1.20.12 Lecture 2 Atoms, Bonds and Water

8/3/2019 1.20.12 Lecture 2 Atoms, Bonds and Water

http://slidepdf.com/reader/full/12012-lecture-2-atoms-bonds-and-water 1/12

1/19/

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

[email protected]

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



1/19/

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



1/19/

• 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



1/19/

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)



1/19/

Strong

Weak (but indispensable for life)

of Methane

electron “cloud”

molecular orbital

another example



1/19/

(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



1/19/

Gecko “Glue”

due to vdW interactions

Gecko

2. Membrane transport of most

molecules

Specific transporter

3. Signal recognition

Receptor for signal molecules



1/19/

Fig. 3.7

Fig. 3.8



1/19/

• H+ and OH- are both very reactive

• Biological functions can only operate within a narrow

range of [H+] and [OH-]

Hydrogen ion or proton



1/19/

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



1/19/

Principle of Le Chatelier (mass action)



1/19/

Buffer

Carbonic Acid Bicarbonate

acetazolamide

carbonicanhydrase

Documents

1.20.12 Lecture 2 Atoms, Bonds and Water