Biochemistry Midterm Study Guide Chapters 1 2 4 7 11 28 31 32 Chapter 1 Biochemistry An Evolving Science DNA proteins are linear polymers with each sugar connected to two phosphate groups Watson Crick deduced the 3D double helix structure of DNA Covalent bonds strongest bonds share a pair of electrons Bond length 1 54 A Bond energy 355 kJ 1 Electrostatic Interactions Noncovalent bonds weaker than covalent bonds another molecule An attraction interaction has a negative energy Charged group on one molecule that can attract an oppositely charged group on Coulomb s Law E kq1q2 D Donor bond atom to which hydrogen is more tightly linked Distribution of electric charge around an atom fluctuates with time Contact distance attraction of atoms to a certain point 2 Hydrogen Bonds base pair formation Acceptor atom less tightly linked Bond length 1 5 A 2 6 A Strong hydrogen bonds are approximately straight 3 Van der Waals Interactions Properties of Water Water is a polar molecule bent not linear Water is highly cohesive Hydrophobic effect when two nonpolar molecules come together some of the water molecules are released allowing them to interact freely with bulk water Acid base reactions H added or removed from molecules pH concentration of H in solution Two strands form a double helix at pH 7 0 As a base is added pH rises pKa falls and the DNA concentration remains relatively constant As the pH approaches 9 0 the double helix begins to dissociate into single strands Dissociation becomes complete around pH 10 0 Hydroxide ions react with bases to remove protons Most susceptible proton is bound to N 1 in guanine Buffers resist changes in pH by absorbing and releasing H Weak acids make good buffers because they partially dissociate When pH pKa deprotonated protonated deprotonation halfway to completion The process of gradually adding known amounts of reagent into solution with which the reagent reacts while monitoring the results is called a titration The pH decreases gradually in the middle of titration because H react with acetate ions to form acetic acid Once all of the acetate ion is converted added H are free in solution pH begins to fall Henderson Hasselbalch equation pH pKa log A HA salt acid Buffers function best when pH is close to the pKa value of its acid component Good buffers are anything between 1 pH unit from the pKa Important buffer H3PO4 it can be deprotonated in 3 steps to form a phosphate ion The relation that links DNA to protein sequence is the genetic code Protein encoding regions account for 3 of the human genome Epigenetic factors are associated with the genome but not simply represented in the sequence of DNA histones DNA modification For CH3COOH at pH 4 8 CH3COOH CH3COO For CH3NH2 at pH 10 63 CH3NH3 CH3NH2 Chapter 2 Protein Composition and Structure Protein Structure 1 Primary sequence of linked amino acids 2 Secondary 3D structure formed by hydrogen bonds between amino acids near one 3 Tertiary long range interactions between amino acids and their folding mechanisms 4 Quaternary protein is composed of several distinct polypeptide chains subunits another Rigid proteins cytoskeleton connective tissue 2 1 Proteins are built from a repertoire of 20 amino acids An alpha amino acid consists of a central carbon called the alpha carbon linked to an amino a carboxylic acid a hydrogen and an R group CHIRAL Configuration Counter clockwise S left Clockwise R right Only L amino acids are constituents of proteins typically have S configuration slightly more soluble Amino acids at neutral pH exist predominantly as dipolar ions or zwitterions Amino group is protonated Carboxylic acid is the first to lose a H then the amino group Carboxyl group is deprotonated pH 0 2 Both groups protonated pH 2 9 Zwitterion carboxylic acid loses a H pH 9 14 Both groups deprotonated amino loses a H Glycine is the only achiral amino acid has no D or L Hydrophobic Amino Acids Methionine contains a largely aliphatic side chain including a thioether C S C Polar Amino Acids contains OH making them much more hydrophilic and reactive Proline has no amino end markedly influences protein architecture because its ring makes it more conformationally restricted than the other amino acids Phenylalanine is purely hydrophobic tryptophan is less so because of its NH group Isoleucine contains a second chiral center Threonine contains a second chiral center Asparagine and Glutamine contain a terminal carboxamide in place of carboxylic acid such as in aspartic acid or glutamic acid Cysteine contains a sulfhydryl or thiol group SH which is much more reactive Histidine contains an imidazole group an aromatic ring that also can be positively Positively Charged Amino Acids highly hydrophilic Negatively Charged Amino Acids charged Aspartic acid protonated aspartate aspartate has a negative charge Glutamic acid protonated glutamate glutamate has a negative charge Amine Containing AAs Lysine Arginine Tryptophan and Histidine NOT Glutamine or Asparagine Amide on a carboxylic acid not amine 2 2 Primary Structure Amino acids are linked by peptide bonds to form polypeptide chains AMINO ACID SEQUENCE Peptide bonds or amide bonds are formed by linking alpha carboxyl group of one amino acid to the alpha amino group of another amino acid Equilibrium of this reaction goes toward hydrolysis rather than synthesis Addition of a peptide bond requires energy Resistant to hydrolysis Ensures that the peptide bond is stable kinetically Each amino acid unit in a polypeptide is a residue Amino residue is the beginning of a polypeptide and carboxyl residue is the end Polypeptide backbone is rich in hydrogen bonding potential Oligopeptides are those that are made of small numbers of amino acids Disulfide bonds are the most common cross links formed by the oxidation of a pair of cysteine residues SH groups link together H released Peptide bond is essentially planar and almost always trans Most common cis peptide bond is X Pro because both cis and trans have steric hindrance 2 3 Secondary Structure Polypeptide chains can fold into regular structures such as the alpha helix the beta sheet and turns and loops CONFORMATION SHAPE Alpha Helix Distance between adjacent amino acids is 1 5 A Tightly coiled backbone inner part of the rod Side chains extend outward Stabilized by hydrogen bonds between NH group and the CO group four residues ahead in the sequence intrachain Almost all main chain CO and NH groups are hydrogen bonded besides those at the ends