BIOLOGY 200 Molecular Biology Students registered for the 9:30AM lecture should NOT attend the 4:30PM lecture.

Transcription

1 BIOLOGY 200 Molecular Biology Students registered for the 9:30AM lecture should NOT attend the 4:30PM lecture. Midterm date change! The midterm will be held on October 19th (likely 6-8PM). Contact Kathy Hewitt at if you have a conflict. You will have 5 hours to take the quiz once initiated through MyCourses. You must take it between 9:00AM Friday and the following Tuesday at 9:00AM. Template versus the final version Powerpoint presentations on MyCourses. Questions on the exams and quizzes are taken ONLY from the lecture materials. You are NOT responsible for the information in the readings not covered in class. Reading assignments are listed on MyCourses follow the Lecture link. Course Outline Professor Thomas Bureau Lecture 1: Introduction Lecture 2: Protein Structure and Function Lecture 3: Basic Molecular Genetic Mechanisms - Nucleic Acids Lecture 4: Basic Molecular Genetic Mechanisms - Transcription and Translation Lecture 5: Basic Molecular Genetic Mechanisms - DNA Replication I Lecture 6: Basic Molecular Genetic Mechanisms - DNA Replication II Lecture 7: Basic Molecular Genetic Mechanisms - DNA Repair and Recombination I Lecture 8: Basic Molecular Genetic Mechanisms - DNA Repair and Recombination II Lecture 9: Molecular Genetics Techniques I Lecture 10: Genes, Genomics, and Chromosomes - Eukaryotic Gene Structure and Noncoding DNA Lecture 11: Genes, Genomics, and Chromosomes - DNA Transposons Lecture 12: Genes, Genomics, and Chromosomes - LTR Retrotransposons, LINEs and SINEs Lecture 13: Genes, Genomics, and Chromosomes - Organellar Chromosomes and Barcoding Lecture 14: Genes, Genomics, and Chromosomes - Eukaryotic Chromosomes Lecture 15: Genomics and Bioinformatics Lecture 16: Gene and Genome Evolution 1

2 Central Dogma DNA RNA Protein DNA Transcription RNA rrna trna mrna mirna Protein Translation Catalysis - catalyze intra- and extracellular chemical reactions Structural - structural rigidity Transport - flow of materials across membrane Regulatory - sensors/switches to control protein activity and gene function Signalling - transmit external signals to cell interior Motor - motion Shape is Important Amino Acids Amino acids Two possible isomers - D and L 2) carboxyl group 20 types properties determined by side chains vary in size, shape, charge, hydrophibicity, and reactivity 4) side chain or R group 1) amino group alpha carbon 3) hydrogen atom 2

3 Fighting drug-resistant bacteria - + Fernando-Lopez et al. (2001) Nature 412, pp Polar - Water soluble Nonpolar Insoluble in water sulfhydryl group symmetrical Can form disulfide bonds (-S-S-) with another cysteine - intra and inter-crosslinking - stabilize folded structure rigid ring structure Proteins Function is derived from the threedimensional structure, and the threedimensional structure is specified by the amino-acid sequence Three-dimensional structure = conformation Hierarchical structure of proteins 3

4 carbonyl C = residue N C alpha C amide N 4

5 Secondary Structure Folding of localized regions of a polypeptide chain Stabilizing noncovalent interactions forming, for instance, alpha helices beta sheets beta turns No noncovalent interactions = random coil Alpha (α) helix H-bond R groups point outward Beta (β) sheet β strands H-bond Laterally packed beta strands beta strand = short, 5 to 8 residues, nearly extended polypeptide segment H-bonding between backbone of the beta strands Directionality - parallel (same orientation) or antiparallel (opposite orientation) Beta sheets are pleated R-groups project outwards Beta Turn Motifs of protein secondary structure H-bond 5

6 Combinations of secondary structures define motifs hydrophobic residues ionic bonds involving Ca 2+ Fibrous proteins Ca 2+ binding proteins RNA and DNA binding proteins Tertiary Structure Long range folding within a polypeptide chain Stabilized by hydrophobic interactions between nonpolar side chains, hydrogen bonds between polar side chains, and disulfide bonds between cysteine residues Provide a compact structure of alpha helices, beta sheets and turns Modular nature of protein domains Structural Domain A region of the protein which is selfstabilizing and can fold independently. Functional Domain A region of the protein that exhibits a particular activity - even when isolated from the rest of the protein. 6

7 STRUCTURE OF RABBIT MUSCLE PYRUVATE KINASE Many polypeptides are composites of different combinations of domains 7

8 Supramolecular Structure Macromolecular assemblies Usually >1 mega daltons in size 10 s to 100 s of polypeptide chains (as well as other macromolecules) Description linear sequence α-helices ß-sheets U-turns and loops motifs domains multimeric interaction macromolecular assemblies (molecular machines) Level supramolecular Course Outline Professor Thomas Bureau Lecture 1: Introduction Lecture 2: Protein Structure and Function Lecture 3: Basic Molecular Genetic Mechanisms - Nucleic Acids Lecture 4: Basic Molecular Genetic Mechanisms - Transcription and Translation Lecture 5: Basic Molecular Genetic Mechanisms - DNA Replication I Lecture 6: Basic Molecular Genetic Mechanisms - DNA Replication II Lecture 7: Basic Molecular Genetic Mechanisms - DNA Repair and Recombination I Lecture 8: Basic Molecular Genetic Mechanisms - DNA Repair and Recombination II Lecture 9: Molecular Genetics Techniques I Lecture 10: Genes, Genomics, and Chromosomes - Eukaryotic Gene Structure and Noncoding DNA Lecture 11: Genes, Genomics, and Chromosomes - DNA Transposons Lecture 12: Genes, Genomics, and Chromosomes - LTR Retrotransposons, LINEs and SINEs Lecture 13: Genes, Genomics, and Chromosomes - Organellar Chromosomes and Barcoding Lecture 14: Genes, Genomics, and Chromosomes - Eukaryotic Chromosomes Lecture 15: Genomics and Bioinformatics Lecture 16: Gene and Genome Evolution 8