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biochem final - Life and Water Types of biomolecules are...

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Life and Water: Types of biomolecules are Proteins: polymers of amino acids Nucleic Acids: heterocyclic nucleic rings on sugar phosphate back bone Lipids: Repeating (-CH2) units ex fatty acids Carbohydrates: poly hydroxyl aldehydes and ketones ex glucose->glycogen Structure of water Polar molecule, geometry is bent. The bond angle is not 109.5 because of lone pairs Water has hydrogen bonding, net dipole b/c of electronegativity Hydrogen bonding potential: sharing H between two electrons atoms Thermodynamics Enthalpy (Delta H) Entropy (Delta S) Acid/Base chemistry PH and H-H Equation Gibbs free Energy Amino Acids: pH of Amino acids The charge on amino acids depends on the pH. pI is the isoelectric point, it’s where the net charge on the molecule is zero (pI= ½(PK1-PK2)) The R-groups the R-groups make amino acids unique. AA are classified on the structure and chemical properties of their R-groups Peptide bonds The peptide bond is an amide bond, it is between –COO- and NH3+ of two amino acids by removing H2O (condensation). Peptide bond has 40% double bond characteristics The peptide bond is TRANS AND PLANAR . it is TRANS because the R-groups are on the opposite sides.
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Proteins- primary structure Protein sequences 1’->2’-3’ Primary structure: its sequences of amino acids (20^60) possible combos. Secondary structure: 3-dimensinaol space taken up by amide back bone. Excludes amino acids R- groups Tertiary structure: 3-D space includes contribution or R-groups Quaternary structure: Association of >1 subunits to make a protein. Ex Hemoglobin is make of 2 alpha and 2 beta subunits. Protein purification Based on charge, size, natural binding affinity and solubility. (I) Base on solubility: (Salt out) lower conc of salt = highly soluble. Higher conc of salt =lower solubility of proteins. (NH4)2SO4 is the salt often used. (II) Ion exchange chromatography: takes advantage of the intrinsic charge of proteins. If beads are negatively charged it will retard the (+) charged proteins (III) Gel Filtrations: Size exclusion chromatography. Smaller proteins go into the beads and take long time to come out. Earlier fraction is large proteins and later fraction will be the small proteins. (IV) Natural Binding Affinity: many proteins naturally bind to small molecules or substrates. Endopeptidases They are enzymes that cut internal of proteins 3-D structure of proteins Secondary structure: (not talking about the R groups) Alpha helix: 10-20 amino acid residue long, 3.6 amino acid residue per turn, hydrogen bond pattern. Alpha helix has a net dipole. Beta sheets: Anti parallel and parallel. Same forces that stabilize alpha helix stabilize beta sheets. Tertiary structure : (Includes the amino acid R-groups) Tertiary structure is determined by only the strong Disulfide (-SH) covalent forces.
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