Philosophical considerations aside


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Philosophical considerations aside

  1. 1. Philosophical considerations aside, organisms are basically orderedaggregations of chemicals and biological processes are merelybiochemical reactions. Therefore an understanding of basic biochemistryis necessary in order to understand biology.I. Matter is composed of elementsA. Matter1. Matter refers to anything that takes up space and has mass2. All matter (living and nonliving) is composed of basic elementsa. Elements = fundamental forms of matter that occupy space and havemass, cannot be broken down to substances with different chemical orphysical propertiesb. There are 92 naturally occurring elementsb. Six elements (C, H, N, O, P, S) make up 98% of most organismsII. Atoms form compounds and moleculesA. Molecules = two or more atoms of same element bonded together (e.g.,O2)B. Compound = two or more different elements bonded together (e.g., H2O)C. Bonds are not physical links, they are links of pure energy. Typesof bonds:1. Covalent bond - involves sharing of electron(s). Electrons possessenergy; bonds that exist between atoms in molecules contain energy. a. Sharing of a pair of electrons creates a single bond representedby single dash, e.g. water H2O is made of two single bonds H-O-H.Sharing two pairs of electrons is represented by two dashes, C=C b. Know the number of covalent bonds each of the six most importantelements can form.Element # of covalent bondsHydrogen (H) 1Oxygen (O) 2Nitrogen (N) 3Carbon (C) 4Phosphorous (P) 5Sulfur (S) 22. Ionic bond - electrons are transferred from one atom to another,e.g. salt NaCl3. Hydrogen bond - weak attractive force between slightly positivehydrogen atom of one molecule and slightly negative atom in another orthe same molecule
  2. 2. a. E.g. in a water molecule the electrons spend more time orbitingthe oxygen than the hydrogens, therefore the oxygen becomes slightlynegative and the two hydrogens become slightly positive b. Such polar molecules attract each other like magnetsBASIC ORGANIC CHEMISTRYBecause carbon needs four electrons to fill its outer shell it can formmillions of different combinations with other atoms - ten times morethan all other atoms put together.I. Organic moleculesA. Life as we know it is based on carbon1. Carbon has four electrons in outer shell; bonds with up to fourother atoms (usually H, O, N, or another C)2. Ability of carbon to bond to itself makes possible carbon chains andrings which serve as the backbones of organic molecules3. Organic molecules - contain carbon and hydrogen, most also containnitrogen, and oxygen 4. Functional groups - clusters of atoms with characteristicstructure and functionsB. Monomers and polymers 1. Most important biological compounds are polymers a. Polymers - large compounds made of identical or nearlyidentical repeating subunits b. Monomers - the subunits of polymers 2. Making and breaking polymers a. Condensation - making polymers by lining up monomers andeliminating a water molecule, a hydroxyl (OH) group is removed from onemonomer and a hydrogen (H) is removed from the other b. Hydrolysis - breaking polymers apart by introducing a watermolecule c. Condensation/hydrolysis movie of sucrose (table sugar)PRINCIPLE ORGANIC POLYMERSI. Carbohydrates- contain C, H and O in the proportion 1:2:1 (CH2O). A. Most abundant organic compounds in nature B. Serve both as structural compounds and as energy reserves tofuel life processes
  3. 3. C. Carbohydrate monomers are called monosaccharides 1. Alpha Glucose, a six carbon sugar (C6H12O6) is the immediateenergy source to cells. You should know its structure D. Carbohydrate polymers are called polysaccharides 1. Starch is straight chain of alpha glucose molecules with fewside branches, mostly from plant sources 2. Glycogen is highly branched polymer of alpha glucose withmany side branches; called "animal starch," it is storage carbohydrateof animals 3. Cellulose is a polymer of beta glucose molecules, it isprimary constituent of plant cell walls E. Disaccharides - 2 monosaccharides linked together 1. Sucrose (table sugar ) - glucose and fructose linkedtogether, transported throughout plants 2. Lactose (milk sugar) is glucose + galactose F. Virtually all carbohydrates come from plants which use the sunsenergy to make alpha and beta glucose.II. Lipids - fats, oils, fatlike substances, some vitamins and steroids A. Primarily energy sources and structural compounds B. Two principle characteristics: 1. Hydrophobic - insoluble in water 2. Large number of bonded hydrogens - therefore release alarger amount of energy than other organic compounds. Fats yield 9 cal/gm, carbohydrates 4 cal/gm C. Major lipids: 1. Triglycerides (fats and oils) - three fatty acids joined toa glycerol molecule: a. Fatty acid - long hydrocarbon chains with terminalcarboxyl (COOH) group Saturated fatty acids have no double bonds betweentheir carbon atoms Unsaturated fatty acids have double bonds in the carbonchain % saturated/unsaturated fat in some common foods Unsaturated
  4. 4. Saturated safflower 72 beef 48 soybean 59 butter 55 corn 53 fish 15 coconut oil 86 chocolate 56 b. Glycerol - three carbon molecule 1) Fats - triglycerides containing saturated fattyacids (e.g. butter is solid at room temperature) 2). Oils - triglycerides with unsaturated fatty acids(e.g. corn oil is liquid at room temperature) c. Triglycerides are synthesized via condensation 2. Phospholipids - two fatty acids attached to phosphate group a. phosphate heads are hydrophilic (water soluble) buttails are hydrophobic (water insoluble) therefore they spontaneouslyline up to form a lipid bilayer b. very important because they form biological membranesIII. Polypeptides - polymers of nitrogen containing molecules calledamino acids, joined together by peptide bondsA. Amino acids consist of: 1. Amino group - NH2 (positive charge) 2. Carboxyl group - COOH (negative charge) 3. Central carbon atom 4. R group - different substitution to the molecule, determinesnature of the amino acid B. About 50,00 different proteins in humans, serve a variety offunctions: 1. Structural - e.g. muscles, hair, fingernails, collagen 2. Enzymes - biological catalysts which regulate biochemicalreactionsC. Proteins - large polypeptides with molecular weights from 10,000 -1,000,000D. Enzymes - large globular proteins from 12,000 to 1 million molecularweights that act as catalysts 1. Catalysts - substances that accelerate chemical reactions butwhich remain unchanged or unused in the process
  5. 5. 2. Enzymes generally named by adding -ase to root name of substratethey react upon, e.g. amylase breaks down amylose (starch)E. Polypeptide structure - due to interactions between adjacenthydrogen bonds and R groups proteins form complex three dimensionalstructuresC. Polypeptides can be denatured1. Both temperature and pH can change polypeptide shapea. Examples: heating egg white causes albumin to congeal; adding acidto milk causes curdling. When such proteins lose their normalconfiguration, the protein is denaturedb. Once a protein loses its normal shape, it cannot perform its usualfunctionIV. Nucleic Acids - polymers of nucleotidesA. Nucleotides made up of: 1. Phosphate group - PO4 2. Five carbon sugar called ribose (or deoxyribose) 3. Nitrogenous base - ring structure containing C & N B. Important Nucleic Acids:1. DNA (deoxyribonucleic acid) - the molecule which stores the geneticinformation passed on form parent to offspring2. RNA (ribonucleic acid) - serves as the translator of the geneticinformation contained in DNA Page 38 in your text summarizes the structure and function of the fourbasic organic molecules in living organisms.SECONDARY METABOLITESI. Proteins, lipids, carbohydrates and nucleic acids are called primarymetabolites because they occur in all plant cells and they arenecessary for the life of the plant.II. Secondary metabolites are an assortment of many different compoundswhich serve a variety of functions, and that are restricted todifferent species of plants. They include: A. Alkaloids - alkaline, nitrogen containing compounds which affectthe human nervous system. At least 10,000 alkaloids have been isolatedfrom plants. Many names end in -ine, e.g. morphine, caffeine, cocaine,nicotine, atropine. B. Terpenoids - polymers of isoprene (see figure 2-26a, p. 33).Isoprene is emitted by leaves, causing a haze over forests on hot days.
  6. 6. Other terpenoids include essential oils (volatile compounds) such asmint and menthol, taxol (cancer drug), digitalis (heart medicine) andrubber. C. Phenolics - compounds based on an aromatic ring with an attachedOH group. Flavonoids are important pigments, tannins are bitter tastingcompounds which probably act as deterrents to herbivores, lignin is animportant compound secreted into the cells of woody plants to providestructural support. Salicylic acid is the active ingredient in aspirin.