Lecture 4: Energetics and Enzymatics

Bio 219:Dr. Adam Ross

Energy

• Most (essentially all) energy on the planet comes from the sun

• Plants harness this energy with chlorophyll

• Animals get energy from plants or other animals• Some animals also use photosynthesis (algae, some nematodes)

First Law of Thermodynamics

• Energy can never be created or destroyed, only transfered

Second Law of Thermodynamics

• Isolated systems will tend toward disorder• Earth is not an isolated system

• Organisms are not isolated systems

• Isolated systems are unable to exchange energy or matter with surrounding systems/ environments

• Energy can be used to fight entropy (disorder)

Gibbs free energy

• In biological systems energy and entropy change together

• Desribed by Gibbs free energy (G) equation:

• If ΔG is negative, reaction can occur spontaneously

• If ΔG is positive, the reaction is non spontaneous

𝑮 = 𝑯 − 𝑻𝑺𝐻 = 𝑒𝑛𝑡ℎ𝑎𝑙𝑝𝑦 𝑗𝑜𝑢𝑙𝑒𝑠

𝑇 = 𝑇𝑒𝑚𝑝𝑒𝑟𝑎𝑡𝑢𝑟𝑒 𝑘𝑒𝑙𝑣𝑖𝑛

𝑆 = 𝑒𝑛𝑡𝑟𝑜𝑝𝑦 ( 𝑗𝑜𝑢𝑙𝑒𝑘𝑒𝑙𝑣𝑖𝑛)

Implications of Gibbs

• Favorable (negative ΔG) reactions can be used to give energy to unfavorable reactions (positive ΔG )

• Allows for coupling of reactions inside the cell.

• Decreases energy wasting in cellular processes.

• Just because a reaction is energetically favorable, does not mean it will happen rapidly, sometimes activation energy is very high• Enzymes can lower activation energy

Metabolism

• Sum of all the chemical reactions that take place in the body• Some consume energy (endergonic)

• Some produce energy (exergonic)

• Some break things down (catabolic)

• Some build things up (anabolic)

Major classes of metabolic reactions

• Dehyrdation/ Hydrolysis• Dehydration synthesis/ Hydrolytic cleavage

• Phosphorylation/ de-phosphorylation• Kinase/ phosphatase

• Oxidation/ Reduction (Redox)• Addition (reduction) or subtraction (oxidation) of electrons

• Oxidation Is Loss Reduction Is Gain (OIL RIG)

Hydrolysis

• Water added to break bonds between monomers

• Catabolic reaction

• A–B + H2O → A–OH + H–B• Sucrose + H2O = glucose + fructose

Dehydration (condensation)

• Removal of water to join monomers

• Anabolic reaction

• A–OH + H–B → A–B + H2O • Peptide bond formation, sugars

• AA1 + AA2 → AA1—AA2 + H2O

Phosphorylation and Dephosphorylation

• Phosphorylation = addition of phosphate group

• Dephosphorylation = removal of phosphate group

• C + Pi → C–P + H2O

• ATP synthesis; • ADP + Pi + energy → ATP + H2O

Redox• Oxidation

• Major energy source of cells: Oxidation of sugars, fatty acids and amino acids

• Redox reactions are coupled• For every oxidation there is a reduction

• Redox rxns usually involve transfer of H atoms not H+ ions

• coenzymes act as temporary carriers of H atoms and their electrons

NAD+ + 2 H → NADH + H+ FAD + 2 H → FADH2

oxidized reduced oxidized reduced

• - oxygen is the ultimate electron acceptor in cellular respiration: ½ O2 + 2 H → H2O

Energy Metabolism

• Cells use chemical energy to drive biological processes:• Movement, synthesis, transport

• Energy is released in exergonic reactions• Convert high energy to low energy molecules

• Oxidation of glucose C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + energy

(high energy) (lower energy)

Enzymes

• Biochemical catalysts• Speed up reactions by lowering activation energy

• Most are proteins

• Name of enzyme denotes function (usually end in –ase)• Phosphatase removes phosphate

• Kinase adds phosphate

• Helicase unwinds DNA

Basic enzymatic reaction

Properties of enzymes

• Substrate specificity:• Enzymes only bind specific substrates

• Specific fit: enzyme active site fit together in native state

• Induced fit: enzyme pulls on chemical bonds of substrate to change shape

Properties of enzymes

• Enzymes are conserved after the reaction• The enzymatic protein is not used during the reaction, and is not altered in

such a way that it cannot perform the reaction again and again.

Properties of enzymes

• Sensitive to temperature, pH, and salt concentration• These things affect the tertiary structure of proteins

• Cause change in shape of enzyme and substrate which decreases substrate binding to active site

Saturation kinetics

• Reaction rate is non-linear• Depends on substrate [S] concentration

• Low [S]- low reaction rate, will increase with additional [S]

• High [S]- high reaction rate, reaction will not increase as much with additional [S]

• Saturated [S]- highest reaction rate, additional [S] will not increase reaction rate, all active sites are occupied by substrate.

Michaelis-Menten kinetics

• Named after German biochemist Leonor Michaelis and Canadian physician Maud Menten

• Relates reaction rate (v) to substrate concentration [S]

•𝑣 = 𝑑[𝑃]𝑑𝑡 = 𝑉𝑚𝑎𝑥[𝑆]

𝐾𝑚+[𝑆]

• Vmax = maximum rate allowed by system (number of active sites)

• Km = Michaelis constant; [S] that gives ½ Vmax

Michaelis-Menten

So what?

• Enzyme kinetics is important-• Helps explain how enzymes work (what they do and how fast they do it)

• Helps predict how enzymes behave in living organisms

• Km and Vmax are attempts at how enzymes work together to control metabolism

• Can incorporate kinetic data with gene expression data

Intermediates

• Often times reactions are not as simple as A+B=C

• Intermediates can be used and steps between original substrate and desired product• Glycolysis and most metabolic pathways behave this way.

Regulation of enzyme activity

• Covalent regulation• Regulates enzyme activity by covalent addition of a chemical group

• Usually involves addition of phosphate group which activates enzyme

• Protein kinases are a class of enzymes that phosphorylate proteins in specific spots (Ser/Thr, Tyr)

• Changes shape of enzyme, which allows active site to interact with substrate

Allosteric regulation

• Regulation by a non-covalent binding of a modulator to a regulatory site of the enzyme• Can be inhibition or activation

• Depends on concentration of substrate(s) and modulator(s)

• Homotropic• Substrate is also regulatory molecule

• Heterotropic• Another molecule (not substrate) is regulatory molecule

Allosteric regulation

Allosteric kinetics

Courtesy: Tim Vickers, Wikimedia commons

Competitive inhibition

• Enzymes can be inhibited by non-substrates binding to the active site

Courtesy: Jeremy Crimson Mann via Wikimedia commons

Feedback inhibition

• Product of reaction or pathway can inhibit an enzyme in an earlier step via allostery,