Includes bibliographical references and index.

Biochemistry helps us to understand our world -- Biochemistry and the unity of life -- Living systems require a limited variety of atoms and molecules -- There are four major classes of biomolecules. Proteins are highly versatile biomolecules ; Nucleic acids are the information molecules of the cell ; Lipids are a storage form of fuel and serve as a barrier ; Carbohydrates are fuels and informational molecules -- The central dogma describes the basic principles of biological information transfer -- Membranes define the cell and carry out cellular functions. Biochemical functions are sequestered in cellular compartments ; Some organelles process and sort proteins and exchange material with the environment ; CLINICAL INSIGHT: Defects in organelle function may lead to disease -- Water, weak bonds, and the generation of order out of chaos -- Thermal motions power biological interactions -- Biochemical interactions take place in an aqueous solution -- Weak interactions are important biochemical properties. Electrostatic interactions are between electrical charges ; Hydrogen bonds form between an electronegative atom and hydrogen ; Van der Waals interactions depend on transient asymmetry in electrical charge ; Weak bonds permit repeated interactions -- Hydrophobic molecules cluster together. Membrane formation is powered by the hydrophobic effect ; Protein folding is powered by the hydrophobic effect ; Functional groups have specific chemical properties -- pH is an important parameter of biochemical systems. Water ionizes to a small extent ; An acid is a proton donor, whereas a base is a proton acceptor ; Acids have differing tendencies to ionize ; Buffers resist changes in pH ; Buffers are crucial in biological systems ; Making buffers is a common laboratory practice -- Section 2: Protein composition and structure -- Amino acids -- Two different ways of depicting biomolecules will be used -- Proteins are built from a repertoire of 20 amino acids. Most amino acids exist in two mirror-image forms ; All amino acids have at least two charged groups -- Amino acids contain a wide array of functional groups. Hydrophobic amino acids have mainly hydrocarbon side chains ; Polar amino acids have side chains that contain an electronegative atom ; Positively charged amino acids are hydrophilic ; Negatively charged amino acids have acidic side chains ; The ionizable side chains enhance reactivity and bonding -- Essential amino acids must be obtained from the diet. Clinical insight: Pathological conditions result if protein intake is inadequate -- Protein three-dimensional structure -- Primary structure: Amino acids are linked by peptide bonds to form polypeptide chains. Proteins have unique amino acid sequences specified by genes ; Polypeptide chains are flexible yet conformationally restricted -- Secondary structure: Polypeptide chains can fold into regular structures. The alpha helix is a coiled structure stabilized by intrachain hydrogen bonds ; Beta sheets are stabilized by hydrogen bonding between polypeptide strands ; Polypeptide chains can change direction by making reverse turns and loops ; Fibrous proteins provide structural support for cells and tissues ; Clinical insight: Defects in collagen structure result in pathological conditions -- Tertiary structure: Water-soluble proteins fold into compact structures. Myoglobin illustrates the principles of tertiary structure ; The tertiary structure of many proteins can be divided into structural and functional units -- Quaternary structure: Multiple polypeptide chains can assemble into a single protein -- The amino acid sequence of a protein determines its three-dimensional structure. Proteins fold by the progressive stabilization of intermediates rather than by random search ; Some proteins are intrinsically disordered and can exist in multiple conformations ; Clinical insight: Protein misfolding and aggregation are associated with some neurological diseases -- Techniques in protein biochemistry -- The proteome is the functional representation of the genome -- The purification of proteins is the first step in understanding their function. Proteins can be purified on the basis of differences in their chemical properties ; Proteins must be removed from the cell to be purified ; Proteins can be purified according to solubility, size, charge, and binding affinity ; Proteins can be separated by gel electrophoresis and displayed ; A purification scheme can be quantitively evaluated -- Immunological techniques are used to purify and characterize proteins. Centrifugation is a means of separating proteins ; Gradient centrifugation provides an assay for the estradiol-receptor complex ; Antibodies to specific proteins can be generated ; Monoclonal antibodies with virtually any desired specificity can be readily prepared ; The estrogen receptor can be purified by immunoprecipitation ; Proteins can be detected and quantified with the use of an enzyme-linked immunosorbent assay ; Western blotting permits the detection of proteins separated by gel electrophoresis -- Determination of primary structure facilitates an understanding of protein function. Mass spectrometry can be used to determine a protein's mass, identity, and sequence ; Amino acid sequences are sources of many kinds of insight -- Section 3: Basic concepts and kinetics of enzymes -- Basic concepts of enzyme action -- Enzymes are powerful and highly specific catalysts. Proteolytic enzymes illustrate the range of enzyme specificity ; There are six major classes of enzymes -- Many enzymes require cofactors for activity -- Gibbs free energy is a useful thermodynamic function for understanding enzymes. The free-energy change provides information about the spontaneity but not the rate of a reaction ; The standard free-energy change of a reaction is related to the equilibrium constant ; Enzymes alter the reaction rate but not the reaction equilibrium -- Enzymes facilitate the formation of the transition state. The formation of an enzyme-substrate complex is the first step in enzymatic catalysis ; The active sites of enzymes have some common features ; The binding energy between enzyme and substrate is important for catalysis ; Transition-state analogs are potent inhibitors of enzymes -- Kinetics and regulation -- Kinetics is the study of reaction rates -- The Michaelis-Menten model describes the kinetics of many enzymes. Clinical insight: Variations in KM can have physiological consequences ; KM and Vmax values can be determined by several means ; KM and Vmax values are important enzyme characteristics ; kcat/KM is a measure of catalytic efficiency ; Most biochemical reactions include multiple substrates -- Allosteric enzymes are catalysts and information sensors. Allosteric enzymes are regulated by products of the pathways under their control ; Allosterically regulated enzymes do not conform to Michaelis-Menton kinetics ; Allosteric enzymes depend on alterations in quaternary structure ; Regulator molecules modulate the T↔R equilibrium ; The sequential model also can account for allosteric effects ; Clinical insight: Loss of allosteric control may result in pathological conditions -- Enzymes can be studied one molecule at a time -- Mechanisms and inhibitors -- A few basic catalytic strategies are used by many enzymes -- Enzyme activity can be modulated by temperature, pH, and inhibitory molecules. Temperature enhances the rate of enzyme-catalyzed reactions ; Most enzymes have an optimal pH ; Enzymes can be inhibited by specific molecules ; Reversible inhibitors are kinetically distinguishable ; Irreversible inhibitors can be used to map the active site ; Clinical insight: Penicillin irreversibly inactivates a key enzyme in bacterial cell-wall synthesis -- Chymotrypsin illustrates basic principles of catalysis and inhibition
Serine 195 is required for chymotrypsin activity ; Chymotrypsin action proceeds in two steps linked by a covalently bound intermediate ; The catalytic role of histidine 57 was demonstrated by affinity labeling ; Serine is part of a catalytic triad that includes histidine and aspartic acid -- Hemoglobin, an allosteric protein -- Hemoglobin displays cooperative behavior -- Myoglobin and hemoglobin bind oxygen in heme groups. Clinical insight: Functional magnetic resonance imaging reveals regions of the brain processing sensory information -- Hemoglobin binds oxygen cooperatively -- An allosteric regulator determines the oxygen affinity of hemoglobin. Clinical insight: Hemoglobin's oxygen affinity is adjusted to meet environmental needs ; Biological insight: Hemoglobin adaptations allow oxygen transport in extreme environments -- Hydrogen ions and carbon dioxide promote the release of oxygen -- Mutations in genes encoding hemoglobin subunits can result in disease. Clinical insight: Sickle-cell anemia is a disease caused by a mutation in hemoglobin ; Clinical insight: Thalassemia is caused by an imbalanced production of hemoglobin chains -- Section 4: Carbohydrates and lipids -- Carbohydrates -- Monosaccharides are the simplest carbohydrates. Many common sugars exist in cyclic forms ; Pyranose and furanose rings can assume different conformations ; Clinical insight: Glucose is a reducing sugar.