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Molecules

Molecules. Chapter 2. Introduction to Biochemistry and Review. Covalent Bonds - SPONCH. Non polar – Equal sharing of the electrons Polar – Unequal sharing of the electrons. Water and Hydrogen Hydrogen Bonds. Water. Water contains polar covalent bonds

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Molecules

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  1. Molecules Chapter 2 Downloaded from www.pharmacy123.blogfa.com

  2. Introduction to Biochemistry and Review Downloaded from www.pharmacy123.blogfa.com

  3. Covalent Bonds - SPONCH • Non polar – Equal sharing of the electrons • Polar – Unequal sharing of the electrons Downloaded from www.pharmacy123.blogfa.com

  4. Water and Hydrogen Hydrogen Bonds Downloaded from www.pharmacy123.blogfa.com

  5. Water • Water contains polar covalent bonds • Oxygen and hydrogen do not share electrons equally • Oxygen exerts a greater pull on the electrons and gains a negative charge • Hydrogen as a result has a positive charge Downloaded from www.pharmacy123.blogfa.com

  6. Dipole • As a result – the water molecule has a positive end the Hydrogens • The oxygen is slightly negative • This forms a dipole – a polar covalent molecule Downloaded from www.pharmacy123.blogfa.com

  7. Hydrogen bonds • One of the most significant consequences of the polar covalent bond is the production of inter molecular bonds with other water molecules Downloaded from www.pharmacy123.blogfa.com

  8. Water as the universal solvent • Water is able to dissolve small non polar covalent molecules, ionic compounds, and other polar covalent molecules • Water soluble molecules are described as hydrophilic • Those molecules that are not soluble in water are hydrophobic Downloaded from www.pharmacy123.blogfa.com

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  10. Properties • Adhesion- water molecules stick to unlike surfaces such as glass or plastic( -) Meniscus • Cohesion – water molecules stick to each other – “ sticky Mickeys” – drop of water • Water exists in three states on Planet earth ( Liquid – aquatic environment outside us and inside us) Downloaded from www.pharmacy123.blogfa.com

  11. More • Specific heat – Water does not change temperature as rapdily as air- high specific heat • Density of water = 1g/ml • Surface tension – • Solutions – universal solvent- • Dissolves – salts( ionic bonds), sugar( non polar covalent), and polar covalent( unequal sharing) Downloaded from www.pharmacy123.blogfa.com

  12. Molecules in water - polar Downloaded from www.pharmacy123.blogfa.com

  13. Yea or Nay • Hydrophilic – water loving • Hydrophobic – water hating or fearing Polar molecule? Downloaded from www.pharmacy123.blogfa.com

  14. Water and hydrogen ions • http://www.biology.arizona.edu/biochemistry/problem_sets/ph/ph.html Downloaded from www.pharmacy123.blogfa.com

  15. Acid and Base • Acids are hydrogen donors or proton donors COOH COO- + H+ • Bases are hydrogen acceptors or proton acceptors NH2 NH3+ Downloaded from www.pharmacy123.blogfa.com

  16. Acids and Bases Downloaded from www.pharmacy123.blogfa.com

  17. pH • pH = The concentration of H+ ions • The negative logarithm of the hydrogen ion concentration in an aqueous solution.  • pH = - log[ H30+] Downloaded from www.pharmacy123.blogfa.com

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  19. pH and measurement-pHydrion paper Downloaded from www.pharmacy123.blogfa.com

  20. pH measurement – pH meter Downloaded from www.pharmacy123.blogfa.com

  21. Carboxylic acids( Organic acids) • The acidic functional group in organic acids is the carboxl group • The carboxyl group is a proton donor • COOH COO- in water solution Downloaded from www.pharmacy123.blogfa.com

  22. Buffering capacity Downloaded from www.pharmacy123.blogfa.com

  23. Organic bases • Proton acceptors – gain a hydrogen and become positively charged in water solution • The amino group - NH2 becomes NH3+ Downloaded from www.pharmacy123.blogfa.com

  24. Amino acids • Contain both an amino group and a carboxyl group • They are amphoteric • “zwitterions” Downloaded from www.pharmacy123.blogfa.com

  25. Amino acids Downloaded from www.pharmacy123.blogfa.com

  26. Amino Acid Structure • Alanine Downloaded from www.pharmacy123.blogfa.com

  27. Amino acids • http://www.johnkyrk.com/aminoacid.html Downloaded from www.pharmacy123.blogfa.com

  28. Formulas • Structural formulas show the atoms and the arrangement of the atoms in the compound • Molecular formulas tell the number of each type of atom in the compound, • C6H12O6 Downloaded from www.pharmacy123.blogfa.com

  29. Structural formula and condensed • Complete Structural Formula • H   H   H|   |   |H - C - C - C - H|   |   |H H-C-H H|H • Condensed Structural Formula CH3CHCH3CH3 orCH(CH3)3 Downloaded from www.pharmacy123.blogfa.com

  30. Isomers • These molecules have the same structural formula but a different arrangement of the atoms Downloaded from www.pharmacy123.blogfa.com

  31. Macromolecules • Proteins • Lipids • Carbohydrates • Nucleic acids Downloaded from www.pharmacy123.blogfa.com

  32.  Structure Summary Page Analyze Classify Help Software Tools File Formats General Information Structural Genomics Browse Database Search Database Download Files Deposit/Validate Data Education & Discussion Structure Explorer Visualize File Summarize 1C1K  Query    >     Explorer Downloaded from www.pharmacy123.blogfa.com

  33. Protein Facts • Proteins: Polymers of Amino Acids • Proteins are polymers of amino acids. They are molecules with diverse structures and functions. • Each different type of protein has a characteristic amino acid composition and order. • Proteins range in size from a few amino acids to thousands of them. • Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids. Downloaded from www.pharmacy123.blogfa.com

  34. Proteins are polymers • Proteins are polymers of amino acids. They are molecules with diverse structures and functions. • Polymers are made up of units called monomers • The monomers in proteins are the 20 amino acids Downloaded from www.pharmacy123.blogfa.com

  35. Proteins: Polymers of Amino Acids • Each different type of protein has a characteristic amino acid composition and order. • Proteins range in size from a few amino acids to thousands of them. • Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids. Downloaded from www.pharmacy123.blogfa.com

  36. Polar side chains Downloaded from www.pharmacy123.blogfa.com

  37. Non Polar Hydrophobic side chains Downloaded from www.pharmacy123.blogfa.com

  38. Electrical charged hydrophilic Downloaded from www.pharmacy123.blogfa.com

  39. Functions of proteins • Hormones – Growth hormone • Receptors – to Receive information so that cell can communicate with other cells • Neurotransmitters – messenger molecules – to send information between neurons • Cytoskeleton – actin, myosin, and collagen – the structure of connective tissue and muscles • Antibodies – Immunoglobulins to fight disease Downloaded from www.pharmacy123.blogfa.com

  40. Function of Proteins - continued • Enzymes – Biological catalysts • Transport of small molecules – Albumin and haptoglobin • Transport of oxygen – hemoglobin and myoglobin • Membrane proteins – to assist in support • Channels in membranes – to allow the passage of molecules or ions • Electron carriers in electron transport in the production of ATP Downloaded from www.pharmacy123.blogfa.com

  41. Functions( continued)i • Clotting proteins • Immune proteins to fight infectious agents • Histones – DNA binding proteins • Toxins to repel or kill other organisms • Bacteriocins – molecules produced by bacteria against bacteria Downloaded from www.pharmacy123.blogfa.com

  42. Biochemical Reactions • Polymerization reaction- condensation and dehydration synthesis – involves the loss of water between two amino acids and the formation of a peptide bond ( OH is lost from the carboxyl group and H is lost from the hydroxyl) requires energy • Hydrolysis – the addition of water causes the peptide bond to break and the amino acids to separate( releases energy) Downloaded from www.pharmacy123.blogfa.com

  43. Polymerization Downloaded from www.pharmacy123.blogfa.com

  44. Hydrolysis Downloaded from www.pharmacy123.blogfa.com

  45. Four levels of Protein Structure • There are four levels of protein structure: primary, secondary, tertiary, and quaternary. • The precise sequence of amino acids is called its primary structure. • The peptide backbone consists of repeating units of atoms: N—C—C—N—C—C. • Enormous numbers of different proteins are possible. Downloaded from www.pharmacy123.blogfa.com

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  49. The causes of Tertiary structure Downloaded from www.pharmacy123.blogfa.com

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