Name:___________KEY______________ 1 2007 7.013 Problem Set 1 KEY Due before 5 PM on FRIDAY, February 16, 2007. Turn answers in to the box outside of 68-120. PLEASE WRITE YOUR ANSWERS ON THIS PRINTOUT. 1. Where in a eukaryotic cell do you think you would find the following proteins residing? Be as specific as you can in terms of subcellular location. (a) an enzyme whose substrate is DNA The nucleus. DNA is found in the nucleus of eukaryotic cells, so an enzyme that acts on DNA would have to be found inside the nucleus. (b) an enzyme that catalyzes protein synthesis The cytoplasm. Proteins are synthesized by ribosomes, which live in the cytoplasm of the cell. Some of these cytoplasmic ribosomes are associated with the membrane of the ER (i.e. the endoplasmic reticulum), the organelle that helps modify and transport any protein that is destined for the cell membrane or the outside of the cell. (c) a protein that allows ions to pass in and out of the cell The cell membrane. Many proteins are found inside the cell membrane (also called the plasma membrane). Some of these cell membrane proteins form protein pores that allow things to come inside the cell from the extracellular environment, or go outside the cell from the cytoplasm. (d) a protein that acts as a receptor for extracellular cell-cell communication molecules that are large and hydrophilic The cell membrane. Many proteins are found inside the cell membrane (also called the plasma membrane). Some of these cell membrane proteins bind to extracellular molecules and induce changes in the inside of the cell when they receive these extracellular signals. (e) a protein that forms a channel through which RNAs can be exported into the cytoplasm The nuclear membrane. Many proteins are found inside the nuclear membrane, which is the membrane that separates the inside of the nucleus from the cytoplasm. Some of these nuclear membrane proteins form nuclear pores that allow things to come inside the nucleus from the cytoplasm, or go outside the nucleus to the cytoplasm. (f) an extracellular matrix proteinName:___________KEY______________ 2 Outside the cell. These proteins, which make up the majority of the dry weight of your body, are the protein glue that holds your cells together into tissues and organs. (g) a protein that adds carbohydrate groups to proteins destined for the outside of the cell The ER (endoplasmic recticulum) and/or the Golgi. The ER and the Golgi are the two organelles that help modify, sort, and transport any protein that is destined for the cell membrane or the outside of the cell. One of the most common modifications that occurs on extracellular proteins is the covalent addition of sugars/carbohydrates to the protein. (h) a protein that synthesizes ATP The mitochondria. The mitochondria are the organelles in which cellular energy (in the form of ATP) is produced. (i) the cytoskeletal protein actin The cytoplasm. Actin is one of the proteins that makes up the cytoskeleton, which is a collection of large protein cables or filaments that give cells shape and structure, and confer upon cells the ability to change shape and move. Actin is the most abundant protein inside cells, and is found throughout the cytoplasm of cells. (j) The major cytoskeletal protein actin is translated as a single polypeptide subunit. Many actins associate together to form actin filaments. These filaments can disassemble and reassemble to help cells move and change shape. During these processes, what is the highest level of actin protein structure that is changing? Your choices (from lowest to highest) are: primary, secondary, tertiary, quaternary. Quaternary. Actin is a monomeric protein, and proteins that are monomers (i.e. consist of only one chain of amino acids) have primary, secondary, and tertiary structure. However monomeric proteins do not have quaternary structure by definition. Quaternary structure is the level of structure that tells you how multiple protein chains interact with each other. Thus, when protein cables or filaments are being formed by the association of many actin monomers, quaternary structure is changing. 2. Below is a molecule called cholesterol, which is a lipid.Name:___________KEY______________ 3 (a) Put a circle around the part of this molecule that is hydrophobic. Circle the entire molecule except the OH. Cholesterol (other than the one OH group) is made entirely of carbons and hydrogens. Hydrocarbons are hydrophobic because they are not polar and thus cannot form Hydrogen bonds with water. (b) Draw a box around the part of this molecule that is hydrophilic. Box the OH group. An OH group is polar and thus can form Hydrogen bonds with water. (c) Cholesterol is transported through your blood. Do you think that cholesterol molecules can be transported in your blood freely, i.e. without requiring any sort of transport protein? Why or why not? No. Blood is aqueous and cholesterol is very hydrophobic. Thus cholesterol cannot be dissolved in blood. Thus cholesterol must be packaged into protein structures (called, for example, HDL and LDL particles) that hide the cholesterol on the inside of the particles, shielding the hydrophobic cholesterol from the aqueous blood. 3. **For this problem, you will need to use a computer program to view the structure of a protein and of DNA.** To begin, go to the site: http://web.mit.edu/star/biochem/index.html and click on “Click here to start Star Biochem.” Once the program Star Biochem has been downloaded onto your computer, go to the site: http://web.mit.edu/viz/7.01x/ This website has several links. Those marked “The Amino Acids,” “The Peptide Bond,” “Secondary Structure,” and “Nucleotides and DNA” contain models of each of these things that will help you understand protein and DNA structure. To do the graded problem, click on “7.013 Problems” and do “Problem 1 (pdf with live links).” To help you learn how to use the program, a tutorial is available under “StarBiochem Tutorial Problem (pdf with live links).” If you do not have a computer easily available, or if you would like to do this problem in the presence of technical staff who are familiar with this computer program, there will be staff present on Thursday 2/15/07 from 4-9pm in a room TBA (see the course website). You are welcome to stop by anytime during that interval to use one of the computers in that room to
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