Test 1

Question 1

Closed System

Answer 1

energy and materials are retained within the system during any reaction or transformation`

Question 2

Open System

Answer 2

materials can be exchanged with the surrounding enviroment during the reaction or transformation

Question 3

why is a cell/organism an open system?

Answer 3

because there can be import of thermal energy, nutrients, chemical signals, as well as export of reaction products and energy as heat

Question 4

1st law of thermodynamics

Answer 4

ENERGY IS CONSERVED

-energy can be converted from one form to another but the total energy remains the same during a reaction

Question 5

Exothermic

Answer 5

Reaction that gives off heat

Question 6

Endothermic

Answer 6

reaction that absorbs heat

Question 7

2nd law of thermodynamics

Answer 7

Systems tend to go to disorder

-the entropy of an isolated system will tend to increase;meaning the system become more disordered

Question 8

Third law of thermodynamics

Answer 8

The entropy of a system goes to 0 as the temperature goes to absolute 0

Question 9

If Delta G is negative then:

Answer 9

• the reaction is spontaneous/folding

- exergonic

Question 10

If Delta G is positive then:

Answer 10

• the reaction is not spontaneous/folding

- endergonic

Question 11

Transition state

Answer 11

is the activated form of the reactants in which there is a partical chemical reaction and represents a molecular intermediate in the chemical reaction.

Question 12

What is the distance in hydrogen bonding of two waters from one oxygen to another?

Answer 12

2.8 to 3.0 angstroms

Question 13

Edman Degradation Steps

Answer 13

• 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

Question 14

What is Edman Degradation good for?

Answer 14

Good for about 20 amino acids If alot of material is available

Question 15

What do you need to do if the polypeptide is longer than 20 amino acids long for Edman Degradation?

Answer 15

Do prelim Fragmentation with CNBr and needs proteases to be done

Question 16

Mass Spec

Answer 16

• 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

Question 17

Tandem Mass Spec (Ms/Ms)

Answer 17

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

Question 18

What are the two advantages of Mass spec when compared to Edman Degradation

Answer 18

• experimnet requires much less material

- the experiment requires much less time

Question 19

Secondary Protein Structure

Answer 19

• Alpha Helices and Betal Sheets
• Involves interactions between amino acid residues that are close together via H-bonding
• other interactions also contribute

Question 20

Tertiary Protein Structure

Answer 20

-involves regions of the protein that fold into 3D-Domains

Question 21

Quaternary Protein Structure

Answer 21

-involves contact and interactions between proteins in a multi subunit complex

Question 22

What are the Noncovalent interactions

Answer 22

Ionic-results in electrostatic interactions
H-bonding
Hydrophobic interactions (entropy driven)
Van Der Waals

Question 23

List the nonequivalent interactions from strongest to weaken

Answer 23

1) Ionic (42 KJ/Mol
2) H-bonding (8-21Kj/mol)
3) Hydrophobic (4-8KJ/MOL)
4) Van Der Waals (4 KJ/Mol)

Question 24

What force/forces are the most importune in their stabilization of the structure in terms of total Energy?

Answer 24

Hydrophobic and Van Der Waals

Question 25

Peptide Bond

Answer 25

Planar

-reduces the amount of free rotations in the protein backbone

Question 26

Type 1 turn

Answer 26

Fuck Pretty Slutty Girls
F P S G
2nd amino acid is proline

Question 27

Type 2 Turn

Answer 27

VRGN

-3rd amino acid is glycine

Question 28

What stabilizes tertiary Structures?

Answer 28

• 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

Question 29

What makes Disulfide bonds unstable?

Answer 29

BME or DTT

Question 30

Why is it important that the interactions between subunits are weak?

Answer 30

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

Question 31

Kd

Answer 31

The equilibrium that occurs between two subunits

Question 32

if Kd/(p2)=(p1)/(p1-p2) when P1=Kd then…

Answer 32

then (p2)=(P1-P2) means that P2 is half saturated when P1 at (P1)=Kd

Question 33

How can denaturation be accomplished?

Answer 33

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

Question 34

What is the overall Delta G for protein folding?

Answer 34

negative