7.012: Introductory Biology-Fall 2004 Instructors: Professor Eric Lander, Professor Robert A Weinberg, Dr. Claudette Gardel Solutions to 7.012 Problem set 2 Question 1 Many intracellular proteins are required to interact or bind to other macromolecules within a bind DNA. Such proteins often have conserved structural features, called motifs, whis at can cell in order to function properly. One class of such proteins is comprised of proteins tha interact with DNA. One such motif consists of two closely aligned a-helices(shown as cylinders below)that each have leucine-rich regions. This motif is referred to as a leucine Figure by MIT OCW a) Based on what you know about leucine, what type of interaction is likely to be holding the two halves of the"zipper"together? Circle one of the following Ionic Covalent Hydrophobic Hydrogen bonds b)DNA-binding proteins often associate with the charged sugar and phosphate backbone of DNA. Which specific amino acids might you find in a DNA-binding protein on the surface that associates with DNA? What kind of interaction do you expect between DNA and these amino acids of the binding protein You would expect to find positively charged amino acids(arginine, lysine, histidine)interacting with the negatively charged phosphate backbone c)In the lab you purify two short pieces of double-stranded DNA (segment 1 and segment 2) Each piece is exactly the same length(100bp), however the nucleotide sequence comprising each strand is different. You don' t want to spend the money to sequence the strands, but you would the two strands of segment 1 disassociate before those of segment 2. Based on what you kla o like to know which 100bp strand has more A-T base pairs. You heat up each piece and find that about the bonds between nucleotides, which DNA segment had more A-T base pairs? Why? Segment I has more A-T base pairs. A-T base pairs are held together by 2 H-bonds, whereas C-G base pairs share 3 H-bonds. The amount of thermal energy, i.e heat, required to dissociate each segment is directly proportional to the overall number of H-bonds holding the 2 stands of the dna segment together. Therefore, since Segnent I required less thermal energy to cause dissociation, it must have had fewer overall H-bonds than Segment 2. As both strands are comprised of an equal number of base pairs, Segment I must have had more A-T base pairings 7012Fall20037.012 Fall 2003 Solutions to 7.012 Problem Set 2 Question 1 Many intracellular proteins are required to interact or bind to other macromolecules within a cell in order to function properly. One class of such proteins is comprised of proteins that can bind DNA. Such proteins often have conserved structural features, called motifs, which interact with DNA. One such motif consists of two closely aligned α-helices (shown as cylinders below) that each have leucine-rich regions. This motif is referred to as a leucine zipper. a) Based on what you know about leucine, what type of interaction is likely to be holding the two halves of the “zipper” together? Circle one of the following: Ionic Covalent Hydrophobic Hydrogen bonds b) DNA-binding proteins often associate with the charged sugar and phosphate backbone of DNA. Which specific amino acids might you find in a DNA-binding protein on the surface that associates with DNA? What kind of interaction do you expect between DNA and these amino acids of the binding protein? You would expect to find positively charged amino acids (arginine, lysine, histidine) interacting with the negatively charged phosphate backbone. c) In the lab you purify two short pieces of double-stranded DNA (segment 1 and segment 2). Each piece is exactly the same length (100bp), however the nucleotide sequence comprising each strand is different. You don’t want to spend the money to sequence the strands, but you would like to know which 100bp strand has more A-T base pairs. You heat up each piece and find that the two strands of segment 1 disassociate before those of segment 2. Based on what you know about the bonds between nucleotides, which DNA segment had more A-T base pairs? Why? Segment I has more A-T base pairs. A-T base pairs are held together by 2 H-bonds, whereas C-G base pairs share 3 H-bonds. The amount of thermal energy, i.e heat, required to dissociate each segment is directly proportional to the overall number of H-bonds holding the 2 stands of the DNA segment together. Therefore, since Segment I required less thermal energy to cause dissociation, it must have had fewer overall H-bonds than Segment 2. As both strands are comprised of an equal number of base pairs, Segment I must have had more A-T base pairings. MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel L L L L L L Figure by MIT OCW