Organic Chemistry, Biochemistry
The diagram above shows a molecule of methane. Lines can be used to represent bonds in the shorthand formula seen in the upper right side of the diagram.
Carbon can form 4 covalent bonds because it has 4 electrons in its outer shell. It can form the following number of bonds. Notice that in each case below, there is a total of four bonds.
Long chains of carbon atoms are common. The chains may be branched or form rings.
Hydrophilic and Hydrophobic
and ionic molecules have positive and negative charges and are therefore attracted to water molecules because water molecules are also polar. They are said to be hydrophilic because they interact with (dissolve in) water by forming hydrogen bonds.
Nonpolar molecules are hydrophobic (means "water fearing"). They do not dissolve in water.
Portions of large molecules may be hydrophobic and other portions of the same molecule may be hydrophilic.
This is a type of reaction in which a macromolecule is broken down into smaller molecules.
It is the reverse of condensation (above).
Importance of proteins
Enzymes are proteins that speed up the rate of chemical reactions.
The presence of an enzyme in the chemical reaction diagrammed below causes hypothetical chemicals A and B to react, producing C.
Proteins are able to function as enzymes due to their shape. For example, enzyme molecules are shaped like the reactants, allowing the reactants to bind closely with the enzyme. The diagrams below show that the enzyme matches the shape of the substrate molecules. The enzyme is therefore able to hold the substrate molecules in the correct orientation needed for the chemical reaction to proceed. The enzyme does not participate in the reaction and is not changed by the reaction.
Amino acids are the building blocks of proteins.
Twenty of the amino acids are used to make protein. Each has a carboxyl group (COOH) and an amino group (NH2).
Each amino acid is different and therefore has its own unique properties.
Some amino acids are hydrophobic, others hydrophilic. The carboxyl or amino group may ionize (forming NH3+ or COO-). The "R" group of some amino acids is nonpolar and the "R" group of some others is polar or it ionizes.
Amino acids are joined together by a peptide bond. It is formed as a result of a condensation reaction between the amino group of one amino acid and the carboxyl group of another.
Click here to view a web page which shows an animation of the formation of a peptide bond.
The large number of charged atoms in a polypeptide chain facilitates hydrogen bonding within the molecule, causing it to fold into a specific 3-dimensional shape.
The 3-dimensional shape is important in the activity of a protein.
Primary structure refers to the sequence of amino acids found in a protein. The following is the primary structure of one of the polypeptide chains of hemoglobin.
The oxygen or nitrogen atoms of the peptide bond are capable of hydrogen- bonding with hydrogen atoms elsewhere on the molecule. This bonding produces two common kinds of shapes seen in protein molecules, coils (called alpha helices) and beta pleated sheets. The alpha helices and beta pleated sheets are referred to as a proteins secondary structure.
Tertiary structure refers to the overall 3-dimensional shape of the polypeptide chain.
Hydrophobic interactions with water molecules are important in creating and stabilizing the structure of proteins. Hydrophobic (nonpolar) amino acids aggregate to produce areas of the protein that are out of contact with water molecules.
Hydrogen bonds and ionic bonds form between R groups to help shape the polypeptide chain.
Disulfide bonds are covalent bonds between sulfur atoms in the R groups of two different amino acids. These bonds are very important in maintaining the tertiary structure of some proteins.
The shape of a protein is typically described as being globular or fibrous. Globular proteins contain both coils and sheets.
Some proteins contain two or more polypeptide chains that associate to form a single protein. These proteins have quaternary structure. For example, hemoglobin contains four polypeptide chains.
Denaturation occurs when the normal bonding patterns are disturbed causing the shape of the protein to change. This can be caused by changes in temperature, pH, or salt concentration. For example, acid causes milk to curdle and heat (cooking) causes egg whites to coagulate because the proteins within them denature.
If the protein is not severely denatured, it may regain its normal structure.
DNA (deoxyribonucleic acid) is the genetic material. An important function of DNA is top store information regarding the sequence of amino acids in each of the bodys proteins. This "list" of amino acid sequences is needed when proteins are synthesized. Before protein can be synthesized, the instructions in DNA must first be copied to another type of nucleic acid called messenger RNA.
Nucleic acids are composed of units called nucleotides, which are linked together to form a larger molecule. Each nucleotide contains a base, a sugar, and a phosphate group. The sugar is deoxyribose (DNA) or ribose (RNA). The bases of DNA are adenine, guanine, cytosine, and thymine. Notice that the carbon atoms in one of the nucleotides diagrammed below have been numbered.
The diagram below shows how nucleotides are joined together to form a "chain" of nucleotides.
DNA is composed of two strands in which the bases of one strand are hydrogen-bonded to the bases of the other. The sugar-phosphate groups form the outer part of the molecule while the bases are oriented to the center.
The strands are twisted forming a configuration that is often referred to as a double helix. The photograph below is of a model of DNA.
Complimentary base pairing
The adenine of one strand is always hydrogen-bonded to a thymine on the other. Similarly, Guanine is always paired with Cytosine.
The end of a single strand that has the phosphate group is called the 5 end. The other end is the 3 end.
ATP (adenosine triphosphate) is a nucleotide that is used in energetic reactions for temporary energy storage.
Energy is stored in the phosphate bonds of ATP. When ATP breaks down to form ADP and Pi, energy is released. Normally, cells use the energy stored in ATP by breaking one of the phosphate bonds, producing ADP. Energy is required to convert ADP + Pi back to ATP.
ATP is continually produced and consumed as illustrated below.
are simple sugars, having 3 to 7 carbon atoms. They can be bonded together to form polysaccharides.
The names of most sugars end with the letters ose.
Example: Glucose, fructose, and galactose are monosaccharides; their structural formula is C6H12O6.
Glucose and other kinds of sugars may be linear molecules as shown below but in aqueous solution they become a ring form.
There are two isomers of the ring form of glucose. They differ in the location of the OH group on the number 1 carbon atom (in red below).
The number 1 carbon atom (numbered in red above) of the linear form of glucose is attached to the oxygen on the number 5 carbon atom.
Simple sugars store energy for cells. Details concerning energy storage and release by glucose are in the chapter on cellular respiration.
Cells also use simple sugars to construct other kinds of organic molecules.
Disaccharides are composed of 2 monosaccharides joined together by a condensation reaction.
Sucrose (table sugar) is composed of glucose and fructose.
Like glucose, sucrose stores energy. Plants synthesize sucrose to transport to nonphotosynthetic parts of the plant.
Lipids are compounds that are insoluble in water but soluble in nonpolar solvents.
Some lipids function in long-term energy storage. One gram of fat stores more than twice as much energy as one gram of carbohydrate.
Lipids are also an important component of cell membranes.
Fats and oils are composed of fatty acids and glycerol.
Fatty acids have a long hydrocarbon (carbon and hydrogen) chain with a carboxyl (acid) group. The chains usually contain 16 to 18 carbons.
Glycerol contains 3 carbons and 3 hydroxyl groups. It reacts with 3 fatty acids to form a triglyceride or fat molecule.
Fats are nonpolar and therefore they do not dissolve in water.
Saturated fatty acids have no double bonds between carbons. Unsaturated fatty acids have at least one double bond. Each double bonds produces a "bend" in the molecule.
Double bonds produce a bend in the fatty acid molecule (see diagram above). Molecules with many of these bends cannot be packed as closely together as straight molecules, so these fats are less dense. As a result, triglycerides composed of unsaturated fatty acids melt at lower temperatures than those with saturated fatty acids. For example, butter contains more saturated fat than corn oil, and is a solid at room temperature while corn oil is a liquid.
Phospholipids have a structure like a triglyceride (see diagram above), but contain a phosphate group in place of the third fatty acid. The phosphate group is polar and therefore capable of interacting with water molecules.
Phospholipids spontaneously form a bilayer in a watery environment. They arrange themselves so that the polar heads are oriented toward the water and the fatty acid tails are oriented toward the inside of the bilayer (see the diagram below).
In general, nonpolar molecules do not interact with polar molecules. This can be seen when oil (nonpolar) is mixed with water (polar). Polar molecules interact with other polar molecules and ions. For example table salt (ionic) dissolves in water (polar).
The bilayer arrangement shown below enables the nonpolar fatty acid tails to remain together, avoiding the water. The polar phosphate groups are oriented toward the water.
Membranes that surround cells and surround many of the structures within cells are primarily phospholipid bilayers.
Steroids have a backbone of 4 carbon rings.
Cholesterol (see diagram above) is the precursor of several other steroids, including several hormones. It is also an important component of cell membranes.
Saturated fats and cholesterol in the diet can lead to deposits of fatty materials on the linings of the blood vessels.
Additional Reading and Help
The Visionlearning website contains good summaries of the material presented in this class. Do Chemistry (level 2), 4, 5, and 6.