Topic 2.1 Molecular Biology

2.1 (U1) Molecular biology explains living processes in terms of chemical substances involved. Molecular biology is a branch of biology that was developed following the discovery of DNA in 1953. Scientists started to realize that they could explain biological processes by studying the structure of molecules and their interactions in living things. Many molecules important to living things have been studied including water molecules, proteins, nucleic acids (DNA & RNA), carbohydrates and lipids.

The reductionist approach… Molecular biology focuses on the variety of biochemical processes in living organisms and breaking these down into their component parts. This type of approach is known as the reductionist approach and it has been very successful for molecular biologists to date. However, some biologists feel this is not always the best approach as there are emergent properties that cannot be studied without looking at the entire system

2.1 (A1) Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized. Urea is an organic compound found in the urine of animals. It is a nitrogen containing compound and it is produced when there are extra amino acids in the body and the organism needs a way to get rid of the extra nitrogen. Urea is produced in the liver and released into the blood stream. The blood stream carries it to the kidneys where it is filtered out of the blood and passes out of the body in urine.

Urea & the falsification of vitalism German chemist Friedrich Wӧhler was trying to synthesize ammonium cyanate (an inorganic salt) in the lab and he ended up making urea instead. This was the first time an organic compound had been synthesized outside of an organism. When Wӧhler published his results it caused quite a stir among vitalists, scientists who believed that organic compounds could only be produced with the help of a “vital principal” (living thing). The theory was known as vitalism and it states that the origin and phenomena of life are due to a vital principal.

Urea & the falsification of vitalism Friedrich Wӧhler’s finding was significant and while it did not lead to the immediate falsification of the theory of vitalism, it was the first evidence against the theory. It took many more experiments and the synthesis of many more complex organic molecules in the laboratory before the principal was finally abandoned.

What do we mean by organic? Carbon containing Living things also contain a lot of: Hydrogen Oxygen Phosphous Nitrogen

2.1 (U2) Carbon atoms can form four bonds allowing a diversity of compounds to exist. While carbon only ranks 15th on the list of the most abundant element on earth, it is found in and used to make a huge range of different molecules, particularily those important to organisms. Due to the fact that carbon atoms have four valence electrons, it forms four covalent bonds with other atoms which allow carbon based molecules such as carbohydrates, lipids and proteins can be produced.

2.1 (U2) Carbon atoms can form four bonds allowing a diversity of compounds to exist. The covalent bonds that form between carbon and other atoms such as hydrogen, oxygen, nitrogen and phosphorous are very strong and this allows for the formation of many complex molecules. These molecules can be chains or rings and the covalent bonds can be single, double or a combination of both.

2.1 (U3) Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids. All living things are composed of the four main classes of carbon compounds. These inlcude carbohydrates, lipids, proteins and nucleic acids. Each of these carbon compounds have different structures but they all contain carbon, hydrogen and oxygen. The differences in their structures also allows them to be used for different purposes.

Carbohydrates Carbohydrates are organic compuinds that contain carbon, hydrogen and oxygen and they consist of one or more simple sugars. Carbohydrate monomers are often ring shaped molecules and have a ratio of two hydrogen atoms for every one oxygen atom.

The chemical formula for glucose is C6H12O6 2.1 (S1) Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid. Glucose is a monosaccharide with a 6 sided ring and is known as a hexose sugar. The chemical formula for glucose is C6H12O6 Monosaccharides are the subunits of disaccharides and polysaccharides (starches).

Ribose is a 5 carbon sugar and is known as a pentose sugar. 2.1 (S1) Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid. Ribose is a 5 carbon sugar and is known as a pentose sugar. Ribose is also a monosaccharide. Ribose can be found in the nucleic acid RNA (ribonucleic acid).

Lipids Lipids include steroids, waxes, fatty acids and triglycerides. They are insoluble in water and are considered fats if they are solid at room temperature and oils if they are liquid at room temperature.

Fatty acids can be found in a group of fats known as lipids. 2.1 (S1) Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid. Fatty acids can be found in a group of fats known as lipids. Lipids contain three fatty acid molecules and one molecule of glycerol.

Proteins Proteins are made up of chains of amino acids held together by peptide bonds. All proteins are composed of amino acids made of carbon, hydrogen, oxygen and nitrogen. Some proteins also contain sulphur in their amino acids.

2.1 (S1) Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid. Amino acids are the sub units of proteins and they bond together to form polypeptides. There are 20 different amino acids and they are distinguished by their R-group but they all have the same generalized structure.

Nucleic Acids There are two types of nucleic acids, DNA and RNA. Nucleic acids are composed of individual units called nucleotides which contain carbon, hydrogen, oxygen, nitrogen and phosphorous.

See handout given in class 2.1(S2) Identification of biochemicals such as carbohydrate, lipid or protein from molecular diagrams. See handout given in class

2.1 (U4) Metabolism is the web of all the enzyme catalyzed reactions in a cell or organism. Metabolism can be defined as the totality of an organism’s chemical reactions. It is an emergent property of life that arises from interactions between molecules within the orderly environment of the cell (Campbell-Reece). Chemical reactions in living things are catalyzed by enzymes and most reactions are intracellular (cell respiration) but some are extracellular (digestion). These metabolic reactions occur in chains or cycles and one type of molecule is transformed into another in a series of reactions.

2.1 (U5) Anabolism is the synthesis of complex molecules including the formation of macromolecules from monomers by condensation reactions. Anabolic metabolism involves the building of larger molecules from smaller components and require energy which is often ATP. Anabolic pathways use up energy which gets stored in the larger molecule. An example is amino acids being joined together by peptide bonds to form proteins. Other examples of anabolic pathways include DNA synthesis, photosynthesis, and the production of large carbohydrates such as starches from simple sugars.

2.1 (U6) Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers. Catabolic metabolism involves the breaking down of larger molecules into their smaller component parts. These pathways release energy as bonds are broken. Examples of catabolic pathways include digestion in organisms, cellular respiration, and the decompostion of organic matter by decomposers.