Chapter 3

Organic Molecules and Cells

The Variety of Organic Molecules Makes Life Diverse

The chemistry of carbon makes diverse molecules possible

• Organic Chemistry – the chemistry of carbon

• Carbon has 6 electrons so it needs to bond with other elements (CHNOPS) to fill its outer shell

• Hydrocarbons – chains of carbons bonded to hydrogen

• Carbon can have single, double, or triple bonds

• Biomolecules are made of 4 classes– Carbohydrates– Lipids– Proteins– Nucleic acids

• Carbon is the essential ingredient to biomolecules

• Functional groups add to the variety of biomolecules– Carbon chain – backbone of a biomolecule– Functional group – specific combination of bonded

atoms that always react in the same way, regardless of the particular carbon backbone

– R – rest of the molecule

-OH (hydroxyl) turns a molecule into alcohol

-COOH (carboxyl) when it ionizes, releases hydrogen ions making a solution more acidic

Isomers – organic molecules that have identical molecular formulas but a different arrangement of atoms

Molecular subunits can be linked to form varied large biomolecules

• Polymer– Largest of the biomolecules

– Made of many monomers– Glucose is a monomer of starch, a polymer– Proteins are made up of many amino acids– Nucleic acids contain many nucleotides

To create a polymer, a dehydration reaction occurs• A water molecule (-OH and –H) is removed• A bond between two monomers results

Degredation of a biomolecule requires a hydrolysis (“water” “breaking apart”) reaction

• -OH attaches to one subunit• -H attaches to the other subunitEnzyme – molecule that speeds a reaction by bringing

reactants together

Carbohydrates are energy sources and structural components

Simple carbohydrates provide quick energy• Monosaccharide

– Single sugar molecule– Carbon backbone of 3-7 carbons

• Glucose (C6H12O6)– Monosaccharide with 6 carbons– Glucose has isomers such as fructose and galactose

• Ribose and deoxyribose– Monosaccarides with 5 carbon atoms– Found in RNA and DNA respectively

• Disaccharide– Contains two monosaccharides joined during a

dehydration reaction– Maltose, sucrose (table sugar), and lactose are

disaccharides– People with lactose intolerance cannot break down

the disaccharide into monosaccharides

– When disaccharides come into the body, a hydrolysis reaction occurs

Complex carbohydrates store energy and provide structural support

Complex carbohydrates are polysaccharides (polymers of monosaccharides)

• Some polysaccharides (glycogen and starch) are storage molecules– Potatoes contain starch during the winter until it is

needed for growth in the spring

• Structural polysaccharides– Cellulose in plants– Chitin in animals

– Peptidoglycan in bacteria

Lipids store energy and have other functions

Fats and oils are rich energy-storage molecules• Fats and oils consist of

– Glycerol – a compound with 3 –OH groups– Fatty acids – a compound with a long hydrocarbon chain with a

–COOH group at one end• Fat or oil formation

– 3 fatty acids (-COOH portion) react with –OH of glycerol during a dehydration reaction

• Saturated fatty acid– No double bonded carbons– No kinks– Tightly packed solid

• Unsaturated fatty acids– Double bonded carbons– Kinks– Liquid

• Trans fats– Double bonds– Hydrogens are on different sides of the chain (trans means across)

Saturated and trans fat cause plaque buildup in blood vesselsUnsaturated protects against plaque buildup

Other lipids have structural, hormonal, or protective functions

Phospholipids, steroids, and waxes• Phospholipids

– Glycerol, 2 fatty acids, phosphate– Fatty acids are hydrophobic– Head is hydrophilic– In water a phospholipid bilayer naturally occurs

• Cell membrane is a phospholipid bilayer

• Steroids– 4 fused carbon rings– Cholesterol – participates in plaque formation– Estrogen and testosterone – sex hormones

• Waxes– Combines fatty acids and alcohols– Hydrophobic so waterproof and resistant to degredation– Plant leaves, animal skin and fun, ear canal, honey storage

Proteins have many vital functions

Proteins are the most versatile of life’s molecules• Proteins – polymers of amino acids

– Support • Structure• Silk, hair, fingernails

– Metabolism• Enzymes – bring reactants together

– Transport• Allow substances to enter and exit cells

– Defense• Antibodies

– Regulation• Hormones• Intercellular messengers

– Motion• Contractile proteins allow parts of the cell to move and cause muscles to

contract

Each protein is a sequence of particular amino acids• A monomer of a protein is an amino acid• Amino acids have

– Central carbon– Hydrogen atom

– -NH2 (amino group)

– -COOH (acid group)– R group

The R group differs in amino acids and make them different

• Amino acids bond via a dehydration reaction• Peptide – two or more amino acids bonded

together• Polypeptide – chain of many amino acids joined

by peptide bonds• Peptide bond – covalent bond between two

amino acids– Oxygen attracts electrons more than nitrogen

– Oxygen is slightly negative– Hydrogen is slightly positive– Polarity allows hydrogen bonds between –CO of one

amino acid and –NH of another amino acid

The shape of a protein is necessary to its function

• Collagen– Provides strength and support– Super-coiled

• Hemoglobin– Globular– Allows it to travel in blood vessels

Extreme temperatures and pH can denature (alter shape) so it can no longer perform its usual function

Alcohol and salts of heavy metals also denature proteins

Levels of Protein Organization

• Primary structure– Linear– Sequence of amino

acids joined by peptide bonds

• Secondary structure– Peptide bond is polar

– Hydrogen bonds form alpha helix (spiral) or pleated sheet

• Tertiary structure– Final shape for

globular proteins– Hydrophobic portions

are packed on the inside

– Hydrophilic portions are on the outside

– Covalent, ionic, and hydrogen bonds between R groups are present

• Quaternary structure– More than one

polypeptide coming together

Nucleic acids are information molecules

DNA stores coded information• Genes

– Hereditary units composed of DNA (deoxyribonucleic acid)

– Control structure and function of cells and organisms by coding for proteins

• Nucleotide contains– Phosphate– Pentose (5 carbon) sugar– Nitrogen containing base

• Nucleic acid– Polymer of nucleotides

• DNA and RNA (ribonucleic acid) are nucleic acids

• DNA structure contains complementary paired bases that are held together by hydrogen bonds– Thymine (T) always pairs with Adenine (A)– Guanine (G) always pairs with Cytosine (C)

• Genome – DNA base sequence of all genes of an organism

Genetic information flows from DNA to RNA to proteins

• RNA bases include adenine, guinine, uracil, and cytosine• RNA is synthesized next to a segment of DNA• Messenger RNA (mRNA) is a copy of a gene that codes

for proteins• DNA to mRNA to protein

Genetic mutations can result in altered proteins

• Genetic mutation– Change in the sequence of bases, can result in an altered amino

acid sequence in a protein• Sickle-cell

– Amino acid valine (Val) appears instead of glutomate (Glu) resulting in sickle shaped red blood cells

– Double mutation inheritance• Hard and jagged cells• Can clog vessels• Pain, organ damage, low red blood cell count

– Single mutation inheritance• Occasionally sickle shaped such as when invaded with malarial

parasite• Shape causes parasite to die• Individual has advantage• More common in Africa where malaria is prevalent

The nucleotide ATP is the cell’s energy carrier

Adenosine triphosphate (ATP)• Adenine base and ribose

– Form adenosine

• 3 phosphate groups• High energy molecule because last two phosphates are

unstable

• ADP (adenosine diphosphate) and phosphate molecule– Created when the last phosphate bond is hydrolyzed

• ATP breaks down, releases energy, which is used by cells to create biomolecules

• Muscle cells use it for muscle contractions

• Nerve cells use it for nerve impulses