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Biol 205 S08 Week 2 Lecture 1 1. Intro to proteins 2. Basic carbon chemistry 3. Functional groups 4. Macromolecules in cells In Alberts: Chapter 2 pp. 50-52, 55-56 Panels 2-1 (chemical bonds), 2-2 (water) 2-5 (amino acids) Chapter 4 - start reading Reading Assignment for next lecture: Text: Chapter 2 pp. 58-65, 74-75, Chapter 4 pp 119-- 143 Panels 2-2 (on water) and 2-7 (on noncovalent bonds) Panel 4-2 on pg 132: Four ways of depicting protein structure Recall that the SRY gene codes for a regulatory protein that orchestrates the production of a testes during the development of a mammalian embryo The SRY protein controls the transcription of specific genes required to build a testes from an “indifferent” gonad >gi|17488858|ref|XM_010627.4| Homo sapiens SRY (sex determining region Y chromosome) Shorthand abbreviation of part of the DNA sequence of the SRY gene GGCATGTGAGCGGGAAGCCTAGGCTGCCAGCCGCGAGGACCGCACGGAGGAGGAG CAGGAGCGCGGAGCCGCGAGCCCCGAGCCCCGAGCCCGGCGCCTGGCTGAGTAGAT GTCCATGAGGAGCCCCATCTCTGCCCAGCTGGCCCTGGATGGCGTTGGCACCATGGT GAACTGCACCATCAAGTCAGAGGAGAAGAAAGAGCCTTGCCACGAGGCCCCCCAGG GCTCAGCCACTGCCGCTGAACCTCAGCCTGGAGACCCAGCCCGGGCCTCCCAGGAT AGTGCTGACCCCCAAGCTCCAGCCCAGGGGAATTTCAGGGGCTCCTGGGACTGTAGCTCTCCAG AGGGTAATGGGTCCCCAGAACCCAAGAGACCAGGAGTGTCGGAGGCTGCCTCTGGAAGCCAGGA GAAGCTGGACTTCAACCGAAATTTGAAAGAAGTGGTGCCAGCCATAGAGAAGCTGTTGTCCAGT GACTGGAAGGAGAGGTTTCTAGGAAGGAACTCTATGGAAGCCAAAGATGTCAAAGGGACCCAAG AGAGCCTAGCAGAGAAGGAGCTCCAGCTTCTGGTCATGATTCACCAGCTGTCCACCCTGCGGGA CCAGCTCCTGACAGCC Proteins are polymers of L amino acids http://www.clunet.edu/BioDev/omm/aa/aa.htm Shorthand abbreviation of the protein sequence coded for by the SRY gene >gi|17384045|emb|CAD13147.1| sex determining region Y [Homo sapiens] MQSYASAMLSVFNSDDYSPAVQENIPALRRSSSFLCTESCNSKYQCET GENSKGNVQDGVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGY QWKMLTEAEKWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPKNCSL LPADPASVLCSEVQLDNRLYRDDCTKATHSRMEHQLGHLPPINAASSP QQRDRY This week we will explore the general structure and function of proteins First we will review some basic chemistry 02_02_atomic number.jpg • The electron configuration of carbon – Gives it covalent compatibility with many different elements Hydrogen Oxygen Nitrogen Carbon (valence = 1) (valence = 2) (valence = 3) (valence = 4) N C H O Figure 4.4 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular Diversity Arising from Carbon Skeleton Variation • Carbon chains – Form the skeletons of most organic molecules – Vary in length and shape H H H H C C C H H H H Propane H H C H H H H H H H (b) Branching H C C C C H H C C C H H H H H H H H 2-methylpropane Butane (commonly called isobutane) H H H H H H H H (c) Double bonds H H C C C C H C C C C H H H H H 1-Butene 2-Butene H H H H C H H C C H C H (d) Rings H C C H H C C H H C C C (a) Length Figure 4.5 A-D H H H C C H H H Ethane Cyclohexane Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Benzene The Functional Groups Most Important in the Chemistry of Life • Functional groups – Are the chemically reactive groups of atoms within an organic molecule Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings – Give organic molecules distinctive chemical properties Estradiol OH CH3 HO Female lion OH CH3 CH3 O Figure 4.9 Male lion Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Testosterone • Six functional groups are important in the chemistry of life – Hydroxyl – Carbonyl – Carboxyl – Amino – Sulfhydryl – Phosphate Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings • Some important functional groups of organic compounds FUNCTIONAL GROUP HYDROXYL CARBONYL CARBOXYL O OH (may be written HO C C OH ) STRUCTURE In a hydroxyl group (—OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule. (Do not confuse this functional group with the hydroxide ion, OH–.) Figure 4.10 O The carbonyl group ( CO) consists of a carbon atom joined to an oxygen atom by a double bond. > Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings When an oxygen atom is doublebonded to a carbon atom that is also bonded to a hydroxyl group, the entire assembly of atoms is called a carboxyl group (—COOH). • Some important functional groups of organic compounds AMINO SULFHYDRYL H O SH N (may be written HS H The amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton. PHOSPHATE ) O P OH OH The sulfhydryl group consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape. Figure 4.10 Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In a phosphate group, a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges; abbreviated P . The phosphate group (—OPO32–) is an ionized form of a phosphoric acid group (—OPO3H2; note the two hydrogens). 02_15_organic molecules.jpg 02_26_Macromolecules.jpg 02_12_polar covalent.jpg 02_14_Protons on move.jpg 02_21_Alanine.jpg A protein is a polymer of amino acids connected by peptide bonds -- also called polypeptides 04_01_peptide bonds.jpg 04_02_polypeptide back.jpg Decoding the SRY sequence: