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The Macromolecules of LifeCarbon.

Life on earth is carbon based. The large molecules that are found in cells all contain carbon. While the chemistry of life is basically water chemistry because of the high percentage of water in cells (70% to 95%) the chemistry of the biological molecules, biochemistry, is carbon chemistry. What makes carbon so important is its ability to form 4 covalent bonds with other atoms. Its atomic number is 6 so its electrons are found in the 2-4 energy shell configuration. Carbon would have to gain or lose 4 electrons to become an ion. This is difficult to do, so instead, it shares electrons to fill its outer energy shell. Carbon can be thought of as the wheel in a tinkertoy set to which other components are attached. They can be joined by single or double bonds and connect in chains or rings, making carbon extremely versatile.

1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic acids

CarbohydratesCarbohydrates are composed mainly of carbon, hydrogen and oxygen in a CH2O proportion. For each carbon and oxygen there are two hydrogen atoms. Carbohydrates are important as short term energy storage molecules (simple sugars such as glucose and fructose), as long term energy storage molecules (starches and glycogen), as structural molecules (e.g. cellulose, which is found in all plant cell walls) and as important components of DNA and RNA.

MonosaccharidesMonosaccharides are simple sugars. The most common monosaccharide is glucose. Glucose is extremely important because it provides energy when broken down by the process known as cellular respiration. Furthermore it is at the crossroad of many chemical reactions. Many other molecules such as amino acids and fatty acids can be synthesized from glucose and many molecules can be broken down to form glucose. Our brains cannot store glucose and must be constantly supplied with it by our blood. If this supply stops for too long, the brain cells will begin to die. Read about some other common monosaccharides in your text.

DisaccharidesA disaccharide is formed when two monosaccharides are joined together by a reaction known as a dehydration, or condensation, synthesis . In this type of reaction water is removed, thus the name "dehydration". A new molecule is formed or "synthesized" from the two previously separate ones. The animation shows a molecule of the disaccharide, maltose, formed from two glucose molecules. An enzyme is required to make the reaction occur. A very common disaccharide is made of a glucose molecule and a fructose molecule. It is called sucrose, but is better known as the table sugar we so love to eat.

This reaction occurs in the reverse direction when you digest maltose, sucrose or other carbohydrates. In that case water is added and the two glucose molecules are split apart by an enzyme different from the one used in the dehydration synthesis. The splitting apart reaction is called hydrolysis.

PolysaccharidesPolysaccharides (poly = many, saccharide = sugar) are made of many sugar molecules joined together by dehydration synthesis reactions. When many repeating units are joined together to make a large molecule, the resulting molecule is called a polymer. There are many polysaccharides, but we will limit ourselves to only four; starch, glycogen, cellulose and chitin. All four of these are made of many repeating units of glucose molecules. They are, therefore, polymers of glucose. they differ from each other in the amount of

branching of the molecules, the way in which the molecules are connected to each other and in the addition of amino groups to the glucose.

1. Starch. Starch is the long term energy storage form of glucose in plants. It is found

in abundance in the grains we eat, (rice, wheat, barley and rye) and in many vegetables, such as potatoes and corn. The diagram shows part of a molecule of the starch amylose. There will be many more glucose molecules similarly connected to complete this polymer of glucose.

2. Glycogen. Glycogen is the animal energy storage form of glucose. This polymer has the glucose molecules linked in the same way as they are in the plant starch. Glycogen molecules tend to be larger and much more branched than are starch molecules and they are found in the liver and muscles of animals. Human beings send their digested food to the liver where it is carefully monitored. If the supply of glucose in the blood is sufficient, glucose will be polymerized into glycogen. After enough glycogen is synthesized to supply glucose for two hours, the excess glucose will be converted into fat and stored in this efficient, but often unsightly way.

3. Cellulose. Cellulose  differs from starch and glycogen in the way in which the glucose molecules are linked together. Compare the diagram below with that of starch and you will see that the position of the hydrogen on the first carbon atom differs. In starch the hydrogen is pointing up (called an alpha-linkage), and in cellulose it is pointing down (beta linkage). This difference in the way the glucose

molecules are linked together gives the two carbohydrates very different properties. Amylose is water soluble and easily digested.  Cellulose is a tough fibrous polymer of glucose which is found in the cell walls of plants. No animal has an enzyme to break down cellulose, so it cannot be digested by them directly. We eliminate ingested cellulose as fiber. Termites, who eat wood, depend upon microorganisms in their digestive tracts to break down the cellulose. Without these, termites would starve to death.

4. Chitin.  Chitin is made of glucose molecules linked in the same way they are linked in cellulose, making it equally indigestible.  It differs from cellulose by having amino groups (NH2) attached to the glucose molecules.  Chitin is an extremely important material.  It forms the exoskeleton of all arthropods (e.g. insects, spiders, lobsters and crabs).  This exoskeleton, and the jointed limbs it permitted arthropods to acquire, is a primary reason for the extreme success of these animals.

LipidsLipids are defined by their solubility. They are molecules that are insoluble in polar solvents (such as water), but will dissolve in non-polar solvents. Lipids are non-polar. Fats, oils, waxes and the steroids are all lipids. They function as energy storage molecules, as insulation and protection for internal organs, as lubricants and as hormones. One group, the phospholipids are the major structural elements of membranes.

Triglycerides (fats).Triglycerides are composed of a glycerol backbone and three fatty acids. A fatty acid is a long chain of 12-24 carbon atoms with hydrogen atoms attached to them. At one end is a carboxyl or organic acid group.

The acid molecule has the structure . The fatty acids are joined to the glycerol by a dehydration synthesis reaction. (If you have forgotten what this is, return to dehydration synthesis.)

As with the carbohydrates, this reaction requires a specific enzyme to make it occur. Fats have differing properties depending on whether their constituent fatty acids are saturated or unsaturated.

1. Saturated fatty acids contain all of the hydrogens they can hold. The fatty acids in the animation above are all saturated with hydrogen. There are no carbon to carbon double bonds in saturated fatty acids. Saturated fatty acids are typical of animal fats and are believed to cause blockage of arteries which can lead to strokes and heart attacks.

2. Unsaturated fatty acids do not contain all of the hydrogen possible. One or more carbon to carbon double bonds will be present in the carbon chain.Linoleic acid is an unsaturated fatty acid because there are two carbon-carbon double bonds in the carbon chain. Note that each carbon involved in the double

bonding has only one bond left for bonding to hydrogen. Such molecules are not completely loaded with hydrogen so they are unsaturated.

 

Phospholipids.The diagram shows a phospholipid. It is formed by replacing one of the terminal fatty acids in a triglyceride with a phosphate group. Because oxygen is so electronegative (see electronegativity) the oxygens in the phosphate make the region around them negative so that the phosphate part of the molecule is polar. Polar molecules are hydrophilic (water soluble), therefore, the phosphate head of the phospholipid. is water

soluble. The fatty acid tails, however, remain nonpolar and hydrophobic (insoluble in water).

 

 

  

Micelles.When a phospholipid is placed in water it usually forms a ball called a micelle. This happens because the hydrophobic parts of the phospholipid try to avoid the water and cluster together in the middle of the droplet. The polar phosphate heads, however, arrange themselves so that they are exposed to the positive hydrogen regions of water molecules. The micelle is the result.

Cell Membranes.  The membranes that surround cells form from a double layer of phospholipids known as a bilayer. This is essentially a fat sandwich, with the fatty acids forming the filling and the phosphate heads forming the "bread". Since cells have much water in them and are surrounded by a watery medium, the phospholipid bilayer separates these two watery areas. The middle region of the membrane will be hydrophobic and the outside and inside will be hydrophilic.

ProteinsProteins are polymers of amino acids. This means that proteins are repeating units of molecules which have an amino (NH2) group at one end and an acid (carboxyl) group at the other end. Between these there is a carbon atom which has a variable group attached to it. The letter R stands for the various units that can be substituted here. Your text has a picture of the 20 amino acids that are most often found in proteins. Note that the R groups can be as simple as CH3 in the amino acid, alanine, and as complicated as the double ring in the amino acid, tryptophan. The diagram shows the key features of an amino acid.

Proteins are formed by dehydration (condensation) synthesis which links amino acids together. In this reaction, water is removed and the nitrogen from the amino end of one amino acid is joined to the oxygen from the other end of another amino acid.

 

 

Since the linked amino acids always have a free acid group at their end, other amino acids can be added by the same reaction to form a polypeptide. A polypeptide is formed when many amino acids are joined together by peptide bonds.

 

A protein is a large polypeptide, or several polypeptides joined together, and having a specific shape and function. Proteins have many important biological functions. Among these are:

1. Support. Many structural materials are proteins such as the collagen that is the supporting framework in animal connective tissue. The matrix in which bone, cartilage and tendons form is protein.

2. Hormones. Some small hormones are proteins. These molecules carry information to various parts of the body.

3. Blood proteins. Albumin and other proteins in the blood are important in regulating the fluid concentration of the circulatory system and in forming blood clots to prevent bleeding. Hemoglobin is important in carrying oxygen to the cells and in regulating pH of the blood. Many other proteins are important carriers of materials such as those that bind with iron.

4. Receptor sites on membranes. Cells incorporate materials through protein channels. Information is transferred to nerve cells by protein receptors in the receiving cells.

5. Movement. The filaments which slide to cause the contraction of muscles are proteins. Other proteins cause cilia and flagella to move.

6. Defense. Antibodies, which fight invading viruses and bacteria, are proteins.7. Enzymes. Perhaps the most important function of proteins is their action as chemical mediators of

reactions. Digestion of food and synthesis of important molecules occur in living cells only in the presence of these proteins. Life is impossible without them

Protein structure. There are four levels of structure for proteins.

1. Primary structure. The name and location of each amino acid in the protein determines its primary structure. What is the first amino acid? the second? etc. When the name of each amino acid in the polypeptide chain or chains is known, the primary structure is known. Primary structure is fundamental to protein function, because the order of the amino acids in a protein determine the other levels of its structure and ultimately its function. A single amino acid that is in the wrong place can cause a vital protein to malfunction and could be lethal. Sickle cell anemia is caused a single amino acid substitution in hemoglobin, the molecule that carries oxygen to the cells.

2. Secondary structure. The coiling, bending or folding of the primary amino acid chain into a helix or into sheets. The coiling and bending is due to hydrogen bonds that form regularly between hydrogen regions of amino groups and oxygen regions of acid groups in the amino acids composing the polypeptide.

3. Tertiary structure. The final three dimensional shape of a single strand protein.  The model on the right shows the tertiary structure of a molecule of hexokinase, a protein found in almost all living organisms. This protein is composed of approximately 6000 atoms or about 240 amino acids.   Tertiary structure is dependent upon interactions between specific amino acids in the molecule, so it is determined by primary structure. Since these amino acids are not spaced at regularly recurring intervals, tertiary structure can be the result of many irregular and complex bends and twists of the secondary coil. One way this occurs is by binding of the sulfur atoms of some amino acids to each other. Another factor in tertiary shaping has to do with the tendency of hydrophobic regions of the molecule to cluster together to avoid water. The sum total of these sorts of interactions provides a specific three dimensional shape to proteins. This shape determines the functionality of single strand proteins.

4. Quaternary structure. Some proteins are composed of more than one polypeptide chain. The final three dimensional shape of proteins composed of more than one chain is the quaternary structure of such proteins.

 

The hemoglobin molecule shown here is composed of four chains each of which has its specific tertiary structure. Quaternary structure is achieved when these four polypeptides come together and form the specific attachments that give the hemoglobin its final shape.

 

1. (Both models are made available through the courtesy of the MIT Biology Hyprtextbook.. http://web.mit.edu/esgbio/www/lm/proteins/structure/structure.htmll.  This site has more information on protein structure.)

Nucleic acids (DNA and RNA) 

 

On the left is a picture of the famous nucleic acid, DNA. DNA is the molecule which carries the genetic information that makes us unique. The structure of DNA is a double helix. It can be imagined as a ladder which has been twisted into a spiral. The alternating red and light blue balls spiraling around in the picture are analogous to the sides of the ladder and are made of alternating red deoxyribose sugars and light blue phosphate groups. The rungs of the ladder are nitrogenous bases. The discovery of the structure of DNA was arguably the most significant biological discovery of the twentieth century. It revolutionized the field of genetics and led to the new discipline of molecular biology. DNA testing for forensic use, genetic engineering, genetic disease diagnosis and treatment and a host of other areas are all the result of the unraveling of the structure of DNA by Watson and Crick in 1954.

 

 

  

Nucleotides.

 

 

DNA and RNA, the two nucleic acids, are polymers of nucleotides. A nucleotide is made of a phosphate, a 5 carbon sugar and a nitrogenous base. The sugar in DNA is deoxyribose and the bases are adenine (A), cytosine (C), guanine (G), and thymine (T). In RNA the sugar is ribose and the bases are A, C, G, and uracil (U) instead of T.

In both DNA and RNA, nucleotides are joined together by covalent bonds between the phosphate of one nucleotide and the sugar of the next one. The result of this linking is a sugar-phosphate backbone with bases projecting inward from the sugars. When many nucleotides are joined together in a chain we have a polymer of nucleotides forming a nucleic acid.

  

 

 

DNA.DNA is composed of two nucleotide chains connected to each other by hydrogen bonds. The diagram on the right shows a portion of one of the strands of a DNA molecule. The d stands for the sugar, deoxyribose, the P for phosphate and A, C, T and G for the nitrogenous bases, adenine, cytosine thymine and guanine. Note that the backbone of this strand is composed of alternating sugar and phosphate molecules.

 

In a double helix of DNA the two strands of DNA are joined together by specific pairings of the bases. Look at the four letters A, C, G, and T. There is only one two-letter English word you can make from these letters.

What is it? If you said at you are correct. That will help you remember that in DNA, A always pairs with T and C always pairs with G.

In this diagram we have shown the complementary strand of DNA as it pairs with the strand shown above. The dashed lines connecting the bases represent hydrogen bonds joining them together. In the diagram, the bases on the left are not labeled. Decide on the name of the top unnamed base. To see if you are correct, move the cursor over the top base and when the hand appears, click once.

 

 

 

RNA.RNA is single stranded, made of  nucleotides with a  ribose sugar, and the base uracil, instead of the thymine found in DNA.

Since genes are DNA and RNA is important in handling the information in the DNA, we will learn more about nucleic acids when we study the molecular basis of genetics.