3 - Thermodynamics and molecular binding

Define Gibbs free energy

how much energy is free in a system

List the 3 things Gibbs free energy is a function of

• enthalpy (H)

• entropy (S)

• temperature (T)

Define enthalpy

the total heat content of a system in terms of bond breaking and making

Define entropy

measure of disorder in a system

State the Gibbs free energy equation

△G = △H - T△S

What explains a negative value of △G

the reaction is spontaneous and energetically favourale

What explains a positive value of △G

the reaction will not occur spontaneously and energetically unfavourale

What explains a negative value of △H

the reaction is exothermic and releases heat energy

What explains a positive value of △H

the reaction is endothermic and absorbs heat energy

What is temperature measured in?

Kelvin

What explains a negative value of △S

reactants will have a higher entropy than products

What explains a positive value of △S

reactants will have a lower entropy than products

Enthalpy in protein folding

since H bonds are stronger in hydrophobic environments there will be increased enthalpy in proteins

Is entropy in a proteins primary structure high or low?

high as single bonds are free to rotate around themselves with lots of possible conformations

Is entropy in a proteins later structures high or low?

low as chains are folded in on themselves

Levinthal’s paradox

in an 100 residue protein if each amino acid can only adopt 1 of 3 conformations

• the total number of possible structures would be 3¹⁰⁰

if we also imagine it takes 10^-13 seconds to sample each configuration

it would take 1.6×10²⁷ years to search all conformations

Lowest energy state (2 points)

• proteins gravitate energetically towards the lowest free energy conformations

• however since there are several naturally found low energy conformations, the ultimately favoured one is dependent on the environments they’re in

Define a ligand/enzyme in terms of thermodynamics

a molecule that forms a complex with a receptor biomolecule to serve a biological purpose

Define a substrate in terms of thermodynamics

a molecule that binds to an enzyme and is converted into product

Define affinity in terms of thermodynamics

a measure of strength of an interaction between molecules

Write the association constant equation

[AB] / [A] + [B] = K_A

where

[A] + [B] are concentration of reactants

[AB] is concentration of product(s)

What is association constant measured in?

M^-1

What does a high K_A value describe?

strong binding affinity between molecules

Write the disassociation constant equation

[A] + [B] / [AB] = K_D

where

[A] + [B] are concentration of reactants

[AB] is concentration of product(s)

What is disassociation constant measured in?

M

What does a low K_D value describe?

strong binding affinity between molecules

How can K_D be found on a graph?

read ligand concentration at which half of the receptor sites are occupied

Define cooperativity (2 points)

• can occur when two or more molecules bind to the same receptor molecule

• binding a molecule changes the affinity for the subsequent binding events

Define allostery

occurs when a molecue binding to a receptor molecule changes its affinity for a separate molecule

Describe the haem cofactor

tetrapyrole ring molecule in association with an Fe²⁺ ion

What happens when oxygen binds to haem in haemoglobin?

Fe²⁺ moves into plane of tetrapyrole ring

Describe cooperative binding in haemoglobin (2 points)

• binding of O₂ to a haem cofactor in one subunit increases the affinity of O₂ to others

• binding of the last O₂ is 200x more effecient than binding of the first

How does haemoglobin change upon binding?

α₁β₁ dimers rotate relative to α₂β₂ by 15^o

What is the deoxygenated form of haemoglobin known as?

T state (tense state)

What is the oxygenated form of haemoglobin known as?

R state (relaxed state)

State the two haemoglobin cooperativity models

• concerted model

• sequential model

Describe the concerted model of cooperativity

proposes that all subunits of hemoglobin switch between the T and R states simultaneously, affecting the entire molecule's affinity for oxygen

Describe the sequential model of cooperativity

suggests that binding of oxygen to one subunit increases the likelihood of neighboring subunits transitioning from the T state to the R state, leading to a gradual change in affinity.

Describe allosteric control of oxygen binding to haemoglobin

2,3 Bisphosphoglycerate stabilises T state, making it harder to transition into R state

What reactions do oxidoreductase enzymes catalyse?

redox reactions

Give an example of an oxidoreductase enzyme

lactate dehydrogenase

What reactions do ligase enzymes catalyse?

formation of covalent bonds

Give an example of a ligase enzyme

DNA ligase

What reactions do transferase enzymes catalyse?

the transfer of functional groups between molecules.

Give an example of a transferase enzyme

kinases

What reactions do hydrolase enzymes catalyse?

hydrolysis

Give an example of a hydrolase enzyme

sucrase

What reactions do isomerase enzymes catalyse?

rearrangements of molecular structures

Give an example of an isomerase enzyme

alanine racemase

What reactions do lyase enzymes catalyse?

removes groups of atoms from molecules

Give an example of a lyase enzyme

oxalate decarboxylase