BIOMOLECULES
The main classes of biomolecules can be introduced by discussing their roles in the cell. While biomolecules play extremely important roles in the functioning of tissues, organs, organ systems, and the organism as a whole, their unique roles at the cellular level give us a way to relate their structures and properties to their biological functions.
A typical eukaryotic cell consists of a plasma membrane surrounding the cytoplasm. The cytoplasm basically consists of an aqueous solution called the cytosol, and the numerous organelles and structural molecules inside the cell. The cytosol is a solution of ionic compounds and soluble proteins.
The plasma membrane, as well as all membranes that surround the organelles, consists mainly of two types of biomolecules, lipids and proteins. While lipid molecules are present in greater numbers than protein molecules, the protein molecules are much larger and heavier, so that proteins take up a greater fraction of the membrane’s mass than lipids. Nucleic acids are found within the nucleus and the ribosomes. Deoxyribonucleic acid (DNA) is found in the nucleus, and stores genetic information. RNA (ribonucleic acid) is found outside the nucleus, surrounding and within the ribosomes, and is involved in the synthesis of proteins.
Proteins synthesized by the ribosomes are often moved into the endoplasmic reticulum where they are modified in various ways. The Golgi apparatus carries out additional protein modifications. Lipids are made in the endoplasmic reticulum, and move as lipid vesicles to other organelles or to the plasma membrane. Molecules are degraded inside the lysosome by a group of catalytic proteins called enzymes, which facilitate the breakdown of biomolecules. Enzymes are found throughout the cell wherever any chemical reaction takes place.
Carbohydrates are biomolecules that have many roles throughout the cell. Some are found attached to membrane proteins, while others act as long-term or short-term energy storage molecules. Carbohydrate molecules are used as building block molecules in nucleic acids or lipids, and some cells secrete carbohydrates as extracellular structural material. Carbohydrates play a varied role throughout the cell, and we will start our model building with the carbohydrate called D-glucose, also known as blood sugar.
1. Glucose is often found in living organisms as a ring structure, shown below.
2. Monosaccharides such as glucose can link together to form disaccharides, oligosaccharides, and polysaccharides. Form a disaccharide from two glucose molecules by linking them together at their hydroxyl groups (-OH). The reaction below shows the linking of two glucose molecules to make the disaccharide called maltose.
3. Polymers of monosacchrides form by the linking of many monosaccharide monomer molecules, with the same type of reaction that formed the disaccharide. Starch, glycogen, and cellulose are all polymers of glucose.
4. Biomolecules classified as lipids all are very insoluble in water. The major classes of lipids are the triglycerides, phospholipids, glycolipids and steroids. A simple triglyceride is shown below. Triglycerides are commonly known as fats, if animal in origin, or oils, if obtained from plants.
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What is the name of the functional group that is circled in the above structure? Compare the hydrocarbon "tail" containing double bonds to the two below it that are "saturated" with hydrogens. The presence of double bonds in triglycerides is very important. Without any carbon-carbon double bonds a triglyceride is known as saturated, and with at least one carbon-carbon double bond the triglyceride is said to be unsaturated.
5. Nucleic acids such as DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are involved in the storage of genetic information, and the transfer and translation of this information for protein synthesis. Both DNA and RNA are polymers built from monomers called nucleotides. But nucleotides have other important functions too. Nucleotides such as adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide (NADH) are involved in transfer of energy from one reaction (and location) to another. Without these nucleotides our cells would quickly die.
Look at the structure shown below for the nucleotide deoxyadenosine monophosphate (dAMP). This and the monomers dTMP, dCMP, and dGMP make up DNA.
Shown below is a short section of a DNA molecule. Note that it is double stranded, and takes on a helical shape. This is why DNA is commonly referred to has having a double helix.
6. The last class of biomolecules that we will look at is the proteins. As with the polysaccharides and the nucleic acids, proteins are polymers. Amino acids are the monomer molecules in proteins, and they contain both carboxylic acid and amine functional groups. When amino acids link, the amine on one molecule reacts with the carboxylic acid on another to form a special type of amide linkage that biochemists call a peptide bond.
Their are 20 known a -amino acids in nature, two of which are shown below How are these amino acids similar, and how do they differ? These two molecules react together (at the groups shown in bold) to form a peptide bond, resulting in what biochemists call a dipeptide molecule. What other small molecule is formed when two amino acids link to form a dipeptide?
Proteins are polymers consisting of many amino acids linked together. Some proteins are fibrous in shape, some are globular. Some form the pores or channels across lipid membranes. Shown below as 3D stereoplots are the structures of two proteins. Can you predict their functions, based on their structures? Use 3D glasses to view these stereoplots (if you pring this out on paper, and if they are available). (Answer- the first is a molecule called porin, it forms pores in cell membranes, and the second is a short section of the protein called collagen, which is a strong rope-like molecule found in connective tissue. Doesn't the first look like it has a hole down its center, and the second look like a rope?)
