APh161: Physical Biology of the CellHomework 2Due Date: Thursday, January 19, 2005“An ounce of application is worth a ton of abstraction.” – Booker T.Washington1. More on the Size of Things(a) Estimate the number of protein units that make up a viral capsid forinfluenza virus. In addition, estimate the number of lipid molecules associ-ated with one of these viruses. The lipid molecules surround the protein coatin lipid bilayer form. Make sure you show a picture of the virus and givea rough description of what the structure is like - where is the nucleic acid,what is the shape, etc..(b) Give a little story about the life style of Dictyostelium when it isstarved and try to estimate the numb er of cells associated with the fruitingbody. You will find it useful to lo ok at the little article by Bonner that ison the website in association with HW2. The bottom line is that a) I wantyou to explain a bit about what happens when these cells are starved andthen b) make a sensible estimate of the number of cells associated with thecollective they form.(c) Use the video entitled “15.1-cell−compartments.mov” from EssentialCell Biology to estimate the size of the vesicles associated with the Golgi andtheir density (i.e. how many of them are there per cubic micron). Later onwe will use these numbers to try and get a sense of the energy cost associatedwith vesicle budding.2. A Feeling for the Numbers: The Rates of ThingsIn the previous homework, we worked hard to get a sense for the physicalsizes of various biological entities. Another interesting angle on all of this isto try and get a feel for the rates at which things happen. Following in thetradition of the previous problems, here you will try to make some estimatesof the rates of some processes. Much of what you will do in this problem I1have already done partially in class - your job is to make it your own now.(a) Consider the division of an E. coli cell. Think of such a cell duringrapid growth phase where the cell is dividing roughly once every 20 minutes.Make estimates of the number of water molecules being taken on board persecond during this phase, the number of lipid molecules that are being addedonto the s urface membranes, the number of proteins being synthesized persecond and how many ribosomes are needed to do so.(b) In this case, think about the motility of the bacterium Listeria mono-cytogenes and a typical eukaryotic cell. In the case of Listeria, the motion ofthe bacterium is mediated by the formation of actin comet tails w hich dependin turn upon the linear polymerization of actin filaments. The formation ofthe actin comet results in a speed for the bacterium of something around0.1 µm/sec. In the eukaryotic setting, the cell extends arms called filopodiawhich permit it to crawl, again by virtue of actin polymerization. For Lis-teria, use the measured rate of motion of the bacterium to estimate the rateof actin polymerization both in microns/sec and monomers/sec. Make sureyou draw a picture of the process and explain your rationale. Now, take thatestimate for the rate of actin polymerization and estimate the rate at whicha filopodium extends on a eukaryotic cell. Anything you can do to comparethese estimates with measurements would be useful - one excellent source isCell Movements by Dennis Bray.(c) Look at fig. 6-9 of Essential Cell Biology and assuming that this isa representative sample of the replication pro c ess, estimate the number ofDNA polymerase molecules in a eukaryotic cell like this one from the fly.Note that the fly DNA is about 1.8 × 109nucleotide pairs in size. Estimatethe fraction of the total fly DNA shown in the micrograph. There are eightforks in the micrograph, numbered 1-8. Estimate the lengths of the DNAstrands between replication forks 4 and 5 where we count the forks from leftto right. If a replication fork moves at a speed of 100 nucleotides/s, how longwill it take for forks 4 and 5 to collide. Also, given the mean spacing of thebubbles, estimate how long it will take to replicate the entire fly genome.3. Biological Sequences2One of the important classes of data that have catapulted biology forward isbiological sequence information. In particular, the se quences of genomes (i.e.the string of letters A, T, G, C) and the sequences of proteins (i.e. the lineararrangement of amino acids that make the protein) have made it possible toreason about the evolutionary and functional relationships of molecules fromdifferent organisms. In this problem, you will do a combination of estimatesand computer exercises.(a) Make an estimate of the total number of bacteriophage that have ex-isted on Earth since the beginning of life. Don’t worry, no one really knows,but even if you are good to within a factor of 106it will still be useful. Now,given that the length of the lambda phage genome is roughly 50kbp, estimatehow many different possible sequences we could make out of a genome that is50kbp long. Finally, estimate the fraction of all possible genomes that all ofthe bacteriophage that have ever existed could explore if every one of thosephage had a completely new sequence (a silly idea, but let’s run with it fora moment)? Compare this to the total number of possible phage sequenceswith a length of 50kbp.(b) A friend of mine and I were chatting about mechanisms of evolution.He told me that he had estimated the total number of cell divisions in thehistory of life. I haven’t tried this yet, but let’s have a go at it. Try toestimate the total number of cell divisions. Above all, be clear about whatassumptions you have made in order to make such an estimate. Note thatthe reason for thinking about this is that these cell divisions are the rawmaterial of evolution and we want to get a sense of the numbers.(c) Please go through the bioinformatics tutorial on the HW2 part of thecourse website. Make sure to carry out all of the operations expected of
View Full Document
Unlocking...