Section 1 Introduction to Biochemical Principles

Chapter 1 Biochemistry: An Introduction

Life: It is a Mystery!  Why study biochemistry?  Foundation of the modern life sciences  At a certain level, biology can only be understood based on the underlying chemical reactions  Our thoughts and emotions are influenced by chemical reactions  Helps us understand the diversity and resiliency of life Figure 1.1 Diversity of Life

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  E.g., DNA as a blueprint, sequence similarities between different organisms  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  C, H, O, and N are the most prominent elements in organic compounds  Biomolecules share similar properties with organic compounds; functional groups work the same way  Trace elements are also important (i.e., Na +, K +, Mg 2+, and Ca 2+ )

Section 1.2: Biomolecules

 Major Classes of Small Biomolecules  Many organic molecules are relatively small (less than 1000 Daltons (Da = 1 amu))  Families of small molecules: amino acids, sugars, fatty acids, and nucleotides Section 1.2: Biomolecules

Organic compounds with amino and carboxylate functional groups Each AA has unique side chain (R) attached to alpha (α) carbon Crystalline solids with high MP’s, water soluble Exist as dipolar, charged zwitterions (ionic form) Exist as either L- or D- enantiomers Almost without exception, biological organisms use only the L enantiomer Section 1.2: Biomolecules Amino Acids

Amino Acids

Monosaccharides: D- aldoses Seager SL, Slabaugh MR, Chemistry for Today: General, Organic and Biochemistry, 7 th Edition, 2011 Chiral C’s? stereoisomers

Glucose (Blood Sugar)  Primary source of energy in cells  Precursor for Vitamin C synthesis  Modified subunits can form long polymer chains  starch, cellulose, glycogen  Beta-hydroxy group: OH attached to anomeric carbon above ring.  Alpha-hydroxy group: OH attached to anomeric carbon below ring. Hemiacetal (on C1) 64% 0.02% 36%

Lipids Waxy, greasy or oily compounds; insoluble in water. Biological Functions:  Energy Storage  Structural component of cell membranes  Signaling molecules

Nucleotides

 The properties of even the simplest cells are remarkable  Autopoiesis describes a system capable of reproducing and maintaining itself (e.g., the properties of living organisms).  Metabolism: Enzyme-catalyzed cellular chemical reactions that allow organisms to grow and reproduce.  Metabolism describes:  The acquisition and utilization of energy  Synthesis of molecules needed for cell structure and function  Growth and development of organism  Removal of waste products Section 1.3: Is the Living Cell a Chemical Factory?

 Summary of Biochemical Reactions  Nucleophilic substitution  Elimination  Addition  Isomerization  Oxidation-Reduction Section 1.3: Is the Living Cell a Chemical Factory? These are all reactions that you have encountered in general chemistry and organic chemistry.

Reactions Nucleophilic Substitution Elimination Addition

Reactions Isomerization (via hemiacetal) Redox (cellular respiration)

 Energy  Energy is defined as the capacity to do work  Cells generate most of their energy via 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: Transform solar or chemical energy into chemical bond energy  Heterotrophs: Degrade food to produce energy 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 Section 1.3: Is the Living Cell a Chemical Factory?

Catabolic pathways convert nutrients into small molecules, producing waste products and energy. Small molecules are then synthesized into more complex molecules during anabolic processes.

 Biological Order  The coherent unity that is observed in all organisms involving integration of millions of molecules.  Four major classifications of the processes that contribute to this order: 1.Synthesis of biomolecules: ATP driven rxns to produce biomolecules for assembly into proteins and lipids, or nucleic acids, or for catalysis. 2.Transport across membranes: Processes that regulate the movement of ions or molecules between cell compartments, or in or out of the cell. 3.Cell movement: Processes that control the movement of cells or cellular components. 4.Waste removal: Processes that eliminate reaction byproducts that may be toxic to the organism (e.g., conversion of carbon dioxide to bicarbonate for transport, followed by exhalation through the respiratory system) Section 1.3: Is the Living Cell a Chemical Factory?

Reductionism vs. Systems Biology Much of our knowledge of biological systems was learned by reducing the scope of our inquiry to individual processes. In this reductionist approach, we may observe a single biochemical process to understand it, but not necessarily understand how this process relates to other processes. Conversely, Systems Biology is a more comprehensive effort to understand how these processes are integrated and affect each other. There are 2 core principles that help us describe and understand the complex biochemical processes of Systems Biology Emergence: Describes properties that manifest only as a result of the interactions between different processes. Robustness: Describes the ability of a biological system to maintain stability despite perturbations (e.g., codon degeneracy that reduces the incidence of DNA mutation).