Biochem Test 2

what is the system in thermodynamics?

the portion of the universe that is being studied

what are the surroundings in thermodynamics

everything in the universe outside the system

what can an isolated system exchange?

neither matter nor energy

what can a closed system exchange?

energy, but not matter

what can an open system exchange?

both energy and matter

what is the 1st law of thermodynamics?

energy is conserved; it cannot be created or destroyed

what is the equation for change in internal energy?

ΔE = Efinal − Einitial.

what does positive q mean?

heat enters the system from the surroundings

what does negative q mean?

heat leaves the system for the surroundings

what does positive w mean

the system does work on the surroundings and loses energy (positive is overall negative bc of subtraction)

what does negative w mean

the surroundings do work on the system (negative is overall positive bc of subtraction in equation)

what is the equation for the first law of thermodynamics

ΔE = q − w.

what is a state function?

a property depending only on initial and final states, not the path

name major state functions

E,V,T,H,S,G,Keq and electrical potential

which quantities are non-state functions

heat q, work w, velocity v

what are non-state functions dependent on?

the path the reaction takes

how is enthalpy defined?

H = E + PV

what does entropy measure conceptually?

the degree of disorder or randomness of a system

what is the second law of thermodynamics?

a spontaneous process increases the entropy of the universe

what is the Gibbs free-energy equation?

ΔG = ΔH − TΔS.

What does ΔG < 0 mean?

The process is spontaneous and exergonic.

What does ΔG > 0 mean?

The process is nonspontaneous and endergonic.

What does ΔG = 0 mean?

The system is at equilibrium.

What does the magnitude of ΔG indicate?

How far the system is from equilibrium.

Does ΔG tell you reaction speed?

No. Reaction speed is a kinetic property.

How are standard free energy and Keq related?

ΔG°′ = −RT ln Keq

What does a large Keq generally favor?

Products at equilibrium.

Is Keq path dependent?

No. Keq is a state function

What pH defines the biochemical standard state?

7

What concentration defines standard solutes?

1M for reactants and products

What pressure is used in the biochemical standard state?

1 atm

What standard temperature is usually used?

298 K unless otherwise specified

what is the nonstandard free energy equation

ΔG = ΔG°′ + RT ln Q.

what two types of biological catalysts are noted

Protein enzymes and RNA ribozymes

What is an enzyme substrate?

The specific molecule an enzyme binds and transforms

What is the active site?

The specific site where an enzyme binds to its substrate

What is enzyme catalytic power?

Catalyzed rate divided by the uncatalyzed rate

What is enzyme specificity?

selective catalysis of a reaction on a particular substrate or substrate class

how can enzyme activity be regulated?

by enzyme amount, reversible inhibitors, and activators

what is a cofactor?

a nonprotein component required by some enzymes

give examples of metal-ion cofactors

Fe 2+, Mg 2+, Zn 2+

What is a coenzyme?

an organic or organometallic cofactor involved in catalysis

What is a prosthetic group?

a tightly or covalently bound coenzyme

what is a holoenzyme?

the catalytically active enzyme with its cofactor

what is an apoenzyme

the protein portion of an enzyme without its required cofactor

what is the nutritional source of many coenzymes?

vitamins from the diet

what are the six major enzyme classes

Oxidoreductase, transferases, hydrolases, lyases, isomerases, ligases

in the systemic naming system what is the number related to each enzyme

1.oxidoreductases

2.transferases

3.hydrolases

4.lysases

5.isomerases

6.ligases

do catalysts change ΔG or equilibrium?

no. they change the pathway and reaction rate

what is the transition state

the high-energy state at the top of the reaction-energy barrier

what is activation energy, ΔG‡?

energy difference between the ground state and transition state

how does activation energy affect reaction rate?

higher ΔG‡ means a slower reaction.

What does chemical kinetics study?

the rate and mechanisms of chemical reactions

what is reaction rate?

change in reactant or product concentration per unit time

what are typical units for reaction rate?

concentration/time, such as M/s or mM/min

what is the general form of a rate law?

Rate = k[A]^a[B]^b[C]^c.

How is overall reaction order determined?

add the exponents in the rate equation

what is the equation to determine rate constant k units?

[Concentration]^-(n-1)[time]^-1

what does molecularity describe?

the number of molecules involved in one elementary reaction

what is a unimolecular elementary step?

an elementary reaction involving one reactant molecule

what is a bimolecular elementary step

an elementary reaction involving two reactant molecules

why are reactions above termolecular extremely rare?

bringing four or more independent particles together is entropically unfavorable

what is the zero-order rate law?

v=k; rate is independent of reactant concentration

when can enzyme reactions become zero order?

when all enzyme active sites are saturated with substrate with substrate

What is the Michaelis-Menten equation?

v = Vmax[S]/(Km + [S])

What does Vmax represent?

maximum reaction rate when enzyme is fully saturated with substrate

How does Vmax depend on enzyme concentration?

Vmax increases linearly with total enzyme concentration

At what [S] is v = ½Vmax?

When [S] = Km.

What does a smaller Km indicate in these notes?

Higher substrate affinity and tighter binding.

What does a larger Km indicate?

Lower substrate affinity and weaker binding

What is Ks?

The true substate dissociation constant, k2,k1.

For E+S ⇌ ES → E+P, what is Km?

Km = (k2 + k3)/k1.

When does Km approximately equal Ks?

When k3 ≪ k2.

What is kcat?

turnover number: Vmax divided by total enzyme concentration

What are the units of kcat?

Time⁻¹, such as s⁻¹

in the simplest mechanism, what does kcat equal?

k3, the product-forming step

what does a larger kcat mean?

the enzyme turns over substrate faster

what does kcat/Km measure?

catalytic efficiency at low substrate concentration

what are the units of kcat/Km?

M⁻¹s⁻¹

what is the approximate diffusion limit kcat/Km?

About 10⁹ M⁻¹s⁻¹

Why is O2 transport needed in tissues thicker than approx. 1 mm?

Passive O2 diffusion becomes too slow to support metabolism

What is O2 solubility in aqueous solution?

Less than about 10⁻⁴ M

About how much hemoglobin is present in blood?

about 150 g/L

How much O2 can blood carry using hemoglobin?

about 0.01 M O2

How does myoglobin increase O2 delivery in muscle?

It raises effective O2 solubility and facilitates diffusion

What analogy do the notes use for myoglobin?

a molecular bucket brigade for oxygen diffusion

what is a heme porphyrin built from?

from pyrrole rings linked by methylene bridges

why is pyrrole nitrogen not strongly basic?

its lone pair is required for aromaticity

what geometry does heme iron prefer with six ligands?

octahedral coordination

what happens to free heme after binding O2?

O2 readily oxidized free Fe 2+ heme to Fe3+

What is the sixth ligand of ferric heme?

a tightly coordinated water molecule

Does iron change oxidation state when normal O2 binds?

No. It remains Fe2+ during oxygenation

What is oxygenated myoglobin called?

Oxymyoglobin

What occupies deoxymyoglobin’s sixth coordination site?

nothing; the site is vacant

at roughly what angle does O2 bind to myoglobin heme?

about 60 degrees relatively to the heme plane

Where is distal His-E7 relative to bound O2?

On the O2 side of heme, too far away to bind iron

What does His-E7 physically do to the ligand pocket?

creates steric hindrance that affects ligand geometry