Chemistry 333 Principles of Biochemistry Fall 2004 First Exam September 21, 2009 J fo NAME: To be eligible for a regrade, the exam must be done in ink.TOTAL: /5 points /12 points /20 points /4 points /5 points /4 points /24 points 126 /2 points (EXTRA CREDIT) /100 pointsHa manna Formic acid HCOOH 178 10-¢ ‘Acetic acid CH;COOH vie i Pyruvic ‘GH,COCOOH i eae EennesOl 1.38 x 10* sh Malic acid HOOC— CH;—CHOH—COOH (3.98 x 107 oH 255 x 107 l ss Citic acid Reece (a4 107% cooH @) 1.78 x 1075 G)39x 107° Carbonic HCO: (1)43 x 107 = apie 2) 56 x ot Phosphoric acid HPO, (1) 2.25 x 107 : ie (2)631 x 107% (@)3.98 x 107 ‘Ammonium ion NHS 5.6 x 10" TABLE 4.2 ‘Table of pX values for the 20 amina acids found in proteins Rie _PKa Glycine 24 98 Alanine 23 as Valine 23 36 Leucine 24 36 Isoleucine 24 87 Methionine 23 92 Phenylatanine 18 91 Proline 20 106 Sorine 21 92 Threonine 26 104 Cysteine 18 108 83 Asparagine 20 88 Glutamine 22 at Tyrosine 22 a1 108 Tryptophan 24 34 Aspartate 20 100 39 Glutamate 22 97 43 Histidine 18 92 60 lysine 22 92 108 Arginine 18 30 125 "pK, values are atsigned to the a-catbory! group, pK values tothe ‘a-amina group, and pK to sonable groups ia the R group (sve chaio) 475, sat 64 10.2 214 720 12.4 925Biological macromolecules are multimers made up of monomeric building blocks. Use arrows to match the monomers used to synthesize these naturally occurring polymers. Each monomer may be used more than once or not at all. (5 points) Multimers Monomers 1. DNA and RNA. a. glucose 2. proteins. b. nucleotides 3. cellulose . amino acids 4, starch ee 4. lipids 5. membranes ¢. vitamins . How many grams each of solid KH;PO, (MW = 136 g/mol) and solid K3HPOs (MW = 174 g/mol) would you use to prepare 2 L of a 0.3 M phosphate butter (phosphoric acid) at pH 6.8? (12 points) Write out and identify the ACID and the CONJUGATE BASE. (Ignore the K* except when calculating the grams needed.) Partial credit will be awarded, so please show all of your work including any equations! Kal 2POy - Adin \ \ \e . K2WP04- Coniuacte Base, 0.17 lle wales x (4g S yok we pk =| Pre pres \ 4.204 A % = 712+ 4224 moles x [Za _ O.4 _ 5.48 yoy (Se: ae g AR> Answer the following questions regarding the peptide LCYRAIDCG (20 points) AL What is the ‘sequence of amino acids written as the THREE letter code? Leu-Cys-Tuy - Arg - Ala. Tr -Asp - Cys- Ge B. Draw the structure of the peptide LCYRAIDCG as it would exist at PH 6.5 under Vv oxidizing conditions. Be sure to draw any aisle bonds that ‘could form, sh ° 2 ¢ o @ ‘ CA (-N-GH- bene os Oa wee psi -mpick anand ~ ned bm-ce ’ " ch cy GH Cs Cy 4 Ne, te 1 1 § 4 ‘ Cte CH cz0 1 oN da t Cg Cha Cte 3 o NH | | @ #N-C=Niz MN 4 -2 Ss Che c Label the N-terminus of the Peptide you drew in 3B above witha D. Label the C-terminus of the Peptide you drew in 3B above with a * E. Calculate the net charge of LCYRAIDG at PH LS. Ay os Net Chovog = +2 4. Calculate the ‘approximate pl of the peptide DSYRLKCF (4 points) oo Hh S-V- RL Kee COOH 185. Draw the form(s) of the amino acid lysine that would exist at pH 10.8. In what relative percentages (% of each) will these forms exits? Why? (5 points) re s < -c-H Hh, N-€ (Wy NAD Wihun pts plea of the arowp Aone 50% of each form 6A&B points) fou wall J There are six forms of a protein; one is normal and five contain different mutations that change the amino acid at position 150 (called mutants), The normal enzyme has a glutamine residue at amino acid position 150 that is located on the protein surface. Each mutant form of the protein has an amino acid substitution at position 150 as indicated: 6A, Which mutant form of the protein is most like the normal form because it contains the most conservative substitution? (i.e. which side chain most resembles that of glutamine?) a. Form A: glutamine has been replaced by alanine Form B: glutamine has been replaced by arginine 6 Form C: glutamine has been replaced by asparagine d. Form D: glutamine has been replaced by glutamate a. Form E: glutamine has been replaced by phenylalanine B. Which mutant form has the highest propensity to place amino acid 150 in the interior of the protein? Form A: glutamine has been replaced by alanine Form B: glutamine has been replaced by arginine Form C: glutamine has been replaced by asparagine Form D: glutamine has been replaced by glutamate © Fom E: glutamine has been replaced by phenylalanine aesMatch the characteristics at left with the best matching amino acids at right by entering each characteristic’s number in the appropriate blank. Unless otherwise stated, all of the amino acids are at physiological pH 7.4. There are more than one characteristic for many of the amino acids and 24 total answers each worth one point. There will be a deduction for incorrect answers, so don’t fill in the lines with unnecessary characteristics. (24 points) 1. acidic side chain Hl leucine 2. non-chiral amino acid 10 aspartate 3. basic side chain 41213. serine 4. side chain can be modified by adding phosphates 38,4 lysine 5. involved in disulfide cross links HY phenylalanine 6. often found in the tums of proteins 9 ZAS asparagine 7. is converted to tyrosine by hydroxylation Zy lo elycine 8. important for the structure of collagen YZ. AY tyrosine 9. has more than one amino group 8 protine 10. has an overall net charge of -1 at pH 8.5 5 NO AZ cysteine 11. only straight or branched hydrocarbons in the side chain 12. polar, non-charged side chain 13. side chain can be modified by adding sugars 14. aromatic side chaini. Multiple Choice: 2 points each (26 points) ‘The primary purpose of membranes in eukaryotic cells is: A. to increase surface area inside the cell © to create compartments to separate biochemical functions C. to provide anchors for the cytoskeleton D. to provide attachment sites for ribosomes E, none of the above What are the energy-producing organelles in eukaryotic cells? A. endoplasmic reticulum B. lysosomes C. mucteus @ mitochondria E, golgi Aspartame (Nutrasweet) is A. deadly in small amounts ® a dipeptide C. amodified sugar D. a carbohydrate E. anamino acid Free rotation about the peptide bond in a protein is restricted primarily because of @ partial double-bond character of the peptide bond. B. hydrogen bonding to the amide backbone groups. C. partial double-bond character of the N-C alpha bond. D. restrictions caused by local folding patterns. E. steric interference of neighboring amino acid side chainsQuaternary structure refers to: A. the overall shape of the polypeptide chain B, the sum of secondary and tertiary interactions C. simple proteins with one subunit the relative orientation of one polypeptide to another polypeptide in a multisubunit protein complex E. the linear sequence of amino acids in a protein Enantiomers are: A. compounds with very different chemical composition B. molecules with both hydrophobic and hydrophilic characteristics © 2 pair of compounds that are non-superimposable mirror images of one another D. not chiral E, superimposable mirror images The lysosome is important for: A. Biosynthesis of amino acids ® Disposal of molecular waste/excess C. Protein translation D. Glucose breakdown E. None of the above The primary structure of a protein describes the number of each type of amino acid (percent composition) A linear sequence of amino acids C. overall three-dimensional shape D. rotation angles for each amino acid E. assembly of protein subunits into complexes10 9. Structural proteins that typically assemble into large cables or threads to provide mechanical support to cells or organisms are classified as proteins, C. globular D. receptor E. a-helical 10. The [H+] concentration at pH 4.4 is: A. 10 times higher than the [H-] concentration at pH 6.4 B. 10 times lower than the [H-] concentration at pH 5.4 C. 100 times higher than the [H-] concentration at pH 3.4 100 times higher than the [H-] concentration at pH64 E, 100 times lower than the [H+] concentration at pH 5.4 11. Ifhuman blood is not maintained at close to pH = 7.4, a person can develop A. Acidosis B. Alkalosis C. Diabetes © Bown aanad E. None of the above 12. Proteins are biopolymers of amino acids in which monomers are linked in a linear fashion with which type of bond? ® amie . ester ether phosphoanhydride moo ® phosphate ester13. Which of the following compounds would you select to construct a buffer at pH 8? A. acetic acid, pKa = 4.8 ©® _Navisthydroxymethylmethylelycine (Tricine), pKa = 8.15 C.__N-2-hydroxyethylpiperazine-N'-ethansulfonic acid, pKa2 = 7.6 D. glycine, pKa2= 9.9 E. _ tris(hydroxymethy!)aminomethane (Tris), pKa = 8.3 9. EXTRA CREDIT: (2 points) 1. If 70 mL of 0.01 M HCI is added to 150 mL of 0.1M acetic acid, pH 5.0, what is the resulting pH? Identify the appropriate acid and conjugate base and determine their concentrations in the final solution. (2 points) CH; COOH = CH 3too- + H® - Dog WI pte pea m8 CAA] Owl = 0.0FL 5.0 = 4.95 +o a 0, FL x Sela 1. Foal GI. gic ze adaed CBS 1S¢\(Gtt2!) obo mal AT Ve lemmal = 0.2 ml (OEY OHH) = Sit mel HR oto. asi 5.4 mol +4 waurol ~ttl Cu9.45] = J4.4M pH = 4749 + Log Gal pl = 4,4