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Section 1

Section 1. Introduction to Biochemical Principles. Chapter 1. Biochemistry: An Introduction. Life: It is a Mystery!. Life: It is a Mystery! Why study biochemistry? Foundation upon which all of the modern life sciences are built Biology can’t be done without biochemistry

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Section 1

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  1. Section 1 Introduction to Biochemical Principles

  2. Chapter 1 Biochemistry: An Introduction

  3. Life: It isa Mystery! • Life: It isa Mystery! • 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 Figure 1.1 Diversity of Life

  4. Section 1.1: What Is Life? • All Life Obeys the Same Chemical and Physical Laws: • Life is complex and dynamic • Life is organized and self-sustaining • Life is cellular • Life is information-based • Life adapts and evolves Figure 1.3 Hierarchical Organization

  5. 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+)

  6. Section 1.2: Biomolecules

  7. 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

  8. 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

  9. Section 1.3: Is the Living Cell a Chemical Factory? • Biochemical Reactions • Nucleophilic substitution • Elimination • Addition • Isomerization • Oxidation-Reduction

  10. 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

  11. 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

  12. Section 1.3: Is the Living Cell a Chemical Factory? Figure 1.22 Anabolism and Catabolism

  13. 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

  14. Section 1.4: Systems Biology • Systems Biology: Living Organisms Regarded asIntegrated Systems • Emergence:Interaction of parts can lead to new properties Figure 1.23 FeedbackMechanisms

  15. Section 1.4: Systems Biology • Robustness:Many biological systems remain stable despite perturbations • Modularity:Complex systems are composed of modules Figure 1.23 FeedbackMechanisms

  16. Chapter 2 Living Cells

  17. 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:

  18. 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

  19. 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

  20. Section 2.1: Basic Themes • Self-Assembly • Many biomolecules spontaneously undergo self-assembly into supermolecular structures • Molecular Machines • Many multisubunit complexes involved in cellular processes function as molecular machines Figure 2.5 Biological Machines

  21. 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%and40% • Signal Transduction • Reception, transduction, and response

  22. 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

  23. Section 2.2: Structure of Prokaryotic Cells Figure 2.8 Bacterial Cell

  24. Section 2.2: Structure of Prokaryotic Cells • Cell Wall • The prokaryotic cell wall is a complex semi-rigid structure primarily for support and protection • The cell wall is primarily composed of peptidoglycan Figure 2.8Bacterial Cell

  25. 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

  26. 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 • Inclusionbodies are large granules that contain organic or inorganic compounds Figure 2.10 Bacterial Cytoplasm

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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

  32. Section 2.3: Structure of Eukaryotic Cells • Two types: • Rough ER functions includeprotein synthesis, folding, and glycosylation • Smooth ER functions include lipid biosynthesis and Ca2+storage Figure 2.15 Endoplasmic Reticulum

  33. 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

  34. 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

  35. 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) • Nuclearmatrix • Nucleolus • Nuclear envelope Figure 2.18 Eukaryotic Nucleus

  36. 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

  37. 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

  38. 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

  39. 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

  40. Section 2.3: Structure of Eukaryotic Cells • Mitochondria • The mitochondria (mitochondrion)are recognized as the site of aerobic metabolism • Mitochondria are the principle source of cellular energy • Have inner and outermembrane surrounding the matrix • Have DNA and ribosomes Figure 2.23 The Mitochondrion

  41. Section 2.3: Structure of Eukaryotic Cells • Peroxisomes • The peroxisome is a small organelle containing oxidative enzymes • Detoxifies peroxides (e.g., H2O2)

  42. Section 2.3: Structure of Eukaryotic Cells • Plastids • Plastids are organelles found only in plants, algae, and some protists • Two types: leucoplasts and chromoplasts • Chloroplasts are chromoplasts specialized for photosynthesis Figure 2.25 Chloroplast

  43. 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 • Intermediatefilaments • Main functions includE cell shape and structure, large- and small-scale cell movement, solid-state biochemistry, and signal transduction

  44. Section 2.3: Structure of Eukaryotic Cells Figure 2.26 The Cytoskeleton

  45. 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

  46. Section 2.3: Structure of Eukaryotic Cells Figure 2.27 Cilia and Flagella

  47. Chapter 3 Water: The Matrix of Life

  48. 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

  49. 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

  50. Section 3.1: Molecular Structure of Water • Larger oxygen atom has partial negative charge (d-) and hydrogen atoms have partial positive charges (d+) Figure 3.4 Water Molecule Figure 3.3 Charges on a Water Molecule

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