Biochem exam 2

A set of vocabulary flashcards covering protein folding energetics, structural types (fibrous vs. globular), and ligand-binding kinetics including hemoglobin and myoglobin states.

Chaotropes

Small molecules, such as Urea and guanidinium chloride, used to denature proteins by disrupting the hydrophobic core.

Native structure

The functional, lowest Gibbs energy state of a protein which is naturally favored during folding.

Structural nucleation

The first step in protein folding based on local structural preferences, which is similar to but not precisely secondary structure.

Molten globule state

A stage in protein folding where local structures undergo hydrophobic collapse.

Protein folding funnel

A model describing folding where the top represents high free energy/entropy (unfolded) and the bottom represents low free energy/entropy (native structure).

Stability

The energy difference between a fully folded complex shape and a denatured protein, driven by the hydrophobic effect.

Specificity

The determination of how a protein folds and what it looks like, which occurs due to H-bonds and other hydrophilic interactions.

$$T_m$$

Melting point; the temperature at which the transition between the folded structure and the unfolded/random coil structure occurs.

Cooperative folding

A phenomenon where disrupting part of a protein structure quickly destabilizes the rest, resulting in instable and transient folding intermediates.

Amphipathic $\alpha$-helix

A helix where hydrophobic residues are located at the $i$, $i+3$, and $i+4$ positions.

Desolvation cost

The energetic penalty of not forming H-bonds for polar groups in the protein interior, which is unfavorable and destabilizes the protein.

Fibrous proteins

Insoluble structural proteins consisting of repeated secondary structures packed into large cables or threads, such as those in bones and skin.

Keratin

A major protein in hair and fingernails composed of coiled-coil $\alpha$-helices based on simple hydrophobic packing and many disulfide bonds.

Silk

A fibrous protein made of Gly-Ala repeats in an extended antiparallel $\beta$-sheet structure that does not stretch easily and is impenetrable by water.

Collagen

A complex protein in connective tissue where three left-handed helices form a right-handed triple helix, containing modified amino acids like hydroxyproline.

Scurvy

A condition resulting in weak collagen fibers because the enzymes catalyzing the hydroxylation of proline and lysine require Vitamin C.

Fibroin

The $\beta$-sheet secondary structure found in fibrous proteins.

Apoprotein

A protein that has been stripped of its cofactor or metal ion.

Induced fit

A binding model where the binding site is similar to the ligand, and binding triggers structural changes in both for a better fit.

Geometric and electronic complementarity

The requirement for molecules to physically fit in shape (geo) and have favorable arrangement of charges and H-bonding groups (elec).

$$K_a$$

Association constant, defined as $\frac{[PL]}{[P][L]}$, where a larger value signifies a tighter bond.

$$K_d$$

Dissociation constant, defined as $\frac{[P][L]}{[PL]}$, where a smaller value signifies a tighter, more stable bond.

Half saturation point ($\theta$)

The point at which the ligand concentration $[L]$ is equal to the $K_d$, meaning half of the binding sites are occupied.

Myoglobin

A monomeric protein in muscle tissue with a $\alpha$-helical structure that binds $O_2$ very tightly ($P_{50}$ of $0.26\,KPa$).

T state

The tense state of hemoglobin that binds $O_2$ poorly, characterized by a high $P_{50}$ and an open center.

R state

The relaxed state of hemoglobin that binds $O_2$ readily, characterized by a low $P_{50}$ and trapped His residues in the middle.

What is allostery?

allosteric proteins show cooperativity between multiple binding sites on the same protein. A modulator (a protein that binds to a protein and regulates its activity) can increase OR decrease ligand Kd

What does homotropic ans heterotropic mean?

homo: modulator and ligand are the same

hetero: are different

When are T and R state favored?

When there are no/few oxygens bound, low affinity T state is favored (when there are more unbound than bound oxygen). When there is an increasing number of oxygen bound, high affinity R state is favored

What is the MWC symmetry model?

All oxygen are R or all are T

How does carbon monoxide interfere with O2 release?

CO binds in a similar manner to O2, reducing the number of avaiable O2 binding sites. It also induces transitions to the high affinity R state, and is nearly irreversible.

Explain the bohr effect:

• Low pH = more H+, less O2 bound

• More CO2 = more H+=less O2 bound

What is BPG>

2,3-biphosphateglycerate; it binds to a region of concentrated positive charge (basic) at the interface of ALL four subunits that is only present in the low affinity T state. Fetal hemoglobin is not regulated by BPG because it lacks the positive cell to bind to (since it has 2 gamma instead of two beta)

What is sickle cell anemia?

A muation in which surface Glu is mutated to Val in the beta subunit. This makes the mutated T state hemoglobin insoluble when deoxygenated.

What is the E6V mutation?

swapping Glu at position 6 for a Val - leads to a hydrophobic surface on the protein and leads to aggregation (insolubility)

What is a catalyst?

A substance, usually in small amounts relative to the reactants, that modifies (usually inc) the rate of a reaction without being consumed. must be reversible

What is an enzyme?

a protein catalyst that exhibits:

1. higher rxn rates

2. milder rxn conditions

3. greater rxn specifcity

What is a ribozyme?

RNA catalyst

Explain substrate specificity?

some enzymes are very specific for one substrate, but most enzymes catalyze rxns for a range of similar substrates. an example is alcohol dehydrogenase

Transition states are:

inherently unstable and high energy, but rxns have to go through them

If favorable gibbs, a reaction will occur, but:

only kinetics tells you how quickly

What is the rate determining step:

the slow step; typcially the formation of the transition state. The larger the value of G, the slower the reaction rate. In a multistep reaction, the step with the largest activation energy is the rate limiting step. Usually the step making/breaking something

How to enzymes work?

They lower the activation rate, which speeds up the rxn, which lowers the energy of the trnasition state. Enzymes reduce G, speeding up rxns.

What interactions are responsible for formation of the enzyme substrate complex:

multiple weak interactions:

• hydrogen bonds

• electrostatic interactions

• van der wallas

  • hydrophobic interactions

Although adding enzymes can inc the number of steps:

its still going to be way faster

What are the 5 classes of rate enhancement?

1. proximity, orientation, entropy reduction

2. preferential binding of the transition state (transition state stabilization)

3. acid-base catalysis

4. covalent catalysis

5. metal ion catalysis

Explain proximity, orientation, entropy reduction

properties that can be manipulated by the enzyme:

proximity: binds substrates by holding them close together to increase the local concentration. less than 5 fold inc

orientation: helps things line up right. typically 100 fold inc

entropy reduction: binding and holding them close together with proximity and orientation for a longer period of time. it reduces entropy which is technically unfavorable, so this is balanced out by the favorable binding interactions in the enzyme-substrate complex. Up to 10^7 inc

this speeds up the overall reaction rate

Enzymes ahve inc preferntial binding for the:

transition state, this inc the rate of the catalyzed rxn. Consequence of this is that the enzymes will often bind non-reactive molecules which are similar to the transition state much more tightly.