Chapter 5 - The Structure and Function of Large Biological Molecules Outline I. Macromolecules II. Carbohydrates simple and complex III. Lipids triglycerides (fats and oils), phospholipids, carotenoids, steroids, waxes IV. Proteins enzymes, keratin, V. Nucleotides ATP, NAD + VI. Nucleic Acids DNA & RNA Overview: The Molecules of Life All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids Macromolecules are large molecules composed of thousands of covalently connected atoms Molecular structure and function are inseparable Macromolecules are polymers, built from monomers A polymer is a long molecule consisting of many similar building blocks These small building-block molecules are called monomers Three of the four classes of life s organic molecules are polymers Carbohydrates Proteins Nucleic acids Polymers Many biological molecules formed by linking a chain of monomers The Synthesis and Breakdown of Polymers A dehydration reaction occurs when two monomers bond together through the loss of a water molecule Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction 1
Figure 5.2a (a) Dehydration reaction: synthesizing a polymer 1 2 3 Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond. 1 2 3 4 Animation: Polymers Right-click slide / select Play Longer polymer Figure 5.2b Examples of Organic Compounds (b) Hydrolysis: breaking down a polymer 1 2 3 4 Hydrolysis adds a water molecule, breaking a bond. 1. Carbohydrates sugars, polymers of sugars 2. Lipids triglycerides (fats and oils), phospholipids, steroids, waxes 3. Proteins enzymes, keratin, actin 1 2 3 4. Nucleic Acids DNA & RNA Simple Carbohydrates Carbohydrates serve as fuel and building material Carbohydrates include sugars and the polymers of sugars The simplest carbohydrates are monosaccharides, or single sugars Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks 2
Functions of Carbohydrates Sugars 1. Rapidly Mobilized Source of Energy Monosaccharides and disaccharides 2. Energy storage Glycogen in animals Starch in plants 3. Structural In cell walls bacteria and plants (Cellulose). In exoskeletons (Chitin). 4. Coupled with protein to form glycoproteins Important in cell membranes Monosaccharides have molecular formulas that are usually multiples of CH 2 O Glucose (C 6 H 12 O 6 ) is the most common monosaccharide Monosaccharides are classified by The location of the carbonyl group (as aldose or ketose) The number of carbons in the carbon skeleton Figure 5.3a Figure 5.3b Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Pentoses: 5-carbon sugars (C 5 H 10 O 5 ) Trioses: 3-carbon sugars (C 3 H 6 O 3 ) Glyceraldehyde Dihydroxyacetone Ribose Ribulose Figure 5.3c Aldose (Aldehyde Sugar) Ketose (Ketone Sugar) Hexoses: 6-carbon sugars (C 6 H 12 O 6 ) Though often drawn as linear skeletons, in aqueous solutions many sugars form rings Monosaccharides serve as a major fuel for cells and as raw material for building molecules Glucose Galactose Fructose 3
Figure 5.4 1 6 6 Disaccharide 2 5 5 3 4 5 4 3 2 1 4 1 2 3 A disaccharide is formed when a dehydration reaction joins two monosaccharides 6 (a) Linear and ring forms This covalent bond is called a glycosidic linkage 6 5 4 1 3 2 (b) Abbreviated ring structure Figure 5.5 1 4 glycosidic 1 linkage 4 Glucose Glucose (a) Dehydration reaction in the synthesis of maltose Maltose 1 2 glycosidic 1 linkage 2 Animation: Disaccharide Right-click slide / select Play Glucose Fructose (b) Dehydration reaction in the synthesis of sucrose Sucrose 4
Reactions where two molecules are linked together and water is removed is Complex Carbohydrates 1. Condensation or dehydration 2. Hydrolysis 50% 50% Condensation Hydrolysis Polysaccharides Complex carbohydrates - Polysaccharide Polysaccharides, the polymers of sugars, have storage and structural roles The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages Types 1. Starch 2. Glycogen 3. Cellulose 4. Chitin Animation: Polysaccharides Right-click slide / select Play Structure of Complex Carbohydrates Polysaccharides - Long chains of saccharides (sugars) 100s to 1000s Cellulose, starch and glycogen consist of chains of only glucose. Chitin consists of chains of glucose with N-acetyl groups Structure of Complex Carbohydrates The differences between the complex carbohydrates is in the structure branched, unbranched, spiral, hydrogen-bonded. Cellulose is tightly packed and hard to digest Starch is coiled and may be branched and is easier to digest Glycogen is coiled with extensive branching and is even easier to digest. 5
Functions of Carbohydrates 1. Rapidly Mobilized Source of Energy Monosaccharides and disaccharides 2. Energy storage - Polysaccharides Glycogen in animals Starch in plants 3. Structural In cell walls bacteria and plants (Cellulose). In exoskeletons (Chitin). 4. Coupled with protein to form glycoproteins Important in cell membranes Figure 5.6 Chloroplast (a) Starch: a plant polysaccharide Mitochondria Starch granules 1 m Glycogen granules (b) Glycogen: 0.5 m an animal polysaccharide Amylose Amylopectin Glycogen Polysaccharides in Plants for Energy Storage Starch Starch, a storage polysaccharide of plants, consists entirely of glucose monomers Plants store surplus starch as granules within chloroplasts and other plastids The simplest form of starch is amylose Starch form stored in plants, coiled, mainly α 1-4 glycosidic linkage. If branched then will also have 1-6 glycosidic linkage, stored in amyloplasts. Plants used for energy storage, easy to digest Potatoes, rice, carrots, corn Types of starches: Amylose not branched Amylopectin branched, more common Glycogen Glycogen form stored in animals for energy, coiled, mainly α 1-4 glycosidic linkage. It is branched therefore also has 1-6 glycosidic linkage, easy to digest Found in animals: stored mainly in liver and muscle Functions of Carbohydrates 1. Rapidly Mobilized Source of Energy Monosaccharides and disaccharides 2. Energy storage - Polysaccharides Glycogen in animals Starch in plants 3. Structural - Polysaccharides Cellulose in cell walls bacteria and plants Chitin in exoskeletons 4. Coupled with protein to form glycoproteins Important in cell membranes 6
Structural Polysaccharides in Plants - Starch Cellulose The polysaccharide cellulose is a major component of the tough wall of plant cells Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ Cellulose straight chains of glucose, -OH groups H-bond to stabilize chains into tight bundles, β 1-4 glycosidic linkage, hard to digest Used by plants for structure and in cell walls. The difference is based on two ring forms for glucose: alpha ( ) and beta ( ) Figure 5.7a Figure 5.7b 1 4 4 1 4 1 (b) Starch: 1 4 linkage of glucose monomers Glucose Glucose (a) and glucose ring structures 1 4 (c) Cellulose: 1 4 linkage of glucose monomers Polymers with glucose are helical Figure 5.8 Cell wall Cellulose microfibrils in a plant cell wall Microfibril Polymers with glucose are straight 10 m In straight structures, H atoms on one strand can bond with OH groups on other strands 0.5 m Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants Cellulose molecules Glucose monomer 7
Why do we care? 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 Some microbes use enzymes to digest cellulose Many herbivores, from cows to termites, have symbiotic relationships with these microbes Structural Polysaccharides - Chitin Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods. Contains N-acetyl group which hydrogen bond. Is cross-linked with protein to form a strong exoskeleton for insects and crustaceans Chitin also provides structural support for the cell walls of many fungi Figure 5.9 The structure of the chitin monomer Glycoproteins Chitin forms the exoskeleton of arthropods. Glycoproteins carbohydrate + protein on outer surface of cell membranes we will return to this when we study cell membranes Chitin is used to make a strong and flexible surgical thread that decomposes after the wound or incision heals. The form of carbohydrate stored in animals is? Which carbohydrate contains nitrogen? 1. Starch 2. Glycogen 3. Cellulose 33% 33% 33% 1. Starch 2. Cellulose 3. Glycogen 4. Chitin 25% 25% 25% 25% Starch Glycogen Cellulose Starch Cellulose Glycogen Chitin 8
Starch is composed of glucose molecules joined by what kind of covalent bond? 1. β 1-4 Glycosidic linkage 2. α 1-4 Glycosidic linkage 50% 50% Lipids Like carbohydrates, lipids are mainly made of carbon, hydrogen and oxygen They are not soluble in water, they are soluble in nonpolar solvents Types: 1. Triglycerides (Fats) 2. Phospholipids 3. Carotenoids 4. Steroids 5. Waxes Lipids are a diverse group of hydrophobic molecules Lipids are the one class of large biological molecules that do not form polymers The unifying feature of lipids is having little or no affinity for water Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds The most biologically important lipids are fats, phospholipids, and steroids I. Lipid - Triglycerides Function Energy storage, insulation, protection Triglycerides (triacylglycerol) are three fatty acids joined to glycerol The fatty acids are covalently linked by an ester linkage through a condensation reaction Figure 5.10a Figure 5.10b Ester linkage Fatty acid (in this case, palmitic acid) Glycerol (a) One of three dehydration reactions in the synthesis of a fat (b) Fat molecule (triacylglycerol) 9
Ester vs Ether Triglycerides Butter, lard (animal fat), and vegetable oils are all triglycerides Differences are in the structure of the fatty acids Fatty Acids Fatty acids vary in length (number of carbons) and in the number and locations of double bonds Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds Unsaturated fatty acids have one or more double bonds Fatty Acids Saturated fatty acids carbon chain has no double bonds CH 3 -(CH 2 -CH 2 ) n -COOH Unsaturated fatty acids carbon chain has a double bond Monounsaturated fatty acids have one double bond Polyunsaturated fatty acids more than one double bond Figure 5.11 (a) Saturated fat (b) Unsaturated fat Animation: Fats Right-click slide / select Play Structural formula of a saturated fat molecule Space-filling model of stearic acid, a saturated fatty acid Structural formula of an unsaturated fat molecule Space-filling model of oleic acid, an unsaturated fatty acid Cis double bond causes bending. 10
Figure 5.11a Figure 5.11b (a) Saturated fat (b) Unsaturated fat Structural formula of a saturated fat molecule Structural formula of an unsaturated fat molecule Space-filling model of stearic acid, a saturated fatty acid Space-filling model of oleic acid, an unsaturated fatty acid Cis double bond causes bending. Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature Most animal fats are saturated Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room temperature Plant fats and fish fats are usually unsaturated 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 Trans fat Hydrogenated oils unsaturated oils that have been chemically saturated so they will be solid at room temperature (Crisco) Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds These trans fats may contribute more than saturated fats to cardiovascular disease 11
Trans Fats Hydrogenation is the process of adding hydrogen to the unsaturated and polyunsaturated oils to saturate them. This process can also create unsaturated fats that now have a different configuration than the original oil Labeled partially hydrogenated oil Fats and Health Heart disease is caused by plaque collecting in the blood vessels leading to the heart. Cholesterol in the blood leads to more plaque building up in the vessels. LDL (bad cholesterol) transports cholesterol to the heart HDL (good cholesterol) transports cholesterol away from the heart Fatty acids and Cholesterol Trans fats worst type of fat, raise the bad cholesterol (LDL) and lower the good cholesterol (HDL) Saturated fats raise the bad cholesterol Sources = animal fats, dairy products, and some plant oils (palm and coconut) Polyunsaturated fats do not raise the bad cholesterol but slightly lower good cholesterol Sources many vegetable oils (corn and safflower) Monounsaturated fats do not increase either Sources olive, canola and peanut oils; avocado Essential fatty acids Certain unsaturated fatty acids are not synthesized in the human body These must be supplied in the diet These essential fatty acids include the omega-3 fatty acids, required for normal growth, and thought to provide protection against cardiovascular disease 12
Omega-3 Fats Function of Triglycerides Omega-3s are a type of unsaturated fat This fat has a carbon double bond located three carbons from the end (end = omega) This is the healthiest type of fat Protect against heart disease by reducing bad cholesterol Sources fatty fish (salmon, tuna), walnuts The major function of fats is energy storage Humans and other mammals store their fat in adipose cells Adipose tissue also cushions vital organs and insulates the body Which of these fats are the least healthy? Which type of fatty acid does not contain a double bond? 1. Polyunsaturated 2. Omega 3 unsaturated 3. Trans fat 4. Saturated 25% 25% 25% 25% 1. Polyunsaturated 2. Omega 3 unsaturated 3. Trans fat 4. Saturated 25% 25% 25% 25% Polyunsaturated Omega 3 unsaturated Trans fat Saturated Polyunsaturated Omega 3 unsaturated Trans fat Saturated II. Lipid - Phospholipids Function Backbone of cell membranes Similar structure as triglycerides but have: Glycerol 2 fatty acids Phosphate group (negatively charged) R group II. Lipid - Phospholipids Phospholipids are amphiphathic Phosphate end of molecule soluble in water - hydrophilic. Lipid (fatty acid) end is not soluble in water - hydrophobic. 13
Figure 5.12 Phospholipid s role in memebranes Hydrophilic head Choline Phosphate Glycerol When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior Hydrophobic tails Fatty acids Hydrophilic head The structure of phospholipids results in a bilayer arrangement found in cell membranes Phospholipids are the major component of all cell membranes Hydrophobic tails (a) Structural formula (b) Space-filling model (c) Phospholipid symbol Figure 5.13 III. Lipid - Carotenoids Consist of isoprene units Hydrophilic head WATER Orange and yellow plant pigments Classified with lipids Some play a role in photosynthesis Animals convert to vitamin A Hydrophobic tail WATER Isoprene-derived compounds IV. Lipids - Steroids Structure: Four fused rings Examples: cholesterol, bile salts, reproductive hormones, cortisol 14
Steroids - Functions IV. Lipids - Steroids Functions include Hormones - Signaling within and between cells (estrogen, testosterone, cortisol) Unlike triglycerides and phospholipids, steroids have no fatty acids Structure is a four ring backbone, with side chains attached Cholesterol Important part of cell membrane Bile salts - Emulsify fat in small intestine Figure 5.14 Cholesterol V. Lipids - Waxes Covers surface of leaves of plants. Functions Minimizes water loss from leaves to air. Barrier against entrance of bacteria and parasites into leaves of plants. This type of lipid is an important component of membranes Proteins include a diversity of structures, resulting in a wide range of functions 1. Triglycerides 2. Phospholipids 3. Waxes 33% 33% 33% Proteins account for more than 50% of the dry mass of most cells Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances Triglycerides Phospholipids Waxes 15
Proteins Functions numerous and varied Page 78 Facilitate chemical reactions (enzymes) Transport Movement of muscles Structure Cell signaling - Hormones (insulin) Nutrition Defense Components of cell membrane Immune response Protein Functions - Enzymes Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life Enzymes Enzymes are proteins that catalyze reactions = help reactions to happen they speed up chemical reactions They can only speed up reactions that would happen eventually (may take years) They are usually specific for their substrates They are not consumed (destroyed) in the process Some enzymes need cofactors to function. Example = iron Substrate = the thing that is being changed in the reaction Active site = Place in the enzyme where the substrate binds. Product = The end result Figure 5.15-a Figure 5.15-b 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. 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. Enzyme Virus Antibodies Bacterium High blood sugar Insulin secreted Normal blood sugar Signaling molecules Receptor protein 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. Ovalbumin Amino acids for 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 Cell membrane Contractile and motor proteins Structural proteins Function: Movement Function: Support Examples: Motor proteins are responsible for the Examples: Keratin is the protein of hair, horns, undulations of cilia and flagella. Actin and myosin feathers, and other skin appendages. Insects and proteins are responsible for the contraction of spiders use silk fibers to make their cocoons and webs, muscles. respectively. Collagen and elastin proteins provide a fibrous framework in animal connective tissues. Actin Myosin Collagen Muscle tissue Connective 100 m tissue 60 m 16
Polypeptides Amino Acids Polypeptides are unbranched polymers built from the same set of 20 amino acids A protein is a biologically functional molecule that consists of one or more polypeptides, each folded and coiled into a three dimensional shape Proteins are made up of amino acids Amino acids are organic molecules with carboxyl and amino groups There are 20 amino acids, each with a different substitution for R. Figure 5.UN01 Ionized amino acid Side chain (R group) carbon Amino group Carboxyl group Ionized form Figure 5.16 Nonpolar side chains; hydrophobic Side chain (R group) Figure 5.16a Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Nonpolar side chains; hydrophobic Side chain Methionine (Met or M) Polar side chains; hydrophilic Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Electrically charged side chains; hydrophilic Basic (positively charged) Acidic (negatively charged) Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P) Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H) 17
Figure 5.16b Polar side chains; hydrophilic Figure 5.16c Electrically charged side chains; hydrophilic Basic (positively charged) Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) 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) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Amino Acid Polymers Figure 5.17 Amino acids are linked by peptide bonds A polypeptide is a polymer of amino acids Polypeptides range in length from a few to more than a thousand monomers Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus) Side chains Backbone Peptide bond Amino end (N-terminus) Peptide bond New peptide bond forming Carboxyl end (C-terminus) Protein Structure and Function Figure 5.18 A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape Groove Groove (a) A ribbon model (b) A space-filling model 18
Protein Structure and Function The sequence of amino acids determines a protein s three-dimensional structure A protein s structure determines its function Four Levels of Protein Structure The primary structure of a protein is its unique sequence of amino acids Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain Tertiary structure is determined by interactions among various side chains (R groups) Quaternary structure results when a protein consists of multiple polypeptide chains Figure 5.20a Amino acids Primary structure Amino end Primary structure of transthyretin Animation: Protein Structure Introduction Right-click slide / select Play Carboxyl end Primary Structure of Proteins Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word Primary structure is determined by inherited genetic information Animation: Primary Protein Structure Right-click slide / select Play 19
Secondary Structure of Proteins The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet Animation: Secondary Protein Structure Rightclick slide / select Play Figure 5.20c Secondary structure Tertiary Structure of Proteins helix Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents pleated sheet Hydrogen bond strand, shown as a flat arrow pointing toward the carboxyl end Hydrogen bond These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions Strong covalent bonds called disulfide bridges may reinforce the protein s structure Figure 5.20e Tertiary structure Animation: Tertiary Protein Structure Right-click slide / select Play 20
Figure 5.20f Quaternary Structure of Proteins Disulfide bridge Hydrogen bond Hydrophobic interactions and van der Waals interactions Ionic bond Quaternary structure results when two or more polypeptide chains form one macromolecule Collagen is a fibrous protein consisting of three polypeptides coiled like a rope Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains Polypeptide backbone Figure 5.20g Quaternary structure Figure 5.20i Heme Iron subunit subunit four identical polypeptides subunit subunit Hemoglobin Figure 5.20j Animation: Quaternary Protein Structure Right-click slide / select Play 21
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 Figure 5.21 Sickle-cell hemoglobin Normal hemoglobin Primary Structure 1 2 3 4 5 6 7 1 2 3 4 5 6 7 Secondary 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 Cell Shape 10 m 10 m What Determines Protein Structure? Figure 5.22 In addition to primary structure, physical and chemical conditions can affect structure tu Alterations in ph, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein s native structure is called denaturation Normal protein Denatured protein A denatured protein is biologically inactive Protein Folding in the Cell Figure 5.23 It is hard to predict a protein s structure from its primary structure Most proteins probably go through several stages on their way to a stable structure Chaperonins or chaperones are protein molecules that assist the proper folding of other proteins Diseases such as Alzheimer s, Parkinson s, and mad cow disease are associated with misfolded proteins Hollow cylinder Cap Polypeptide Correctly folded protein Chaperonin Steps of Chaperonin2 The cap attaches, causing 3 The cap comes (fully assembled) Action: the cylinder to change off, and the 1 An unfolded polypeptide enters the shape in such a way that properly folded it creates a hydrophilic protein is cylinder from environment for the released. one end. folding of the polypeptide. 22
Determining the Structure of Proteins Scientists use X-ray crystallography to determine a protein s structure Figure 5.24 EXPERIMENT X-ray source X-ray beam Diffracted X-rays Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization RESULTS RNA Crystal Digital detector X-ray diffraction pattern DNA Bioinformatics uses computer programs to predict protein structure from amino acid sequences RNA polymerase II Nucleic acids store, transmit, and help express hereditary information The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid made of monomers called nucleotides The Roles of Nucleic Acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA provides directions for its own replication DNA directs synthesis of messenger RNA (mrna) and, through mrna, controls protein synthesis Protein synthesis occurs on ribosomes Figure 5.25-1 DNA Figure 5.25-2 DNA 1 Synthesis of mrna mrna 1 Synthesis of mrna mrna NUCLEUS CYTOPLASM NUCLEUS CYTOPLASM 2 Movement of mrna into cytoplasm mrna 23
Figure 5.25-3 DNA The Components of Nucleic Acids 1 2 3 Synthesis of mrna NUCLEUS Movement of mrna into cytoplasm Synthesis of protein Polypeptide mrna mrna CYTOPLASM Ribosome Amino acids Nucleic acids are polymers called polynucleotides Each polynucleotide is made of monomers called nucleotides Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups The portion of a nucleotide without the phosphate group is called a nucleoside Nucleotides Their functions include: Energy (ATP) Coenzymes that aid enzyme function (NAD + ) Messengers within cells (GTP) Nucleotides consists of a sugar, phosphate groups, and a base. There are 5 nucleotide bases: Adenine, Thymine, Uracil, Guanine, Cytosine Nucleic Acids Figure 5.26 Sugar-phosphate backbone 5 end Nitrogenous bases Pyrimidines Nucleic Acids are a chain or chains of nucleotides 5 C 3 C Nucleoside Nitrogenous base Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) The nucleotides are covalently bonded by phosphodiester linkage between the phosphates and sugars 5 C 3 C Phosphate group (b) Nucleotide 5 C 3 C Sugar (pentose) 1 C Adenine (A) Purines Guanine (G) 3 end Sugars (a) Polynucleotide, or nucleic acid Deoxyribose (in DNA) Ribose (in RNA) (c) Nucleoside components 24
Figure 5.26ab 5 end 5 C Sugar-phosphate backbone Figure 5.26c Nitrogenous bases Pyrimidines 3 C Nucleoside 5 C Nitrogenous base Cytosine (C) Thymine (T, in DNA) Purines Uracil (U, in RNA) Sugars 1 C 5 C 3 C Phosphate group (b) Nucleotide 3 C Sugar (pentose) Adenine (A) Guanine (G) Deoxyribose (in DNA) Ribose (in RNA) 3 end (a) Polynucleotide, or nucleic acid (c) Nucleoside components The Components of Nucleotides Nucleoside = nitrogenous base + sugar There are two families of nitrogenous bases Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring Purines (adenine and guanine) have a sixmembered ring fused to a five-membered ring In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose Nucleotide = nucleoside + phosphate group Nucleotide Polymers Nucleotides are linked together to build a polynucleotide polymer Adjacent nucleotides are joined by covalent bonds that form between the OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages The sequence of bases along a DNA or mrna polymer is unique for each gene The Structures of DNA and RNA Molecules RNA molecules usually exist as single polynucleotides chains DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix In the DNA double helix, the two backbones run in opposite 5 3 directions from each other, an arrangement referred to as antiparallel One DNA molecule includes many genes The Structures of DNA and RNA Molecules 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 25
Figure 5.27 DNA and Proteins as Measures of Evolution 5 3 Sugar-phosphate backbones Hydrogen bonds The linear sequences of nucleotides in DNA molecules are passed from parents to offspring Base pair joined by hydrogen bonding Two closely related species are more similar in DNA than are more distantly related species 3 (a) DNA 5 Base pair joined by hydrogen bonding (b) Transfer RNA Molecular biology can be used to assess evolutionary kinship Figure 5.UN02 Figure 5.UN02a Figure 5.UN02b Fatty acids are joined to glycerol by what kind of linkage? 1. Peptide 2. Gycosidic 3. Phosphodiester 4. Ester 25% 25% 25% 25% Peptide Gycosidic Phosphodiester Ester 26
Important Concepts Know the vocabulary of the lecture and reading What are the different types of biological molecules, their functions and be able to identify their structures What are the types of carbohydrates and what types of organisms they are found in, what are their functions, identify their structures Be able to describe the differences in the carbohydrates structures and the implications these difference have on our ability to digest them Important Concepts What are the types of starches and what structure stores starch? What are the different types of lipids and their biological functions What are the types of dietary triglycerides and which are healthy know the order from healthiest to least healthy What is the structure of amino acids, what bond links amino acids together, how they link together. Be able to draw and amino acid structure. Important Concepts Be able to describe protein structure including primary, secondary etc. Know what forces hold alpha helixes and beta sheets together, know the forces that help shape tertiary structure. Know examples of steroids and functions of each type of steroids. What are enzymes, what is their function, what are their properties, what are the active site, the substrates, and the products. Important Concepts What is the structure of nucleotides, you should be able to identify the bases but you don t need to draw their structure. What are nucleic acids what are their functions. Know the examples of nucleic acids and nucleotides Which molecules join together to form what molecules (monomer and polymers) what are the linkages called 27