DOC PREVIEW
CALTECH APH 161 - Lecture notes

This preview shows page 1-2-3-26-27-28 out of 28 pages.

Save
View full document
View full document
Premium Document
Do you want full access? Go Premium and unlock all 28 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 28 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 28 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 28 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 28 pages.
Access to all documents
Download any document
Ad free experience
View full document
Premium Document
Do you want full access? Go Premium and unlock all 28 pages.
Access to all documents
Download any document
Ad free experience
Premium Document
Do you want full access? Go Premium and unlock all 28 pages.
Access to all documents
Download any document
Ad free experience

Unformatted text preview:

BE/APh161 – Physical Biology of the Cell!Rob Phillips Applied Physics and Bioengineering California Institute of Technology Surreal game of telephone – my lecture slides were made by someone else who was teaching out of our book. In some cases, a little more a repeat of book relative to my usual tendency.http://www.rpgroup.caltech.edu/courses/aph161/2010/index.html Username: aph161winter2010 Password: bythenumbers“The most fascinating subject at the time that I was a student was Maxwell's theory” - Einstein. !! “His (Weber’s) lectures on classical physics were lively, but we waited in vain for a presentation of Maxwell’s theory. We knew that it confirmed the identity of transmission of electricity and light and that Hertz’s investigations on electric waves had confirmed the theory. Einstein above all was disappointed.” – Einstein fellow student L. Kollros quoted in “Einstein: The Formative Years” by Don Howard and Jon Stachel ! What about our time? From “Feynman Lectures on Physics”Classification of Cells: The three domains of Life!Cells Bacteria Archaea Eukarya • Classification based on similarities and differences in ribosomal RNA seq.: • < 3µm • diverse habitats Geothermal vent on the Atlantic ocean floor Permafrost in Antarctica • animals, plants, fungi (e.g., mushrooms, mold) • definition: a cell that contains its DNA genome within a membrane-bound nucleusIdealizations of living Cells!The cell can be modeled as… Receptor array Swimmer Random walk Genetic network • how a bacterium swims through water • cell’s large-scale motion • how cells alter the expression of their polymer languages in response to changing conditions E. coliAn ode to E.coli!• To understand the basic rules governing metabolism and replication (and life in general): focus on a few representatives. Although not everyone is mindful of it, all cell biologists have two cells of interest: the one they are studying and Escherichia coli. !!!F. Neidhardt"Image: NBBC library portal E.Coli • Bacteria E.coli: human intestinal inhabitant ! easy to isolate ! is able to grow well in the presence of O2 (unlike most other bacteria) ! replicates rapidly in vitro, easily adjusts to changes in its envir. ! routine to produce mutants (changes in DNA seq. =>biol. signif. differences,e.g. resistance to antibiotics)e.coli as The bacterial standard ruler!• All cells share with E.coli the fundamental biol. directive to convert Eenvir into struct. order and to perpetuate their species. • Min requirements for the perpetuation of cellular life, as observed on Earth: ! DNA-based genome ! mechanisms for DNA→ RNA → proteins ribosomes AFM image of an E.coli cell Electron micrograph the E.coli ruler Human hair 1/500 E.coli DNA E.coli as a standard ruler: • Note: size of E.coli depends on the nutrients provided: richer media => larger size. • Biochem. studies usually use “minimal medium”: salts+glucoseBacterial Shapes!• Here we simply note that the diversity of cell shapes and sizes is immense. Star%Square%! Every time I show you a picture of a cell, ask yourself how the architecture works. ! For cyanobacteria, we are going to examine several remarkable specializations related to their ability to perform photosynthesis. (Cannon et al.)Eukaryotic Cells: a rogue’s gallery!Yeast as the model eukaryote!A budding yeast cell: a model eukaryotic cell • Budding yeast (S. cerevisiae): Fungi - most closely related to animals in terms of evolutionary descent and similarity of protein functions. • Although there are no single-cell animals, there are some single-cell fungi. • ~5µm Electron microscopy image of a cross-section of a budding yeast cell A scanning electron micrograph of budding yeastSize and shape of fibroblasts!! One of my favorite marine organisms is Emiliana huxleyi, a single-celled, eukaryote that performs photosynthesis to make a living. ! These organisms also have a peculiar morphology (mineral shell) that scatters light and gives characteristic appearance to the ocean from space known as a “bloom” Eukaryotic Phytoplankton!Cell Size: Beyond the Mean!• Careful measurements of the size of yeast cells (for different mutants corresponding to different genes being knocked out) reveal a broad distribution of sizes. • Compare these sizes to the mean sizes of bacterial cells. • See reading in HW1 for similar characterization of bacteria. Cell size distribution of mammalian cells, Kirschner et al. Yeast cell size distribution, Jorgensen et al.An Environmental sample!• Here we simply note that the diversity of cell shapes and sizes is immense.The Inventory of cells!• Cells: variety of shapes and sizes, yet many common features of their mol. inventories <=> underlying biochemical unity of life. • Physicists: fundamental unit of matter is the atom (at least for chem. transactions) • Life ≡ metabolism + replication • Biologists: indivisible unit of life is the cell L2!consump. & use of energy from envir. generating offspring that resemble the orig. Image: nobelprize.org Drawing of the structure of cork as it appeared under the microscope to Hooke.!Microscopic section through 1-yr old ash tree wood, drawing by Leeuwenhok 17th cent.: microscopic observations by Hooke and Leeuwenhoek 19th cent.: modern cell theory by Schwann, Schleiden, Virchow; confirmed by PasteurTaking the molecular census of e.coli: why?!• For most cases of interest, it suffices to attribute to E.coli VE.coli ≈ 1µm3 = 1 fL AE.coli ≈ 6µm2 femto = 10 -15 • Estimating the number of molecules of diff. kinds that are in an E.coli cell… …Why care about these numbers? ! a realistic physical picture of a bio phenomena demands understanding of the individual particles involved + the spatial dimensions over which they can interact (crowded? dilute? homogeneous?) ! a prerequisite to beginning to answer questions such as: How fast is a genome replicated? What is the aver. rate of protein synthesis? How do the ribosomes maintain this rate? ! To understand many experiments in biology. Most experimentation is comparative (“normal” behavior vs. “perturbed” behavior, compared by observing some measurable property) ! “a lot” vs. “a few” copies of a molecule => describe


View Full Document

CALTECH APH 161 - Lecture notes

Documents in this Course
Lecture 2

Lecture 2

12 pages

Lecture 3

Lecture 3

18 pages

Load more
Download Lecture notes
Our administrator received your request to download this document. We will send you the file to your email shortly.
Loading Unlocking...
Login

Join to view Lecture notes and access 3M+ class-specific study document.

or
We will never post anything without your permission.
Don't have an account?
Sign Up

Join to view Lecture notes 2 2 and access 3M+ class-specific study document.

or

By creating an account you agree to our Privacy Policy and Terms Of Use

Already a member?