BMCB 658A EXAM 2

Which of the following is most directly related to the speed of a reaction?

Which of the following is most directly related to the speed of a reaction?

The ΔG0‡ of the reaction

Why can the breakdown of A T P power cellular processes?

As an exergonic reaction, it releases energy to spare.

∆G < 0

Spontaneous exergonic

∆G > 0

Nonspontaneous endergonic

_____ is a measure of a system’s instability, its tendency to change to a more stable state.

Free energy

During a spontaneous change free energy ….. and the stability of a system ….

decreases, increases

∆G = 0

Equilibrium

What conditions are necessary for the free energy change to predict the spontaneity of a reaction?

Free energy change can be used to predict spontaneity of reaction under the conditions of constant TEMPERATURE and PRESSURE

Gibbs free energy equation

∆G = ∆H - T∆S

If the ∆G is negative than the ….

reaction is spontaneous

Standard states

Standard set of conditions used for comparisons of chemical reactions

If [H+] = 1 M then

pH=0

Standard state for [H+] is

[H+] = 10-7 M and pH = 7.0

Modified standard state for free-energy change is

∆G°ʹ

Spontaneous reaction occurs without

added energy

How to make endergonic reactions proceed?

Couple endergonic reaction to an exergonic reaction

Enzymes do not affect the change \n in free energy (ΔG); they only …..

speed up reactions that would eventually occur without them

Standard free energy change (ΔG°)

Difference between energies of reactants and products \n under standard conditions

Reaction rate depends on its …

activation energy (ΔG°‡),which is the energy input required to initiate a reaction

Lock-and-key model

Substrate binds to that portion of the enzyme with a \n complementary shape

Induced fit model

Binding of the substrate induces a change in the conformation of the enzyme that results in a complementary fit

Proximity and orientation of the substrate …..

speed up the reaction

Once enzyme and substrate bind (ES) and attain the transition state \n complex (EX‡) …..

catalysis can occur

The active site can lower activation energy and speed up reactions by

• Orienting substrates correctly

• Straining substrate bonds

• Providing a favorable microenvironment

• Non-covalent bonding to the substrate

The rate of catalysis can usually be sped up by

Increasing the substrate concentration

Enzyme is saturated when …..

all enzyme molecules in a solution are bonded with substrate

Competitive Inhibition

\n Decrease in enzymatic activity caused by binding of \n a substrate analogue to the active (catalytic) site \n

Inhibitor competes with the substrate for the active \n site on the enzyme

Noncompetitive Inhibition

Form of enzyme inactivation in which a substance binds \n to a site other than the active site but distorts the \n active site to inhibit reaction

Involves two distinct binding sites, one for the substrate \n and one for the inhibitor

Increasing substrate concentration cannot ….

overcome noncompetitive inhibition

Uncompetitive Inhibition

Inhibitor can bind to the ES complex but not to the free E

Allosteric enzyme

Oligomer whose biological activity is affected by other substances binding to it

Allosteric effector

Substance that modifies the behavior of an allosteric enzyme by binding to it

Binding of O2 to hemoglobin exhibits

positive cooperativity

Instead of relying on heat, organisms carry out _____ to selectively speed up reactions

catalysis

Enzymes are biological catalysts that are usually

globular proteins

Enzyme and substrate must bind to form the

ES complex

E + S -→ ES

First order

Description of a reaction whose rate depends on the first power of the concentration of a single reactant

Second order

Description of a reaction whose rate depends on the product of the concentrations of TWO reactants

Zero Order

rate of reaction does NOT depend on concentration of substrate, it instead relies on the presence of catalysts

Steady state

Condition in which the [ES] remains constant in spite of continuous turnover

KM – Michaelis constant

describes the affinity of enzyme for substrate

Vmax

maximum velocity of reaction

When [S] << KM

• First-order kinetics \n • Double [S], Vinit doubles

When [S] = KM

Vinit = Vmax/2

When [S] >> KM

Vinit= Vmax \n • enzyme is saturated with substrate \n • Zero-order kinetics

Inhibitors

substances that decrease the rate of an enzyme-catalyzed reaction

Reversible Inhibitors

Substances that bind to an enzyme and subsequently are released

Irreversible inhibitors

Substances that react with enzymes to produce proteins that are not enzymatically active and from which original enzymes cannot be regenerated

Competitive Inhibition

Decrease in enzymatic activity caused by binding of a substrate analogue to the active (catalytic) site DOESNT AFFECT CATALYSIS

In the presence of a competitive inhibitor:

• Vmax is unchanged

• apparent increase in KM

Because substrate and inhibitor are competing for the same location, a sufficiently high amount of substrate will outcompete inhibitor

Noncompetitive Inhibitor

Form of enzyme inactivation in which a substance binds to a site other than the active site but distorts the active site to inhibit a reaction

Involves two distinct binding sites: one for the substrate and one for the inhibitor

Increasing substrate concentration cannot

overcome noncompetitive inhibition causing the Vmax to decrease and the value of kM to stay unchanged

A biologist working in a lab adds a compound to a solution that contains an enzyme and its substrate. This compound binds to the enzyme and decreases the rate at which the enzyme converts substrate to product. However, this decrease can be overcome by increasing the concentration of substrate in the reaction mix. Therefore, which of the statements is true of the compound?

The compound is a competitive inhibitor

Under steady state conditions the ES …..

remains constant

____ can be used to compare the relative affinity of an enzyme for a substrate if the Vmax values for the enzymes are similar.

KM

Regulation of Enzyme Activity can

Alter enzyme concentration \n

-rate of synthesis \n -rate of degradation \n

Alter enzyme activity \n

-allostery (activation, inhibition) \n -phosphorylation \n -post-translational processing \n -sequestration

____ describes allosteric behavior

sigmoidal curve

Types of Inhibition

K systems

V systems

K 0.5

K systems

Enzyme for which the substrate concentration that yields \n one-half Vmax is altered by the presence of inhibitors or activators

V systems

Enzyme in which the presence of inhibitor/activator \n changes the maximal velocity of the enzyme but not the substrate level that yields one-half Vmax

K0.5

Substrate level at one-half Vmax in a K system

Homotropic effects

Allosteric effects that occur when several IDENTICAL molecules are bound to a protein

Heterotropic effects

Allosteric effects that occur when DIFFERENT substances are bound to a protein

Binding of O2 to hemoglobin exhibits

positive cooperativity

Concerted Model

Description of allosteric activity in which the conformations of all subunits change simultaneously

Zymogen

Inactive protein that can be activated by specific hydrolysis of peptide bonds

Negative Cooperativity

Cooperative effect whereby binding of the first ligand \n to an enzyme or protein causes the affinity for the next ligand to be lower

Transition-state analog

Synthesized compounds that mimic the form \n of the transition state of an enzyme reaction

Abzymes

Antibodies that are produced against a transition-state analog and that have catalytic activity similar to that of a naturally occurring enzyme

Coenzymes

Nonprotein substances that take part in enzymatic reactions and are regenerated at the end of the reaction

Amphipathic

Molecule that has one end with a polar or charged, water-soluble group and another end with a nonpolar hydrocarbon group that is insoluble in water

Fatty Acids

Unbranched chain carboxylic acids

• Amphipathic compounds

• 12–20 carbons long

• Unsaturated fatty acids - Contain \n carbon–carbon double bonds

• Saturated fatty acids - Contain only \n single bonds

Triacylglycerols

Lipids formed by the esterification of \n three fatty acids to glycerol

Ester groups form the polar part of the molecule, and the tails are nonpolar

Phosphatidic Acid

Compound in which two fatty acids and phosphoric acid are esterified to the three hydroxyl groups of glycerol

Phosphoacylglycerols

•Polar head group is charged \n

•Phosphate group is ionized at \n neutral pH \n

•Positively charged amino group is \n contributed by an amino alcohol \n esterified to the phosphoric acid

Waxes

•Complex mixtures of esters of long-chain carboxylic acids and long- \n chain alcohols \n

•Serve as protective coatings for plants and animals

Sphingolipids

•Contain sphingosine, a long- \n chain amino alcohol \n

•Found in plants and animals and \n are abundant in the nervous \n system

Glycolipids

•Lipid to which a sugar moiety is bonded

Steroids

•Lipids with a characteristic fused-ring structure •Three six-membered rings (the A, B, and C rings) \n •One five-membered ring (the D ring)

Four fused rings in total

What are important steroids?

Cholesterol is an important steroid, it acts as a precursor for other steroids

Interaction between lipid bilayers and membrane proteins determines….

membrane function

Lipid Bilayer

Aggregate of a lipid molecule in which the polar head groups are in contact with water and the hydrophobic parts are not that is held together by noncovalent interactions (van der waals and hydrophobic interactions)

When considering the Lipid Bilayer and cholesterol it is important to remember …….?

That the hydrocarbon interior of saturated and unsaturated fatty acid chains and the fused-ring system of cholesterol

Which of the following lipids is not \n found in biological membranes?

triacylglycerols

What is important regarding the OUTER layer of the lipid bilayer?

Sphingolipids, gangliosides, cerebrosides have larger hydrophilic groups and are more likely to be found on the outer layer of a curved bilayer

What is important regarding the INNER layer of the lipid bilayer?

phosphoacylglycerols with smaller hydrophilic groups are more common on the inner layer.

The most abundant open-chain lipids found in typical membranes are

phosphoacylglycerols such as phosphatidylethanolamine and phosphatidylcholine

Membrane fluidity can differ due to the composition of the bilayer for instance …..

Saturated fatty acids have a LINEAR arrangement of hydrocarbon chains leading rigidity

Unsaturated fatty acids have a KINKY arrangement that causes disorder in its packing and leads to greater fluidity

With membrane fluidity and cholesterol …….

The presence of cholesterol can enhance order and rigidity due to the fused ring structure of cholesterol

Receptor proteins in the membrane ….

detect extracellular signals and trigger intracellular signaling pathway

Peripheral proteins are …

Loosely bound to the outside of a membrane