Overview: The Molecules of Life

¥           All living things are made up of four classes of large biological molecules: carbohydrates, lipids, proteins, and nucleic acids

¥           Macromolecules are large molecules composed of thousands of covalently connected atoms

¥           Molecular structure and function are inseparable

Concept 5.1: Macromolecules are polymers, built from monomers

¥           A polymer is a long molecule consisting of many similar building blocks

¥           These small building-block molecules are called monomers

¥           Three of the four classes of lifeÕs organic molecules are polymers

          Carbohydrates

          Proteins

          Nucleic acids

The Synthesis and Breakdown of Polymers

¥           A dehydration reaction occurs when two monomers bond together through the loss of a water molecule

¥           Polymers are disassembled to monomers by hydrolysis, a reaction that is essentially the reverse of the dehydration reaction

The Diversity of Polymers

¥           Each cell has thousands of different macromolecules

¥           Macromolecules vary among cells of an organism, vary more within a species, and vary even more between species

¥           An immense variety of polymers can be built from a small set of monomers

Concept 5.2: Carbohydrates serve as fuel and building material

¥           Carbohydrates include sugars and the polymers of sugars

¥           The simplest carbohydrates are monosaccharides, or single sugars

¥           Carbohydrate macromolecules are polysaccharides, polymers composed of many sugar building blocks

Sugars

¥           Monosaccharides have molecular formulas that are usually multiples of CH2O

¥           Glucose (C6H12O6) is the most common monosaccharide

¥           Monosaccharides are classified by

          The location of the carbonyl group (as aldose or ketose)

          The number of carbons in the carbon skeleton

¥           Though often drawn as linear skeletons, in aqueous solutions many sugars form rings

¥           Monosaccharides serve as a major fuel for cells and as raw material for building molecules

¥           A disaccharide is formed when a dehydration reaction joins two monosaccharides

¥           This covalent bond is called a glycosidic linkage

Polysaccharides

¥           Polysaccharides, the polymers of sugars, have storage and structural roles

¥           The structure and function of a polysaccharide are determined by its sugar monomers and the positions of glycosidic linkages

Storage Polysaccharides

¥           Starch, a storage polysaccharide of plants, consists entirely of glucose monomers

¥           Plants store surplus starch as granules within chloroplasts and other plastids

¥           The simplest form of starch is amylose

¥           Glycogen is a storage polysaccharide in animals

¥           Humans and other vertebrates store glycogen mainly in liver and muscle cells

Structural Polysaccharides

¥           The polysaccharide cellulose is a major component of the tough wall of plant cells

¥           Like starch, cellulose is a polymer of glucose, but the glycosidic linkages differ

¥           The difference is based on two ring forms for glucose: alpha (a) and beta (b)   

          Polymers with a glucose are helical

          Polymers with b glucose are straight

          In straight structures, H atoms on one strand can bond with OH groups on other strands

          Parallel cellulose molecules held together this way are grouped into microfibrils, which form strong building materials for plants

¥           Enzymes that digest starch by hydrolyzing a linkages canÕt hydrolyze b linkages in cellulose

¥           Cellulose in human food passes through the digestive tract as insoluble fiber

¥           Some microbes use enzymes to digest cellulose

¥           Many herbivores, from cows to termites, have symbiotic relationships with these microbes

¥           Chitin, another structural polysaccharide, is found in the exoskeleton of arthropods

¥           Chitin also provides structural support for the cell walls of many fungi

Concept 5.3: Lipids are a diverse group of hydrophobic molecules

¥           Lipids are the one class of large biological molecules that do not form polymers

¥           The unifying feature of lipids is having little or no affinity for water

¥           Lipids are hydrophobic because they consist mostly of hydrocarbons, which form nonpolar covalent bonds

¥           The most biologically important lipids are fats, phospholipids, and steroids

Fats

¥           Fats are constructed from two types of smaller molecules: glycerol and fatty acids

¥           Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon

¥           A fatty acid consists of a carboxyl group attached to a long carbon skeleton

          Fats separate from water because water molecules form hydrogen bonds with each other and exclude the fats

          In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a triacylglycerol, or triglyceride

¥           Fatty acids vary in length (number of carbons) and in the number and locations of double bonds

¥           Saturated fatty acids have the maximum number of hydrogen atoms possible and no double bonds

¥           Unsaturated fatty acids have one or more double bonds

¥           Fats made from saturated fatty acids are called saturated fats, and are solid at room temperature

¥           Most animal fats are saturated

¥           Fats made from unsaturated fatty acids are called unsaturated fats or oils, and are liquid at room temperature

¥           Plant fats and fish fats are usually unsaturated

¥           A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits

¥           Hydrogenation is the process of converting unsaturated fats to saturated fats by adding hydrogen

¥           Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds

¥           These trans fats may contribute more than saturated fats to cardiovascular disease

¥           Certain unsaturated fatty acids are not synthesized in the human body

¥           These must be supplied in the diet

¥           These essential fatty acids include the omega-3 fatty acids, required for normal growth, and thought to provide protection against cardiovascular disease

¥           The major function of fats is energy storage

¥           Humans and other mammals store their fat in adipose cells

¥           Adipose tissue also cushions vital organs and insulates the body

Phospholipids

¥           In a phospholipid, two fatty acids and a phosphate group are attached to glycerol

¥           The two fatty acid tails are hydrophobic, but the phosphate group and its attachments form a hydrophilic head

¥           When phospholipids are added to water, they self-assemble into a bilayer, with the hydrophobic tails pointing toward the interior

¥           The structure of phospholipids results in a bilayer arrangement found in cell membranes

¥           Phospholipids are the major component of all cell membranes

Steroids

¥           Steroids are lipids characterized by a carbon skeleton consisting of four fused rings

¥           Cholesterol, an important steroid, is a component in animal cell membranes

¥           Although cholesterol is essential in animals, high levels in the blood may contribute to cardiovascular disease

Concept 5.4: Proteins include a diversity of structures, resulting in a wide range of functions

¥           Proteins account for more than 50% of the dry mass of most cells

¥           Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances

¥           Enzymes are a type of protein that acts as a catalyst to speed up chemical reactions

¥           Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

Polypeptides

¥           Polypeptides are unbranched polymers built from the same set of 20 amino acids

¥           A protein is a biologically functional molecule that consists of one or more polypeptides

Amino Acid Monomers

¥           Amino acids are organic molecules with carboxyl and amino groups

¥           Amino acids differ in their properties due to differing side chains, called R groups

Amino Acid Polymers

¥           Amino acids are linked by peptide bonds

¥           A polypeptide is a polymer of amino acids

¥           Polypeptides range in length from a few to more than a thousand monomers

¥           Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)

Protein Structure and Function

¥           A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape

¥           The sequence of amino acids determines a proteinÕs three-dimensional structure

¥           A proteinÕs structure determines its function

Four Levels of Protein Structure

¥           The primary structure of a protein is its unique sequence of amino acids

¥           Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain

¥           Tertiary structure is determined by interactions among various side chains (R groups)

¥           Quaternary structure results when a protein consists of multiple polypeptide chains

¥           Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word

¥           Primary structure is determined by inherited genetic information

¥           The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone

¥           Typical secondary structures are a coil called an a helix and a folded structure called a b pleated sheet

¥           Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents

¥           These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions

¥           Strong covalent bonds called disulfide bridges may reinforce the proteinÕs structure

¥           Quaternary structure results when two or more polypeptide chains form one macromolecule

¥           Collagen is a fibrous protein consisting of three polypeptides coiled like a rope

¥           Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains

Sickle-Cell Disease: A Change in Primary Structure

¥           A slight change in primary structure can affect a proteinÕs structure and ability to function

¥           Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin

What Determines Protein Structure?

¥           In addition to primary structure, physical and chemical conditions can affect structure

¥           Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel

¥           This loss of a proteinÕs native structure is called denaturation

¥           A denatured protein is biologically inactive

Protein Folding in the Cell

¥           It is hard to predict a proteinÕs structure from its primary structure

¥           Most proteins probably go through several stages on their way to a stable structure

¥           Chaperonins are protein molecules that assist the proper folding of other proteins

¥           Diseases such as AlzheimerÕs, ParkinsonÕs, and mad cow disease are associated with misfolded proteins

¥           Scientists use X-ray crystallography to determine a proteinÕs structure

¥           Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization

¥           Bioinformatics uses computer programs to predict protein structure from amino acid sequences

Concept 5.5: Nucleic acids store, transmit, and help express hereditary information

¥           The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene

¥           Genes are made of DNA, a nucleic acid made of monomers called nucleotides

The Roles of Nucleic Acids

¥           There are two types of nucleic acids

          Deoxyribonucleic acid (DNA)

          Ribonucleic acid (RNA)

¥           DNA provides directions for its own replication

¥           DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis

¥           Protein synthesis occurs on ribosomes

The Components of Nucleic Acids

¥           Nucleic acids are polymers called polynucleotides

¥           Each polynucleotide is made of monomers called nucleotides

¥           Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups

¥           The portion of a nucleotide without the phosphate group is called a nucleoside

¥           Nucleoside = nitrogenous base + sugar

¥           There are two families of nitrogenous bases

          Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring

          Purines (adenine and guanine) have a six-membered ring fused to a five-membered ring

¥           In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose

¥           Nucleotide = nucleoside + phosphate group

Nucleotide Polymers

¥           Nucleotide polymers are linked together to build a polynucleotide

¥           Adjacent nucleotides are joined by covalent bonds that form between the —OH group on the 3¢ carbon of one nucleotide and the phosphate on the 5¢ carbon on the next

¥           These links create a backbone of sugar-phosphate units with nitrogenous bases as appendages

¥           The sequence of bases along a DNA or mRNA polymer is unique for each gene

The Structures of DNA and RNA Molecules

¥           RNA molecules usually exist as single polypeptide chains

¥           DNA molecules have two polynucleotides spiraling around an imaginary axis, forming a double helix

¥           In the DNA double helix, the two backbones run in opposite 5¢→ 3¢ directions from each other, an arrangement referred to as antiparallel

¥           One DNA molecule includes many genes

¥           The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T), and guanine (G) always with cytosine (C)

¥           Called complementary base pairing

¥           Complementary pairing can also occur between two RNA molecules or between parts of the same molecule

¥           In RNA, thymine is replaced by uracil (U) so A and U pair

DNA and Proteins as Tape Measures of Evolution

¥           The linear sequences of nucleotides in DNA molecules are passed from parents to offspring

¥           Two closely related species are more similar in DNA than are more distantly related species

¥           Molecular biology can be used to assess evolutionary kinship

The Theme of Emergent Properties in the Chemistry of Life: A Review

¥           Higher levels of organization result in the emergence of new properties

¥           Organization is the key to the chemistry of life