Topic 2: Molecular Biology Subtitle

The essential idea:  Living organisms control their composition using a complex web of chemical reactions.

All living organisms control their composition by a complex web of chemical reactions. These reactions form the basis of life. Every aspect and structure of living cells is based on the results of chemical reactions.

Some of the metabolic reactions in a cell

Molecular Biology It is a part of biology that is associated with biological activity at molecular level. It explains living processes in terms of chemical substances involved.

Molecular Biology aims to solve problems associated with living processes by balancing the chemical substances involved. Phenylketonuria Rare inherited disorder (fewer than 20.000/year) Causes an amino acid called phenylalanine to build up in your body. Caused by a defect in the gene that helps create the enzyme needed to break down phenylalanine. Controlled consumption of protein.

2.1.1 Carbon and the basis of organic chemistry The majority of chemical substances in living organisms contain carbon. AKA Organic Compounds Carbon containing, non-organic compounds: Carbon dioxide, carbon monoxide, carbonates and hydrogen carbonates.

Carbon Atomic number 6 Makes 4 bonds Very stable: Tetrahedron shape 109.5 degree angles

Carbon can form be very diverse molecules, from simple to complex Methane Butane Benzene ring

Carbon-based compounds found in living organisms include: Lipids Carbohydrates Nucleic acids Proteins

2.1.2 Carbohydrates, lipids and amino acids Living organisms are made of organic compounds. Be able to recognize and draw: Glucose Ribose Saturated fatty acid Generalized amino acid Be able to recognize: Lipids such as triglycerides, phospholipids and steroids Proteins or parts of polypeptides showing amino acids linked by peptide bonds

Alpha-D-Glucose & Beta-D-glucose Carbon 6 is CH2OH, and is attached to C5 Oxygen atom at the top -OH aBove 6 6 5 5 4 1 4 1 4 3 2 2 3 -OH below The difference between alpha and beta-D-glucose is that in beta-D-glucose the hydroxyl group is above the plane of the ring.

2H:1C ratio = monomer is a sugar Ribose – 5 carbon sugar 2H:1C ratio = monomer is a sugar

Fatty Acids Hydrocarbon chain is nonpolar, which means they are hydrophobic Remember –COOH is a carboxylic acid group! Carboxylic acid groups are polar, which means they are hydrophilic CH3(CH2)16COOH (keep the total number of carbon atoms in the molecule between 12-24)

Amino Acids Remember –COOH is a carboxylic acid group! NH2 is called an amino group

2.1.3 Metabolism, anabolism and catabolism Metabolism is the total of the enzymatic reactions that take place inside a living organism. It consists of pathways by which one type of molecule is transformed into another, in a series of small steps.

2.1.3 Metabolism, anabolism and catabolism

Catabolism Breakdown of complex molecules into simpler molecules. Includes the hydrolysis of macromolecules into monomers. Hydrolysis = breaking molecules down by adding water Energy is released. The breakdown of sugars (including glycolysis) or fats to release energy are all examples of catabolic reactions. It is a process during which energy is released.

Anabolism Synthesis of complex molecules from simpler molecules. Requires the input of energy. Includes the formation of macromolecules from monomers by condensation reactions. Condensation = combining two smaller molecules to make a larger one, usually producing water or some other simple molecule in the process. Ex: proteins are made from amino acids starches are made from glucose. DNA synthesis using ribosomes.

Anabolism vs Catabolism

2.1.4 Urea - CO(NH₂)₂ Is a waste product of many living organisms. Major organic component of human urine. This is because it is at the end of chain of reactions which break down the amino acids that make up proteins. These amino acids are metabolized and converted in the liver to ammonia, CO2, water and energy. But the ammonia is toxic to cells, and so must be excreted from the body. Aquatic creatures, such as fish, can expel the ammonia directly into the water, but land-based animals need another disposal method. So the liver converts the ammonia to a non-toxic compound, urea, which can then be safely transported in the blood to the kidneys, where it is eliminated in urine.  As urea goes stale, bacteria convert it back into ammonia, which gives the familiar pungent smell of lavatories

2.1.4 Urea - CO(NH₂)₂ Organic compound Formula CO(NH₂)₂ Also know as carbamide. It is used by the human body in nitrogen excretion because it is non-toxic and highly soluble. Widely used as a nitrogen fertilizer. This application of urea has led to its artificial synthesis on large scale. 

Commercial production of synthetic Urea Produced by the reaction of ammonia and carbon dioxide under high pressure (approximately 150 atm) and at high temperatures (approximately180°C). The reaction is summarized  below: 2NH3 + CO2 -----> CO2NH4NH2 -----> CO(NH2)2 + H2O The product, ammonium carbamate (CO2NH4NH2), is then dehydrated to yield urea. Urea

Theories can be falsified by new evidence According to the theory of vitalism, organic compounds could only be synthesized by living organisms as they possessed an 'element' that non-living things did not have. That element has been referred to as the “vital principle”, “divine principle” or “the life spark” by some. Friedrich Wohler accidentally synthesized urea in 1828. Two important concepts from his experiment: a by-product of life could be artificially synthesized in a laboratory. First experiment to show that the synthesis of an organic compound from two inorganic molecules was achievable.