1.20.12 lecture 2 atoms, bonds and water
TRANSCRIPT
8/3/2019 1.20.12 Lecture 2 Atoms, Bonds and Water
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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
BryanT.PhillipsPhD
Asst.ProfessorofBiology
Office200BBE;phone335-2071
Lab214BBE
Officehours:TuesdayandWednesday9:30-11am
B.Sc.1998inBiologyfromUniversityofIllinois
PhD2004inBiology/DevelopmentalGenecsfromTexasA&MUniversity
Dissertaon:Cellsignalingduringzebrafishhindbrainandinnereardevelopment
Postdoc2004-2009UW-Madison/HowardHughesMedicalInstute
CellsignalingandasymmetriccelldivisionduringC.elegansdevelopment
ProfessoratUnivofIowa,DeptofBiologysince2009
Caenorhabditis elegans
Topics covered over the next 4 weeks:
Biological molecules
Cell structure and functionInheritance of genetic informationCellular energetics
8/3/2019 1.20.12 Lecture 2 Atoms, Bonds and Water
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Acknowledgements
This unit’s 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 tounderstand the whole
Reductionism
synthetic wild-type
Predicts that once the parts areunderstood well enough and
assembled in the correct pattern, thewhole should be reproducible.
Examples:
virusesbacteria: Mycoplasma mycoides
Reconstruction is instrumental-
identifies gaps filled by newproperties of the parts
Gibson et al 2010
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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)
8/3/2019 1.20.12 Lecture 2 Atoms, Bonds and Water
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Strong
Weak (but indispensable for life)
of Methane
electron “cloud”
molecular orbital
another example
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(shared hydrogen)
A polar molecule-
orients in an electrical
field
inter-water distance larger
Energy of vdW interaction between two atoms is weak but if many
atoms interact the energy is additive and can result in significant
binding.
any two molecules can interact via vdW
because all molecules can have positively or negatively charged regions
attraction
Inter-atomic distance
average charge
instantaneouscharge
or
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Gecko “Glue”
due to vdW interactions
Gecko
2. Membrane transport of most
molecules
Specific transporter
3. Signal recognition
Receptor for signal molecules
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Fig. 3.7
Fig. 3.8
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• H+ and OH- are both very reactive
• Biological functions can only operate within a narrow
range of [H+] and [OH-]
Hydrogen ion or proton
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pH Value [H+] in M [OH-] in M 1 10-1 10-13 2 10-2 10-12 3 10-3 10-11 4 10-4
10-10
5 10-5 10-9 6 10-6 10-8 7 10-7 10-7 8 10-8 10-6 9 10-9 10-5
10 10-10 10-4 11 10-11 10-3 12 10-12 10-2 13 10-13 10-1
Decreasing pH
Increasing pH
pH ≡ -log10 [H+]
7.4
Milk of magnesia pH = 10.5
pH changes can cause problems to living organisms
Buffers keep pH stable
Carbonic Acid Bicarbonate
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Principle of Le Chatelier (mass action)
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Buffer
Carbonic Acid Bicarbonate
acetazolamide
carbonicanhydrase