The Chemistry of Biology

Chapter 2

Organic Chemistry and the Importance of Carbon to Life

Inorganic Molecules

• Molecules that lack the basic framework of the elements of carbon and hydrogen– NaCl

– Mg3(PO4)2

– CaCO3

– CO2

Organic Molecules

• Molecules that contain the basic framework of the elements of carbon and hydrogen– Simplest: CH4

– Complex: antibody molecules with a molecular weight of 1,000,000

The Chemistry of Carbon

• Carbon is the fundamental element of life:

– Ideal atomic building block to form the backbone of organic molecules

– Four electrons in outer orbital can be shared with for other atoms, including carbon

Functional Groups

• Molecular groups or accessory molecules that bind to organic compounds– Help define the class of certain groups of

organic compounds– Confer unique reactive properties on the

whole molecule– Reactions of an organic compound can be

predicted by knowing its functional group

Functional Groups

Check Your Understanding• Explain the relationship between atoms and elements.• List and describe the three particles associated with

atoms. What properties do each give to an atom?• Explain the difference between a molecule and a

compound.• List and describe four types of chemical bonds.• Differentiate between a solute and a solvent. What role

does water often play in the creation of solutions?• Provide a brief definition of pH. Differentiate between

acids and bases chemically and in terms of the pH scale.• Describe three ways in which carbon is the fundamental

element of life. What role do functional groups often play in organic molecules?

Macromolecules:The Superstructures of Life

Section 2.2

Macromolecules

• Biochemistry: explores the compounds of life

• Four main families of biochemicals:– Carbohydrates– Lipids– Proteins– Nucleic acids

Macromolecules

• Macromolecules: – Assembled from smaller molecular subunits or

building blocks– Often very large compounds

• Polymerization:– Monomers (repeating subunits) are bound

into varying lengths called polymers

Role of Macromolecules

• Structural components

• Molecular messengers

• Energy sources

• Enzymes (biochemical catalysts)

• Nutrient stores

• Sources of genetic information

CarbohydratesA Source of Fuel and Structure

Types of Carbohydrates

• Saccharide: a sugar

• Monosaccharide: a simple sugar containing from 3 – 7 carbons

• Disaccharide: combination of two monosaccharides

• Polysaccharide: polymer of five or more monosaccharides

Types of Carbohydrates

Identifying Carbohydrates

• Monosaccharides and disaccharides are described with the suffix –ose

• Hexose: composed of 6 carbons

• Pentose: composed of 5 carbons

Carbohydrate Bonds

• Glycosidic bonds: carbons on adjacent sugar units are bonded to the same oxygen atom like links in a chain

• Dehydration synthesis: occurs in the polymerization process when one carbon group gives up an H and the other carbon group gives up an OH, forming water

Carbohydrate Bonds

Cellulose

• Long, fibrous polymer• Gives strength and rigidity to plants and

microscopic algae• One of the most common organic substances on

Earth• Digestible only by bacteria, fungi, and protozoa

Agar

• Important in preparing solid culture media

• Natural component of seaweed

• Polymer of galactose and sulfur-containing carbohydrates

Chitin

• Polymer of glucosamine

• Found in the exoskeletons of certain fungi

Peptidoglycan

• Polysaccharides are linked to peptide fragments

• Provides the main source of structural support to the bacterial cell wall

Lipopolysaccharide (LPS)

• Complex of lipid and polysaccharide found in the outer membrane of gram-negative bacteria

• Responsible for symptoms of fever and shock

Glycocalyx

• Composed of polysaccharides bounds in various ways to proteins

• Functions in attachment to other cells or as a site for receptors

Glycogen / Starch

• Storage molecules in cells– Glycogen in animal cells– Starch in plant cells

• Must be broken down by appropriate enzymes for use by the cell

• Hydrolysis: digestion or breakdown of polysaccharides that requires the addition of water

LipidsLife’s Hydrophobic Molecule

Lipids

• Operational term for substances that are not soluble in polar solvents but are soluble in nonpolar solvents

• Long or complex hydrocarbon chains that are hydrophobic

Lipids

• Triglycerides:– Storage lipids that includes fats and oils– Composed of a single molecule of glycerol

bound to three fatty acids– Glycerol: 3-carbon alcohol with three OH

groups that serve as binding sites– Fatty acids: long chain hydrocarbons with a

carboxyl group at the end

Lipids

Lipids

• Saturated fatty acid: – All carbons in the fatty acid chain are single-

bonded to 2 other carbons and 2 hydrogen atoms

• Unsaturated fatty acid: – a fatty acid in which at least one double bond

exists between carbon atoms

Phospholipids

• Contain only two fatty acids attached to a glycerol

• Third binding site holds a phosphate group bound to an alcohol

• Have a hydrophilic region and a hydrophobic region

• Allows the molecule to form bilayers and membranes

Phopsholipid Bilayers

• Hydrophilic face orients itself toward the solution

• Hydrophobic tails immerse themselves in the bilayer

• These characteristics allow selective permeability and fluidity

Steroids

• Ringed compounds commonly found in membranes and hormones

• Cholesterol: reinforces cell membranes in animal cells and cell-wall deficient bacteria

• Ergosterol: found in the cell membranes of fungi

Waxes

• Ester formed between a long-chain alcohol and a fatty acid

• Soft and pliable when warmed, waterproof when cold

• Natural waterproofing of skin, fur, feathers, etc.• Unique wax found in certain species of bacteria

confers natural pathogenicity

ProteinsThe Shapers of Life

Proteins

• Predominant molecule in cells– Determine structure, behavior, and unique

qualities of organisms

• Amino acids:– Building blocks of proteins– Exist in 20 different naturally-occurring forms– Linked by peptide bonds

Amino Acid Structure

• α (alpha) carbon

• Amino group (NH2)

• Carboxyl group (COOH)

• Hydrogen atom (H)• R group: imparts

unique characteristics to the amino acid

Protein Structure

• Peptide:– Molecule composed of short chains of amino

acids

• Polypeptide:– Has more than 20 amino acids– Not all polypeptides are large enough to be

considered proteins

Protein Structure and Diversity

• Primary (1°) structure: – The type, number, and order of amino acids.

• Secondary (2°) structure: – Arises when functional groups on the outer

surface of the molecule interact with each other.

• α helix• β pleated sheet

Protein Structure and Diversity

• Tertiary (3°) structure: – Torsion caused by interaction between

functional groups– Covalent sulfide bonds

• Quaternary (4°) structure: – Large multiunit proteins formed by more than

one polyprotein

Protein Structure and Diversity

Selected Protein Roles

• Enzymes:– Catalysts for chemical reactions in cells– Specificity comes from the unique patterns in

enzyme binding sites

• Antibodies:– Complex glycoproteins with specific

attachment regions for microorganisms

Protein Structure Determines Function

• Native state: – The functional, three-dimensional form of a

protein

• Denature: – Disruption of the native state of a protein

through heat, chemicals, acid or other means, making the protein non-functional

Prions

Infectious Proteins! – Creutzfeldt-Jakobs Disease (CJD)Chapter 6 and Chapter 18

Spongiform Encephalopathies

• Implicated in chronic, persistent disease in humans and animals

• Brain tissue removed from affected animals resembles a sponge

• Often caused by prions– Distinct protein fibrils

deposited in brain tissue of affected animals

Infections by Prions

• Exact mode of infection is unknown• Protein composition of prions has

revolutionized ideas of what can constitute an infectious agent

• Scientists still do not know how prions replicate given that they have no nucleic acid

Creutzfeldt-Jakob Disease (CJD)

• Affects the central nervous system of humans• Causes gradual degeneration and death• Transmissible by an unknown mechanism• Several animals are victims of similar diseases:

– Scrapies: Sheep, mink elk– Bovine spongiform encephalopathy: cows

Nucleic AcidsBearer’s of Life’s Genetic Code

Nucleic Acids

• Deoxyribonucleic Acid (DNA):– Contains a special coded genetic program

with detailed instructions for each organism’s heredity

• Ribonucleic Acid (RNA):– Helper molecules responsible for translating

and carrying out the instructions of DNA

Nucleic Acids

• DNA and RNA are composed of repeating nucleotide subunits– Nitrogen base– Pentose (5-carbon)

sugar– Phosphate

Nucleic Acids

• Purines:– Nitrogen bases

composed of two rings– Adenine and Guanine

• Pyrimidines:– Nitrogen bases

composed of one ring– Thymine, Cytosine,

and Uracil

DNA vs. RNA

• DNA: – Contains all of the nitrogen bases except uracil– Nitrogen bases are covalently bonded to

deoxyribose

• RNA:– Contains all of the nitrogen bases except thymine– Nitrogen bases are covalently bonded to ribose

The Double Helix of DNA

RNA: Organizer of Protein Synthesis

• Long, single strand of nucleotides

• Three major types of RNA:– mRNA: copy of a gene– tRNA: carrier that transports the correct

amino acids to the ribosome– rRNA: major component of ribosome

ATP: Energy Molecule

• Adenosine Triphosphate (ATP):– Adenine– Ribose– Three phosphate

molecules

• Releases energy when the bond is broken between the 2nd and 3rd phosphates

Check Your Understanding• List and describe the four main biochemicals.• Why are phospholipids important biological molecules?• Differentiate among primary, secondary, tertiary, and

quaternary levels of protein structure.• List the three components of nucleic acids. Identify the

nucleotides of DNA and RNA.• List the three components of ATP. Why is ATP an

important energy molecule for cells?• Provide examples of cell components made from each of

the families of biochemicals.

Cells:Where Chemicals Come to Life

Section 2.3

Cells: Where Chemicals Come to Life

• Cell:– Fundamental unit of life– Huge aggregate of carbon, hydrogen, oxygen,

nitrogen, and other atoms– Follows the basic laws of chemistry and

physics– Produces characteristics, reactions, and

products that can only be described as living

Fundamental Characteristics of Cells

• Three basic categories:– Bacteria– Archaea– Eukarya: animals, plants, fungi, protozoans

Fundamental Characteristics of Cells

• Eukaryotic cells:– Compose plants, animals, and fungi

– Contain a nucleus and organelles that perform functions for growth, nutrition, or metabolism

• Bacteria and Archaea:– Do not contain a nucleus or organelles

– Structurally very complex

– Can engage in every activity eukaryotic cells can and some that they can’t

Check Your Understanding

• What is the basic definition of a cell?

• What are the basic shapes of cells?

• How are bacteria and archaea different than eukarya?

• Recall three characteristics common to all cells.