Test 1 Flashcards
Closed System
energy and materials are retained within the system during any reaction or transformation`
Open System
materials can be exchanged with the surrounding enviroment during the reaction or transformation
why is a cell/organism an open system?
because there can be import of thermal energy, nutrients, chemical signals, as well as export of reaction products and energy as heat
1st law of thermodynamics
ENERGY IS CONSERVED
-energy can be converted from one form to another but the total energy remains the same during a reaction
Exothermic
Reaction that gives off heat
Endothermic
reaction that absorbs heat
2nd law of thermodynamics
Systems tend to go to disorder
-the entropy of an isolated system will tend to increase;meaning the system become more disordered
Third law of thermodynamics
The entropy of a system goes to 0 as the temperature goes to absolute 0
If Delta G is negative then:
- the reaction is spontaneous/folding
- exergonic
If Delta G is positive then:
- the reaction is not spontaneous/folding
- endergonic
Transition state
is the activated form of the reactants in which there is a partical chemical reaction and represents a molecular intermediate in the chemical reaction.
What is the distance in hydrogen bonding of two waters from one oxygen to another?
2.8 to 3.0 angstroms
Edman Degradation Steps
- react peptide with PITC @ ph=9
- N-terminus is uniquely NH2 at this pH
- N terminal peptide bond will selectively cleave in formic acid
- Treat with aqueous acid to stabilize product
- identify amino acid R1 on the products by chromatography
What is Edman Degradation good for?
Good for about 20 amino acids If alot of material is available
What do you need to do if the polypeptide is longer than 20 amino acids long for Edman Degradation?
Do prelim Fragmentation with CNBr and needs proteases to be done
Mass Spec
- accurately measures the Mass/Charge Ration (m/z) of molecules up to 10 kDs
- works by manipulating charge molecules through a voltage and electrical field which measures the M/z ratio
Tandem Mass Spec (Ms/Ms)
involves two stages of Ms
1) lions of a desired M/Z are isolated from the rest of the ions
2) The selected ions are subject to a chemical reaction that leads to dissociation to form product ions that are analyzed by the 2nd stage Ms
What are the two advantages of Mass spec when compared to Edman Degradation
- experimnet requires much less material
- the experiment requires much less time
Secondary Protein Structure
- Alpha Helices and Betal Sheets
- Involves interactions between amino acid residues that are close together via H-bonding
- other interactions also contribute
Tertiary Protein Structure
-involves regions of the protein that fold into 3D-Domains
Quaternary Protein Structure
-involves contact and interactions between proteins in a multi subunit complex
What are the Noncovalent interactions
Ionic-results in electrostatic interactions
H-bonding
Hydrophobic interactions (entropy driven)
Van Der Waals
List the nonequivalent interactions from strongest to weaken
1) Ionic (42 KJ/Mol
2) H-bonding (8-21Kj/mol)
3) Hydrophobic (4-8KJ/MOL)
4) Van Der Waals (4 KJ/Mol)
What force/forces are the most importune in their stabilization of the structure in terms of total Energy?
Hydrophobic and Van Der Waals
Peptide Bond
Planar
-reduces the amount of free rotations in the protein backbone
Type 1 turn
Fuck Pretty Slutty Girls
F P S G
2nd amino acid is proline
Type 2 Turn
VRGN
-3rd amino acid is glycine
What stabilizes tertiary Structures?
- hydrophobic and Van Der waals in the interior
- hydrophilic interactions at the protein surface
- Fold structures can be stabilized by disulfide bond forms between cysteins
What makes Disulfide bonds unstable?
BME or DTT
Why is it important that the interactions between subunits are weak?
1) so that association and dissociation reactions can occur
- association can activate or deactivate the function
- different combinations of subunits in heterodimers can occur and this leads to different activities or specificities
2) Bc conformational changes are important in the function of the complex
Kd
The equilibrium that occurs between two subunits
if Kd/(p2)=(p1)/(p1-p2) when P1=Kd then…
then (p2)=(P1-P2) means that P2 is half saturated when P1 at (P1)=Kd
How can denaturation be accomplished?
1) heating the protein-incrases the values of -TdeltaS so folded stat is less stable
2) add chaotrophic agent (urea, SDS, Alcohol): reacts favorably with the unfolded protein resulting in a large Delta S change in going from folded to unfolded state
3) extreme pH: result in charge change and will decrease delta H of folding
What is the overall Delta G for protein folding?
negative
