Lecture 4 - Protein Folding, Chemical Energy, Enzymes

BIOLOGY 173, Exam 1, Lecture 4

Chemical Energy Source

• Comes from breaking and making covalent bonds

• Energy comes from: movement of electrons from higher energy states to lower energy states

• Electrons = source of chemical energy

• Changing bonds from NON-POLAR TO POLAR COVALENT releases energy

  • Non-polar covalent generally = more potential energy than polar covalent

Chemical Reactions

• Allow proteins/molecules to do work

• Reactants converted to products

  • Forward reactions: Reactants = more energy than products

Kinetic and Potential Energy

• Potential Energy (Free Energy): capacity of molecule/object to do work

• Kinetic Energy: energy molecule/object has while moving

Potential (Free) Energy

• Can be use to do work

• Molecules tend to move from high free energy to lower free energy

  • More order to less order

• Higher vs. Lower Potential (Free) Energy

  • Higher Potential (Free) Energy

    • Less stable

    • More concentrated

    • More ordered (less entropy)

    • Greater work capacity

  • Lower Potential (Free) Energy

    • More stable

    • Less concentrated

    • Less ordered (more entropy)

    • Less work capacity

• Amount of potential (free) energy molecules in chemical reaction dictates important properties of reaction

“Gibbs” Free Energy

• Amount of free energy molecule has

Gibbs Free Energy Change

• ∆G

• ∆G = G_(Products) - G_(Reactants)

  • Spontaneous reaction = -∆G

  • Reactants = higher Gibbs Free Energy than products when -∆G

Spontaneous Reactions

• Energy-releasing reactions

  • Exergonic (work)

  • Exothermic (heat)

• ∆G < 0

• Do not occur immediately or without kickstart

• Requires activation energy

Non-Spontaneous Reaction

• Energy-consuming reaction

  • Endergonic (work)

  • Endothermic (heat)

Chemical Reaction Types (Based on Changes in Free Energy)

• Spontaneous

  • Energy-releasing reactions

    • Exergonic (work)

    • Exothermic (heat)

• Non-spontaneous

  • Energy-consuming reaction

    • Endergonic (work)

    • Endothermic (heat)

Exergonic Reactions

• Reactants have more potential (free) energy than products

Activation Energy (E_A)

• Energy required for reactants to reach transition state

  • transition state = unstable intermediate

• Can be overcome by hear or catalyst

Enzymes Definition

• PROTEIN CATALYST

• Overcome activation energy

Enzyme Effect on Reaction

• DOES NOT change amount of energy released

• DOES NOT change equilibrium constant (K_^eq)

• DOES lower the activation energy E_A

• DOES increase rate of reaction

• IS NOT changed by reaction itself

Properties of Enzyme

• Proteins

• Substrate-Specific

• Bring substrates together so can react

  • ACTIVE SITE: region binding substrate

• Involves interactions between enzyme’s R-groups and substrate

• Binding destabilizes bond(s) in substrate

Enzyme Process Explanation

• Initiation

  • Reactants bind to active site

  • Specific orientation

  • Forms enzyme-substrate complex

• Transition State Facilitation

  • Interactions b/w enzyme and substrate lower E_A required

• Termination

  • Produce = lower affinity for active site and released

  • Enzyme unchanged after reaction

Enzyme Function and Role

• Active site binds substrates (reactants)

  • Substrate specificity

• Binding destabilizes chemical bonds in substrate

  • Lowers activation energy

  • Reaction proceeds faster

• Changes reactants into products via catalysis (speeding chem rxn with catalyst)

Active Site

• Where substrate(s) bind and catalysis (speeding chem rxn with catalyst) occurs

• Induced Fit: Binding b/w enzyme and substrate causing shape change in enzyme protein

Enzyme Efficiency

Dependent on:

• Active site matching shape and chemistry of substrate

  • How good it enzyme binds to substrate

• Enzyme efficacy in driving catalysis for substrate

• *Can only catalyze reactions where ∆G < 0

How Enzyme Binds to Substrate

ACTIVE SITE

• Substrates can physically fit in active site

• Substrate can make chemical interactions w/ R-groups present in active site

Folding Enzymes

• Amino acids in active site usually far apart when linearly sequenced in unfolded enzyme

• Protein folding brings specific amino acids closer to each other and create active site

• DENATURING protein enzyme: active site doesn’t form and enzyme NOT FUNCTIONAL

Reaction Coupling

• Involves 2 reactions

• One releases energy (exergonic) and drives energy consuming (endergonic) reaction

• Overall ∆G < 0 (spontaneous)

Hydrolysis

• Chemical reaction where water is used to break down chemical bonds in a compound

Hydrolysis of Phosphate Groups Off Nucletoides

• Releases energy

• ATP (nucleotide) commonly used by enzymes as source of potential/free energy

  • ATP = high free energy molecule

  • Much PE comes from 3 negatively charged and crowded phosphate groups

  • ATP = 3 phosphate groups, ribose, adenine

Enzymes and Reaction Coupling

• Enzymes can mediate reaction coupling

• Exergonic and endergonic reaction coupled

  • Example: ATP + H2O + (Substrate A&B)→ ADP + P(Substrate A&B)

    • ATP loses 1 P (exergonic)

    • Substrate gains P

Energy Moving Through Biological Systems

• More chemical energy: Less disorder/entropy in bonds

  • Energy concentrated in bonds

• Less chemical energy: More disorder/entropy in bonds

  • Stored energy converted to dispersed heat

Anabolic vs. Catabolic

• Anabolic: Building molecules

• Catabolic: Breaking molecules down