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Chapter 3

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McMaster University
Lovaye Kajiura

BIO 1AA3 Chapter 3 Khizar Karim Chapter 3 – Protein and Function Key Terms Peptide backbone Prebiotic Soup _____________________________________________________________________________________________ - Proteins made up of amino acids, and the difference in structure and function are due to the differences in side chain composition - Chemical Evolution began with production of small organic compounds such as H2CO, HCN from reactants H2, C02, CH4, NH3 - H2C0 and HCN and other molecules combined to form amino acids, sugars, and nitrogenous bases which accumulated in ocean creating the prebiotic soup (monomers) - The various amino acids, sugars and nitrogenous bases combined to form macromolecules; proteins, nucleic acids and carbohydrates - Life started when one of these molecules gained the ability to self-replicate by the using the chemical reactions it could control 3.1 What do proteins do? - Most diverse in terms of function Defence Antibodies protein attack and destroy viruses and bacteria Movement Myosin, actin examples of contractile proteins Catalysis Enzymes; speed up reactions Signalling Hormones; act as signals coordinating the activity of cells Structure Provide support for cells and tissues Transport Moving substances across the membrane and throughout the cell body 3.2 Early Origin of Life Experiments - Stanley Miller wanted to recreate ancient earth in terms of the elements present in the atmosphere; mainly CO2, NH3, CH4, which were contained in a large flask - The large flask was connected to a smaller flask containing sea water which was heated up so that the water vapour could react with the gases in the larger flask, as they reacted, the gases condensed which stimulated “rain” that went back into the flask with boiling water Q: Why was it essential to boil water? - Initially there was no reaction as the reactants did not react spontaneously, but when he added electrodes to create sparks to stimulate lightning, it provided the BIO 1AA3 Chapter 3 Khizar Karim energy to start the reactions Q: Why was the addition of electrodes essential in his experiment? - After days the solution had turned pink, and after weeks it turned red and cloudy - When he examined which products were in the apparatus, he found HCN and H2CO, these reactants were required for the synthesis for more complex molecules - Complex molecules like amino acids were found in the miniature ocean Q: What was so significant about the initial products, HC0 and H2CO he found in the mini ocean flask? Q: How did the amino acids he found relate to the prebiotic soup? - Strong consensus that amino acids and other components of the prebiotic soup are readily produced under conditions that accurately stimulate the atmosphere and oceans of early earth 3.3 Amino Acids and Polymerization Structure of Amino Acids - NH2 – Amino Functional Group - COOH- is the carboxyl functional group - The COOH- is acidic; The oxygen atoms are highly electronegative; they have a strong attraction for shared electrons. The carboxyl group is acid because the high electronegative oxygen atoms pull the electrons away from the H atom in the O-H bond. When the electrons are pulled away from the H, it leaves the group as an H+ ion. Thus, the -COOH group is acidic (donates a proton). - When in water, the NH2 acts as a base to form NH3+ and the COOH loses an H to become COO - Q. Relate the properties of the functional groups found on the amino acid Q. How do they behave in water, and why? Q. Draw the amino acid in as many variations as possible (google images of different ways they represent amino acids) Nature of the Side Chains - The R group is what differentiates the properties of various amino acids into hydrophobic, hydrophilic, and electrically charged - The nature of the side chain dictates nature of the whole amino acid - Hydrophobic side chains render the whole amino acid nonpolar and thus incapable to react in water - With polar side chains, they readily react with water BIO 1AA3 Chapter 3 Khizar Karim - Polarity of the R group correlates with the amino acids ability to react with water (solubility) - R groups with carbon and hydrogen atoms are relatively non-reactive - R groups with OH-, H2N, COOH-, SH- are reactive Q. why are the side chains important? Q. How do they affect properties of the amino acid? Isomers - Molecules with the same molecular formula but different structures Structural Isome
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