1. “Molecules of life” - Fundamentals of proteins, carbohydrates, lipids, nucleic acids
All life on Earth is built from four different types of molecules. These four types of molecules are often referred to as the molecules of life. The four molecules of life are proteins, carbohydrates, lipids and nucleic acids. Each of the four groups is vital for every single organism on Earth. Without any of these four molecules, a cell or an organism would not be able to live. All of the four types of molecules of life are important either structurally or functionally for cells and, in most cases, they are important in both ways.
Proteins are the building blocks of life. They are the most common molecules found in cells. If all the water is removed from a cell, proteins make up more than half of the remaining weight. The diversity and abundance of proteins within biological systems contribute to the large range of functions for which proteins are responsible. In fact, the large variety of protein structures inform their wide range of functions. Such functions include muscle movement, storage of energy, digestion, immune defense and much more.
Among their many functions, proteins provide structural support to specific tissues and organs within an organism. Keratin, for example, is the protein found in the outer layers of skin, making the skin a strong protective layer to the outside world. Keratin is also the structural protein that comprises the vast majority of tissues like hair, horns and nails.
Digestion is a function that is driven by proteins, specifically a protein type known as enzymes. Enzymes facilitate digestion by speeding up chemical reactions and cleaving large molecules into small and consumable molecules. Digestion specifically, is the breakdown of food from large, insoluble molecules into smaller molecules that can dissolve in water. These water-soluble molecules can enter the bloodstream and are transported throughout the body.
A very important protein for animals, both mammals and birds is hemoglobin. It is the protein in blood that binds to oxygen so that oxygen can be transported around the body.
The primary structure of a protein is a long chain made of many smaller molecules called amino acids. There are 20 different amino acids that are used to build proteins. The different amino acids can be arranged into trillions of different sequences that each creates a unique protein. The long chain of amino acids twists and folds on itself to produce the final shape of a protein (8).
An amino acid consists of a carboxyl group (chemical structure -COOH), an amine group (-NH₂), and a sidechain made mostly from carbon and hydrogen. The sidechain is often referred to as the R group. The differences in the R group make the 20 amino acids different from each other.
An amino acid can be water-soluble (polar), water insoluble (non-polar), or contain a positive or negative charge. These characteristics determine how the amino acids behave as they link up and influence the overall shape and function of a protein.
All 20 amino acids are necessary for good health. If an organism is low in one of the 20 amino acids, certain proteins are not built, causing health issues for the organism.
Some amino acids can be created by the body using other molecules while other amino acids must be sourced from food. The amino acids that must be eaten are known as the “essential amino acids” because they are an essential part of a healthy diet. The amino acids that can be made by the human body are known as “non-essential amino acids”.
The simplest form of a protein is called a polypeptide. A polypeptide consists of a chain of amino acids. Amino acids are bonded together between the amine group (-NH₂) of one amino acid and the carboxyl group (-COOH) of a second amino acid. The order the amino acids link together determines the final shape and structure of the polypeptide chain.
Carbohydrates are an important source of energy. They provide structural support for cells and help with communication between cells. A carbohydrate molecule is made of atoms of carbon, hydrogen and oxygen. They are found in the form of either a sugar or many sugars linked together.
Carbon atoms have the ability to bond to four other atoms. In carbohydrates, carbon atoms form a linear chain by bonding to two other carbon atoms. The chain ends when a carbon uses three of their bonds with oxygen and hydrogen rather than bonding to two carbons.
The oxygen atoms of a carbohydrate can be bonded to carbon with double or single bonds. If an oxygen forms a double bond to a carbon atom (C=O), this is known as the carbonyl group. Oxygen can form a single bond to a carbon atom when is part of hydroxyl group (-OH). A carbohydrate can contain more than one hydroxyl group.
Hydrogen atoms take up most of the remaining carbon bonds. Generally, there is around twice as many hydrogen atoms in a carbohydrate as there are oxygen atoms.
The most basic carbohydrates known as simple sugars are called monosaccharides. They include sugars such as glucose and fructose. Monosaccharides are the building blocks for larger carbohydrates, and are also used in cells to produce proteins and lipids. Sugars that are not used for production of cells’ energy are often stored as lipids or more complex carbohydrates.
The monosaccharides are compounds used by cells to get energy. Glucose is arguably the most important monosaccharide because it is used in respiration to provide energy for cells.
Two monosaccharides joined together form a disaccharide. The best known disaccharide is sucrose, commonly used as sugar because of its sweetness. Sucrose is made by bonding together one fructose and one glucose molecule. Another well-known disaccharide is lactose, the sugar found in dairy products. Lactose is made from one molecule of glucose and one molecule of galactose. It is not uncommon for humans to have difficulties breaking down lactose into glucose and galactose after eating dairy products. This is the cause of the health condition known as lactose intolerance which can cause diarrhea, bloating, gas and vomiting.
The names of monosaccharide and disaccharide carbohydrates end with the suffix -ose. For example fructose, glucose, galactose, sucrose and lactose.
Polysaccharides are made out of three or more monosaccharides joined together. A single monosaccharide in a polysaccharide is referred to as a monomer. A polysaccharide, which is made from many monomers, can be called a polymer. Some polymers are more than 1000 monomers (or monosaccharides) long.
Polysaccharides have a range of biological functions. A key function they fill is as a temporary storage of energy. Plants store energy in the form of a polysaccharide known as 'starch'. Many crops, such as corn, rice and potatoes, are important because of their high starch content. Humans and other animals store energy in their muscles and liver using a polysaccharide known as glycogen.
Using carbohydrates to produce energy prevents proteins being used for that purpose. This is important because it allows proteins to be used for other functions, such as metabolism and muscle contraction.
Lipids are a group of molecules that include fats, oils, waxes and steroids. These molecules are made mostly from chains of carbon and hydrogen, called fatty acids. Fatty acids bond to different types of atoms to form many lipids. Cells require lipids for a number of functions that include insulation of heat, storing energy, protection and cellular communication.
Fatty acids are a defining feature of lipids. A fatty acid is a long hydrocarbon (alkyl) chain with an acidic end. The acidic end is known as a “carboxylic acid” and has the chemical structure RCOOH, the same structure that makes vinegar acidic.
A fatty acid can be saturated or unsaturated. If two carbon atoms of the hydrocarbon chain share a double bond, then a fatty acid is known as “unsaturated”. If there is no double bonds along the alkyl chain, the fatty acid is saturated. This is because all of the carbon atoms bond to as many hydrogen atoms as possible. The alkyl chain is therefore saturated in hydrogen. The presence of a double bond makes a fatty acid unsaturated because it is possible for the alkyl chain to bond to more hydrogen atoms.
Fats and Oils
Fats are a well-known form of lipids. They are made by bonding fatty acids to an alcohol. The most common fat is a triacylglycerol. A triacylglycerol is a fat made from three fatty acids bonded to an alcohol called “glycerol”. Glycerol is a three carbon alcohol, and each of the carbons bond to one fatty acid.
The structure of fatty acids in a fat determine if that fat is saturated or unsaturated. Double bonds in one or more alkyl chains of the fatty acids create an unsaturated fat. A fat molecule with no double bonds in any of its alkyl chains is known as a saturated fat.
A double bond creates a bend in an alkyl chain. This reduces how tightly fat molecules can be packed together. Loosely packed fats have lower melting points which is why unsaturated fats, such as vegetable oils, are commonly liquid at room temperature. Saturated fats on the other hand have higher melting points, and are more likely to be found as solids at room temperature.
The main function of a fat is to store energy. They are most common in animals because they contain a very large amount of energy for their weight. A fat molecule will hold far more energy than a carbohydrate molecule of the same weight. For mobile animals, carrying extra weight is not ideal, so storing energy in lightweight molecules is beneficial. Fats are stored in tissue known as adipose tissue and in cells known as adipose cells.
Phospholipids are less known than fats and oils but are essential to life on Earth. They are the molecules used to build the membranes found around and inside cells. Without a membrane, a cell would not be able to survive.
A phospholipid is similar in structure to a triacylglycerol. It contains two fatty acids plus a phosphate group bonded to the three carbons of a glycerol molecule. The sole difference between a phospholipid and a fat is the replacement of one fatty acid with a phosphate group (-PO4). A phosphate group has a negative charge (3-) so many other molecules can attach themselves to the phosphate group. This makes a large variety of different possible phospholipids.
Steroids are a particular type of lipid with a unique chemical structure. They are characterized by having carbon atoms arranged into four adjacent rings - three rings made from six carbon atoms and the final ring made from five carbon atoms. Steroids are produced naturally in the body. Examples include cholesterol and the sex hormones testosterone, progesterone and estrogen. Cholesterol is the most abundant steroid in the body and is produced in brain, blood and nerve tissue.
Nucleic acids are long chains made from many smaller molecules called nucleotides. Each nucleotide is made of a sugar, a base and a phosphate group. There are two types of nucleic acids that are essential to all life. These are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). DNA is a very well-known type of molecule that makes up the genetic material of a cell. DNA is responsible for carrying all the information an organism needs to survive, grow and reproduce.
For animals, plants, fungi and other eukaryotic organisms, the majority of DNA is found within the cell nucleus (chromosomes). In organisms which have prokaryotic cells, such as bacteria, DNA can be found coiled together anywhere within the cell in a nucleus-like structure called a nucleoid.
Structure of DNA
A DNA is a large molecule (macromolecule) and is made up of many smaller molecules connected together to form a long chain. The smaller molecules are known as nucleotides and each nucleotide consists of a sugar (deoxyribose), a base and a phosphate group. Nucleotides are bonded together by the phosphate group of one nucleotide and the sugar on the next nucleotide.
One strand of DNA is almost always found bonded to another strand in a structure known as the double helix. The double helix DNA structure is sort of the unofficial emblem of biology.
Two strands of DNA bind together to form the double helix because of the way each strand is both attracted and repelled by the other strand. The two strands bind through the bonding of the bases of each nucleotide (the bases from one strand bond to the bases of the second strand of DNA). This makes the two chains run anti-parallel to each other and gives the DNA the spiraling structure that makes the double helix.
The bases that are responsible for the bonding of two DNA strands are known as nitrogenous bases. Each nucleotide has one nitrogenous base but there are a total of four different nitrogenous bases in DNA molecules. The nitrogenous base molecules are bonded to the deoxyribose sugar of a nucleotide.
Differences in the arrangement of these four bases along a strand of DNA is how different genes are formed. A specific sequence of nitrogenous bases provides the information for a cell to produce a specific protein. The four different bases are adenine (A), thymine (T), guanine (G), or cytosine (C). The nitrogenous bases of one DNA strand bonds to the opposite bases in the second strand. This brings the two DNA strands together to form the double helix.
The bases bond in pairs and will only bond with one of the three other bases, that means adenine only bonds with thymine and guanine only bonds with cytosine. The size of a double stranded DNA molecule is measured by the number of base pairs it contains and a single strand is measured by the number of nucleotides it has. As humans, we have a total of 6,000,000,000 base pairs in all of our chromosomes and the entire sequence of base pairs was published by the Human Genome Project in 2003.
RNA is a less-known molecule but it also plays an important role in cells. RNA molecules are used to translate the information stored in DNA molecules and use the information to help build proteins. Without RNA, the information in DNA would be useless.
The two differences between DNA and RNA are their sugars and their bases. DNA has a deoxyribose sugar while RNA has a ribose sugar. DNA has four different bases – adenine (A), thymine (T), guanine (G), and cytosine (C). RNA has three of the same bases but the thymine base is replaced with a base called uracil (U).
2. Producing food and alcohol through fermentation
People used biotechnology techniques for thousands years to produce food and drinks. For example, ancient Egyptians applied fermentation technologies to make dough rise during bread-making. Due in part to this application, there were more than 50 varieties of bread in Egypt more than 4,000 years ago.
The first beer known to humans was brewed by Sumerians in Mesopotamia (modern-day Irak) approximately 7,000 years BC (9). Egyptians made also beer and wine using fermentation techniques based on an understanding of the microbiological processes that occur in the absence of oxygen. In wetter parts of the Nile Valley, Egyptians bred geese and cattle to meet their society's nutritional and dietary needs. Yogurt was made at homes but the reason of the conversion of milk into yogurt was unknown to old people.
Scientists proved that yogurt is made due to the action of yeast added to milk, which is also biotechnology as it uses a micro-organism for fermentation of lactic acid.
3. Genetic engineering, artificial tissues
Genetic engineering, also called genetic modification (GMO), is the direct manipulation of an organism's genome using biotechnology methods. Through genetic engineering, organisms can be given targeted combinations of new genes, and therefore new combinations of traits that do not occur in nature and cannot be developed by natural means. Such an approach is different from classical plant and animal breeding, which operates through selection across many generations for traits of interest.
The new genes can be obtained through any one of the following methods: cloning, hybridization, reverse transcription of the RNA, chemical synthesis (if the sequence of the gene is known), or by polymerase chain reaction (PCR) if the gene specific primer is available (10).
With the advancement of methods of genetic engineering in the 1980s, it became possible to transfer specific genes from other organisms including microbes and animals into plant cells and protoplasts and regenerate the whole plant - that is the transgenic plants. The introduction of transgenic plants or genetically-modified crop plants with improved agronomic characteristics is a real boost to agriculture and may be responsible for the second green revolution. In addition to the applications in agriculture, genetic engineering of plants has also helped to understand the basic mechanism of gene expression and its involvement in various activities such as morphogenesis and differentiation (11).
A relatively new field in biotechnology is tissue culture. It is a method in which fragments of tissue from an animal or plant are transferred to an artificial environment in which they can continue to survive and function. The cultured tissue may consist of a single cell, a population of cells, or a whole or part of an organ. Cells in culture may multiply, change size, form, or function. They can exhibit specialized activity or interact with other cells. Many tissues such as cardiac muscle, heart valves, and blood vessels have distinct elastomeric properties, so engineering these tissues has been a continuous effort in the tissue engineering community (12).
The ability to generate functional tissues and organs as replacements for their damaged or diseased counterparts is a rapidly advancing pursuit in the field of tissue engineering and regenerative medicine. Interest in this field has been motivated by clinical needs: an increase in chronic disease due to increased life expectancy, the low availability of suitable donor tissue for transplantation and the fact that medical implants cannot fully replicate all of the functions of a replaced tissue and have a finite life. Recent scientific and technological developments in materials, particularly at the nanoscale level have had a great impact in the development of tissue engineering (13). One application is represented by the organ transplant.
Due to the scarcity of organs available for donations and incompatibility of donor organs with hosts, many research groups are currently working to develop Extra Cellular Matrix (ECM)-like scaffolds for engineered tissues or whole organs. One of the biggest challenges in the field of tissue engineering is biocompatibility, which is critical to ensure that patients do not develop an immune response and reject the implant.
First, the tissues and organs must be size matched to have the appropriate dimensions that allow for true biocompatibility with the recipient. One solution to this problem is the development of advanced synthetic materials incorporating biomimetic ECM components for cellular recolonization. Polymers and polymer blends are, today, the most commonly used base for creating synthetic soft tissue ECM scaffolds, and many are already being used for functional in vivo studies to assess their utility for tissue regeneration. Polymers are an ideal material for biomedical applications because their properties are highly adjustable and can be engineered to have a variety of mechanical and biological properties. Polymers can be modified via surface functionalization to control wettability, electric charge, morphology, and roughness. Some polymers are also biodegradable and have modifiable degradation rates (14).
However, synthetic polymers inherently lack cell recognition signals, and this presents a hurdle to their adoption as scaffold materials (15). This limitation can be addressed by chemical modification of the polymer before scaffold formation, or surface treatment after scaffold formation, to make the material functional.
Although still largely in the research and development phase, a number of fibrous self-assembling peptide hydrogels are candidates for new biomaterials (16). Utilizing natural amino acids in designed sequences, it may be possible to achieve biocompatibility and safe degradability without provoking any immune response from the receiving organism. The range of amino acid side chains allows tuning to specific uses by varying the primary structure, for example, altering self-assembly may influence the physical properties (pore size, fiber thickness and mechanical properties), different side chains may influence chemical properties (pH and surface properties), and biologically relevant peptide sequences can be included to modify the material’s biological properties. Certain types of self-assembling peptides (ex. RAD16 sequences) have been widely studied, tested in areas as diverse as nerve repair, heart and endothelial treatments and model skin replacements (17).