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BIO EXAM NOTES.pdf

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Department
Biology
Course
BIOLOGY 1A03
Professor
Jeffery Donaldson
Semester
Winter

Description
BIO 1A03 EXAM NOTES : Chapter 3 Protein Structure and Function: • 1953 - Stanley Miller performed an experiment to see whether simple molecules and kinetic energy lead to chemical evolution • hypothesis: if kinetic energy is added to a mix of simple molecules with high free energy, reactions will occur that produce more complex molecules, perhaps including some with C-C bonds • large flask represented the atmosphere and contained the gases methane (CH4), ammonia (NH4), and hydrogen (H2). large flask was connected to a smaller flask by glass tubing. the small flask held a tiny ocean - 200 millilitres (mL) of liquid water • water was boiled constantly, adding water vapour to the mix of gases in the large flask. as the vapour cooled and condensed, it flowed back into the smaller flask, where it boiled again. water vapour circulated continuously through the system • electrical discharges were sent across the electrodes inserted in the atmosphere, creating pulses of intense electrical energy • after a day of continuous boiling and sparking, the solution in the boiling flask began to turn pink. after a week, it was deep red and cloudy • large quantities of hydrogen cyanide (HCN) and formaldehyde (H2CO) were found in the mini ocean. these are key compounds in chemical evolution because they are required for reactions that lead to the synthesis of more complex organic molecules. the sparks and heating had led to the synthesis of compounds that are the building blocks of proteins: amino acids • conclusion: chemical evolution occurs readily if simple molecules with high free energy are exposed to a source of kinetic energy • controversy rose, as researchers pointed out that because volcanism would have been common at the time, the early atmosphere was dominated by volcanic gases like CO, CO2, and H2, not the CH4 and NH3 in Miller’s experiment • current consensus is that amino acids were abundant in the early oceans • there are 20 amino acids, all have a common structure • amino acids have a carbon atom that forms bonds to the following four groups or atoms: NH2 (amino functional group), COOH (carboxyl functional group), H (a hydrogen atom), and an “R group” (an atom or group of atoms called a side chain). each R group varies • the charges on these functional groups are important for two reasons: (1) they help amino acids stay in solution, where they can interact with one another and with other solutes; (2) they alter amino acid chemical reactivity • functional groups affect reactivity • several side chains found in amino acids contain the carboxyl, sulphydryl, hydroxyl, or amino functional groups, and under the right conditions can participate in chemical reactions • some amino acids contain side chains consisting entirely of carbon and hydrogen atoms, and these R-groups rarely participate in chemical reactions • the polarity of side chains affects solubility •amino acids with nonpolar side chains lack charged or electronegative atoms capable of forming hydrogen bonds with water. these R-groups are hydrophobic, and tend to coalesce in aqueous solution •amino acids with polar or charged side chains interact readily with water and are hydrophilic, and are easily dissolved in water • amino acids polymerize to form proteins; proteins are known as macromolecules •polymerization decreases entropy of the molecules involved •polymers are energetically much less stable than their component monomers; polymerization reactions are endergonic and nonspontaneous • monomers polymerize through condensation reactions (also known as dehydration reactions), which results in the loss of a water molecule • the reverse reaction, hydrolysis, breaks polymers apart by adding a water molecule • the peptide bond • amino acids polymerize when a bond forms between the carboxyl group of one amino acid and the amino group of another •the C-N bond that results is called a peptide bond •since water is lost in the condensation reaction, the carboxyl group of the amino acid is converted to a carbonyl functional group in the polymer •peptide bonds are unusually stable because the electrons involved are partially shared between the peptide bond and the neighbouring carbonyl functional group; the degree of electron sharing is great enough that peptide bonds actually have some of the characteristics of a double bond •when amino acids are linked by peptide bonds into a chain, the amino acids are referred to as residues and the resulting molecule is called a polypeptide •three key points to note about the peptide-bonded backbone of a polypeptide: • R-group orientation • directionality • flexibility • primary structure •R-groups affect that molecule’s properties and function; in some cases a single change in the sequence of amino acids can cause radical changes in the way the macromolecule as a whole behaves •example: the hemoglobin protein in humans. in some individuals, hemoglobin has a valine instead of a glutamate. valine’s side chain is radically different from the R-group in glutamate. this change produces a protein that tends to crystalize instead of staying in solution when oxygen concentrations in the blood are low. when hemoglobin crystallizes, the red blood cells that carry the protein adopt a sickled shape. sickled red blood cells get stuck in the small blood vessels called capillaries. in people whose hemoglobin contains this single amino acid change, cells downstream of blocked capillaries become st
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