1P2-1 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

1P Biochemical Processes Metabolism is the sum of all biochemical reactions. Functions of metabolism are: 1.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.

1P2-3 Bio Rxns: By Mechanism-1 Nucleophilic Substitution-acyl Sulfur nucleophile attacks C=O

1P2-4 Bio Rxns: By Mechanism-1 Nucleophilic Substitution-alkyl Sulfur nucleohile attacks alkyl C

1P2-5 Bio Rxns: By Mechanism-2 Addition: two molecules combine to give one. One molecule usually multiple bonded. Addition occurs at C=C

1P2-6 Bio Rxns: By Mechanism-3 Elimination- a molecule loses atoms usually in the form of a small molecule like water. Water is lost to form phosphoenolpyruvate

1P2-7 Bio Rxns: By Mechanism-4 Isomerization: molecule rearranges atoms 3-phosphoglycerate to 2-phosphoglycerate

1P2-8 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.

1P2-9 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.

1P2-10 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.

1P2-11 Bio Rxns: By Redox Nature-3 Oxidation Lactate is oxidized. NAD + is oxidizing agent.

1P2-12 Bio Rxns: By Redox Nature-4 Reduction The double bond is reduced. NADPH is the reducing agent.

1P2-13 Quiz Classify the reactions: by mechanism and by redox character. Mech: addition Not redox (add 2H and 1 O) Mech: elimination Oxidation (remove 2H)

1P2-14 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.

1P2-15 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.

1P2-16 Biological Order Processes can be classified in the following categories. 1.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.

1P2-17 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.

1P2-18 Biological Order-3 4. Waste removal Excess CO 2, H 2 O, and NH 3 must be removed. CO 2 is exhaled, H 2 O is excreted by the kidneys, and NH 3 is converted to urea. Hydrophobic molecules such as the steroid hormones are converted to water soluble derivatives.

1P Genetic Information “Central dogma” of molecular biology The chemical information in a gene (DNA) directs the assembly of amino acids into polypeptides (proteins).

1P2-20 Information Flow DNARNAProtein Transcription: RNA is made on a DNA template Translation: Protein is synthesized from AAs and the three RNAs.

1P2-21 Transcription RNA polymerases and proteins copy the coded instructions in genes into RNA molecules.

1P2-22 Translation The nucleotide base code of messenger RNA binds to ribosomes where it is decoded into the amino acids sequence of proteins.