Biochemistry Exam 1 Review 2

Function of Globular Proteins

Binding: Interaction strength can be expressed by:

• Association (binding) constant: Ka, units M^-1

• Dissocation constant: Kd, units M, Kd = 1/Ka

• Ka = [PL]/[P][L]

• Kd = [P][L]/[PL]

Binding: Magnitudes - strong and weak

• Strong binding: Kd < 10nM

• Weak binding: Kd > 10 uM

Proteins typically have high specificity: only certain ligands ___.

bind

High specificity can be explained by the ____ of the binding site and the ligand.

Complementary

Complementary of the binding site and the ligand in ….

• size

• shape

• charge

• hydrophobic/hydrophilic character

What is induced fit? Induced fit allows for ____ binding of the ligand. Induced fit allows for ___ affinity of different glands.

• the adaptation where conformational changes may occur upon ligand binding.

• tighter

• high

T/F? Both the ligand and the protein can change their conformations.

TRUE

_____ is a special case of allosteric regulation.

Cooperativity

Allosteric Proteins:

Binding of a ____ to one site affects the binding

Can they be positive? negative? both?

What is it called when a normal ligand of the protein is the allosteric regulator?

What is it called when a different ligand affects binding of the normal ligand?

• ligand

• both

• homotropic

• heterotropic

Cooperativity = ?

positive homotropic regulation

Hemoglobin binds O2 _____.

cooperatively

Hemoglobin is a ___ of two subunits.

Each subunit is similar to ____.

• tetramer

• myoglobin

Are the sequences of hemoglobin and myoglobin similar?

They are not very similar.

Subunit interactions of Hemoglobin:

What molecule is in the T state?

deoxyhemoglobin - hemoglobin without oxygen bound.

Define R and T states of hemoglobin.

Do they have more or less interactions?

Are they more stable or flexible?

Low or high affinity for O2?

T = tense state

• more interactions

• more stable

• Lower affinity

R = relaxed state

• fewer interactions

• more flexible

• higher affinity

O2 binding triggers a ___ → ___ conformational change.

T → R

Conformational change from the T state to the R state involves breaking ____ ___ between the a1-B2 interface.

ion pairs

Hemoglobin (Hb) affinity for O2 depends on __.

H+ binds to Hb and stabilizes the __ state.

Protonates His146 which then forms a ____ _____ with Asp94.

Leads to release of ___.

• pH

• T

• salt bridge

• O2

The pH differences between ____ and ____ _____ increases efficiency of the O2 transport.

• lungs

• metabolic tissues

pH effect on O2 Binding to Hemoglobin is known as the ____ ____.

Bohr Effect

2,3-Bisphosphoglycerate regulates O2 binding:

_____ heterotrophic regulator of Hb function.

Present at mM concentrations in _____.

• Produced from an intermediate in ____.

Small ____ charged molecule, binds to the ____ charged central cavity of Hb.

Stabilizes the ___ states.

• Negative

• erythrocytes

• glycolysis

• negatively

• positively

• T

2,3-BPG binds to the …

central cavity of Hb

2,3-BPG allows for ___ release in the tissues and adaptation to changes in altitude:

Hemoglobin binds to O2 quite tightly when ___ is entirely absent.

At high altitudes, O2 delivery _____ by about ¼ to 30% of max.

Increase in BPG concentration _____ affinity of hemoglobin for O2.

• O2

• BPG

• declines

• decreases

Sickle-Cell anemia is due to a mutation in ____.

Hemoglobin

What are enzymes?

Enzymes are catalysts that increase rates without being used up.

Most enzymes are ____ proteins and ____.

• globular

• soluble

Apoenzyme

protein part of the enzyme

Holoenzyme

complete function including coenzyme and metal ions

In light produced by fireflies:

_____ provides energy

____ is the enzyme

_____ is the cofactor

• ATP

• luciferase

• Mg+2

Six Classes of Enzymes:

Enzymes act by binding _____.

• The non covalent enzyme substrate complex is known as the _____ _____.

• substrates

• Michaelis complex

Do enzymes affect equilibrium?

_____ reactions face significant activation barriers (delta G++) that must be surmounted during rxn.

Enzymes ____ reaction rates (k) by decreasing deltaG++

• No

• Slow

• Increase

What are inhibitor?

compounds that decrease enzymes activity

Irreversible inhibitors ____ with the enzyme

• One inhibitor can permanently ____ ____ one enzyme molecule.

• They are often ____ _____ but may be used as drugs.

react

• shut off

• powerful toxins

Reversible inhibitors ____ to and can ____ from enzyme.

• they are often structural analogs of ____ or ____.

• They are often used as ____ to slow down a specific enzyme.

bind, dissociate

• substrates, products

• drugs

Reversible inhibitor can bind to:

• to the free enzyme and prevent binding of the substrate

• to the enzyme-substrate complex and prevent rxn.

Competitive Inhibition:

• Competes with ____ for binding.

  • Binds ___ site

  • Does/Doesn’t affect catalysis?

• No change in ____ ; apparent increase in ___.

• In Linweaver-Burk: lines intersect at the _-axis.

• substrate

  • active

  • doesn’t

  • Vmax; Km

  • y

Mixed Inhibition:

• Binds enzyme with/without/both substrate?

  • Inhibits what two things?

  • Binds to ___ site.

• Decrease in ____; apparent change in ____.

• In lineweaver-burk: lines intersect ____ from y-axis/

• ______ inhibitors are mixed inhibitors such that there is no change in Km.

• both

  • catalysis and substrate binding

  • regulatory

• Vmax; Km

• left

• Noncompetitive

Hexokinase undergoes ____ ____ on substrate binding.

induced fit

How does hexokinase under induced fit on substrate binding?

Starts in open U-shape and when entering catalytic active form, the ends pinch together after binding of D-glucose.

General Acid-Base Catalysis:

Charged intermediates are stabilized by transfer of ____ to or from the substrate or intermediate to form a species that breaks down more readily to products.

protons

Covalent Catalysis:

• A transient covalent bond between the ____ and the ____.

• Changes the rxn ____

• Requires a _____ on the enzyme.

  • a nucleophile is a chemical species that donates an ____ ____ to an electrophile to form a chemical bond in relation to a rxn.

  • Can be reactive ___, ___, ___, or ____.

• enzyme and the substrate

• pathway

• nucleophile

• electron pair

• Serine, thiolate, amine, or carboxylate