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Proteins - Département de Biologie
1.0 Organisation of the course « Introduction to biology » Faculty • Patrick Charnay • Morgane Thomas-Chollier • Régis Ferrière Students Course and tutorials Reference book • Savada et al. (2010). Life. Sinauer associates Home work (Charnay + Thomas-Chollier) • Every week, in tutorials, presentation of an important point of the previous course in 5 min by two groups of two students (20% of the final note) Evaluation (Charnay + Thomas-Cholier) • Oral (30 min) for mathematicians, discussion on the course • Written for chemists (course + exercises) 1.0 Organisation of the course « Introduction to biology » 1.0 Organisation of the course « Introduction to biology » • 1 General introduction-Proteins • 2 Carbohydrates, Lipids and Nucleic Acids • 3 Cells • 4 Metabolism and Cell Cycle • 5 Organisms in their environment • 6 Populations, communities, ecosystems • 7 Inheritance and DNA • 8 Gene Expression and Mutation • 9 Regulation, Genomes and Recombinant DNA • 10 Introduction to Development • 11 Introduction to Evolution • 12 Adaptation 1.1 General introduction • Related Sadava’s chapters: 1) Studying life 2) Small Molecules and the Chemistry of Life 3) Proteins, Carbohydrates, and Lipids 1.2 What is Biology? Characteristics of living organisms: • Consist of one or more cells • Contain genetic information • Use genetic information to reproduce themselves • Are genetically related and have evolved • Can extract energy from the environment 1.2 What is Biology? Evolution: a central theme of biology • Living systems evolve through differential survival and reproduction • The processes of evolution have generated the enormous diversity of life on Earth 1.2 What is Biology? entérobactérie diatomée tardigrade 1 µm 10 µm insecte 100 µm champignon oiseau "reptile" 1 cm BMC 12-13 1.2 What is Biology? • Unicellular organisms: a single cell carries out all the functions of life • Multicellular organisms: made of many cells that are specialized for different functions 1.2 What is Biology? • The study of cells was made possible by the invention of microscopes. • Robert Hooke in the 1600s described repeating units of plant material as cells. 1.2 What is Biology? Cell Theory: Matthias Schleiden and Theodore Schwann (1838) • Cells are the basic structural and physiological units of all living organisms. • Cells are both distinct entities and building blocks of more complex organisms. • All cells come from preexisting cells • All cells are similar in chemical composition • Most of the chemical reactions of life occur within cells • Complete sets of genetic information are replicated and passed on during cell division 1.2 What is Biology? 1.2 What is Biology? • Evolution: change in the genetic makeup of biological populations through time • Charles Darwin proposed that all living organisms are descended from a common ancestor by the mechanism of natural selection • Species: a group of organisms that can produce viable and fertile offspring with one another 1.2 What is Biology? • Humans select for desired traits when breeding animals • Darwin postulated that natural selection could occur through differential survival and reproductive success 1.2 What is Biology? • Genome: sum of all the DNA in a cell • DNA: the information that is passed from parent to daughter cells • All cells in a multicellular organism have the same genome 1.2 What is Biology? • DNA consists of repeating subunits called nucleotides • Gene: a specific segment of DNA that contains information for making a protein • Mutations are alterations in the nucleotide sequence 1.2 What is Biology? 1.2 What is Biology? • Metabolism: the sum total of all chemical transformations and other work done in all the cells of an organism • The reactions are integrally linked – the products of one are the raw materials of the next 1.2 What is Biology? • Multicellular organisms have an internal environment that is not cellular • Their cells are specialized or differentiated, and organized into tissues; tissues are organized into organs • Organ systems are groups of organs with interrelated functions 1.2 What is Biology? 1.2 What is Biology? • Model systems: using one type of organism to understand others • This is possible because all life is related by descent from a common ancestor, shares a genetic code, and consists of similar building blocks: cells 1.2 What is Biology? • Earth formed 4.6 to 4.5 billion years ago but it was 600 million years or more before life evolved • The history of Earth can be pictured as a 30-day month 1.2 What is Biology? 1.2 What is Biology? • For 2 billion years, life consisted of single cells called prokaryotes. • These cells were in the oceans, protected from UV radiation. • There was little or no oxygen (O2) in the atmosphere, and hence no protective ozone (O3) layer. 1.2 What is Biology? cellule procaryote typique flagelle membrane cellulaire cytoplasme nucleoide paroi pili ~ 1 µm Campbell & Reece BMC 12-13 1.2 What is Biology? Consequences of photosynthesis: • O2 accumulated in the atmosphere • Aerobic metabolism began • Ozone layer formed, which allowed organisms to live on land 1.2 What is Biology? • Eukaryotic cells evolved from prokaryotes • These cells have intracellular compartments called organelles with specialized cellular functions • The nucleus contains the genetic information 1.2 What is Biology? cellule eucaryote typique noyau reticulum endoplasmique rugueux centrosome reticulum endoplasmique lisse vesicules cis-Golgi cytosol trans-Golgi mitochondrie lysosome ~ 10-50 µm endosome trans-Golgi network membrane cellulaire matrice extracellulaire BMC 12-13 1.2 What is Biology? 1.2 What is Biology? La biologie*, une science récente Les disciplines à l’intérieur de la biologie (XIXe et XXe siècles) étaient traditionnellement définies par leurs objets, ou le niveau de leur analyse, ou leurs méthodes, ou leur échelle de temps caractéristique ... exemples: biochimie, génétique, biologie cellulaire, physiologie, écologie, botanique, zoologie, microbiologie, évolution (incluant la génétique des populations) et des sous-disciplines plus spécialisées: immunologie, neurosciences ... Lamarck (1744-1829) ces sous-disciplines sont désormais beaucoup mieux intégrées (depuis moins de trente ans) * Jean-Baptiste de Lamarck (1802) "Recherches sur l’organisation des êtres vivants" BMC 12-13 1.2 What is Biology? Biologists use many methods to expand our understanding of life. • Observation: improved by new technologies • Experimentation 1.2 What is Biology? 1.2 What is Biology? • Biological knowledge allows advances in human pursuits such as medicine and agriculture • These advancements can raise ethical and policy questions • Biological knowledge contributes to our understanding of human influences on our environment • Biologists are called on to advise governments making policy decisions 1.2 What is Biology? Distinguishing science and nonscience: • Scientific hypotheses must be testable, and have the potential of being rejected • Science depends on evidence that comes from reproducible and quantifiable observations 1.3 Small molecules and the chemistry of life 1.3 Small molecules and the chemistry of life 1.3 Small molecules and the chemistry of life • Polar molecules that form hydrogen bonds with water are hydrophylic (“water-loving”) • Nonpolar molecules such as hydrocarbons that interact with each other, but not with water, are hydrophobic (“water-hating”) • Individual interactions are brief and weak, but summed over a large molecule, can be substantial 1.4 Proteins 1.4 Proteins • Proteins: combinations of 20 amino acids • Carbohydrates: sugar monomers (monosaccharides) are linked to form polysaccharides • Nucleic acids: 4 kinds of nucleotide monomers • Lipids: noncovalent forces maintain interactions between lipid monomers 1.4 Proteins • Polypeptide chain: single, unbranched chain of amino acids. • The chains are folded into specific three dimensional shapes defined by the sequence of the amino acids. 1.4 Proteins Functions of proteins include: • Enzymes—catalytic proteins • Structural proteins provide physical stability and movement. • Defensive proteins (e.g., antibodies) • Receptor proteins—receive and respond to molecular signals • Transport proteins carry substances within the organism (e.g., hemoglobin). • Genetic regulatory proteins regulate when, how, and to what extent a gene is expressed. 1.4 Proteins Amino acids have carboxyl and amino groups—so they function as both acid and base 1.4 Proteins The peptide bond is inflexible—no rotation is possible. 1.4 Proteins These hydrophylic amino acids attract ions of opposite charges. 1.4 Proteins Hydrophylic amino acids with polar, but uncharged side chains form hydrogen bonds. 1.4 Proteins 1.4 Proteins Hydrophobic amino acids 1.4 Proteins • The primary structure of a protein is the sequence of amino acids • The sequence determines secondary and tertiary structure—how the protein is folded • The number of different proteins that can be made from 20 amino acids is enormous! 1.4 Proteins 1.4 Proteins Secondary structure: • α helix—right-handed coil resulting from hydrogen bonding between N—H groups on one amino acid and C=O groups on another • β pleated sheet—two or more polypeptide chains are aligned; hydrogen bonds from between the chains 1.4 Proteins • Tertiary structure: Bending and folding results in a macromolecule with specific three-dimensional shape • The outer surfaces present functional groups that can interact with other molecules 1.4 Proteins Tertiary structure is determined by interactions of R-groups: • Disulfide bridges • Hydrogen bonds • Aggregation of hydrophobic side chains • van der Waals forces • Ionic bonds 1.4 Proteins Complete descriptions of tertiary structure have been worked out for many proteins (in this case Lysozyme) 1.4 Proteins Proteins bind noncovalently with specific molecules. The specificity is determined by: • Protein shape—there must be a general “fit” between the 3-D shapes of the protein and the other molecule • Chemistry—R groups on the surface interact with molecules via ionic bonds, hydrophobically, or hydrogen bonds 1.4 Proteins Quaternary structure results from the interaction of subunits by hydrophobic interactions, van der Waals forces, ionic bonds, and hydrogen bonds. Each subunit has its own unique tertiary structure. 1.4 Proteins 1.4 Proteins • If a protein is heated, the secondary and tertiary structure is broken down; the protein is said to be denatured • When cooled, the protein may return to normal tertiary structure, demonstrating that the information to specify protein shape is contained in its primary structure 1.4 Proteins Conditions that affect secondary and tertiary structure: • High temperature • pH changes • High concentrations of polar molecules • Nonpolar substances 1.4 Proteins Lectures utiles Savada et al. Life (9th, Freeman, 2009, ~1200p) + online material Stryer Biochemistry (4th, Freeman, 1995, ~1.000p) Biochimie (4e, Flammarion, 1997) Biochemistry (6th, with collaborators) Alberts et al. Molecular biology of the cell (5th, Garland, 2007) Biol. moléc. de la cellule (4e, Flammarion, 2004, 1472p) Brown Genomes (3rd, Bios, 2006, ~700p) Genomes (2e, Flammarion, 2004, 585p) Gilbert Developmental biology (9th, 2010, ~700p) BMC 12-13
