1. Chapter 5 The Structure and Function of Large Biological Molecules

2. A. Introduction  Atoms ---> molecules ---  compound  large molecules composed of smaller molecules called macromolecules  complex in their structures  most are polymers, built from monomers  “The whole is greater than the sum of its parts” is a phenomenon referred to as “emergent properties.”  a property that a collection or complex system has but which the individual members do not possess

3.  Four classes of life’s organic molecules are polymers  Carbohydrates – CHO  Lipids - CHO  Proteins - CHON  Nucleic acids - CHONPS

4. Monomers Make Up Polymers LIPIDS Fatty acids 9 cal/g PROTEIN Amino acids 4 cal/g CARB Mono- saccharide 4 cal/g NUCLEIC ACID Nucleotide 0 cal/g

5.  Monomers form larger molecules by condensation reactions called dehydration synthesis H2OH2O HO H HH enzyme Dehydration synthesis

6.  Polymers can disassemble by hydrolysis H2OH2O HOH H H enzyme Hydrolysis

7.  All organisms share 4 monomer types, but each organism is unique based on arrangement of monomers into polymers  immense variety of polymers can be built from a small set of monomers

8. B. CARBOHYDRATES  Monomer is monosaccharide or simple sugar  Many functions:  Immediate energy  raw materials  energy storage  structural compounds  Examples  glucose, starch, cellulose, glycogen glycosidic bond

10.  Carbohydrates have formula C 1 H 2 O 1, usually end in suffix “-ose”  Monosaccharide = 1 sugar (C 6 H 12 O 6 or glucose)  Disaccharide = 2 sugars (C 12 H 22 O 11 or sucrose)  Joined by covalent bond through glycosidic linkage  Polysccharide = 3 or more

12.  Monosaccharides may be linear or form rings  Classified by number of carbons  6Cs = hexose (ex: glucose)  5Cs = pentose (ex: ribose)  3Cs = triose (ex: glyceraldehyde) OH H H HO CH 2 OH H H H OH O Glucose H OH HO O H H H Ribose CH 2 OH Glyceraldehyde H H H H OH O C C C

13. 1' 2' 3' 4' 5' 6' C C C C C C O  Carbons numbered after positions using (‘) prime symbol  Energy stored in C-C bonds

14.  Polysaccharides made of 100s to 1000s of monosaccharides joined by glycosidic bonds serve different purposes:  Storage  Ex: starch in plants; glycogen in animals  Main starches in corn/maize, wheat, rice, potatoes  Liver converts glucose  glycogen for cell use  Structural  Ex: cellulose in plants; chitin in animals/fungi  Cellulose is insoluble fiber making cell wall of plants  Chitin is exoskeleton of arthropods and walls in fungi

15. Glucose ($1) Glycogen ($60,000) blood liver glycogenesis Fats/protein (£100) gluconeogenesis Neo new Lyse break apart Genesis creation

16. Blood Sugar Regulation

19. o isomers of glucose o structure determines function… in starchin cellulose

20. C. LIPIDS  Lipids are a diverse group of hydrophobic molecules  Only macromolecules that do not consist of polymers  big molecules made of smaller subunits, not a continuing chain  Function is to 1.Store energy - 9 cal/g concentrated in H-C bonds 2.Protect/cushion organs 3.Insulate body

21.  Eight categories of lipids but will focus on three: 1.fats 2.phospholipids 3.steroids

22. 1. fats  constructed from two types of smaller molecules, a single glycerol (3-C alcohol) and usually three fatty acid chains  fatty acid = long HC “tail” with carboxyl (COOH) group “head”

23. Dehydration synthesis! dehydration synthesis enzyme H2OH2O

24.  Two types of fatty acids  1. Saturated  Have the maximum number of hydrogen atoms possible  Have no double bonds  Solid at room temperatures (a) Saturated fat and fatty acid Stearic acid Figure 5.12

25.  2. Unsaturated  Have one or more double bonds  Liquid at room temperature  One = mono  Two+ = poly (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid Figure 5.12

26. Animal fats Butter Cheese Red meats Saturated fat Plant fats Almonds Fish Olive Unsaturated fat

27. 2. Phospholipids  Constructed from glycerol and two fatty acids  Have a phosphate group (PO 4 ) instead of a third fatty acid  PO 4 is negatively charged

28.  Heads are hydrophilic  Tails are hydrophobic  can self-assemble into bubbles called micelles  also form a phospholipid bilayer making up cell membranes  early evolutionary stage of cell? bilayer water

29. Phospholipid Bilayer (Membrane)

30. 3. Steroids  lipids characterized by carbon skeleton consisting of four fused rings  different steroids created by attaching different functional groups to rings  different structure creates different function  Two main types: cholesterol, sex hormones  Cholesterol: precursor to many hormones, vitamin D, build cell membranes (with phospholipids)  Sex hormones: regulate physiology & behavior, bring about secondary sex characteristics

31. Cholesterol Sex hormones Vitamin D

32.  What a difference a few atoms make!

33. D. PROTEINS  Most structurally & functionally diverse group resulting in a wide range of functions  Function: involved in almost everything (see chart)  Proteins are made of monomers called amino acids  Proteins do most of the work in cells and also act as enzymes

34. Protein Functions

35.  Proteins are a polymer called polypeptide made of chains of amino acid monomers  20 different amino acids  protein is one or more polypeptide chains folded & bound together by peptide bonds  Forms large & complex molecules  complex 3-D shape Rubisco hemoglobin growth hormones

36.  Structure of amino acids:  central carbon  amino group  carboxyl group (acid)  R group (side chain)  variable group  different for each amino acid  confers unique chemical properties to each amino acid  like 20 different letters of an alphabet  can make many words (proteins) H H C—OH || O R | —C— | H N

38. 38 Four Levels of Protein Structure  Primary (1°) structure  unique sequence of amino acids in a polypeptide Figure 5.20 – Amino acid subunits + H 3 N Amino end o Carboxyl end o c Gly ProThr Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Val Arg Gly Ser Pro Ala Gly lle Ser Pro Phe His Glu His Ala Glu Val Phe Thr Ala Asn Asp Ser Gly Pro Arg Tyr Thr lle Ala Leu Ser Pro Tyr Ser Tyr Ser Thr Ala Val Thr Asn Pro Lys Glu Thr Lys Ser Tyr Trp Lys Ala Leu Glu Lle Asp

39. 39 O C  helix  pleated sheet Amino acid subunits N C H C O C N H C O H R C N H C O H C R N H H R C O R C H N H C O H N C O R C H N H H C R C O C O C N H H R C C O N H H C R C O N H R C H C O N H H C R C O N H R C H C O N H H C R C O N H H C R N H O O C N C R C H O C H R N H O C R C H N H O C H C R N H C C N R H O C H C R N H O C R C H H C R N H C O C N H R C H C O N H C  Secondary (2°) structure  folding or coiling of polypeptide into a repeating configuration  Includes  helix and  pleated sheet H H Figure 5.20

40. 40  Tertiary (3°) structure  overall three-dimensional shape of a polypeptide  Results from interactions between amino acids and R groups CH 2 CH OHOH O C HO CH 2 NH 3 + C -O-O CH 2 O SS CH CH 3 H3CH3C H3CH3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond CH 2 Disulfide bridge

41. 41 Polypeptide chain Collagen  Chains  Chains Hemoglobin Iron Heme  Quaternary (4°) structure  overall protein structure results from aggregation of two or more polypeptide subunits

42. Protein Function Depends on Structure amino acid sequence peptide Z 1° determined by DNA R groups H bonds R groups hydrophobic interactions disulfide bridges (H & ionic bonds) multiple polypeptides hydrophobic interactions 4° 2° 3°

43.  Sulfur-containing amino acids methionine & cysteine form disulfide (S-S) bridges  covalent cross links between sulfhydryls  stabilizes 3-D structure  Concentrated in eggs (sulfur smell), curly hair (kinks)

44.  Chaperonins are protein molecules that assist in the proper folding of other proteins Hollow cylinder Cap Chaperonin (fully assembled) Steps of Chaperonin Action: An unfolded poly- peptide enters the cylinder from one end. The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. Correctly folded protein Polypeptide 2 1 3

45.  X-ray crystallography is used to determine a protein’s three-dimensional structure

46. Building Proteins  Dehydration synthesis occurs directionally in polypeptide chains  N-terminus = NH 2 end  C-terminus = COOH end  repeated sequence (N- C-C) is the polypeptide backbone  can only grow in one direction

47.  Unfolding a protein alters its 2°, 3° or 4° shape thereby altering (or destroying) its function  conditions that disrupt H bonds, ionic bonds, disulfide bridges will alter shape  temperature  pH  salinity  Rarely can proteins can return to their functional shape after denaturation Denaturing (Breaking) Proteins

48. Paperclip Demo 1.Examine the folds of your paperclip. 2.Use it to clip 2 pieces of paper together. Notice the folds determine the function. 3.Denature your paperclip. Make it as straight as you can. Notice the function is lost. 4.Attempt to refold your paperclip. See if you can clip the same 2 pieces of paper together.

49. Enzymes – Specialized Proteins  Type of protein that acts as a catalyst, speeding up chemical reactions  Does not get used up in process – can catalyze multiple reactions before degrading  Many enzymes help digestion of macromolecules!

50.  acts on chemical called substrate which binds to enzyme, causing chemical reaction to take place but cleaving substrate  involved in almost all metabolic processes

52.  Only ONE enzyme attaches to ONE specific substrate to power the reaction – just like a lock, it never gets destroyed.

53. An Error In Folding Proteins Causes Disease  Sickle-cell anemia results from a single amino acid substitution in the protein hemoglobin  Natural circular shape can carry 4 O 2 molecules  Mutated hemoglobin is a straight structure

54. E. Nucleic Acids  Nucleic acids store and transmit hereditary information  Genes are the units of inheritance  Program the amino acid sequence of polypeptides  Are made of nucleotide sequences on DNA  There are two types of nucleic acids  Deoxyribonucleic acid (DNA)  Ribonucleic acid (RNA)

55.  Nucleic acids exist as polymers called polynucleotides  Each of monomers called nucleotides  1 nucleotide = Sugar + phosphate + nitrogen base

56.  DNA stores information for the synthesis of specific proteins  Found in nucleus of cells  Functions  Directs RNA synthesis (transcription)  Directs protein synthesis through RNA (translation) 1 2 3 Synthesis of mRNA in the nucleus Movement of mRNA into cytoplasm via nuclear pore Synthesis of protein NUCLEUS CYTOPLASM DNA mRNA Ribosome Amino acids Polypeptide mRNA

57.  nucleotides linked by the–OH group on the 3´ carbon of one nucleotide and the phosphate on the 5´ carbon on the next

58.  Nitrogen bases vary; four types in DNA, four types in RNA  DNA  Cytosine  THYMINE  Guanine  Adenine  RNA  cytosine  URACIL  Guanine  adenine purines pyrimidines

59.  DNA is structured as a double helix ; RNA is found as a single strand  H bonds between bases  DNA is found in the nucleus; RNA is synthesized in the nucleus but travels outside it (into the cytoplasm)