BIBC 102 - Quiz 1

R

Arg Arginine positively charged r groups

N

Asn Asparagine polar uncharged r groups

D

Asp Aspartate negatively charged r groups

C

Cys Cysteine polar uncharged r groups

Negatively Charged R Groups

DE aspartate, glutamate

DE

Domain Expansion Aspartate, Glutamate negatively charged r groups

General theory of enzyme

ES is a theoretical value (enzyme + substrate) Assume at Vmax [ES] = [Et]

ΔG

Gibb's Free Energy

Q

Gin Glutamine polar uncharged r groups

E

Glu Glutamate negatively charged r groups

G

Gly Glycine nonpolar aliphatic r group

H

His Histidine positively charged r groups

I

Ile Isoleucine nonpolar aliphatic group

Michaelis-Menten Graph

Initial velocity vs substrate conc Vmax 1/2Vmax and Km this curve suggested that there are two entities binding each other

Positively Charged R Groups

KRH Lysine, Arginine, Histidine

KRH

Kugisaki Rams Hammer Lysine, Arginine, Histidine positively charged r groups

L

Leu Leucine nonpolar aliphatic r group

K

Lys Lysine positively charged r groups

Nonpolar Aliphatic R Groups

MIAPLVG methionine, isoleucine, alanine, proline, leucine, valine, glycine

MIAPLVG

Megumi, Itadori, And Panda Likely Value Gojo Nonpolar Aliphatic R Groups methionine, isoleucine, alanine, proline, leucine, valine, glycine

M

Met Methionine nonpolar aliphatic r group

Polar Uncharged R Groups

NQTCS Asparagine, Glutamine, Threonine, Cysteine, Serine

NQTCS

Nanami Questions The Conservative Sorcerers Asparagine, Glutamine, Threonine, Cysteine, Serine polar uncharged R groups

Do enzymes affect transition state differently?

No, enzymes affect transition state in the same way for forward and reverse reactions.

Do enzymes affect thermodynamic favorability or the equilibrium?

No, they do not affect thermodynamic favorability or the eq. They do not change Keq or ΔG.

F

Phe Phenylalanine aromatic r groups

P

Pro Proline nonpolar aliphatic r group

Steady State Assumption

Rate of ES formation is equal to rate of ES breakdown

S

Ser Serine polar uncharged r groups

What dos it mean when Km is small?

Smaller the Km is, the smaller the substrate concentration you need to get to 1/2 Vmax. Small Km means efficient enzyme

Tertiary Protein Structure

Structure based on weak interactions between far-away R groups and describes 3D folding of entire polypeptide - hydrophobic interactions - disulfide bonds - ionic bonds

T

Thr Threonine polar uncharged r groups

W

Trp Tryptophan aromatic r groups

Y

Tyr Tyrosine aromatic r groups

V

Val Valine nonpolar aliphatic r group

Quaternary Protein Structure

Weak interactions between polypeptide chains when protein has 2 or more polypeptide subunits - not always present

What happens at 1/2 Vmax?

When V0=1/2Vmax Km=[s] Km is equal to the substrate concentration at which the initial velocity is one-half the maximum velocity

Aromatic R Groups

YWF tyrosine, tryptophan, phenylalanine

YWF

Yuta Wins Fushiguro Tyrosine, Tryptophan, Phenylalanine aromatic r groups

Free Energy

amount of energy capable of doing work during reaction (ΔG)

Primary Protein Structure

covalent bonds linking amino acid residues in polypeptide chain

entropy

degree of randomness in a system (ΔS)

enthalpy

energy stored in chemical bonds (ΔH)

ΔH

enthalpy

ΔS

entropy

Secondary Protein Structure

local structural factors that are driven by hydrogen bonding - 𝜶-helixes - β-pleated sheet

Endergonic Reactions

reacting systems that take up heat from their surroundings when ΔG > 0 (change in free energy is positive) and ΔH>0 and Keq<1 thermodynamically unfavorable

Equilibrium Constante (Keq)

relates specific concentrations of all reactants and products and equilibrium at a given temperature and pressure. Keq=K1/K-1 Keq large=favors products, Keq small=favors reacntants

What do enzymes do?

they lower the activation energy ΔG‡, increasing the reaction rate and rate constant

Exergonic Reactions

when chemical reaction releases heat when ΔG < 0 (change in free energy is negative) and ΔH < 0 and Keq > 1 thermodynamically favorable

Michaelis-Menten Equation

x-value is [s]

Free energy that links ΔG and ΔGº'

ΔG = ΔGº' + RTln(K) K=[p]/[s] K can also equal Q

Calculate Free Energy

ΔG = ΔH - TΔS

when Keq >>1

ΔGº' <<0 large and negative free energy change thermodynamically favorable

Free energy at standardized biological conditions

ΔGº' = -RTln(Keq) T=310K 1mM Mg2+ ions pH=7

when Keq << 1

ΔGº' >> 0 large and positive free energy change thermodynamically unfavorable

Mass Action Ratio

"Q" describes the effects of the concentration on the reaction ΔG = ΔGº' + RTln(Q) Q = [p]/[s] decrease products and increase substrates cells change the mass action ratio to promote reactions that would be unfavorable at equilibrium

Competitive Inhibition

-Reversible Inhibition -1 substrate -Km is increased (inhibitor is stealing enzyme away) -Vmax is not affected (add enough substrate, can overcome inhibitor) *alpha is proportional to [I]

Non-competitive Inhibition

-Reversible Inhibition -2 or more substrates -inhibitor is competitive for one of these substrates -Uncompetitive or mixed (depends on whether the binding of two substrates are ordered) -all non-competitive inhibitors affect both Km and Vmax

Mixed Inhibition

-Reversible Inhibition -> Uncompetitive Inhibition -can bind to E or ES -inhibitor will bind to the free and substrate-bound enzyme with different rate constants -affect Km (inhibitor is stealing enzyme away) -affect Vmax (add as much S1 but won't overcome inhibitor)

Uncompetitive Inhibition

-Reversible Inhibition -> Uncompetitive Inhibition -only bind to ES (enzyme + substrate 1) -Km is decreased (product formation step is blocked) -Vmax also affected (add as much S1 but won't overcome inhibitor) -same slopes bc Km and Vmax are changing by the same amount

Irreversible Inhibitors

-Undergoes chemical reaction with the enzyme (that may form a covalent bond) - destroys the enzyme -> preventing enzyme activity

How do cells push thermodynamically unfavorable reactions forward?

-adjusting local product and substrate concentrations (mass action ratio) -linking multiple reactions together (linking)

Reversible Inhibition

-reversible interactions between inhibitor -weak binding to enzyme, doesn't form covalent bonds (H-bonds) -driven by inhibitor concentration -Competitive or Non-competitive (Mixed or Uncompetitive)

Lineweaver-Burk Plot

1/v = (Km/Vmax)(1/[S]) + 1/Vmax inverse of michaelis-menten equation X-intercept = -1/Km

Michaelis-Menten Kinetics

A kinetic pattern in which the initial rate of an enzyme-catalyzed reaction exhibits a hyperbolic dependence on substrate concentration.

A

Ala Alanine nonpolar aliphatic r group