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Organic Chemistry, Biochemistry

Introduction

Organic molecules are molecules that contain carbon and hydrogen.

All living things contain these organic molecules: carbohydrates, lipids, proteins, and nucleic acids. These molecules are often called macromolecules because they may be very large, containing thousands of carbon and hydrogen atoms and because they are typically composed of many smaller molecules bonded together. These four macromolecules will be discussed in the second half of this chapter.. 

Carbon

Carbon has four electrons in its outer shell.

Hydrogen has one electron and one proton.

Carbon can bond by covalent bonds with as many as 4 other atoms.

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 also form double covalent (shares 2 pairs of electrons) or triple covalent bonds (shares 3 pairs).

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.

  • 4 single bonds
  • two double bonds
  • one double bond and two single bonds
  • one triple and one single bond

Long chains of carbon atoms are common. The chains may be branched or form  rings.

Hydrophilic and Hydrophobic

Polar 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.

Nonpolar molecules are hydrophobic.
Polar and ionic molecules are hydrophilic.

Portions of large molecules may be hydrophobic and other portions of the same molecule may be hydrophilic.

Functional Groups

Organic molecules may have functional groups attached. A functional group is a group of atoms of a particular arrangement that gives the entire molecule certain characteristics. Functional groups are named according to the composition of the group. For example, COOH is a carboxyl group.

Organic chemists use the letter "R" to indicate an organic molecule. For example, the diagram below can represent a carboxylic acid. The "R" can be any organic molecule.

Some functional groups are polar and others can ionize. For example, if the hydrogen ion is removed from the COOH group, the oxygen will retain both of the electrons it shared with the hydrogen and will have a negative charge. The hydrogen that is removed leaves behind its electron and is now a hydrogen ion (proton).

If polar or ionizing functional groups are attached to hydrophobic molecules, the molecule may become hydrophilic due to the functional group. Some ionizing functional groups are: -COOH, -OH, -CO, and -NH2.

Some important functional groups are shown below.

NameStructure
Non-ionizedIonized
Hydroxyl 
Carboxyl
Amino
Phosphate
Sulfhydryl 
Aldehyde

 

Ketone 

Isomers

Different molecules that are composed of the same number and kinds of atoms are called isomers. Glucose and fructose (shown below) are both C6H12O6 but the atoms are are arranged differently in each molecule. Three kinds of isomers are described below.

Structural isomers differ in their overall construction as shown above for glucose and fructose. 

Geometric isomers maintain the same carbon skeleton but a double bond occurs between carbon atoms. The location of atoms bonded to a double-bonded carbon atom differs. The two molecules below are geometric isomers because the double bond cannot rotate. If the bond between the two carbon atoms below were a single bond, they would not be isomers because atoms attached by single bonds can rotate. The carbon atoms would be able to rotate from one orientation to another if the bond were a single bond.

Enantiomers are molecules that are mirror images of each other. The molecules shown below are enantiomers.

Condensation

In order to bond the two molecules shown below together, you must first remove a hydrogen from each one. This is necessary because carbon has a maximum of 4 bonds and hydrogen can have only one.

In biological systems, macromolecules are often formed by removing H from one atom and OH from the other (see the diagram below). The H and the OH combine to form water. Small molecules (monomers) are therefore joined to build macromolecules by the removal of water. The diagram below shows that sucrose (a sugar) can be produced by a condensation reaction of glucose and fructose.

Sucrose:

This is called a condensation or dehydration reaction.

Energy is required to form the bond.

Hydrolysis

This is a type of reaction in which a macromolecule is broken down into smaller molecules.

It is the reverse of condensation (above).

Macromolecules and Monomers

Many of the common large biological molecules (macromolecules) are synthesized from simpler building blocks (monomers). Each of the types of molecules listed in the table are discussed below.

Example of a MacromoleculeMonomer
polysaccharide (complex carbohydrate)monosaccharide (simple sugar)
fat (a lipid)glycerol, fatty acid
proteinamino acid
nucleic acidnucleotide

Proteins

Importance of proteins

Some important functions of proteins are listed below.

enzymes (chemical reactions)

hormones

storage (egg whites of birds, reptiles; seeds)

transport (hemoglobin)

contractile (muscle)

protective (antibodies)

membrane proteins (receptors, membrane transport, antigens)

structural

toxins (botulism, diphtheria)

Enzymes

Enzymes are proteins that speed up the rate of chemical reactions.

Example:

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

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) attached to the same carbon atom, called the alpha carbon.

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.

Polypeptides

A short chain of amino acids bonded together is called a peptide. A longer chain of many amino acids, typically 50 or more,  is referred to as a polypeptide.  The complete product, consisting of one or more polypeptides, is called a protein.

There is unequal sharing of electrons in a peptide bond. The O and the N are negative and the H is positive.

Levels of structure

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

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.

val his leu thr pro glu glu lys ser ala val thr ala leu tyr gly lys val asn val asp glu val gly gly glu ala leu gly arg leu leu val val tyr pro try thr gln arg phe phe glu ser phe gly asp leu ser thr pro asp ala val met gly asn pro lys val lys ala his gly lys lys val leu gly ala phe ser asp gly leu ala his leu asp asp leu lys gly thr phe ala thr leu ser gln leu his cys asp lys leu his val asp pro glu asn phe arg leu leu gly asn val leu val cys val leu ala his his phe gly lys glu phe thr pro pro val gln ala ala tyr gln lys val val ala gly val ala asp ala leu ala his lys tyr his

Secondary structure

The amino and carboxyl groups of the polypeptide backbone are capable of hydrogen-bonding with each other. This bonding produces two common kinds of shapes seen in protein molecules- coils , called alpha helices, and beta sheets. A single polypeptide may contain many of these helices and sheets. Hydrogen bonding between amino and carboxyl groups that produces alpha helices and beta sheets is referred to as secondary structure.

Tertiary 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.

Hydrophilic (polar and ionized) amino acids form hydrogen bonds with water molecules due to the polar nature of the water molecule.

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.

Quaternary structure

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.

Other Kinds of Proteins

Simple proteins contain only amino acids. Conjugated proteins contain other kinds of molecules. For example, glycoproteins contain carbohydrates, nucleoproteins contain nucleic acids, and lipoproteins contain lipids. 

Denaturation

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.

Nucleic Acids

DNA

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 body’s 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.

Structure of DNA

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.

DNA.jpg (94691 bytes)

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.

A-T

G-C

Antiparallel

The end of a single strand that has the phosphate group is called the 5’ end. The other end is the 3’ end.

The two strands of a DNA molecule run in opposite directions. Note the 5’ and 3’ ends of each strand in the diagram.

RNA

RNA (ribonucleic acid) is similar to DNA and is involved in the synthesis of polypeptides and proteins as discussed above.

RNA is single-stranded as shown below.

 

RNA contains the base Uracil instead of Thymine.

The table below lists differences between DNA and RNA.

 

DNA

RNA

# Strands

2

1 (see diagram below)

Sugar

deoxyribose

ribose

Bases

A, T, G, C

A, U, G, C

Codons

One strand of DNA (the anti-sense strand) is used as a template to produce a single strand of mRNA. The bases in the mRNA strand are opposite (complimentary) to the bases in the DNA template strand; it resembles the sense strand of DNA except that the base thymine is replaced by uracil. The mRNA contains three-letter (three-base) codes used to determine the sequence of amino acids in the polypeptide that it codes for. For example, in the diagram below, GUG is the code for valine. The sequence of codes in DNA therefore determines the sequence of amino acids in the protein.

transcription, translation

Each three-letter code in mRNA is a codon. It is the code for one amino acid.

Click here for details on how information is stored in DNA.

ATP

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.

Carbohydrates

The general formula for carbohydrates is (CH2O)n.

Monosaccharides

Monosaccharides 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

Disaccharides are composed of 2 monosaccharides joined together by a condensation reaction.

Examples:

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.

Lactose is found in milk. It is formed when glucose bonds to galactose.

The digestion of complex carbohydrates (polysaccharides) typically involves hydrolysis reactions in which the molecules are broken down to maltose, a disaccharide. Maltose is then further broken down to produce two glucose molecules.

Polysaccharides

Monosaccharides may be bonded together to form long chains called polysaccharides.

Ten or more monosaccharides may be bonded together to form long chains called polysaccharides. The chains are typically composed of hundreds of monosaccharaides.

Starch and Glycogen

Starch and glycogen are polysaccharides that function to store energy. They are composed of glucose monomers bonded together producing long chains.

Animals and some bacteria store extra carbohydrates as glycogen.

In animals, glycogen is stored in the liver and muscle cells. Between meals, the liver breaks down glycogen to glucose in order to keep the concentration of glucoses in the blood stable. After meals, as glucose levels in the blood rise, it is removed from and stored as glycogen.

Plants and some algae produce starch to store carbohydrates.

Amylopectin is a form of starch that is very similar to glycogen. It is branched but glycogen has more branches. Amylose is a form of starch that is unbranched.

Below: Glycogen or Starch

Cellulose and Chitin

Cellulose and Chitin are polysaccharides that function to support and protect the organism. The cell walls of plants are composed of cellulose. The cell walls of fungi and the exoskeleton of arthropods are composed of chitin.

Cellulose is composed of beta-glucose monomers; starch and glycogen are composed of alpha-glucose. The bond orientation between the glucose subunits of starch and glycogen allows the polymers to form compact spirals. The monomers of cellulose and chitin are bonded together in such a way that the molecule is straight and unbranched. The molecule remains straight because every other glucose is twisted to an upside-down position compared to the two monomers on each side. Cellulose fibers are composed of long parallel chains of these molecules. The chains are attached to each other by hydrogen bonds between the hydroxyl groups of adjacent molecules.

Below: Cellulose

The glucose monomers of chitin (N-acetyl glucosamine) have a side chain containing nitrogen.

Cellulose is the most abundant carbohydrate on earth. Cotton and wood are composed mostly of cellulose.  They are the remains of plant cell walls.

Digestibility of Cellulose and Chitin

Humans and most animals do not have the necessary enzymes needed to break the linkages of cellulose or chitin.

Some bacteria and some fungi produce enzymes that digest cellulose. Some animals have microorganisms in their gut that digest cellulose for them.

Fiber is cellulose, an important component of the human diet.

Lipids

Lipids are compounds that are insoluble in water but soluble in nonpolar solvents. 

Lipids are also an important component of cell membranes.

Some lipids function in long-term energy storage. One gram of fat stores more than twice as much energy as one gram of carbohydrate.

Fats and Oils (Triglycerides)

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 and Unsaturated Fat

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

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

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.

Waxes

Waxes are composed of a long-chain fatty acid bonded to a long-chain alcohol

They form protective coverings for plants and animals (plant surface, animal ears).

Review

Use the symbols below to draw a disaccharide, polysaccharide, triglyceride, phospholipid, polypeptide, and DNA. Use short, straight lines to represent covalent bonds.

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.