metabolism enzymes metabolism and metabolic pathways

Metabolism

Enzymes

Metabolism and Metabolic Pathways

Enzymes

Proteins which function as biological catalysts

Each biochemical transformation in a cell has a specific enzyme associated with it

Enzymes and Activation Energy

Lock and Key Model

Interaction between enzyme and substrate analogous to a lock and key

Active site Allosteric sites

Kinetics of an Enzymatically Catalyzed Reaction

Conversion of substrate to product

Concentration of substrate and enzyme constant

All experimental conditions (pH, temp) constant

Effect of [S] on V0

Initial linear relationship between increasing [S] and initial reaction velocity

Saturation kinetics Overall a hyperbolic

curve

Michaelis-Menton Kinetics

Vmax

– Maximum reaction rater

KM

– Affinity constant

– [S] when V0 = 1/2 Vmax

Values can be estimated from hyperbolic graph

Lineweaver - Burke Plots

Linearizes Michaelis-Menton plot

Plot 1/V0 vs 1/[S]

Monod Equation

Metabolism

Definitions Metabolism: The sum of the

biochemical reactions which occur in a cell

Pathway: – A series of connected reactions– A --> B--> C-->D-->E

Catabolism: – Breakdown complex substrates– Generally oxidations

– Energy yielding– Generate reduced electron carriers

Anabolism– Build up complex molecules from

precursors– Generally reductions– Energy requiring– Oxidize electron carriers

ATP and Energy Transfer ATP <---> ADP <--->

AMP High energy (squiggle)

phosphate bonds 7.3 kcal to make or

break these bonds Transfer energy from

energy yielding reactions to energy requiring reactions

Mechanisms of Energy Generation

Substrate level phosphorylation

Oxidative phosphorylation Photophosphorylation

Electron Carriers

Coenzymes– NAD/NADH + H+

– FAD/FADH2

Transfer electrons from oxidation to reduction reactions

Need for initial electron donor and terminal electron acceptor

NAD/NADH + H+

Understanding Metabolic Pathways

Keep track of:– Elements– Energy (ATP/ADP)– Electrons

Why are there so many steps in the pathways– Energetic constraints– Generation of intermediates

Central Metabolic Pathways

Essential pathways Found in all organisms Include:

– Glycolysis (EMP)– TCA (Kreb’s) cycle– ETS

Other Pathways Specific catabolic pathways not

found in all organisms If an organism can convert a

compound into an intermediate in Central metabolism, complete mineralization (catabolism to carbon dioxide and water) is possible.

Overview of Pathways

Glycolysis

Conversion of glucose to 2 pyruvate

Most common pathway for initial metabolism of glucose

Anaerobic pathway Substrate level

phosphorylation

Low energy yield/incomplete oxidation

Production of NADH + H+

Fermentation Reoxidation of NADH

+ H+ to NAD Organic compound

functions as a terminal electron acceptor

Important in– Industrial production of

chemicals– Food production: bread,

wine, etc.

TCA Cycle Oxidation of

pyruvate to carbon dioxide

Low direct energy yield

Generates large amounts of reduced coenzymes

Produces biosynthetic intermediates

Respiration

Transfer of electrons from electron acceptors to terminal electron acceptors– Aerobic organisms: oxygen– Anaerobic organisms: other inorganic

compounds• Nitrate• Sulfate• Iron• Carbonate

Electron Transport System Series of compounds

which are alternatively reduced and oxidized

Orientation in the membrane. Net translocation of charge and hydrogen across the membrane

Chemiosmosis

Couples electron transport with ATP generation

Development of transmembrane potential by transfer of electrons and hydrogens

Where H+ reenters the cell, ATP synthease is present