Biological Molecules: Structures and Functions PDF

Biological Molecules Structures and Functions  Walkthrough: Content Content Performance Learning Competencies Standards Standards BIOLOGICAL Structures and Prepare a Simple 1. Categorize the biological MOLECULE...

Biological Molecules Structures and Functions  Walkthrough: Content Content Performance Learning Competencies Standards Standards BIOLOGICAL Structures and Prepare a Simple 1. Categorize the biological MOLECULES Function of Activity on molecules (carbohydrates, Biological Biochemical tests to lipids, proteins and nucleic Molecules detect the presence acids) according to their Carbohydrates of biomolecules in structure and function Lipids variety of foods 2. Explain the role of each Proteins biological molecule in Enzymes specific metabolic processes Nucleic Acids 3. Describe the components of an enzyme 4. Explain oxidation reduction reactions 5. Determine how factors such as pH, temperature, and substrate affect enzyme activity Have you been exposed to these food labels? Important Elements in Organisms Element % of Human Function in Life weight Oxygen 65 Part of water and most organic molecules, also O 2 Carbon 18 The backbone of all organic molecules Hydrogen 10 Part of all organic molecules and of water Nitrogen 3 Components of proteins and nucleic acids Calcium 2 Constituents of bone, essential for the action of nerves and muscles Phosphorus 1 Part of cell membrane & energy storage molecules; constituent of bone Potassium 0.3 Important in nerve action Sulfur 0.2 Structural component of most proteins Sodium 0.1 Primary ion in body fluids; important in nerve action Chlorine 0.1 Component of digestive tract; also major ion in body fluids Biomolecules  Molecules of Life  Provide the structural framework for all living things, as well as the mechanisms needed to perform various biological processes. 5  Organic Compounds Compounds that contain CARBON are called organic. Diverse and varied structural organization of carbon atoms, there is a great variations in biological system 6 Most common elements Macromolecules Large organic molecules. Also called POLYMERS. Made up of smaller “building blocks” called MONOMERS. 8 Major biomolecules: 1. Carbohydrates 2. Lipids 3. Proteins-includes enzymes 4. Nucleic acids (DNA and RNA Distribution of molecules in cells Carbohydrates CARBO HYDROG OXYGE N EN N 1 2 1 “HYDRATED CARBON” E.F.= CX(H2O)Y OR CH2O  Carbohydrates TRIOSE – contains 3-carbon atoms Ex. glyceraldehyde PENTOSE– contains 5-carbon atoms Ex. ribose and deoxyribose HEXOSE– contains 6-carbon atoms Ex. glucose and fructose 1 3 Carbohydrates 1. Monosaccharide: one sugar unit Examples: glucose (C6H12O6) deoxyribose ribose glucose Fructose Galactose 1 4  GLUCOSE blood sugar universal cellular fuel FRUCTOSE GALACTOSE -converted to glucose for use by body cells RIBOSE DEOXYRIBOSE -form part of the structure of the structure of nucleic acid DISACCHARIDE S “DOUBLE SUGAR” -Formed when 2 simple sugars are joined by a synthesis reaction “DEHYDRATION SYNTHESIS” - Forms a “GLYCOSIDIC BOND” SUCRO (GLUCOSE-FRUCTOSE) SE Cane sugar LACTO (GLUCOSE-GALACTOSE) SE Milk MALTO SE Malt sugar (GLUCOSE-GLUCOSE) “Hydrolysis ”  Because double sugars are too large to pass through the cell membrane, they must be broken down (digested) to their monosaccharide units to be absorbed from the digestive tract.  Water molecule is added. 3. Polysaccharides “MANY SUGAR” -are long, branching chains of linked simple sugars -ideal storage products -they lack the sweetness of the simple and double sugars Starc h -storage of polysaccharide formed by plants -ingested to form starchy products :grain products, root crops and specialized parts of some plants  Glycosidic linkages between many sugar molecules create complex carbohydrates, such as starch. What is the scientific term for many monomers linked together? Glycogen -polysaccharide found in animal tissues Cellulose -chief component of cell walls in plants - Uses: cotton, pharmaceuticals, cellophane, energy drinks etc. Cellulose Hemp Cotton Rayon Dietary Linen “fiber” What do you see in the structure of cellulose that tells you that it is a carbohydrate? How is cellulose similar to starch? Cellulose vs. Starch Chitin Pectin Hydrolysis A dimer such as...can be broken maltose, or any apart into its other polymer... constituent monomers. Dehydration Synthesis Two glucose molecules...can bond (monomers)... together to make maltose (dimer). Making/Breaking Molecules Monomers or Polymers? The process The process occurring occurring between C and between A and A is: Hydrolysis C is: Dehydratio n Synthesis What is What is taken up given off here? here? H2O H2O Monomer or Polymer? Lipids LIPIDS: FATS, OILS & WAXES Oily, greasy materials that have a glistening appearance. Made up of Carbon, Hydrogen & Oxygen Soluble in organic solvents as dry cleaning fluid and chloroform FATS Solid at room temperature Usually have animal sources Butter, lard, tallow OILS Liquid at room temperature Extracted from plants Corn, peanut and vegetable oils WAXES Made of polymers Pliable and can be molded when they are warm Occur in nature as protective covering of plants  When Fats and Oils are hydrolyzed, they form GLYCEROL & FATTY ACIDS.  FATTY ACIDS  Made up of a methyl (omega) end and a carboxyl end Have you been exposed to these food labels? TYPES OF FATTY ACIDS 1. Saturated  With high molecular weight and made of single bonds  These are fatty acids which contain the maximum possible number of hydrogen atoms. SATURATED FATTY ACID: Each carbon in the chain has two hydrogen atoms attached to it. It is "saturated" with hydrogen atoms. Saturated fatty acids:  TYPES OF FATTY ACIDS 2. Unsaturated ◦ With low Molecular Weight and with the occurrence of double bonds Unsaturated Fatty Acid:  These are fatty acids which contain carbon-to-carbon "double" bonds.  Therefore, since a carbon atom can have only 4 covalent bonds, there is one less bond available for hydrogen, thus, there is one less hydrogen. (The carbons are NOT "saturated" with hydrogen atoms.) Unsaturated fatty acids  Typesof Unsaturated Fatty Acids a. MONOUNSATURATED FATTY ACID  Two adjacent carbon atoms are missing hydrogen atoms and have a double bond b. POLYUNSATURATED FATTY ACID  There are two or more carbon double bonds Unsaturated fatty acids are chemically more active and unstable than saturated fatty acids.  There is a numbering system used to identify where chemical bonds occur on the fatty chain.  The term "Omega", being the end letter of the Greek alphabet, indicates that the count starts from the end of the chain (the CH3 side).  The location of the carbon double bond determines the type of Omega fatty acid. Omega 3 means a double bond occurs at the third carbon from the end carbon of the chain. Omega 9 means a double bond occurs at the 9th carbon from the end carbon. Trans Fats: What's up with that? Fatty Acid Configurations  What are Trans Fats? ◦ Double bonds bind carbon atoms tightly and prevent rotation of the carbon atoms along the bond axis. ◦ This gives rise to configurational isomers which are arrangements of atoms that can only be changed by breaking the bonds. Cis and Trans configurational isomers  The Latin Cis Configuration prefixes Cis and Trans describe the orientation of the hydrogen atoms with respect to the Trans Configuration double bond.  Cis means "on the same side" and Trans means "across" or "on the other  Naturally occurring fatty acids generally have the Cis configuration. The natural form of 9- octadecenoic acid (oleic acid) found in olive oil has a "V" shape due to the Cis configuration at position 9. The Trans configuration Cis-9-octadecenoic acid (Oleic acid) Trans-9-octadecenoicacid (Elaidicacid) What is Hydrogenation and Partial Hydrogenation?  Unsaturated fats exposed to air becomes oxidized to create compounds that have rancid, stale, or unpleasant odors or flavors.  Hydrogenation is a commercial chemical process to add more hydrogen to natural unsaturated fats to decrease the number of double bonds and retard or eliminate the potential for rancidity. Hydrogenation Process  Fully saturated fats are too waxy and solid to use as food additives, so manufacturers use partially hydrogenated oils.  These oils are also produced at high temperatures with metal catalysts and pressurized hydrogen, but the process is stopped when the oil has the proper consistency for its application. The high temperatures and catalysts used for this chemical reaction weaken the double bonds and, as a side effect, cause a large percentage of the natural Cis double bonds to change to Trans double bonds.  Trans fatty acids are present mainly in partially hydrogenated fats, but they are also present in hydrogenated fats because chemical reactions never achieve 100% efficiency. The Triglycerides  Both fats and oils are "triglycerides". These molecules are made up of 3 long chain "fatty acids" attached to a 3 carbon molecule called "glycerol".  The carboxyl and the fatty acids are attached to the -OH groups of the Glycerol via a "dehydration synthesis" reaction to yield an "ester" bond.  Function: storage of energy - "fat" in animals, and "oils" in plants. The Triglycerides Phospholipids  These molecules are structurally similar to the triglycerides, but they differ in one important respect. Triglycerides have 3 fatty acid chains, but the phospholipids have only 2 fatty acid chains and one phosphate (-) group.  The negatively charged phosphate group (and its various end groups) cause this end of the molecule to form a "polar" covalent bond with glycerol.  That is this end of the phospholipid molecule is "polar" while the fatty acid chain is "non-polar". Therefore one end of the molecule is charged (-), i.e. polar and the other end of the molecule is not charged (neutral), i.e. non-polar.  Sincewater isalso a polar moleculethepolar end of thephospholipid is"attracted" to the + ends of the water molecules. It issaid to be"hydrophilic" (or water loving).  While the neutral end of the phospholipid molecule is non-polar, i.e. isrepelled by the"polar" water molecules, it is said to be"hydrophobic" (water fearing). Membrane Lipids Membrane lipids Evidences: Amphiphilic or amphipathic nature STEROIDS Steroids are lipids containing a steroid nucleus (core structure) The steroid nucleus is a fused ring system consisting of three cyclohexane rings and one cyclopentane ring The rings are designated A, B, C and D Attachment of different groups to the core steroid structure leads to a wide variety of steroid compounds, including cholesterol, D bile salts and steroid hormones C A B Protein Structure and Functions Monomers Amino Carboxylic acid group group Amino acids are the monomers of proteins. Amino Acids: The building blocks of protein Side chain Carboxyl Amine Acid group group  Each amino acid has an amine group at one end ◦ The nitrogen-containing part  An carboxyl acid group at the other end  A distinctive side chain attached to the carbon at the center Proteins  Make up about 15% of the cell  Have many functions in the cell: Structural Enzymes Transport Motor Storage Signaling Receptors Gene regulation Special functions 82 Functions of proteins as biological molecules: a. Structural Proteins in the diet serve primarily to build and maintain cells, but their chemical breakdown also provides energy, yielding close to the same 4 calories per gram as do carbohydrates  Collagen and keratin are structural proteins. Collagen holds the tissues together throughout the body and strengthens ligaments and tendons.  Keratin – found in skin. Hair, fingernails b. As Enzymes they catalyze specific chemical reactions Enzymes are referred to as catalysts. A catalyst is a substance that assists other chemical reactions to occur without being chemically changed itself. In the example to the right, molecule A and molecule B are joined together to form a new substance AB. Enzymes are needed to permit every chemical reaction in the body to occur. The most important characteristic of an enzyme molecule is its shape. The shape of the enzyme molecule must fit the shape of the specific molecules the enzyme works on like a key fits into a lock. c. They function as regulatory molecules controlling various physiological processes such as growth and development, as neurotransmitter ex. (hormones, GF, gene activator) d. As membrane components; function as receptor in signal transduction, carriers, channels e. As contractile molecules: form the machinery for coordinated movement  Actin  Myosin  Tropomyosin f. Storage –such as ferritin storing iron in the liver g. Miscellaneous functions :  Immunological -as antibodies & interleukins  Transport – such as hemoglobin ; transports oxygen and carbon dioxide throughout the body  Form blood clots such as fibrinogen and thrombin  absorbs/ reflects light Amino acids are building blocks for proteins H C N O S O H H H N C C O H By attaching various combinations of the 5 above atoms at this location, living things make a total of 20 amino acids that then build all the proteins they need.  R-groups determine the properties of individual amino acids. What process do you see happening here to create this peptide bond between the two amino acids? What is the scientific term for many monomers linked together? Amino acids are building blocks for proteins H C N O S O H H H N C C O H By attaching various combinations of the 5 above atoms at this location, living things make a total of 20 amino acids that then build all the proteins they need. Protein Shape = Amino Acid Sequence  Proteins are made of 20 amino acids linked by peptide bonds  Polypeptide backbone is the repeating sequence of the N-C-C-N-C-C… in the peptide bond  The side chain or R group is not part of the backbone or the peptide bond 93 Amino acids are building blocks for proteins H C N O S H H O H H O H N C C O H N C C O H H H H H Glycine Glycine Amino acids connect as a water molecule is released. What stabilize protein structures? 1. Weak, Non-covalent Interactions  Weak Non-covalent Interactions or Bonds hold the protein in its functional shape – these are weak and will take many to hold the shape. 96 Non-covalent Bonds in Proteins 97 2. Hydrogen Bonds in Proteins 98 Hydrogen Bonds in Globular Proteins  The side chains will help determine the conformation in an aqueous solution 99 3. Disulfide Bonds: Stabilizing Cross Links  Cross linkages can be between 2 parts of a protein or between 2 subunits  Disulfide bonds (S-S) form between adjacent -SH groups on the amino acid cysteine 10 0 “The peptide bond allows for rotation around it and therefore the protein can fold R Groups and orient the or SIDE CHAINS in favorable positions.” 10 1  Refolding of Proteins  Molecular chaperones are small proteins that help guide the folding and can help keep the new protein from associating with the wrong partner 10 2 If proteins can be denatured and refolded to its original conformation, then what is its shape? 10 3 Protein Folding  2 regular folding patterns have been identified – formed between the bonds of the peptide backbone  -helix – protein turns like a spiral – fibrous proteins (hair, nails, horns)  -sheet – protein folds back on itself as in a ribbon –globular protein 10 4 Levels of Organization  Primary structure  Amino acid sequence of the protein  Secondary structure  H bonds in the peptide chain backbone  -helix and -sheets  Tertiary structure  Non-covalent bonds between the R groups within the protein  Quaternary structure  Interaction between 2 polypeptide chains 10 5 Primary Structure Amino acids bonded together by peptide bonds (straight chains) Amino Acids (aa) aa1 aa2 aa3 aa4 aa5 aa6 Peptide Bonds copyright cmassengale 1 0  Secondary Structure 3-dimensional folding arrangement of a primary structure into coils and pleats held together by hydrogen bonds. Two examples: Alpha Helix Beta Pleated Sheet Hydrogen Bonds copyright cmassengale 1 0  Tertiary Structure Secondary structures bent and folded into a more complex 3-D arrangement of linked polypeptides Bonds: H-bonds, ionic, disulfide bridges (S-S) Call a “subunit”. Alpha Helix Beta Pleated Sheet copyright cmassengale 1 0  Quaternary Structure Composed of 2 or more “subunits” Globular in shape Form in Aqueous environments Example: enzymes (hemoglobin) subunits copyright cmassengale 1 0 Parts of Protein Structure  Non-covalent bonds can form interactions between individual polypeptide chains Binding site – where proteins interact with one another Consists of a cavity formed by a specific arrangement of amino acids Subunit – each polypeptide chain of large protein Dimer – protein made of 2 subunits  Can be same subunit or different subunits 11 2 Different Subunit Proteins  Hemoglobin 2  globin subunits 2  globin subunits Heme = non- protein structure that contains Iron & binds with molecular oxygen 11 3 Protein Assemblies  Proteins can form very large assemblies  Can form long chains if the protein has 2 binding sites – link together as a helix or a ring  Actin fibers in muscles and cytoskeleton – is made from thousands of actin molecules as a helical fiber 11 5 Cytoskeleton Types of Proteins as to Structure 1. Globular Proteins – Compact shape like a ball with irregular surfaces  Enzymes are globular  Myoglobin – muscle tissues  Cytoglobin – neurons & connective tissues  Neuroglobin – brain & nerve tissues Human adult skeletal muscle: cytoglobin neuroglobin immunohistochemical staining for myoglobin 11 7 Types of Proteins as to Structure 2. Fibrous Proteins – usually span a long distance in the cell 3-D structure is usually long and rod shaped 11 8 Important Fibrous Proteins Extracellular matrix Bind cells together to make tissues Secreted from cells and assemble in long fibers Collagen – fiber with a glycine in every third amino acid in the protein Connective tissue, bones, skin Elastin – unstructured fibers that gives connective tissues an elastic characteristic 11 9 Animal Cells  Animal cells lack cell walls. ◦ form extracellular matrix  provides support, strength, and resilience Collagen and Elastin 12 1 Proteins at Work  The conformation of a protein gives it a unique function  To work, proteins must interact with other molecules, usually 1 or a few molecules from the thousands to 1 protein  Ligand – the molecule that a protein can bind  Binding Site – part of the protein that interacts with the ligand Consists of a cavity formed by a specific arrangement of amino acids 12 2 Ligand Binding 12 3 Enzymes Enzymes as Biological Catalysts)  Enzymes are proteins that increase the rate of reaction by lowering the energy of activation  They catalyze nearly all the chemical reactions taking place in the cells of the body.  Not altered or consumed during reaction.  Reusable ACTIVE SITES  Enzyme molecules contain a special pocket or cleft called the active sites.  Lock-and-Key Model  In the lock-and-key model of enzyme action: - the active site has a rigid shape - only substrates with the matching shape can fit - the substrate is a key that fits the lock of the active site This explains enzyme specificity This explains the loss of activity when enzymes denature APOENZYME and HOLOENZYME  The enzyme without its non protein moiety is termed as apoenzyme and it is inactive.  Holoenzyme is an active enzyme with its non protein component. Important Terms to Understand Biochemical Nature And Activity of Enzymes  Cofactor: ◦ A cofactor is a non-protein chemical compound that is bound (either tightly or loosely) to an enzyme and is required for catalysis. ◦ Types of Cofactors:  Coenzymes.  Prosthetic groups. Enzyme Specificity  Enzymes have varying degrees of specificity for substrates  Enzymes may recognize and catalyze: - a single substrate - a group of similar substrates - a particular type of bond Types of Cofactors  Coenzyme: The non-protein component, loosely bound to apoenzyme by non-covalent bond.  Examples : vitamins or compound derived from vitamins.  Prosthetic group The non-protein component bound to the apoenzyme by covalent bonds Mechanism of Action of Enzymes Enzymes increase reaction rates by decreasing the Activation energy: Enzyme-Substrate Interactions: ‒Formation of Enzyme substrate complex by: ‒Lock-and-Key Model ‒Induced Fit Model Enzymes Lower a Reaction’s Activation Energy  Active Site of an Enzyme The active site is a region within an enzyme that fits the shape of substrate molecules Amino acid side-chains align to bind the substrate through H-bonding, salt- bridges, hydrophobic interactions, etc. Products are released when the reaction is complete (they no longer fit well in the active site)  Lock-and-Key Model  In the lock-and-key model of enzyme action: - the active site has a rigid shape - only substrates with the matching shape can fit - the substrate is a key that fits the lock of the active site  This is an older model, however, and does not work for all enzymes Induced Fit Model  In the induced-fit model of enzyme action: - the active site is flexible, not rigid - the shapes of the enzyme, active site, and substrate adjust to maximize the fit, which improves catalysis - there is a greater range of substrate specificity  This model is more consistent with a wider range of enzymes  Example of an Enzyme Catalyzed Reaction The reaction for the sucrase catalyzed hydrolysis of sucrose to glucose and fructose can be written as follows: E + S  ES E + P1 + P2 where E = sucrase, S = sucrose, P1 = glucose and P2 = fructose  Factors Affecting Enzyme Activity  Three factors: 1. Environmental Conditions 2. Cofactors and Coenzymes 3. Enzyme Inhibitors 143 1. Environmental Conditions 1. Extreme Temperature are the most dangerous - high temps may denature (unfold) the enzyme. 2. pH (most like 6 - 8 pH near neutral) 3. substrate concentration. 144 Environmental factors  Optimum temperature The temp at which enzymatic reaction occur fastest. Temperature and Enzyme Activity  Enzymes are most active at an optimum temperature (usually 37°C in humans)  They show little activity at low temperatures  Activity is lost at high temperatures as denaturation occurs Environmental factors  pH also affects the rate of enzyme- substrate complexes ◦ Most enzymes have an optimum pH of around 7 (neutral)  However, some prefer acidic or basic conditions Optimum pH for Selected Enzymes  Most enzymes of the body have an optimum pH of about 7.4  However, in certain organs, enzymes operate at lower and higher optimum pH values Substrate Concentration and Reaction Rate  The rate of reaction increases as substrate concentration increases (at constant enzyme concentration)  Maximum activity occurs when the enzyme is saturated (when all enzymes are binding substrate) 2. Cofactors and Coenzymes  Inorganic substances (zinc, iron) and vitamins (respectively) are sometimes need for proper enzymatic activity.  Example: Iron must be present in the quaternary structure - hemoglobin in order for it to pick up oxygen. 150 Enzyme Inhibitors  Inhibitors (I) are molecules that cause a loss of enzyme activity  They prevent substrates from fitting into the active site of the enzyme: E + S  ES E + P E + I  EI no P formed Enzyme Inhibitors  Competive - mimic substrate, may block active site, but may dislodge it. Enzyme Inhibitors  Noncompetitive  Naming Enzymes  The name of an enzyme in many cases end in –ase  For example, sucrase catalyzes the hydrolysis of sucrose  The name describes the function of the enzyme For example, oxidases catalyze oxidation reactions  Sometimes common names are used, particularly for the digestion enzymes such as pepsin and trypsin  Some names describe both the substrate and the function  For example, alcohol dehydrogenase oxides ethanol Enzymes Are Classified into six functional Classes (EC number Classification) by the International Union of Biochemists (I.U.B.). on the Basis of the Types of Reactions That They Catalyze  EC 1. Oxidoreductases  EC 2. Transferases  EC 3. Hydrolases  EC 4. Lyases  EC 5. Isomerases  EC 6. Ligases  Principle of the international classification Each enzyme has classification number consisting of four digits: Example, EC: (2.7.1.1) HEXOKINASE  EC: (2.7.1.1) these components indicate the following groups of enzymes:  2. IS CLASS (TRANSFERASE)  7. IS SUBCLASS (TRANSFER OF PHOSPHATE)  1. IS SUB-SUB CLASS (ALCOHOL IS PHOSPHATE ACCEPTOR)  1. SPECIFIC NAME ATP,D-HEXOSE-6-PHOSPHOTRANSFERASE (Hexokinase)  6 CH 2 O H 6 CH O PO 2  2 3 ATP ADP 5 O 5 O H H H H H H 4 1 4 H 1 OH H OH M g 2+ OH OH OH OH 3 2 3 2 H OH H ex o k in ase H OH glu co se glu co se -6 -p h o sp h ate 1. Hexokinase catalyzes: Glucose + ATP  glucose-6-P + ADP Oxidoreductases, Transferases and Hydrolases Lyases, Isomerases and Ligases Nucleic Acid NUCLEIC ACID - group of complex organic compounds found in all living cells, consisting a combination of: 1. Phosphate NUCLEOTIDE 2. Pentose Sugar 3. Nitrogenous Base DNA – deoxyribonucleic acid - master plan or program that specifies all the proteins that will be synthesized in an organism 1. Phosphate 2. Deoxyribose 3. Purine: Adenine, Guanine Pyrimidine: Thymine, Cytosine Deoxyribonuclei c Acid A nucleic acid present in chromosomes of the nuclei of cells. It is the chemical basis of heredity and the carrier of genetic information Deoxyribonucleic Acid A nucleic acid present in chromosomes of the nuclei of cells. It is the chemical basis of heredity and the carrier of genetic information DNA molecules DNA molecules: is an enormously long, unbranched, linear polymer that can contain many millions of nucleotides arranged in human irregular but nonrandom sequence and that the genetic information of a cell is contained in the linear order of the nucleotides.  Cellular Organization organ cell tissue nucleus DNA chromosome Chromatin Packing  Chromatin packing. This model shows some of the many levels of chromatin packing postulated to give rise to the highly condensed mitotic chromosome. Bending of DNA in a Nucleosome  The bending of DNA in a nucleosome. The DNA helix makes 1.65 tight turns around the histone octamer. This diagram is drawn approximately to scale, illustrating how the minor groove is compressed on the inside of the turn. Owing to certain structural features of the DNA molecule, A-T base pairs are preferentially accommodated in such a narrow minor groove RNA – ribonucleic acid - nucleic acid found in the cytoplasm and nucleus 1. Phosphate 2. Ribose 3. Purine: Adenine, Guanine Pyrimidine: Uracil, Cytosine  Components of Nucleotides A. PENTOSE SUGAR RIBOSE DEOXYRIBOS E - The 2’ position of deoxyribose is distinguished from ribose in that it lacks a hydroxyl (-OH) group on the 2' carbon. - DNA is made up of nucleotides that lack the -OH group at this position. B. NITROGENOUS BASES Purine – double-ring Pyrimidine – single-ring Cytosine Thymine Uracil in DNA in RNA In DNA: In RNA: C. PHOSPHATE GROUP - The phosphate group is attached to the nucleoside via an ester linkage to the 5' carbon - the oxygen of the phosphate group are negatively charged  NB P SUGAR Glycosidic Bond Ester Bond - Nucleotides can contain one or more phosphate groups i) nucleoside monophosphates, ii) nucleoside diphosphates, and iii) nucleoside triphosphates. DNA vs RNA  Components of DNA ◦ Sugar (deoxyribose) ◦ Base (A,G,C,T) ◦ Phosphate group  Components of RNA ◦ Sugar (ribose) ◦ Base (A,G,C,Uracil)  RNA does not contain thymine ◦ Phosphate group DNA vs RNA continued  Structural Characteristics of DNA ◦ Double stranded ◦ Base-pairing rules apply (A:T & G:C)  Structural Characteristics of RNA ◦ Primarily single stranded ◦ Limited base-pairing (G:C & A:U) RNA RNA has the same primary structure as DNA. It consists of a sugar-phosphate backbone, with nucleotides attached to the 1' carbon of the sugar. The differences between DNA and RNA are that: 1. RNA has a hydroxyl group on the 2' carbon of the sugar (thus, the difference between deoxyribonucleic acid and ribonucleic acid. 2. Instead of using the nucleotide thymine, RNA uses another nucleotide called uracil: DNA vs. RNA 3. Because of the extra hydroxyl group on the sugar, RNA is too bulky to form a stable double helix. RNA exists as a single- stranded molecule. However, regions of double helix can form where there is some base pair complementation (U and A , G and C), resulting in hairpin loops. The RNA molecule with its hairpin loops is said to have a secondary structure. 4. Because the RNA molecule is not restricted to a rigid double helix, it can form many different stable three-dimensional tertiary structures. STRUCTURE OF THE DOUBLE HELIX 1. DNA is DOUBLE-STRANDED - held together by Hydrogen Bond - Standard Watson-Crick base pairing A always pairs with T G always pairs with C 2. DNA is ANTIPARALLEL - 5' end of one strand is paired with the 3‘ end of the other strand 3. Two strands of a DNA double helix are COMPLEMENTAR Y  CENTRAL DOGMA OF MOLECULAR BIOLOGY DNA mRNA PROTEIN TRANSCRIPTION TRANSLATION References:  Alberts, B.A., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Watson, J. (2015). Molecular Biology of the Cell. New York: Garland Publishing, Inc.  Campbell, N.A. and Reece, J.B. (2012). Biology. 7th Ed. Singapore: Pearson Education and South-Asia Pte Ltd.  Weaver, Robert F. (2012). Molecular Biology. 5th Ed. New York: McGraw-Hill.