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Biochemistry Midterm 1 Notes.docx

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BCHM 2020
Mark Bayfield

Biochemistry Midterm #1 Notes  SPONCH: key elements in organic molecules (sulfur, phosphorus, oxygen, nitrogen, carbon, hydrogen)  Covalent bonds are strong, rigid, not easily broken  Single bond between carbons=rotation around the bond  Double bond between carbons=planar, no rotation  Effects of non-covalent bonds are often additive  Weakness allows for continual breakage and forming of new bonds  H-bonds occur between hydrogen donors and acceptors NOT CARBON ATOMS  Occur within a distance of 3 A  Donor is atom with H-atom attached to it  Water creates H-bonds (how it dissolves polar molecules)  Non polar groups will orient themselves accordingly to minimize contact with H2O  Amphiphilic: contain both polar and non polar sections (polar head, non polar tail)  most reactions take place between pH of 6.5 and 8.0  at half ionization pH=pka  isoelectric point is the pH where the net charge is 0 on a molecule  pK1 is where COOH becomes COO-  pK2 is where NH3 becomes NH2  pKr is side chain pKa  energy of interaction: energy required to separate two charged particles from a distance to infinite distance  H-bonds are the strongest, most specific non covalent interaction  Low pKa =very strong acid, high Ka=strong acid as well  Proteins are soluble when they have a net charge (not at isoelectric point)  “zwitterion” both positive and negative charges  all amino acids are chiral except for glycine  active sites of enzymes are chiral  aromatic R-groups in amino acids tend to be in the center of protiens  UV light is used to determine concentration of amino acids (esp. tryptophan which emits light)  Cysteine: special case a.acid, contains sulfur in its R group and ionizes at moderately high pH  Histadine: basic a.acid contains imidazole as R-group that can be ionized at physiological pH  Proteins are written from N to C terminus  Peptide bonds are rigid, will not rotate, if they do however, trans conformation is favored  Proline is less resistant to rotation  Trypsin cleaves basic amino acids  Chromeotrypsin cleaves aromatic residues  Cyanogen bromide cleaves methionines  Glycine is an exception to rotation rules because it is so small (r-group is H)  Alpha-helix is most common secondary structure o Formation driven by H-bonds between NH of one residue and C=O of residue 4 amino acids ahead  Beta sheet is planar, R-groups alternatively project from either side, antiparallel sheets are more common because less looping occurs  B-turns reverse the direction of the chain (praline and glycine turn chain)  Fibrous proteins: ex. Collagen (P-G-X) form tight triple helix intertwined with each other held together by covalent bonds  Vitamin c is crucial for these covalent bonds to be formed  Misfolded or denatured proteins are typically non functional  Afinson’s dogma: all information needed to determine native fold is in primary sequence  If disulfide bonds in a protein are broken (by reduction w a salt), then use urea to unfold it, you will denature the protein  If you remove urea and then oxidize, it will fold back into native fold  If you oxidize first and then remove urea, it will fold into a random shape  A-keritins=a-helice structure  Fibron: beta sheet structure  Collagen=every third residue is glycine usually accompanied by proline  Elastin: rich in glycine, alanine, valine  Heme group composed of 4 polypeptide chains, iron atom bound in poryphrin ring  Oxygen site is buried to protect the iron atom from diffusing away and creating oxygen radicals  Hemoglobin binds 4 heme groups and four oxygen molecules  Hemoglobin has a higher affinity for oxygen in the relaxed state  Binding of oxygen shifts plane of the poryphrin ring, which pulls histadine and its helix with it (changes the molecule into relaxed state)  Binding of oxygen is inhibited at low pH  Protons are negative allosteric effector (binding of proton inhibits binding of oxygen)  BPG is highly acidic, and holds hemoglobin in its tense form…in order to bind O2 we must remove BPG molecule  Vmax is the turnover number times the total concentration of enzyme  Catalytic efficiency = kcat/km  Protein without prosthetic group=apoprotein  Protein with prosthetic group= holoprotein  Iron-poryphrin ring accounts for red colour of meat and blood  Henry’s law concentration of any gas dissolved in a fluid is proportional to the partial pressure of that gas above the fluid  Bohr effect: hemoglobin detect a change in pH and releases O2  Concentration of substrate, pH and t
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