Chapter 1 The Foundations of Biochemistry Biochemistry asks how the properties of life arise from the thousands of different biomolecules Biochemistry also shows how the collections of inanimate molecules that make up living organisms interact to maintain life animated solely by the physical and chemical laws that govern the nonliving universe Distinguishing properties of living organisms o A high degree of chemical complexity and microscopic organization o Systems for extracting transforming and using energy from the environment to do mechanical chemical osmotic and electrical work o Defined functions for each of an organism s components and regulated interactions among them o Mechanisms for sensing and responding to alterations in their surroundings by adapting their internal chemistry o A capacity for precise self replication and self assembly o A capacity to change over time by gradual evolution 1 1 Cellular Foundations Plasma membrane the surroundings barrier Cells Are the Structural and Functional units of All Living Organisms the periphery of the cell separating its contents from o Composed of lipid and protein molecules that form a hydrophobic o The membrane is a barrier to the free passage of inorganic ions and most other charged or polar compounds o Transport proteins allow passage of certain ions and molecules o Receptor proteins transmit signals into the cell o Membrane enzymes participate in some reaction pathways the internal volume enclosed by the plasma membrane which is Cytoplasm composed of an aqueous solution cytosol and a variety of suspended particles In the cytosol o Enzymes and the RNA molecules that encode them o Amino acids and nucleotides to build macromolecules o Metabolites intermediates in biosynthetic and degradative pathways compounds essential to many enzyme catalyzed found in the cytosol reactions found in the cytosol o Coenzymes o Inorganic ions o Ribosomes o Proteasomes the sites of protein synthesis degrade proteins that are no longer needed by the cell All cells have for at least a part of their life o Either a nucleus or a nucleoid in which the genome the complete set of genes is stored and replicated o Eukaryotes have membrane bound nuclei while prokaryotes have a Cellular Dimensions Are Limited by Diffusion The upper limit of the size of a cell is limited by the rate of diffusion of solute molecules in aqueous systems o Want a large surface to volume ratio so cytoplasm is more easily nucleoid accessed There Are Three Distinct Domains of Life Bacteria Archaea inhabit extreme environments such as salt lakes hot springs highly inhabit soils surface waters and the tissues of other living or decaying organisms acidic bogs and the ocean depths Eukaryotes are more closely related to Archaea In aerobic habitats some organisms derive energy from the transfer of electrons from fuel molecules to oxygen In anaerobic environments microorganisms adapt by obtaining energy by transferring electrons to nitrate forming N2 sulfate forming H2S or CO2 forming CH4 Phototrophs Chemotrophs trap and use sunlight derive their energy from oxidation of a chemical fuel o Some the lithotrophs oxidize inorganic fuels Organotrophs oxidize a wide array of organic compounds Phototrophs and chemotrophs can also be divided into two categories o Autotrophs o Heterotrophs organisms that can obtain all needed carbon from CO2 organisms that require organic nutrients Escherichia coli Is the Most Studied Bacterium The plasma membrane and the layers outside it constitute the cell envelope The cytoplasm contains one or more circular segments of DNA called plasmids environment o Sometimes confer resistance to toxins and antibiotics in the Eukaryotic Cells Have a Variety of Membranous Organelles Which Can Be Isolated for Study Eukaryotes have a nucleus and a variety of membrane bound organelles unlike prokaryotes o Mitochondria o Endoplasmic reticulum o Golgi complexes o Peroxisomes o Lysosomes o Plant cells also have vacuoles and chloroplasts In cell fractionation cells or tissues in solution are disrupted by physical shear leaving most organelles intact Isopycnic centrifugation is when organelles of different buoyant densities are separated by centrifugation through a column of solvent with graded density The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic The cytoskeleton is a crisscrossing network of protein filaments in a eukaryotic cell and is made up of three different types of filaments o All types provide structure organization and shape o Actin filaments and microtubules also help produce the motion of organelles or the whole cell and endocytosis movement out of and into cells respectively Exocytosis involve membrane fusion and fission and provide paths between the cytoplasm and the surrounding medium Cells Build Supramolecular Structures The monomeric subunits of proteins nucleic acids and polysaccharides are joined by covalent bonds but macromolecules are held together by noncovalent interactions hydrogen bonds ionic interactions and van der Waals interactions In Vitro Studies May Overlook Important Interactions among Molecules In vitro study is much different than in vivo study because the enzymes in vivo can be affected by many other proteins influencing its activity 1 2 Chemical Foundations In general the lightest elements form the strongest bonds Biomolecules Are Compounds of Carbon with a Variety of Functional Groups No other chemical element can form molecules of such widely different sizes shapes and compositions than carbon Cells Contain a Universal Set of Small Molecules Thousands of different small organic molecules central metabolites in the major pathways in almost all cells are dissolved in the cytosol o Amino acids o Nucleotides o Sugars and their phosphorylated derivatives o Mono di and tricarboxylic acids Vascular plant cells also contain secondary metabolites which play roles specific to plant life Metabolome the entire collection of small molecules in a given cell Macromolecules Are the Major Constituents of Cells Macromolecules assembled from relatively simple precursors polymers with molecular weights above 5 000 that are o Proteins o Nucleic acids o Polysaccharides shorter polymers Oligomers Proteins water of a cell o Catalytic activity functioning as enzymes o Structure elements o Signal receptors o Transporters polymers of amino acids constitute the largest fraction besides A sum of all the proteins functioning in a cell is called a