98aMTReviewPacket - Marilyn Le Bio 98A Midterm Review Bio...

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Unformatted text preview: Marilyn Le Bio 98A Midterm Review Bio 98A Midterm Review 1-5-08: Lecture 1 Noncovalent forces and water Proteins types o Enzymes : slow down or speed up rxns o Transport proteins Example: hemoglobin o Hormones (for cell communication) bind to receptor proteins (usually on surface) o Structural proteins : just there Ex. keratin in hair Biochemical forces o Covalent: Strong bonds Bonds that hold molecules together o Noncovalent: Weak bonds can change easily = dynamic Bonds between molecules Ionic bonds Non-directional: can be rotated Hydrogen bonds Fixed length Made between H---O or H---N Involved in protein folding Hydrophobic interactions Interactions b/t non-polar molecules in water Van der Waals forces Induced dipoles: + and - Relative strength: Ionic> H-bond Hydrophobic > Van der Waals Water o High amount of H-bonds responsible for high b.p. and m.p. o Density of liquid > ice o Can make 4 H-bonds 1 Marilyn Le Bio 98A Midterm Review 1-7-09: Lecture 2 Acid-base equilibria, pH, and buffers Weak acids and bases o Only a small portion will dissociate (1-2%) o Vs. strong acid assume all of acid/base will dissociate o K a = [H + ][A- ] / [HA] Henderson-Hasselbalch Equation o pH = pK a + log ([HA]/[A- ]) When pK a = pH o [HA] = [A- ] To find pH of a weak acid (when pK a and concentration given) o Assume Ka = [H + ] 2 / [HA] Find [H + ] take log of this Buffers resist change in pH Best buffer is when pH = pK a (or close) To make a buffer o How much acid? Find amount desired moles of acid convert to mL with given concentration o How much base? Use HH eq to find % of A- Multiply moles of acid by %A- = moles of base needed convert to mL of base o Add mL of water to get to desired volume Finding net charge on an amino acid o If pH >> pKa deprotonated o If pH << pKa protonated o If pH is w/in 1 unit of pKa use HH eq to find % of HA and A- figure out which form (HA or A- ) is charged o Add all charges together HA (protonated) A- (deprotonated) Amino group, Lys, Arg, His +1 Carboxyl group, Cys, Tyr, Glu, Asp-1 2 Marilyn Le Bio 98A Midterm Review 1-9-09: Lecture 3 Amino Acids (abbreviated in notes as AA) 20 amino acids o Building blocks of proteins o Precursors to other molecules o Some AA must be provided from diet Structure o Identical in all AA: amino group, -C, carboxyl o Each AA differs in R group Peptide bond formed between carboxyl of one AA and amino of another o Formation by losing H 2 O Some special AA: o Cystine : R group (--SH) makes disulfide bonds o Tyrosine and tryptophan absorb light at high wavelengths Insulin o 2 polypeptides folded conformation dictated by disulfide bonds Amino acid titration curve o When pK a = pH 50% protonated and 50% deprotonated Draw horizontal (flat) regions at pH = pK a Happens for each ionizable group...
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98aMTReviewPacket - Marilyn Le Bio 98A Midterm Review Bio...

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