Ch3-Organic_Molecules_of_Life.pdf

1 Chapter 3 Biology: The Organic Molecules of Life Adapted from Textbook, Essentials of Biology, 7 th Edition, McGraw Hill ...

1 Chapter 3 Biology: The Organic Molecules of Life Adapted from Textbook, Essentials of Biology, 7 th Edition, McGraw Hill  2 Content of the Chapter : Organic Molecules The Biological Molecules of Life o Carbohydrates o Lipids o Proteins o Nucleic Acids Learning 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 Content of the Chapter : Organic Molecules The Biological Molecules of Life o Carbohydrates o Lipids o Proteins o Nucleic Acids Learning 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. 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 (ex: H2O and NaCl). Organic Molecules - Hydrocarbons Hydrocarbons are organic molecules consisting of only carbon and hydrogen Hydrocarbons can undergo reactions that release large amounts of energy Many organic molecules, such as fats, have hydrocarbon components Nucleus Fat droplets 10 µm (a) Part of a human adipose cell (b) A fat molecule  6 With an atomic number of 6, how many valence electrons does a carbon atom have? A. 0 B. 2 C. 4 D. 6 Carbon atom: The backbone of life Carbon is unparalleled in its ability to form large, complex, 6 electrons and diverse molecules 4 in outer shell 1. has 4 valence electrons → can bond with as many as 4 other elements o can share electrons with other carbon atoms forming carbon skeletons o can share electrons with elements other than carbon such as hydrogen, nitrogen, and oxygen 2. relatively small in size Carbon atom: The backbone of life Diversity in organic compounds arises from variations in carbon skeletons o Carbon skeletons vary in length and shape o Carbon skeletons can contain single, double or triple bonds Carbon atom: The backbone of life Name and Molecular Structural Ball-and- Space-Filling o In molecules with multiple carbons, each Comment Formula Formula Stick Model Model carbon bonded to four other atoms has a (a) Methane CH4 tetrahedral shape o When two carbon atoms are joined by a (b) Ethane double bond, the atoms joined to the C2H6 carbons are in the same plane as the carbons (c) Ethene (ethylene) o When two carbon atoms are joined by a C2H4 triple bond, the atoms joined to the carbons are in the linear form. (d) Ethyne (Acetylene) C2H2 Carbon atom: The backbone of life Isomers are compounds with the same chemical formula (types of atoms) but different structures and properties Structural Isomers Cis-trans Isomers Enantiomers Isomers have different covalent have the same covalent are isomers that are arrangements of their bonds but differ in spatial mirror images of each atoms (a) Structural isomers arrangements other (c) Enantiomers (b) Cis-trans isomers CO2H CO2H H NH2 NH2 H cis isomer: The two Xs trans isomer: The two Xs CH3 CH3 C5H12 C5H12 are on the same side. are on opposite sides. L isomer D isomer Functional Groups and Organic Molecules Reactivity of organic molecule largely depends on attached functional groups Functional group—specific combination of bonded atoms that always has the same chemical properties and therefore always reacts in the same way A Functional group always reacts the same way regardless of the carbon skeleton to which it is attached Five functional groups that are most important in the chemistry of life: 1. Hydroxyl group 2. Carboxyl group 3. Amino group 4. Sulfhydryl group 5. Phosphate group Functional Groups and Organic Molecules  13 Content of the Chapter : Organic Molecules The Biological Molecules of Life o Carbohydrates o Lipids o Proteins o Nucleic Acids Learning 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. The Biological Molecules of Life There are four categories of biological molecules: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids These molecules that distinguish living matter are all composed of carbon compounds The Biological Molecules of Life The 4 biological molecules of life are Macromolecules → large and complex molecules Carbohydrates, proteins, and nucleic acids are polymers → long molecules consisting of many similar building blocks (monomers) joined together. oMonomers are repeating subunits that serve as building blocks Lipids are not made up of repeating units (monomers) and thus are not polymers (but are still macromolecules because they are large and complex) 16 The synthesis and breakdown of polymers Dehydration/synthesis reaction o Joins monomers to form polymers; equivalent of losing a water molecule Hydrolysis Reaction o Breaks bonds in a polymer; essentially the reverse of a dehydration reaction where OH group attaches to one monomer and H from water attaches to the other monomer Dehydration Monomer Polymer Hydrolysis  18 Content of the Chapter : Organic Molecules o The Biological Molecules of Life o Carbohydrates o Lipids o Proteins o Nucleic Acids Learning 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. Carbohydrates Carbohydrates include sugars and the polymers of sugars Carbohydrates are mainly used for an immediate energy source May also be used as a structural component Carbohydrates are classified as Monosaccharides Disaccharides Polysaccharides Carbohydrates: Monosaccharides Are single sugar molecules also called simple sugars or simply sugars Monosaccharides have molecular formulas that are usually multiples of CH2O → (CH2O)n Glucose (C6H12O6) is the most common monosaccharide o Cells use glucose as the energy source of choice. ▪ Glucose has two isomers: fructose and galactose Two types of sugars: ribose and deoxyribose are found in RNA and DNA. Carbohydrates: Monosaccharides Though often drawn as linear skeletons, in aqueous solutions many sugars form rings 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 Carbohydrates: Polysaccharides Polymers of monosaccharides (3+ monosaccharides joined together) Some function as energy storage molecules. o Plants store glucose as starch. o Animals store glucose as glycogen (mainly in liver and muscle cells) Some function as structural components o Cellulose— found in plant cell walls ▪ Most abundant of all organic molecules ▪ Digested only by some microbes o Chitin—found in crab, lobster, insect exoskeletons Carbohydrates: Polysaccharides Energy Storage Starch Glycogen Structural Components Cellulose α-Chitin  25 Content of the Chapter : Organic Molecules o The Biological Molecules of Life o Carbohydrates oLipids o Proteins o Nucleic Acids Learning 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. Lipids Lipids are the one class of large biological molecules that are not true polymers The unifying feature of lipids is that they mix poorly, if at all, with water (hydrophobic). Lipids are hydrophobic because 1. They consist mostly of hydrocarbons, which form nonpolar covalent bonds 2. Relatively, they almost lack hydrophilic functional groups Lipids have very diverse structures and functions The most biologically important lipids are fats and oils, phospholipids, and steroids Lipids: Fats and Oils Fats and oils are made up of molecules called triglycerides which contain two subunit molecules: 1- Glycerol is a three-carbon alcohol (a hydroxyl group (OH) attached to each carbon) 2- Fatty acid consists of a carboxyl group (COOH) attached to a long carbon skeleton A triglyceride forms when the carboxyl portions of three fatty acids react with the OH groups of glycerol and are joined by an ester linkage. This structure contains a lot of energy. Lipids: Fats and Oils Fats and oils are the body’s primary long-term energy storage molecules. Humans and other mammals store their long-term food reserves in adipose cells. Adipose tissue also cushions vital organs and insulates the body. Oil may help waterproof skin, hair, and feathers. Fats and oils separate from water because water molecules hydrogen-bond to each other and exclude the fats and oils Lipids: Fats and Oils Fatty acids are the primary component of fats and oils. Saturated fatty acids have no double bonds between carbon atoms. o Most animal fats are saturated Unsaturated fatty acids have double bonds in the carbon chain wherever the number of hydrogens is less than two per carbon atom. o Plant fats and fish fats are usually unsaturated o Trans fat is an unsaturated fat (C=C) bond has H’s located on opposite side of bond. Lipids: Fats and Oils Unsaturated; liquid at room temperature Saturated; Solid at room temperature Unsaturated trans-fat Semi-solid at room temperature Lipids: Phospholipids Are a class of lipids whose molecules have a hydrophilic "head" containing a phosphate group and two hydrophobic "tails" derived from fatty acids Are Amphipathic (have hydrophilic parts and hydrophobic parts) o Phosphate head ▪ Polar, hydrophilic (water soluble) o Fatty acid tails ▪ Non-polar, hydrophobic (water- insoluble) Are structural components → form the bulk of the plasma membrane Lipids: Steroids Are lipids made of four fused rings (3 cyclohexane and one cyclopentane). Have no fatty acids but are insoluble in water Are derived from cholesterol Have a common ring structure → differ only in functional groups Are mainly signaling molecules Lipids: Steroids Cholesterol is an amphipathic molecule Useful: functions to separate phospholipid tails and so prevent crystallization of the membrane Cholesterol Harmful: High blood cholesterol is associated with increased risk of Myocardial Infarction Cholesterol Build up  34 Content of the Chapter : Organic Molecules o The Biological Molecules of Life o Carbohydrates o Lipids oProteins o Nucleic Acids Learning 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. Proteins Proteins are composed of monomers called amino acids. Proteins account for more than 50% of the dry mass of most cells Proteins have many functions: support, metabolism, transport, defense, regulation, and motion Antibodies Proteins Amino Acids are organic molecules consisting of a central carbon bonded to hydrogen atom, amino group, carboxyl group, and a side chain, or R group. Amino acids differ in their properties due to differing side chains (R groups) Proteins The 20 different amino acids Proteins are constructed by linking amino acids together o constructed from the same set of 20 amino acids – different combinations Proteins Amino acids are linked by covalent bonds called 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) Proteins 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 Secondary Tertiary Quaternary Amino acid sequence Portions of chain form 3D shape of interacting more than one polypeptide helices or pleated sheets secondary structures chain interacting Proteins The Amino acid sequence (primary structure) determines the final three-dimensional shape of protein. However, physical and chemical conditions can alter the structure of the protein o Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel o This loss of a protein’s native structure is called denaturation  41 Content of the Chapter : Organic Molecules o The Biological Molecules of Life o Carbohydrates o Lipids o Proteins oNucleic Acids Learning 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. Nucleic Acids Nucleic acids are polymers made up of monomers called nucleotides Nucleotides consist of: a phosphate, 5-carbon sugar, and nitrogen-containing base Nucleic Acids Nitrogenous bases are grouped into two families: Pyrimidines (cytosine, thymine, & uracil) have a single six-membered ring Purines (adenine & guanine) have a six-membered ring fused to a five-membered ring C always binds with a G A always binds with a T or U depending on the type of nucleic acid Nucleic Acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) 1. stores genetic information 1. helps to make proteins 2. 5 carbon sugar is deoxyribose 2. 5 carbon sugar is ribose 3. Nitrogenous bases 3. Nitrogenous bases are Adenine, are Adenine, Guanine, Thymine, Guanine, Uracil, Cytosine Cytosine 4. Single stranded 4. Double stranded (2 strands arranged in a helix) C—G C—G A—T A—U Nucleic Acids 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 Relation between Nucleic Acids and Proteins 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. o Ex: Sickle-cell disease Sickle-Cell Disease 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 Chapter Recap – What did we learn? Carbon and hydrogen are the basis of organic molecules found in living organisms Carbohydrates are short-term energy storage molecules and are structural components (in some organisms) Lipids are long-term energy storage molecules, are structural components (phospholipids) and are signaling molecules (steroids) Proteins have many functions including support, metabolism, transport, defense, regulation, and motion Nucleic Acids contain the information to direct the synthesis of proteins What’s next?  50 Revision Questions What type of chemical bond joins a functional group to the carbon skeleton of a large molecule? a) covalent bond b) hydrogen bond c) ionic bond d) double bond e) disulfide bond What type of isomer is propanal compared to acetone? a) cis-trans isomer b) structural isomer c) enantiomer d) none of the above What kind of bond would be present in a completely flat section of a biological molecule? a) single bond b) double bond c) triple bond d) b or c e) a or c Which of the following can carbon-based molecules do because of the versatile bond structures formed by carbon? a) make three-dimensional shapes b) branch c) have mirror-image versions d) all of the above Which polysaccharide has the greatest number of branches? a) cellulose b) chitin c) amylose d) amylopectin e) glycogen A polysaccharide you are studying contains unbranched β glucose molecules and cannot be digested by humans. Which polysaccharide are you studying? a) cellulose b) DNA c) chitin d) starch e) glycogen All lipids a) are made from glycerol and fatty acids. b) contain nitrogen. c) have low energy content. d) are acidic when mixed with water. e) do not dissolve well in water. How does RNA differ from DNA? a) DNA encodes hereditary information; RNA does not. b) DNA forms duplexes; RNA does not. c) DNA contains thymine; RNA contains uracil. d) 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) RNA b) DNA c) protein d) lipid e) carbohydrate In which pair does the first molecule determine the structure of the second? a) DNA, protein b) RNA, carbohydrate c) Lipid, DNA d) DNA, RNA e) a and d Thank You ku.ac.ae