Biological Molecules PDF

CARBON: The Framework of Biological Molecules Hydrocarbons ⮚the simplest organic compounds ⮚Made up of only carbon and hydrogen ⮚(ex: methane, CH4 ) ⮚Hydrocarbons can undergo reactions that release large amount of energy ⮚Hydrocarbons are classified as either saturated or unsaturated ❑Saturate...

CARBON: The Framework of Biological Molecules Hydrocarbons ⮚the simplest organic compounds ⮚Made up of only carbon and hydrogen ⮚(ex: methane, CH4 ) ⮚Hydrocarbons can undergo reactions that release large amount of energy ⮚Hydrocarbons are classified as either saturated or unsaturated ❑Saturated – All carbon atoms have 4 single bonds * Unsaturated – at least 2 carbons has a double bond or triple bond - (example, ethene )856`7 FUNCTIONAL GROUPS * Functional groups are the components of organic molecules that are most commonly involved in chemical reactions * The number and arrangement of functional groups give each molecule its unique properties * Functional groups have definite chemical properties that they retain no matter where they occur  The Primary Functional Groups * Hydroxyl group * Carbonyl group * Carboxyl group * Amino group * Sulfhydryl group * Phosphate group * Methyl group Hydroxyl STRUCTUR Example: E Found in: carbohydrates, Ethan proteins, ol nucleic acids, lipids Carbonyl Exampl Structure e: Propanal, Acetone, an the simplest aldehyde ketone Found in: carbohydrates, nucleic acids  Types of Unsaturated Hydrocarbons * Alkenes – contain carbon- carbon double bonds * Alkynes – contain carbon- carbon triple bonds * Aromatic hydrocarbons – contain benzene ring Carboxyl Structur Exampl e e Acetic acid Found in: proteins, lipids Amino Structur Exampl e e Glycine Found in: proteins, nucleic acids Sulfhydryl Structur e Exampl e: Ethaneth Found in: iol proteins, Phosphate Structur Exampl e e Found in: nucleic acids Methyl Example Structure Methanol Found in : proteins  ISOMERS * Isomers are compounds with the same molecular formula but different structures and properties: – Structural isomers have different covalent arrangements of their atoms – Stereoisomers have same molecular formula, same Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane. C2H60  cis trans isomer isomer Geometric isomers differ in arrangement about a double bond.  Enantiomers * stereoisomers whose molecules are nonsuperimposable mirror images * also known as optical isomers Examples of enantiomers  Chiral Molecule * A molecule that has mirror-image versions * Commonly comprise a carbon atom attached to four different substituent A chiral molecule: 2-butanol I and II are mirror images of each other I and II are not superposable and so are enantiomers Carbon, C. -a naturally non-metallic element that occurs in all organic compounds -capable of chemical self- bonding to form an enormous number of chemically, biologically, and commercially important molecules -can bond to as many as 4 of the same or different atom or * Chiral compounds are characterized by their effect on polarized light. * Polarized light has a single plane and chiral molecules rotate this plane either to the right or left. We call the two chiral forms D for dextrorotatory and L for levorotatory  Macromolecules Subunit Function Examples CARBOHYDRATES Starch, glycogen Glucose Energy storage potatoes Cellulose Glucose Structural support Strings of celery in plant cell walls Chitin Modified Structural support Crab cells glucose NUCLEIC ACIDS DNA Nucleotides Encodes genes Chromosomes RNA Nucleotides Needed for gene Messenger RNA expression Macromolecul Subunits Functions Examples es PROTEINS Functional Amino acids Catalysis; transport Hemoglobin Structural Amino acids Support Hair; silk LIPIDS Fats Glycerol and three Energy storage Butter, corn oil fatty acids Phospholipids Glycerol, two fatty Cell membranes Phosphatidychlolin acids, phosphate, an e Prostaglandins 5 carbon rings with Chemical Prostaglandin E two nonpolar messengers (PGE) Macromolecules Subunits Functions Examples Prostaglandins 5 carbon rings Chemical Prostaglandin E with two nonpolar messenger (PGE) Steroids Four fused carbon Membranes, Cholesterol; rings hormones estrogen Terpenes Long carbon Pigments, Carotene; rubber chains structural support * All macromolecules are polymers (chains) of repeating links called monomers. POLYMER – is a large molecule composed of many repeated subunits MONOMER - is a molecule that is able to bond in long chains The Dehydration Reaction * defined as a chemical reaction that involves the loss of a water molecule from the reacting molecule. The Hydrolysis Reaction * It is a process by which a hydrogen atom is attached to one subunit and a hydroxyl group to the other, breaking a specific covalent bond in the macromolecule CARBOHYDRATES : Energy Storage and Structural Molecules  Carbohydrates * are a loosely defined group of molecules that all contain CARBON , HYDROGEN , and OXYGEN. * its molar ratio is 1:2:1 * its empirical formula is (CH2O)n, where n is the number of carbon atoms. * carbohydrates are a major source of metabolic energy, both for plants and for animals Monosaccharide ⮚ Greek mono, “single” and Latin saccharum, “sugar” ⮚ simple sugars ⮚ simplest of the carbohydrates ⮚ simple sugars contain as few as three carbon atoms and this are often used as building blocks to form larger molecules, but those that play the central role in energy storage have six. Examples of monosaccharide : * Triose ⮚ glyceraldehyde – C3H6O3 ⮚ deoxyribose Glucose is a linear, six-carbon molecule that forms a six- membered ring in solution. Ring closure occurs such that two forms can result α- glucose and β-glucose. * Pentose ⮚ ribose – C5H10O5  hexoses ⮚ glucose- also called “dextrose” (blood sugar) ⮚ Galactose ⮚ fructose- also called levulose “fruit sugar”. Found commonly in fruits. ❑ sugar isomers have structural differences * fructose is a structural isomer that differs in the position of the carbonyl carbon ( C= =O)  galactose is a stereoisomer that differs in the position of – OH and –H groups relative to the ring. DISACCHARIDES ⮚ Greek di, “two” ⮚ serve as transport molecules in plants and provide nutrition in animals ⮚ serve as effective reservoirs of glucose because the enzymes that normally use glucose in the organism cannot break the bond linking the two monosaccharide su units.  Condensation or Dehydration synthesis ⮚ the chemical process where by two monosaccharide are joined together to form a disaccharide with the loss of water molecules Hydrolysis or hydrolytic reaction ⮚ the chemical process where by disaccharide is broken down into simple sugar by heating it with acid.  example of disaccharide: ⮚ when glucose forms a disaccharide with the structural isomer fructose, the resulting disaccharide is sucrose or table sugar. ⮚ when glucose is linked to the stereoisomer galactose, the resulting disaccharide is lactose, or milk sugar. POLYSACCHARIDE ⮚ poly means “many” ⮚ provide energy storage and structural components. ⮚ are longer polymers made up of monosaccharide that have been joined through dehydration reaction. ⮚ examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose and chitin.  Starch * a storage polysaccharides, consists entirely α-glucose molecules linked in long chains. * Starch has α-linkages. This polysaccharide is produced by all green plants as an energy store. * Starch with the simplest structure is amylose. Amylose ❖ composed of many hundreds α-glucose molecules linked together in long, unbranched chains. Amylopectin ❖ complicated varient of amylose.  Cellulose a structural polysaccharide, also consists of glucose molecules linked in chains, but these molecules are β glucose * Cellulose has β linkages * Cellulose is the chief component of plant walls * Because cellulose cannot be broken down readily by most creature, it works well as a biological structural material Cellulose Glycogen - the comparable molecule to starch in animals - like amylopectin, glycogen is an insoluble polysaccharide containing branched amylose chains. - has much longer average chain length and more branch than plant starch. Chitin -structural material found in arthropods and in fungi. * Is a polymer of N-acetylglucosamine- a substitute version of glucose * When cross-linked by proteins, it forms a tough resistant surface material that serves as the exoskeleton of insects and crustaceans.  Proteins: Molecules with Diverse Structures and Functions Functions of Proteins  1. Enzyme catalysis Enzymes- biological catalysts that facilitate specific chemical reaction. - (3D)Three dimensional globular proteins that fit snugly around the molecules they act on. This fit facilitates chemical reactions by stressing particular chemical bonds. - Its appearance is one of the most important events in the evolution of life. Examples Example of Use Glycosidases Cleave polysaccharides Proteases Break down proteins Polymerases Synthesize nucleic acid Kinases Phosphorylate sugar and proteins  2. Defense ‘Antibodies’ are specialized proteins involved in defending the body from antigen( foreign invaders). Other globular proteins use their shapes to “recognize” foreign microbes and cancer cells. These cell-surface form the core of the body’s endocrine and immune system. Class of Protein Examples Example of Use Immunoglobulin Antibodies Mark foreign s proteins for elimination Toxins Snake Venom Blocks nerve function Cell-surface MHC* *Self *recognition antigens proteins  3. Transport A variety of globular proteins transport small molecules and ions from one place to another around the body. Examples: The transport protein hemoglobin transports oxygen in the blood. Membrane transport proteins help move ions and molecules across the Class of Protein Example Example of Use Circulating Hemoglobin Carries O2 and Transporters CO2 In blood Myoglobin Carries O2 and CO2 in muscles Cytochromes Electron transport Membrane Sodium- Excitable Transporters potassium pump membranes Proton pump Chemiosmosis Glucose Transports Transporter glucose into cells  4. Support Protein fibers plays structural roles. Structural proteins are fibrous and stringy and provide support. Example: The collagen , forms the matrix of skin, ligaments, tendons, and the bones and is the most abundant protein in the vertebrate body. Class of Examples Example of Protein Use Fibers Collagen Forms cartilage Keratin Forms hair, nails, quills, feathers , horns, beaks Fibrin Forms blood clots  5. Motion Muscles contract through the sliding motion of two kinds of protein filaments: 1. Actin 2. Myosin Contractile protein also plays key roles in the cells cytoskeleton and in moving materials within the cells. Class of Example Example of Protein use Muscle Actin Contraction of muscle fiber Myosin Contraction of muscle fiber  6. Regulation Hormones- small proteins that serve as intercellular messengers in animals. Proteins plays many regulatory roles within the cell- turning on and shutting off genes during development. Also receive information acting as cell- surface receptors.  7. Storage Storage proteins store amino acids. Calcium and iron are stored in the body by building as ions to storage proteins. Examples: Ovalbumin and Casein. Ovalbumin is found in egg whites and casein is a milk-based protein. Class of Protein Example Example of Use Osmotic proteins Serum albumin Maintains osmotic concentration of blood Gene Iac Repressor Regulates Regulators transcription Hormones Insulin Controls blood glucose levels Vasopressin Increases water retention by kidneys Oxytocin Regulates uterine contractions and milk production Building Block: Amino Acid * There are 20 well known amino acids. Because of this, it can form various sizes and shapes each with unique functions. H NH2 C COOH R  Amino Acid Structure The structure as shown are Amino Acid and Carboxyl groups bonded to a Central Carbon Atom, with an additional Hydrogen and a functional Side group indicated by R. R Group determined the unique character of each amino acid. 5 Chemical classes of Amino acid base on their R Group: 1. Nonpolar amino acids, Such as leucine, often have R groups that contain –CH2 OR –CH3 2. Polar uncharged amino acids, Such as threonine, have R group that contain oxygen (or –OH).  3. Charged amino acids, Such as glutamic acid, have R groups that contain acids and bases that can ionize. 4. Aromatic amino acids, such as phenylalanine, have R groups that contain an organic (carbon) ring with alternating single and double bonds. 5. Amino acids that have special functions have unique properties. Some examples are methionine, which is often the first amino acid in a chain or amino acids; proline, which causes kinks in chains; and cysteine which links chains together. ❑Peptide Bond. Covalent bond that links two amino acids. Forms when the amino end of one amino acid joins to carboxyl end of another. ❑Polypeptide Bond. A protein composed of one or more long unbranched chains and is composed of amino acids linked by peptide bonds. Proteins Levels of Structure 1. PRIMARY STRUCTURE: amino acid sequence 2. SECONDARY STRUCTURE: Hydrogen bonding patterns - Parts of the polypeptide coil or fold into a local pattern. 3. TERTIARY STRUCTURE: Folds and links - Refers to the over-all three dimensional shape of the polypeptide.  4. QUATERNARY STRUCTURE: Subunit arrangements -Two or more polypeptide chains associate to form a functional protien,the individual chains are referred to as subunits of the protein  20 Common Amino Acids Amino Acid Name: Alanine Type: Nonpolar Amino Acid Name: Arginine Type: Ionic Amino Acid Name: Asparagine Type: Polar Amino Acid Name: Aspartic Acid Type: Ionic Amino Acid Name: Cysteine Type: Polar Amino Acid Name: Glutamic Acid Type: Ionic Amino Acid Name: Glutamine Type: Polar Amino Acid Name: Glycine Type: Nonpolar Amino Acid Name: Histidine Type: Ionic Amino Acid Name: Isoleucine Type: Nonpolar Amino Acid Name: Leucine Type: Nonpolar Amino Acid Name: Lysine Type: Ionic Amino Acid Name: Methionine Type: Nonpolar Amino Acid Name: Phenylalanine Type: Nonpolar Amino Acid Name: Proline Type: Nonpolar Amino Acid Name: Serine Type: Polar Amino Acid Name: Threonine Type: Polar Amino Acid Name: Tryptophan Type: Nonpolar Amino Acid Name: Tyrosine Type: Polar Amino Acid Name: Valine Type: Nonpolar ❑ Motifs and domains are combinations of secondary structures. ❑ Motifs only consist out of few secondary structures. They may but need not have a function. A domain is more complex or larger structure. It is usually defined as a modular functional unit folding independently. THE PROCESS OF FOLDING RELIES ON CHAPERONE PROTEINS. Chaperone proteins assist in the folding proteins. Example: Heat Shock Proteins How one type of chaperone protein works: Denaturation - process in which proteins change its shape or even unfold completely. - Proteins can be denatured when the pH, temperature, or ionic concentration of the surrounding solution change. * In this state proteins are biologically inactive. Disassociation refers to separation of quaternary subunits with no changes to their tertiary structure. NUCLEIC ACIDS: INFORMATION MOLECULES  NUCLEIC ACIDS * CARRY INFORMATION INSIDE CELLS * HAVE TWO MAINS VARIETIES, DEOXYRIBONUCLEIC ACID (DNA) and RIBONUCLEIC ACID (RNA)  DNA * ENCODES THE GENETIC INFORMATION USED TO ASSEMBLE PROTEINS WHERE IS DNA FOUND?  Nucleotides and the double helix * Nucleotides are arranged in two long strands that form a spiral called a double helix. * This looks like a twisted ladder and the base pairs form the rungs of the ladder and the sugar and phosphate molecules form the sides of the ladder. * CONTAINS THE GENETIC INFORMATION NECESSARY TO BUILD SPECIFIC ORGANISMS * What is DNA made of? DNA contains four chemical bases: * Adenine (A) * Guanine (G) * Cytosine (C) * Thymine (T) NITOGENOUS BASES  How does DNA replicate itself? The DNA can make copies of itself. Both the strands of the DNA open up and make a copy of each and become two DNA stands. Thus each new DNA has one copy of the old DNA from where the copy is made. * Watch video of DNA and ANTIPARALLEL  PROCESS: * DNA replication. The double helix is unwind and each strand acts as a template for the next strand. Bases are matched to synthesize the new partner strands. * Watch video of DNA REPLICATION  Semiconservative replication Describes the mechanism by which DNA is replicated in all known cells. This mechanism of replication was one of three models originally proposed for DNA replication: * Semiconservative replication would produce two copies that each contained one of the original strands and one new strand. * Conservative replication would leave the two original template DNA strands together in a double helix and would produce a copy composed of two new strands containing all of the new DNA base pairs. * Dispersive replication would produce two copies of the DNA, both containing distinct regions of DNA composed of either both original strands or both new strands. * Show video of SEMICONSERVATIVE  PROOFREADING * Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.  RNA * THE STRUCTURE OF RNA IS SIMILAR TO THAT OF DNA. HOWEVER, RNA DIFFERS FROM DNA IN 3 WAYS: * RNA IS SINGLE- STRANDED. * URACIL IS FOUND IN ITS PLACE, IT IS A PYRIMIDINE AND IS COMPLEMENTARY TO ADENINE. * THE SUGAR MOLECULES IN RNA ARE RIBOSE SUGAR.  RNA HAS MULTIPLE ROLES IN GENE EXPRESSION * MESSENGER RNA (mRNA)- COPIES THE MESSAGE FROM THE DNA AND BRINGS IT TO THE RIBOSOMES LOCATED IN THE CYTOPLASM. THE CODE DICTATES THE ORDER IN WHICH AMINO ACIDS MUST BE LINKED TO MAKE A SPECIFIC PROTEIN. * RIBOSOMAL RNA(rRNA)- COMPONENT OF RIBOSOME. * TRANSFER RNA (tRNA)- PICKS UP AND CARRIES THE SPECIFIC AMINO ACIDS TO THE mRNA AT THE RIBOSOMES. TRANSCRIPTION DNA RNA DNA RNAP mRNA (Show video)  TRANSLATION RNA PROTEINS mRNA CYTOPLASM RIBOSOME tRNA AMINO ACIDS (show video)  (review) NUCLEIC ACIDS ARE NUCLEOTIDE POLYMERS * NUCLEOTIDES – ARE REPEATING SUBUNITS OF NUCLEIC ACIDS WITH LONG POLYMERS * EACH NUCLEOTIDE CONSISTS OF 3 COMPONENTS: 1. PENTOSE OR FIVE- CARBON SUGAR ( RIBOSE IN RNA AND DEOXYRIBOSE IN DNA) 2. PHOSPHATE (---PO4) GROUP 3. ORGANIC NITROGENOUS (NITROGEN- CONTAINING) BASE A NUCLEIC ACID, THEN, IS SIMPLY A CHAIN OF FIVE-CABON SUGARS LINKED TOGETHER BY PHOSPHODIESTER BONDS WITH A NITOGENOUS BASE PROTRUDING FROM EACH SUGAR 2 TYPES OF NITROGENOUS BASE 1. PURINES- ARE LARGE, DUOBLE RING MOLECULES FOUND IN BOTH DNA AND RNA 2 TYPES OF PURINES * ADENINE (A) * GUANINE (G) 2. PYRIMIDINES- ARE SMALLER, SINGLE- RING MOLECULES INCLUDE: * CYTOSINE (C, IN BOTH DNA AND RNA) * THYMINE (T, IN DNA ONLY) * URACIL (U, IN RNA ONLY) DNA CARRIES THE GENETIC * ORGANISMS USE SEQUENCES OF NUCLEOTIDES IN DNA TO ENCODE THE INFORMATION SPECIFYING THE AMINO ACID SEQUENCES OF THEIR PROTEINS * THE CODE OF DNA MOLECULECONSISTS OF DIFFERENT COMBINATIONS OF THE FOUR TYPES OF NUCLEOTIDES IN SPECIFIC SEQUENCE:  CGCTTACG * THE INFORMATION ENCODED IN DNA IS USED IN THE EVERYDAY FUNCTIONING OF THE ORGANISM’S DESCENDANTS. * DNA HAS 2 CHAINS WRAPPED ABOUT EACH OTHER IN A LONG LINEAR MOLCULE IN EUKARYOTES AND A CIRCULAR MOLECULE IN MOST PROKARYOTES. * TWO STRANDS OF A DNA POLYMER WIND AROUND EACH OTHER LIKE THE OUTSIDE AND INSIDE RAILS OF A SPIRAL STAIRCASE CALLED DOUBLE HELIX * EACH STEP IN DNA’S HELICAL STAIRCASE IS COMPOSED OF A BASE-PAIR, IT CONSISTS OF A BASE IN ONE CAHIN ATTRACTED BY HYDROGEN BONDS TO A BASE OPPOSITE IT ON THE OTHER CHAIN * THE BASE-PAIRING RULES ARE RIGID: ADENINE CAN PAIR ONLY WITH THYMINE (IN DNA) OR WITH URACIL (IN RNA), AND CYTOSINE CAN PAIR ONLY WITH GUANINE. * THE BASES THAT PARTICIPATE IN BASE- PAIRING ARE SAID TO BE COMPLEMENTARY TO EACH OTHER * ADDITIONAL DETAILS OF THE STRUCTURE OF DNA AND HOW IT INTERACT WITH RNA IN THE PRODUCTION OF RNA IS A TRANSCRIPT OF A DNA STRAND (comparing) * RNA IS SIMILAR TO DNA, BUT WITH TWO MAJOR CHEMICAL DIFFERENCES: 1. RNA MOLECULES CONTAIN RIBOSE SUGAR, IN WHICH THE C-2 IS BONDED TO A HYDROXYL GROUP 2. RNA MOLECULE USE URACIL IN PLACE OF THYMINE  OTHER NUCLEOTIDES ARE VITAL COMPONENTS * ADENINE IS A KEY COMPONENT OF THE MOLECULE ADENOSINE TRIPHOSPHATE (ATP) ATP * THE ENERGY CURRENCY OF THE CELL * USED TO DRIVE ENERGETICALLY UNFAVORABLE CHEMICAL REACTION. TO POWER TRANSPORT ACROSS MEMBRANES, AND * TO POWER THE MOVEMENT OF CELLS  LIPIDS HYDROPHOB IC MOLECULES LIPIDS ✔Insoluble in water. ✔Storage of energy ✔Have a very high proportion of nonpolar carbon-hydrogen (C-H) bonds.  8 Categories: 1. Fatty acids 2. Glycerolipids 3. Glycerophospholipid 4. Sphingolipids 5. Saccharolipids 6. Polyketides 7. Sterol lipids 8. Prenol lipids COMPOSED OF ✔Fatty : acids - long chain hydrocarbon with carboxylic acid (COOH) at one end. ✔Glycerol - three carbon polyalcohol (three-OH group) ✔Saturated -refers to its having all the hydrogen atoms possible. ✔Unsaturated -fatty acid that has double bonds between one or more pairs of successive carbon atoms. ✔Monounsaturated - fatty acids with one double bond. ✔Polyunsaturated -those with more than one SATURATED FATS: UNSATURATED FATS: MONOUNSATURATED : POLYUNSATURATED : Other kinds of lipid ✔Terpenes - are long-chain lipids of many biologically important pigments. EXAMPLE: -chlorophyll -visual pigment retinal ✔Steroids - composed of four carbon rings. - most animal cell membranes contain the steroid cholesterol. EXAMPLE: -testosterone -estrogen ✔Prostaglandins - group of about 20 lipids that are modified fatty acids, with two nonpolar tails attached to a five carbon ring. - act as local chemical messengers in many vertebrate tissues.  Facts in Fats ✔Efficient molecules for storing chemical energy. ✔Contain over 40 carbon atoms. ✔Fats yield about 9 kilocalories(kcal) of chemical energy per gram, as compared with about 4 kcal/g for carbohydrates. ✔Most fats produced by animals are saturated (except some fish 3 kinds of phospholipids ✔GLYCEROL - a three-carbon alcohol, in which each carbon bears a hydroxyl group. Glycerol forms the backbone of the phospholipids molecule ✔FATTY ACIDS - long chain of -CH₂ groups (hydrocarbon chains) ending in a carbolyx (-COOH) group. Two fatty acids are attached to the glycerol backbone in a phospholipid molecule. ✔A phosphate group - (-PO₄2-) attached to one end of the glycerol. The charged phosphate group usually has a charged organic molecule linked m