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MIT 7 012 - Study Guide

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Name__________________________ TA____________Section____7.012 F’04 Problem Set 1 September 10th 2004 This completed problem set must be turned into the wooden box outside Problem sets will not be accepted late.Solutions will appear on the web after the due time.Question 1A.a) Explain what an ion is.b) Explain what a van der Waals force is.c) Match the atoms and molecules listed below with the appropriate descriptive.Choose from:cation anion polar non-charged nonpolar non-chargedCl-H2ONa+CH4d) Circle the “side chain” in each of the amino acids given below.CCOOHNH3CH2CH2OOC-+-GLUTAMIC ACIDCCOOHNH3CH2CH2CH2CH2NH3+-+LYSINE CCOOHNH3H-+GLYCINECCOOHNH3CH2CH2OCNH2-+GLUTAMINEMIT Biology Department7.012: Introductory Biology - Fall 2004Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel2e) Check the following terms to describe the side chains of the amino acids you circledabove.Side Chain of…ChargedNon ChargedPolarNon PolarHydrophobicHydrophilicGlutamic AcidLysineTyrosineAsparagineGlycineGlutaminef) Explain why ethane (C2H6) is a non-polar molecule while ethanol (C2H5 - OH) is a polarmolecule. (A diagram of each molecule may help.)B.a) What are two main differences between prokaryotic cells and eukaryotic cells?b) Match the letter of the organelle on the left with the function or characteristic onthe right.Complex orOrganelleFunction or Characteristica. Mitochondria Site of lipid synthesis; where hydrophobictoxins‡ water soluable and thus excretableb. Nucleus Digests macromolecules and degrades worn-outorganellesc. Smooth Endoplasmic Reticulum Catalyzes protein synthesisd. Golgi Apparatus Contains all genomic DNA in eukaryotic celle. Lysosome Uses sunlight to build sugarf. Ribosome Where ribosomal RNA is madeg. Chloroplast Prepares proteins for export from the cellh. Nucleolus Powerhouse of the cell; where the Krebs Cycleoccurs3Question 2One day in lab while studying your favorite enzyme, Votase, you discover the followingpotential interactions that could occur between this amazing enzyme and its substrate ofchoice.a) At each site between the chemical group on the substrate and the closest side chain ofan amino acid on Votase determine if a favorable interaction is likely to take place. If afavorable interaction is likely to take place, give the name for the strongest directintermolecular interaction. Choose from ionic interaction, covalent bond, hydrogen bond,and van der Waals force.Amino AcidWill a favorableinteraction take place?Circle one.If yes, Name the StrongestInteractionionic interaction, covalent bond,hydrogen bond, or van derWaals force.GlnYes/NoAspYes/NoIleYes/NoLysYes/NoArgYes/NoHOGlnH3N +AspNH3+C-O-OLysH3C CH3SubstrateVotaseIleArgCH34b) For all cases where a potential interaction seemed unfavorable, explain why.Question 3a) In your continuing work with the enzyme votase you discover that the enzyme is also atransmembrane protein (part of the protein crosses the lipid bilayer of the cell). Circlethe portion of the sequence below that you would expect to be the transmembrane regionof the protein.+NH3 - glu - trp - asp - arg - his - asp - phe - glu - ser - gly – pro - thr - phe -ile - trp - leu - ile - trp - leu - val - ile - ala – val - leu - phe - leu - leu - ile -trp – ala - val - leu – arg - pro - gly - cys - ser - lys - ala - tyr - ala - lys -- val- cys - ala - gly - cys - ser - asp - lys - gly - glu - COOHb) Why will the section you circled be embedded in the membrane?c) Draw a schematic of the phospholipid bilayer. Label the lipid hydrocarbon chains,phosphate hydrophilic heads, and water.5Question 4a) In the peptide below, circle the peptide bonds. What are the amino acids in thispeptide?b) What is the name of the macromolecule below? ________________c) What is the chemical difference between the pentose sugar in DNA and the pentosesugar in RNA? (See page 48 in text book.)6 CCOOHNH3CH2CH2CH2CH2NH3+ALANINE(ala)ARGININE(arg)ASPARAGINE(asn)+-ASPARTIC ACID(asp)CYSTEINE(cys)-+CNCH2CH2CH2HHH-COO+GLUTAMIC ACID(glu)GLUTAMINE(gln)GLYCINE(gly)HISTIDINE(his)ISOLEUCINE(ile)LEUCINE(leu)LYSINE(lys)METHIONINE(met)PHENYLALANINE(phe)PROLINE(pro)SERINE(ser)THREONINE(thr)TRYPTOPHAN(trp)TYROSINE(tyr)VALINE(val)STRUCTURES OF AMINO ACIDS at pH 7.0CNHHHHHHCCOOHNH3CH3-+CCOOHNH3CH2CH2CH2NHCNH2NH2-+CCOOHNH3CH2CONH2-+CCOOHNH3CH2COO-+CCOOHNH3CH2SH-+CCOOHNH3CH2CH2OOC-+CCOOHNH3CH2CH2OCNH2-+CCOOHNH3H-+CCOOHNH3CH2CNCNHHHH-+CCOOHNH3CHCH3CH2CH3-+CCOOHNH3CH2CHCH3CH3-+-+CCOOHNH3CH2CH2S CH3-+CCOOHNH3CH2H HHHH-+CCOOHNH3CH2OH-+CCOOHNH3CHOHCH3-+CCOOHNH3CH2-+CCOOHNH3CH2OHH


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MIT 7 012 - Study Guide

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