Atoms are the basic units of matter and all life is based on them. Life on earth is based on the element carbon. It is a highly versatile atom able to form four covalent bonds with itself or other atoms such as hydrogen and water. Atoms combine to form molecules and those that are carbon based are referred to as organic molecules. Organic molecules occur in four different types in living cells; carbohydrates, lipids, proteins and nucleic acids. They are also known as hydrocarbons due to the presence of both hydrogen and carbon. Carbohydrates are made up of carbon, hydrogen and oxygen in the ratio 1:2:1. They are important sources of energy and are classified in three main groups; monosaccharides, disaccharides and polysaccharides. Lipids contain high proportions of carbon-hydrogen bonds. The electrons in the bonds are shared equally giving it no charge. As a result they are non polar and insoluble in water, which is highly polar. They are also grouped into three classes; triglycerides, phospholipids and steroids. Proteins are the most abundant of the organic molecules found in cells and have a wide range of cell functions. They consist of chains of amino acids covalently bonded and differ from each other by the number and arrangement of the 20 different amino acids that exist in living organisms. Nucleic acids are polymers made of nucleotide monomers. They can either be Deoxyribonucleic Acid (DNA) or Ribonucleic Acid (RNA). All these organic molecules carry out various essential functions within the body and their absence or lack of proper functionality greatly affects how the body works.
The purpose of this experiment was to test different substances to determine the organic molecules they contain. Different reagents were used for the tests with the reagents reacting with the molecules in a specific way indicated by a change of color. Controls were provided to ensure integrity of the process. The results indicated the presence or absence of the organic molecules in the various substances provided. They proved that using these tests, one can accurately determine what organic molecules a substance contains. This will help in determining the composition of various substances within the cell or even outside the body and how they affect normal cell function.
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Introduction
Organic molecules are defined as those molecules that are carbon based. However , not all compounds containing carbon are organic molecules. There are a few exceptions such as carbon monoxide, carbon dioxide, carbonates (e.g. calcium carbonate), carbides (e.g. calcium carbide) and cyanides (e.g. sodium cyanide). Diamond and graphite, which are pure carbon compounds are also not classified as organic compounds ( Alberts B., Johnson A., Lewis J., 2002). Our bodies largely constitute of organic molecules. These organic compounds occur naturally and can also be synthetic (man-made). They are present in our foods, clothes, medicines, washing powders and much more. Inorganic molecules are not composed of chains of carbon atoms and are relatively less complex. Living things regularly utilize inorganic molecules e.g. water, carbon dioxide and oxygen and even assimilate them into organic molecules. Plants utilize carbon dioxide assimilating the carbon into sugar (a carbohydrate). Each carbon atom can covalently bond with four other atoms at any given time but mostly oxygen, hydrogen, nitrogen, sulfur, and phosphorus atoms. It can also bond to other carbon atoms forming extremely long chains. As a result, a huge number and great variety of molecules can be built from carbon atoms. No other element even comes close (Alberts et al., 2002).
The four types of organic molecules found in cells are carbohydrates, lipids, proteins and nucleic acids. They are all polymers made during dehydration synthesis reactions from monomers. These reactions result in the loss of water forming strong covalent bonds. They are referred to as endergonic reactions since they require an input of energy. Hydrolytic reactions are the opposite as they break polymers into single unit monomers using water and in the process releasing energy thus referred to as exergonic reactions (Gorrod, 1985). The monomer form of carbohydrates is a monosaccharide e.g. glucose (used for energy in cells), fructose and ribose. When two monosaccharides undergo a dehydration synthesis reaction they form a disaccharide e.g. sucrose, which is a combination of glucose and fructose. Sucrose is used for transport in plants. Polysaccharides consist of three or more covalently bonded monosaccharides. Starch and glycogen are good examples and are both used in energy storage in plants and animals respectively. Monomers of lipids are fatty acids and glycerol while amino acids are monomers of proteins. Amino acids mainly function to regulate different cell functions as well as catalyze various cell reactions. Nucleotides are the monomers of nucleic acids and they function in storing the genetic information of a cell (DNA) and synthesis of proteins (RNA). All these monomers undergo dehydration synthesis reactions to form their corresponding polymers and are used in different cell functions (Organic Molecules Lab Manual, 2017). RNA differs from DNA in a number of ways. Firstly, the sugar present in the nucleotides that make an RNA molecule is ribose, not deoxyribose as it is in DNA. Secondly, the thymine nucleotide is not found in RNA but has been replaced by uracil. Furthermore, RNA is a single ‐ stranded molecule while DNA is double-stranded (Gorrod, 1985).
Figure 1. Examples of amino acids. Figure 2. Examples of carbohydrates
The above examples show the different molecular structures of amino acids and carbohydrates ( Lodish H., Berk A., Zipursky S., 2000).
In the analysis of scientific data, either qualitative or quantitative tests carried out. Qualitative tests involve the use of results that cannot be measured but observed e.g. color changes. One records the qualities of what is under study. Quantitative analysis involves the study of measurable parameters e.g. change in numbers, amounts etc. Controls are another important aspect of scientific analysis. They confirm that the experiment is working correctly. In the lab, a positive control is usually a substance that contains the molecule that is being tested for while a negative control does not contain the molecule. The positive control shows how a positive result should look like while a negative control shows how a negative result should look like. If the controls do not react as expected, the test results cannot be trusted and is repeated (Organic Molecules Lab Manual, 2017).
The purpose of this experiment was to test different substances to determine what organic molecules they contain. Unknown substances were compared to known substances to determine their composition of organic molecules.
Hypothesis: Using these tests, we will be able to accurately determine the presence of proteins, monosaccharides, starch, lipids and DNA molecules in the substances.
In our experiment, different tests were conducted to establish presence of various organic molecules;
Benedict’s test - This is a monosaccharide test. During the test, when heated the Benedict’s solution will turn from blue to green, yellow, orange then finally red depending on the amount of reducing sugars (monosaccharides) present. Disaccharides do NOT react with the Benedict’s Solution.
Iodine Test - This is a starch test. When starch (amylose) interacts with iodine it produces a blue / black color. When iodine does NOT interact with any starch it may have a yellow-brownish color.
Grease spot test /Brown paper test - The test is done by applying the sample on a brown piece of paper. The residue is observed. If it dries within a few minutes it is aqueous (water-based). If the spot is still looking wet after a few minutes, it is most likely a lipid.
Sudan IV test - Sudan IV is a fat-soluble dye that stains lipids red when mixed together. Using Sudan red can show the amount and the location of lipids.
Biuret test - Biuret agent is used to test proteins. The reagent is blue in color but when it reacts with the peptide bonds of the proteins it turns purple/ violet in color. The intensity of the color is directly proportional to the number of peptide bonds in the solution.
Dische diphenylamine test - Under acidic conditions, the deoxyribose moiety of DNA binds to diphenylamine to form a molecule that is blue in color. The intensity of the resulting color indicates the concentration of DNA in the solution.
The significance of accurately testing solutions and substances for organic molecules cannot be understated. Industries dealing with medicines, food and even cosmetics rely on the accurate determination of the presence of organic molecules in numerous compounds, their location in the body and how they react with other substances. The accuracy of these tests is therefore paramount and more advanced ways of testing for organic molecules continue to be invented (Lodish et al., 2000)
References
Alberts B., Johnson A., Lewis J., (2002). Molecular Biology of the Cell. 4th edition. New York: Garland science
Gorrod J. W., (1985). Biological Oxidation of Nitrogen in Organic Molecules: Chemistry, Toxicology and Pharmacology (Ellis Horwood Health Science Series) . Vch Publishers
Lodish H., Berk A., Zipursky S., (2000). Molecular Cell Biology. 4th edition. New York: W. H. Freeman. Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK21514/ on 05 March 2017.
Organic Molecules Lab Manual 2017
