Chapter 3: The Chemical Basis of Life II: Organic Molecules PDF

CHAPTER 3 THE CHEMICAL BASIS OF LIFE II: ORGANIC MOLECULES From atom to molecule to macromolecule Matter( anything that takes up space and has mass) composed of atoms Atoms make molecule Molecules join together to make macromolecules (proteins, carbo, lipids) Cells contain thousan...

CHAPTER 3 THE CHEMICAL BASIS OF LIFE II: ORGANIC MOLECULES From atom to molecule to macromolecule Matter( anything that takes up space and has mass) composed of atoms Atoms make molecule Molecules join together to make macromolecules (proteins, carbo, lipids) Cells contain thousands of molecules 2 Organic molecules carbon containing molecules and are found in all forms of life. Carbon- containing molecules are collectively referred to as organic molecules. 3  Organic Chemistry The science of carbon-containing molecules is known as organic chemistry. Organic molecules contain Carbon (C) and Hydrogen (H) Organic molecules are mainly abundant in living organisms Macromolecules are large, complex organic molecules Four categories of Macromolecules: - Carbohydrates - Lipids - Proteins - Nucleic Acids Bacterial cell contains about 5000 different organic molecules and Plant or animal cell contains twice that number 4 Covalent bond with carbon carbon atoms most commonly form covalent bonds with other carbon atoms and with hydrogen, oxygen, nitrogen, and sulfur atoms. Bonds between two carbon atoms, between carbon and oxygen, or between carbon and nitrogen can be single or double, or in the case of C≡C and C≡N bonds, triple. Carbon bonds may occur in configurations that are linear, ringlike, or highly branched and such molecules perform variety of functions. *Carbon n hydrogen combine bc of covalent bonding. *Sometimes u see nitrogen, oxygen and sulfur bonded w carbon *Ring = pentagon structure = glucose (6 carbon) or in linear structure or in a 5 ring structure, they will possibly make a lot of molecules thanks to many structures carbon makes so it’s the most essential cell needs. 5 Nonpolar and polar bonds in an organic molecule Carbon and hydrogen have similar electronegativities. Therefore, carbon-carbon and carbon-hydrogen bonds are nonpolar. molecules with a high amount of hydrogen- carbon bonds, called hydrocarbons, are hydrophobic and poorly soluble in water because they r forming nonpolar bonding so they do equal sharing, so they r neutral and Carbon not attract anything forms , so theybonds polar covalent don’t with attract more electronegative water such as oxygen or nitrogen. atoms, Polar molecule is much more soluble in water due to the electrical attraction of polar water molecules. The ability of carbon to form both polar and nonpolar bonds contributes to its ability to serve as the backbone for an astonishing variety of biologically important molecules. 6 Isomers Two molecules with an identical chemical formula but different structures and characteristics are called isomers. If carbon structure is arranged diff but in a same formula, then it makes a new molecule Structural isomers contain the same atoms but in different bonding relationships. Stereoisomers have identical bonding relationships.  the two hydrogen atoms linked to the two carbons of a C=C double bond may be on the same side of the carbons, in which case the C=C bond is called a cis double bond.  If the hydrogens are on opposite sides, it is a Same bonding but the molecules r in trans double bond. diff order or place Cis = same direction  enantiomer, exists as a pair of Trans = opposite direction 7 molecules that are mirror images.  Inorganic Molecules Organic Molecules Usually contains positive and negative ions Always contains carbon and hydrogen Usually ionic bonding Always covalent bonding Always contains small number of atoms Often quite large, with many atoms Often associated with non living matter Usually associated with living organisms 8 The four class of organic molecules and macromolecules 1. Carbohydrates, 2. lipids, 3. proteins, 4. nucleic acids Polymers are made up of monomers. Protein (polymer) can contain hundreds of amino acids (monomers) and nucleic acid can contain hundreds of nucleotides. 9 The four class of organic molecules and macromolecules How can polymers get so large? Many smaller molecules called monomers are linked together to form polymers. 10 Polymer formation: Dehydration - Removal of water Monomer combined together molecule. as polymer and water is release as the process is happening Polymer degradation: Hydrolysis - Addition of water molecule. To break DNA, water is needed, DNA Is a polymer 11 dehydration reaction To form a polymer, a water molecule removed for adding each monomer Example: long strand of DNA where nucleotides are joined to form polynucleotide 12  Stearic acid (fatty acid) Glycerol dehydration reaction to form fat (triglyceride) Triglyceride hydrolysis reaction The process by which a polymer is broken down into monomers water is added back each time a monomer is released 14 hydrolysis reaction hydrolysis  Carbohydrates An immediate energy source in living organisms Large molecule Composed of C, H, and O atoms General formula: Cn(H2O)n Most of the C atoms in a carbohydrate are linked to a H atom and a OH group Plays structural roles in a variety of organisms The term carbohydrates include single sugar molecules and also chains of sugars (polysaccharide) 16  Carbohydrates: Monosaccharides Simplest sugars. Monosaccharides (monos, single and sacchar, sugar). Ready energy Molecular formula for a single sugar is a multiple of CH2O. Sugars have many hydroxyl groups, and this polar functional group makes them soluble in water. Most common are 5 or 6 carbons  Pentoses: 5C (component of RNA and DNA molecules)  ribose (C5H10O5); found in RNA  deoxyribose (C5H10O4); found in DNA  Hexose: 6C  glucose (C6H12O6); water soluble Different ways to depict structures  Ring or linear 17  Glucose isomers Structural isomers: different arrangement of same elements Glucose and galactose Stereoisomers: glucose Geometric isomers:above or below ring α- and β-glucose Enantiomers: mirror image D- and L-glucose d-Glucose is the isomer of glucose that is commonly found in living cells. By comparison, l-glucose is rarely found in living cells, and it binds poorly to enzymes that recognize d-glucose. 18  Carbohydrates: Disaccharides Composed of 2 monosaccharides Joined by dehydration/condensation reaction Broken apart by hydrolysis Examples:. Sucrose = Glucose (6C) + Fructose (5C), -Sucrose is the form in which sugar is transported in plants; -Sugar we use to sweeten our food. Maltose = Glucose + Glucose [malt sugar]. Lactose = Glucose + Galactose) [milk sugar] 19  Carbohydrates: Polysaccharides Many monosaccharides linked together to form long polymers Short term energy storage Large molecules can’t pass through plasma membrane (not soluble in water, and much larger than sugar) when an organism requires energy, polysaccharides are broken down to release sugar molecules Glucose molecules can be stored by organisms as different macromolecules. Energy storage molecules: Starch in plants, (energy storage) Glycogen in animals, (energy storage) Structural role : Cellulose (plants), chitin (insects and fungi), glycosaminoglycans (animals) 20  Starch and glycogen are polymer of alpha-d- glucose Cellulose is a polymer of β-d- glucose 21  Carbohydrates: Polysaccharides (Energy Storage Molecules) Starch: is a mixture of two complex carbohydrates: amylose and amylopectin, both of which are polymers of glucose. It is used by plants as a way to store excess glucose. Glycogen: Animals store glucose as Glycogen (granules in liver). polysaccharide of glucose which functions as the primary short term energy storage in animal cells. Hormones control release and storage of glucose: Insulin released from the pancreas promotes the storage of the glucose as glycogen. Glucagon, another hormone released from the pancreas stimulates glycogen breakdown into glucose. 22  Carbohydrates: Polysaccharides (Structural Molecules) Cellulose:. Most abundante of all the carbohydrates. Cellulose. Polymer of b-glucose. Cell walls in plants contain Cellulose.. Parallel glucose chains  cellulose Chitin:. Form the external skeleton of many insects and the cell wall of fungi.. The sugar monomer of chitin have nitrogen-containing groups attached to them. Glycosaminoglycans:. Found in animals.. Abundantly found in cartilage.. Tend to have sugar monomers with carboxyl and sulfate groups. 23  Lipids Organic molecules Composed predominantly of H and C atoms (hydrocarbon chains). Defining feature of lipids is that they are nonpolar (Hydrogen bonded only to carbon have no tendency to form hydrogenated bonds with water molecules) and therefore very insoluble in water. Lipids (fats) used for both insulation and long-term energy storage by animals. Plants use oil instead of fat for a long-term energy storage Phospholipids and steroids: other important lipids found in living things. 24  Lipids: Fats Mixture of triglycerides (Also known triacylglycerols), Long-term Energy storage Formed by bonding glycerol to three fatty acids; joined by dehydration or condensation reaction Broken apart by hydrolysis Glycerol: compound with three OH groups (OH is polar group- glycerol soluble in water). Fatty acid consists of long hydrocarbon (R) chain with a carboxyl (-COOH) group at one end. Chemical formula: R-COOH Fat and oils formation: Acid portions of the three fatty acids react with the OH group of glycerol during a dehydration reaction.  Lipids: Fats (contd) The three fatty acids can be all different, all the same, or only two the same. 26  Lipids: Fats (contd) Fatty acids are either saturated or unsaturated. Saturated fatty acids:. Have no double bonds between the carbon atoms. All carbons are linked by single covalent bonds.. Tend to be solid at room temperature Unsaturated fatty acids:. contain one or more double bonds in the carbon chain - 1 double bond: monounsaturated - 2 or more: polyunsaturated. Tend to be liquids at room temperature (plant oils) Fats are important for energy storage: 1g of fat stores twice as much energy as 1g of glycogen or starch Fats can also be structural in providing cushioning and insulation Saturated and unsaturated fatty acids 28 Lipids: Phospholipids Phospholipids: membrane components, contains phosphate group. Instead of third fatty acid attached to glycerol as in fat, there is a polar phosphate group. Amphipathic molecule Hydrophilic heads (phosphate region) hydrophobic tails ( Fatty acid chains) Arrange themselves so polar heads are adjacent to water. Bulk of cell plasma membrane consists of phospholipid bilayer. 29  Lipids: Steroids Have skeletons of 4 interconnected carbon rings Usually not very water soluble Cholesterol, estrogen and testosterone Cholesterol is the precursor of several other steroids, such as testosterone and estrogen. Testosterone and estrogen differ only by the functional group attached to the same carbon skeleton, and yet have a profound effect on the body and the sexuality of an animal. 30  Waxes Long-chain fatty acid bonds with a long-chain alcohol, secreted onto plant leaves and insect cuticles Very nonpolar and exclude water: provide a barrier to water loss High melting point: Solid at normal temperature. Waterproof Resistant to degradation Structural elements in colonies (bee hives) 31  Proteins Enzymes r proteins Diverse functions: - Support: keratin (hair, nail, ligaments..) - Enzymes: bring reactants together - Transport: channel and carrier protein (plasma membrane) allow substance to enter and exit cells. Hemoglobin: transport of oxygen. - Defense: antibodies (combine with foreign subjects and prevent them from destroying cells) - Hormones: eg. insulin regulates blood glucose - Motion: eg. actin and myosin allow parts of cells to move and cause muscles to contract This is covalent bond Composed of C, H, O, N, and small amounts of other elements, notably S Amino acids are the monomers of proteins. Common structure with variable R-group. 20 amino acids. Side-chain determines structure and function. Bond to a hydrogen atom, an amino group -NH2, an acidic group -COOH, and an R (remainder) group. 32 Proteins: Amino Acids Structure Amino acids are usually classified by properties of the side chain into four groups: acidic, basic, hydrophilic (polar), and hydrophobic (nonpolar). 33 34  Proteins: Peptide bond formation. Amino acids are joined by dehydration or condensation reaction through a covalent bond called “peptide bond”.. Peptide: Two or more amino acids bonded together.. Polypeptide : Chain of many amino acids joined by peptide bonds.. Proteins are made up of 1 or more polypeptides. Peptide bonds are broken apart by hydrolysis 35 1 more amino acid than the bond so if the bond is 7 then the animo acid is 8 36  Protein Structure Primary: Sequence of amino acids. Secondary: Polypeptide coils or folds in a particular fashion. Hydrogen bonding often holds the secondary structure Tertiary: Folding and twisting that results in final three dimensional shape of a polypeptide. Quaternary: They r functional, the Consists of more than one only functional structure in most of the cases polypeptide. because most proteins have to be a quaternary structure 37  Protein structure Primary structure:. Amino acid sequence. Determined by genes Secondary structure:. Chemical and physical interactions cause folding. Irregular or repeating. α helices and β pleated sheets - Key determinants of a protein’s characteristics. “Random coiled regions” - Not α helix or β pleated sheet - Shape is specific and important to function When 1 is connecting to 3, and 5 is connecting to 9 38 like that.  The five factors promoting protein folding and stability 1. H bonds: promotes protein folding and stability (when 1 and 5 connect by bond by hydrophobic reasons)?? 2. Ionic bonds: ionic and polar interactions promote folding and stability 3. Hydrophobic effects: avoid water contact 4. Van der Waals forces: atoms that have weak attarctions 5. Disulfide bridges: covalent bonds that link 2 cysteine aminoi acids that contain sulfthydryl group 39  Protein-protein interactions Many cellular processes involve steps in which two or more different proteins interact with each other Very specific binding at surface Use first 4 factors 40  Proteins Contain Functional Domains Within Their Structures RNA polymers Module or domains in proteins have distinct structures and function which is a protein makes RNA and need dna-binding Signal transducer and activator of transcription (STAT) protein example domain to bind Each domain of this protein is involved in a distinct biological function Proteins that share one of these domains also share that function  Nucleic Acids Responsible for the storage, expression, and transmission of genetic information Two classes. Deoxyribonucleic acid (DNA) Store genetic information coded in the sequence of their monomer building blocks. Ribonucleic acid (RNA) Involved in decoding this information into instructions for linking together a specific sequence of amino acids to form a polypeptide chain Monomer is a nucleotide Made up of phosphate group, a 5C sugar (either ribose or deoxyribose), and a single or double ring of C and N atoms known as a base Sugar-phosphate backbone 42  Nucleotides r bonded by phosphoester, nucleotides 1 and 2 r added by phosphoester bond (both DNA and RNA, in any base, doesn’t matter) between sugar and phosphate Bases r outside and add tg by hydrogen bond A and t – two hydrogen bond C and g – 3 hydrogen bond Structure of a DNA strand The double-stranded structure of DNA 43  DNA vs. RNA DNA RNA Deoxyribonucleic acid Ribonucleic acid Deoxyribose Ribose Thymine (T) Uracil (U) Adenine (A), guanine (G), cytosine (C) used in both 2 strands- double helix Single strand 1 form Several forms 44