Lecture 6-10

Question 1

Specific binding

Answer 1

Intensive variable defined as mol substance bound (ligand) per mol protein

Question 2

Specific activity

Answer 2

Intensive variable defined as µmol rxn product formed per minute per mg enzyme

Question 3

Foldases

Answer 3

ATP-dependent mechanoenzymes that facilitate protein folding (ex: molecular chaperones) into active conformation

Question 4

Levinthal paradox

Answer 4

High number of degrees of freedom in unfolded protein means extremely large number of possible conformations. If folding happened step-wise, time would be astronomically long. Predicts massive parallel search of local conformation

Question 5

Folding funnnel

Answer 5

Hypothetical depiction of converging paths to native protein structure

Question 6

GroES/EL

Answer 6

Chaperonin protein complex that hydrolyzes 7 ATP in order to assist folding of other proteins. GroES = cap. GroEL = chamber

Question 7

Prion diseases

Answer 7

Prion = (Pr)oteinaceous (I)nfectious (ON)ly. Found in CNS. Normal protein = PrPc. Aberrant protein form = PrPSc. PrPSc has infectious B-sheet fold and promotes the folding of PrPc into PrPSc

Question 8

Kd

Answer 8

Dissociation constant. Kd = [P][L]/[PL]

Question 9

Saturation equation

Answer 9

[PL]/[Ptotal] = 1/(1 + Kd/[L])

Question 10

Hemoglobin (Hb)

Answer 10

8-helix polypeptide subunits. Tetramer of two alpha and two beta subunits. Heme group between helices E and F. Transports O2 from lungs to tissues in RBCs

Question 11

Myoglobin (Mb)

Answer 11

8-helix polypeptide subunits. Heme group between helices E and F. Muscles use Mb to bind and store O2 for emergency needs. Higher affinity for O2 drives O2 transfer from Hb to Mb in muscles

Question 12

Hb and Mb structure similarities

Answer 12

Only share 27 identical residues. Demonstrates that extensive sequence similarity is not required for structure similarity. Only require similar residues in critical locations

Question 13

Monod model

Answer 13

Aka concerted cooperativity model. Hb has two states: T-state and R-state with no hybrid forms (all-or-nothing transition from T to R). T-state preferred when O2 is not bound. O2 binding stabilizes R-state and increases number of Hb in R-state.

Question 14

Hb-T

Answer 14

More stable conformation of Hb due to more subunit interactions. Lower affinity for O2 because T-conformation pulls Fe2+ out of heme group plane

Question 15

Hb-R

Answer 15

Higher affinity for O2 because R-conformation aligns Fe2+ in plane with heme ring. Conformation change transmitted to other subunits through subunit interface and leads to changes in all subunit tertiary structures

Question 16

Koshland model

Answer 16

Aka sequential model. Describes a series of conformational changes as ligand binds. Affinity for O2 increases as more O2 binds to Hb subunits.

Question 17

Oxidoreductases

Answer 17

Class 1. Catalyze oxidation-reduction rxns.

Ex: ethanol + NAD+ <> acetaldehyde + NADH + H+

Question 18

Transferases

Answer 18

Class 2. Catalyze transfer of functional groups.

Ex: glucose + ATP <> glucose-6-P + ADP

Question 19

Hydrolases

Answer 19

Class 3. Catalyze hydrolysis of covalent bonds.

Ex: glucose-6-P + H2O <> glucose + Pi

Question 20

Lyases

Answer 20

Class 4. Catalyze elimination/addition of functional groups (creation/removal of double bonds).
Ex: malate <> H2O + fumarate

Question 21

Isomerases

Answer 21

Class 5. Catalyze intramolecular rearrangements.

Ex: glucose-6-P <> fructose-6-P

Question 22

Ligases

Answer 22

Class 6. Catalyze joining of molecules (or molecular groups).
Ex: Glutamate + NH3 + ATP <> Glutamine + ADP + Pi

Question 23

Ergases

Answer 23

Unofficial class 7. Convert chemical bond energy into mechanical work.
Ex: ATP + Myosin at pos1 <> Myosin at pos2 + ADP + Pi

Question 24

Keq

Answer 24

Equilibrium constant. Keq = [products]/[reactants]. Unaffected by enzymatic catalysis

Question 25

Delta G (double dagger)

Answer 25

Reaction energy barrier (activation energy)

Question 26

Covalent catalysis

Answer 26

Covalent bond forms transiently between enzyme and substrate. Helps preserve chemical bond energy during catalysis. Forms adducts or intermediates
AA side-chains modified: Lys, His, Cys, Asp, Thr, Ser

Question 27

Metal ion catalysis

Answer 27

Use of metal ions in active sites as template, Lewis acid, or redox reagent. Acts as template to bind and orient substrates. Shields and stabilizes negative charges in transition state. Increases acidity of bound water/alcohols. Mediates redox rxns by changing oxidation state. Exploits the Lewis acid and redox properties of active site metal ions

Question 28

Chymotrypsin active site

Answer 28

Hydrophobic pocket helps bind aromatic ring and dehydrate active site. Catalytic triad: Asp102, His57, Ser195. Ser195 participates in covalent catalysis with help of Asp102 and His 57 to make Ser Oh more nucleophilic. Gly193 and Ser195 use NH atoms to stabilize transition state in oxy-anion hole with H-bonds

Question 29

Orientation

Answer 29

Arranging active-site for optimal activity

Question 30

Induced fit

Answer 30

Binding substrate in ways that stabilize chemical and conformational intermediates of catalysis

Question 31

Acid-base catalysis

Answer 31

Donating/abstracting protons

Question 32

Conformational catalysis

Answer 32

Creating a dynamic environment that facilitates chemical changes during catalysis

Question 33

Transition-state stabilization

Answer 33

Various catalytic elements working together to lower activation energy for each step in catalytic mechanism