Chemistry of Life

1. Chemistry of Life Chapter 2

2. An Intro to Chemistry

3. 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

4. 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

5. 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)

6. 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

7. 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

8. Electron Shell Models SODIUM 11p+ , 11e- CHLORINE 17p+ , 17e- electron proton neutron CARBON 6p+ , 6e- OXYGEN 8p+ , 8e- NEON 10p+ , 10e- HYDROGEN 1p+ , 1e- HELIUM 2p+ , 2e-

9. 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)

10. 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

11. Covalent Bonds • Atoms share outer pair or pairs of valence electrons • Single, double, or triple covalent bond • Strong bonds

12. What’s Mine is Yours or Just Mine Nonpolar Covalent Bonds Polar Covalent Bonds Electrons spend more time near the nucleus with the most protons (electronegativity) Example: water (H20) • Electrons shared equally • Example: carbon dioxide(CO2), hydrogen gas (H2)

13. 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

14. 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.

15. An Intro to Biochemistry

16. 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

17. 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

18. 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 • H2CO3HCO3- + H+

19. 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

20. Making and Breaking Polymers Dehydration reaction Hydrolysis reaction Breaks polymers Addition of water for each broken bond • Links monomers • Loss of water for each monomer added • Forms a covalent bond 1 2 4 3 4 1 2 3 1 4 2 3 1 2 3 4

21. 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

22. 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

23. 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)

24. Protein Types • Fibrous (structural proteins) • Building materials of the body • Keratin, elastin, and collagen • Movement • Actin and myosin • Globular (functional proteins) • Enzymes • Transport • Immunity

25. 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

26. Nucleic Acids • DNA and RNA • Composed of nucleotides with 3 components • Pentose sugar • Phosphate group (PO4) • Nitrogenous base form complementary pairs

27. How DNA and RNA Differ DNA (deoxyribonucleic acid) 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 • 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

28. 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