N-terminus is to the LEFT AND C-TERMINUS IS TO THE RIGHT!!!N-terminus is to the LEFT AND C-TERMINUS IS TO THE RIGHT!!!QUESTION: Sigma factors binds ______ and initiates ________A. DNA / DNA synthesisB. RNA / RNA synthesisC. DNA/ RNA synthesisMicrobio Exam Study Guide Chapter 6: Molecular Biology of BacteriaThe functional unit of genetic information is the gene.Genes are found in cells and are composed of DNADNA  RNA  PROTEINGenetic information flow can be divided into three stages:Replication: DNA is dulplicatedTranscription: DNA  RNATranslation: RNA  polypeptidesBackbone of the DNA chain is composed of alternating phosphates and the pentose sugar deoxyribose (contains 5-carbons)6.2 The Double Helix:- All cells have some viruses and DNA in doubl-stranded molecules- Two strands are antiparallel, meaning they have complementary bases- Two strands have complementary base sewuencesINVERTED REPEATS:- Repeated sequences that are arranged in an inverse orientation. An example would be TTCHCCG and then AAGCGGCSTEM LOOPS:- Short, double-helical regions caused by nearby inverted repeats in a DNA or RNA molecule- Stem loops are very common forms of secondary structure in RNA molecules, which liketo fold over on themselves.When there are more G/C bonds in a DNA molecule, DNA melts at higher temperatures because G/C bonding pairs have more hydrogen bonds.6.4 Plasmids and Other Genetic ElementsPLASMIDS: replicate separately from chromosomesTRANSPOSABLE ELEMENTS: can move around in DNA; there are insertion sequences whichinsert themselves into important areas, transposons, and special viruses6.5 The Escherichia coli Chromosome:- Echerichia coli is a useful model organism for the study of biochemistry, genetics, and bacterial pathophysiology- The E. coli chromosome has been mapped using conjugation, transduction, molecular cloning, and gene sequencing.FEATURES OF THE E. coli CHROMOSOME:- Many genes that encode the enzymes for a single biochemical pathway are clustered into operons- Operons are usually equally distributed on both strands of the chromosome- About 5 Mbp in size- 40% of predicted proteins are of unknown function- Average protein contains about 300 amino acids- Insertion sequences (IS elements) – insertion sequences are small, short sequences that act as transposable elements6.6 Plasmids: General Principles- Plasmids are genetic elements that replicate independently of the host chromosome- Small circular or linear DNA molecules- Carry a variety of nonessential, but very helpful genes- Their abundance (COPY NUMBER) is variable in cells. Meaning how many of them are present in each cell.6.7 The Biology of Plasmids:- Genetic information encoded on plasmids is NOT ESSENTIAL FOR CELL FUNCTION,but may confer a selective growth advantage under certain conditions- R plasmids: Resistance plasmids; R plasmids confer resistance to antibiotics and other growth inhibitors- R plasmids (resistance plasmids) are often conjugative  which means that antibiotic resistance can be transferred to other cells nearby the cells that contain those plasmids.6.8 Templates and Enzymes:- DNA replication is semiconservative.- Semiconservative: each of the two progeny double helices have one parental and one new strand. (each complementary chain acts as a template for a new daughter strand)- THE PRECURSOR OF EVERY NEW DNA STRAND IS A DEOXYNUCLEOSIDE 5’-TRIPHOSPHATE. (dNTPs)(a deoxynucleoside 5’-triphosphate)6.9 The Replication Fork:- DNA synthesis begins at the ORIGIN OF REPLICATION (ORI) in prokaryotes.- Replication fork: the zone of unwound DNA where the DNA replication machinery is binding and where replication of DNA thus occurs- DNA polymerase: catalyze the addition of dNTPs - DNA polymerases require a PRIMER!!!! (DNA replication requires primers)- DNA helicase – unwinds the DNA molecules- Extension of DNA: occurs continuously on the leading strand, and discontinuously on the lagging strand, which requires the addition of “Okazaki fragments” onto the lagging strand.6.10 Bidirectional Replication and the Replisome:- DNA synthesis is bidirectional in prokaryotes!!!!!!!- Two replication forks move in opposite directions.NOTE: DnaA binds at the origin of replication and then allows the DNA replication machinery to bind there and replicate the DNA.6.10 Bidirectional Replication and the Replisome:- DNA Polymerase III adds nucleotides to the growing daughter strand.- DNA polymerase III adds about 1000 nucleotides per second.- Replisome: complex of multiple proteins involved in DNA replication.  DNA is pulled through the replisome. The REPLISOME consists of DNA Polymerase III, DNA helicase,DNA gyrase, Tau proteins, and DNA primase (adds primers).DNA Polymerase can detect mismatch pairs through incorrect hydrogen bonding.6.11 The Polymerase Chain Reaction: (PCR)- PCR is also known as DNA amplificationSTEPS IN PCR INCLUDE:- Add a long, DNA template strand- Add primers (manmade)- Add DNA polymerase (Taq or Pfu polymerase)- Heat, cool, and repeatApplications of PCR:- Phylogenetic studies- Amplifying small amounts of DNA for forensics- Identifying a specific bacteria- Looking for a specific gene6.12 Overview of Transcription:- Transcription is carried out by RNA polymerase- Only one of the two strands are transcribed for any DNA molecule- RNA polymerase recognizes important and very specific DNA sites called promoters.- Promoters are the initiation sites of transcription. - Promoter regions are recognized by sigma factors- Transcription strops at specific sites called transcription terminators.SIGMA FACTORS BIND BETWEEN TWO VERY SHORT AND SPECIFIC SEQUENCES CALLED CONSENSUS SEQUENCES.Two types of consensus sequences: Pribnow box and the ~35 region. The Pribnow box is located about 10 bases for the start site of transcription.The Unit of Transcription is the unit of chromosome that is bounded by sites where the transcription of DNA to RNA is initiated and terminated. (reaches from the promoter region to the transcription stop site)An mRNA molecule encoding a group of co-transcribed genes is called a polycistronic mRNA.Operons: a group of related genes that are co-transcribed on a polycistronic mRNA molecule6.16 Polypeptides, Amino Acids, and the Peptide Bond.- Proteins play a major role in cell function.There are catalytic proteins (enzymes), as well as structural proteins (histones)- Proteins are polymers of amino acids (amino acid chains)- Amino acids are linked by PEPTIDE