Biochemistry: Unit 1

• For biology, non-polarity results in strong, stable bonds that convey non-polarity and avoidance of water to molecules, making them good components for cell membranes and other structures not needing too much water.
• Polar: ionized, dipoles, unequal sharing of electrons.
• Ionic bonds are held together by electrostatic attractions and are water soluble.
• Intramolecular force: forces that bond atoms together within a molecule to hold it together (harder to break).
• Nonpolar covalent: no dipoles, are hydrophobic.
• Ionic bond: transfer of electrons; ionize or dissociate readily in aqueous environments, creating electrochemical gradients.
• For biology, polarity results in strong, stable bonds that are interactive and hydrophilic, and can attract molecules.
• Electronegativity: the tendency for an atom to attract electrons to itself. Nonpolar covalent: 0-0.5; electrons are evenly distributed no dipoles. Polar covalent: 0.5-1.9; electrons shared unequally results in +/- dipoles; able to attract other atoms. Ionic bond: > 2.0; electrons pulled away from one atom to the other; results in loss/gain of electrons.
• Intermolecular force: forces that exist between different molecules to bond them together. Hydrogen bonds: weak interactions don’t react electrons are shared unequally between hydrogen atoms and a highly electronegative atom (F Cl O N). In biology: very strong in large numbers bind DNA strands are responsible for the strong properties of water. Dipole movement: the direction the polar bond in a molecule is; arrow points toward more elec. neg. atom.
• How do water's properties help plants take in water? Cohesion: intermolecular force in liquids where particles are united/connected together. Adhesion: forces between liquid entities and the container and other substances; liquid is attracted to other substances. Transport of water in xylem: water molecules are attracted to the stem of a plant moving the water up to the plant for hydration.
• Alcohol: contains OH- hydroxyl, in place of one or more hydrogens.
• Carbonyl: contains C=O. Ketones: O is in the middle; ‘-one’. Aldehydes: O is in the beginning of the molecule; ending is ‘-al’.
• Amine: NH2; commonly found in amino acids- replace H.
• Carboxylic acids: COOH; acids
• Amino acid: 2 functional groups; amine and carboxyl, and NH2CH[R]COOH, where R is a different group. Each R group changes the properties of the amino acid; can be polar or nonpolar.
• Sulfhydryl: sulfur and hydrogen bond, attached to R group.
• Phosphate: P and O bonded with 3 single bonds and one double bond.
• 1. Ether: formed between 2 alcohols, an oxygen between 2 carbon atoms; builds carbohydrates’ polymers.
• 2) Ester: formed between an alcohol and carboxyl, bond between OCO; builds lipids. 
• 3) Phosphate ester: formed between alcohol and phosphoric acid; builds DNA. 
• 4) Peptide: forms proteins from long chains of amino acids- form the primary structure in proteins.
• CARBS: Functional groups: hydroxyl & carbonyl. Water solubility: Mostly; are hydrophilic due to many charged OH’s, making carbs polar. but, the more complex the carb, the less soluble. Linkages in monomers: ether, glycosidic linkage; 1-2 or 1-4 carbons; monomers switch arrangements for different carbon linkages
• Phagocytosis: (“cellular eating”): cells engulf bacteria, dead cells or other foreign particles- vacuole fuses with a lysosome- and forms a food vacuole with the engulfed material.
• Pinocytosis: (“cellular drinking”): water from outside the cell is taken in.
• Receptor-mediated endocytosis: molecules are taken in by being bound to the outer cell surface binding of ligands to receptor proteins. A ligand is any molecule that binds specifically to a receptor site of another molecule.
• PROTEINS: Functional groups: amine, carboxyl, & some hydroxyl. Water solubility: depends on the R group and whether it has charged regions. Linkages in monomers: peptide bonds of two or more amino acids linked in a chain to form proteins.
• LIPIDS: Functional groups: hydroxyl, carboxyl, & carbonyl. Water solubility: not soluble in water; C-H hydrocarbon structure is nonpolar; hydrophobic. Make up a cell membrane to keep water out and prevent the cell from dissolving. Linkages in monomers: ester links; formed between an alcohol and carboxyl, bond between OCO.
• Symport: If transport is in the same direction. Antiport: If transport is in the opposite direction.
• Starches: 𝝰-glucose, 1-4, 1-6; energy storage in plants. Glycogen: 𝝰 glucose, 1-4, 1-6; energy storage in the liver of animals. Cellulose: 𝜷-glucose, 1-4; found in plants, allow them to be rigid and provide standing support. Chitin: 𝜷 glucose, 1-4; straight shape, found in insect exoskeletons.
• Cell Membrane Structure- phospholipid amphipathic bilayer (both hydrophobic and philic). hydrophobic fatty acid tail; hydrophilic phosphate head. Cholesterol: help build the cell membrane and keep it fluid and firm. Proteins (amphipathic): Peripheral proteins on surface of the membrane act as sites for attachment. Integral proteins go through the hydrophobic core and act as transporters for molecule.
• Lipids: used for long term energy storage. Hydrocarbons with no OH’s. C-H bonds contain a high amount of stored energy. Monomer unit: fatty acids; attach to a glycerol molecule. Saturated fats: 2 H bonded to each C atom with only single bonds; no bending, rigid structure, solid at room temperature, linear- unhealthy fats. Unsaturated fats: C bonded to each other with at least one double bond; causes fat to bend, liquid at room temperature, found in plants- healthy fats.
• When hydrogen is covalently bonded to the remaining open bonds on a carbon, it forms a hydrocarbon. A nonpolar molecule forms, lacking charged areas, making them insoluble in water, uncharged.
• Triglycerides (fats and oils): Made of one glycerol and 3 fatty acids in a series of reactions (unsat. or sat.). Phospholipids: components of the cell membrane; made of glycerol and 2 fatty acids (insoluble in water) and a phosphate group (soluble in water).
• Waxes: Composed of long fatty acid chains attached to alcohol or carbon rings, hydrophobic; Used as waterproof protection. Steroids: made of 4 carbon rings linked together, hydrophobic; make up body components like hormones, cholesterol (found in cell membranes).
• Free Ribosomes– float “freely” in the cytoplasm of a cell. Make proteins that will stay inside the cell for use by the cell, like enzymes associated with metabolism or DNA replication. Bound Ribosomes – attached to the endoplasmic reticulum. These make proteins that will leave the cell to be used elsewhere. 
• Alpha 𝝰 glucose: OH groups are pointing down on a monomer. Beta 𝜷 glucose: OH groups are pointing up (at least one) on a monomer
• Cohesion: intermolecular force in liquids where particles are united/connected together. Adhesion: forces between liquid entities and the container and other substances; liquid is attracted to other substances. 
• Exocytosis: transport vesicles migrate to the end of the membrane, fuse with it, and release their contents outside the cell. Many secretory cells use exocytosis to export their products. Endocytosis: the cell takes in extracellular macromolecules by forming vesicles from the membrane and brings them into the cell.