7.012 Problem Set 1 Solutions

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1 ame TA Section Problem Set 1 Solutions Your answers to this problem set must be inserted into the large wooden box on wheels outside by 4:30 PM, Thursday, September 15. Problem sets will not be accepted late. Solutions will be posted on the web. ( Question 1 A. a) Define.. i) hydrogen bond_ A noncovalent bond in which a hydrogen atom of one molecule is attracted to an electronegative atom like nitrogen or oxygen ii) covalent bond a bond formed by the sharing of one or more electrons, between atoms.. iii) ion An ion is an electrically charged particle that forms when an atom gains or loses one or more electrons iv) isotope The term isotope describes a situation where atoms of the same element have the same number of protons in their nuclei, but differ in their number of neutrons. b) Which of the following bonds is a covalent bond? ircle the correct answers. ionic hydrogen van der Waals disulfide bond none of these c) Write in the appropriate descriptive term(s) from below adjacent to the molecules listed. hoose from: cation anion polar noncharged nonpolar noncharged 2 a l 4 Polar noncharged ation Anion onpolar noncharged d) Explain why ethane ( 2 6 ) is a nonpolar molecule while ethanol ( 2 5 ) is a polar molecule. Ethanol is a polar molecule because there is a partial charge separation associated with the bond between the hydrogen and the oxygen. The higher electronegativity of oxygen pulls the electrons in the bond closer to the oxygen resulting in a greater electron density around the oxygen. This provides a slight negative charge for the oxygen and a slight positive charge for the ydrogen. The molecule is polar because these opposite charges are separated at the two ends of the bond. Ethane, on the other hand, is nonpolar because there are no such charge separations present in this molecule. The electronegativity difference between carbon and hydrogen are not significant enough to cause this type of charge separation.

2 B. Match the letter of the organelle or structure on the left with the function or characteristic on the right. rganelle/structure Function or haracteristic a. ucleolus G Prepares proteins for export from the cell b. ucleus D Digests macromolecules c. Plasma Membrane F rganelle catalyzing protein synthesis d. Lysosome B ontains all genomic DA e. Rough Endoplasmic Reticulum Surrounds cells f. Ribosome A Where ribosomal RA is made g. Golgi Apparatus E Site of exported protein synthesis. h. Mitochondria "Powerhouse" of the cell a) What is the general name of this macromolecule above? Polypeptide DA RA Lipid arbohydrate b) What is the chemical difference between the pentose sugar in DA and the pentose sugar in RA? (See pages 47 and 55 in the text book.) The sugar in RA has a hydroxyl () group in the 2' position while the sugar in DA has a hydrogen in the 2' position. 2

3 Question 2 The following structure is found in many biological systems P Professor Eric Lander drew a representation of this molecule like this. a) This is an example of what type of biological molecule? Phospholipid b) Where exactly are these molecules found in a living cell? Plasma Membrane, other membranes c) If you were to add many of these molecules to the glass of water shown below, draw one of three configurations these molecules would assume. bilayer bilayer micelle vesicle d) What is the name of your configuration? e) Explain briefly why the molecules take this shape. A phospholipid molecule has a hydrophobic tail and a hydrophilic head. When many molecules are placed in an aqueous solution, the most energy efficient configuration is for these molecules is to align tailtotail and headtohead. 3

4 Question 3 ne day in lab while studying an enzyme, Bioroxase, you discover the following potential interactions that could occur between this amazing enzyme and its substrate. Asn 3 Asp Substrate Substrate 3 Lys Arg Ile Bioroxase a) Determine if a favorable interaction is likely to take place, at each site between the chemical group on the substrate and the closest side chain of an amino acid on Bioroxase. If, and only if, a favorable interaction is likely to take place, give the name for the strongest direct intermolecular interaction. hoose from ionic interaction, covalent bond, hydrogen bond, and van der Waals force. Amino Acid Will a favorable interaction take place? ircle one. Strongest Interaction ionic interaction, covalent bond, hydrogen bond, or van der Waals force. Asp Yes/o ionic bond Asn Yes/o hydrogen interaction Ile Yes/o van der Waals Arg Yes/o ionic interaction Lys Yes/o b) For all cases where a potential interaction seemed unfavorable, explain why that interaction may be unfavorable. The interaction between the side chain of lysine and the 3 group is unfavorable because both are positively charged. The positive charge of the 3 group will repel and not attract the positive charge of the lysine side chain. 4

c) Explain what a van der Waals force is. A very weak attraction between molecules resulting from a momentary shift of the electron density in a molecule thus establishing a dipole moment.

d) Recent studies have suggested that geckos (small lizards) can stick to walls and ceilings using van der Waals forces alone. ow might this be possible? http://www.sciam.com/article.cfm?

5 c) Explain what a van der Waals force is. A very weak attraction between molecules resulting from a momentary shift of the electron density in a molecule thus establishing a dipole moment. The dipoles induced by the effect of one molecule on the others lead to a net electrostatic attraction. d) Recent studies have suggested that geckos (small lizards) can stick to walls and ceilings using van der Waals forces alone. ow might this be possible? 8E1809E588EF e) In your continuing work with Bioroxase you discover that this enzyme is also a transmembrane protein (the protein transverses the lipid bilayer of the cell). Box the portion(s) of the protein sequence below from Bioroxase that you would expect to be found in the membrane. 3 arg pro gly cys ser lys ala tyr ala lys ile val leu leu phe ala trp val leu ala leu ala phe phe leu ile trp val ile phe leu glu trp asp arg his asp phe glu ser gly pro val cys ala gly cys ser asp lys gly glu f) Why would the section(s) you boxed likely to be found in the membrane? The lipid bilayer of the cell is largely nonpolar, and thus it is expected that the region of the protein that passes through this nonpolar layer will also be nonpolar and generally hydrophobic. The section boxed above represents the largest consecutive stretch of nonpolar amino acids of the residues given and would most likely be the transmembrane region or domain. 5

6 Question 4 Which of the following substrates would fit favorably in the enzyme binding site depicted below? W ormal Substrate (binds to protein) Analog 1 (does Xnot bind) Analog 2 (binds) Y Analog 3 (does Znot bind) This is the simplest correct bonding arrangement of the atoms and charges. 1 Solution Protein Substrate S

7 STRUTURES F AMI AIDS at p ALAIE (ala) ARGIIE (arg) ASPARAGIE (asn) 2 3 ASPARTI AID (asp) 2 S 3 YSTEIE (cys) GLUTAMI AID (glu) GLUTAMIE (gln) 2 3 GLYIE (gly) 2 3 ISTIDIE (his) ISLEUIE (ile) 2 3 LEUIE (leu) LYSIE (lys) 2 2 S 3 3 METIIE (met) 3 3 TREIE (thr) TRYPTPA (trp) PEYLALAIE (phe) PRLIE (pro) TYRSIE (tyr) 2 3 SERIE (ser) VALIE (val)

7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells?

7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells? ame 7.01 Problem Set 1 Section Question 1 a) What are the four major types of biological molecules discussed in lecture? Give one important function of each type of biological molecule in the cell? b)