Chapter 3 The Molecules of Cells

1. Chapter 3 The Molecules of Cells

2. Organic Chemistry: Carbon Based Compounds A. Inorganic Compounds: Compounds without carbon. B. Organic Compounds: Compounds synthesized by cells and containing carbon (except for CO and CO2). • Diverse group:Several million organic compounds are known and more are identified every day. • Common: After water, organic compounds are the most common substances in cells. • Over 98% of the dry weight of living cells is made up of organic compounds. • Less than 2% of the dry weight of living cells is made up of inorganic compounds.

3. Carbon: unique element for basic building block of molecules of life • Carbon has 4 valence electrons: Can form four covalent bonds • Can form single , double, triple bonds. • Can form large, complex, branching molecules and rings. • Carbon atoms easily bond toC, N, O, H, P, S. • Huge variety of molecules can be formed based on simple bonding rules of basic chemistry

4. Organic Compounds are Carbon Based Carbon Can Form 4 Covalent Bonds

5. Different Carbon Skeletons of Organic Compounds

6. Diversity of Organic Compounds • Hydrocarbons: • Organic molecules thatcontain C and H only. • Good fuels, but not biologically important. • Undergo combustion (burn in presence of oxygen). • In general they are chemically stable. • Nonpolar: Do not dissolve in water (Hydrophobic). Examples: • (1C) Methane: CH4 (Natural gas). • (2C) Ethane: CH3CH3 • (3C) Propane: CH3CH2CH3 (Gas grills). • (4C) Butane: CH3CH2CH2CH3 (Lighters). • (5C) Pentane: CH3CH2CH2CH2CH3 • (6C) Hexane: CH3CH2CH2CH2CH2CH3 • (7C) Heptane: CH3CH2CH2CH2CH2CH2CH3 • (8C) Octane: CH3CH2CH2CH2CH2CH2CH2CH3

7. Hydrocarbons have C and H only

8. Isomers: Compounds with same chemical formula but different structure (arrangement of atoms) • Isomers have different physical and chemical properties • Structural Isomers: Differ in bonding arrangements Butane (C4H10) Isobutane (C4H10) CH3 | CH3--CH2--CH2--CH3 CH3---CH---CH3 • Number of possible isomers increases with increasing number of carbon atoms.

9. Functional groups play pivotal role in chemical & physical properties of organic molecules Compounds that are made up solely of carbon and hydrogen are not very reactive. Functional groups: • One or more H atoms of the carbon skeleton may be replaced by a functionalgroup. • Groups of atoms that have unique chemical and physical properties. • Usually a part of molecule that is chemically active. • Similar activity from one molecule to another. • Together with size and shape, determine unique bonding and chemical activity of organic molecules.

10. Functional Groups Determine Chemical & Physical Properties of Organic Molecules Four Important Functional Groups: • Hydroxyl (-OH) • Carbonyl (=C=O) • Carboxyl (-COOH) • Amino (-NH2) • Notice that all four functional groups are polar.

11. A. Hydroxyl Group (-OH) • Is a polar group: Polar covalent bond between O and H. • Can form hydrogen bonds with other polar groups. • Generally makes molecule water soluble. Example: • Alcohols:Organic molecules with a simple hydroxyl group: • Methanol (wood alcohol, toxic) • Ethanol (drinking alcohol) • Propanol (rubbing alcohol)

12. B. Carbonyl Group (=CO) • Is a polar group: O can be involved in H-bonding. • Generally makes molecule water soluble. Examples: • Aldehydes:Carbonyl is located at end of molecule • Ketone: Carbonyl is located in middle of molecule Examples: • Sugars (Aldehydes or ketones) • Formaldehyde (Aldehyde) • Acetone (Ketone)

13. Sugars Have Both -OH and =CO Functional Groups

14. C. Carboxyl Group (-COOH) • Is a polar group • Generally makes molecule water soluble • Acidic because it can donate H+ in solution Example: • Carboxylic acids: Organic acids,can increase acidity of a solution: • Acetic acid: Sour taste of vinegar. • Ascorbic acid (Vitamin C): Found in fruits and vegetables. • Amino acids: Building blocks of proteins.

15. D. Amino Group(-NH2) • Is a polar group • Generally makes molecule water soluble • Weak base because N can accept a H+ • Amine -general term given to compound with (-NH2) Example: • Amino acids: Building blocks of proteins.

16. Amino acid Structure: • Central carbon with: • H atom • Carboxyl group • Amino group • Variable R-group Amino Acid Structure: H | (Amino Group)NH2---C---COOH (Carboxyl group) | R (Varies for each amino acid)

17. Amino Acids Have Both -NH2 and -COOH Groups

18. The Macromolecules of Life: Carbohydrates, Proteins, Lipids, and Nucleic Acids

19. I. Most Biological Macromolecules are Polymers • Polymer: Large molecule consisting of many identical or similar “subunits” linked through covalent bonds. • Monomer: “Subunit” or building block of a polymer. • Macromolecule: Large organic polymer. Most macromolecules are constructed from about 70 simple monomers. • Only about 70 monomers are used by all living things on earth to construct a huge variety of molecules • Structural variation of macromoleculesis the basis for the enormous diversity of life on earth.

20. Relatively few monomers are used by cells to make a huge variety of macromolecules Macromolecule Monomers or Subunits 1. Carbohydrates20-30 monosaccharides or simple sugars 2. Proteins 20 amino acids 3. Nucleic acids (DNA/RNA)4 nucleotides (A,G,C,T/U) 4. Lipids (fats and oils) ~ 20 different fatty acids and glycerol.

21. Making and Breaking Polymers • There are two main chemical mechanisms in the production and break down of macromolecules. • Condensation or Dehydration Synthesis • Hydrolysis • In the cell these mechanisms are regulated by enzymes.

22. Making Polymers A. Condensation or Dehydration Synthesis reactions: • Synthetic process in which a monomer is covalently linked to another monomer. • The equivalent of a water molecule is removed. General Reaction: X - OH + HO - Y --------> X - O - Y + H2O Monomer 1 Monomer 2 Dimer Water (Unlinked) (or Polymer) (or Polymer) • Anabolic Reactions: Used by cells to make large molecules from smaller ones. • Require energy (endergonic) • Require catalysis by enzymes

23. Condensation Synthesis: Monomers are Linked and Water is Removed

24. Breaking Polymers B. Hydrolysis Reactions: “Break with water”. • Degradation of polymers into component monomers. • Involves breaking covalent bonds between subunits. • Covalent bonds are broken by adding water. General Reaction: X - O - Y + H2O ----------> X - OH + HO - Y Polymer Water Monomer 1 Monomer 2 (or Dimer) • Catabolic Reactions: Used by cells to break large molecules into smaller ones. • Release energy (exergonic) • Reactions catalyzed by enzymes

25. Hydrolysis: Polymers are Broken Down as Water is Added Hydrolysis

26. Making and Breaking Polymers Examples: Dehydration Synthesis (Condensation): Enzyme Glucose + Fructose ---------> Sucrose + H2O (Monomer) (Monomer) (Dimer) Water Hydrolysis: Enzyme Sucrose + H2O ---------> Glucose + Fructose (Dimer) Water (Monomer) (Monomer)

27. Synthesis and Hydrolysis of Sucrose

28. III. Carbohydrates: Molecules that store energy and are used as building materials • General Formula: (CH2O)n • Simple sugars and their polymers. • Diverse group includes sugars, starches, cellulose. • Biological Functions: • Fuels, energy storage • Structural component (cell walls) • DNA/RNA component • Three types of carbohydrates: A. Monosaccharides B. Disaccharides C. Polysaccharides

29. A. Monosaccharides: “Mono” single & “sacchar” sugar • Preferred source of chemical energy for cells (glucose) • Can be synthesized by plants from light, H2O and CO2. • Store energy in chemical bonds. • Carbon skeletons used to synthesize other molecules. Characteristics: 1. May have 3-8 carbons. -OH on each carbon; one with C=0 2. Names end in -ose. Based on number of carbons: • 5 carbon sugar: pentose • 6 carbon sugar: hexose. 3. Can exist in linear or ring forms 4. Isomers: Many molecules with the same molecular formula, but different atomic arrangement. • Example: Glucose and fructose are both C6H12O6. Fructose is sweeter than glucose.

30. Monosaccharides Can Have 3 to 8 Carbons

31. Linear and Ring Forms of Glucose

32. B. Disaccharides: “Di” double & “sacchar” sugar • Covalent bond formed by condensation reaction between 2 monosaccharides. • Examples: • 1. Maltose: Glucose + Glucose. • Energy storage in seeds. • Used to make beer. • 2. Lactose: Glucose + Galactose. • Found in milk. • Lactose intolerance is common among adults. • May cause gas, cramping, bloating, diarrhea, etc. • 3. Sucrose: Glucose + Fructose. • Most common disaccharide (table sugar). • Found in plant sap.

33. Maltose and Sucrose are Disaccharides

34. C. Polysaccharides: “Poly” many (8 to 1000) Functions: Storage of chemical energy and structure. • Storage polysaccharides: Cells can store simple sugars in polysacharides and hydrolyze them when needed. 1. Starch: Glucose polymer (Helical) • Form of glucose storage in plants (amylose) • Stored in plant cell organelles called plastids 2. Glycogen: Glucose polymer (Branched) • Form of glucose storage in animals (muscle and liver cells)

35. Three Different Polysaccharides of Glucose

36. Structural Polysaccharides: Used as structural components of cells and tissues. 1. Cellulose: Glucose polymer. • The major component of plant cell walls. • CANNOT be digested by animal enzymes. • Only microbes have enzymes to hydrolyze. 2. Chitin: Polymer of an amino sugar (with NH2 group) • Forms exoskeleton of arthropods (insects) • Found in cell walls of some fungi

37. Cellulose: Polysaccharide Found in Plant and Algae Cell Walls

38. Proteins: Large three-dimensional macromolecules responsible for most cellular functions • Polypeptide chains: Polymers of amino acids linked by peptide bonds in a SPECIFIC linear sequence • Protein: Macromolecule composed of one or more polypeptide chains folded into SPECIFIC 3-D conformations

39. Proteins have important and varied functions: • 1. Enzymes: Catalysis of cellular reactions • 2. Structural Proteins: Maintain cell shape • 3. Transport: Transport in cells/bodies (e.g. hemoglobin). Channels and carriers across cell membrane. • 4. Communication: Chemical messengers, hormones, and receptors. • 5. Defensive: Antibodies and other molecules that bind to foreign molecules and help destroy them. • 6. Contractile: Muscular movement. • 7. Storage: Store amino acids for later use (e.g. egg white). • Protein function is dependent upon its 3-D shape.

40. Polypeptide: Polymer of amino acids connected in a specific sequence A. Amino acid: The monomer of polypeptides • Central carbon • H atom • Carboxyl group • Amino group • Variable R-group

41. Protein Function is dependent upon Protein Structure (Conformation) CONFORMATION: The 3-D shape of a protein is determined by its amino acid sequence. Four Levels of Protein Structure 1. Primary structure: Linear amino acid sequence, determined by gene for that protein. 2. Secondary structure: Regular coiling/folding of polypeptide. • Alpha helix or beta sheet. • Caused by H-bonds between amino acids.

42. Primary Structure of Protein: Amino Acid Sequence is Determined by Gene

43. Secondary Structure of Protein: Regular Folding Patterns (Alpha Helix or Pleated Sheet)

44. 3. Tertiary structure: Overall 3-D shape of a polypeptide chain. 4. Quaternary structure: Only in proteins with 2 or more polypeptides. Overall 3-D shape of all chains. • Example: Hemoglobin (2 alpha and 2 beta polypeptides)

45. Tertiary Structure: Overall 3-D Shape of Protein Tertiary Structure of Lysozyme

46. Quaternary Structure: Overall 3-D Shape of Protein with 2 or More Subunits

48. What determines a protein’s shape? A. Primary structure: Exact location of each amino acid along the chain determines the protein’s folding pattern. Example: Sickle Cell Hemoglobin protein • Mutation changes amino acid #6 on the alpha chain. • Defective hemoglobin causes red blood cells to assume sickle shape, which damages tissue and capillaries. • Sickle cell anemia gene is carried in 10% of African Americans.

49. B. Chemical & Physical Environment:Presence of other compounds, pH, temperature, salts. Denaturation:Process which alters native conformation and therefore biological activity of a protein. Several factors can denature proteins: • pH and salts:Disrupt hydrogen, ionic bonds. • Temperature:Can disrupt weak interactions. • Example:Function of an enzyme depends on pH, temperature, and salt concentration.

50. Nucleic acids store and transmit hereditary information for all living things There are two types of nucleic acids in living things: A. Deoxyribonucleic Acid (DNA) • Contains genetic information of all living organisms. • Has segments called geneswhich provide information to make each and every protein in a cell • Double-stranded molecule whichreplicates each time a cell divides. B. Ribonucleic Acid (RNA) • Three main types called mRNA, tRNA, rRNA • RNA molecules are copied from DNA and used to make gene products (proteins). • Usually exists in single-stranded form.