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Chemistry of Life Chapter 2 AN INTRO TO CHEMISTRY Matter • Substance that has mass and takes up space – Compose all living things • Generally found in 1 of 3 states • Composed of 1 or more elements Elements • Can’t be broken down by ordinary chemical processes • 92 occur naturally on Earth – 96% of the human body is (CHON) – 25 are essential to life • Composed of atoms Atoms • Smallest particles that retains properties of an element • Made up of subatomic particles: – Protons (+) in nucleus – Electrons (-) orbits nucleus – Neutrons (no charge) in nucleus • Protons and neutrons – Mass of about 1 • Electrons – Mass is negligible (1/2000) Reading A Periodic Table • Elements differ depending on the number of subatomic particles • Atomic symbol – 1st letter or 2 (usually) • Atomic number – Determined by number of protons – Element specific • Mass number – Determined by number of protons + neutrons Chemical Properties of Atoms • Electrons are key – Move in orbitals called shells – Repel one another, but attracted to protons • Electron shells – Outermost (valence) determines chemical properties • Closer to the nucleus = lower energy and are filled first – Holds up to 2 or 8 electrons (Octet Rule) • Filled are unreactive • Unfilled are reactive – Number differs between atoms • Chemical reactions are making and breaking bonds Electron Shell Models SODIUM 11p+ , 11e- CHLORINE 17p+ , 17e- electron proton neutron CARBON 6p+ , 6e- OXYGEN 8p+ , 8e- HYDROGEN 1p+ , 1e- HELIUM 2p+ , 2e- NEON 10p+ , 10e- Chemical Bonds • Hold 2 or more atoms together – Complete outer shells – By sharing, donating, or receiving electrons • Form molecules (H2, I2, and O2) or compounds (H20, NaCl, C6H12O6) – Demonstrates emergent properties • 2 H+ (gas) + O- (gas) = H2O (water) • Na+ (metal) + Cl- (poisonous gas) = NaCl (table salt) Ionic Bond • One atom loses electrons cation (charge?) • Another atom gains these electrons anion (charge?) • Charge difference attracts the two – Very weak bond – Table salt (NaCl) cation anion Covalent Bonds • Atoms share outer pair or pairs of valence electrons – Single, double, or triple covalent bond • Strong bonds What’s Mine is Yours or Just Mine Polar Covalent Bonds • Electrons spend more time • Electrons shared equally near the nucleus with the • Example: carbon dioxide(CO2), most protons hydrogen gas (H2) (electronegativity) • Example: water (H20) Nonpolar Covalent Bonds Hydrogen Bond • Positive charge on H attracts negative charge on another atom • Individually weak, but often numerous = strong • Important to many biological compounds – E.g. water • Makes up 70 – 90% of all living things • Bonds create unique properties Chemical Reactions • Chemical equation: reactant(s) + reactant(s) = product(s) – May be reversible – Move to equilibrium • Types – Synthesis: (A + B AB) usually anabolic and endergonic – Decomposition: (AB A + B) usually catabolic and exergonic – Exchange: (AB + CD AD + BC) may or may not be endergonic/exergonic – Redox: may gain or lose electrons • Oxidized – loses electrons (LEO) • Reduced – gains electrons (GER) • Affected by temperature, concentration, catalysts, etc. AN INTRO TO BIOCHEMISTRY Biologically Important Compounds • Inorganics lack carbon (generally) – E.g. salts, water, acids, and bases • Organics contain carbon, are covalently bonded, and generally large – E.g. carbs, lipids, proteins, and nucleic acids Properties of Water • High heat capacity – Absorb and release water with little temp. change – Environmental changes (internal and external) • High heat of vaporization – Lots of heat required to transform water to steam – Sweating • Polarity – Slightly negative AND slightly positive ends – Dissociation of salts, hydration layers, and transport • Reactant – Solubility – Dehydration and hydrolysis • Cushion/shock absorber – Acts as a barrier/buffer – CSF and joints Electrolytes • Ions able to conduct electrical current – Kidneys regulate • Salts contain ions other than H+ or OH– E.g. NaCl, KCl, and calcium phosphates • Acids are hydrogen ion (H+) donors – Concentration determines acidity of a solution – E.g. pH < 7; HCl, H2CO3 • Bases are hydrogen ion (H+) acceptors – Form water upon disassociation – E.g. pH > 7; Mg(OH) 2, HCO3-, and NH3 • Buffers release H + with increasing pH and accept H + when decreasing – H2CO3 HCO3- + H+ Building Organic Molecules • Monomers: small repeating units – Universal, similar in all forms of life • Polymers: chains of monomers, functional components of cells (macromolecules) – DNA is composed of 4 monomers (nucleotides) • Variation based on arrangement – Proteins are composed of 20 different amino acids (AA’s) • Variation distinguishes within and between species Making and Breaking Polymers Dehydration reaction • Links monomers • Loss of water for each monomer added • Forms a covalent bond 1 2 Hydrolysis reaction • Breaks polymers • Addition of water for each broken bond 4 3 1 1 2 3 2 3 4 4 1 2 3 4 Carbohydrates • General (CH2O)n ratio, ends in ‘ose’ • Fuel source for cells • Glycosidic bonds – Dehydration vs. hydrolysis • Monosaccharides – Pentoses – Glucose, fructose, & galactose • Disaccharides – Maltose, lactose, & sucrose • Polysaccharides – Glycogen – Starch Lipids • Composed of fatty acids (long carbon chains) and a glycerol (3 carbons) • Triglycerides – – – – 3 FA’s Most usable form of energy Fats (animal) and oils (plants) Saturated or unsaturated (mono- or poly-) • Phospholipids – 2 FA’s and a phosphate group – Amphipathic molecule • Steroids – Hydrocarbon rings – Cholesterol and sex hormones Proteins • Chains of amino acids joined by peptide bonds – 20 different types (alphabet) – Peptides, polypeptides, and proteins (words) are all slightly different • Structural levels – Primary (1°) – sequence of amino acids – Secondary (2°) – primary level folds to form alpha (α) – helixes and beta (β) - pleated sheets – Tertiary (3°) – folding of secondary structures on each other – Quaternary (4°) – 2+ polypeptides interact to form a protein • Denaturation destroys structure which alters or inhibits function – Changes in pH and temperature – Reversible or permanent depending on extend of change (fevers) Protein Types • Fibrous (structural proteins) – Building materials of the body • Keratin, elastin, and collagen – Movement • Actin and myosin • Globular (functional proteins) – Enzymes – Transport – Immunity Enzymes • Globular proteins acting as catalysts to speed a reaction – Lowers energy of activation (EA) • End in ‘ase’ and named for substrate • Mechanism of enzyme action: – Enzyme binds substrate at its active site on the enzyme. – Enzyme-substrate complex undergoes an internal rearrangement that forms a product. – Product released and now catalyzes another reaction Nucleic Acids • DNA and RNA • Composed of nucleotides with 3 components – Pentose sugar – Phosphate group (PO4) – Nitrogenous base form complementary pairs How DNA and RNA Differ DNA (deoxyribonucleic acid) • Directs protein synthesis; replicates self; genetic material • Sugar is deoxyribose – Has –H • Bases are adenine (A), cytosine (C), guanine (G), and thymine (T) • Double-stranded helix • Only in nucleus • 1 type RNA (ribonucleic acid) • Carries out protein synthesis • Sugar is ribose – Has -OH • Bases are adenine (A), cytosine (C), guanine (G), and uracil (U) • Single-stranded • Not confined to nucleus • 3 major types Adenosine Triphosphate (ATP) • RNA nucleotide with 3 phosphate groups • Stores energy from break down of glucose – Transfers phosphate groups to release energy = phosphorylation – Controls energy release