Ap Bio, Chapter Five, Guide

1 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Five: The Structure and Function of Macromolecules (Text from Biology , 6 th Edition, by Campbell and Reece)

The Structure and Function of Macromolecules (Chapter Five)

POLYMER PRINCIPLES

Most Macromolecules are Polymers

The four main classes of macromolecules are carbohydrates, lipids, proteins and nucleic acids. The large molecules in carbohydrates, proteins, and nucleic acids are polymerspolymers, long molecules consisting of similar or identical building blocks linked by covalent bonds. These blocks are small molecules called monomersmonomers.

Monomers are connected by a condensation reactionreaction, also known as a dehydration reactionreaction, where a water molecule is lost to allow the two monomers to bond together. One monomer loses a hydroxyl group (-OH), while the other loses a hydrogen (-H). Enzymes help to speed up these dehydration reactions.

Hydrolysis is the process that reverses the dehydration reaction and breaks polymers back into monomers. By adding a water molecule to the bond, a hydrogen atom will attach to one monomer and the hydroxyl will attach to the other monomer. Digestion works through hydrolysis: enzymes work to speed up hydrolysis and break apart large polymers into monomers that can be absorbed into the bloodstream.

An Immense Variety of Polymers Can Be Built From a Small Set of Monomers

There is an amazing number of different combinations of polymers that result from the approximately 40 to 50 common monomers. The variation in the linear sequence the units follow result in unique macromolecules from small molecules common to all life.

CARBOHYDRATES – FUEL AND BUILDING MATERIAL

Carbohydrates include both sugars and their polymers. Monosaccharides are single sugars (also known as simple sugars) and disaccharides are double sugars. Polysaccharides are carbohydrates.

Sugars, the Smallest Carbohydrates, Serve as Fuel and Carbon Sources

Monosaccharides generally have molecular formulas that are a multiple of CH 2O. Glucose is the most common monosaccharide. A sugar has a carbonyl group and multiple hydroxyl groups. Depending on the location of the carbonyl group, the sugar is either an aldose or a ketose. Another criterion for grouping sugars is the size of the carbon skeleton, which can be from three to seven carbons long. Those with three carbons are trioses, five carbons are pentoses, and six carbons are hexoses. 2 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Five: The Structure and Function of Macromolecules (Text from Biology , 6 th Edition, by Campbell and Reece)

Simple sugars can also differ in the spatial arrangement of their parts around asymmetric carbons. Glucose can be drawn in a linear carbon skeleton, but this is not really an accurate representation. In aqueous solutions, most sugars form rings.

Monosaccharides are major nutrients in the cell. They fuel cellular work and the carbon skeletons work as raw material for other types of small organic molecules. A disaccharide consists of two monosaccharides joined by a glcyosidic linkagelinkage, a covalent bond formed between two monosaccharides by a dehydration reaction. Two glucoses bonded together result in maltose, while glucose and fructose bond together to create a sucrose. Lactose is created from galactose and glucose.

Polysaccharides, the Polymers of Sugars, Have Storage and Structural Roles

PolysacPolysaccharidescharides are macromolecules, composed of a few hundred to a few thousand monosaccharides joined by glycosidic linkages. Some polysaccharides store energy for the cells, while others are building materials for structures.

Storage Polysaccharides

Starch is a storage polysaccharide in plants and consists entirely of alpha glucose molecules. Amylose, the simplest form of starch consists of 1-4 glycosidic linkages. Amylopectin, a more complex type of starch, is branched and has 1-6 linkages at the branch points. Starch represents stored energy which can be released by breaking the bonds between the glucose monomers. Most animals can hydrolyze plant starch. Starch is usually helical.

Animals store energy in glycogenglycogen, a polymer even more branched than amylopectin. Humans and other vertebrates store glycogen mainly in liver and muscle cells.

Structural Polysaccharides

Cellulose is created from beta glucose molecules. Because of the slightly different ring structure in beta glucose, when they bond, every other glucose monomer is upside down in respect to the other. Cellulose are grouped into microfibrils in plant cells, which are a strong building material for plants. It is the most abundant organic compound on Earth. Most animals do not have the beta enzyme necessary to break down cellulose. Some microbes are able to break down cellulose – cows have cellulose-digesting bacteria in the first compartment in its stomach.

Chitin is the carbohydrate used by arthropods to build exoskeletons. While pure chitin is leathery, it becomes hardened when encrusted with calcium carbonate.

3 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Five: The Structure and Function of Macromolecules (Text from Biology , 6 th Edition, by Campbell and Reece)

LIPIDS – DIVERSE HYDROPHOBIC MOLECULES

Lipids have little or no affinity for water and have no monomers. They consist mostly of hydrocarbons.

Fats Store Large Amounts of Energy

A fatfatfat consists of glycerol and fatty acids. Glycerol is an alcohol with three carbons, each with its own hydroxyl group. A fatty acid has a long carbon skeleton, with a carboxyl group at the end of a long hydrocarbon chain. The nonpolar carbon-hydrogen bonds in the hydrocarbon chains are the reason why fats are hydrophobic.

To make a fat, three fatty acids join together and bond to the glycerol through ester linkage (bond between hydroxyl and carboxyl group). The resulting Triacylglycerol has three fatty acid tails linked to one glycerol head. The terms saturated fats and unsaturated fats refer to the nature of the bonds between the carbon and hydrogen in the fatty acid tails. If there are no double bonds, then there are as many hydrogens as possible bonded to the carbon skeleton – this structure is a saturated fatty acidacid. An unsaturated fatty acid has one or more double bonds and will have a kink in its tail wherever there is a double bond.

Most saturated fats are animal fats – these are solid at room temperature. Fat from plants and fishes are generally unsaturated and are liquid at room temperature – they are oils.

Fats are used for energy storage. A gram of fat stores more than twice as much energy as a gram of a polysaccharide. Since animals must carry energy stores with them, it is more economic to have fat for energy storage, since it takes up less space.

Phospholipids are Major Components of Cell Membranes

Phospholipids are similar to fats, but they only have two fatty acids tails. The third hydroxyl group of glycerol is instead joined to a phosphate group. When phospholipids are added to water, they self- assemble into micelles: a phospholipid droplet with the hydrophobic tails inside and the hydrophilic heads facing the water.

Steroids Include Cholesterol and Certain Hormones

Steroids are characterized by a carbon skeleton of four fused rings. One steroid, cholesterolcholesterol, is a common component of animal cell membranes.

PROTEINS – MANY STRUCTURES, MANY FUNCTIONS

Proteins are the workhorses of the cell and are used for structural support, storage, transport of substances, signaling, movement, and defense. They are also used as enzymes. All proteins are 4 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Five: The Structure and Function of Macromolecules (Text from Biology , 6 th Edition, by Campbell and Reece) constructed out of the same set of 20 amino acids. Polymers of amino acids are called polyppolypeptideseptideseptides. Proteins consist of one or more polypeptides folded and coiled into specific shapes.

A Polypeptide is a Polymer of Amino Acids Connected in a Specific Sequence

Amino acids are organic molecules possessing both carboxyl and amino groups. The general formula for an amino acid: The alpha carbon is in the center, bonded to an amino group, a carboxyl group, a hydrogen atom, and a variable R group. The R group is also known as the side chain.

The physical and chemical properties of the side chain determine how a particular amino acid will behave. When two amino acids are positioned so that the carboxyl group of one is adjacent to the amino group of the other, an enzyme can begin the dehydration reaction that will form the peptide bond (type of covalent bond).

When this process is repeated over and over, a polypeptide will result. At one end of the chain is a free amino group, and the other end has a free carboxyl group.

A Protein’s Function Depends on Its Specific Conformation

A polypeptide is not quite the same as a protein. A functional protein is one or more polypeptides twisted, folded, and coiled into a uniquely shaped molecule. The amino acid sequence determines what three-dimensional shape the protein will take. Some proteins are globular while others are fibrous.

Four Levels of Protein Structure

When a cell creates a polypeptide, the chain automatically folds to achieve the shape it needs to carry out its function. This shape is held together by a variety of different bonds between parts of the chain.

Primary StructureStructure. The primary structure of a protein is the sequence of amino acids. Even a slight change in the order of amino acids can affect the protein’s ability to function. Frederick Sanger was the pioneer in determining the primary structure of proteins. 5 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Five: The Structure and Function of Macromolecules (Text from Biology , 6 th Edition, by Campbell and Reece)

Secondary Structure. Most proteins have segments of their chain repeatedly coiled or folded – these coils and folds are referred to as the secondary structurestructure.structure They are the result of hydrogen bonds at regular intervals along the polypeptide backbone. This is limited to the atoms of the backbone, not the side chains. One main type of secondary structure is the α helixhelix, a coil held together by hydrogen bonding between every fourth amino acid. The other main type of secondary structure is the β pleated sheetsheet, where two or more regions of polypeptide chain lie parallel to each other. Hydrogen bonds between parts of the backbone in the parallel regions hold the structure together. Pleated sheets make up the inner part of many globular proteins and are seen in some fibrous proteins.

Tertiary Structure. A protein’s tertiary structure consists of irregular contortions because of interactions between side chains. A hydrophobic interaction occurs when amino acid with hydrophobic side chains become grouped into the core – the water molecules bond to each other and to hydrophilic parts of the protein. When the nonpolar amino acid side chains are brought together, van der Waals interactions help hold them together.

Strong covalent bonds called disulfide bridges form where amino acids with sulfhydryl groups are brought close together. Ionic bonds can also occur between side chains.

Quaternary Structure. Proteins that consist of two or more polypeptide chains also have quaternary structstructureureureure, where polypeptides can be coiled into a triple helix or bunched into a roughly spherical shape. Collagen is a fibrous protein while hemoglobin is a globular protein.

What Determines Protein Conformation? pH, salt concentration, temperature, and other aspects of a protein’s environment can affect what happens to a protein. Changes in its environment can cause a protein to become denatured and biologically inactive. Denaturation agents can disrupt the bonds that hold the protein together. Excessive heat can also overpower the weak interactions that stabilize the shape of the protein. Some proteins can return to normal after conditions are fixed. 6 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Five: The Structure and Function of Macromolecules (Text from Biology , 6 th Edition, by Campbell and Reece)

The Protein-Folding Problem

Biologists have discovered that chaperonins are protein molecules that help other proteins fold correctly. They work to keep the new polypeptide away from other influences that could affect the polypeptide’s development.

Determining the Structure of a Protein

XXX-X---rayray crystallography depends on the diffraction of an X-ray beam by the individual atoms in the crystal of the protein. A model can then be built of the protein.

NUCLEIC ACIDS – INFORMATIONAL POLYMERS

The amino acid sequence of a polypeptide is programmed by genesgenes. Genes consist of DNA, which is a polymer belonging to the class of compounds known as nucleic acidsacids.

Nucleic Acids Store and Transmit Hereditary Information

The two types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)(RNA).(RNA) They enable living organisms to reproduce their complex components from one generation to the next. DNA provides directions for its own replication.

A DNA molecule consist of hundreds or thousands of genes. DNA molecules are copied and passed when cells reproduce by dividing. Genes along the length of DNA direct mRNA (messenger RNA) to produce a polypeptide.

A Nucleic Acid Strand is a Polymer of Nucleotides

Monomers of nucleic acids are nucleotidesnucleotides. They are each composed of a nitrogenous base, a pentose, and phosphate group.

A pyrimidine has a six-membered ring of carbon and nitrogenous atoms – they are cytosine, thymine, and uracil. Purines are larger and have a six-membered ring fused to a five-membered ring – adenine and guanine.

The pentose connected to the nitrogenous base is riboseribose in the nucleotides of RNA and deoxyribose in DNA. Because deoxyribose does not have an oxygen atom on one of its carbons, it receives the name deoxy ribose.

A phosphate group is attached to the number five carbon of the sugar.

In a nucleic acid polymer, or polynucleotidepolynucleotide, nucleotides are joined by covalent bonds called phosphodiester linkages between the phosphate of one nucleotide and the sugar of the other.

7 UNIT ONE: THE CHEMISTRY OF LIFE Chapter Five: The Structure and Function of Macromolecules (Text from Biology , 6 th Edition, by Campbell and Reece)

Inheritance is Based on Replication of the DNA Double Helix

The RNA molecules of cells consist of a single polynucleotide chain. However, DNA molecules have two polynucleotides that spiral around an imaginary axis to form a dddodooouuuubbbblllleeee hhheheeelllliiiixxxx. According to the base-pairing rules, Adenine always pairs with Thymine, and Guanine always pairs with Cytosine (ATGC). The two strands are complementary.

We Can Use DNA and Proteins As Tape Measures of Evolution

Genes and their products document the hereditary background of an organism. Since DNA molecules are passed through generations, related individuals have greater similarities in their DNA than unrelated individuals do. Thus, two species that appear closely related based on fossil and anatomical evidence also share a greater proportion of their DNA and protein sequences than do more distantly related species.