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Chapter 3: Organic Molecules Carbon I.

Carbon has 4 electrons in its outer shell therefore needs 4 more electrons to fill the shell A. Ability of Carbon to form both polar and non-polar bonds contributes to its ability to serve as the backbone for a variety of molecules B. Carbon bonds are stable at the different temperatures associated with life from Earths icy poles to deep-sea vents 1. Carbon atoms are relatively small compared to other atoms a) Carbon-Carbon bonds are short (1) therefore bonds are strong C. makes 4 bonds with other atoms, single and double bonds 1. Non-polar bonds a) poorly water soluble 2. Polar bonds a) water soluble Functional groups (FG) I. Groups of atoms with special chemical features that are functionally important A. Each type of FG exhibits the same properties in all molecules in which it occurs B. When FGs are added to a carbon backbone, its biological and biochemical properties are changed, same goes for removing FGs. 1. Compounds may have more than on FG a) Carboxylic Acid (charged or uncharged) (1) Important because as pH changes within a cell the hydrogen atom can dissociate and the carboxylic acid will be negatively charged. (a) Proteins that may have recognized the uncharged molecule will not be able to function or recognize the charged molecule. Isomers I. Identical molecular formula but different structure and characteristics A. these often subtle differences in physical arrangements have huge implications on biological processes as enzymes can be every specific 1. Stereoisomers a) identical bonding relationships, but the spatial positioning the atoms differs in the two isomers (1) Enantiomers (a) mirror image of another molecule (2) Geometric isomers (a) positioning around double bond i) no rotation around the double bond 2. Structure isomers a) contain the same atom but in different bonding relationship and different properties

Chapter 3: Organic Molecules Macromolecules Carbohydrates (sugars -ose) I. Composed of C,H,O: [Cn(H2O)n] II. Most of the carbon atoms in the carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group 1. certain carbohydrates have amino and carboxyl groups B. Monosaccharides 1. Simplest sugars a) Pentose - 5 Carbons (1) Ribose (C5H10O5) (RNA) (2) Deoxyribose (C5H10O4) (DNA) b) Hexose - 6 Carbons (1) Glucose (C6H12O6) (a) Essential sugar present in cells (b) Very water soluble i) can move readily to different parts of the organism 2. Can be in a ring or linear structure a) ring forms in aqueous solution (1) glucose, fructose, ribose C. Disaccharides 1. Sucrose, maltose, lactose a) composed of two monosaccharides (1) bind together via condensation reaction (2) can be broken apart by hydrolysis D. Polysaccharides 1. Monosaccharides linked together to form long polymers a) can be highly branched (B), unbranched (UB) (straight chain), or moderately branched (MB) which effects the function b) Structural role (1) cellulose (UB) (a) linked by beta 1-4 glycosidic bonds (b) single chains allow for greater strength and is very resistance to breakdown/attack. (2) chitin (3) glycosaminoglycans c) Quick Energy storage (B/MB) (a) branching allows the molecule to be soluble in tissues i) glucose can be readily removed by hydrolysis (2) Starch (MB) (a) alpha 1-4 bonds (3) glycogen (B)

Chapter 3: Organic Molecules Lipids I. Composed predominantly of H&C II. Non-polar: very insoluble in water A. Fats 1. Mixture of triglycerides/triglycerols 2. Formed by bonding glycerol to three fatty acids (ester bonds) a) Fatty Acids (1) Saturated (a) solid at room temperature (2) Unsaturated (a) liquids and room temperature (oils) i) monounsaturated (1) one double bond ii) polyunsaturated (1) two or more double bonds 3. joined by dehydration, broken by hydrolysis 4. Can be structural: provide cushioning and insulation for cells 5. important for energy storage a) 1 gram of fat stores twice as much as much energy as 1 gram of glycogen or starch (1) more energy rich bonds 6. Essential fatty acids a) fatty acids that are necessary for good health but cannot be synthesized by the body and must be obtained in the diet B. Phospholipids 1. Glycerol, 2 fatty acids and phosphate group a) phosphate group is linked to third hydroxy group of the glycerol 2. Important in membrane structure: signaling a) is essential for the compartmentation within cells 3. Amphiphatic molecule a) Allows for the organization of bilayers (1) hydrophilic head (Polar phosphate group) b) hydrophobic tail (non-polar fatty acid chains) C. Steroids 1. Four interconnected rings of carbon atoms 2. Usually not very water soluble a) Cholesterol (1) essential component of cellular membranes and found in the blood of animals b) Estrogen and testosterone (1) Tiny differences in chemical structure can lead to profoundly different biological properties (female or male characteristics)

Chapter 3: Organic Molecules Proteins I. Composed of COHN, some S, often modified II. Machines of the cell III. Have 4 main structures [Hierarchy structure - each level is dependent on the level above] A. Primary 1. sequence of AA determined by gene a) ultimately determines 2nd degree and 3rd degree B. Secondary 1. alpha-helices, beta-sheets C. Tertiary 1. 3-D shape a) determined by the totality of the amino acid interactions with one another and the aqueous and non aqueous environment surrounding them D. Quaternary 1. 2 or more subunits, multi-meric complexes IV. 5 Factors promote protein folding and stability A. Hydrogen bonds 1. form between atoms in the polypeptide backbone and atoms in different side chains a) adds up to a strong force that promotes protein folding and stability B. Ionic bonds 1. form between oppositely charged side chains C. Hydrophobic effects 1. Non-polar amino acids in the center of the protein avoid contact with water a) Anchors proteins in the hydrophobic portion of membranes D. Van der Waals forces 1. Attractive forces occur between atoms that are optimal distances apart E. Disulfide bridges 1. covalent bond forms between 2 cysteine side chains V. Composed of 2 or more polypeptides A. Monomers are Amino Acids 1. common structure with variable R-group 2. 20 L-amino acids (used in proteins) 3. Side-chain determines structure and function 4. Joined by dehydration reaction and broken by hydrolysis a) forms peptides with peptide bonds in between amino acids VI. Protein-Protein interactions are very specific A. The surface of one protein precisely fits into the surface of another 1. Critically important so that cellular processes can occur in a series of defined steps 2. Important in building large cellular structure that provide shape and organization to cells

Chapter 3: Organic Molecules Proteins Contain Functional Domains within their structures I. Module or domains in proteins have distinct structures and function A. ie.: Signal transducer and activator of transcription (STAT) protein 1. each domain of the protein is involved in a distinct biological function 2. proteins that share one of these domains also share that function

Nucleic Acids I. Responsible for the storage, expression, and transmission of genetic information II. Two classes A. Deoxyribonucleic acid (DNA) (deoxyribose more stable) 1. store genetic information coded in the sequence of their monomer building blocks B. Ribonucleic acid (RNA) 1. involved in decoding this information into instructions for linking together a specific sequence of amino acids to form a polypeptide chain III. Monomer is a nucleotide A. Made up of a phosphate group, a five-carbon sugar, and a single or double ring of carbon and nitrogen atoms know as a base 1. Sugar-phosphate back bone