Chapter 3: The Chemistry of Organic Molecules - Biology - PDF

Because learning changes everything. ® Biology Sylvia S. Mader...

Because learning changes everything. ® Biology Sylvia S. Mader Michael Windelspecht Chapter 3 The Chemistry of Organic Molecules Copyright 2022 © McGraw Hill LLC. All rights reserved. No reproduction or distribution without the prior written consent of McGraw Hill LLC.  Outline 3.1 Organic Molecules 3.2 Carbohydrates 3.3 Lipids 3.4 Proteins 3.5 Nucleic Acids  3.1 Organic Molecules Organic molecules contain carbon and hydrogen atoms. Four classes of organic molecules (biomolecules) exist in living organisms: – Carbohydrates – Lipids – Proteins – Nucleic Acids – Functions of the four biomolecules in the cell are diverse. 3 Inorganic vs. Organic  The Carbon Atom - C can form 4 covalent bonds. -It bonds with many elements (CHNOPS), including itself. -C-C bond is very stable & allows formation of long C chains Rings  The Carbon Skeleton and Functional Groups The carbon chain of an organic molecule is called its skeleton or backbone. Functional groups are clusters of specific atoms bonded to the carbon skeleton with characteristic structures and functions. They determine the chemical reactivity and polarity of organic molecules. Ex.: Replace H by OH in ethane changes it to ethanol, a hydrophobic molecule became hydrophilic 6  Table 3.1 Functional Groups Group Structure Compound Significance Hydroxyl Alcohol as in Polar, forms ethanol hydrogen bond Present in sugars, some amino acids Carbonyl Aldehyde as in Polar formaldehyde Present in sugars Ketone as in Polar acetone Present in sugars Carboxyl Carboxylic acid Polar, acidic (acidic) as in acetic acid Present in fatty acids, amino acids 7  Table 3.1 Functional Groups Group Structure Compound Significance Amino Amine as in Polar, basic, forms tryptophan hydrogen bonds Present in amino acids Sulfhydryl Thiol as in Forms disulfide ethanethiol bonds Present in some amino acids Phosphate Organic Polar, acidic Phosphate as in phosphorylated molecules Present in nucleotides, phospholipids R = remainder of molecule 8  Isomers Isomers are organic molecules that have identical molecular formulas but a different arrangement of atoms, so different functional groups. glyceraldehyde dihydroxyacetone H H O H O H H C C C H H C C C H OH OH OH OH  Same formula C3H6 O3, different functional groups 9 Biomolecules Category Subunits (monomers) Polymer Carbohydrates* Monosaccharide Polysaccharide Lipids Glycerol and fatty acids N/A Proteins* Amino acids Polypeptide Nucleic acids* Nucleotide DNA, RNA *form polymers Usually consist of many repeating units called a monomer. A molecule composed of monomers is called a polymer (many parts). Ex. amino acids (monomer) are joined together to form a protein (polymer) Lipids are not polymers because they contain two different types of subunits  Synthesis and Degradation Dehydration reaction is a chemical reaction in which subunits are joined together by the formation of a covalent bond and water is produced during the reaction. Ex. Forms starch from glucose. Hydrolysis reaction is a chemical reaction in which a water molecule is added to break a covalent bond. Ex. Digestion of starch into glucose monomers. Both processes require enzymes Synthesis of Biomolecules Figure 3.3 Access the text alternative for slide images. 13 Synthesis of Biomolecules Figure 3.3 Access the text alternative for slide images. 14 Synthesis of Biomolecules Figure 3.3 15 Synthesis and Degradation of Biomolecules a. Synthesis of a biomolecule b. Degradation of a biomolecule 16  Enzymes Special molecules called enzymes are required for cells to carry out dehydration synthesis and hydrolysis reactions. An enzyme is a molecule that speeds up a chemical reaction. Enzymes are not consumed in the reaction. Enzymes are not changed by the reaction. Enzymes are catalysts. 17  3.2 Carbohydrates - C-H-O at a ratio of 1:2:1 - Can be small soluble chains or long chains or rings. - Short term & long term energy source & has a structural role.  Types:- Monosaccharide - Disaccharide - Polysaccharide -  1. Monosaccharides A monosaccharide is a single sugar molecule, a simple sugar. It has a backbone of 3 to 7 carbon atoms. Ex: Glucose (blood sugar), fructose (fruit sugar), & galactose. Hexoses – six carbon atoms. Ribose and deoxyribose (sugars contained in nucleotides, the monomer of DNA). Pentoses – five carbon atoms Ribose Deoxyribose  Disaccharides A disaccharide contains two monosaccharides joined together during a dehydration reaction. Examples: Lactose (milk sugar) is composed of galactose and glucose. Sucrose (table sugar) is composed of glucose and fructose. Maltose is composed of two glucose molecules. Lactose-intolerant individuals lack the enzyme lactase which breaks down lactose into galactose and glucose. 20 Synthesis and Degradation of Maltose Jump to Synthesis and Degradation of Maltose (8) Long Descri ption  2. Disaccharides Contains 2 monosaccharides joined togther by a dehydration reaction. 2. Disaccharides The sugar transported in plants.  Polysaccharide is a polymer of monosaccharides Starch, energy storage in plants. Glycogen, energy storage in animals. Cellulose , in the cell walls of plants. Most abundant organic molecule on earth Animals are unable to digest cellulose. Chitin is found in the cell walls of fungi and in the exoskeleton of some animals. Peptidoglycan in the cell walls of bacteria. Monomers contain an amino acid chain.  Amylose: nonbranched starch granule Amylopectin: branched a. Starch 250 m glycogen granule b. Glycogen 150 nm Glycogen is much more branched than starch a: © Jeremy Burgess/SPL/Photo Researchers, Inc.; b: © Don W. Fawcett/Photo Researchers, Inc. Cellulose  3.3 Lipids Large, nonpolar molecule. Hydrophobic= insoluble in water, repels water. soluble in organic solvents contain large sections of only C & H. Functions: Long-term energy storage, fats store more E than CHO. Structural components, cell membrane. Heat retention. Cell communication and regulation. Protection, waxes. Ex. Fats, oils, phospholipids, steroids, waxes Major types of lipids: 1. Triglycerides: fats & oils 2. Phospholipids 3. Steroids 4. Waxes  Table 3.3 Types of Lipids Type Functions Human Uses Fats Long-term energy storage and Butter, lard insulation in animals Oils Long-term energy storage Cooking oils in plants and their seeds Phospholipids Component of plasma Food additive membrane Steroids Component of plasma Medicines membrane (cholesterol), sex hormones Waxes Protection, prevention of Candles, polishes water loss (cuticle of plant surfaces), beeswax, earwax 2 9 1. Triglycerides: Fats & oils Long-term energy storage and insulation Consist of one glycerol molecule linked to three fatty acids by dehydration synthesis 1. Triglycerides  Fatty acids may be either unsaturated or saturated. Unsaturated – one or more double bonds between carbons. Liquid at room temperature Ex: plant oils Can have chemical groups on the same (cis) or opposite (trans) side of the double bond. Saturated – no double bonds between carbons Solid at room temperature Ex.: butter, lard  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. H H H H H H H O H H H H H O 3 H2O C C C C C C H H C O C C C C C C H H C OH HO H H H H H H H H H H Fig. 3.10 H H H H H H H O H H H H H H H O + C C C C C C C C H H C H C C C C C C C C H H C OH HO H H H H H H H H H H H H H H H H H O H H H O H H C C C C H H C O C C C C H C 3 H2O C H C OH HO C C H H H H H H H H H H in in glycerol 3 fatty acids 3 water fat molecule molecules a.Formation of a fat corn corn oil H H H H H H H H H H H H H H H O C C C C C C C C C C C C C C C C C C H HO H H H H H H H H H H H H H unsaturated fatty acid with double bonds (yellow) unsaturated fat mil butter H H H H H H H H H H H H H H H O C C C C C C C C C C C C C C C C H HO H H H H H H H H H H H H H H H saturated fatty acid with no double bonds saturated fat b. Types of fatty acids c.Types of fats  Trans-Fats and Cardiovascular Health Trans-fats (a type of fat, or lipid) Are made by hydrogenation = adding hydrogen to unsaturated fats. – Are used to increase food shelf life and flavor/texture. – May cause worse health effects than saturated fat in an individual’s diet. 34  2. Phospholipids: Structure is similar to triglycerides – Consist of one glycerol molecule linked to two fatty acids and a modified phosphate group The fatty acids are nonpolar and hydrophobic. The modified phosphate group is polar and hydrophilic. Function: form plasma membranes – Polar phosphate heads are oriented towards the water. – Nonpolar fatty acid tails are oriented away from water and form a hydrophobic core. 35 Phospholipids Form Membranes Jump to Phospholipids For m Membranes Long Descr iption  3. Steroids -    Testosterone and estrogen are sex hormones differing only in the functional groups attached to the same carbon skeleton. OH CH3 CH3 O b. Testosterone CH3 HC CH3 (CH2)3 OH HC CH3 CH3 CH3 CH3 HO HO c.Estrogen a.Cholesterol  4. Waxes - Long-chain fatty acids connected to carbon chains containing alcohol functional groups Solid at room temperature Waterproof Resistant to degradation Function: protection Ex.: earwax (contains cerumin), plant cuticle, beeswax  3.4 Proteins Proteins are polymers of amino acids linked together by peptide bonds. A peptide bond is a covalent bond between amino acids. As much as 50% of the dry weight of most cells consists of proteins. Long chains of amino acids joined together are called polypeptides. A protein is a polypeptide that has folded into a particular shape, which is essential for its proper functioning.  Functions of Proteins Metabolism, Most enzymes are proteins that act as catalysts to accelerate chemical reactions within cells. Support, Some proteins have a structural function, for example, keratin and collagen. Transport, Membrane channel and carrier proteins regulate what substances enter and exit cells. Hemoglobin protein transports oxygen to tissues and cells. Defense , Antibodies are proteins of our immune system that bind to antigens and prevent them from destroying cells. Regulation , Hormones are regulatory proteins that influence the metabolism of cells. Motion, Microtubules move cell components to different locations. Actin and myosin contractile proteins allow muscles to contract. There are 20 different common amino acids. Amino acids differ by their R, or variable groups, which range in complexity  Proteins Two amino acids are joined together by a peptide bonds to form a dipeptide. Many peptides form a polypeptide. Shape of Proteins and Levels of Protein Structure Proteins cannot function properly unless they fold into their proper shape. When a protein loses it proper shape, it said to be denatured. Exposure of proteins to certain chemicals, a change in pH, or high temperature can disrupt protein structure. Proteins can have up to four levels of structure: Primary Secondary Tertiary Quaternary 4 5 Polypeptides can have 4 levels of structure before becoming proteins:  Primary structure is amino acid chain  Secondary structure (fibrous proteins) 2 types of folding: 1. α helix 2. β sheet Hydrogen bonding holds the secondary structure in place. Examples of Fibrous Proteins  Tertiary structure (Globular proteins): is the overall three-dimensional shape of a polypeptide. It is stabilized by the presence of hydrophobic interactions, hydrogen, ionic, and covalent bonding.  Quaternary structure: consists of more than one polypeptide e.g. hemoglobin. Quaternary Tertiary Four Levels of Protein Structure Primary structure This level of structure is determined by the linear sequence of amino acids, coded for in the genes of the DNA. Secondary Structure Hydrogen bonding between amino acids causes the polypeptide to form an alpha helix or a pleated sheet. Tertiary Structure Interactions of amino acid side chains with water, covalent bonding between R groups, and other chemical interactions determine the folded three-dimensional shape of a protein. Quaternary Structure This level of structure occurs when two or more folded polypeptides interact to perform a biological function. The Importance of Protein Folding and Protein-Folding Diseases Chaperone proteins help proteins fold into their normal shapes and may also correct misfolding of new proteins. Defects in chaperone proteins may play a role in several human diseases, such as Alzheimer’s disease and cystic fibrosis. Prions are misfolded proteins that have been implicated in a group of fatal brain diseases known as TSEs. Ex. MCD Prions are believed to cause other proteins to fold the wrong way. Protein folding disease:  Chaperon proteins bind to proteins and help them fold into their normal shape & prevent incorrect interactions & even correct misfolding of a new protein.  Many misfolded proteins can cause diseases. Ex. Prions cause Mad Cow Diseases.  3.5 Nucleic Acids Nucleic acids are polymers of nucleotides. Two varieties of nucleic acids: DNA (deoxyribonucleic acid) Genetic material that stores information for its own replication and for the sequence of amino acids in proteins RNA (ribonucleic acid) Performs a wide range of functions within cells which include protein synthesis and regulation of gene expression  A Nucleotide  Nucleotides c. Pyrimidines versus purines Figure 3.18 5 4 Nucleotides Figure 3.18 5 5 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. RNA Structure Fig. 3.19 N O N G N P N NH2 S H Nitrogen-containing bases O N O P U N CH3 S Backbone N NH2 P N A N S N C Cytosine S Ribose G Guanine A Adenine NH2 O N P Phosphate U Uracil P C N S  Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. DNA Structure T A C G A T G C C Cytosine C S Sugar GGuanine G A Adenine A PPhosphateT Thymine T a. Space-filling model b.Double helix H ― N ― N H O ― ― N H ― N N Complementary N ― N sugar ― ― ― O ― sugar H N H Base Pairing in DNA cytosine (C) guanine (G) H ― ― ― N N H O CH3 ― C N N H N sugar N N ― ― O sugar adenine (A) thymine (T) c. Complementary base pairing © Photodisk Red/Getty RF  A Special Nucleotide: ATP ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates. ATP is a high-energy molecule due to the presence of the last two unstable phosphate bonds. Hydrolysis of the terminal phosphate bond yields: – The molecule ADP (adenosine diphosphate) – An inorganic phosphate – Energy to do cellular work ATP is called the energy currency of the cell. 59  ATP Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. adenosine triphosphate c. NH2 NH2 N N H2O N N N N P P P N N P P + P + ENERGY adenosine triphosphate adenosine diphosphate phosphate b. ATP ADP c: © Jennifer Loomis / Animals Animals / Earth Scenes