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Nick Ehrecke is the Supplemental Instruction instructor this semester. Sessions are: Mondays 10:30 - 11:20 in 234 BHC Tuesdays 2 - 2:50 in 140 BHC Wednesdays 3:30 - 4:20 in 240 BHC Sessions will start the 2nd week of classes

Bryan T. Phillips PhD Asst. Professor of Biology Oce 200 BBE; phone 335-2071 Lab 214 BBE bryan-phillips@uiowa.edu Oce hours: Tuesday and Wednesday 9:30-11am B.Sc. 1998 in Biology from University of Illinois PhD 2004 in Biology/Developmental GeneTcs from Texas A&M University DissertaTon: Cell signaling during zebrash hindbrain and inner ear development Postdoc 2004-2009 UW-Madison/Howard Hughes Medical InsTtute Cell signaling and asymmetric cell division during C. elegans development Professor at Univ of Iowa, Dept of Biology since 2009

Caenorhabditis elegans

Topics covered over the next 4 weeks: Biological molecules Cell structure and function Inheritance of genetic information Cellular energetics

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Acknowledgements
This units powerpoints are the product of former lecturers in this course:
Dr. John Menninger Dr. Mark Holbrook Myself

Material Composition of Organisms

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Ecosystem Organism Organs Tissues Cells Organelles Molecules Atoms

Reductionism Goal is to understand the parts in order to understand the whole

Reductionism
Predicts that once the parts are understood well enough and assembled in the correct pattern, the whole should be reproducible.
Gibson et al 2010

Examples: viruses bacteria: Mycoplasma mycoides Reconstruction is instrumentalidentifies gaps filled by new properties of the parts

synthetic

wild-type

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Emergent properties
At each step in the hierarchy, new properties of how the parts work together are revealed (they emerge)

These emergent properties of how the parts work together can be essential for understanding the whole, and as a result, understanding life.

Few elements used as such in organisms: o N2, O2 Most mass, energy obtained as molecules Some molecules essential: o 8/20 common amino acids (human) o vitamins (e.g., folic acid, niacin)

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Strong Weak (but indispensable for life)

electron cloud

of Methane

molecular orbital

another example

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(shared hydrogen)

A polar moleculeorients in an electrical field

inter-water distance larger

average charge

any two molecules can interact via vdW because all molecules can have positively or negatively charged regions

instantaneous charge

or
Inter-atomic distance

attraction

Energy of vdW interaction between two atoms is weak but if many atoms interact the energy is additive and can result in significant binding.

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Gecko Glue
due to vdW interactions

2. Membrane transport of most molecules

Specific transporter

3. Signal recognition
Receptor for signal molecules

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Fig. 3.8 Fig. 3.7

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Hydrogen ion or proton

H+ and OH- are both very reactive Biological functions can only operate within a narrow range of [H+] and [OH-]

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pH Value

[H+] in M 10-1 10-2 10-3 10-4 10-5 10-6 10-7 10-8 10-9 10-10 10-11 10-12 10-13

[OH-] in M 10-13 10-12 10-11 10-10 10-9 10-8 10-7 10-6 10-5 10-4 10-3 10-2 10-1

pH -log10 [H+]
Increasing pH

1 2 3 4 5 6 7 8 9

Decreasing pH

10 11 12 13

7.4

Milk of magnesia pH = 10.5 pH changes can cause problems to living organisms

Buffers keep pH stable

Carbonic Acid

Bicarbonate

10

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Principle of Le Chatelier (mass action)

11

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Buffer

carbonic anhydrase acetazolamide

Carbonic Acid

Bicarbonate

12