012: Introductory Biology-Fall 2004 Instructors: Professor Eric Lander, Professor Robert A Weinberg, Dr. Claudette Gardel Name Section: 7.012 Problem set 2 Please print out this problem set and record your answers on the printed copy. Answers to this problem set are to be turned in at the box outside by 4: 10 Wednesday, September 17. Problem sets will not be accepted late. Solutions will be posted on the web september 18 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 L 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? 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 7012Fall2003Name:___________________________________ Section:_____ 7.012 Fall 2003 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? 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 Please print out this problem set and record your answers on the printed copy. Answers to this problem set are to be turned in at the box outside by 4:10 Wednesday, September 17. Problem sets will not be accepted late. Solutions will be posted on the web September 18, 2003. 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