Organic Molecules of Living Systems (N=4)

1. Organic Molecules of Living Systems (N=4) • Principles of carbon chemistry • Principle of polymers • Hydrocarbons (book; not responsible) • Organic chemistry in living systems: biochemistry • Carbon metabolism and energy • Minerals and vitamins (book; not responsible)

3. Covalent Bonds and Carbon C C – C – C C C C - C 612C is a unique case Valence electrons for C are 4 (one in each orbit of the 2nd shell) C – C: single covalent bond; share orbit + shared electron C – C – C: two covalent bonds for center carbon atom Covalent bond: energy stores (excited electron)

4. Significance: increases diversity of carbon compounds

5. More Principles of Carbon Chemistry: Functional Groups • Features of C macromolecules • Carbon skeleton (chains, branches, rings) • Groups of atoms attached to carbon skeleton - functionalgroups • Hydroxyl (OH) • Amino (NH2) • Phosphate (PO4) C C – C – OH C C C – C – NH2 C phosphate (what molecule from last week/this week also had phosphate group?)

6. Principle of Polymers • Small molecules joined together to form large molecules up to 1,000’s of carbon atoms (macromolecules) • Array of combinations, each with its own unique chemistry (e.g., polarity, solution chemistry, three dimensional structure, reactivity, passage through membranes, etc.)

7. Simple to Complex Polymers of Carbon Methane - 1 C atom Ethane – 2 C atoms Green atoms = Carbon White atoms = Hydrogen Red atoms = Nitrogen Fullerene – 60+ C atoms (Buckyballs)

8. More Complex Carbon Polymers: Macromolecules nicotine caffeine aspirin

9. Principle of Polymers • Polymers of carbon: four major classes of macromolecules in all cells (N=4) • Carbohydrates • Proteins • Nucleic acids • Lipids • Diversity of carbon polymers: effectively unbounded

10. Question There are millions of organic compounds but only a few thousand inorganic compounds because ____? • Organic compounds are formed by living critters • There is more C on the Earth’s surface than most other elements • Atoms of elements other than C never combine with themselves (e.g., oxygen never combines with another oxygen atom – O2) • C atoms combine with up to four other atoms, notably other C atoms

11. Question The diversity of functional features of carbon macromolecules is a consequence of ___? nitrogen carbon skeleton oxygen functional groups B and D

12. Functionality of Hydrocarbons! • Carbon skeleton • Functional groups (e.g., hydroxyl - OH, amine group – NH2, phosphate or PO4)

13. Organic Chemistry and Biochemistry • Introduction to organic chemistry • Principles of carbon chemistry • Principle of polymers • Organic chemistry in living systems: biochemistry • Carbon metabolism and energy

14. Organic Chemistry and Biochemistry: a Template • Keys: • Structure of basic unit (monomer) • Polymer structure (i.e., macromolecule) • Functional group (e.g., OH, PO4 or NH2) • Four types of carbon polymers -macromolecules - in living systems (N=4) • Carbohydrates • Lipids • Proteins • Nucleic acids

15. Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (e.g., glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate and phosphate (PO4) • Lipids • Monomer: fatty acid + glycerol • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)

16. Biochemistry: Carbohydrates • Keys • Monosaccharide (monomer); Glucose (C6H12O6) • Functional unit: hydroxyl or OH-

17. Monomer Unit: Monosaccharide

18. Polymer: Polysaccharide (Glycogen) Monomer

19. Question Any individual sugar molecule that is a monomer of a carbohydrate macromolecule is generically called ___. A glucose B starch C monosaccharide

20. Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (e.g., glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate and phosphate (PO4) • Lipids • Monomer: fatty acid + glycerol • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)

21. Biochemistry: Proteins Monomer = amino acid Keys Amino acid (monomer) Polypeptide (polymer) Functional unit: amine or NH2 Polypeptide bond serine – lysine – arginine – tryptophan – glutamic acid – etc. Polymer called _____?

22. Amino Acids: The Building Blocks of Proteins • Side group makes each amino acid unique What is distinction between a polypeptide and a protein?

23. Amino Acids • Bonding • Two amino acids • Forms peptide bond • Polypeptide -not functional … yet (I am getting there!) • Chain of amino acids • Protein – functional now! • Large molecule • Chain of amino acids • Only 20 different amino acids in all living organisms

24. Proteins: Linear Sequence of Amino Acids (Monomers) GLY Type of bond? LEU VAL LYS LEU ALA

25. Protein Conformation(1 and 2nd) The “slinky” structure

26. Protein Conformation (3rd & 4rd)

27. Protein Conformation

28. Question Proteins are made up of strings of monomers called ___. A amino acids B monosaccharides C nucleotides D lipids

29. Question How many different amino acids appear in the proteins of all living organisms on Earth? A 10 B 20 C 50 D 200

30. Question The exact sequence of amino acids that goes into a protein is called its __. A primary structure B secondary structure C tertiary structure D quaternary structure

31. Organic Chemistry and Biochemistry • Introduction to organic chemistry • Principles of carbon chemistry • Principle of polymers • Organic chemistry in living systems: biochemistry • Carbon metabolism and energy

32. Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate, and phosphate • Lipids • Monomer: fatty acid + glycerol unit • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)

33. Special Proteins Called Enzymes: How They Work • Base case for reactions to occur • Reactants • Products • Activation energy • Energy analysis (thermodynamics) • Energy to cause reaction to occur (“hill” or activation energy) Without enzyme Enzyme mediated

34. How Enzymes Work • Efficacy of enzymes • “Hill” height/activation energy • Mechanism • Lower the height of the “hill” • Selectivity/specificity • Rate of a reaction • Absence of enzyme: minutes to hours to days to years • Presence of enzyme: 1,000 - 10,000 times per second! • Increase in rate > 106 orders of magnitude (1,000,000)

35. Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate, and phosphate • Lipids • Monomer: fatty acid + glycerol unit • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)

36. Biochemistry: Nucleic Acids Keys Monomer: Nucleotides Functional units (N=3): organic N base, sugar, and phosphate

37. Nucleic Acids as Polymers:DNA Double Helix Monomer: Nucleotide BASES A T C G

38. Nitrogen Base Monomer: Nucleotide

39. Biochemistry Cheat Sheet • Carbohydrates • Monomer: monosaccharide (glucose or C6H12O6) • Polymer: polysaccharide • Functional unit: hydroxyl or OH- • Proteins • Monomer: amino acid (peptide) • Polymer: polypeptide and protein • Functional unit: amine or NH2 • Nucleic Acids • Monomer: nucleotide • Polymer: polynucleotide - DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) • Functional units: organic N base, carbohydrate, and phosphate • Lipids • Monomer: fatty acid + glycerol unit • Polymer: fats, phospholipids and steroids • Functional unit: glycerol (3 OH- groups)

40. Biochemistry: Lipids Keys Monomer: Fatty acids - C16-18 Functional unit: glycerol (3 OH- groups)

41. Special Case: Cell Membranes • Cell membrane • Hydrophobic (phosphate) • Hydrophilic (lipid) • Lipid bilayer = cell membrane

42. Organic Chemistry and Biochemistry • Introduction to organic chemistry • Principles of carbon chemistry • Principle of polymers • Organic chemistry in living systems: biochemistry • Carbon metabolism and energy

43. Carbon Metabolism Biosynthesis (photosynthesis) CO2 + H2O + Energy CH2O + O2 (light) (C - C Bonds/excited electron) Catabolism CH2O + O2 CO2 + H2O + Energy (C - C Bonds/excited electron) (heat + chemical energy) Key: C-C covalent bonding, which in turn is determined by electrons in the valence state, which in turn is underpinned by energy of electrons in their respective shells (remember the granola bar!)

44. Question Hearing is a process that is best categorized as being staccato (absence of sound then bursts of sound …) What bonds are likely to be involved in hearing if sound is best characterized as being staccato? How might those bonds operate in the inner ear and brain, and what element is likely to be involved?