacking interactions with bases, are often “read” as additional bases, creating insertion mutations 3.) UV- induced thymine dimers 4.) Ionizing radiation, creates double stranded DNA breaks, can be difficult to repair and may still result in an insertion or deletion --- mutagenesis is the process of purposely mutating an organism, “wreck and check” strategy of protein study

The Ames Test: --- measuring how mutagenic a substance is