Biology - Unit 2: Metabolism

Metabolism

• all the chemical reactions in a living cell to sustain life

Metabolic Pathways

• a series of biochemical reactions in cells that are catalyzed by an enzyme

Catabolism

• the process of breaking down compounds into smaller molecules to release energy

Anabolism

• the process of using energy to make larger compounds

Endergonic Reactions

• non-spontaneous, requires energy to occur

Exergonic Reactions

• spontaneous, occurs on their own

• e.g. ATP hydrolysis

Coupled Reactions

• pairing an endergonic reaction with an exergonic reaction to drive the endergonic one

• e.g. ATP hydrolysis releases free energy which can be used by another reaction

Redox Reactions

• transfer of electrons between substances using cofactors

• “reduction-oxiation” reactions

Oxidation

• loss of electrons

Reduction

• gain of electrons

Cofactor

• inorganic compound needed by an enzyme to catalyze a reaction

Coenzyme

• organic molecule needed by enzyme to catalyze a reaction

• e.g. NAD+/NADH functioning as an electron carrier/acceptor for oxidation of energy rich molecules

ADP & ATP

• energy storing/releasing molecules

• ADP - energy poor, ATP - energy rich

• adding P_i stores energy, removing P_i releases energy

• energy used for photosynthesis, protein synthesis, active transport, muscle contractions

Substrate-Level Phosphorylation

• phosphate removed from substrate to phosphorylate ADP → ATP

Oxidative Phosphorylation

• oxidizes NADH and FADH₂ to create gradient for ATP synthesis

Aerobic Respiration

• needs O₂

Anaerobic Respiration

• does not need O₂

Cellular Respiration

• break down glucose in presence of oxygen

• C₆H₁₂O₆ + O₂ → CO₂ + H₂O + ATP

• energy released in small, controlled steps → 36/38 ATP made

Matrix

• space within the inner membrane of the mitochondria

• lower [H+] than intermembrane space

• ADP + P_i enters ATP synthase and exits as ATP from matrix

Cristae

• folds of the mitochondrial inner membrane

Intermembrane Space

• space between outer and inner membrane

• higher [H+] than mitochondrial matrix

Glycolysis

• net equation: 1 glucose → 2 ATP + 2 NADH

• 2 NADH → 2 FADH₂ in eukaryotes (since mitochondrial inner membrane is impermeable to NADH, needs energy to shuttle)

Pyruvate Oxidation

• Net products per 1 glucose: 2 NADH

Krebs Cycle

• net products: 6 NADH, 2 FADH₂, 2 ATP

Electron Transport Chain (ETC)

• uses free energy from electrons transferred by NADH and FADH₂ to pump H+ to intermembrane space

• electrochemical gradient is created → chemical potential energy

• 36/38 H+ are pumped

• oxygen is final electron acceptor

Chemiosmosis

• 1 H+ pumped → 1 ATP made in matrix via ATP synthase

• ATP synthase spins from chemical potential energy

Fermentation

• occurs in anaerobic conditions

• alternative to oxidize NADH since ETC is not working (no oxygen = no final acceptor to oxidize)

• inefficient ATP synthesis (2 ATP vs 36/38 ATP)

Alcohol Fermentation

• NADH is oxidized by acetylaldehyde to make NAD+

• acetylaldehyde is reduced to ethanol (ethyl alcohol)

Lactic Acid Fermentation

• pyruvate oxidizes NADH to form NAD+

• pyruvate is reduced to lactic acid (lactate)

Phosphofructokinase (PFK)

• main control in glycolysis

• converts F6P to F1,6BP via phosphorylation

• extra ADP → binds to allosteric site to increase enzyme activity

• extra ADP → binds to same allosteric site as ADP to decrease enzyme activity

• extra citrate → binds to different allosteric site as ADP to decrease enzyme activity

Pyruvate Dehydrogenase

• main control in pyruvate oxidation

• pyruvate + NAD+

• extra NADH binds to active site to compete against NAD+ → decrease enzyme activity

Mobile Carriers

• transports electrons between enzymes (complexes)

• e.g. Ubiquinone (Q) and Cytochrome C (C)

Deamination

• removal of a amino group from an amino acid

• amino → ammonia → urea

• organic acid → molecule in cellular respiration

Leucine

• becomes acetyl-CoA after undergoing deamination

Alanine

• becomes pyruvate after undergoing deamination

Proline

• becomes α-ketoglutarate after undergoing deamination

Beta-Oxidation

• occurs in mitochondria

• fatty acids (triglycerides/free fatty acid tails) are broken into acetyl-CoA

• 1 β-oxidation → 1 acetyl-CoA, 1 NADH, 1 FADH₂

Glycerol

• becomes glucose via gluconeogenesis

• becomes DHAP with help of enzymes → G3P (DHAP is unstable)

Gluconeogenesis

• making glucose from non-carbohydrate precursors

Friederich’s Ataxia

• autosomal recessive → mutation in FXN gene → less frataxin production

• lack of ATP made, loss of movement (neurological, cardiovascular, muscular)

Frataxin

• a protein responsible for making iron-sulfur clusters

• important for ETC to prevent accumulation of iron

• iron accumulation → oxidative stress and ETC damage

Omaveloloxone

• treatment for Friederich’s Ataxia

• activates Nrf2 pathways → increases antioxidants → lowers oxidative stress & inflammation

Cyanide Poisoning

• cyanide binds to and inhibits cytochrome oxidase complex

• prevents oxidation of the complex → can’t pass electrons to oxygen → obstructs ETC

• lack of ATP production

• dizziness, restlessness, rapid/slow breathing