Chemistry of Life

1. Chemistry of Life Chapter 2

2. An Intro to Chemistry

3. Matter • Any substance that has mass and takes up space • Composed of 1 or more elements • Found in 1 of 3 states • Gas – no definite shape or volume • Liquid – shape conforms to container • Solid – definite shape

4. Elements Human Oxygen 61.0% Carbon 23.0 Hydrogen 10.0 Nitrogen 2.6 Calcium 1.4 Phosphorus 1.1 Potassium 0.2 Sulfur 0.2 96% • Substances that can’t be broken down by ordinary chemical processes • 92 occur naturally on Earth • About 25 are essential to life • 96% of human body, as well as other living organisms, from 4 elements (CHON) • Composed of atoms • 2+ of same atoms is a molecule (O2) • 2+ of different atoms is a compound (NaCl, H2O) • Metal + poisonous gas = edible product • Gas + gas = liquid

5. Atoms • Smallest particles that retain the 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 dalton (atomic mass unit, amu) • Electrons • Mass is negligible (1/2000 amu)

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 • Neutral atoms contain equal # of electrons • Element specific • Mass number • Determined by number of protons + neutrons • Atomic weight: average of relative weights of all isotopes, versions of the element

7. The Periodic Table Most Common Elements in Living Organisms

8. Chemical Bonds • Energy relationship between electrons • Energy is the capacity to do work, cause change, or move matter • Kinetic: energy of motion • Potential: energy due to location or structure; capability • Electrons repel one another (magnets), but attracted to protons (opposites attract) • Determine chemical properties, reactivity, of atoms • Orbitals are key • Closer to the nucleus = lower energy and filled first • Octet rule: hold up to 8 electrons (not 1st = 2) • Outermost is valence shell • Chemical reactions are making and breaking bonds

9. Electron Shell Models • Inert versus reactive elements • Valence electrons

10. Ionic Bonds cation anion • One atom loses electron(s) to become _____ charge? • Another atom gains these electrons to become _____ charge? • Charge difference attracts the two ions to each other • Clinically called electrolytes • Very weak bond • E.g. Salts

11. Covalent Bonds • Atoms share a pair(s) of electrons to fill valence shell • Form single, double, or triple covalent bond, based on number of electrons shared • Strong bonds

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

13. Hydrogen Bonds • Special case of covalent bonds • Attractions between molecules • Polar hydrogen (slightly ‘+’ charge) attracted to another polar molecule (slightly ‘-’ charge) • Hold large molecules in a specific 3D shape

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. carbohydrates, lipids, proteins, and nucleic acids

17. Properties of Water • Temperature-stabilizing effects • Absorbs and releases large amounts of heat w/o significant change • Sun, wind, muscle activity • High heat of evaporation • Absorption of heat breaks bonds; liquid  gas • Sweating • Polar molecule • Hydrophobic and hydrophilic • Solvent/solute relationship • Blood circulation, waste disposal, and cleaning • Reactivity • Hydrolysis and dehydration reactions

18. Electrolytes • Ions able to conduct electrical current • Kidneys regulate • Salts contain ions other than H+ or OH- • E.g. NaCl, CaCO3, and calcium phosphates • Acids are hydrogen ion (H+) donors • Concentration determines acidity of a solution • E.g. pH < 7; HCl, H2CO3 • Bases are hydrogen 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 from 20 different amino acids (AA’s) • Variation distinguishes within and between species

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

21. Carbohydrates • General (CH2O)n ratio, end in ‘ose’ • Fuel source for cells • Glycosidic bonds • Dehydration vs. hydrolysis • Monosaccharides (simple) • Pentoses: ribose and deoxyribose • Hexoses: glucose, fructose, & lactose (energy production) • Disaccharides (simple) • Maltose, lactose (glu + gal), & sucrose (glu + fru) • Polysaccharides (complex) • Glycogen (animal storage) • Starch (plant storage)

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 • Cell membranes • Steroids • Hydrocarbon rings • Cholesterol and sex hormones • Eicosanoids • In all cell membranes • Prostaglandins role in blood clotting, inflammation, and labor contractions

23. Proteins • Chains of amino acids joined by peptide bonds • 20 different types (alphabet) • Peptide, 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 • Globular (functional proteins) • Enzymes • Transport • Immunity

25. Enzymes • Globular proteins acting as catalysts to speed a reaction • Lower 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 complementray pairs • Purines (2 rings): adenine (A) and guanine (G) • Pyrimidines (1 ring): thymine (T), cytosine (C), and uracil (U)

27. How DNA and RNA Differ DNA (deoxyribonucleic acid) RNA (ribonucleic acid) • Directs protein synthesis; replicates self; genetic material • Sugar is deoxyribose • Has –H • Bases are A,C, G, and T • Double-stranded helix • Only in nucleus • 1 type • Carries out protein synthesis • Sugar is ribose • Has -OH • Bases are A, C, G, and U • Single-stranded • Not confined to nucleus • 3 major types

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