Lecture 3


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Lecture 3

  1. 1. Lecture 3: Biological (Organic) Molecules Covers Chapter 3
  2. 2. Organic Molecules Contain CARBON* • Organic molecules have a carbon skeleton bonded to hydrogen atoms. • The term “organic: is derived from the ability of living organisms to synthesize and use these types of molecules. • Life is created, sustained, and propagated due to the fact that organic molecules can interact in complex ways.
  3. 3. Carbon • Carbon (6) has 6 electrons and 6 protons • 2 electrons in inner shell, 4 in outer shell • Room for 4 more electrons in outer shell to become stable. • Carbon can form single bonds with 4 other molecules, double bonds with 2 other molecules, and even triple bonds.
  4. 4. Carbon bonds • C C H H H H H H e t h a n e ( a n a l k a n e ) C C H H H H e t h e n e ( a n a lk e n e ) C C HH e t h y n e ( a n a l k y n e )
  5. 5. Functional Groups* • Once carbon has formed these molecules, the atoms that attach to the carbon become functional groups of the molecule. Since carbon is so stable, it is the functional groups which are most likely to react chemically with other substances.
  6. 6. Example of Organic Molecule with blue functional groups
  7. 7. Table 3-1 Common Functional Groups and how they interact with other molecules
  8. 8. Organic molecules react with other organic & non-organic molecules • The structure of a molecule as well as the chemical properties of that molecule (which are a result of its structure) determine how it will react with other molecules • Result of this is organic molecules with complex shapes: branched chains, rings, sheets, etc
  9. 9. Example of organic reaction
  10. 10. Molecules can do work!* • In addition, molecules can change structure and chemical properties as a result of interactions with other molecules. • These changes in structure and properties give cells the ability to: – Eliminate waste – Move – Grow – Reproduce – EVOLVE?
  11. 11. Living organisms prefer small molecules • Living organisms prefer to assemble small molecules and hook them together to make large intricate molecules • Ex: trains are made up of individual cars… • Individual subunits of organic molecules are called monomers. • Chains of monomers are called polymers
  12. 12. Monomers join together via DS • Subunits are joined together via a chemical reaction called dehydration synthesis (DS) • A hydrogen atom is removed from one subunit and a hydroxyl ion is removed from the second subunit, and a molecule of water is created, as a by product, while the two monomers become bonded together.
  13. 13. Dehydration Synthesis Fig. 3-1 dehydration synthesis + +
  14. 14. Reverse of DS is hydrolysis • Long subunits sometimes need to break down into small units (ex: the food we eat) • Our bodies like to break down long subunits and use the small pieces • Hydrolysis is the donation of a water molecule to a polymer. H and OH break apart, and are added to the ends of each monomer that is created. • Digestive enzymes use hydrolysis to digest food.
  15. 15. Hydrolysis Fig. 3-2 + hydrolysis
  16. 16. What types of organic molecules exist in living organisms?* • There are 4 types of molecules (monomers)that living organisms use: – Carbohydrates – Lipids – Proteins – Nucleic Acids
  17. 17. Carbohydrates (Sugars) • A molecule with C, H, and O in approximately a 1:2:1 ratio. • Major functions of carbs: – Store energy in cells – Strengthen cell walls in bacteria, fungi and plants – Form protective armor for insects, crabs and other animals.
  18. 18. Monosaccharides: monomers of carbohydrates • Monosaccharides are single units of carbs. They have the ability to join with other monosaccharides to form polysaccharides • Monosaccharides have between 3 and 7 carbon atoms arranged in a “backbone.” • Glucose is the most common monosaccharide. Structure is C6 H12 O6
  19. 19. Monosaccharides Fig. 3-5 galactosefructose 6 5 4 3 2 12 3 4 5 1 6
  20. 20. Non-humans make different monosaccharides – Fructose: monosaccharide made by fruit – Galactose: monosaccharide found in milk
  21. 21. Disaccharides • 2 monosaccharides joined together by dehydration synthesis. • Often used for short term energy storage in plants. • When energy is needed, disaccharide is broken into 2 monosaccharides (via hydrolysis) and each monosaccharide can be broken down to release energy that is stored in chemical bonds • Sucrose, Lactose, maltose are examples
  22. 22. Synthesis of a Disaccharide Fig. 3-7 glucose fructose sucrose dehydration synthesis  
  23. 23. Polysaccharides* • Long chain of monosaccharides, used for energy storage – Starch: made by plants – Glycogen: made by animals (stored in muscle and liver) – Cellulose: made by plants but used as a STRUCTURAL molecule (tree bark) – Chitin:made by bugs and crabs, used as a STRUCTURAL molecule (crunchy body)
  24. 24. Starch is an Energy-Storing Plant Polysaccharide (b) A starch molecule (a) Potato cells (c) Detail of a starch molecule starch grains Fig. 3-8
  25. 25. Fig. 3-9
  26. 26. Lipids* • Diverse group of molecules that contain regions composed almost entirely of carbon and hydrogen • Functions: – Store energy – Waterproof coverings on plant or animal bodies – Primary component of cell membranes – Hormones
  27. 27. Fatty Acids: monomers of Lipids • Molecules containing long chains of C & H with carboxylic functional groups (-COOH) • If chain contains carbon-carbon double bond, the FA is said to be unsaturated. • If no double bonds, it is considered saturated.
  28. 28. Fatty Acid
  29. 29. Lipid Classification* • 3 major groups – 1.) Oils, fats, and waxes – 2.) Phospholipids – 3.) Steroids
  30. 30. 1.) Oils, Fats, Waxes • Also known as triglycerides • Oils and fats are primarily for energy storage • Formed by dehydration synthesis by linking 3 fatty acids to a molecule of glycerol (a three carbon molecule.) • Fats produced by animals, oils produced by plants
  31. 31. glycerol fatty acids triglyceride + + Fig. 3-12
  32. 32. Oils are liquids, Fats are solids • In oils, the carbons of the fatty acids are joined by single bonds, while in fats, the carbons in the fatty acids are joined by double bonds, making them solids at room temp.
  33. 33. An Oil Fig. 3-13b
  34. 34. Fig. 3-13a
  35. 35. 2.) Phospholipids* • Component of cell membranes • Similar to a fatty acid, except one of the three fatty acid tails is replaced by a functional group that contains nitrogen. • Structure is fatty acid tails on one end (insoluble in water) and phosphate-nitrogen head (polar and water soluble)
  36. 36. Phospholipids Fig. 3-14 polar head glycerol backbone phosphate group variable functional group (hydrophilic) (hydrophobic) fatty acid tails
  37. 37. 3.) Steroids* • Composed of 4 rings of carbon atoms, fused together, with multiple functional groups protruding. • Functions: – Regulate metabolism – Regulate immune response – Regulate reproduction
  38. 38. Steroids Fig. 3-15
  39. 39. Proteins* • Diverse group of molecules composed of one or more chains of amino acids. (AA’s)
  40. 40. Functions of Proteins* • Promote chemical reactions: these proteins are called enzymes. • Provide structure to organisms: ex: keratin – principle protein of hair, horns, nails, scales and feathers • Help organisms move: ex: actin/myosin in muscle • Provide defense for an organism: ex: antibodies in our immune system • Provide food for developing animals ex: albumin in egg white-feeds growing chick • Relay signals to other parts of the body: ex: insulin released from pancreas, promotes glucose uptake
  41. 41. Amino Acids: monomers of proteins • Amino acids are molecules that have a common structure: central carbon bonded to three different functional groups – Nitrogen-containing amino group (NH2) – Carboxylic acid group (COOH) – An “R” group that varies among the different amino acids • 20 common amino acids • The “R” group gives the amino acid its distinctive properties: – Some are hydrophobic – Some are hydrophilic
  42. 42. Amino Acid Structure Fig. 3-17 amino group hydrogen variable group carboxylic acid group
  43. 43. glutamic acid (glu) aspartic acid (asp) (a) Hydrophilic functional groups (b) Hydrophobic functional groups (c) Sulfur-containing functional group leucine (leu)phenylalanine (phe) cysteine (cys) Fig. 3-18
  44. 44. How are proteins made? • Amino acids linked together via dehydration synthesis (the NH2 group of one AA is joined to the carbon in the carboxylic group of another AA) • This is called a peptide bond • Proteins can be three to thousands of AA’s long
  45. 45. Protein Synthesis Fig. 3-19 amino acid amino group amino group carboxylic acid group amino acid peptide water peptide bond  + dehydration synthesis
  46. 46. Proteins exhibit up to 4 levels of structure • Primary structure: the sequence of amino acids • Secondary structure: shape of protein: helix, pleated sheet, etc (result of primary structure and caused by hydrogen bonding between the amino acids making up the protein)
  47. 47. Proteins exhibit up to 4 levels of structure • Tertiary structure: folds in the protein caused by interaction of functional groups BETWEEN different AA’s AND the environment the protein is in (if protein normally exists in watery environment, hydrophilic functional groups will “point” outward and hydrophobic groups will “point” inward.)
  48. 48. Proteins exhibit up to 4 levels of structure • Quaternary structure: only happens with some proteins where more than one AA chain exists • Interaction between DIFFERENT AA chains (polypeptides)
  49. 49. Fig. 3-20 (a) Primary structure: The sequence of amino acids linked by peptide bonds (c) Tertiary structure: Folding of the helix results from hydrogen bonds with surrounding water molecules and disulfide bridges between cysteine amino acids (d) Quaternary structure: Individual polypeptides are linked to one another by hydrogen bonds or disulfide bridges (b) Secondary structure: Usually maintained by hydrogen bonds, which shape this helix helix hydrogen bond heme group leu val lys lys gly his ala lys val lys pro
  50. 50. Structure confers function • Ex: Hemoglobin • The type, position and number of AA’s with specific functional groups determine its function • Specific R groups allow heme group to bind oxygen • Polar amino acids on outside of molecule allow it to remain dissolved in watery environment of RBC
  51. 51. Nucleic Acids* • Large organic molecules that are responsible for encoding, transmitting and expressing genetic information EX: DNA/RNA. The sequence of nucleotides in the DNA of living organisms carries hereditary information. DNA is a double-stranded molecule made up of 2 nucleotide strands. RNA is single stranded.
  52. 52. Nucleotides: monomers of nucleic acids* • A nucleotide has a basic 3-part structure: – 5 carbon sugar – Phosphate functional group – Nitrogen-containing base (5 different bases exist) • Nucleotides fall into 2 categories, depending on which sugar is present – Deoxyribose – Ribose
  53. 53. Nucleotide •
  54. 54. The Energy-Carrier Molecule Adenosine Triphosphate (ATP) is also a nucleotide (3 phosphate groups instead of one) Fig. 3-23