The Foundations of Biochemistry PDF

The Foundations of Biochemistry Recommended reading: Chapter 1 (Lehninger Principles of Biochemistry. Nelson & Cox-7th Edition) Course Proficiencies covered: 1. Analyze, evaluate and interpret information and ideas about biochemistry 2. Interpret tabular and graphical information relating t...

The Foundations of Biochemistry Recommended reading: Chapter 1 (Lehninger Principles of Biochemistry. Nelson & Cox-7th Edition) Course Proficiencies covered: 1. Analyze, evaluate and interpret information and ideas about biochemistry 2. Interpret tabular and graphical information relating to biochemistry Slides are adapted from Dr. Narendra Kumar Jayshree Mishra PhD Office: Rm. 213 Poll Everywhere login: mishra Syllabus and Expectations  How to make an “A” in the course Attendance Attention Notes Video Study Review self/instructor Reading NOT to do (org/outside-work) Pre-lecture assessment/ attendance Learning goals: 1. Distinguish the features of living organisms 2. Describe the roles of small & large biomolecules 3. Describe the structural & functional parts of cells 4. Describe biological reactions and free energy (G) 5. Describe biochemical basis for the perpetuation of living organism and evolution. Key concept: The purpose of existence of life in every cell and the common molecular denominators that defines it are the foundations of biochemistry. Cellular Foundation What is the biochemical basis?  Biochemistry Is the Chemistry of Living Matter Living matter is characterized by: a high degree of complexity and organization the extraction, transformation, and systematic use of energy to create and maintain structures and to do work the interactions of individual components being dynamic and coordinated the ability to sense and respond to changes in surroundings a capacity for fairly precise self-replication while allowing enough change for evolution All Cells Share Some Common Features Bacterial Cell Structure and Functions Read Animal Cell Structure and Functions Cells and Minimal Components (Summary) Plasma membrane Cytoplasm – Enzymes – RNA – Metabolites – Coenzymes – Ribosomes Nucleus (Eukaryote) or nucleoid (Prokaryote) (genome) Organelles in eukaryote cytoplasm, not in Prokaryotes *Viruses: Are they cells? Structure and Bio-molecular Hierarchy Know the differences Chemical Foundation  Functional Groups in Biological Molecules Methyl, ethyl, phenyl Amino, amido Ether Carbonyl (aldehyde, Ester ketone) Sulfhydryl, disulfide Carboxyl Phosphoryl Hydroxyl (alcohol) Phosphoanhydride Phenol 6. Which of the following fruit group is most abundant in phenolic phytochemicals? Citrus, Pome, Stone, Tropical, Berries Functional Groups in Biological Molecules This symbol means you need to know S the structure! Functional Groups in Biological Molecules Archaeal membrane S Bacterial membrane  Functional Groups in Biological Molecules S Phenol Know How is an alcohol different from a phenol? (a) Structurally & (b) Chemically  Functional Groups in Biological Molecules S Insulin maturation Is the sulfhydryl group also present as another form?  Functional Groups in Biological Molecules S Phosphoanhydride Give an example of metabolite with bond? Clue: one of the most abundant metabolite in human. Biological Molecules Typically Have Several Functional Groups The ABCs of Life Sub-cellular hierarchy AA Protein Ribosome Organelle Cell Tissue Organ Human body  Stereoisomers Compounds differing only in the spatial arrangement (configuration) of their atoms. Have different physical and chemical properties. Configuration is conferred by either: Double bonds, around which there is no freedom of motion (cis-trans isomers) Chiral centers, around which substituent groups are arranged in a specific sequence (enantiomers and diastereomers)  Cis vs. Trans The chemical basis of visual phototransduction. ?? Source of retinal: Vit-A Enantiomers and Diastereomers Optical plane Physical Foundation  Unfavorable and Favorable Reactions Synthesis of complex molecules and many other metabolic reactions requires energy (endergonic). – A reaction might be thermodynamically unfavorable (G°> 0). Creating order requires work and energy. ‡ – A metabolic reaction might have too high an energy barrier (G > 0). Metabolite is kinetically stable. The breakdown of some metabolites releases a significant amount of energy (exergonic). – Such metabolites (ATP, NADH, NADPH) can be synthesized using the energy from sunlight and fuels. – Their cellular concentration is far higher than their equilibrium concentration. Genetic Foundation The Central “Dogma” of Biochemistry: DNA → RNA → Protein Evolutionary Foundation  Natural Selection Favors Some Mutations Mutations occur more or less randomly in DNA and RNA. Mutated polynucleotides may be transcribed and translated into molecular machinery like proteins. Mutations that give organisms an advantage in a given environment are more likely to be propagated.  At this time you should know 1. Describe the structural and functional components of prokaryotic and eukaryotic cells. 2. Describe the key similarities and differences between bacteria, archaea, eukaryotes and viruses. 3. Identify the key differences between the common functional groups in biological molecules. 4. Distinguish between a favorable and an unfavorable reaction based on its delta G value. 5. Described the Central Dogma, and define replication, transcription and translation.