A.C.E. Biology Spring 2011

1. A.C.E. BiologySpring 2011 CHAPTER III: The Chemistry of Organic Molecules

2. CARBOHYDRATES • Carbohydrate = “CARBON + WATER” • (CH2O)n = the empirical formula • MONOSACCHARIDES = simple sugars, of which there are several; C6H12O6 is a simple sugar that exists in several isomeric forms (organic molecules with identical molecular formulas but different arrangements of the atoms comprising the molecules)

3. GLUCOSE – a simple sugar in the form of a six-sided ring (a hexose); holds a place of special significance in the chemistry of living organisms; it is broken down to release the energy needed for metabolic reactions through the process of CELLULAR RESPIRATION

4. FRUCTOSE – another simple sugar, this time a five-sided sugar, with one carbon forming a KETONE GROUP; this is a member of the Ketose Family • Two other five-sided sugars, found in RNA and DNA respectively, are RIBOSE and DE-OXIRIBOSE

5. DISACCHARIDES = “double sugars” with an empirical formula of C12H22O11 • Two monosaccharides covalently bond during a dehydration (synthesis) reaction • The linkage formed between the 2 monosaccharides is known as a GLYCOSIDIC LINKAGE • As with all reactions, this one requires the presence of biologically active protein catalysts = ENZYMES • SUCROSE= “table sugar” – comprised of one glucose molecule and one fructose molecule

6. MALTOSE – disaccharide comprised of 2 glucose sub-units • LACTOSE = “milk sugar” – comprised of one glucose molecule and one galactose molecule • EVOLUTIONARY HISTORY: “Lactose Intolerance” – milk is a mammary product designed to sustain newborns of specific species; humans did not evolve to consume milk of other species; appear to have adapted to its consumption during one of the relatively recent glaciations; Lactose Intolerance occurs due to the absence of the enzyme LACTASE needed to digest lactose. Lactose Intolerance is more predominent in people of non-Caucasian ancestry

7. POLYSACCHARIDES = longer chains of covalently bonded simple sugars with the general empirical formula (CH2O)n – can be very large • GLYCOGEN – a common polysaccharide used by animals as a way to store glucose in the liver and muscle tissue; a highly branched chain; short-term energy storage • PLANT STARCHES – stored food reserves • AMYLOSE = simplest plant storage starch; unbranched chain of glucose subunits; 20% of potato starch [1-4 linkages] • AMYLOPECTIN = other 80% of potato starch; highly branched large polymer [1-6 linkages]

8. CELLULOSE – the structural polymer in plants; the most abundant polysaccharide on the planet • Made from BETA (β) GLUCOSE isomer – has a difference in the position of the –H and the –OH on the primary carbon unit – which results in every other glucose unit being inverted • The molecule does not coil, it remains linear & draws together to form cable-like MICROFIBRILS, then larger FIBRILS due to hydrogen bonding; this results in greater tensile strength & flexibility

9. CELLULOSE is insoluble/indigestible to most animals; requires a specific enzyme – CELLULASE – to hydrolyze the molecule • TERMITES & UNGULATES (cows, etc.) have resident fauna within their intestines that secrete CELLULASE, allowing them to digest the molecule • CHITIN = 2nd most abundant polysaccharide on the planet; used by insects to form exoskeletons and by fungi for cell walls; also undigestible by most animals

10. LIPIDS • Greasy, oily, fat-soluble • HYDROPHOBIC – defined by their solubility rather than their structure • Generally NON-POLAR; so dissolve in non-polar solvents like CHLOROFORM & ETHER • Can be large or small molecules • Energy storage molecules • Structural molecules • Hormones; lubricants • Parts of proteins and carbohydrates

11. I. TRIGLYCERIDES = Fats & Oils • FATS – have a higher melting point and are solid at room temperature • OILS – have a lower melting point and are liquid at room temperature • Both are comprised of 3 FATTY ACID CHAINS attached to a GLYCEROL molecule • GLYCEROL = an ALCOHOL with 3 carbons and 3 hydroxyl side groups • FATTY ACID = a hydrocarbon chain with a CARBOXYL (ACID) GROUP at one end; can be of different lengths, but commonly 14, 16, 18 or 20 carbons long; not very water soluble

12. TRIGLYCERIDES form through a DEHYDRATION REACTION; 3 fatty acids covalently bond with a glycerol molecule, forming ESTER LINKAGES and releasing 3 water molecules

13. SATURATED FATS = triglycerides whose fatty acids contain all the HYDROGEN ATOMS possible – no double bonds on the chain; all single covalent bonds • High melting point • Solid at room temperature • Most often of animal origin • Consumption of these saturated fats is associated with circulatory disorder and heart disease

14. UNSATURATED FAT = a triglyceride that has at least one double bond between carbons in the chain and producing a rigid point in the chain; liquid at room temperature and resists freezing; usually found in PLANTS; also found in the most exposed regions in animals that live in extremely cold environments (feet of penguin & reindeer to guard against freezing) • POLYUNSATURATED FATS = fats containing multiple carbon to carbon double bonds; multiple rigid points

15. ESSENTIAL FATTY ACIDS = certain unsaturated fats we need for our cell membranes that WE CANNOT SYNTHESIZE; we are unable to synthesize double bonds in triglycerides beyond the 9th carbon in the chain; only two for humans: • LINOLEIC ACID (an Omega-6 fatty acid) found in cotton seed oil • ALPHA-LINOLENIC ACID (an Omega-3 fatty acid) found in linseed (flaxseed) oil • Other food sources for these essential fatty acids include: • hemp oil/seed, shell fish, canola (rapeseed) oil, chia seeds, pumpkin seeds, sunflower seeds, leafy vegetables, & walnuts

16. II. PHOSPHOLIPIDS = component of the cell, and other plasma, membranes • Comprised of 2 FATTY ACIDS (one saturated, the other not) attached to a GLYCEROL molecule with an PHOSPHATE-BEARING COMPLEX • PLASMA MEMBRANE = comprised of two PHOSPHOLIPID layers arranged tails to tails = a PHOSPHOLIPID BI-LAYER; also includes GLYCOLIPIDS (sugar lipids) and GLYCOPROTEINS (sugar proteins); the center has oily characteristics

17. Phosphate head has negative charge & is HYDROPHILIC • The tails are HYDROPHOBIC • Individual phospholipid molecules will spontaneously assemble into BI-LAYERS and aggregate as hollow spheres called MICELLS • Interaction of the polar heads & water = electrostatic attraction & hydrogen bonding • Hydrophobic interaction = clumping & packing together of non-polar tails • May have been one of the mechanisms in the evolution of the first cells

18. Bilayer continued . . . . . . • VanDerWaals Forces = being generated by large numbers of molecules being drawn together • PROPERTIES OF PHOSPHOLIPID BI-LAYER: • Tend to self-perpetuate & be extensive • Tend to close in on themselves • Automatically repair any holes or tears III. WAXES = one fatty acid covalently joined by ester linkage (C-O-C) to a long chain alcohol • HYDROPHOBIC – even more so than fats – and “harder” • EX: beeswax; cerumen (ear wax); waxy cuticle on leaves and fruit

19. IV. STEROIDS = comprised of 4 interlocking rings of carbon & hydrogen; hydrophobic & non-polar; another component of cell membranes; all steroids are derived from CHOLESTEROL • CHOLESTEROL = an important nutrient with several vital functions: • Used to form bile acids • A derivative is converted into Vitamin D • Used to synthesize all other steroid hormones • Estrodiols and testosterones

20. PROTEINS • PROTEINS are the heavyweights among the molecules of life; huge MACROMOLECULES comprised of one or more POLYPEPTIDES (which are made of a linear chain of AMINO ACIDS covalently bonded by PEPTIDE BONDS – enormous variation in size of the chains) • PEPTIDE – a short chain of amino acids joined by peptide bonds • DIPEPTIDE – 2 amino acids joined by a single peptide bond

21. PROTEINS – many functions – of primary importance to the structure and function of cells • SUPPORT: structural proteins • KERATIN – makes up hair & nails • COLLAGEN – lends support to ligaments, tendons & skin • ENZYMES: bring reactants together and speed up chemical reactions; specific for one type of reaction; function at body temperature; CATALYSTS • DEFENSE: ANTIBODIES are proteins; identify foreign proteins known as ANTIGENS, to prevent these antigens from destroying cells, causing disease & thus upsetting homeostasis

22. TRANSPORT: plasma membrane contains CHANNEL & CARRIER PROTEINS allow substances to enter and exit cells. Other proteins transport molecules in the blood of animals • HEMOGLOBIN – huge globular 4˚ level protein pigment on RBCs that transports O2 in the blood • HORMONES: regulatory proteins; intercellular messengers that influence the metabolism of cells • INSULIN – regulates level of glucose in blood & cells • HUMAN GROWTH HORMONE – determines height of individual • MOTION: contractile proteins ACTIN & MYOSIN allow parts of cells to move & cause muscles to contract; enables animals to move from place to place

23. TWO GENERAL CATEGORIES OF PROTEIN SHAPE • GLOBULAR: folds spontaneously into compact globs – usually has a large preponderance of ALPHA HELIX sections in its structure • ENZYMES, HORMONES & ANTIBODIES • FIBROUS: remains linear, but zig-zags or fan-folds; occurs in MUSCLES, LIGAMENTS & TENDONS; preponderance of BETA-PLEATED SHEET segments • COLLAGEN – makes up most of the structure of ligaments and tendons and is the most common protein in the vertebrate body

24. AMINO ACIDS: basic building blocks of PROTEINS • There are 20 PRIMARY AMINO ACIDS • Additional secondary amino acids are derived from the primary amino acids • All of them have the same basic structure –

25. Amino Acids continued . . . . • Readily ionize in standard physiological conditions; carboxyl group gives off a proton and the amine group takes on a proton – so it has both a (+) and a (-) charge • The R-GROUPS are where the 20 amino acids differ; their structure and properties affect protein’s shape • 8 NON-POLAR R-GROUPS: hydrophobic - mainly hydrocarbons that cluster together in a water environment • 7 POLAR R-GROUPS: hydrophilic – form HYDROGEN BONDS with water and with other polar R-groups • 5 R-GROUPS IONIZE WITH WATER and thus bear additional (+) and (-) charges • (+) charged amino acids within a protein will interact with one another to form IONIC BONDS

27. CONFORMATION: a protein’s specific 3-dimensional shape; determined by amino acid content and their various interactions • Many proteins work through RECOGNITION & BONDING • RECOGNITION = by protein’s shape • BONDING = of substance & protein at a particular site or location • POLYPEPTIDES: the carboxyl group of one amino acid linked in a peptide bond to the amine group in the next amino acid • N-TERMINAL = “beginning” of peptide chain; free amine • C-TERMINAL = “end” of peptide chain; free carboxyl

28. FOUR LEVELS OF PROTEIN STRUCTURE • 1˚-PRIMARY – determined by the number, type & order of amino acids in the chain – determined by genetic sequence • 2˚-SECONDARY – occurs spontaneously as the protein forms; EITHER . . . • ALPHA HELIX: a right-hand coil formed as a result of hydrogen bonding along strand; number of bonds leads to stable configuration; occurs in GLOBULAR PROTEINS • BETA SHEETS: back & forth folding; maintained by hydrogen bonds between adjacent strands; principally found in FIBROUS PROTEINS

29. Levels of Protein Structure continued . . . . • 3˚TERTIARY: highly specific looping & folding due to interactions of various R-Groups; each unique; tertiary structure is rigidly set & determined by the primary structure • 4 forces influence folding • HYDROPHOBIC INTERACTIONS among non-polar amino acids • HYDROGEN BONDS between adjacent polar R-Groups • IONIC ATTRACTIONS between oppositely charged R-Groups • COVALENT BONDING when 2 cystine amino acids form DISULFIDE LINKAGES

30. Levels of Protein Structure continued . . . . • 4˚QUATERNARY: when 2 or more polypeptides join to form the finished protein • HEMOGLOBIN: comprised of 4 poly peptides – 2 pairs – a virtual giant among proteins

31. Proteins can readily be DENATURED = have their conformation (and thus their effectiveness) altered by a chemical or physical agent • Loses biological function • Causes old bonds to break and new bonds to form randomly • HEAT (egg white ALBUMEN) • INTENSE COLD – usually reversible • Alkalinity & ACIDITY “Can’t unboil an egg”

32. STRUCTURAL PROTEINS: maintain the physical form of organisms • INTRACELLULAR: within cells • KERATIN – fills the growing cells of hair, feathers, claws, nails, horns, antlers & scales; dead cell layers are pushed out by growing cells beneath • EXTRACELLULAR: outside of cell • COLLAGEN – long, fibrous molecules wound together to make long fibers; 25% of protein in humans ; tendons, ligaments & muscles

33. ELASTIN – gives elasticity to connective tissue - EARS & SKIN – loses elasticity with aging; wrinkling; the “pinch” test • CONJUGATED PROTEIN: one that contains chemical components other than amino acids; generally named for the added chemical component • HEMOPROTEINS: hemoglobin; contains HEME GROUPS (iron-containing nitrogen rings • LIPOPROTEINS: possesses lipid components • GLYCOPROTEINS: possesses carbohydrate components • PHOSPHOPROTEINS: possesses phosphate components

34. NUCLEIC ACIDS • DNA = Deoxy-Ribonucleic Acid = molecular core of life – contains GENES (units of heredity) that specify the types of proteins the organism produces - it’s DOUBLE-STRANDED & SELF-REPLICATING • RNA = Ribonucleic Acid = a related molecule - it’s SINGLE-STRANDED & is vital in translating information from DNA into assembled proteins

35. NUCLEOTIDE = the subunit of which nucleic acids are comprised; includes a 5-CARBON SUGAR (ribose or deoxyribose), a PHOSPHATE GROUP & one of 4 NITROGENOUS BASES • NITROGENOUS BASE – can be either a single (PURINES) or double ringed (PYRIMIDINES) molecule (2 of each) • ADENINE - purine • GUANINE - purine • CYTOSINE - pyrimidine • THYMINE - pyrimidine • URACIL - pyrimidine (only in RNA)

36. NUCLEOTIDES form polymer chains by covalently bonding between the sugar of one molecule and the phosphate group of the next • In DNA, the polymer chains are drawn together and form WEAK HYDROGEN BONDS between the nitrogenous bases in one with the nitrogenous bases in the other. They then are spontaneously twist into a DOUBLE HELIX • CHARGAFF’S RULES: • The amount of A, T, G & C in DNA varies from species to species • In each species, the amount of A = T, and the amount of C = G

37. ENZYMES “-ase” • ORGANIC CATALYSTS – accelerates the rate of chemical reactions by lowering the ACTIVATION ENERGY necessary for the reaction to take place • ACTIVATION ENERGY – the minimum energy sufficient to form new bonds A catalyst is not changed by the reaction & can be used over & over again • METABOLISMS = chemical reactions that occur in biological systems

38. CATABOLISM = breaking down of substances • ANABOLISM or SYNTHESIS = formation of new products CHEMICAL EQUALIBRIUM: when the rate of the forward reaction = the rate of the reverse reaction; therefore no net production of either reactants or products

39. ENZYMES are specific for particular reactions because of shape • INDUCED-FIT MODEL (formerly LOCK &KEY MODEL) of enzyme action • ACTIVE SITE on enzyme binds with SUBSTRATE (substance upon which the enzyme acts) MOLECULE due to SHAPE, POLARITY or other characteristics of the active site • Enzyme then changes its shape slightly & lowers activation energy of reaction

40. Enzymes operate at an optimum temperature (37˚C for humans) and pH (varies by species & area in body) • DENATURING – destroys enzyme’s shape and therefore its function • Sometimes ELASTIC, as with freezing • Mainly permanent, as in spiking a fever above 104.5˚F • ATP – Common source of ACTIVATION ENERGY for metabolic reactions; break high energy bonds between SECOND & THIRD phosphate groups • CO-FACTORS = non-protein molecules that assist enzyme action • COENZYMES: organic co-factors such as VITAMINS • INORGANIC CO-FACTORS: often metal ions (Fe++)

41. REGULATING ENZYME ACTION • ALLOSTERIC ENZYMES • Two types of ACTIVE SITES • For Substrate • For ALLOSTERIC EFFECTOR – presence or absence of either activates or inhibits enzyme action • FEED-BACK INHIBITION = end product of reactions acts as allosteric effectors to inhibit enzyme and shutdown reaction • COMPETITIVE INHIBITION = substance inhibits enzyme by occupying its active site – this displaces the substrate