Chapter 3 The Molecules of Cells

Got Lactose? Lactose intolerance illustrates the importance of biological molecules to the functioning of living cells and to human health Molecular interactions, such as those between the gene for lactase production, the enzyme lactase, and the milk sugar lactose, drive all biological processes

INTRODUCTION TO ORGANIC COMPOUNDS 3.1 Life's molecular diversity is based on the properties of carbon Organic compounds contain at least one carbon atom Covalent bonding enables carbon to form complex structures – A carbon atom has four electrons in its outer shell – To complete the shell, it can form four covalent bonds – The way bonding occurs among atoms determines the overall shape of the molecule

LE 3-1a Structural formula Ball-and-stick model Space-filling model Methane The 4 single bonds of carbon point to the corners of a tetrahedron.

LE 3-1b EthanePropane Carbon skeletons vary in length.

LE 3-1c ButaneIsobutane Skeletons may be unbranched or branched.

LE 3-1d 1-Butene2-Butene Skeletons may have double bonds, which can vary in location.

LE 3-1e Skeletons may be arranged in rings. CyclohexaneBenzene

Animation: Carbon Skeletons Animation: Carbon Skeletons Animation: Isomers Animation: Isomers Animation: L-Dopa Animation: L-Dopa

Hydrocarbons are composed of only hydrogen and carbon – A series of covalently bonded carbons forms the carbon skeleton of the molecule – Isomers are molecules with the same molecular formula but different structures and properties

3.2 Functional groups help determine the properties of organic compounds Functional groups are groups of atoms attached to the carbon skeleton of molecules – Usually participate in chemical reactions – Give organic molecules their particular properties

LE 3-2 Estradiol Female lion Male lion Testosterone

Five main functional groups are important in the chemistry of life: – Hydroxyl group – Carbonyl group – Carboxyl group – Amino group – Phosphate group These groups are all polar and make compounds containing them hydrophilic (water- loving)

3.3 Cells make a huge number of large molecules from a small set of small molecules Four main classes of biological macromolecules – Carbohydrates – Lipids – Proteins – Nucleic acids

Cells make the most of their large molecules by joining smaller organic monomers into chains called polymers – Monomers are usually linked by dehydration reactions A water molecule is removed Animation: Polymers Animation: Polymers

LE 3-3a Short polymerUnlinked monomer Dehydration reaction Longer polymer

– Polymers are broken down to monomers by the reverse process, hydrolysis A water molecule is added

LE 3-3b Hydrolysis

CARBOHYDRATES 3.4 Monosaccharides are the simplest carbohydrates Monosaccharides (single sugars) are carbohydrate monomers A monosaccharide has a formula that is a multiple of CH 2 O – Contains hydroxyl groups and a carbonyl group – May be isomers, such as glucose and fructose – May take chain or ring forms

LE 3-4b Glucose Fructose

LE 3-4c Structural formula Abbreviated structure Simplified structure

3.5 Cells link two single sugars to form disaccharides Two monosaccharides can join to form a disaccharide – Linked by a dehydration reaction – Example: two glucose monomers form the disaccharide maltose Animation: Disaccharides Animation: Disaccharides

LE 3-5 Glucose Maltose

CONNECTION 3.6 How sweet is sweet? We perceive a sweet taste when a chemical binds to the sweet receptor on the tongue – The structure of a compound determines how well it fits into a receptor – The more strongly the chemical binds to the receptor, the sweeter it is perceived to be – The chemical can be sugar or another compound, such as aspartame

3.7 Polysaccharides are long chains of sugar units Polysaccharides are polymers of monosaccharides linked together by dehydration reactions Some polysaccharides are storage molecules – Starch in plants – Glycogen in animals Some polysaccharides serve as structural compounds – Cellulose in plants Animation: Polysaccharides Animation: Polysaccharides

LE 3-7 Starch granules in potato tuber cells Glycogen granules in muscle tissues Cellulose fibrils in a plant cell wall Cellulose molecules G LYCOGEN C ELLULOSE S TARCH Glucose monomer

LIPIDS 3.8 Fats are lipids that are mostly energy-storage molecules Lipids are diverse compounds consisting mainly of carbon and hydrogen atoms – Linked by nonpolar covalent bonds – Hydrophobic (water-fearing) Animation: Fats Animation: Fats

Fats, also called triglycerides, are lipids whose main function is energy storage – Polymers of fatty acids (usually three molecules) and one glycerol molecule – Formed by dehydration reactions

Saturated fatty acids – Contain the maximum number of hydrogens – Have no double bonds between carbons Unsaturated fatty acids – Contain fewer than the maximum possible hydrogens – Have double bonds between carbons Oils are liquid fats

3.9 Phospholipids, waxes, and steroids are lipids with a variety of functions – Phospholipids – Contain two fatty acid groups and the element phosphorus – Are a major component of cell membranes Waxes – Consist of a single fatty acid linked to an alcohol – Form waterproof coatings

Steroids – Have backbones bent into rings, as in cholesterol – Are often hormones or the basis of hormones

CONNECTION 3.10 Anabolic steroids pose health risks Anabolic steroids are natural and synthetic variants of the male hormone testosterone – Build up bone and muscle mass – Can cause serious health problems

PROTEINS 3.11 Proteins are essential to the structures and activities of life A protein is a polymer constructed from amino acid monomers The structure of the protein determines its function The seven major classes of protein are – Structural: hair, cell cytoskeleton – Contractile: producers of movement in muscle and other cells

– Storage: sources of amino acids, such as egg white – Defense: antibodies, membrane proteins – Transport: carriers of molecules such as hemoglobin, membrane proteins – Signaling: hormones, membrane proteins – Enzymes: regulators of the speed biochemical reactions

Animation: Structural Proteins Animation: Structural Proteins Animation: Storage Proteins Animation: Storage Proteins Animation: Transport Proteins Animation: Transport Proteins Animation: Receptor Proteins Animation: Receptor Proteins Animation: Contractile Proteins Animation: Contractile Proteins Animation: Defensive Proteins Animation: Defensive Proteins Animation: Enzymes Animation: Enzymes Animation: Hormonal Proteins Animation: Hormonal Proteins Animation: Sensory Proteins Animation: Sensory Proteins Animation: Gene Regulatory Proteins Animation: Gene Regulatory Proteins

3.12 Proteins are made from amino acids linked by peptide bonds Protein diversity is based on different arrangements of a common set of 20 amino acid monomers Each amino acid contains – An amino group – A carboxyl group – One of twenty functional ("R") groups The three groups and a hydrogen atom are bonded to a central "alpha" carbon

LE 3-12a Carboxyl (acid) group Amino group

The structure of the R group determines the specific properties of each amino acid An amino acid may be hydrophobic or hydrophilic, depending on the characteristics of the R group

LE 3-12b Leucine (Leu) Serine (Ser) HydrophobicHydrophilic Aspartic acid (Asp)

Cells link amino acids together by dehydration synthesis The bonds between amino acid monomers are called peptide bonds Dipeptides are two amino acids long; polypeptides are from several to more than a thousand amino acids long

LE 3-12c Amino acid Dipeptide Amino acid Peptide bond Dehydration reaction Amino group Carboxyl group

3.13 A protein's specific shape determines its function A protein consists of one or more polypeptide chains spontaneously folded into a unique shape

LE 3-13 Groove

The folding of a polypeptide creates grooves that enable other molecules to bind to it In denaturation, chemical or physical changes can cause proteins to lose their shape and thus their specific function

3.14 A protein's shape depends on four levels of structure Primary structure: the unique sequence of amino acids forming the polypeptide Secondary structure: the coiling or folding of the chain, stabilized by hydrogen bonding – May be alpha helix or pleated sheet (which dominates the silk protein of a spider's web)

Tertiary structure: the overall three-dimensional shape of the polypeptide Quaternary structure: the association of two or more polypeptide chains (subunits)

LE 3-14a Levels of Protein Structure Amino acids

LE 3-14b Levels of Protein Structure Amino acids Hydrogen bond Alpha helix Pleated sheet

LE 3-14c Levels of Protein Structure Amino acids Hydrogen bond Alpha helix Pleated sheet Polypeptide (single subunit of transthyretin)

LE 3-14d Levels of Protein Structure Amino acids Hydrogen bond Alpha helix Pleated sheet Polypeptide (single subunit of transthyretin) Transthyretin, with four identical polypeptide subunits

Animation: Protein Structure Introduction Animation: Protein Structure Introduction Animation: Primary Protein Structure Animation: Primary Protein Structure Animation: Secondary Protein Structure Animation: Secondary Protein Structure Animation: Tertiary Protein Structure Animation: Tertiary Protein Structure Animation: Quarternary Protein Structure Animation: Quarternary Protein Structure

Collagen is an example of a protein with a quaternary structure – Three subunits wound into a helix – Structure provides great strength to long fibers

TALKING ABOUT SCIENCE 3.15 Linus Pauling contributed to our understanding of the chemistry of life Felt that the study of individual parts must come first, then putting the parts together Began his career by studying chemical bonding First described the alpha helix and pleated sheet protein structures Discovered how abnormal hemoglobin causes sickle cell disease Won two Nobel prizes, for chemistry and for peace (for helping produce a nuclear test ban treaty)

NUCLEIC ACIDS 3.16 Nucleic acids are information-rich polymers of nucleotides There are two types of nucleic acid-DNA and RNA Nucleic acids are polymers of nucleotide monomers composed of – A five-carbon sugar – A phosphate group – A nitrogenous base-adenine (A), thymine (T), cytosine ( C), and guanine (G) in DNA; A, G, C, and uracil (U) in RNA

LE 3-16a Nitrogenous base (A) Sugar Phosphate group

Nucleotide monomers are formed into a polynucleotide with a sugar-phosphate backbone and attached nitrogenous bases

LE 3-16b Nucleotide Sugar-phosphate backbone

Hydrogen bonding between nitrogenous bases creates the final structure of the nucleic acid – RNA usually consists of a single polynucleotide strand – DNA is a double helix Two polynucleotides are twisted around each other Nitrogenous bases protruding from the backbone pair with each other, A with T and G with C

LE 3-16c Base pair

– Specific sequences of DNA make up genes that program the amino acid sequences of proteins