3.1 Organic Molecules
Organic molecules contain carbon and hydrogen atoms bonded to other atoms.
Four types of organic molecules (biomolecules) exist in organisms: carbohydrates, lipids, proteins, and nucleic acids.
Organic molecules are a diverse group; even a simple bacterial cell contains some 5,000 organic molecules.
A. The Carbon Atom
1. The chemistry of the carbon atom allows it to form covalent bonds with as many as four other elements (generally with the CHNOPS elements).
2. Hydrocarbons are chains of carbon atoms bonded exclusively to hydrogen atoms; hydrocarbons can be branched and they can form ringed (cyclic) compounds.
3. Carbon atoms can form double or triple bonds with certain atoms (carbon, nitrogen).
B. The Carbon Skeleton and Functional Groups
1. The carbon chain of an organic molecule is called its skeleton or backbone.
2. Functional groups are clusters of specific atoms bonded to the carbon skeleton with characteristic structure and functions.
a. For example, the addition of an –OH (hydroxyl group) to a carbon skeleton turns the molecule into an alcohol.
b. Ethyl alcohol (ethanol) is hydrophilic (dissolves in water) because the hydroxyl group is polar.
Nonpolar organic molecules are hydrophobic (cannot dissolve in water) unless they contain a polar functional group (ex., ethane), while hydrophilic compounds (such as ethanol) can dissolve in water because the –OH functional group is polar.
d. Depending on its functional groups, an organic molecule may be both acidic and hydrophilic. For example, a hydrocarbon that contains a carboxyl group; carboxyl groups ionize in solution by releasing hydrogen ions, becoming both polar and acidic.
e. Because cells are 70–90% water, the degree to which an organic molecule interacts with water affects its function.
3. Isomers are molecules with identical molecular formulas but different arrangements of their atoms (e.g., glyceraldehyde and dihydroxyacetone).
a. Isomers have different chemical properties and react differently with other molecules.
C. The Biomolecules of Cells
Carbohydrates, lipids, proteins, and nucleic acids are biomolecules; certain foods are known to be rich in them.
The largest biomolecules are called polymers, constructed by linking many of the same type of small subunits, called monomers. Examples: amino acids (monomers) are linked to form a protein (polymer); many nucleotides (monomers) are linked to form a nucleic acid (polymer).
Cellular enzymes carry out dehydration reactions to synthesize biomolecules. In a dehydration reaction, a water molecule is removed and a covalent bond is made between two atoms of the monomers.
In a dehydration reaction, a hydroxyl (— OH) group is removed from one monomer and a hydrogen (— H) is removed from the other.
This produces water, and, because the water is leaving the monomers, it is a dehydration reaction.
Hydrolysis (“water breaking”) reactions break down polymers in reverse of dehydration.
A hydroxyl (— OH) group from water attaches to one monomer and hydrogen (— H) attaches to the other.
Enzymes are molecules that speed up chemical reactions by bringing reactants together; an enzyme may even participate in the reaction but is not changed by the reaction.
A. Monosaccharides: Ready Energy
1. Monosaccharides are simple sugars with a backbone of three to seven carbon atoms.
a. Most monosaccharides of organisms have six carbons (hexose).
b. Glucose, fructose, and galactose are hexoses, but are isomers of one another; each has the same molecular formula (C6H12O6 ) but they differ in arrangement of the atoms.
c. Glucose is found in the blood of animals; it is the source of biochemical energy (ATP) in nearly all organisms.
2. Ribose and deoxyribose are fivecarbon sugars (pentoses); they contribute to the backbones of RNA and DNA, respectively.
Disaccharides: Varied Uses
1. Disaccharides contain two monosaccharides joined by a dehydration reaction.
2. Maltose is composed of two glucose molecules; it forms in the digestive tract of humans during starch digestion.
3. Sucrose (table sugar) is composed of glucose and fructose; it is used to sweeten food for human consumption.
4. Lactose is composed of galactose and glucose and is found in milk.
C. Polysaccharides: Energy Storage Molecules
1. Polysaccharides are polymers of monosaccharides. They are not soluble in water and do not pass through the plasma membrane of the cell.
2. Starch, found in many plants, is a straight chain of glucose molecules with relatively few side branches. Amylose and amylopectin are the two forms of starch found in plants.
3. Glycogen is a highly branched polymer of glucose with many side branches. It is the storage form of glucose in animals.
D. Polysaccharides: Structural Molecules
1. Cellulose is a polymer of glucose which forms microfibrils, the primary constituent of plant cell walls.
Cotton is nearly pure cellulose.
Cellulose is indigestible by humans due to the unique bond between glucose molecules.
Grazing animals can digest cellulose due to special stomachs and bacteria.
Cellulose is the most abundant organic molecule on Earth.
Chitin is a polymer of glucose with an amino group attached to each glucose molecule.
Chitin is the primary constituent of the exoskeleton of crabs and related animals (lobsters, insects, etc.).
Chitin is not digestible by humans.
3. Peptidoglycan is a polymer of glucose derivatives and is found in bacteria.
1. Lipids are varied in structure.
a. Lipids are hydrocarbons that are insoluble in water because they lack polar groups.
b. Fat provides insulation and energy storage in animals.
c. Phospholipids form plasma membranes and steroids are important cell messengers.
d. Waxes have protective functions in many organisms.
A. Triglycerides: Long-Term Energy Storage
1. Fats and oils contain two molecular units: glycerol and fatty acids.
2. A fatty acid is a long hydrocarbon chain with a carboxyl (acid) group at one end.
a. Most fatty acids in cells contain 16 to 18 carbon atoms per molecule.
b. Saturated fatty acids have no double bonds between their carbon atoms.
c. Unsaturated fatty acids have double bonds in the carbon chain where there are less than two hydrogens per carbon atom.
i. The double bonds in unsaturated fatty acids may have chemical groups arranged on the same side (cis configuration) or on opposite sides (trans configuration). These two configurations affect the unsaturated fatty acids biological activity.
3. Glycerol is a water-soluble compound with three hydroxyl groups.
4. Triglycerides are glycerol joined to three fatty acids by dehydration reactions.
5. Fats contain saturated fatty acids and are solid at room temperature (e.g., butter).
6. Oils contain unsaturated fatty acids and are liquid at room temperature.
7. Animals use fat rather than glycogen for long-term energy storage; fat stores more energy.
B. Phospholipids: Membrane Components
1. Phospholipids are constructed like neutral fats except that the third fatty acid is replaced by a polar (hydrophilic) phosphate group; the phosphate group usually bonds to another organic group (designated by R).
2. The hydrocarbon chains of the fatty acids become the nonpolar (hydrophobic) tails.
3. Phospholipids arrange themselves in a double layer in water, so the polar heads face toward water molecules and nonpolar tails face toward one other, away from water molecules.
4. This property enables phospholipids to form an interface or separation between two solutions (e.g., the interior and exterior of a cell); the plasma membrane is a phospholipid bilayer.
C. Steroids: Four Fused Rings
1. Steroids have skeletons of four fused carbon rings and vary according to attached functional groups; these functional groups determine the biological functions of the various steroid molecules.
2. Cholesterol is a component of an animal cell’s plasma membrane, and is the precursor of several other steroids (aldosterone, testosterone, estrogen, calcitriol, etc.).
3. A diet high in saturated fats and cholesterol can lead to circulatory disorders.
1. Waxes are long-chain fatty acids bonded to long-chain alcohols.
2. Waxes have a high melting point, are waterproof, and resist degradation.
3. Waxes form a protective covering in plants that prevents water loss in leaves and fruits.
4. In animals, waxes maintain animal skin and fur, trap dust and dirt, and form the honeycomb.
1. Proteins are of primary importance to the structure and function of cells:
a. Metabolism Enzyme proteins act as organic catalysts to accelerate chemical reactions within cells.
b. Support Some proteins have a structural function, examples are keratin, which makes up hair and nails, and collagen fibers, which support many of the body’s structures (e.g., ligaments, tendons, skin).
c. Transport Channel and carrier proteins in the plasma membrane regulate what substances enter and exit cells. Hemoglobin transports oxygen in red blood cells.
d. Defense Antibodies are proteins that prevent infection.
e. Regulation Some hormones are regulatory proteins that influence the metabolism of cells. For example, insulin regulates glucose content of blood and within cells.
f. Motion The contractile proteins actin and myosin allow parts of cells to move and cause muscles to contract.
1. A peptide bond is a covalent bond between two amino acids.
2. Atoms of a peptide bond share electrons unevenly (oxygen is more electronegative than nitrogen).
3. The polarity of the peptide bond permits hydrogen bonding between different amino acids in a polypeptide.
4. A peptide is two or more amino acids bonded together.
5. Polypeptides are chains of many amino acids joined by peptide bonds.
6. A protein may contain more than one polypeptide chain; it can thus have a very large number of amino acids.
The three-dimensional shape of a protein is critical; an abnormal sequence will have the wrong shape and will not function normally.
Frederick Sanger determined the first protein sequence (of the hormone insulin) in 1953.
B. Amino Acids: Protein Monomers
1. Amino acids contain an acidic group (— COOH) and an amino group (—NH2).
2. Amino acids differ according to their particular R group, ranging from single
hydrogen to complicated ring compounds.
3. The R group of the amino acid cystine ends with a sulfhydryl (— SH) that serves to connect one chain of amino acids to another by a disulfide bond (— S— S—).
4. There are 20 different amino acids commonly found in cells.
C. Shape of Proteins
1. Protein shape determines the function of the protein in the organism; proteins can have up to four levels of structure (but not all proteins have four levels).
2. The primary structure is the protein’s own particular sequence of amino acids.
a. Just as the English alphabet contains 26 letters, 20 amino acids can join to form a huge variety of “words.”
3. The secondary structure results when a polypeptide coils or folds in a particular way.
a. The ( (alpha) helix was the first pattern discovered.
i. In a peptide bond, oxygen is partially negative, hydrogen is partially positive.
ii. This allows for hydrogen bonding between the C=O of one amino acid and the N—H of another.
iii. Hydrogen bonding between every fourth amino acid holds the spiral shape of an ( helix.
b. The ( (beta) sheet was the second pattern discovered.
i. Pleated ( sheet polypeptides turn back upon themselves.
ii. Hydrogen bonding occurs between extended lengths.
c. Fibrous proteins (e.g., keratin) are structural proteins with helices and/or pleated sheets that hydrogen bond to one another.
4. Tertiary structure results when proteins are folded, giving rise to the final three-dimensional shape of the protein. This is due to interactions among the R groups of the constituent amino acids.
a. Globular proteins tend to ball up into rounded shapes.
b. Strong disulfide linkages maintain the tertiary shape; hydrogen, ionic, and covalent bonds also contribute.
c. Enzymes are globular proteins and have specific conditions for optimal functionality. There are conditions in which the enzyme, or protein, will lose its natural shape (i.e. high temperatures). This is called denaturation.
5. Quaternary structure results when two or more polypeptides combine.
a. Hemoglobin is a globular protein with a quaternary structure of four polypeptides; each polypeptide has a primary, secondary, and tertiary structure.
D. Protein-Folding Diseases
1. As proteins are synthesized, chaperone proteins help them fold into their correct shapes; chaperone proteins may also correct misfolding of a new protein and prevent them from making incorrect shapes.
2. Certain diseases (e.g., the transmissible spongiform encephalopathies, or TSEs) are likely due to misfolded proteins, called prions.
3.5 Nucleic Acids
1. Nucleic acids are polymers of nucleotides, which store information in cells.
2. DNA (deoxyribonucleic acid) stores the genetic code for its own replication and for the amino acid sequences in proteins.
3. RNA (ribonucleic acid) allows for translation of the genetic code of DNA into the amino acid sequence of proteins; other functions for RNA in the cell exist.
4. Some nucleotides have independent metabolic functions in cells.
a. Coenzymes are molecules which facilitate enzymatic reactions.
b. ATP (adenosine triphosphate) is a nucleotide used to supply energy for synthetic reactions and other energy-requiring metabolic activities in the cell.
A. Structure of DNA and RNA
1. Nucleotides are a molecular complex of three types of molecules: a phosphate (phosphoric acid), a pentose sugar, and a nitrogen-containing base.
2. DNA and RNA differ in the following ways:
a. Nucleotides of DNA contain deoxyribose sugar; nucleotides of RNA
b. In RNA, the base uracil occurs instead of the base thymine. Both RNA and DNA contain adenine, guanine, and cytosine.
c. DNA is double-stranded with complementary base pairing; RNA is single-stranded.
i. Complementary base pairing occurs when two strands of DNA are held together by hydrogen bonds between purine and pyrimidine bases.
ii. The number of purine bases always equals the number of pyrimidine bases.
iii. In DNA, thymine is always paired with adenine; cytosine is always paired with guanine. Thus, in DNA: A + G = C + T.
d. Two strands of DNA twist to form a double helix; RNA does not form a helix.
B. ATP (Adenosine Triphosphate)
1. ATP (adenosine triphosphate) is a nucleotide in which adenosine is composed of ribose and adenine.
2. Triphosphate derives its name from three phosphate groups attached together and to the ribose.
3. ATP is a high-energy molecule because the last two phosphate bonds release energy when broken.
In cells, the terminal phosphate bond is hydrolyzed, leaving ADP (adenosine diphosphate); energy is released when this occurs.
The energy released from ATP breakdown is used in the energy-requiring processes of the cell, such as synthetic reactions, muscle contraction, and the transmission of nerve impulses.
C. Everyone Needs a Little Fat, Right? (Nature of Science reading)
Dietary fat provides energy, builds and maintains cell membranes, and provides padding for internal organs.
Saturated fats, which are from animals and solid at room temperature, stick together and have been associated with coronary heart disease (CHD).
Unsaturated fats, which are from plants and liquid at room temperature, do not stick together and do not clog arteries
A Food Revolution
Although unsaturated fat is thought to be healthier than saturated fat, plant oils can go bad and since they are liquid at room temperature, are difficult to use in solid food products.
To solve this problem, food manufacturers hydrogenated unsaturated fatty acids.
The hydrogenation process involves heating and exposing oil to hydrogen gas.
A consequence of the hydrogenation process is the formation of trans-fats, which increase LDL (“bad”) cholesterol and lower HDL (“good”) cholesterol, and increases the risk of CHD.
Scientific Evidence Changes our Perceptions
Since there has been scientific evidence to support the health risks associated with intake of trans-fat, the food service industry has clear labeling of trans-fats on food products, and many restaurants use trans-fat-free oil.