Red Cross: 1-800-HELP-NOW or www.redcross.orgAmeriCares: www.americares.orgEpiscopal Relief & Development: 1-800-334-7626 or www.er-d.orgUnited Methodist Committee on Relief: 1-800-554-8583 or gbgm-umc.org/umcor/emergency/hurricanes/2005Salvation Army: 1-800-SAL-ARMY or www.salvationarmyusa.orgCatholic Charities: 1-800-919-9338 or www.catholiccharitiesusa.orgFEMA Charity tips: www.fema.gov/rrr/help2.shtmNational Voluntary Organizations Active in Disaster: www.nvoad.orgLouisiana Society for the Prevention of Cruelty to Animals: www.la-spca.orgOperation Blessing: 1-800-436-6348 or www.ob.orgAmerica's Second Harvest: 1-800-344-8070 or www.secondharvest.orgAdventist Community Services: 1-800-381-7171 or www.adventist.communityservices.orgChristian Disaster Response: 1-941-956-5183 or 1-941-551-9554 or www.cdresponse.org/cdrhome.html

Christian Reformed World Relief Committee: 1-800-848-5818 or www.crwrc.orgChurch World Service: 1-800-297-1516 or www.churchworldservice.orgConvoy of Hope: 1-417-823-8998 or www.convoyofhope.orgLutheran Disaster Response: 1-800-638-3522 or www.elca.org/disasterMennonite Disaster Service: 1-717-859-2210 or www.mds.mennonite.netNazarene Disaster Response: 1-888-256-5886 or www.nazarenedisasterresponse.orgPresbyterian Disaster Assistance: 1-800-872-3283 or www.pcusa.org/pdaSouthern Baptist Convention - Disaster Relief: 1-800-462-8657, ext. 6440 or www.namb.net

Any questions regarding material from the last lecture?Any questions regarding material from the last lecture?

Bioinformatic approaches are widely used to “guess”

function since the structure of functionally-similar proteins is shared.

It is dependent on the ability to query what is now very large databases of both

primary and tertiary protein structures.

BLAST analysis demo

The function of a protein is determined by its structure. Ligand binding is specific and tight because of complimentary structures at interaction faces. Lots of noncovalent weak bonds are involved.“Hand-in-glove.

It is the binding site (pocket) that allows a protein to interact with a specific ligand.

It does so with stereo-specificity

Example: immunoglobulin, binds antigen tightly to inactivate or mark for destruction

3 ways that binding pockets favor reactions, but all threework by stabilizing a transition state.

Learn terms in table 4-1!!!

Don’t sweat the details fig 4-34,Lysozyme mechanism

“Extensions” to proteins give them special functions. Take for example, retinal of rhodopsin and heme of hemoglobin.

Vitamin A cis retinal (photoisomerization to all-trans retinal)http://www.elmhurst.edu/~chm/vchembook/533cistrans.html

Some extensions bond with the substrateBiotin, metals so-called co-enzymes

Take for example: hemoglobin, four oxygen carrier, heterotetramer

Four O2; each affect binding of another

How are proteins controlled?

Catalytic properties controlled*Feedback inhibitionAllostery & conformational changesMost enzymes are allosteric 2 conform.

*but positive feedback also occurs such as ADP stimulation of glucose breakdownsee Fig. 4-40

Allostery, feedback inhibition- example, aspartyl transcarbamoylase and cytosine triphosphate, a product of this pathway. ATC makes the nucleotide ring for pyrimidine. CTP is a product of this pathway

Phosphorylation can control protein activity by triggering a conformational change.

GTP binding proteins are self regulating. They are controlled by the loss(hydolysis) and gain (GTP/GDP exchange) of a phosphate group.

The additional phosphate (highly negative) can cause a major conformational change. This is an amplification mechanism, like a lever.

Nucleotide binding and hydrolysis allows motor proteins to produce large movements.

Same idea: phosphate alters gross conformation

Essentially irreversible

NOW, let’s put “working proteins”

in their setting.

Compartmentalization solved many problems.Surface area vs. volumeConcentration dependenceToxic reaction productsSelective barriersStored energy across compartments

Dynamic: Information gate, site of transport, flux for movement

The PM has properties that make it an unusual barrier. Fluid mosaic, 50 atoms thick.

Lipid bilayer

Phospholipids are amphipathic.