Ch. 2 continued. Biological Molecules. 4 Classes of ORGANIC MACROMOLECULES

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2 Ch. 2 continued. Biological Molecules 4 Classes of ORGANIC MACROMOLECULES

3 Carbon: The Backbone of Life Living organisms consist mostly of carbon-based compounds (ORGANIC) Organic chemistry- study of compounds containing carbon, bonded to H and O (CHO) 2011 Pearson Education, Inc.

4 WHY Carbon??? With 4 valence electrons, C forms 4 covalent bonds with a variety of atoms (wants 8!) ability makes large, complex molecules 2011 Pearson Education, Inc.

5 Carbon Atom = protons - Positively charged = electrons - electrons - travel in regions outside the nucleus called orbitals = neutrons - No charge = Nucleus center of an atom. Home to protons and neutrons.

6 Figure 4.5 (a) Length (c) Double bond position Ethane Propane 1-Butene 2-Butene (b) Branching (d) Presence of rings Butane 2-Methylpropane (isobutane) Cyclohexane Benzene

7 Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Lipid (fats)- have long hydrocarbon chains Hydrocarbon chains = many bonds = release a large amount of energy when broken apart 2011 Pearson Education, Inc.

8 Figure 4.6 Nucleus Fat droplets 10 m (a) Part of a human adipose cell (b) A fat molecule

9 Chemical Functional Groups Functional groups parts of organic molecules that are most commonly involved in chemical reactions The number and arrangement of functional groups = unique properties of molecule 2011 Pearson Education, Inc.

10 Figure 4.UN02 Estradiol Testosterone

11 The 7 functional groups most important in the chemistry of life: 1. Hydroxyl group 2. Carbonyl group 3. Carboxyl group 4. Amino group 5. Sulfhydryl group 6. Phosphate group 7. Methyl group *NEED TO MEMORIZE WHAT IT LOOKS LIKE, WHERE TO FIND IT (macromolecule), and HOW IT WILL INTERACT (particularly with H2O) 2011 Pearson Education, Inc.

12 Figure 4.9-a CHEMICAL GROUP Hydroxyl Carbonyl Carboxyl STRUCTURE (may be written HO ) NAME OF COMPOUND Alcohols (Their specific names usually end in -ol.) Ketones if the carbonyl group is within a carbon skeleton Carboxylic acids, or organic acids Aldehydes if the carbonyl group is at the end of the carbon skeleton EXAMPLE Ethanol Acetone Acetic acid Propanal FUNCTIONAL PROPERTIES Is polar as a result of the electrons spending more time near the electronegative oxygen atom. Can form hydrogen bonds with water molecules, helping dissolve organic compounds such as sugars. A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal. Ketone and aldehyde groups are also found in sugars, giving rise to two major groups of sugars: ketoses (containing ketone groups) and aldoses (containing aldehyde groups). Acts as an acid; can donate an H + because the covalent bond between oxygen and hydrogen is so polar: Nonionized Ionized Found in cells in the ionized form with a charge of 1 and called a carboxylate ion.

13 Figure 4.9-b Amino Sulfhydryl Phosphate Methyl (may be written HS ) Amines Thiols Organic phosphates Methylated compounds Glycine Cysteine Glycerol phosphate 5-Methyl cytidine Acts as a base; can pick up an H + from the surrounding solution (water, in living organisms): Nonionized Found in cells in the ionized form with a charge of 1+. Ionized Two sulfhydryl groups can react, forming a covalent bond. This cross-linking helps stabilize protein structure. Cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be permanently curled by shaping it around curlers and then breaking and re-forming the cross-linking bonds. Contributes negative charge to the molecule of which it is a part (2 when at the end of a molecule, as above; 1 when located internally in a chain of phosphates). Molecules containing phosphate groups have the potential to react with water, releasing energy. Addition of a methyl group to DNA, or to molecules bound to DNA, affects the expression of genes. Arrangement of methyl groups in male and female sex hormones affects their shape and function.

14 Figure 4. UN04 Adenosine What is this structure?? What does it do for cells?

15 Figure 4. UN05 Adenosine Reacts with H 2 O Adenosine Energy ATP Inorganic phosphate ADP

16 Is this molecule soluble in water? A.yes B.no

17 Is this molecule soluble in water? A.yes B.no

18 The general structure of amino acids are shown in this figure. What functional groups are highlighted in salmon and yellow, respectively? a) Amino and carboxyl b) Amino and carbonyl c) Hydroxyl and carbonyl d) Methyl and carboxyl e) Methyl and hydroxyl

19 The general structure of amino acids are shown in this figure. What functional groups are highlighted in salmon and yellow, respectively? a) Amino and carboxyl b) Amino and carbonyl c) Hydroxyl and carbonyl d) Methyl and carboxyl e) Methyl and hydroxyl

20 What functional group is commonly used in cells to transfer energy from one organic molecule to another? a) carboxyl b) sulfhydryl c) hydroxyl d) phosphate e) amino

21 What functional group is commonly used in cells to transfer energy from one organic molecule to another? a) carboxyl b) sulfhydryl c) hydroxyl d) phosphate e) amino

22 Review Identify the functional groups in this structure. What macromolecule is it?

23 ALL living things are made up of 4 classes of large biological molecules: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids 2011 Pearson Education, Inc.

24 Macromolecules, polymers, monomers Polymer - long molecule consisting of many smaller building blocks Monomers- smaller building-block molecules of polymers Polymers: Carbohydrates Proteins Nucleic acids *Lipids consider an exception; but usually built from smaller pieces 2011 Pearson Education, Inc.

25 Analogy of macromolecules

26 The Synthesis & Breakdown of Polymers Condensation reaction (AKA dehydration synthesis)- when two monomers bond together through the LOSS of a water molecule (DEHYDRATES!) Hydrolysis- breaks chemical bonds of polymers into monomers, USING water; essentially the reverse of the dehydration reaction ( Lyse - break, loosen) 2011 Pearson Education, Inc.

27 Animation: Polymers Right-click slide / select Play 2011 Pearson Education, Inc.

28 Figure 5.2 (a) Dehydration reaction: synthesizing a polymer Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond Longer polymer (b) Hydrolysis: breaking down a polymer Hydrolysis adds a water molecule, breaking a bond

29 The Diversity of Polymers Macromolecules vary among cells of an organism, HO vary more within a species, and vary even more between species An immense variety of polymers can be built from a small set of monomers Macromolecules Tutorial/ Animations 2011 Pearson Education, Inc.

30 Section 2-3 Concept Summary Carbon Compounds include Carbohydrates Lipids Nucleic acids Proteins that consist of that consist of that consist of that consist of Monosaccharides which contain Carbon, hydrogen, oxygen Types of Bonds: - Covalent (Alpha or beta glycosidic) - Hydrogen (b/w Go to Section: Fatty acids & Glycerol Nucleotides Amino Acids which contain which contain which contain Carbon, hydrogen, Oxygen * Carbon,hydrogen, oxygen, nitrogen, phosphorus Carbon, hydrogen,oxygen, Nitrogen * * Phosphorus = phospholipid (2 tails) * Sulfur Types of Bonds: - Covalent and hydrogen - Ester linkages b/w hydrocarbon FA chain tails and glycerol head Types of Bonds: - Covalent (b/w sugar/ phosphates and sugar/bases) - Hydrogen (b/w base pairs) Types of Bonds: - PEPTIDE (b/w a.a.) PRIMARY - Hydrogen (b/w R groups of a.a) SECONDARY - disulfide bridges/ionic/ H bonds, hydrophobic interactions (b/w R groups of a.a) _TERT

31 Class: Lipids Elements made from: C,H,O 1:2:1 Mostly C, H Very little O Example: Functions: (SUBUNITS) Monomer and Basic Structural Diagrams GLUCOSE C 6 H 12 O 6 Carbohydrate Mono- Fructose Glucose Galactose Di- Lactose Sucrose Poly- Starch Glycogen Cellulose FATS OILS WAXES STEROIDS Testosterone Estrogen Cholesterol 1.Stores Short Term Energy - Animals ONLY= GLYCOGEN - Plants ONLY= STARCH 2. Structural support within cells: - PLANT CELL WALLS (CELLULOSE) MONOSACCHARIDE = SINGLE SUGAR Mono + mono = DISACCHARIDES Mono + mono + +mono (X 100) = POLYSACCHARIDE CHITIN ( KITE-IN ) -(INSECT EXOSKELETON; Fungi cell walls) 1. Stores LONG TERM Energy 2. Form cell membranes 3. Waterproof coverings 4. Chemical messengers 5. Insulation 6. Protection 1 glycerol 3 fatty acids Saturated- NO DOUBLE BONDS IN FATTY ACID (SINGLE bonds=straight lines = solids) LEAST 1 DOUBLE BOND (double = kink in the leg; can t fit closely= liquids) Saturated fat!

32 CLASS: Elements made of: Examples: Functions: Monomer and Structural diagrams: Nucleic acids C H O P N DNA/RNA Stores and transmits hereditary information Help in reproduction of cells NUCLEOTIDES = C SUGAR PHOSPHATE GROUP NITROGENOUS BASE ProteiNs C H O N *S Hemoglobin Insulin Collagen Lactase Trypsin Pepsin Shape of protein s determine their functions: 1. HELPS CONTROL RATE OF REACTIONS (ENZYMES) 2. pump small molecules in and out of the cell 3. Aids in cell movement 4. Structural supportmuscles (ACTIN/MYOSIN) 5. Antibodies of immune system AMINO ACIDS = 20 DIFFERENT KINDS HELD TOGETHER BY PEPTIDE BONDS! *R GROUP- variable that identifies each of the 20 a.a.

33 Carbohydrates ( -ose ) Serve as fuel and building material in cell walls Carbohydrates- include sugars and polymers of sugars Monosaccharides- single sugars; simplest carbohydrates Disaccharides 2 monosaccharides held together by glycosidic bond Polysaccharides- macromolecules composed of hundreds of monosaccharide building blocks 2011 Pearson Education, Inc.

34 Monosaccharides Usually have molecular formulas that are multiples of CH 2 O (1 C: 2 H: 1 O) Glucose (C 6 H 12 O 6 )- most common 2011 Pearson Education, Inc.

35 Figure 5.3c Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Hexoses: 6-carbon sugars (C 6 H 12 O 6 ) Glucose Galactose Fructose

36 FUNCTION: Monosaccharides serve as a major fuel for cells and as raw material for building molecules 2011 Pearson Education, Inc.

37 Figure (a) Linear and ring forms (b) Abbreviated ring structure

38 Disaccharides Formed when a CONDENSATION reaction Joins 2 monosaccharides = covalent bond called a glycosidic linkage 2011 Pearson Education, Inc.

39 Figure glycosidic 1 linkage 4 Alpha Glucose Alpha Glucose Maltose (a) Dehydration reaction in the synthesis of maltose 1 2 glycosidic 1 linkage 2 Alpha Glucose Beta Fructose Sucrose (b) Dehydration reaction in the synthesis of sucrose

40 2011 Pearson Education, Inc. Animation: Disaccharide Right-click slide / select Play

41 Polysaccharides Polymers of sugars storage and structural roles Structure and function determined by sugar monomers AND the positions of glycosidic linkages 2011 Pearson Education, Inc.

42 Polysaccharides: Storage in PLANTS Starch- storage polysaccharide of PLANTS, consists entirely of glucose monomers store starch as granules within chloroplasts and other plastids or in roots (i.e. carrots, potatoes ) NEVER FOUND IN ANIMALS! Combination of AMYLOSE and AMYLOPECTIN Amylose = Alpha glucose = Unbranching chain ( STRAIGHT ) = Carbons #1, 4 bonding Amylopectin = Alpha glucose = branching chain = 1, 4 AND Carbons #1, 6 bonding 2011 Pearson Education, Inc.

43 Figure 5.6 Chloroplast Starch granules Amylopectin (a) Starch: a plant polysaccharide 1 m Amylose Mitochondria Glycogen granules (b) Glycogen: 0.5 m an animal polysaccharide Glycogen

44 Polysaccharides: Storage in ANIMALS Glycogen - storage polysaccharide in animals Stores mainly in liver and muscle cells Like Amylopectin = Alpha glucose = branching chain= Carbons #1, 4 and 1, 6 bonding Difference = more branching chains 2011 Pearson Education, Inc.

45 Figure 5.6 Chloroplast Starch granules Amylopectin (a) Starch: a plant polysaccharide 1 m Amylose Mitochondria Glycogen granules (b) Glycogen: 0.5 m an animal polysaccharide Glycogen

46 Polysaccharides: Structural in PLANTS Cellulose - major component of the tough cell wall in plant. (ie celery, corn) Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ! The difference is based on two ring forms for glucose: alpha ( ) and beta ( ) 1, 4 bonds! 2011 Pearson Education, Inc.

47 Figure 5.7 (a) and glucose ring structures C1 = the carbon to the right of the O Glucose Glucose (b) Starch: 1 4 linkage of glucose monomers (c) Cellulose: 1 4 linkage of glucose monomers = OH BELOW the ring on C1; same side = OH ABOVE the O; alternation of sides

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49 Polysaccharides: Structural in ANIMALS * not in Cambridge book! Chitin- major component of the tough exoskeletons of invertebrates (ie cockroaches, crabs) AND cell walls of many fungi Like cellulose (1, 4 BETA bonds); ALSO HAS NITROGEN!

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51 2011 Pearson Education, Inc.

52 Figure 5.9 Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals.

53 Glycosidic Linkages and Shape Polymers with glucose are helical Starch (amylose/amylopectin) Glycogen Polymers with glucose are straight Cellulose- parallel strands of long cellulose molecules group into microfibrils (strong building structure for plants) Chitin 2011 Pearson Education, Inc.

54 Figure 5.8 Cell wall Cellulose microfibrils in a plant cell wall Microfibril Starch and Cellulose Animation 10 m 0.5 m Cellulose molecules Glucose monomer

55 Hydrolysis of Cellulose NOT EASY for animals to break bonds of cellulose! Enzymes that digest starch by hydrolyzing linkages; can t hydrolyze linkages in cellulose! Cellulose in human food passes through the digestive tract as insoluble fiber (ie celery, corn) *Many herbivores, from cows to termites, have symbiotic relationships with these microbes to help break down the bonds in plant cell walls Pearson Education, Inc.

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57 Which polysaccharide has the greatest number of branches? a) cellulose b) starch c) amylose d) glycogen

58 Which polysaccharide has the greatest number of branches? a) cellulose b) starch c) amylose d) glycogen

59 If actively growing cells are fed 14 C-labeled glucose, what macromolecules will become radioactive first? a) proteins b) starch c) nucleic acids d) fatty acids

60 If actively growing cells are fed 14 C-labeled glucose, what macromolecules will become radioactive first? a) proteins b) starch c) nucleic acids d) fatty acids

61 Why are human enzymes that digest starch unable to digest cellulose? a) Cellulose is made of amino-containing sugars that cannot be metabolized. b) Cellulose is only in plants, therefore humans do not have enzymes to break plant polysaccharides. c) Cellulose has beta-glycosidic linkages; starch-digesting enzymes break only alpha-glycosidic linkages. d) Cellulose has alpha-glycosidic linkages that only bacterial enzymes can break.

62 Why are human enzymes that digest starch unable to digest cellulose? a) Cellulose is made of amino-containing sugars that cannot be metabolized. b) Cellulose is only in plants, therefore humans do not have enzymes to break plant polysaccharides. c) Cellulose has beta-glycosidic linkages; starch-digesting enzymes break only alpha-glycosidic linkages. d) Cellulose has alpha-glycosidic linkages that only bacterial enzymes can break.

63 Carbohydrate Lab Tests POTENTIAL Practical Q! 1. Reducing/Non- Reducing Sugar test 2. Starch test Read p in sugar and starch lab tests Cambridge chapter Predict the results of the various test you will be doing of unknowns (write in left margin of data table)

64 Carbohydrate Tests Reducing and Non-Reducing Sugars Reducing sugar Benedicts test (Most mono, disaccharides) Non-reducing sugar no reaction to reducing; Acid/ base needed; neutral for Benedicts to work (SUCROSE)

65 Carbohydrate Tests Presence of Starch test Potassium-Iodide (K 2 I) Solution= Strong + only for plant tissues (Storage carbohydrate in starchy plants- carrots, potatoes, etc)

66 LIPIDS

67 Lipids *Sometimes considered the class of macromolecules NOT formed of polymers Diverse group of hydrophobic molecules having little or no affinity for water consist mostly of hydrocarbons (formed of nonpolar covalent bonds) The most biologically important lipids: Fats (Triglycerides) Phospholipids cell membranes Steroids hormones; cholesterol in cell membranes 2011 Pearson Education, Inc.

68 Fats (TRIGLYCERIDES) Made from smaller molecules: 1 glycerol head and 3 fatty acids tails A fatty acid consists of a carboxyl (-COOH) group attached to a long carbon skeleton 2011 Pearson Education, Inc.

69 Figure 5.10 Fatty acid (in this case, palmitic acid) Glycerol (a) One of three dehydration reactions in the synthesis of a fat Ester linkage cov. bond in fats holding glycerol head to tails (b) Fat molecule (triacylglycerol)

70 SATURATED VS. UNSATURATED FATS Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds - SATURATED = SINGLE bonds= Straight lines of hydrocarbon chains = Solids at room temp (can pack together tightly) Lard, butter Unsaturated fatty acids have one or more double bonds - Double bonds= kink in the hydrocarbon chains liquids at room temp (can t pack together tightly) -olive, vegetable, fish oils 2011 Pearson Education, Inc.

71 2011 Pearson Education, Inc. Animation: Fats Right-click slide / select Play

72 Figure 5.11 (a) Saturated fat (b) Unsaturated fat Structural formula of a saturated fat molecule Space-filling model of stearic acid, a saturated fatty acid A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty acid Cis double bond causes bending.

73 Functions of Lipids Long term energy storage in adipose cells Structure of cell membranes Cushions vital organs Insulates the body Chemical messengers- Hormones 2011 Pearson Education, Inc.

74 Phospholipids In a phospholipid, two fatty acids and a phosphate group are attached to glycerol The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head 2011 Pearson Education, Inc.

75 Figure 5.12 Hydrophobic tails Hydrophilic head Choline Phosphate Glycerol Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol

76 Figure 5.13 Fluid mosaic model Hydrophilic head WATER Hydrophobic tail WATER Phospholipids are the component of all cell membranes

77 Steroids Steroids are lipids characterized by a carbon skeleton consisting of 4 fused carbon rings Sex hormones estrogen and testosterone Cholesterol- important component in animal cell membranes; helps maintain structure and shape of cell 2011 Pearson Education, Inc.

78 Figure 5.14

79 PROTEINS

80 Proteins Proteins account for more than 50% of the dry mass of most cells Many functions include : 1. Structural support (hair/fingernails, skeletal muscle) 2. Storage (albumin in eggs, seeds,milk) 3. Transport (channels in cell membranes, hemoglobin) 4. Cellular communications (hormones- insulin, enzymes) 5. Movement (skeletal muscle, flagella, centrioles) 6. Defense against foreign substances (ie. Enzymes and antibodies) 2011 Pearson Education, Inc.

81 Figure 5.15-a Enzymatic proteins Function: Selective acceleration of chemical reactions Example: Digestive enzymes catalyze the hydrolysis of bonds in food molecules. Defensive proteins Function: Protection against disease Example: Antibodies inactivate and help destroy viruses and bacteria. Antibodies Enzyme Virus Bacterium Storage proteins Function: Storage of amino acids Examples: Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Transport proteins Function: Transport of substances Examples: Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to other parts of the body. Other proteins transport molecules across cell membranes. Transport protein Ovalbumin Amino acids for embryo Cell membrane

82 Figure 5.15-b Hormonal proteins Function: Coordination of an organism s activities Example: Insulin, a hormone secreted by the pancreas, causes other tissues to take up glucose, thus regulating blood sugar concentration Receptor proteins Function: Response of cell to chemical stimuli Example: Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells. High blood sugar Insulin secreted Normal blood sugar Signaling molecules Receptor protein Contractile and motor proteins Function: Movement Examples: Motor proteins are responsible for the undulations of cilia and flagella. Actin and myosin proteins are responsible for the contraction of muscles. Structural proteins Function: Support Examples: Keratin is the protein of hair, horns, feathers, and other skin appendages. Insects and spiders use silk fibers to make their cocoons and webs, respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Actin Myosin Collagen Muscle tissue Connective 100 m tissue 60 m

83 2011 Pearson Education, Inc. Animation: Structural Proteins Right-click slide / select Play

84 2011 Pearson Education, Inc. Animation: Storage Proteins Right-click slide / select Play

85 2011 Pearson Education, Inc. Animation: Transport Proteins Right-click slide / select Play

86 2011 Pearson Education, Inc. Animation: Receptor Proteins Right-click slide / select Play

87 2011 Pearson Education, Inc. Animation: Contractile Proteins Right-click slide / select Play

88 2011 Pearson Education, Inc. Animation: Defensive Proteins Right-click slide / select Play

89 2011 Pearson Education, Inc. Animation: Hormonal Proteins Right-click slide / select Play

90 2011 Pearson Education, Inc. Animation: Sensory Proteins Right-click slide / select Play

91 2011 Pearson Education, Inc. Animation: Gene Regulatory Proteins Right-click slide / select Play

92 Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions Enzymes function as workhorses that carry out the processes of life 2011 Pearson Education, Inc.

93 2011 Pearson Education, Inc. Animation: Enzymes Right-click slide / select Play

94 Structure of Proteins Monomers = Amino acids organic molecules with carboxyl and amino groups differ in their properties due to differing side chains, called R groups Side chain (R group) carbon Amino acids are linked by peptide bonds Polypeptides are unbranched polymers built from the same set of 20 amino acids Amino group Carboxyl group 2011 Pearson Education, Inc.

95 Figure 5.16 Nonpolar side chains; hydrophobic 20 Different Amino Acids separated by their R groups; properties of each are indicative of R group Side chain (R group) Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) BASIC RULES TO KNOW: Charges or OH attached = hydrophilic (+ bases, - acids) Rings, CH3 or H = nonpolar, hydrophobic Methionine (Met or M) Polar side chains; hydrophilic Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) NONPOLAR and POLAR (water!) DON T MIX well!! Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Electrically charged side chains; hydrophilic Tyrosine (Tyr or Y) Asparagine (Asn or N) Basic (positively charged) Glutamine (Gln or Q) Acidic (negatively charged) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

96 Figure 5.17 Peptide bond New peptide bond forming Side chains Backbone Amino end (N-terminus) Peptide bond Carboxyl end (C-terminus)

97 Protein Shape and Function A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape The sequence of amino acids determines a protein s 3-D structure; structure determines its function 2011 Pearson Education, Inc.

98 Figure 5.18 Groove Groove (a) A ribbon model (b) A space-filling model

99 Figure 5.19 Antibody protein Protein from flu virus

100 4 Levels of Protein Structure 1. Primary structure- the protein s unique sequence of amino acids (met-leu-gly-..) 2. Secondary structure- consists of coils and folds in the polypeptide chain (H-bonds to form alpha helix and beta pleated sheets) 3. Tertiary structure- interactions among various side chains (R groups- hydrogen, disulfide bonds, ionic bonds, etc.) 4. Quaternary structure- when a protein consists of multiple polypeptide chains (fibrous or globular structure) 2011 Pearson Education, Inc.

101 2011 Pearson Education, Inc. Animation: Protein Structure Introduction Right-click slide / select Play

102 Figure 5.20a Primary structure Amino acids Amino end Primary structure of transthyretin Carboxyl end

103 2011 Pearson Education, Inc. Animation: Primary Protein Structure Right-click slide / select Play

104 Figure 5.20b Secondary structure Tertiary structure Quaternary structure helix pleated sheet Hydrogen bond strand Hydrogen bond Transthyretin polypeptide Transthyretin protein

105 2011 Pearson Education, Inc. Animation: Secondary Protein Structure Right-click slide / select Play

106 Figure 5.20c Secondary structure helix pleated sheet Hydrogen bond strand, shown as a flat arrow pointing toward the carboxyl end Hydrogen bond

107 2011 Pearson Education, Inc. Animation: Tertiary Protein Structure Right-click slide / select Play

108 Figure 5.20f Disulfide bridge Hydrogen bond Hydrophobic interactions and van der Waals interactions Ionic bond Polypeptide backbone

109 Figure 5.20g Quaternary structure Transthyretin protein (four identical polypeptides)

110 Figure 5.20h Collagen

111 Figure 5.20i Heme Iron subunit subunit subunit subunit Hemoglobin

112 Quaternary structure Collagen is a fibrous protein consisting of three polypeptides coiled like a rope Hemoglobin is a globular protein consisting of four polypeptides: 2 alpha and 2 beta chains Globular vs. fibrous proteins *CAMBRIDGE LIKES TO ASK ABOUT HOW YOU WOULD IDENTIFY EACH! (DIFFERENCES) 2011 Pearson Education, Inc.

113 2011 Pearson Education, Inc. Animation: Quaternary Protein Structure Right-click slide / select Play

114 Sickle-Cell Disease: A Change in Primary Structure A slight change in primary structure can affect a protein s structure and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin 2011 Pearson Education, Inc.

115 Figure 5.21 Primary Structure Secondary and Tertiary Structures Quaternary Structure Function Red Blood Cell Shape Sickle-cell hemoglobin Normal hemoglobin subunit Exposed hydrophobic region subunit Normal hemoglobin Sickle-cell hemoglobin Molecules do not associate with one another; each carries oxygen. Molecules crystallize into a fiber; capacity to carry oxygen is reduced. 10 m 10 m

116 Denaturation of Proteins This loss of a protein s native structure is called denaturation; becomes biologically inactive Alterations in ph salt concentration temperature other environmental factors can cause a protein to unravel 2011 Pearson Education, Inc.

117 Figure 5.22 tu Normal protein Denatured protein

118 Nucleic Acids

119 Functions of Nucleic acids: store, transmit, and help express hereditary information DNA and RNA programmed unit of inheritance called a gene = a.a. sequence for protein synthesis Monomers = nucleotides 2011 Pearson Education, Inc.

120 Figure DNA 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM

121 Figure DNA 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM 2 Movement of mrna into cytoplasm mrna

122 Figure DNA 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM 2 3 Movement of mrna into cytoplasm Synthesis of protein mrna Ribosome Polypeptide Amino acids

123 Figure end 5 C Sugar-phosphate backbone Nitrogenous bases Pyrimidines 3 C Nucleoside Nitrogenous base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) 5 C Purines 5 C 3 C 3 end (a) Polynucleotide, or nucleic acid Phosphate group (b) Nucleotide 3 C Sugar (pentose) 1 C EACH nucleotide= 1) a nitrogenous base 2) a pentose sugar, 3) one or more phosphate groups Adenine (A) Guanine (G) Sugars Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components

124 2 Group of nitrogenous bases: 1. Pyrimidines (cytosine, thymine, and uracil) have a single ring (SMALLER) 2. Purines (adenine and guanine) ring fused to a another ring (BIGGER!) In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose 2011 Pearson Education, Inc.

125 The Structures of DNA and RNA Molecules RNA molecules - single polypeptide chains DNA molecules - double helix One DNA molecule includes many genes 2011 Pearson Education, Inc.

126 The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C) Called complementary base pairing Complementary pairing can also occur between two RNA molecules or between parts of the same molecule In RNA, thymine is replaced by uracil (U) so A and U pair 2011 Pearson Education, Inc.

127 Figure Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 3 (a) DNA 5 Base pair joined by hydrogen bonding (b) Transfer RNA *Be able to COMPARE/CONTRAST The structures of DNA and RNA!

128 REVIEW QUESTIONS!

129 Lipids All lipids a) are made from glycerol and fatty acids. b) contain nitrogen. c) have low energy content. d) are acidic when mixed with water. e) do not dissolve well in water.

130 Lipids Compared to tropical fish, arctic fish oils have a) more unsaturated fatty acids. b) more cholesterol. c) fewer unsaturated fatty acids. d) more trans-unsaturated fatty acids. e) more hydrogenated fatty acids.

131 Subunits and Metabolic Labeling If you want to selectively label nucleic acids being synthesized by cells, what radioactive compound would you add to the medium? a) 35 S-labeled sulfate b) 32 P-labeled phosphate c) 14 C-labeled leucine d) 3 H-labeled thymidine e) 14 C-labeled guanine

132 Protein Structure and Amino Acids Sickle-cell disease is caused by a mutation in the betahemoglobin gene that changes a charged amino acid, glutamic acid, to valine, a hydrophobic amino acid. Where in the protein would you expect to find glutamic acid? a) on the exterior surface of the protein b) in the interior of the protein, away from water c) at the active site, binding oxygen d) at the heme-binding site

133 Protein Structure The sickle-cell hemoglobin mutation alters what level(s) of protein structure? a) primary b) tertiary c) quarternary d) all of the above e) primary and tertiary structures only

134 Macromolecular Structures and Bonds Ceviche is prepared by marinating fresh raw fish in citrus juice for several hours, until the flesh becomes opaque and firm, as if cooked. How does citrus juice render the seafood safe to eat? a) Acidic ph denatures (unfolds and inactivates) proteins by disrupting their hydrogen bonds. b) Citrus juice denatures proteins by disrupting their ionic bonds. c) Citrus juice contains enzymes that hydrolyze peptide bonds to break apart proteins. d) Citrus juice dissolves cell membranes by disrupting hydrophobic interactions.

135 RNA and DNA How does RNA differ from DNA? a) DNA encodes hereditary information; RNA does not. b) DNA forms duplexes; RNA does not. c) DNA contains thymine; RNA contains uracil. d) all of the above