Chapters 1 and 2 - Chapter 1 : The Foundations of...

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Chapter 1 : The Foundations of Biochemistry * A. Distinguishing features of living organisms a. Highly complex and microscopically organized b. Systems for extracting and transforming energy from the environment c. Functions for each component of the organism and regulated interactions between them d. Mechanisms for sensing and responding to alterations in surroundings e. Capacity for precise self-replication for lots of generations f. Capacity to change over time, gradual evolution B. 1.1 : Cellular Foundations a. Plasma membrane a.i. Defines periphery a.ii. Lipids and proteins a.iii. Cytoplasm —internal volume enclosed by the plasma membrane a.iii.1. Cytosol —aqueous solution making up cytoplasm that is highly concentrated with enzymes and RNA molecules a.iii.1.a. Metabolites —organic molecules that are intermediates in biosynthetic and degradative pathways a.iii.1.b. Proteasomes —degrade proteins that are no longer needed b. What determines cell size? b.i. Lower limit: minimum number of each type of biomolecules required by the cell b.ii. Upper limit: rate of diffusion of solute molecules in aqueous systems c. Three domains of life c.i. Bacteria c.i.1. Aerobic and anaerobic c.ii. Archaea: extreme environments c.iii. Eukarya: all eukaryotics d. Structural hierarchy d.i. Level 4: Cell and organelles d.ii. Level 3: Supramolecular complexes: Chromatin, cell wall (noncovalent) d.iii. Level 2: Macromolecules: DNA, protein, cellulose d.iv. Level 1: Monomeric units: proteins, nucleic acids, polysaccharides (covalent) C. Chemical Functions a. Lightest elements form the strongest bonds b. Biomolecules Are Compounds of Carbon with a Variety of Functional Groups b.i. Tetrahedral b.i.1. Angle: 109.5 b.i.2. Bond length: 0.154 nm (single), 0.134 nm (double) b.ii. Derivatives of hydrocarbons b.ii.1. Hydrogen atoms replaced by functional groups b.ii.2. Alcohols - One or more hydroxyl groups b.ii.3. Amines - Amino groups b.ii.4. Aldehydes and Ketones – Carbonyl groups
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b.ii.5. Carboxylic acids – Carboxyl groups b.iii. Many are polyfunctional —2 or more functional groups c. Cells Contain a Universal Set of Small Molecules c.i. Common AAs, nucleotides, sugars (and phosphorylated derivatives), and mono-, di-, and tricarboxylic acids c.ii. Characteristics c.ii.1. Polar or charged c.ii.2. Water soluble c.ii.3. Present in micromolar to millimolar concentrations c.ii.4. Trapped in cell because membrane is impermeable to them c.iii. Some biomolecules are specific to cells or organisms c.iii.1. Secondary metabolites —play roles specific to vascular plant life c.iii.1.a. Include compounds that give plants their smell c.iii.1.b. Include compounds like morphine, quinine, nicotine, and caffeine c.iii.2. ** “The entire collection of small molecules in a given cell has been called that cell’s metabolome , in parallel with the term “genome.” c.iv. Macromolecules Are the Major Constituents of Cells c.iv.1. Macromolecules —polymers with molecular weights about
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This note was uploaded on 12/10/2011 for the course BCH 5045 taught by Professor Guy during the Fall '08 term at University of Florida.

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Chapters 1 and 2 - Chapter 1 : The Foundations of...

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