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BIOCHEMISTRY REVIEW Water, carbon and more…. About 25 elements are essential for life Four elements make up 96% of living matter: • carbon (C) • hydrogen (H) • oxygen (O) •nitrogen (N) Four elements make up most of remaining 4%: • phosphorus (P) • calcium (Ca) • sulfur (S) • potassium (K) Weak bonds hydrogen bonds attraction between + and – hydrophobic & hydrophilic interactions interaction with H2O van derWaals forces (ionic) Strong bonds covalent bonds – – H2 (hydrogen gas) Why are covalent bonds strong bonds? two atoms share a pair of electrons both atoms holding onto the electrons very stable Forms molecules H Oxygen H H2O molecules form H-bonds with each other +H attracted to –O creates a sticky molecule Special properties of water 1. cohesion & adhesion surface tension, capillary action 2. good solvent many molecules dissolve in H2O hydrophilic vs. hydrophobic 3. lower density as a solid ice floats! 4. high specific heat water stores heat 5. high heat of vaporization heats & cools slowly Cohesion H bonding between H2O molecules water is “sticky” surface tension drinking straw Adhesion H bonding between H2O & other substances capillary action meniscus water climbs up paper towel or cloth Polarity makes H2O a good solvent polar H2O molecules surround + & – ions solvents dissolve solutes creating solutions Most (all?) substances are more dense when they are solid, but not water… Ice floats! H bonds form a crystal H2O resists changes in temperature high specific heat takes a lot to heat it up takes a lot to cool it down H2O moderates temperatures on Earth H+ Ion Concentration pH Examples of Solutions 100 0 10–1 1 10–2 2 Stomach acid, Lemon juice 10–3 3 Vinegar, cola, beer 10–4 4 Tomatoes 10–5 5 Black coffee, Rainwater 10–6 6 Urine, Saliva 10–7 7 Pure water, Blood 10–8 8 Seawater 10–9 9 Baking soda 10–10 10 Great Salt Lake 10–11 11 Household ammonia 10–12 12 Household bleach 10–13 13 Oven cleaner 10–14 14 Sodium hydroxide Hydrochloric acid pH pH of cells must be kept ~7 pH affects shape of molecules shape of molecules affect function pH affects cellular function Control pH by buffers reservoir of H+ donate H+ when 9 [H+] falls 8 absorb H+ when 7 [H+] rises 6 5 Buffering range 4 3 2 1 0 0 1 2 3 4 Amount of base added 5 All of life is built on carbon Cells ~72% H2O ~25% carbon compounds carbohydrates lipids proteins nucleic acids ~3% salts Na, Cl, K… HYDROCARBONS Combinations of C & H non-polar not soluble in H2O hydrophobic stable very little attraction between molecules a gas at room temperature METHANE Simplest hydrocarbon 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 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 January 17, 2014 Guided Reading due Monday Get ready for QQ POLYMERS • Long molecules built by linking repeating building blocks in a chain – monomers • building blocks • repeated small units – covalent bonds H 2O HO HO H HO H H Dehydration Synthesis- HOW TO BUILD A POLYMER • Synthesis – joins monomers by “taking” H2O out • one monomer donates OH– • other monomer donates H+ • together these form H2O – requires energy & enzymes H 2O DEHYDRATION SYNTHESIS HO HO H HO H H HOW TO BREAK DOWN A POLYMER • Digestion – use H2O to breakdown polymers • reverse of dehydration synthesis • cleave off one monomer at a time • H2O is split into H+ and OH– – H+ & OH– attach to ends – requires enzymes – releases energy H2O HO HO HYDROLYSIS H H HO H CARBOHYDRATES • Structure / monomer – monosaccharide • Function – energy – raw materials – energy storage – structural compounds • Examples – glucose, starch, cellulose, glycogen CH2OH H O H OH H HO H OH CH2OH O H H OH Glucose HO H O C H HO OH H H C OH Ribose H C OH H H Glyceraldehyde GLUCOSE + GLUCOSE MALTOSE GLUCOSE + FRUCTOSE SUCROSE POLYSACCHARIDES • Polymers of sugars – costs little energy to build – easily reversible = release energy Glycogen-glucagon-glycogenolysis; How are these terms related to each other? LIPIDS • Structure / building block – glycerol, fatty acid, cholesterol, H-C chains • Function – energy storage – membranes – hormones • Examples – fat, phospholipids, steroids STEROIDS PROTEINS • Structure / monomer – amino acids – levels of structure • Function – enzymes – transport – signals -defense -structure -receptors • Examples – digestive enzymes, membrane channels, insulin, actin Structure central carbon amino group carboxyl group (acid) R group (side chain) variable group different for each amino acid confers unique chemical properties to each amino acid like 20 different letters of an alphabet can make many words (proteins) PROTEIN STRUCTURE • Function depends on structure – 3-D structure • twisted, folded, coiled into unique shape PRIMARY STRUCTURE – slight change in amino acid sequence can affect protein’s structure & its function • even just one amino acid change can make all the difference! – amino acid sequence determined by gene (DNA) IS PRIMARY STRUCTURE IMPORTANT? SECONDARY STRUCTURE TERTIARY STRUCTURE QUATERNARY STRUCTURE NUCLEIC ACIDS • Function: – genetic material • stores information – genes – blueprint for building proteins » DNA RNA proteins • transfers information – blueprint for new cells – blueprint for next generation G C T A A C G T A C G T A Examples: RNA (ribonucleic acid) single helix DNA (deoxyribonucleic acid) double helix Structure: monomers = nucleotides • 3 parts NUCLEOTIDES – nitrogen base (CN ring) – pentose sugar (5C) • ribose in RNA • deoxyribose in DNA – phosphate (PO4) group 2 types of nucleotides different nitrogen bases purines double ring N base adenine (A) guanine (G) pyrimidines single ring N base cytosine (C) thymine (T) uracil (U) NUCLEIC POLYMER • Backbone – sugar to PO4 bond – phosphodiester bond • new base added to sugar of previous base • polymer grows in one direction – N bases hang off the sugar-phosphate backbone Nucleotides bond between DNA strands H bonds purine :: pyrimidine A :: T 2 H bonds G :: C 3 H bonds DNA DOUBLE HELIX • Double helix – H bonds between bases join the 2 strands • A :: T • C :: G DNA REPLICATION “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.” James Watson Francis Crick 1953