Biochem 415 Exam 1 Review

Biochem 415 Exam 1 Review - Ch.1 DNA Structure and Function...

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Ch.1 DNA Structure and Function – Stabilizing forces Chemical bonds - bases linked to polymer by glycosidic bonds H-bonds – specific base pairing between bases, bases stack on top of each other Electrostatic interactions – phosphates have negative charges, causes repulsion, they are far away from each other on backbone Van der Waals – bases stack on each other at Van der Waals distance Hydrophobic effect – more complete base-stacking moves nonpolar surfaces of bases out of water into contact with each other pH – extreme pH can alter DNA structure Henderson-Hasselbalch: pH = pKa + log([A-]/[HA]) When pH=pKA, [A-]=[HA] Ch.2 Protein Composition and Structure Peptide Bond Planar, no free rotation due to resonance (has alkene character) Psi-phi angles o Psi angle – rotation angle around carbonyl C and alpha-C o Phi angle – rotation angle around N and alpha-C o Ramachandran diagram shows favorable combinations of psi-phi angles Trans conformation of peptide bond favored (to avoid steric hindrance) except Proline Protein Structure Primary – amino acid sequence Secondary - local conformation of peptide backbone o α helix CO and NH groups of peptide bonds H-bonded (i+4) Right handed helix All residues on outside Can be asymmetric Coiled coil – quaternary structure built on helical secondary structure o β pleated sheet Each strand called β stand Parallel or antiparallel Antiparallel stands often connected by β turns ( i+1) Form β barrels o Loops between α helices and β sheets are important functional domains of proteins Tertiary – interaction of secondary structures on same polypeptide o Globular proteins have hydrophobic interior and hydrophilic exterior o EcoR1, TATA-binding protein (TBP) o Domain – coded by distinct exon in gene, discrete part of protein Quartenary o Several subunits o Cro (dimer) o Hemoglobin (tetramer)
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Sequence determines structure Native form of enzyme is most thermodynamically stable form Protein Folding Denaturants – urea, guanidinium chloride Highly cooperative Progressively stabilization of correct interactions between amino acids (typing monkey analogy) Diseases from misfolding of proteins o Bovine Spongiform Encephalitis (Mad Cow Disease) o Creutzfeldt-Jacob Disease – PrP monomers stick together to form plaques Protein Chaperones o Isolates (encapsulates) protein to facilitate correct folding Protein Modification Give added functionality Ch.3 Protein Purification Protein Properties Used for Isolation Solubility Lengths of amino acid chain (molecular weight) Charges 3D shapes Surface features
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Biochem 415 Exam 1 Review - Ch.1 DNA Structure and Function...

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