APh161: Physical Biology of the CellHomework 1Due Date: Tuesday, January 16, 2007“Chance only favours the mind which is prepared.” ” – Louis PasteurReading:Read chap. 1 of Physical Biology of the Cell (PBOC) and write a refereereport. Your referee report should be submitted by email to me and bothTAs. The referee report should be divided into two sections: i) general com-ments - this should provide an overview of your impressions on the chapter,ii) specific comments - call attention to particular issues that need to be fixed.This first homework has as its main objective the development of a feel forthe numbers associated with various biological problems and the beginningof an ability to use important software for visualizing biological structuresand examining biological sequence information. This particular homeworkwill probably involve more searching around on the web than others. Pleasemake sure to report your sources.1. A Feeling for the Numbers: The Parts List of a White Blood CellIn the figures attached to this homework, there is an electron micrographof a white blood cell. Your goal in this problem is to imitate the molecu-lar census I did in class for E. coli, but this time for this mammalian cell.In particular, use the picture to estimate the size of the nucleus (includingits volume). Estimate the number of nucleosomes that wrap up the humangenome in these cells. Estimate the number of proteins in the cytoplasm ofone of these cells. Also, estimate the area of the plasma membrane and thenthe number of lipid molecules making up this membrane (Note: assume thathalf the mass of the plasma membrane is lipids, the other half is proteins).2. A Feeling for the Numbers: Microbes as the Unseen MajorityOne of the key arguments that I will make throughout the course is that1sometimes just having a feel for magnitudes is a useful guide to intuition. In-deed, our model building will usually follow the sequence: simple estimatesand feeling for the numbers, simple toy models, more realistic models. Forthis problem, read the article entitled ”Prokaryotes: The Unseen Majority”as the basis for your estimates.(a) I argued that we will think of E. coli as our biological standard ruler.This cell has hall of fame status in biology and it is important that you havea sense of what these cells are like. Justify the assumption that a typical (i.e.E. coli) bacterial cell has a volume of 1 µm3. Also, express this volume infemtoLiters. The claim is made (see the paper on prokaryotes as the unseenmajority on the course website) that in the top 200 m of the world’s oceans,there are roughly 1028prokaryotes. Work out the total volume taken up bythese cells in m3and km3.(b) In his famed book The Story of Mankind, Hendrik Willem van Loonmakes an amazing estimate of the size of a box that all of the humans fromall of history would have fit into. I read this when I was about 15 years oldand found it really odd, but cool! Your task is to work out the size of a boxthat would hold (close packing) all of the current human inhabitants of theEarth. Compare this number to the volume of the box that will hold all ofthe bacteria in the top 200 m of the oceans.(c) Also, recall that roughly 2-3 kg of bacteria are to be found in thewaste factory of your large intestine. Make an estimate of the total numberof bacteria inhabiting your intestine and then all of the intestines of all ofthe humans currently on the Earth.(d) On the course website, there is a fascinating paper by Zimmerman andTrach in which they attempt to measure the crowding in the cellular interior.In table 3 they tell us their estimated macromolecular concentrations in thecellular interior. Use these numbers to make an estimate of the mean proteinspacing. Also, estimate the number of lipid molecules in the cell membrane ofE. coli by computing the approximate area of the cell membrane and dividingby the area taken up by each lipid (note: be careful because there are twolipid bilayer membranes in these cells ), the total number of protein moleculesand the number of water molecules. What is the number of base pairs of the2E. coli genome and what is the circumference of its circular chromosome?Comment on the relative size of the DNA molecule and the bacterium.(e) If a particular protein in an E. coli cell is found there at nM concen-trations, how many molecules are there per cell? Are you happy with thenotion of a “concentration” in this case? Explain your reasoning. Make aplot of the numb er of copies of a molecule in an E. coli cell as a function ofthe concentration - make the plot for concentrations from nM to mM.(f) Bacteriophage are the viruses that infect bacteria. Given that theconcentration of phage is tenfold or more higher than that of bacteria, re-port the concentration of phage in the ocean in mg/mL. Then, use this tomake an estimate of the total number of phage on the Earth. This numberwill come in handy in our initial estimates about evolution.3. Manipulating Atomic CoordinatesVisualization of the various structures populating the cell is a key part of ful-filling the objective of structural biology to connect structure and function.In this problem, you will learn how to manipulate pdb files from the ProteinDatabank and to view them using one of the various plotting programs.(a) Obtain coordinates for ATP, phosphatidylcholine, B-DNA, G-actin,the lambda repressor/DNA complex or lac repressor/DNA complex, hemoglobin,HIV gp120 complexed to an antibody, green fluorescent protein (GFP) andRNA polymerase. We will provide most of these coordinates for you with thishomework - a few will be left for you so that you can at least see how this isdone. You can do this by visiting sites such as “http://chemistry.gsu.edu/glactone/PDB/pdb.html”and the Protein Databank itself. You may have to search around a bit. Givea brief description of each one of these molecules and its role in cellular life.(b) Download a structural viewing code such as VMD (University of Illi-nois), Rasmol (University of Massachusetts) or DeepView (http://www.expasy.ch/spdbv/)and create a plot of each of the molecules you downloaded above. You candownload one of these programs under the “General Interest” part of theAPh161 webpage. Experiment with the orientation of the molecule and makesure you print out pictures of each and every molecule.3(c) Later we will see that phosphatidylcholine is one of the molecules thatcan self assemble to form a lipid bilayer (see
View Full Document
Unlocking...