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Essentials of Biochemistry Chemistry 360 Thomas J. Wiese, Ph.D. Assistant Professor of Chemistry Fort Hays State University
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Agenda Roll Call Questionnaire Syllabus
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Definition of Biochemistry “Chemistry of Life” Living Things are composed of lifeless molecules Doesn’t fully take into account what chemistry is Biochemistry- Study of the structure, properties and changes of biomatter
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1. Complex and highly ordered 2. Everything has a function 3. Living things transform their environment (extract energy) 4. Self-replicating 5. Reactions occur at constant temperature, pressure and pH; in an aqueous environment Special Considerations
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Biomolecules - Elements C, H, O, N99% of mass of most cells P, S Mg 2+, Na +, K +, Ca 2+, Cl - Fe, Zn, Mn, Co, Cu
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Biomolecules - Macromolecules 1. Carbohydrates- made up mostly of 7 monosaccharides 2. Proteins - 5 10 6, made up of 20 amino acids 3. Nucleic Acids - 1,000, made up of 4 nucleotides 4. Lipids
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70% of most organisms polar –favors solubility –directionality holds macromolecules in given conformations Water
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hydrogen bond –half-life < 1/1,000,000 sec –holds water together without being viscous high specific heat colligative properties weakly ionizable Water
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Cell Structure
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Cell Membrane Appears as 3 layers by EM 7.5-10 nm thick “Unit membrane” These three things are explained on a molecular level as a phospholipid bilayer Function: osmotic barrier Present in all cells Further consideration in lipid material.
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Nucleus Bounded by a porous nuclear membrane Function: contain DNA Present in all eukaryotic cells 1 per cell Often 1-4 nucleoli
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Cell Wall No picture thick, tough wall Function: rigidity Present in plant and prokaryotic cells
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Mitochondria Shape varies, size varies 500-2,000 per cell
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Mitochondria Function: “powerhouse of the cell” Present in all eukaryotic cells Structure: compartments Further consideration in metabolism.
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Endoplasmic Reticulum Rough and Smooth Phospholipid bilayer surrounding a lumen ± ribosomes Function: protein synthesis (rough) lipid synthesis (smooth) Present in all eukaryotic cells (lots)
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Rough Endoplasmic Reticulum Surface looks rough because of the presence of ribosomes, another organelle (present in all cells)
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Golgi Apparatus Historically cis, medial and trans: trans-golgi network Function: protein processing and secretion Present in all eukaryotic cells (lots)
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Lysosomes About as big as a mitochondrion not much to see Function: degradation of proteins Present in animal cells, plant cells have similar organelle called peroxisome Number per cell varies enormously
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Chloroplasts Stacks of “grana” grana composed of thylakoid disks Function: photosynthesis Present in photosynthetic cells 50-200 per cell
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Cytoplasm Aqueous, solute-containing contents within the plasma membrane Contains soluble proteins, salts, organelles Cytosol- is the supernate of a centrifugation process
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Microtubules Polymer of a protein called actin Gives shape to cell, also functions in transport around the cell
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pH and Buffers
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Water is Weakly Ionizable 2 H 2 O OH – + H 3 O + Weakly means this doesn’t happen often [OH – ] = [H 3 O + ] = 1 10 -7 M, [OH – ] [H 3 O + ] = 1 10 -14, the basis of the pH scale
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Equilibrium Constants Mathematically Represent Degree of Dissociation Keq’ is used in biochemistry to denote modified standard state.
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pKa’ Values are Used to Describe Ionization of Acids CH 3 COOH + H 2 O CH 3 COO – + H 3 O + Keq’ = Ka’ = 1.74 x 10 -5 = pKa’ = 4.76
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Graphical Determination of pKa’ The pKa’ is the pH at the point where buffering occurs
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Buffers Buffer- a compound that does not allow the pH to change even if acid or base is added to the system. Amphiprotic compounds are also good buffers. Amphiprotic compound- a compound that can act as a proton donor or as a proton acceptor.
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[HA] [A – ] pH = pKa’ + log [acid] [salt] or pH = pKa’ + log The Henderson-Hasselbalch Equation is Used to Determine the pH of Buffered Solutions
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When pH = pKa’, There is Equal Amounts of A – and HA Proof on board
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pH Problems What will the pH of a solution be if 0.1 mL of 6 M HCl is added to 100. mL of H 2 O? What will the pH of a solution be if 0.1 mL of 6 M HCl is added to 100. mL of 1 M HEPES initially at pH 7.6? What will the pH of a solution be if 0.1 mL of 6 M HCl is added to 100. mL of 50 mM HEPES initially at pH 7.6?
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Choosing a Buffer pKa ± 0.5 pH units ionic strength: use 50 or 100 mM metal ion chelation, etc.
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