06 molecular biology.ppt

06 molecular biology.ppt - CEE 266 ENVIRONMENTAL...

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Unformatted text preview: CEE 266 ENVIRONMENTAL BIOTECHNOLOGY Lecture 6 (Molecular Biology Fundamentals: DNA, RNA, proteins) Macromolecules and Genetic Information   Genetic information flow can be divided into three stages   Replication: DNA is duplicated   Transcription: information from DNA is transferred to RNA   mRNA (messenger RNA): encodes polypeptides   tRNA (transfer RNA): plays role in protein synthesis   rRNA (ribosomal RNA): plays role in protein synthesis   Translation: information in RNA is used to build polypeptides Synthesis of the Informational Macromolecules Figure 7.1 Macromolecules and Genetic Information  Central dogma of molecular biology   DNA to RNA to protein  Eukaryotes: each gene is transcribed individually  Prokaryotes: multiple genes may be transcribed together The Double Helix   Four nucelotides found in DNA:   Adenine (A)   Guanine (G)   Cytosine (C)   Thymine (T)   Backbone of DNA chain is alternating phosphates and the pentose sugar deoxyribose   Phosphates connect 3′- carbon of one sugar to 5′ of the adjacent sugar DNA Structure Figure 7.4 Thermal Denaturation of DNA Figure 7.7 The Double Helix   Size of DNA molecule is expressed in base pairs   1,000 base pairs = 1 kilobase pairs = 1 kbp   1,000,000 base pairs = 1 megabase pairs = 1Mbp   E. coli genome = 4.64 Mbp   Each base pair takes up 0.34 nm of length along the helix   10 base pairs make up 1 turn of the helix Supercoiling   Supercoiled DNA: DNA is further twisted to save space   Negative supercoiling: double helix is underwound   Positive supercoiling: double helix is overwound   Relaxed DNA: DNA has number of turns predicted by number of base pairs   Negative supercoiling is predominantly found in nature   DNA Gyrase: introduces supercoils into DNA Supercoiled DNA Figure 7.8a-c Supercoiled DNA Figure 7.8d DNA Gyrase Figure 7.9 Templates and Enzymes   DNA replication is semiconservative   Each of the two progeny double helices have one parental and one new strand   Precursor of each nucleotide is a deoxynucleoside 5′ triphosphate (dNTP)   Replication ALWAYS proceeds from the 5′ end to the 3′ end Overview of DNA Replication Figure 7.10 Events at the DNA Replication Fork Figure 7.13 Major Enzymes Involved in DNA Replication in Bacteria Enzyme Genes Function Gyrase gyrAB Unwinds supercoils ahead of replisome Helicase dnaB Unwinds double helix at replication fork Polymerase III dnaE, dnaQ Strand elongation and proofreading Polymerase I polA Excises RNA primer and fills gaps Ligase ligA, ligB Seals nicks in DNA Sealing Two Fragments on the Lagging Strand Figure 7.15 Bidirectional Replication and the Replisome   DNA synthesis is bidirectional in prokaryotes   Two replication forks moving in opposite directions   DNA Pol III adds 1,000 nucleotides per second   Replisome complex of multiple proteins involved in replication   DNA pulled through the replisome Replication of Circular DNA: The Theta Structure Figure 7.16 Proofreading and Termination   DNA replication is extremely accurate   Proofreading helps to ensure high fidelity   Mutation rates in cells are 10-8–10-11 errors per base inserted   Polymerase can detect mismatch through incorrect hydrogen bonding   Proofreading occurs in prokaryotes, eukaryotes and viral DNA replication systems Overview of Transcription   Promoters: site of initiation of transcription   Promoters are recognized by sigma factor of RNA polymerase   Transcription stops at specific sites called transcription terminators   Unlike DNA replication, transcription involves smaller units of DNA   Often as small as a single gene   Allows cell to transcribe different genes at different rates Transcription: Steps in RNA Synthesis Figure 7.21a Sigma Factors and Consensus Sequences   Sigma factors recognize two highly conserved regions of promoter   Two regions within promoters are highly conserved   Pribnow box aka Pribnow-Schaller box: located 10 bases before the start of transcription (-10 region)   Sequence is always TATAAT   -35 region: located ~35 bases upstream of transcription The Interaction of RNA Polymerase with the Promoter Figure 7.22 The Unit of Transcription   Prokaryotes often have genes related to the same process clustered together   These genes are transcribed all at once as a single mRNA   An mRNA encoding a group of cotranscribed genes is called a polycistronic mRNA   Operon: a group of related genes cotranscribed on a polycistronic mRNA   Allows for expression of multiple genes to be coordinately regulated The Genetic Code   Translation: the synthesis of proteins from RNA   Genetic code: a triplet of nucleic acid bases (codon) encodes a single amino acid   Specific codons for starting and stopping translation   Degenerate code: multiple codons encode a single amino acid   Anti-codon on tRNA recognizes codon   Wobble: irregular base pairing allowed at third position of tRNA The Genetic Code as Expressed by Triplet Bases of mRNA The Wobble Concept Figure 7.25 The Genetic Code   Stop codons: signal the termination of translation (UAA, UAG, and UGA)   Start Codon: translation begins with AUG   Reading frame: triplet code requires translation to begin at the correct nucleotide   Shine-Dalgarno sequence: ensures proper reading frame   Open Reading Frame (ORF): AUG followed by a number of codons and a stop codon in the same reading frame Possible Reading Frames in an mRNA Figure 7.26 Transfer RNA   Transfer RNA: at least one tRNA per amino acid   Bacterial cells have 60 different tRNAs   Mammalian cells have 100–110 different tRNAs   Specific for both a codon and its cognate amino acid   tRNA and amino acid brought together by aminoacyl-tRNA synthetases   ATP is required to attach amino acid to tRNA   tRNA is cloverleaf in shape Structure of a Transfer RNA Figure 7.27 Transfer RNA   Anti-codon: three bases of tRNA that recognize three complementary bases on mRNA   Fidelity of recognition process between tRNA and aminoacyl-tRNA synthetase is critical   Incorrect amino acid could result in a faulty/nonfunctioning protein Translation: The Process of Protein Synthesis 1) Initiation: two ribosomal subunits assemble with mRNA   Begins at an AUG start codon 2) Elongation: amino acids are brought to the ribosome and are added to the growing polypeptide   Translocation: movement of the tRNA holding the polypeptide from the A to the P site 3) Termination: occurs when ribosome reaches a stop codon   Release factors (RF): recognize stop codon and cleave polypeptide from tRNA   Ribosome subunits then dissociate The Ribosome and Protein Synthesis Figure 7.29a The Ribosome and Protein Synthesis Figure 7.29b ...
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This note was uploaded on 02/02/2012 for the course CEE 266 taught by Professor Shailymahendra during the Fall '11 term at UCLA.

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