Organic Macromolecules of Life PDF

1 Chapter 3: The Organic Molecules of Life 2 Outline : Organic Molecules The Biological Molecules of Cells Objectives Distinguish between organic and inorganic molecules. Summarize the structure and function of each category of carbohydrates. Summarize the structure and function of each category of...

1 Chapter 3: The Organic Molecules of Life 2 Outline : Organic Molecules The Biological Molecules of Cells Objectives Distinguish between organic and inorganic molecules. Summarize the structure and function of each category of carbohydrates. Summarize the structure and function of each category of lipids. Summarize the structure and function of proteins. Summarize the two categories of nucleic acids, and describe their biological functions. 3 Organic Molecules Living organisms are made up of chemicals based mostly on the element carbon. Organic chemistry is the study of compounds that contain carbon Organic compounds range from simple molecules to complex ones Most organic compounds contain hydrogen atoms in addition to carbon atoms Inorganic molecules do not contain a combination of carbon and hydrogen (H2O and NaCl). 4 Organic Molecules Have a Variety of Functions Carbohydrates form fiber that provides support to plants. Proteins help form the cell walls of bacteria Lipids, such as oils, are used for energy storage for plant Nucleic acids form DNA which acts to store genetic information. 5 Carbon atom: The backbone of life Carbon atoms always shares electrons with elements such as carbon, hydrogen, nitrogen, and oxygen Can bond with as many as four other elements Carbon is unparalleled in its ability to form large, complex, and diverse molecules Proteins, DNA, carbohydrates, and other molecules that distinguish living matter are all composed of carbon compounds six electrons four in outer shell ku.ac.ae 6 The Formation of Bonds with Carbon In molecules with multiple carbons, each carbon bonded to four other atoms has a tetrahedral shape When two carbon atoms are joined by a double bond, the atoms joined to the carbons are in the same plane as the carbons Name%and Comment Molecular Formula (a)%Methane CH4 (b)%Ethane C2 H6 (c)%Ethene (ethylene) C2 H4 When two carbon atoms are joined by a triple bond, the atoms joined to the carbons are in the linear form. Structural Formula Ball9and9 Stick%Model Space9Filling Model ku.ac.ae Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Nucleus Fat*droplets Many organic molecules, such as fats, have hydrocarbon components 10* µm (a)*Part*of*a*human* adipose* cell Hydrocarbons can undergo reactions that release a large amount of energy (b)*A*fat*molecule © 2014 Pearson Education Inc 7 ku.ac.ae 8 Isomers Isomers are compounds with the same molecular formula but different structures and properties Structural Isomers (a)$Structural$isomers Structural isomers have different covalent arrangements of their atoms Cis-trans Isomers Cis-trans isomers have the same covalent bonds but differ in spatial arrangements Enantiomers Isomers Enantiomers are isomers that are mirror images of each other (b)$Cis$trans isomers cis isomer:$The$two$Xs are$on$the$same$side. trans isomer:$The$two$Xs are$on$opposite$sides. (c)$Enantiomers CO2H CO2H © 2014 Pearson Education Inc H NH2 CH3 L$isomer NH2 H CH3 D$isomer ku.ac.ae Carbon skeleton: Molecular diversity arising for carbon skeleton variation Carbon chains form the skeletons of most organic molecules Carbon chains vary in length and shape 9 10 A few chemical groups are key to the function of biological molecules Functional group—specific combination of bonded atoms that always has the same chemical properties and always reacts the same way Reactivity of organic molecule largely dependent on attached functional groups Often use R to stand for the remainder of the molecule Five functional groups that are most important in the chemistry of life: Hydroxyl group Carboxyl group Amino group Sulfhydryl group Phosphate group 11 Common Functional Groups ku.ac.ae ATP: an important source of energy for cellular processes One phosphate molecule, adenosine triphosphate (ATP), is the primary energy-transferring molecule in the cell ATP consists of an organic molecule called adenosine attached to a string of three phosphate groups ATP stores the potential to react with water where energy is released as a result. 12 13 The Molecules of Life There are four categories of biological molecules Carbohydrates Lipids Proteins Nucleic Acids 14 Building Complex Biological Molecules (macromolecules) Macromolecules are large molecules and are complex Large biological molecules have unique properties that arise from the orderly arrangement of their atoms Monomers are repeating subunits that serve as building blocks Polymers are long molecule consisting of many similar building blocks (monomers) joined together. 15 Synthesis and Breakdown of Polymers Dehydration=synthesis reaction Joins monomers to form polymers; equivalent of losing a water molecule Hydrolysis Reaction OH group attaches to one monomer and H from water attaches to the other monomer; used to break bonds in a polymer. 16 Carbohydrates Carbohydrates include sugars and the polymers of sugars Carbohydrates are mainly used for immediate energy source. May also be used for structural component Carbohydrates are classified as Monosaccharides disaccharides polysaccharides 17 Carbohydrates: Monosaccharides Are Single sugar molecule also called Simple sugars Monosaccharides have molecular formulas that are usually multiples of CH2O Glucose (C6H12O6) is the most common monosaccharide Cells use glucose as the energy source of choice. Ribose and deoxyribose are found in RNA and DNA. Two isomers—fructose and galactose Sugars Though often drawn as linear skeletons, in aqueous solutions many sugars form rings 19 Carbohydrates :Disaccharides A disaccharide is formed when a dehydration reaction joins two monosaccharides together This covalent bond between two monosaccharides is called a glycosidic linkage Maltose = glucose-α-1,4-glucose Sucrose = glucose-α-1,2-fructose Lactose = galactose-β-1,4-glucose 20 Polysaccharides Many polysaccharides are used as energy storage molecules. Polymers of monosaccharides Some function as energy storage molecules. Plants store glucose as starch. Animals store glucose as glycogen (mainly in liver and muscle cells) Some function as structural components. Cellulose—plant cell walls Most abundant of all organic molecules Digested only by some microbes Chitin—crab, lobster, insect exoskeletons Starch and Glycogen, Cellulose Structure and Function Energy storage Starch Glycogen Structural components Cellulose (photos): (a): Dr. Jeremy Burgess/Science Source; (b): Don W. Fawcett/Science Source 21 22 Lipids All are insoluble in water. Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds. Relative lack of hydrophilic functional groups Very diverse structures and functions Fats is used for long-term energy storage. Oil may help waterproof skin, hair, and feathers. 23 Fats and Oils: Long-Term Energy Storage Fats and oils are made up of molecules called triglycerides which contain two subunit molecules: Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon Fatty acid consists of a carboxyl group attached to a long carbon skeleton A triglyceride forms when the carboxyl portions of three fatty acids react with the O H groups of glycerol and are joind by by an ester linkage. 24 Fats are hydrophobic molecules for energy storage This structure contains a lot of energy. Fats and oils are the body’s primary long-term energy storage molecules. Fats separate from water because water molecules hydrogen-bond to each other and exclude the fats Adipose tissue also cushions vital organs and insulates the body. 25 Fatty Acids: Saturated vs Unsaturated Fatty acids are the primary component of fats and oils. Saturated fatty acids have no double bonds between carbon atoms. Most animal fats are saturated Unsaturated fats have double bonds in the carbon chain wherever the number of hydrogens is less than two per carbon atom. Plant fats and fish fats are usually unsaturated Trans fat is an unsaturated fat (C=C) bond has H’s located on opposite side of bond. 26 Fatty Acids liquid at room temperature solid at room temperature 27 Structural Lipids: Phospholipids Form the bulk of the plasma membrane One end of the molecule is watersoluble. Polar phosphate head Other end of the molecule is not watersoluble. Nonpolar fatty acid tails 28 Signaling lipids: Steroids Lipids made of four fused rings. No fatty acids but are insoluble in water Derived from cholesterol Differ only in functional groups Cholesterol High blood cholesterol is associated with increased risk of Myocardial Infarction Cholesterol Cholesterol is an amphipathic molecule It functions to separate phospholipid tails and so prevent crystallization of the membrane 30 Proteins and Nucleic Acids Proteins account for more than 50% of the dry mass of most cells Many functions: support, metabolism, transport, defense, regulation, and motion Proteins are composed of amino acid monomers. ku.ac.ae Proteins are chains of amino acids Central carbon bonded to hydrogen atom, amino group, carboxyl group, and a side chain, or R group. Amino group Proteins are all constructed from the same set of 20 amino acids that Differ according to R group E.g. If the R group is just a H atom, we call this amino acid glycine Carboxyl group Amino acids 31 ku.ac.ae Amino acids Amino acids are organic molecules with amino and carboxyl groups Amino acids differ in their properties due to differing side chains, called R groups 32 33 Amino Acids and Peptides Peptide are two or more amino acids covalently linked Peptide bond—formed by dehydration reaction between two amino acid monomers Polypeptide (a polymer)—chain of many amino acids joined by peptide bonds Amino acid sequence determines the final three-dimensional shape of protein. ku.ac.ae Protein structure and function Amino acid sequence determines the final three-dimensional shape of protein. A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape Primary amino acid sequence Secondary portions of chain form helices or pleated sheets Tertiary Quaternary 3D shape of interacting secondary structures more than one polypeptide chain interacting 34 What Determines Protein Structure? In addition to primary structure, physical and chemical conditions can affect structure 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 Methods to determine protein structure Scientists use X-ray crystallography to determine a protein’s structure Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization Bioinformatics is another approach to prediction of protein structure from amino acid sequences 37 Nucleic Acids Genetic information stored in sequence of bases Deoxyribonucleic acid (DNA) stores genetic information Ribonucleic acid (RNA), helps to make proteins nucleic acids are polymers of nucleotide monomers 38 DNA Structure Nucleotide composed of a phosphate, 5-carbon sugar, and nitrogen-containing base Deoxyribose as sugar Five types of bases—adenine (A), guanine (G), cytosine (C), and thymine (T) [DNA only], Uracil (U) [RNA only] 39 Structure of DNA Double helix Complementary base pairing Adenine (A) with thymine (T) Cytosine (C) with guanine (G) 40 Nucleotide polymers Nucleotides are linked together to build a polynucleotide Adjacent nucleotides are joined by a phosphodiester linkage, which consists of a phosphate group that links the sugars of two nucleotides These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages C always binds with a G and A with a T The sequence of bases along a DNA or mRNA polymer is unique for each gene ku.ac.ae There are two families of nitrogenous bases There are two families of nitrogenous bases Pyrimidines (cytosine, thymine, & uracil) have a single sixmembered ring Purines (adenine & guanine) have a six-membered ring fused to a five-membered ring 41 42 RNA Bases RNA ribonucleic acid Ribose as sugar Single-stranded Uses uracil (U) instead of thymine (T) 44 Comparing Proteins and Nucleic Acids Sequence of bases in DNA determines sequence of amino acids in a protein. Sequence of amino acids determines a protein's structure and function. Small changes in the DNA may cause large changes in a protein. E.g, Sickle-cell disease Sickle-Cell Disease: A Change in Primary Structure Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin The abnormal hemoglobin molecules cause the red blood cells to aggregate into chains and to deform into a sickle shape 46 47 Nucleotide polymers Recap: 48 Revision Questions What type of chemical bond joins a functional group to the carbon skeleton of a large molecule? a) b) c) d) e) covalent bond hydrogen bond ionic bond double bond disulfide bond What type of isomer is propanal compared to acetone? a) b) c) d) cis-trans isomer structural isomer enantiomer none of the above What kind of bond would be present in a completely flat section of a biological molecule? a) b) c) d) e) single bond double bond triple bond b or c a or c Which functional group is most important for DNA molecules? a) b) c) d) e) phosphate sulfhydryl hydroxyl carbonyl carboxyl Which of the following can carbon-based molecules do because of the versatile bond structures formed by carbon? a) b) c) d) make three-dimensional shapes branch have mirror-image versions all of the above Which polysaccharide has the greatest number of branches? a) b) c) d) e) cellulose chitin amylose amylopectin glycogen A polysaccharide you are studying contains unbranched β glucose molecules and cannot be digested by humans. Which polysaccharide are you studying? a) b) c) d) e) cellulose DNA chitin starch glycogen All lipids a) b) c) d) e) are made from glycerol and fatty acids. contain nitrogen. have low energy content. are acidic when mixed with water. do not dissolve well in water. How does RNA differ from DNA? a) b) c) d) DNA encodes hereditary information; RNA does not. DNA forms duplexes; RNA does not. DNA contains thymine; RNA contains uracil. all of the above If you heat a cell to a moderately higher temperature than it is normally used to, which molecule will stop working first? a) b) c) d) e) RNA DNA protein lipid carbohydrate In which pair does the first molecule determine the structure of the second? a) b) c) d) e) DNA, protein RNA, carbohydrate Lipid, DNA DNA, RNA a and d Thank You ku.ac.ae