Biochemistry Topics Inorganic chemistry Water Organic chemistry (macromolecules) Carbohydrates Lipids Proteins Nucleic acids Why are we studying chemistry? Biology has chemistry at its foundation SI Unit Prefixes Everything is made of matter Matter is made of atoms Atoms are made of: protons+mass of 1 nucleus neutrons0mass of 1 nucleus electrons- mass [ - OH], water is acidic If [ - OH] > [H + ], water is basic pH scale = how acidic or basic a solution is pH & Biology pH of a neutral solution = 7 Acidic solutions =pH 7 Most biological fluids have pH 6 8 pH values in human stomach can reach 2 Each pH unit represents a 10-fold difference in H + & OH - concentrations. small change in pH actually indicates a substantial change in [H + ] & [OH - ] Buffers Have properties that allow them to act as either an acid or a base (minimizing changes in pH) Biological molecules/rxns are very sensitive to changes in pH (ex: pH of blood must stay between 7.4 and 7.2. If brought to 7 cause a coma) * Without buffers, a very small amount of an acid (1x10 -6) will cause a large change in pH (a whole unit) 10. Importance of Water ~ makes up 70-90% of living things ~ all life occurs in water: every cell is bathed in water for rxns to occur ~ water has unique physical properties b/c of Its hydrogen bonding 1. stable & polar 2. three forms: ice, solid, gas 3. high heat capacity & retains heat 4. universal solvent 5. cohesion and high surface tension (elastic film) 6. expands when freezes 7. dissociates to form protons H+ and hydroxide ions OH- 9. effective buffer against extreme temperature fluctuations Stable & Polar polar covalent bonds (pair of electrons not shared equally by 2 atoms) + & poles Oxygen has a stronger attraction for the H Oxygen has a higher electronegativity Polar covalent bonds 2 hydrogens in the water molecule form an angle Water molecule is polar oxygen end is hydrogen end is + Leads to many interesting properties of water. Water molecules form H bonds with each other + attracted to creates a sticky molecule Hydrogen bonds Positive H atom in 1 water molecule is attracted to negative O in another Can occur wherever an -OH exists in a larger molecule Weak bonds Cohesion (think cuddle) H bonding between H 2 O creates cohesion water is sticky surface tension drinking straw can you suck sugar up a straw? Adhesion (think attach) H 2 O molecules form H bonds with other substances capillary action meniscus water climbs up fiber ex. paper towel How does H 2 O get to top of tree? (transpiration) Transpiration Lets go to the video tape! (play movie here)play movie here Water is the solvent of life H 2 O is a good solvent due to its polarity polar H 2 O molecules surround + & ions solvents dissolve solutes creating aqueous solutions Hydrophilic substances have affinity for H 2 O polar or non-polar? ionic Hydrophobic substances do not have affinity for H 2 O polar or non-polar? non-ionic fat (triglycerol) The special case of ice Most (all?) substances are more dense when they are solid But not water Ice floats! H bonds form a crystal with loose structure Ice floats Why is ice floats important? Oceans & lakes dont freeze solid if ice sank eventually all ponds, lakes & even ocean would freeze solid during summer, only upper few inches would thaw surface ice insulates water below allowing life to survive the winter seasonal turnover of lakes cycling nutrients Specific heat H 2 O has high specific heat due to H bonding H 2 O resists changes in temperature takes a lot to heat it up takes a lot to cool it down H 2 O moderates temperatures on Earth Evaporative cooling Organisms rely on heat of vaporization to remove heat Water is a polar molecule The special properties of water make life on Earth possible The chemical behavior of water governs how organisms function Punchline Any Questions?? I norganic Chemistry ~ small and very reactive compounds ~ about 20,000 different compounds Organic Chemistry Contains carbon & hydrogen 2. Can form chains (weakest), rings (strongest) & helixes 3. React slowly & most are insoluble in water Why study Carbon? All living things are made of cells Cells ~72% H 2 O ~3% salts (Na, Cl, K) ~25% carbon compounds carbohydrates lipids proteins nucleic acids Chemistry of Life Organic chemistry is the study of carbon compounds C atoms are versatile building blocks bonding properties 4 stable covalent bonds Complex molecules assembled like TinkerToys Hydrocarbons Simplest C molecules = hydrocarbons combinations of C & H Simplest HC molecule = methane 1 carbon bound to 4 H atoms non-polar not soluble in H 2 O hydrophobic stable very little attraction between molecules a gas at room temperature Hydrocarbons can grow adding C-C bonds straight line ethane hexane branching isohexane ring cyclohexane ethane hexane cyclohexane isohexane methane Diversity of organic molecules Isomers Molecules with same molecular formula but different structures different chemical properties Structural isomers Molecules differ in structural arrangement of atoms Geometric isomers Molecules differ in arrangement around C=C double bond same covalent partnerships Enantiomer (stereo) isomers Molecules which are mirror images of each other C bonded to 4 different atoms or groups assymetric left-handed & right-handed versions L versions are biologically active 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 Form affects function Thalidomide prescribed to pregnant women in 50s & 60s reduced morning sickness, but stereoisomer caused severe birth defects Diversity of molecules Substitute other atoms or groups around the C ethane vs. ethanol H replaced by an hydroxyl group (OH) nonpolar vs. polar gas vs. liquid biological effects! ethanol ethane Functional Groups Functional groups Components of organic molecules that are involved in chemical reactions give organic molecules distinctive properties ex: male & female hormones Viva la difference! Basic structure of male & female hormones is identical identical C skeleton attachment of different functional groups interact with different targets in the body Types of functional groups 6 functional groups most important to chemistry of life: hydroxyl u amino carbonyl u sulfhydryl carboxyl u phosphate Affect reactivity hydrophilic increase solubility in water Hydroxyl OH organic compounds with OH = alcohols names typically end in -ol ethanol Carbonyl C=O O double bonded to C if C=O at end molecule = aldelhyde if C=O in middle of molecule = ketone Carboxyl COOH C double bonded to O & single bonded to OH group compounds with COOH = acids fatty acids amino acids Amino -NH 2 N attached to 2 H compounds with NH 2 = amines amnio acids NH 2 acts as base ammonia picks up H + from solution Sulfhydryl SH S bonded to H compounds with SH = thiols SH groups stabilize the structure of proteins Phosphate PO 4 P bound to 4 O connects to C through an O PO 4 are anions with 2 negative charges function of PO 4 is to transfer energy between organic molecules (ATP)