The Foundations of Biochemistry PDF

The Foundations of Biochemistry  Chapter outline 1.1 Cellular Foundations 1.2 Chemical Foundations 1.3 Physical Foundations 1.4 Genetic Foundations 1.5 Evolutionary Foundations  Introduction ▪ The study of the chemical substances and processes that occ...

The Foundations of Biochemistry  Chapter outline 1.1 Cellular Foundations 1.2 Chemical Foundations 1.3 Physical Foundations 1.4 Genetic Foundations 1.5 Evolutionary Foundations  Introduction ▪ The study of the chemical substances and processes that occur in plants, animals, and microorganisms, as well as the changes that occur during development and life, is known as biochemistry. ▪ Living organs are made-up from biological molecules that we called biochemical compounds. The vast number of biochemical compounds can be grouped into just four major classes: Carbohydrate, protein, Lipid, and nucleic acids.  Introduction Biochemical compounds are carbon-based compounds found in living things. They make up and other structures of organisms and carry out life processes. Most biochemical compounds are macro- molecules that consist of many repeating units of smaller micro-molecules. There are millions of biochemical compounds, but all of them fall into four major classes: carbohydrates, lipids, proteins, and nucleic acids.  Introduction Proteins Carbohydrate Food Energy Vitamins Building materials Lipids Human Growth 5  1.1 Cellular Foundations The unity and diversity of organisms become apparent even at the cellular level. The smallest organisms consist of single cells and are microscopic.  1.1 Cellular Foundations Cells Are the Structural and Functional Units of All Living Organisms 1.1 Cellular Foundations  1.1 Cellular Foundations The Cell Membrane is a barrier to the free passage of inorganic ions and most other charged or polar compounds. Transport proteins in the plasma membrane allow the passage of certain ions and molecules; receptor proteins transmit signals into the cell; and membrane enzymes participate in some reaction pathways.  1.1 Cellular Foundations The internal volume enclosed by the plasma membrane, the cytoplasm is composed of an aqueous solution, the cytosol, and a variety of suspended particles with specific functions. Group study  1.1 Cellular Foundations - Most cells are microscopic, invisible to the unaided eye. - Animal and plant cells are typically 5 to 100 mm in diameter, and many unicellular microorganisms are only 1 to 2 mm long. - Eukaryotic cells contain a variety of membrane-bounded organelles (mitochondria, chloroplasts) and large particles (ribosomes, for example)  1.1 Cellular Foundations All living organisms fall into one of three large groups (domains) that define three branches of the evolutionary ▪ Eukaryotic cells have a variety of membranous organelles, which can be isolated for study.  1.1 Cellular Foundations Cytoskeleton provides essentially support structures composed of numerous smaller proteins linked together. The structure of cytoskeleton composed of microfilaments, intermediate filaments, and microtubules. Endothelial cells from the bovine pulmonary artery. Bundles of actin filaments called “stress fibers” are stained red; microtubules, radiating from the cell center, are stained green; and chromosomes (in the nucleus) are stained blue. The cytoskeleton of animal cells is one of the most complicated and functionally versatile structures, involved in processes such as endocytosis, cell division, intra-cellular transport, motility, force transmission, reaction to external forces, adhesion and preservation, and adaptation of cell shape. 1.1 Cellular Foundations The organic compounds from which most cellular materials are constructed: the ABCs of biochemistry. Shown here are (a) six of the 20 amino acids from which all proteins are built (the side chains are shaded light red); (b) the five nitrogenous bases, two five-carbon sugars, and phosphate ion from which all nucleic acids are built; (c) five components of membrane lipids; and (d) d-glucose, the simple sugar from which most carbohydrates are derived. Note that phosphate is a component of both nucleic acids and membrane lipids. FIGURE 1–8 Subcellular fractionation of tissue.  1.2 Chemical Foundations Biochemistry aims to explain biological form and function in chemical terms. Elements essential to animal life and health. Bulk elements (shaded light red) are structural components of cells and tissues and are required in the diet in gram quantities daily. For trace elements (shaded yellow), the requirements are much smaller: for humans, a few milligrams per day of Fe, Cu, and Zn, even less of the others. The elemental requirements for plants and microorganisms are similar to those shown here; the ways in which they acquire these elements vary.  1.2 Chemical Foundations Biomolecules Are Compounds of Carbon with a Variety of Functional Groups 1.2 Chemical Foundations Cells Contain a Universal Set of Small Molecules  1.2 Chemical Foundations ▪ Macromolecules are the major constituents of cells.  III. Physical Foundations Living cells and organisms must perform work to stay alive and to reproduce themselves. The synthetic reactions that occur within cells, like the synthetic processes in any factory, require the input of energy. ▪ Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings. The constancy of concentration is the result of a dynamic steady state, a steady state that is far from equilibrium. Maintaining this steady state requires the constant investment of energy; when the cell can no longer generate energy, it dies and begins to decay toward equilibrium with its surroundings. We consider below exactly what is meant by “steady state” and “equilibrium.” ▪ Organisms Transform Energy and Matter from Their Surroundings. ▪ The Flow of Electrons Provides Energy for Organisms. Nearly all living organisms derive their energy, directly or indirectly, from the radiant energy of sunlight, which arises from thermonuclear fusion reactions carried out in the sun. ▪ Creating and Maintaining Order Requires Work and Energy. DNA, RNA, and proteins are informational macromolecules. In addition to using chemical energy to form the covalent bonds between the subunits in these polymers, the cell must invest energy to order the subunits in their correct sequence. ▪ Creating and Maintaining Order Requires Work and Energy. ▪ Energy Coupling Links Reactions in Biology. The central issue in bioenergetics (the study of energy transformations in living systems) is the means by which energy from fuel metabolism or light capture is coupled to a cell’s energy-requiring reactions. FIGURE 1–26a Energy coupling in mechanical and chemical processes. FIGURE 1–26b Energy coupling in mechanical and chemical processes. ▪ Enzymes Promote Sequences of Chemical Reactions. FIGURE 1–27 Energy changes during a chemical reaction. FIGURE 1–28 The central roles of ATP and NAD(P)H in metabolism. ▪ Metabolism Is Regulated to Achieve Balance and Economy. Metabolism is the sum of many interconnected reaction sequences that interconvert cellular metabolites. Each sequence is regulated so as to provide what the cell needs at a given time and to expend energy only when necessary.  IV. Genetic Foundations ▪ The Structure of DNA Allows for Its Replication and Repair with Near-Perfect Fidelity. FIGURE 1–30 Complementarity between the two strands of DNA. ▪ The Linear Sequence in DNA Encodes Proteins with Three- Dimensional Structures.  V. Evolutionary Foundations Nothing in biology makes sense except in the light of evolution. —Theodosius Dobzhansky, The American Biology Teacher, March 1973 ▪ Changes in the Hereditary Instructions Allow Evolution. FIGURE 1–32 Gene duplication and mutation: one path to generate new enzymatic activities. ▪ Biomolecules First Arose by Chemical Evolution. ▪ Chemical Evolution Can Be Simulated in the Laboratory. FIGURE 1–33 Abiotic production of biomolecules. Spark-discharge apparatus of the type used by Miller and Urey in experiments demonstrating abiotic formation of organic compounds under primitive atmospheric conditions. After subjection of the gaseous contents of the system to electrical sparks, products were collected by condensation. Biomolecules such as amino acids were among the products. ▪ RNA or Related Precursors May Have Been the First Genes and Catalysts. FIGURE 1–34: A possible “RNA world” scenario. ▪ Biological Evolution Began More Than Three and a Half Billion Years Ago. ▪ The First Cell Was Probably a Chemoheterotroph. ▪ Eukaryotic Cells Evolved from Prokaryotes in Several Stages. FIGURE 1–35 Landmarks in the evolution of life on Earth. FIGURE 1–36 Evolution of eukaryotes through endosymbiosis.