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Organic Molecules and Biomolecules: Structure, Function, and Interactions, Study notes of Chemistry

Chemistry

An overview of organic molecules, focusing on biomolecules such as carbohydrates, lipids, proteins, and nucleic acids. Topics include the chemistry of carbon, functional groups, hydrolysis and dehydration reactions, enzymes, and the structure and functions of various biomolecules. The text also covers the importance of water in cellular processes and the concept of isomers.

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Chapter 3
3.1 Organic Molecules
Organic molecules contain carbon and hydrogen atoms bonded to other atoms.
1. Four types of organic molecules (biomolecules) exist in organisms:
carbohydrates, lipids, proteins, and nucleic acids.
2. 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. As an 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.
c. 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. An example is 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).
C. The Biomolecules of Cells
1. Carbohydrates, lipids, proteins, and nucleic acids are called biomolecules
because certain foods are known to be rich in them.
2. 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.
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Chapter 3

3.1 Organic Molecules

Organic molecules contain carbon and hydrogen atoms bonded to other atoms.

1. Four types of organic molecules ( biomolecules ) exist in organisms : carbohydrates, lipids, proteins, and nucleic acids.

  1. Organic molecules are a diverse group; even a simple bacterial cell contains some 5,000 organic molecules. A. The Carbon Atom
  2. The chemistry of the carbon atom allows it to form covalent bonds with as many as four other elements (generally with the CHNOPS elements).
  3. Hydrocarbons are chains of carbon atoms bonded exclusively to hydrogen atoms; hydrocarbons can be branched and they can form ringed (cyclic) compounds.
  4. Carbon atoms can form double or triple bonds with certain atoms (carbon, nitrogen). B. The Carbon Skeleton and Functional Groups
  5. The carbon chain of an organic molecule is called its skeleton or backbone.
  6. Functional groups are clusters of specific atoms bonded to the carbon skeleton with characteristic structure and functions. a. As an 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. c. 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. An example is 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.
  7. Isomers are molecules with identical molecular formulas but different arrangements of their atoms (e.g., glyceraldehyde and dihydroxyacetone). C. The Biomolecules of Cells
  8. Carbohydrates, lipids, proteins, and nucleic acids are called biomolecules because certain foods are known to be rich in them.
  9. 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.
  1. 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.
  2. 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.
  3. 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). a. In a dehydration reaction, a hydroxyl (— OH) group is removed from one monomer and a hydrogen (— H) is removed from the other. b. This produces water, and, because the water is leaving the monomers, it is a dehydration reaction.

3.2 Carbohydrates

A. Monosaccharides: Ready Energy

  1. Monosaccharides are simple sugars with a backbone of 3 to 7 carbon atoms. a. Most monosaccharides of organisms have 6 carbons (hexose). b. Glucose and fructose are hexoses, but are isomers of one another; each has the formula (C 6 H 12 O 6 ) 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 five-carbon sugars (pentoses); they contribute to the backbones of RNA and DNA, respectively. B. Disaccharides: Varied Uses
  3. Disaccharides contain two monosaccharides joined by a dehydration reaction.
  4. Maltose is composed of two glucose molecules; it forms in the digestive tract of humans during starch digestion.
  5. Sucrose (table sugar) is composed of glucose and fructose; it is used to sweeten food for human consumption.
  6. Lactose is composed of galactose and glucose and is found in milk. C. Polysaccharides: Energy Storage Molecules
  7. Polysaccharides are polymers of monosaccharides. They are not soluble in water and do not pass through the plasma membrane of the cell.
  8. 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.
  9. 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
  10. Cellulose is a polymer of glucose which forms microfibrils, the primary constituent of plant cell walls. a. Cotton is nearly pure cellulose.
  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 the steroid hormone (aldosterone, testosterone, estrogen, calcitriol, etc.).
  3. A diet high in saturated fats and cholesterol can lead to circulatory disorders. D. Waxes
  4. Waxes are long-chain fatty acids bonded to long-chain alcohols.
  5. Waxes have a high melting point, are waterproof, and resist degradation.
  6. Waxes form a protective covering in plants that retards water loss in leaves and fruits.
  7. In animals, waxes maintain animal skin and fur, trap dust and dirt, and form the honeycomb. 3.4 Proteins

Protein Functions

  1. Metabolic enzymes are proteins that act as organic catalysts to accelerate chemical reactions within cells.
  2. Support proteins include keratin, which makes up hair and nails, and collagen fibers, which support many of the body’s structures (e.g., ligaments, tendons, skin).
  3. Transport functions include channel and carrier proteins in the plasma membrane, and hemoglobin that transports oxygen in red blood cells.
  4. Defense functions include antibodies that prevent infection.
  5. Hormones are regulatory proteins that influence the metabolism of cells. For example, insulin regulates glucose content of blood and within cells.
  6. Motion within cells and by muscle contraction is provided by the proteins myosin and actin. A. Peptides
  7. A p eptide bond is a covalent bond between two amino acids.
  8. Atoms of a peptide bond share electrons unevenly (oxygen is more electronegative than nitrogen).
  9. The polarity of the peptide bond permits hydrogen bonding between different amino acids in a polypeptide.
  10. A peptide is two or more amino acids bonded together.
  11. Polypeptides are chains of many amino acids joined by peptide bonds.
  12. A protein may contain more than one polypeptide chain; it can thus have a very large number of amino acids. a. The three-dimensional shape of a protein is critical; an abnormal sequence will have the wrong shape and will not function normally. b. Frederick Sanger determined the first protein sequence (of the hormone insulin) in 1953. B. Amino Acids: Proteins Monomers
  13. Amino acids contain an acidic group (— COOH) and an amino group (— NH 2 ).
  1. Amino acids differ according to their particular R group, ranging from single hydrogen to complicated ring compounds.
  2. The R group of 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—).
  3. There are 20 different amino acids commonly found in cells. C. Shape of Proteins
  4. 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).
  5. 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.”
  6. The secondary structure results when a polypeptide coils or folds in a particular way. a. The αααα (alpha) helix was the first pattern discovered.
  1. In a peptide bond, oxygen is partially negative, hydrogen is partially positive.
  2. This allows for hydrogen bonding between the C=O of one amino acid and the N—H of another.
  3. Hydrogen bonding between every fourth amino acid holds the spiral shape of an α helix. b. The ββββ (beta) sheet was the second pattern discovered.
  4. Pleated β sheet polypeptides turn back upon themselves.
  5. 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.
  1. 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.
  2. Quaternary structure results when two or more polypeptides combine. a. Hemoglobin is globular protein with a quaternary structure of four polypeptides; each polypeptide has a primary, secondary, and tertiary structure. D. Protein Folding Diseases
  3. 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.
  4. Certain diseases (e.g., the transmissible spongiform encephalopathies, or TSEs) are likely due to misfolded proteins, called prions. 3.5 3ucleic Acids
  5. Nucleic acids are polymers of nucleotides with very specific functions in cells.