Ch 4 Molecular Basis of Living Organisms

After water, cells consists mostly of carbon-based compounds= organic molecules Examples Carbohydrates, lipids, proteins, nucleic acids (DNA, RNA)

Carbon Bonds Consequence: Four valence electrons--> allows 4 covalent single bonds Or 2 double bonds Consequence: Potential to form complex molecules

Molecular Formula Structural Formula Ball-and-Stick Model Space-Filling Model Methane Ethane Ethene (ethylene)

Shape of carbon complex Tetrahedron When C bonded to 4 other groups Groups can rotate around single bonds Linear/Flat/Planar When C is double bonded to another C Unable to rotate

Common Carbon Bonding Partners in Biological Molecules Hydrogen Oxygen Nitrogen

Molecular Diversity of Organic Molecules Due in part to Formation of carbon chain Differences in length and organization of chain

(commonly called isobutane) Ethane Propane Length Butane 2-methylpropane (commonly called isobutane) Branching 1-Butene 2-Butene Double bonds Note: molecular abbreviation Cyclohexane Benzene Rings

Isomers different covalent arrangements of atoms Compounds with same molecular formula but different structures/ properties Structural isomers different covalent arrangements of atoms Geometric isomers same covalent arrangements;different spatial arrangements Enantiomers mirror images of each other

Structural isomer Geometric Enantiomers Stereoisomers Mirror images LE 4-7 Structural isomer Structural isomers differ in covalent partners, as shown in this example of two isomers of pentane. Geometric cis isomer: The two Xs are on the same side. trans isomer: The two Xs are on opposite sides. Geometric isomers differ in arrangement about a double bond. In these diagrams, X represents an atom or group of atoms attached to a double-bonded carbon. Enantiomers Stereoisomers Mirror images L isomer D isomer Enantiomers differ in spatial arrangement around an asymmetric carbon, resulting in molecules that are mirror images, like left and right hands. The two isomers are designated the L and D isomers from the Latin for left and right (levo and dextro). Enantiomers cannot be superimposed on each other.

Enantiomers (effective against Parkinson’s disease) (biologically LE 4-8 Enantiomers L-Dopa (effective against Parkinson’s disease) D-Dopa (biologically Inactive)

Functional Groups Molecules attached to carbon chains that are involved in reactions Determine distinctive properties of organic molecule

LE 4-9 Estradiol Female lion Testosterone Male lion

The six functional groups that are most important in the biological chemistry: Hydroxyl group Carbonyl group Carboxyl group Amino group Phosphate group Sulfhydryl group

FUNCTIONAL PROPERTIES LE 4-10aa STRUCTURE Ethanol, the alcohol present in alcoholic beverages NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Alcohols (their specific names usually end in -ol) polar as a result of the electronegative oxygen atom drawing electrons toward itself. Attracts water molecules, helping dissolve organic compounds such as sugars

STRUCTURE EXAMPLE NAME OF COMPOUNDS Acetone, the simplest ketone LE 4-10ab Acetone, the simplest ketone STRUCTURE EXAMPLE Acetone, the simplest ketone Propanal, an aldehyde NAME OF COMPOUNDS Ketones if the carbonyl group is within a carbon skeleton FUNCTIONAL PROPERTIES Aldehydes if the carbonyl group is at the end of the carbon skeleton A ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal.

LE 4-10ac STRUCTURE EXAMPLE Acetic acid, which gives vinegar its sour taste NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Carboxylic acids, or organic acids Has acidic properties because it is a source of hydrogen ions. The covalent bond between oxygen and hydrogen is so polar that hydrogen ions (H+) tend to dissociate reversibly; for example, Acetic acid Acetate ion In cells, found in the ionic form, which is called a carboxylate group.

LE 4-10ba STRUCTURE EXAMPLE Glycine Because it also has a carboxyl group, glycine is both an amine and a carboxylic acid; compounds with both groups are called amino acids. NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Amine Acts as a base; can pick up a proton from the surrounding solution: (nonionized) (ionized) Ionized, with a charge of 1+, under cellular conditions

STRUCTURE EXAMPLE NAME OF COMPOUNDS LE 4-10bc STRUCTURE EXAMPLE Glycerol phosphate NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Organic phosphates Makes the molecule of which it is a part an anion (negatively charged ion). Can transfer energy between organic molecules.

STRUCTURE EXAMPLE NAME OF COMPOUNDS LE 4-10bb STRUCTURE EXAMPLE (may be written HS—) Ethanethiol NAME OF COMPOUNDS FUNCTIONAL PROPERTIES Thiols Two sulfhydryl groups can interact to help stabilize protein Structure.

LE 4-10bc Cccccccccc ccccccc ccc PO4_ COOH Questions? OH SH

Ch 5 Overview: The Molecules of Life Within cells small organic molecules bond together to form larger molecules Macromolecules large molecules composed of thousands of covalently connected atoms

long molecule consisting of similar building blocks called monomers What is the structure of most organic macromolecules? Polymer long molecule consisting of similar building blocks called monomers Three of the four classes of life’s organic molecules are polymers: Carbohydrates Proteins Nucleic acids

LE 5-2 Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond Longer polymer Dehydration reaction in the synthesis of a polymer Hydrolysis adds a water molecule, breaking a bond Hydrolysis of a polymer

The Synthesis and Breakdown of Polymers Synthesis (Construction) Monomers link together through dehydration reactions (aka condensation rxn) Breakdown Polymers disassemble into monomers by hydrolysis (reverse of dehydration)

Carbohydrates Functions Fuel Construction and support Structure Simple sugars: monosaccharides Formula (CH2O)n Polymers Disaccharides (relatively short) Polysaccharides (long)

Monosaccharides

Triose sugars (C3H6O3) (C5H10O5) Hexose sugars (C5H12O6) LE 5-3 Triose sugars (C3H6O3) Pentose sugars (C5H10O5) Hexose sugars (C5H12O6) Aldoses Glyceraldehyde Ribose Glucose Galactose Ketoses Dihydroxyacetone Ribulose Fructose

Structures Monosaccharides Functions linear ---> ring major fuel for cells raw material for building larger molecules Structures linear ---> ring

LE 5-4 Glucose Linear and ring forms Abbreviated ring structure

Disaccharide Nomenclature of bond glycosidic linkage forms by a dehydration reaction between two monosaccharides Nomenclature of bond glycosidic linkage

Disaccharide formation LE 5-5 Disaccharide formation Dehydration reaction in the synthesis of maltose 1–4 glycosidic linkage Glucose Glucose Maltose Dehydration reaction in the synthesis of sucrose 1–2 glycosidic linkage Glucose Fructose Sucrose

Polysaccharides

Storage Polysaccharides Fuel storage molecule in plants Polymer of glucose-->Starch -glycosidic linkage Stored in chloroplasts and other plastids

What kind of isomer is this? Geometric LE 5-7 Glucose  Glucose and  glucose ring structures Geometric Starch: 1–4 linkage of  glucose monomers. Cellulose: 1–4 linkage of  glucose monomers.

Starch: a plant polysaccharide LE 5-6a Chloroplast Starch 1 µm Amylose Amylopectin Starch: a plant polysaccharide

Glycogen storage polysaccharide of glucose in ANIMALS Stored in liver and muscle

Glycogen: an animal polysaccharide LE 5-6b Mitochondria Glycogen granules 0.5 µm Glycogen Glycogen: an animal polysaccharide

Structural Polysaccharides Cellulose found in plant cell walls Polymer of glucose -glycosidic linkages

alpha Starch beta Cellulose LE 5-7 Glucose  Glucose and  glucose ring structures alpha Starch Starch: 1–4 linkage of  glucose monomers. beta Cellulose Cellulose: 1–4 linkage of  glucose monomers.

Structural difference of glucose isomers Polymers of alpha glucose helical Polymers with beta glucose Straight Pack together well in microfibrils Stabilized by H-bonds Strong

Cellulose microfibrils in a plant cell wall LE 5-8 Cellulose microfibrils in a plant cell wall Cell walls Microfibril 0.5 µm Plant cells Cellulose molecules b Glucose monomer

-unable to breakdown cellulose -lack hydrolytic enzymes Many animals -unable to breakdown cellulose -lack hydrolytic enzymes -insoluble fiber results Some bacteria Possess enzymes to breakdown cellulose Live in symbiotic relationship in guts of animals (from cow to termite)

Chitin structural polysaccharide in the exoskeleton of arthropods cell walls of many fungi used as surgical thread!

Assignment Due Friday 1. Bring to class a substance made of or containing a carbohydrate. 2. Identify the carbohydrate and do research on its structure, function and uses. Find reliable sources on Google and various science databases like PubMed. Provide a short typed description properly citations.