1. Polymers. What are Polymers? 2/13/2016. Chapter 5: The Structure and Function of Large Biological Molecules

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1 hapter 5: The Structure and Function of Large Biological Molecules 1. Polymers 2. arbohydrates 3. Proteins 4. Lipids 5. Nucleic Acids 1. Polymers hapter Reading pg. 67 What are Polymers? Polymers are chains of smaller molecules: 1

2 Dehydration Synthesis Building biological polymers involves the loss of H 2 O: (a) Dehydration reaction: synthesizing a polymer Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond Longer polymer Hydrolysis of Polymers Breaking down polymers requires water: (b) Hydrolysis: breaking down a polymer Hydrolysis adds a water molecule, breaking a bond arbohydrates hapter Reading pp

3 Overview of arbohydrates Made of H 2 O (1 arbon : 2 Hydrogen : 1 Oxygen) lucose ( 6 H 12 O 6 ) structural formula abbreviated structure simplified structure Functions: source of energy structural support Examples of arbohydrates: sugars cellulose starch glycogen arbohydrate Monomers & Polymers monosaccharides, disaccharides & polysaccharides ( saccharide is reek for sugar) 2 monosaccharides lucose lucose 1 disaccharide Important monosaccharides: LUOSE & FRUTOSE Important disaccharides: Maltose SUROSE, LATOSE & MALTOSE Linear and Ring Forms (a) Linear and ring forms Monosaccharides that can adopt the ring form have 5 carbons (pentoses) or 6 carbons (hexoses) (b) Abbreviated ring structure 3

4 Some Important Monosaccharides Aldose (Aldehyde Sugar) lyceraldehyde Ketose (Ketone Sugar) Trioses: 3-carbon sugars ( 3 H 6 O 3 ) Dihydroxyacetone Aldoses have a terminal carbonyl (aldehyde) group Ketoses have an internal carbonyl (ketone) group Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Pentoses: 5-carbon sugars ( 5 H 10 O 5 ) Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Hexoses: 6-carbon sugars ( 6 H 12 O 6 ) Ribose Ribulose lucose alactose Fructose Disaccharides 1 4 glycosidic linkage lucose lucose (a) Dehydration reaction in the synthesis of maltose Maltose 1 2 glycosidic linkage lucose Fructose Sucrose (b) Dehydration reaction in the synthesis of sucrose Polysaccharides hloroplast Starch granules Amylopectin (a) Starch: 1 m a plant polysaccharide Amylose Mitochondria lycogen granules (b) lycogen: 0.5 m an animal polysaccharide lycogen 4

5 & forms of lucose (a) and glucose ring structures lucose lucose (b) Starch: 1 4 linkage of glucose monomers (c) ellulose: 1 4 linkage of glucose monomers Starch and glycogen are polymers of glucose ellulose is a polymer of glucose ell wall Structure of ellulose ellulose microfibrils in a plant cell wall Microfibril 10 m 0.5 m ellulose molecules lucose monomer hitin (a) The structure (b) hitin forms the (c) hitin is used to make of the chitin exoskeleton of a strong and flexible monomer. arthropods. surgical thread. hitin is a polymer of an unusual nitrogen-containing sugar: found in exoskeletons of insects, cell walls of fungi 5

6 3. Proteins hapter Reading pp Overview of Proteins Proteins are polymers of amino acids and have a tremendous variety of functions. proteins carry out most of the activities toward maintaining homeostasis in cells and staying alive made from elements, H, O, N & S Functions of Proteins Proteins have a wide variety of functions and carry out most of the biochemical activities in cells: ENZYMATI 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 STORAE PROTEINS Function: Storage of amino acids Examples: asein, 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 ell membrane 6

7 more Protein Functions HORMONAL PROTEINS Function: oordination 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 REEPTOR 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 ONTRATILE 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. STRUTURAL 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. ollagen and elastin proteins provide a fibrous framework in animal connective tissues. Actin Myosin ollagen Muscle tissue onnective 100 m tissue 60 m Side chain (R group) Amino Acids Amino acids are the monomers from which the polymers we call proteins are made. carbon Each amino acid has a central carbon atom to which is attached: an amino group a carboxyl group Amino group arboxyl group a hydrogen atom a variable R group NONPOLAR SIDE HAINS HYDROPHOBI Side chain Hydrophobic Amino Acids D favors avoidance of H 2 O by non-polar R groups. * lycine (ly or ) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) * Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) 7

8 POLAR SIDE HAINS HYDROPHILI Serine (Ser or S) Polar Amino Acids Threonine (Thr or T) * ysteine (ys or ) The R groups on all of these AAs are polar because they have polar chemical groups Tyrosine (Tyr or Y) Asparagine (Asn or N) lutamine (ln or Q) The R groups of these AAs mix well with water and other polar substances harged Amino Acids The R groups of these AAs are acidic or basic and as a result have a net charge at neutral ph. interact well with water, oppositely charged substances ELETRIALLY HARED SIDE HAINS HYDROPHILI Acidic (negatively charged) Basic (positively charged) Aspartic acid (Asp or D) lutamic acid (lu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) Polypeptides Polypeptides are polymers of AAs Peptide bond New peptide bond forming Each AA is joined to the next by the loss of H 2 O (dehydration) Side chains Backbone Amino end (N-terminus) Peptide bond arboxyl end (-terminus) OH from the carboxyl group, H from the amino group Polypeptides have N-termini & -termini 8

9 Primary (1 o ) structure Four Levels of Protein Structure Amino acids Protein Structure Secondary (2 o ) structure Hydrogen bond Protein function depends on its structure: Tertiary (3 o ) structure Quaternary (3 o ) structure Polypeptide (single subunit of transthyretin) Alpha helix Transthyretin, with four identical polypeptide subunits Pleated sheet ea polypeptide must be folded properly polypeptides in a protein must interact in the right way If this is not the case, proteins don t work! Primary Protein Structure Amino acids PRIMARY STRUTURE The 1 o structure of a protein is simply the AA sequence of each polypeptide it contains Higher orders of protein structure are dependent on the AA sequence changes in AA sequence (i.e., mutations) will affect overall protein structure Amino end Primary structure of transthyretin arboxyl end Higher Levels of Protein Structure Secondary (2 o ) structure Tertiary (3 o ) structure Quaternary (4 o ) structure helix pleated sheet Hydrogen bond strand Hydrogen bond Transthyretin polypeptide Transthyretin protein reflect 3-D arrangements on successively larger scales 9

10 Secondary Structure SEONDARY STRUTURE helix Involves H-bonding between =O & N H within the backbone of the polypeptide pleated sheet Hydrogen bond strand, shown as a flat arrow pointing toward the carboxyl end Hydrogen bond Tertiary & Quaternary Structure 3 o structure overall 3-D shape of a single polypeptide due to R group interactions Tertiary Structure 4 o structure 3-D arrangement of multiple polypeptides in a single protein Quaternary Structure R-group Interactions in Tertiary (& Quaternary) Structure Disulfide bridge Hydrogen bond Hydrophobic interactions and van der Waals interactions Ionic bond Polypeptide backbone 10

11 Modeling Protein Structure roove roove (a) A ribbon model of lysozyme (b) A space-filling model of lysozyme Ribbon models reveal the 2 o structure: coils = -helices arrows = -pleated sheets intervening regions = loops MH Variety in Protein Shape Polypeptide chain hains Iron Heme hains ollagen Hemoglobin Mutations & Protein Structure Sickle-cell hemoglobin Normal hemoglobin Primary Secondary Structure and Tertiary Structures subunit Exposed hydrophobic region subunit Quaternary Structure Normal hemoglobin Sickle-cell hemoglobin Function Molecules do not associate with one another; each carries oxygen. Molecules crystallize into a fiber; capacity to carry oxygen is reduced. Red Blood ell Shape 10 m 10 m 11

12 Denaturation of Proteins Denaturation Normal protein Renaturation Denatured protein Proteins can be denatured by: extreme temperature extreme ph high [salt] non-polar solvent 4. Lipids hapter Reading pp Lipids glycerol fatty acid Hydrophobic, made mostly of & H. Functions: source of energy insulation hormones membranes Includes: fatty acids (FA) triglycerides phospholipids steroids triglyceride 12

13 Fatty Acid Saturation depends on whether or not = double bonds are present (a) Saturated fat (b) Unsaturated fat Structural formula of a saturated fat molecule Space-filling model of stearic acid, a saturated fatty acid Polyunsaturated fats have >1 = double bond Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty acid is double bond causes bending. Triglycerides (triacylglycerol) Fatty acid (palmitic acid) lycerol (a) Dehydration reaction in the synthesis of a fat Ester linkage 3 fatty acids connected via ester linkages to a molecule of glycerol (b) Fat molecule (triacylglycerol) Phospholipids Phospholipids are the major component of biological membranes. Hydrophobic tails Hydrophilic head holine Phosphate lycerol Fatty acids Hydrophilic head Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol 13

14 Membrane Structure Phospholipids in water will form a phospholipid bilayer. Hydrophilic head WATER Hydrophobic tail WATER Steroids All steroids contain the same core 4 ring structure. cholesterol Important Steroids: estradiol cholesterol estrogens testosterone testosterone 5. Nucleic Acids hapter Reading pp ,

15 Overview of Nucleic Acids The main function of Nucleic Acids is to store and express enetic Information: includes DNA & RNA DNA & RNA are linear polymers of nucleotides made from elements, H, O, N & P Nucleic Acids & ene Expression DNA is used to store genetic information RNA is used in gene expression & regulation Synthesis of mrna in the nucleus NULEUS Movement of mrna into cytoplasm via nuclear pore Synthesis of protein Polypeptide DNA mrna mrna YTOPLASM Ribosome Amino acids All nucleotides have this basic structure. Nucleotides nitrogenous base (adenine) phosphate group sugar 15

16 Sugars in Nucleotides SUARS * * Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components: sugars Deoxyribose and Ribose differ only in what is attached to the 2 carbon. Purines & Pyrimidines NITROENOUS BASES Pyrimidines Pyrimidines have 1 ring ytosine () Thymine (T, in DNA) Uracil (U, in RNA) Purines Purines have 2 rings Adenine (A) uanine () (c) Nucleoside components: nitrogenous bases DNA & RNA: Nucleotide Polymers 5' 3' 5' end Nucleotide polymers or strands are connected through an alternating sugar-phosphate backbone 5' Nucleoside Nitrogenous base 5 end has a free phosphate group 5' 3' 3' end (a) Polynucleotide, or nucleic acid Phosphate group (b) Nucleotide 3' Sugar (pentose) 3 end has a free hydroxyl group 16

17 DNA & RNA Structure DNA is double-stranded and RNA is single-stranded. 5 3 Sugar-phosphate backbones Hydrogen bonds Base pair joined by hydrogen bonding 3 5 Base pair joined by hydrogen bonding (a) DNA (b) Transfer RNA Structure of Double-stranded DNA the 2 strands are anti-parallel and interact via base pairs 5 end Hydrogen bond 3 end T A T A 3.4 nm A T 1 nm T A A T A T 3 end T A A T 0.34 nm 5 end (a) Key features of DNA structure (b) Partial chemical structure (c) Space-filling model DNA Base-Pairing Base pairs are held together by hydrogen bonds. Why only A:T and :? Sugar Adenine (A) Sugar Thymine (T) the position of chemical groups involved in H-Bonds the size of the bases (purine & pyrimidine) Purine purine: too wide Sugar uanine () Sugar ytosine () Pyrimidine pyrimidine: too narrow Purine pyrimidine: width consistent with X-ray data 17

18 Key Terms for hapter 5 polymer, monomer, dehydration synthesis, hydrolysis carbohydrate; mono-, di-, polysaccharide aldose, ketose, triose, pentose, hexose lipid, fatty acid, triglyceride, phospholipid, sterol protein, amino acid, polypeptide, denatured nucleic acid, nucleotide, purine, pyrimidine, antiparallel, base pair Relevant hapter Questions