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Biochemistry

Biochemistry. Concept 1: Analyzing and the chemistry of life (Ch 2, 3, 4, 5) Let’s go back a few steps…. The Chemical Context of Life (Ch 2). The three subatomic particles and their significance.

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Biochemistry

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  1. Biochemistry Concept 1: Analyzing and the chemistry of life (Ch 2, 3, 4, 5) Let’s go back a few steps…

  2. The Chemical Context of Life (Ch 2) • The three subatomic particles and their significance. • The types of bonds (covalent: nonpolar and polar, ionic, Hydrogen, Van der Waals interations) how they form, and their relative strengths.

  3. Back to the basics… • All matter is made of particles (air, plants, your pen, you… etc…)

  4. Back to the basics… • All matter is made of particles • A particle could be: • Atoms(made of protons, neutrons, and electrons)

  5. Back to the basics… • All matter is made of particles • A particle could be: • Atoms (made of protons, neutrons, and electrons) • Ions (atoms or groups or atoms that have electrons added or taken away… charged + or -)

  6. Back to the basics… • All matter is made of particles • A particle could be: • Atoms (made of protons, neutrons, and electrons) • Ions (atoms or groups or atoms that have electrons added or taken away… charged + or -) • Molecules (of atoms bonded together covalently)

  7. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • Atoms want ‘full outer shells of electrons’ to be stable

  8. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • Atoms want ‘full outer shells of electrons’ to be stable • The strongest type of bond is an intramolecular (within molecules) bond formed by a shared pair of electrons

  9. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • Atoms want ‘full outer shells of electrons’ to be stable • The strongest type of bond is an intramolecular (between molecules) bond formed by a shared pair of electrons • COVALENT BOND

  10. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • Atoms want ‘full outer shells of electrons’ to be stable • Another way for atoms to stabilize is by transferring electrons from one atom to another, forming ions (charged particles) and the intermolecular attraction between charged particles

  11. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • Atoms want ‘full outer shells of electrons’ to be stable • Another way for atoms to stabilize is by transferring electrons from one atom to another, forming ions (charged particles) and the intermolecular attraction between charged particles • IONIC BOND

  12. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • In some molecules, the shared pair of electrons in covalent bonds are pulled to one side by a strongly positive nucleus • This leaves one end of the molecule slightly negative and the other slightly positive

  13. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • In some molecules, the shared pair of electrons in covalent bonds are pulled to one side by a strongly positive nucleus • This leaves one end of the molecule slightly negative and the other slightly positive • POLAR MOLECULE • Ex: WATER

  14. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • With water, it is SO POLAR that weak intermolecular bonds form between the slightly negative end of one water molecule and the slightly positive end of another water molecule

  15. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • With water, it is SO POLAR that weak intermolecular bonds form between the slightly negative end of one water molecule and the slightly positive end of another water molecule • HYDROGEN BONDS

  16. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • HYDROGEN BONDS • It is the hydrogen bonding between polar water molecules that gives water its special properties

  17. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • HYDROGEN BONDS • It is the hydrogen bonding between polar water molecules that gives water its special properties • Solvent • Temperature regulator • Lubricant • Involvement in chemical reactions

  18. Types of Bonding • What IS ‘bonding’? • It’s all about electrons! • Let’s recap: • COVALENT BONDS: intramolecular, strong • IONIC BONDS: intermolecular • HYDROGEN BONDS: intermolecular, relatively weak

  19. Polar vs Nonpolar

  20. Polar vs Nonpolar • Polar molecules • Do not share their covalent bonds equally and are slightly negative at one end and slightly positive at the other (though neutral overall) • Nonpolar molecules • do not have one end more charged than the other (and neutral overall)

  21. Polar vs Nonpolar • Polar molecules do not mix with nonpolar molecules (ex: water and oil)

  22. Polar vs Nonpolar • Polar molecules do not mix with nonpolar molecules (ex: water and oil) • Polar and ionic substances are known as hydrophilic (water loving) • Nonpolar substances are known as hydrophobic (water fearing)

  23. Polar vs Nonpolar • Hydrophobic and hydrophilic interactions are important: • in the cell membrane phospholipid bilayer

  24. Polar vs Nonpolar • Hydrophobic and hydrophilic interactions are important • In the tertiary structure of proteins

  25. Water and the Fitness of the Environment (Ch 3) • The importance of hydrogen bonds to the properties of water. • Four unique properties of water and how each contributes to life on Earth. • How to interpret the pH scale. • The importance of buffers in biological systems.

  26. Bryson p. 270-272

  27. The importance of hydrogen bonds to the properties of water. • Polar!

  28. Four unique properties of water and how each contributes to life on Earth. • Cohesion • Adhesion • Transpiration • TemperatureRegulator • Ex: sweat • Insulation • By ice • Solvent

  29. Four unique properties of water and how each contributes to life on Earth.

  30. How to interpret the pH scale

  31. The importance of buffers in biological systems.

  32. Carbon and the Molecular Diversity of Life (Ch 4) • The properties of carbon that make it so important.

  33. Carbon – The atom of Life! • What a beautiful thing! • The four electrons in the outer orbital want to form covalent bonds with electrons of other elements

  34. Carbon – The atom of Life! • What a beautiful thing! • Carbon needs 4 covalent bonds to ‘feel satisfied’ (to complete its electron shell)

  35. Carbon – The atom of Life! • What a beautiful thing! • Carbon needs 4 covalent bonds to ‘feel satisfied’ (to complete its electron shell)

  36. Carbon – The atom of Life! • What a beautiful thing! • Instead of drawing the electrons all the time, we draw sticks to represent a shared electron pair (covalent bond)

  37. Carbon – The atom of Life! • What a beautiful thing! • Instead of drawing the electrons all the time, we draw sticks to represent a shared electron pair (covalent bond)

  38. Carbon – The atom of Life! • What a beautiful thing! • The four covalent bonds can be arranged in singles, doubles, or triples

  39. Carbon – The atom of Life! • What a beautiful thing! • The four covalent bonds can be arranged in singles, doubles, or triples

  40. Carbon – The atom of Life! • What a beautiful thing! • Other important atoms: • Carbon (C) : needs 4 bonds • Nitrogen (N): needs 3 bonds • Oxygen (O): needs 2 bonds • Hydrogen (H): needs 1 bond

  41. Carbon – The atom of Life! • What a beautiful thing! • Other important atoms: • Carbon (C) : needs 4 bonds • Nitrogen (N): needs 3 bonds • Oxygen (O): needs 2 bonds • Hydrogen (H): needs 1 bond

  42. Carbon – The atom of Life! • What a beautiful thing! • If arranged in single bonds, the carbon molecule can be straight. • Ex: saturated fatty acid • If arranged in double bonds, the carbon molecule must be bent. • Ex: Unsaturated fatty acid

  43. Carbon – The atom of Life! • What a beautiful thing! • Functional Groups

  44. Carbon – The atom of Life! • What a beautiful thing! • Functional Groups: can you find the alcohol, and carboxylic acids?

  45. Carbon – The atom of Life! • What a beautiful thing! • Reactions: dehydration synthesis and hydrolysis

  46. Carbon and the Molecular Diversity of Life • The properties of carbon that make it so important. • Can form, large, complex, diverse molecules, including isomers! • Various functional groups allow for diverse properties

  47. Next Class: The Structure and Function of Macromolecules To prepare: • Read Holtzclaw p 38-42 • Campbell • Examine at figures from Chapter 5 • Read “Exploring Protein Structure” Pg. 82-83 • Read “Inquiry 5.25” p. 86

  48. The Structure and Function of Macromolecules (Ch 5) • The role of dehydration synthesis in the formation of organic compounds and hydrolysis in the digestion of organic compounds. • How to recognize the four biologically important organic compounds (carbohydrates, lipids, proteins, and nucleic acids) by their structural formulas. • The cellular functions of all four organic compounds. • The four structural levels of proteins and how changes to any level can affect the protein. • How proteins reach their final shape (conformation), the denaturing impact that heat and pH can have on a protein structure, and how these changes may affect the organism.

  49. OK, so now what questions do you have about: • Carbohydrates • Monosaccharides (glucose), disacchariades (maltose), polysaccharides (glycogen, starch, cellulose) • Lipids • Glycerol, fatty acids (unsaturated, saturated), neutral fats, phospholipids, steroids • Proteins • Amino acids, dipeptides, tripeptides, polypeptides, levels of structural organization (primary, secondary, tertiary, quaternary) • Nucleic Acids • Nucleotides, phosphate-sugar-base, deoxyribose, ribose, adenine, thymine, uracil, guanine, cytosine, DNA, RNA, ATP

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