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2/5 Notes

by: Cara Cahalan

2/5 Notes Bios 312

Cara Cahalan
GPA 3.8

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About this Document

First notes on Exam 2.
Karrie Weber
Class Notes
25 ?




Popular in Microbiology

Popular in Biology

This 3 page Class Notes was uploaded by Cara Cahalan on Thursday April 7, 2016. The Class Notes belongs to Bios 312 at University of Nebraska Lincoln taught by Karrie Weber in Spring 2016. Since its upload, it has received 10 views. For similar materials see Microbiology in Biology at University of Nebraska Lincoln.


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Date Created: 04/07/16
2/5: Molecular Microbiology   Readings: 4.1­4.6 I: Blueprint of Life: Structure of Bacterial Genome  4.1 Macromolecules and Genes  Components of nucleotide: o Pentose sugar­ ribose or deoxyribose o Nitrogen base  4­ o Phosphate molecule PO 3  Purines­ A and G, two fused heterocyclic rings   Pyrimidines­ T, C, and U, single six­membered rings, fuse with purines   A=T and G triple bonded to C (more stable)   Nitrogen base attached to pentose sugar by glycosidic linkage between C 1 of sugar and N in base   Nucleotides covalently bonded by P between 3’ C of one sugar and 5’ C of next  o Phosphodiester bond­ phosphate connects two sugar molecules by ester linkages   Types of RNA:  o mRNA­ messenger, carries genetic information from DNA to ribosome  o tRNA­ convert genetic information into nucleotide sequences of RNA defined by amino acids  o rRNA­ ribosomal, catalytic and structural components of ribosome   Flow of genetic information: DNA  RNA  protein  o Replication­ DNA replicated o Transcription­ transfer of information from DNA to RNA  o Translation­ Synthesis of protein from RNA template 4.2 Double Helix   Left strand: runs 5’ to 3’ top to bottom. Right strand: 3’ to 5’ from top to bottom   0.34 nm per base pair and 10 base pairs in 1 turn   Supercoiling­ allowing DNA to be packed in cells, topoisomerases­ insert or remove supercoils, can be relaxed  o Positive­ overwound o Negative­underwound, predominant in nature, inserted by DNA gyrase  4.3 Genetic Elements  Genetic elements include chromosomes, virus genomes, plasmids, organelle genomes, and transposable elements   Plasmids­ replicate separately from chromosome, smaller than chromosomes, contain non­essential genes, one to  hundreds of copies, 1 to over 400 kbp o Carry genes that influence host cell physiology  o R plasmids­ confer resistance to antibiotics or other growth inhibitors  o Virulence is plasmid encoded   Transposable elements­ can move around in genome, either on same or different DNA molecule, jumping genes II: Transmission of Genetic Information: DNA Replication 4.4 Templates and Enzymes  Semiconservative­ one parent and one daughter strand in each molecule   Replication proceeds from 5’ end to 3’ end 5’ phosphate of incoming attaches to free 3’ –OH  DNA pol­ catalyze addition of deoxynucleotides, cannot initiate a new chain o DNA Pol III­ primary enzyme in chromosomal replication  Primer­ DNA pol attaches here, allowing initiation of  a new chain, free 3’ –OH where DNA pol adds    Primase­ makes short stretch of RNA complementary to DNA 4.5 Replication Fork  Replication fork­ zone of unwound DNA where replication occurs   DNA helicase­ unwinds double helix, exposing short region of DNA, just in front of replication fork  o Causes positive supercoiling, undone by DNA gyrase inserting negative supercoiling   Helicases added  2 primers and 2 DNA Pol behind helicase  replication   Leading strand­ 5’ P to 3’ OH, continuously due to free 3’ –OH  Lagging strand­ discontinuously because no free 3’ –OH, RNA primers needed multiple times, Okazaki fragments  DNA Pol I­ exonuclease activity that removes RNA primer preceding it, can repair DNA    DNA ligase­ seals nicks in DNA, repairs DNA 4.6 Bidirectional Replication and the Replisome   Circular DNA­ 2 replication forks moving in opposite directions, creates theta structures   Replisome­ aggregation of replication proteins to form large replication complex.   Proofreading­ by DNA Pol I and III (I directly, III indirectly)  o If incorrect base has been inserted, double helix is slightly distorted  remove  insert correct nucleotide  o DNA Pol III pauses by abnormal H bond (DnaQ performs proofreading)  proofreading exonuclease  removes mismatched nucleotide   Terminus of replication­ 2 replication forks collide as new circles of DNA are completed, 2 circular molecules are linked  Lecture:   GC­rich DNA melts at higher temperatures than AT­rich due to 3 H bonds between G and C  1,000 base pairs= 1 kilobase pair (kbp). 1,000,000 base pairs= 1 megabase pair (Mbp)  Gene: functional unit of genetic information contained in DNA   Minor and major grooves determine how proteins interact with DNA, most proteins bind to major groove   Supercoiling:  o Class I topoisomerases­ make single stranded break in DNA, responsible for removal of supercoiling   Break one strand­ rotate one end of broken around helix and seal  supercoil o Class II: DNA gyrase, double stranded breaks in DNA, double helix remains intact passes through break   Circular DNA twisted  DNA gyrase makes 2x stranded break  intact chain passes through   resealed   Antibiotics that inhibit DNA gyrase in Bacteria­ inhibit growth  o Quinolones (nalidixic acid) o Fluoroquinolone (ciprofloxacin) o Novobiocin  (also effective against some Archaea)  Viruses­ DNA or RNA genomes can be circular or linear   Single stranded binding proteins­ stabilize the unwound parental DNA   DNA Pol III­ replaces primase and adds the first nucleotide at 3’­OH and continues synthesizing RNA o Activity of DNA Pol III stops when reaches synthesized DNA o DNA Pol I replaces Pol III, removes RNA primer, adds nucleotide to the gap  o DNA ligase makes the last phosphodiester bond sealing nicks   Key concepts:  o Chromosome is replicated bidirectionally in prokaryotes.   o Multiple replication forks allow for increased growth rate or doubling time of cells.  o Error rate in DNA replication is low due to the proofreading activity of DNA polymerase. 


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