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Chemistry Big Idea 2: Biological systems utilize free energy and molecular building blocks to grow, to reproduce, and to maintain dynamic homeostasis P.S. In Biology we talk mainly about Organic Chemistry: The chemistry of molecules containing Carbon.

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Chemistry Joke of the Day a Poem. Susan was in chemistry. Susan is no more, for what she thought was H 2 O was really H 2 SO 4.

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Essential knowledge 2.A.3: Organisms must exchange matter with the environment to grow, reproduce and maintain organization. a. Molecules and atoms from the environment are necessary to build new molecules Carbon moves from the environment to organisms where it is used to build carbohydrates, proteins, lipids, or nucleic acids. Carbon is used in storage compounds and cell formation in all organisms.. Nitrogen moves from the environment to organisms where it is used in building proteins and nucleic acids. Phosphorus moves from the environment to organisms where it is used in nucleic acids and certain lipids.

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Living systems depend on properties of water that result from its polarity and hydrogen bonding. Cohesion Adhesion High specific heat capacity Universal solvent to support reactions Heat of vaporization Heat of fusion (exo vs.endo) Waters thermal conductivity.

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Review of Chemistry Review of Chem Review of Water

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Essential knowledge 4.a.1: the subcomponents of biological molecules and their sequence determine the properties of that molecule. a. Structure and function of polymers are derived from the way their monomers are assembled. Lipids are nonpolar; however phospholipids exhibit structural properties, with polar regions that interact with other polar molecules such as water, and with nonpolar regions where differences in saturation determine the structure and function of lipids.. Carbohydrates are composed of sugar monomers whose structures and bonding with each other by dehydration synthesis determine the properties and functions of the molecules. Cellulose vs. Starch. Why does one dissolve? Lipids Trans fats

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Is this a carbohydrate or a lipid? How can your tell?

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Is this a carbohydrate or a lipid? How can you tell?

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What is the difference between Linear vs. branched polysaccharides? starch (plant) glycogen (animal) energy storage What does branching do? slow release fast release

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Cow can digest cellulose well; no need to eat other sugars Gorilla cant digest cellulose well; must add another sugar source, like fruit to diet

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How do animals break down cellulose? How can herbivores digest cellulose so well? Mutualism BACTERIA live in their digestive systems & help digest cellulose- rich (grass) meals Ruminants Coprophage I eat WHAT! Tell me about the rabbits, again, George!

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a. Structure and function of polymers are derived from the way their monomers are assembled. In nucleic acids, biological information is encoded in sequences of nucleotide monomers. Each nucleotide has structural components: a five-carbon sugar (deoxyribose or ribose), a phosphate and a nitrogen base (A,T,C,G,U). DNA and RNA differ in function and differ slightly in structure, and these structural differences account for the differing functions. In proteins, the specific order of amino acids in a polypeptide (primary structure) interacts with the environment to determine the overall shape of the protein, which also involves secondary tertiary and quaternary structure and, thus, its function. The R group of an amino acid can be categorized by chemical properties (Hydrophobic/philic, ionic), and the interactions of these R groups determine structure and function of that region of the protein.

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What are the three parts of Nucleotides? nitrogen base (C-N ring) pentose sugar (5C) ribose in RNA deoxyribose in DNA phosphate (PO 4 ) group Are nucleic acids charged molecules ? Nitrogen base Im the A,T,C,G or U part!

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How are Proteins structured? monomer = amino acids 20 different amino acids polymer = polypeptide protein can be one or more polypeptide chains folded & bonded together large & complex molecules complex 3-D shape RuBisCO cant do photosynthesis without it! hemoglobin H2OH2O Because everybody needs a Chaperonin!

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Sickle cell anaemia Im hydrophilic! But Im hydrophobic! Just 1 out of 146 amino acids!

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Isomers Molecules with same molecular formula but different structures (shapes) different chemical properties different biological functions 6 carbons

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Form affects function Structural differences create important functional significance amino acid alanine L-alanine used in proteins but not D-alanine medicines L-version active but not D-version sometimes with tragic results stereoisomers

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Form affects function Thalidomide prescribed to pregnant women in 50s & 60s reduced morning sickness, but stereoisomer caused severe birth defects

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b. Directionality influences structure and function of the polymer. Nucleic acids have ends, defined by the 3 and 5 carbons of the sugar in the nucleotide, that determine the direction in which complementary nucleotides are added during DNA synthesis and the direction in which transcription occurs (from 5 to 3) Proteins have an amino (NH2) end and a carboxyl (COOH) end, and consist of a linear sequence of amino acids connected by the formation of peptide bonds by dehydration synthesis between the amino and carboxyl groups of adjacent monomers. The nature of the bonding between carbohydrate subunits determines their relative orientation in the carbohydrate, which then determines the secondary structure of the carbohydrate.

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Learning Objectives: LO 4.1: The student is able to explain the connection between the sequence and the subcomponents of a biological polymer and its properties. LO 4.2: The student is able to refine representations and models to explain how the subcomponents of a biological polymer and their sequence determine the properties of that polymer

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2007-2008 Chemistry of Carbon Building Blocks of Life A Review for You!

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Why study Carbon? All of life is built on carbon Cells ~72% H 2 O ~25% carbon compounds carbohydrates lipids proteins nucleic acids ~3% salts Na, Cl, K

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Chemistry of Life Organic chemistry is the study of carbon compounds C atoms are versatile building blocks bonding properties 4 stable covalent bonds HH C H H

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Diversity of molecules Substitute other atoms or groups around the carbon ethane vs. ethanol H replaced by an hydroxyl group (OH) nonpolar vs. polar gas vs. liquid biological effects! ethane (C 2 H 6 ) ethanol (C 2 H 5 OH)

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Functional groups Parts of organic molecules that are involved in chemical reactions give organic molecules distinctive properties hydroxyl amino carbonyl sulfhydryl carboxyl phosphate Affect reactivity makes hydrocarbons hydrophilic increase solubility in water

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Viva la difference! Basic structure of male & female hormones is identical identical carbon skeleton attachment of different functional groups interact with different targets in the body different effects

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Hydroxyl OH organic compounds with OH = alcohols names typically end in -ol ethanol

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Carbonyl C=O O double bonded to C if C=O at end molecule = aldehyde if C=O in middle of molecule = ketone

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Carboxyl COOH C double bonded to O & single bonded to OH group compounds with COOH = acids fatty acids amino acids

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Amino -NH 2 N attached to 2 H compounds with NH 2 = amines amino acids NH 2 acts as base ammonia picks up H + from solution

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Sulfhydryl SH S bonded to H compounds with SH = thiols SH groups stabilize the structure of proteins

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Phosphate PO 4 P bound to 4 O connects to C through an O lots of O = lots of negative charge highly reactive transfers energy between organic molecules ATP, GTP, etc.

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2007-2008 Macromolecules Building Blocks of Life

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Macromolecules Smaller organic molecules join together to form larger molecules macromolecules 4 major classes of macromolecules: carbohydrates lipids proteins nucleic acids And a minor one: ATP

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H2OH2O HO H HH Polymers Long molecules built by linking repeating building blocks in a chain monomers building blocks repeated small units covalent bonds Dehydration Synthesis http://sciencestage.com/v/621/chemis try-experiment- science- dehydration- sugar.html http://sciencestage.com/v/621/chemis try-experiment- science- dehydration- sugar.html Dehydration Synthesis http://sciencestage.com/v/621/chemis try-experiment- science- dehydration- sugar.html http://sciencestage.com/v/621/chemis try-experiment- science- dehydration- sugar.html

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H2OH2O HO H HH How to build a polymer Synthesis joins monomers by taking H 2 O out one monomer donates OH other monomer donates H + together these form H 2 O requires energy & enzymes enzyme Dehydration synthesis Condensation reaction You gotta be open to bonding!

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H2OH2O HOH H H How to break down a polymer Digestion use H 2 O to breakdown polymers reverse of dehydration synthesis cleave off one monomer at a time H 2 O is split into H + and OH H + & OH attach to ends requires enzymes releases energy Breaking up is hard to do! Hydrolysis Digestion enzyme

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2007-2008 Any Questions?? And now on to Acids and Bases

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Ph Scale Fig 2.9, pg. 43 potential hydrogen Measured on grams of Hydrogen (H+) pH of 1=.1g of H+, pH of 2=.01g of H+ Acid: form hydronium ions (H+) pH of less than 7 ( 1 to 6.9) Base: form hydroxide ions (OH-) pH of more than 7 (7.1 to 14) Acid + Base: salt & water, the solution is neutral with a pH of 7. NaOH + HCl = H 2 O + NaCl with a pH of 7

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pH Scale

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What is a Buffer? Chemical substances that neutralizes small amounts of an acid or base added to a solution. Why are these important to your body? Think Blood pH 7.45

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What is a Buffer? three main buffers in the body:three main buffers bicarbonate buffer system: in the blood and stomach to neutralize acids protein buffer system: inter and extra cellular buffering used with hemoglobin and blood phosphate buffer system: used in the urinary system to remove H+ ions and make urine acidic

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Enzymes (most are Proteins) pg. 21 Barrons Catalysts: Lower activation energy needed to start a chemical reaction. See fig 2.22, pg.54 Nonspecific Inhibitors: Temperature, pH, radiation, electricity: Terms: substrate, active site, product Can be denatured Induced fit

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Enzymes continued Characteristics: Globular proteins (tertiary structure) Substrate specific Not destroyed /reused Named after substrate with ase ending Catalyze in both directions Catalyze with help Cofactor: inorganic Coenzyme: vitamin Control of Enzyme Activity Competitive Inhibition: competes for the space with the substrate Noncompetitive Inhibition/ Allosteric: secondary site stops enzyme from functioning PFK too much ATP Cooperativity: amplifies the response of an enzyme to its substrate. Hemoglobin, more oxygen it has.

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