Chapter 1: Outline • The Living World • Bacteria, Archaea, Eukarya, (Viruses) • Biomolecules • Functional Groups • Major Classes of Biomolecules • Biochemical Processes (We are here.) • Reactions, Energy, Metabolism, Order • Genetic Information Processing
1.3 Biochemical Processes • Metabolism is the sum of all biochemical reactions. • Functions of metabolism are: • Synthesis of biomolecules. • 2. Transport of ions and molecules across cell membranes. • 3. Production of force and movement. • 4. Removal of metabolic waste and other toxic substances.
Bio Rxns: By Mechanism-1 • Nucleophilic Substitution-acyl Sulfur nucleophile attacks C=O
Bio Rxns: By Mechanism-1 Nucleophilic Substitution-alkyl • Sulfur nucleohile attacks alkyl C
Bio Rxns: By Mechanism-2 Addition occurs at C=C • Addition: two molecules combine to give one. • One molecule usually multiple bonded.
Bio Rxns: By Mechanism-3 Water is lost to form phosphoenolpyruvate • Elimination- a molecule loses atoms usually in the form of a small molecule like water.
Bio Rxns: By Mechanism-4 • Isomerization: molecule rearranges atoms 3-phosphoglycerate to 2-phosphoglycerate
Bio Rxns: By Mechanism-5 • Hydrolysis: water cleaves (splits) a covalent bond and inserts itself. Hydrolysis of a fat Hydrolysis is a variant of acyl substitution.
Bio Rxns: By Redox Nature • Redox reactions involve the transfer of electrons. • Oxidation: a loss of electrons • Reduction: a gain of electrons • Oxidizing agent: the electron acceptor • Reducing agent: the electron donor • Note: Reactions may fall into both classification categories, mechanism and redox.
Bio Rxns: By Redox Nature-2 • In biochemistry redox reactions are usually recognized by the following changes: • Oxidation occurs when a molecule loses two hydrogens and/or gains an oxygen. • Reduction occurs when a molecule gains two hydrogens and/or loses an oxygen.
Bio Rxns: By Redox Nature-3 Oxidation Lactate is oxidized. NAD+ is oxidizing agent.
Bio Rxns: By Redox Nature-4 Reduction The double bond is reduced. NADPH is the reducing agent.
Quiz • Classify the reactions: by mechanism and by redox character. Mech: addition Not redox (add 2H and 1 O) Mech: elimination Oxidation (remove 2H)
Energy • Energy is the capacity to do work. • Cells generate most of their energy from redox reactions. • When electrons are transferred to an electron deficient molecule, energy is lost. Several redox reactions provide enough energy for ATP synthesis. • The ultimate source of energy used by most organisms on earth is the sun.
Metabolism • Metabolism is the sum of all the enzyme- catalyzed reactions in a living organism. • In anabolic (biosynthetic) pathways large complex molecules are synthesized from smaller molecules. • In catabolic pathways large complex molecules are degraded into simpler products. A portion of the energy produced drive anabolic reactions.
Biological Order • Processes can be classified in the following categories. • Synthesis of biomolecules • Many reactions are integrated into carefully regulated pathways. Energy is supplied either directly or indirectly by breaking phospho-anhydride bonds of ATP.
Biological Order-2 • 2. Transport across membranes. • Cell membranes regulate the passage of ions and molecules from one compartment to another. • Much of this is accomplished by membrane bound proteins. • 3. Cell movement • Examples include cell division, organelle movement and even movement of enzymes along a DNA strand.
Biological Order-3 • 4. Waste removal • Excess CO2, H2O, and NH3 must be removed.CO2 is exhaled, H2O is excreted by the kidneys, and NH3 is converted to urea. • Hydrophobic molecules such as the steroid hormones are converted to water soluble derivatives.
1.4 Genetic Information • “Central dogma” of molecular biology • The chemical information in a gene (DNA) directs the assembly of amino acids into polypeptides (proteins).
Information Flow Transcription: RNA is made on a DNA template Translation: Protein is synthesized from AAs and the three RNAs. • DNA RNA Protein
Transcription • RNA polymerases and proteins copy the coded instructions in genes into RNA molecules.
Translation • The nucleotide base code of messenger RNA binds to ribosomes where it is decoded into the amino acids sequence of proteins.