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Section 1 Introduction to Biochemical Principles Chapter 1 Biochemistry: An Introduction Life: It is a Mystery! Life: It is a Mystery! Figure 1.1 Diversity of Life Why study biochemistry? Foundation upon which all of the modern life sciences are built Biology can’t be done without biochemistry Life and its Diversity Life is Resilient Section 1.1: What Is Life? All Life Obeys the Same Chemical and Physical Laws: Life is complex and dynamic Life is organized and selfsustaining Life is cellular Life is information-based Life adapts and evolves Figure 1.3 Hierarchical Organization Section 1.2: Biomolecules Living organisms composed of inorganic and organic molecules Water is the matrix of life Six principal elements: carbon, hydrogen, oxygen, nitrogen, phosphorous, and sulfur Trace elements are also important (i.e., Na+, K+, Mg2+, and Ca2+) Section 1.2: Biomolecules Section 1.2: Biomolecules Major Classes of Small Biomolecules Many organic molecules are relatively small (less than 1000 Daltons (Da)) Families of small molecules: amino acids, sugars, fatty acids, and nucleotides Section 1.3: Is the Living Cell a Chemical Factory? The properties of even the simplest cells are remarkable Autopoiesis has been coined to describe the remarkable properties of living organisms Metabolism is defined as: The acquisition and utilization of energy Synthesis of molecules needed for cell structure and function Growth and development Removal of waste products Section 1.3: Is the Living Cell a Chemical Factory? Biochemical Reactions Nucleophilic substitution Elimination Addition Isomerization Oxidation-Reduction Section 1.3: Is the Living Cell a Chemical Factory? Energy Energy is defined as the capacity to do work Cells generate most of their energy with redox reactions The energy captured when electrons are transferred from an oxidizable molecule to an electron-deficient molecule is used to drive ATP synthesis Acquiring energy from the environment happens in distinct ways: Autotrophs Heterotrophs Section 1.3: Is the Living Cell a Chemical Factory? Overview of Metabolism Metabolic pathways come in two types: anabolic and catabolic Anabolic: large complex molecules synthesized from smaller precursors Catabolic: large complex molecules degraded into smaller, simpler products Energy transfer pathways capture energy and transform it into a usable form Signal transduction pathways allow cells to receive and respond to signals Figure 1.21 A Biochemical Pathway Section 1.3: Is the Living Cell a Chemical Factory? Figure 1.22 Anabolism and Catabolism Section 1.3: Is the Living Cell a Chemical Factory? Biological Order The coherent unity that is observed in all organisms: Synthesis of biomolecules Transport across membranes Cell movement Waste removal Section 1.4: Systems Biology Systems Biology: Living Organisms Regarded as Integrated Systems Emergence: Interaction of parts can lead to new properties Figure 1.23 Feedback Mechanisms Section 1.4: Systems Biology Robustness: Many biological systems remain stable despite perturbations Modularity: Complex systems are composed of modules Figure 1.23 Feedback Mechanisms Chapter 2 Living Cells Section 2.1: Basic Themes Figure 2.2 Hydrophobic Interactions Between Water and a Nonpolar Substance Understanding of the biological context of biochemical processes is enhanced by examining six key concepts: Section 2.1: Basic Themes Figure 2.2 Hydrophobic Interactions Between Water and a Nonpolar Substance Water Unique polar structure Among its most important properties is interaction with a wide range of substances Section 2.1: Basic Themes Biological Membranes Thin, flexible, and stable sheet-like structures Selective physical barrier Phospholipid bilayer with integral and peripheral membrane proteins Figure 2.3 Membrane Structure Section 2.1: Basic Themes Self-Assembly Many biomolecules spontaneously undergo selfassembly into supermolecular structures Molecular Machines Many multisubunit complexes involved in cellular processes function as molecular machines Figure 2.5 Biological Machines Section 2.1: Basic Themes Figure 2.6 Volume Exclusion Macromolecular Crowding The interior space within cells is dense and crowded The excluded volume may be between 20% and 40% Signal Transduction Reception, transduction, and response Section 2.2: Structure of Prokaryotic Cells Figure 2.7 Typical Bacterial Cell Prokaryotes include bacteria and archaea They have common features: cell wall, plasma membranes, circular DNA, and no membrane-bound organelles Section 2.2: Structure of Prokaryotic Cells Figure 2.8 Bacterial Cell Section 2.2: Structure of Prokaryotic Cells Cell Wall The prokaryotic cell wall is a complex semirigid structure primarily for support and protection The cell wall is primarily composed of peptidoglycan Figure 2.8 Bacterial Cell Section 2.2: Structure of Prokaryotic Cells Figure 2.9 Bacterial Plasma Membrane Plasma Membrane Directly inside the cell wall is the plasma membrane, a phospholipid bilayer A selectively permeable membrane that may be involved in photosynthesis or respiration Section 2.2: Structure of Prokaryotic Cells Cytoplasm Prokaryotic cells do have functional compartments Nucleoid, which is centrally located and contains the circular chromosome Also contains small DNA plasmids Inclusion bodies are large granules that contain organic or inorganic compounds Figure 2.10 Bacterial Cytoplasm Section 2.2: Structure of Prokaryotic Cells Figure 2.7 Typical Bacterial Cell Pili and Flagella Many bacteria have external appendages Pili (pilus) are for attachment and sex Flagella (flagellum) are used for locomotion Section 2.3: Structure of Eukaryotic Cells Eukaryotic cells are structurally complex Membrane-bound organelles and the endomembrane system increase surface area for chemical reactions Figure 2.11 Animal Cell Section 2.3: Structure of Eukaryotic Cells Important structures: plasma membrane, endoplasmic reticulum, Golgi apparatus, nucleus, lysosomes, mitochondria, chloroplasts, ribosomes, and the cytoskeleton Figure 2.12 Plant Cell Section 2.3: Structure of Eukaryotic Cells Figure 2.13 Plasma Membrane Plasma Membrane Isolates the cell and is selectively permeable Outside the plasma membrane are the glycocalyx and the extracellular matrix Section 2.3: Structure of Eukaryotic Cells Endoplasmic Reticulum The endoplasmic reticulum (ER) is a series of membranous tubules, vesicles, and flattened sacks The internal space is the ER lumen Figure 2.15 Endoplasmic Reticulum Section 2.3: Structure of Eukaryotic Cells Two types: Rough ER functions include protein synthesis, folding, and glycosylation Smooth ER functions include lipid biosynthesis and Ca2+ storage Figure 2.15 Endoplasmic Reticulum Section 2.3: Structure of Eukaryotic Cells Golgi Apparatus The Golgi apparatus is formed of large, flattened, sac-like membranous vesicles Processes, packages, and distributes cell products Has a cis and a trans face (cisternae) Figure 2.16 The Golgi Apparatus Section 2.3: Structure of Eukaryotic Cells Cisternal maturation model vesicles are recycled back to the cis Golgi from the trans Golgi Secretory products concentrated at the trans Golgi into secretory vesicles Involved in exocytosis Figure 2.17 Exocytosis Section 2.3: Structure of Eukaryotic Cells Nucleus The nucleus is the most prominent organelle Contains the hereditary information Site of transcription Nuclear components: Nucleoplasm Chromatin (genome) Nuclear matrix Nucleolus Nuclear envelope Figure 2.18 Eukaryotic Nucleus Section 2.3: Structure of Eukaryotic Cells The nuclear envelope surrounds the nucleoplasm The nuclear envelope has nuclear pores referred to as nuclear pore complexes Structures through which pass most of the molecules that enter and leave the nucleus Figure 2.19 The Nuclear Pore Complex Section 2.3: Structure of Eukaryotic Cells Vesicular Organelles The eukaryotic cell has vesicles Vesicles originate in the ER, Golgi and/or via endocytosis Figure 2.20 Receptor-Mediated Endocytosis Section 2.3: Structure of Eukaryotic Cells Phagocytosis Receptor-mediated endocytosis Endocytic cycle is used for recycling and remodeling of membranes Figure 2.20 Receptor-Mediated Endocytosis Section 2.3: Structure of Eukaryotic Cells Vesicular Organelles Continued Lysosomes are vesicles that contain digestive enzymes Enzymes are acid hydrolases Degrade debris in cells and involved in autophagy Figure 2.21 Lysosomes Section 2.3: Structure of Eukaryotic Cells Mitochondria Figure 2.23 The Mitochondrion The mitochondria (mitochondrion) are recognized as the site of aerobic metabolism Mitochondria are the principle source of cellular energy Have inner and outer membrane surrounding the matrix Have DNA and ribosomes Section 2.3: Structure of Eukaryotic Cells Peroxisomes The peroxisome is a small organelle containing oxidative enzymes Detoxifies peroxides (e.g., H2O2) Section 2.3: Structure of Eukaryotic Cells Plastids Figure 2.25 Chloroplast Plastids are organelles found only in plants, algae, and some protists Two types: leucoplasts and chromoplasts Chloroplasts are chromoplasts specialized for photosynthesis Section 2.3: Structure of Eukaryotic Cells Cytoskeleton The cytoskeleton is an intricate supportive network of fibers, filaments, and associated proteins Three main components: Microtubules Microfilaments Intermediate filaments Main functions includE cell shape and structure, large- and small-scale cell movement, solid-state biochemistry, and signal transduction Section 2.3: Structure of Eukaryotic Cells Figure 2.26 The Cytoskeleton Section 2.3: Structure of Eukaryotic Cells Cytoskeleton Cilia and flagella, whip-like appendages encased in plasma membrane, are highly specialized for their roles in propulsion Bending occurs via ATP-driven structural changes in dynein molecules Section 2.3: Structure of Eukaryotic Cells Figure 2.27 Cilia and Flagella Chapter 3 Water: The Matrix of Life Section 3.1: Molecular Structure of Water Water is essential for life Water’s important properties include: Chemical stability Remarkable solvent properties Role as a biochemical reactant Hydration Section 3.1: Molecular Structure of Water Water has a tetrahedral geometry Oxygen is more electronegative than hydrogen Figure 3.2 Tetrahedral Structure of Water Section 3.1: Molecular Structure of Water Larger oxygen atom has partial negative charge (d-) and hydrogen atoms have partial positive charges (d+) Figure 3.3 Charges on a Water Molecule Figure 3.4 Water Molecule Section 3.1: Molecular Structure of Water Bond between oxygen and hydrogen is polar Water is a dipole because the positive and negative charges are separate Figure 3.5 Molecular Dipoles in an Electric Field Section 3.1: Molecular Structure of Water An electron-deficient hydrogen of one water is attracted to the unshared electrons of water forming a hydrogen bond Can occur with oxygen, nitrogen, and fluorine Has electrostatic (i.e., opposite charges) and covalent (i.e., electron sharing) characteristics Figure 3.6 Hydrogen Bond Section 3.2: Noncovalent Bonding Noncovalent interactions are electrostatic Weak individually, but play vital role in biomolecules because of cumulative effects Section 3.2: Noncovalent Bonding Three most important noncoavalent bonds: Ionic interactions Van der Waals forces Hydrogen bonds Section 3.2: Noncovalent Bonding Ionic Interactions Oppositely charged ions attract one another Ionized amino acid side chains can form salt bridges with one another Biochemistry primarily investigates the interaction of charged groups on molecules, which differs from ionic interactions like those of ionic compounds (e.g., NaCl) Section 3.2: Noncovalent Bonding Hydrogen Bonds Electron-deficient hydrogen is weakly attracted to unshared electrons of another oxygen or nitrogen Large numbers of hydrogen bonds lead to extended network Figure 3.7 Tetrahedral Aggregate of Water Molecules Section 3.2: Noncovalent Bonding Van der Waals Forces Occur between neutral, permanent, and/or induced dipoles Three types: Dipole-dipole interactions Dipole-induced dipole interactions Induced dipole-induced dipole interactions Figure 3.8 Dipolar Interactions Section 3.3: Thermal Properties of Water Water’s melting and boiling points are exceptionally high due to hydrogen bonding Each water molecule can form four hydrogen bonds with other water molecules Extended network of hydrogen bonds Section 3.3: Thermal Properties of Water Figure 3.9 Hydrogen Bonding Between Water Molecules in Ice Maximum number of hydrogen bonds form when water has frozen into ice Open, less-dense structure Section 3.3: Thermal Properties of Water Water has an exceptionally high heat of fusion and heat of vaporization Helps to maintain an organism’s internal temperature Section 3.4: Solvent Properties of Water Figure 3.10 Solvation Spheres Water is the ideal biological solvent Hydrophilic Molecules, Cell Water Structuring, and Sol-Gel Transitions Water can dissolve ionic and polar substances Shells of water molecules form around ions forming solvation spheres Section 3.4: Solvent Properties of Water Figure 3.11 Diagrammatic View of Structured Water Structured Water Water is rarely free flowing Water is associated with macromolecules and other cellular components Forms complex threedimensional bridges between cellular components Section 3.4: Solvent Properties of Water Figure 3.12 Amoeboid Movement Sol-Gel Transitions Cytoplasm has properties of a gel (colloidal mixture) Transition from gel to sol important in cell movement Amoeboid motion provides an example of regulated, cellular, sol-gel transitions Section 3.4: Solvent Properties of Water Figure 3.13 The Hydrophobic Effect Hydrophobic Molecules and the Hydrophobic Effect Small amounts of nonpolar substances are excluded from the solvation network forming droplets This hydrophobic effect results from the solvent properties of the water and is stabilized by van der Waals interactions Section 3.4: Solvent Properties of Water Amphipathic Molecules Contain both polar and nonpolar groups Amphipathic molecules form micelles when mixed with water Important feature for the formation of cellular compartments Figure 3.14 Formation of Micelles Section 3.4: Solvent Properties of Water Figure 3.15 Osmotic Pressure Osmotic Pressure Osmosis is the spontaneous passage of solvent molecules through a semipermeable membrane Osmotic pressure is the pressure required to stop the net flow of water across the membrane Osmotic pressure depends on solute concentration Section 3.4: Solvent Properties of Water Can be measured with an osmometer or calculated ( =iMRT) Cells may gain or lose water because of the environmental solute concentration Solute concentration differences between the cell and the environment can have important consequences Isotonic solution Hypotonic solution Hypertonic solution Figure 3.17 Effect of Solute Concentration on Animal Cells Section 3.4: Solvent Properties of Water Proteins with ionizable amino acid side chains affect cellular osmolarity by attracting ions of opposite charge There is asymmetry of charge across the membrane due to ions forming an electrical gradient (membrane potential) Unlike animal cells, plant cells use osmotic pressure to drive growth via turgor pressure Section 3.5: Ionization of Water Water can occasionally ionize, forming a hydrogen ion (H+) and a hydroxide ion (OH-) In an aqueous solution, a proton combines with a water molecule to form H3O+ (hydronium ion) H2O H+ + OH- (reversible) Section 3.5: Ionization of Water The ion product of water is referred to as Keq[H2O] or Kw = [H+][OH-] Kw at 25°C and 1 atm pressure is 1.0 10-14 Kw is temperature-dependent; therefore, pH is temperature-dependent as well Section 3.5: Ionization of Water Acids, Bases, and pH An acid is a proton donor A base is a proton acceptor Most organic molecules that donate or accept protons are weak acids or weak bases A deprotonated product of a dissociation reaction is a conjugate base Section 3.5: Ionization of Water The pH scale can be used to measure hydrogen ion concentration pH=-log[H+] Figure 3.18 The pH Scale and the pH Values of Common Fluids Section 3.5: Ionization of Water pKa is used to express the strength of a weak acid Lower pKa equals a stronger acid pKa=-logKa Ka is the acid dissociation constant Figure 3.18 The pH Scale and the pH Values of Common Fluids Section 3.5: Ionization of Water Section 3.5: Ionization of Water Buffers Regulation of pH is universal and essential for all living things Certain diseases can cause changes in pH that can be disastrous Acidosis and Alkalosis Buffers help maintain a relatively constant hydrogen ion concentration Commonly composed of a weak acid and its conjugate base Section 3.5: Ionization of Water Buffers Continued Establishes an equilibrium between buffer’s components Follows Le Chatelier’s principle Equilibrium shifts in the direction that relieves the stress Figure 3.19 Titration of Acetic Acid with NaOH Section 3.5: Ionization of Water Henderson-Hasselbalch Equation Establishes the relationship between pH and pKa for selecting a buffer Buffers are most effective when they are composed of equal parts weak acid and conjugate base Best buffering occurs 1 pH unit above and below the pKa Henderson-Hasselbalch Equation pH = pKa + log [A-] [HA] Section 3.5: Ionization of Water Worked Problem 3.5 (Page 91) Calculate the pH of a mixture of 0.25 M acetic acid (CH3COOH) and 0.1 M sodium acetate (NaC2H3O2) The pKa of acetic acid is 4.76 Solution: pH = pKa + log pH = 4.76 + log [acetate] [acetic acid] [0.1] [0.25] = 4.76 + 0.398 = 4.36 Section 3.5: Ionization of Water Figure 3.20 Titration of Phosphoric Acid with NaOH Weak Acids with Multiple Ionizable Groups Each ionizable group can have its own pKa Protons are released in a stepwise fashion Section 3.5: Ionization of Water Physiological Buffers Buffers adapted to solve specific physiological problems within the body Bicarbonate Buffer One of the most important buffers in the blood CO2 + H2O H+ + HCO3- (HCO3- is bicarbonate): This is a reversible reaction Carbonic anhydrase is the enzyme responsible Section 3.5: Ionization of Water Phosphate Buffer Consists of H2PO4-/HPO42(weak acid/conjugate base) H2PO4- H+ + HPO42Important buffer for intracellular fluids Protein Buffer Proteins are a significant source of buffering capacity (e.g., hemoglobin) Figure 3.21 Titration of H2PO4- by Strong Base Chapter 4 Energy Section 4.1: Thermodynamics Energy is the basic constituent of the universe Energy is the capacity to do work In living organisms, work is powered with the energy provided by ATP Thermodynamics is the study of energy transformations that accompany physical and chemical changes in matter Bioenergetics is the branch that deals with living organisms Section 4.1: Thermodynamics Bioenergetics is especially important in understanding biochemical reactions These reactions are affected by three factors: Enthalpy—total heat content Entropy—state of disorder Free Energy—energy available to do chemical work Section 4.1: Thermodynamics Three laws of thermodynamics: First Law of Thermodynamics—Energy cannot be created nor destroyed, but can be transformed Second Law of Thermodynamics—Disorder always increases Third Law of Thermodynamics—As the temperature of a perfect crystalline solid approaches absolute zero, disorder approaches zero Section 4.1: Thermodynamics First two laws are powerful biochemical tools Thermodynamic transformations take place in a universe composed of a system and its surroundings Energy exchange between a system and its surroundings can happen in two ways: heat (q) or work (w) Figure 4.2 A Thermodynamic Universe Work is the displacement or movement of an object by force Section 4.1: Thermodynamics First Law of Thermodynamics Expresses the relationship between internal energy (E) in a closed system and heat (q) and work (w) Total energy of a closed system (e.g., our universe) is constant DE = q + w Unlike a human body, which is an open system Enthalpy (H) is related to internal energy by the equation: H = E + PV DH is often equal to DE (DH = DE) Section 4.1: Thermodynamics First Law of Thermodynamics Continued If DH is negative (DH <0) the reaction gives off heat: exothermic If is DH positive (DH >0) the reaction takes in heat from its surroundings: endothermic In isothermic reactions (DH =0) no heat is exchanged Reaction enthalpy can also be calculated: DHreaction = SDHproducts SDHreactants Standard enthalpy of formation per mole (25°C, 1 atm) is symbolized by DHf° Section 4.1: Thermodynamics Figure 4.3 A Living Cell as a Thermodynamic System Second Law of Thermodynamics Physical or chemical changes resulting in a release of energy are spontaneous Nonspontaneous reactions require constant energy input Section 4.1: Thermodynamics As a result of spontaneous processes, matter and energy become more disorganized Gasoline combustion The degree of disorder is measured by the state function entropy (S) Figure 4.4 Gasoline Combustion Section 4.1: Thermodynamics Second Law of Thermodynamics Continued Entropy change for the universe is positive for every spontaneous process DSuniv = DSsys + DSsurr Living systems do not increase internal disorder; they increase the entropy of their surroundings For example, food consumed by animals to provide energy and structural materials needed are converted to disordered waste products (i.e., CO2, H2O and heat) Organisms with a DSuniv = 0 or equilibrium are dead Section 4.2: Free Energy Free energy is the most definitive way to predict spontaneity Gibbs free energy change or DG Figure 4.5 The Gibbs Free Energy Equation Negative DG indicates spontaneous and exergonic Positive DG indicates nonspontaneous and endergonic When DG is zero, it indicates a process at equilibrium Section 4.2: Free Energy Standard Free Energy Changes Standard free energy, DG°, is defined for reactions at 25°C,1 atm, and 1.0 M concentration of solutes Standard free energy change is related to the reactions equilibrium constant, Keq DG° = -RT ln Keq Allows calculation of DG° if Keq is known Because most biochemical reactions take place at or near pH 7.0 ([H+] = 1.0 10-7 M), this exception can be made in the 1.0 M solute rule in bioenergetics The free energy change is expressed as DG°′ Section 4.2: Free Energy Figure 4.6 A Coupled Reaction Coupled Reactions Many reactions have a positive DG°′ Free energy values are additive in a reaction sequence If a net DG°′ is sufficiently negative, forming the product(s) is an exergonic process Section 4.2: Free Energy The Hydrophobic Effect Revisited Understanding the spontaneous aggregation of nonpolar substances is enhanced by understanding thermodynamic principles The aggregation decreases the surface area of their contact with water, increasing its entropy The free energy of the process is negative; therefore, it proceeds spontaneously Spontaneous exclusion of water is important in membrane formation and protein folding Section 4.3: The Role of ATP Figure 4.7 Hydrolysis of ATP Adenosine triphosphate is a nucleotide that plays an extraordinarily important role in living cells Hydrolysis of ATP ADP + Pi provides free energy Section 4.3: The Role of ATP Drives reactions of several types: 1. Biosynthesis of biomolecules 2. Active transport across membranes 3. Mechanical work such as muscle contraction Figure 4.8 The Role of ATP Section 4.3: The Role of ATP Structure of ATP is ideally suited for its role as universal energy currency Its two terminal phosphoryl groups are linked by phosphoanhydride bonds Specific enzymes facilitate ATP hydrolysis Figure 4.9 Structure of ATP Section 4.3: The Role of ATP Figure 4.10 Transfer of Phosphoryl Groups The tendency of ATP to undergo hydrolysis is an example of its phosphoryl group transfer potential ATP acts as energy currency, because it can carry phosphoryl groups from high-energy compounds to low-energy compounds Section 4.3: The Role of ATP Section 4.3: The Role of ATP Figure 4.11 Contributing Structure of the Resonance Hybrid of Phosphate Several factors need to be considered to understand why ATP is so exergonic: 1. At physiological pH, ATP has multiple negative charges 2. Because of resonance stabilization, the products of ATP hydrolysis are more stable than resonance-restricted ATP Resonance is when a molecule has two or more alternative structures that differ only in the position of their electrons 3. Hydrolysis products of ATP are more easily solvated 4. Increase in disorder with more molecules