Organic Substances

Carbohydrates: • •

Sugars and their Molecules Monosaccharide, disaccharides, and polysaccharides ○ Monosaccharides:  Multiple of CH2O  Carbonyl group and hydroxyl group  Carbon skeleton length: 3-7  Different arrangements around asymmetric carbon  Ex. Glucose vs. galactose ○ Dissacharides:  Polymer of sugars  Storage and structural roles  Macromolecules of many monomers linked by glycosidic linkages.  Starch: Helical, storage polysaccharide in plants made of only glucose monomers with some branches. • Plants store them in plastids (issued by hydrolysis) • Animals store them in glycogen (issued by hydrolysis)  Cellulose: Structural polysaccharide used in cell walls of plants. • Microfibrils: Made by binded cellulose which cannot be digested —good for digestive system? • Some microbes can hydrolyze cellulose (Ex. Bacteria in cow, termites).  Chitin: Exoskeleton material in insects, etc. Hard because of calcium carbonate. Cell wall function in fungi.

Lipids: •

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Made of Glycerol (alcohol with 3 carbons and hydroxyl group at end) and Fatty Acid (carboxyl group with hydrocarbon chain). Hydrophobic. Triaglycerol? ○ Composes fats and oils. ○ Bonded by ester linkage. Saturated Fatty Acid: ○ No double bonds ○ As many H as possible ○ Saturated Fats-solid in room temperature Unsaturated Fatty Acid: ○ At least one double bond ○ Not as many H as possible ○ Unsaturated Fats-Liquid in room temperature. Hydrogenate: ○ To add H synthetically to an unsaturated fat to make it solid in room temperature. Fat: Major energy storage (like gasoline) ○ Animals need fat because they move.

Stored in adipose cells ○ Cushion and insulation Phospholipids: ○ Like fats; two tails; structural differences. ○ Hydrocarbon tail ○ Hydrophilic head ○ Assemble with tail inside:  Micelle cluster  Phospholipid bilayer • Found in plasma membrane Steroids: ○ Lipids with four fused rings on carbon skeleton ○ Vary with functional group on rings ○ Ex. Cholesterol:  A steroid found in animal membranes and precursor from which steroids are made. ○

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Proteins: • • • •

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Purposes of Protein: Support, storage, transport, signaling, movement, defense against foreign substances, enzymes. Vary in 3-D structure ○ Most complex ○ Made of polymers from 20 amino acids-polypeptides. Definition: One or more polypeptide folded/coiled into specific conformations. Amino Acid: ○ Organic molecule ○ Asymmetric carbon center (alpha carbon) ○ For Parts:  Amino Group  Hydrogen Group  Carboxyl Group  R (variable) Group • R property determines the type of amino acid. • Ex. Nonpolar, polar, acidic (+), basic (-) • Describes R, not other parts of amino acid. Peptide Bond: ○ Links two amino acids (carboxyl group next to amino group) by enzyme (dehydration reaction). ○ Forms Polypeptide. ○ 1 End (free amino group): N- Terminus ○ Other end (carboxyl): C- Terminus Polypeptide Backbone: ○ Has different appendages/side chains ○ Vary in length Polypeptide Chains

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○ A group that forms a functional protein. ○ The ability of a protein to recognize and bind to certain things determines its purpose (it depends on molecular order and levels of structure. ○ Folds/conforms as it is synthesized by a cell Primary Structure: ○ A protein’s unique sequence of amino acids. ○ Ex. Lysozene has 129 amino acids chain. ○ The order is determined genetically, and an error can cause deformation/disease  Ex. Sickle Cell ○ Sanger: Worked out amino acid sequence of insulin with chromatography and fragments of polypeptide. Secondary Structure: ○ The coils and folds of polypeptide chains that contribute to the protein’s conformation/ ○ Polypeptide Backbone:  H Bonds, partial negative charge. H bonds with N determine shape.  Alpha Helix: • Coils • H bond ever 4th amino acid.  Beta pleated sheet: • Two or more regions of polypeptide chain • Parallel to each other • H bonds between parallel regions hold them together. • Ex. Spider silk  One protein can have both shapes in polypeptides. Tertiary Structure: ○ Irregular contortions from interactions between side chains of various amino acids. ○ Hydrophobic Interaction:  Non polar amino acid side chains cluster together with Van der Waals forces, excluding water which H bonds to itself. This gives protein its shape. ○ Disulfide Bridges:  Covalent bonds that link two cysteine monomers (amino acids with sulfhydryl group [--SH]) when they meet as protein folds.  Two sulfides bond, folding the protein (-S-S-) Quaternary Structure: ○ Overall protein structure that results from the aggregation of polypeptide units. ○ Ex. Collagen: helical proteins make triple helix. ○ Ex. Hemoglobin: A lobular protein. Protein Conformation: ○ Determined by amino acids, secondary, and tertiary structures. ○ Also depends on environment. Denaturation: ○ Protein loses conformity because of environment. ○ Ex. Salt, pH, etc

Biologically inactive usually because it leaves aqueous environment to organic solvent; bond disruption. ○ Remove denaturation agent back to normal because shape is intrinsic in proteins. Difficult to trace “folding” path of protein. ○ Final step doesn’t show steps. Chaperonins/chaperone proteins: ○ Help proteins fold by making sure nothing bad happens to new protein (no bad influence). ○ IBM computer Blue Gene to illustrate protein with amino acids. ○ X-ray Crystallography: Deflected beams from protein atoms in crystal to make model. ○

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Nucleic Acids: