Biology Basics

What is a Cell?

Of the millions of different types of organisms that inhabit the earth, all have at least one thing in common: they are made of cells. Cells are the basic unit of life. They are very small. A bacterium, which consists of only one cell, is generally 1 micron (æm) in diameter. To get an idea of the length of one micron, imagine dividing the smallest division on a ruler (1 millimetre) into 1000 equal egments; each of these segments is 1æm. Humans are made up of trillions of cells. A typical cell though 10 times the size of a bacterial cell (10 æm) still cannot be seen by the human eye but can be seen by microscope.

Not all the cells within large organisms (like humans) are alike. Different cells look and function very differently because they have become specialized at performing very different tasks. For example, T-cells, which are part of our immune system, look very different from our nerve cells. T-cells are structured to help fight infection, while nerve cells need to be capable of transmitting and receiving the electrical impulses that characterize brain function. But one thing that all human cells have in common - from brain to eye to muscle to skin cells is that they contain DNA , the "blueprint of life". And each cell, regardless of its form or function, contains a complete set of DNA. This is the same DNA as is found in every other cell in a person's body. Medical research is the key factor in the discoveries of the human body. .

Genes: The DNA Sentence

A gene is a set of nucleotides (DNA "words") which constitutes a unit of hereditary information. Each of the chromosomes within the nucleus of a human cell contains thousands of genes. All of the DNA contained on the 23 pairs of chromosomes within a single human cell contains all of the 80,000 genes (and therefore all of the genetic instructions) that make up the human genome.

But what do we mean by "a unit of hereditary information?" A more precise definition of a gene is a region of DNA that is transcribed. Transcription, a biological process that is carried out by enzymes, is the first step of the Protein Synthesis process. As its name implies, the protein synthesis process results in the production of a protein. Proteins are the biological molecules that give living cells their diverse forms and functions. So, a gene is a sequence of A's, T's, C's and G's - in a particular order - that codes for a defined biochemical function, usually through the production of a particular protein. It is the proteins produced using genes as atemplate, that are responsible for the characteristics of a particular cell or organism.

Genes have specific jobs, at specific times. Not all genes are "turned on" all the time. For example, many genes are turned on' (causing proteins to be produced) only during the development of the human fetus. Once the child is born, the proteins associated with these particular genes are no longer needed, and the genes are "turned off," perhaps never to be used again, except when passed on to future generations.

Other genes are turned on' only in times when they are needed by the body. As an example, a gene for producing insulin is regulated by the amount of glucose (sugar) in a person's bloodstream. Following the consumption of a meal, there is a higher concentration of glucose in the blood, which triggers higher levels of insulin being produced by pancreatic cells. Insulin stimulates the uptake of glucose by tissues like skeletal muscle and adipose (fatty) tissue, which brings the concentration of glucose in the bloodstream back to normal levels. Once the blood-glucose level has returned to normal, the amount of insulin secreted by pancreatic cells is also reduced.

What is RNA?

RNA is short for RiboNucleic Acid. Like DNA , RNA molecules are manufactured in the nucleus of the cell . However, unlike DNA, RNA is not restricted to the nucleus. It can migrate out into other parts of the cell. Some RNA, called messenger RNA (mRNA) communicate the genetic message found in the DNA out to the rest of the cell for the purpose of promoting the synthesis of proteins . How a gene sequence in DNA is ultimately translated into its corresponding protein is discussed in the Protein synthesis section.

Like DNA, RNA molecules are composed of nucleotides. However, while DNA molecules consist of two parallel strands of nucleotides, an RNA molecule consists of only one strand.

In addition, the chemical structure of the RNA nucleotide 'backbone' is slightly different from the structure of the DNA nucleotide backbone. The DNA backbone contains deoxyribose sugar molecules (hence the "D" in DNA) and the RNA backbone contains ribose sugar molecules (hence the "R" in RNA).

Three of the four nitrogen bases that can be attached to the RNA backbone are the same as those for DNA. Just like DNA, RNA nucleotides can have Guanine (G) and Cytosine (C) bases and just like in DNA nucleotides, Guanine is complementary (binds) to Cytosine (G-C). A third base found in RNA - Adenine (A) - is also the same as in DNA. But instead of Thymine (T), RNA has Uracil (U) which binds with Adenine (U-A).

Proteins

What Are Proteins For?

Many genes code for particular polypeptide chains. And proteins consist of one or several of these polypeptide chains.

It is the proteins that are responsible for a cell or organism's characteristics. The way in which proteins are constructed, based on a genetic template, is described in the Protein Synthesis section.

Proteins serve a variety of purposes, and give living cells their diverse forms and functions. Some proteins have a structural function; such proteins make up cartilage, hair and nails, for example. A special class of proteins, called enzymes catalyze important chemical reactions for the cell that could not normally occur in their absence. Some proteins serve as membrane channels which facilitate the passage of molecular particles into and out of the cell. Some hormones, like insulin, are proteins, and serve to regulate body functions (insulin controls blood-sugar levels). Proteins are also needed for muscle contraction and to aid in the defence of body cells against foreign invaders. The above are only a few of the many diverse functions of proteins.

Protein Structure

All proteins are made up of one or several long molecules called polypeptides. Each polypeptide, in turn, is made up of small molecules attached end to end called amino acids. All of the 20 types of amino acids used by living cells have identical "backbone" structures which serve to attach the amino acids together in long chains. Each type of amino acid also has what is referred to as a side group, which is chemically distinct, depending on the amino acid type. While we need not concern ourselves with the fine points of how the structures of the side groups vary, it is important to note that they can be grouped into several categories.

For example, some side groups are non-polar, while others are polar. Polar and non-polar molecules generally stay away from each other. (Have you ever noticed that cooking oil, when added to water, doesn't mix with it, but stays together in large globs? This is because oil molecules are non-polar and water molecules are polar.) Water molecules are polar, and since non-polar molecules don't like to associate with polar molecules, we often call non-polar molecules hydrophobic (derived from Greek, and meaning "water-fearing"). On the other hand, polar molecules are hydrophilic (derived from Greek, meaning "water-loving"), because they love to interact with water.

Proteins, which are floating around within a cell, or just about anywhere else in your body, are surrounded by an environment which is mostly water. What happens to the long chain of amino acids, some of which are hydrophobic and others hydrophilic?

What happens is that the protein folds into a 3-D structure where most of the hydrophobic amino acids are pointing into the inside of the structure (and away from the water) and where most of the hydrophilic amino acids are on the surface, pointing out into the water. Therefore, the types of amino acids and the order in which they are located in the chain, will determine how the protein will ultimately fold in water, and therefore what its 3-D structure will be in your body.

This 3-D structure is essential for the correct functioning of the protein. A membrane transport protein, for example, is embedded in the cell membrane and is in the shape of a tunnel or passageway from one side of the membrane to the other. Its job is to allow certain molecules that fit correctly to pass into or out of the cell. Obviously, the transport protein's shape is going to be very important so that it can do its job correctly! A misformed transport protein may have a "blocked" passageway, meaning that important molecules could not pass into or out of the cell. Another example of a class of proteins whose shape is crucial for their proper function is enzymes.

Enzymes

What is an Enzyme?

An enzyme is a biological catalyst. But what is a catalyst?

A catalyst is a substance that speeds up the rate of a chemical reaction without being consumed in the process. There are hundreds of different types of chemical reactions going on all the time inside our cells and within our bodies. In our stomach and small intestine, chemical reactions occur which break up the food we eat into smaller particles that can be absorbed by our cells. For example a complex sugar molecule found in milk products called lactose must first be broken up into two molecules - glucose and galactose - before absorption by the body's cells. This reaction normally occurs with help from an enzyme called lactase in the small intestine.

Many chemical reactions, including the break-up of lactose, don't happen spontaneously. Lactose will not break into its component parts if it resides long enough in milk or cheese. This is because the reaction requires that the molecules involved possess a certain amount of energy before the reaction can occur. The amount of energy needed for a given reaction to occur is called the activation energy. So although the break-up of lactose is possible, it will not occur unless the individual lactose molecules have the required energy. Within milk or cheese or ice cream, the average lactose molecule simply doesn't have enough energy to undergo the break-up reaction, and we would have to wait a very long time before this happens on its own!

So how do catalysts speed up chemical reactions? They permit the reaction to occur at a lower activation energy. In other words, in the presence of an appropriate catalyst, the reactant molecules will require less energy to be converted into products. The catalyst does not react in itself, and does not get used up by the reaction. So catalysts, are more like 'reaction helpers' which will help one set of reactant molecules be converted into products and then scoot off to help another set undergo that same reaction. Some biological catalysts (enzymes) are so effective that only one is needed to help over 600,000 reactant molecules be converted to product molecules every second!

We should note that enzymes are very specific. The lactase enzyme, which helps lactose molecules to be broken into galactose and glucose molecules, is especially constructed so that it can only catalyze that one type of reaction. Enzymes are so selective that they ignore the thousands of molecules in body cells and fluids for which they were not designed. A molecule which an enzyme is designed to help react is called the substrate. So lactose is the substrate for the lactase enzyme. To understand how enzymes can be specific, we should consider enzyme structure and theLock and Key Model of enzyme function.

Enzyme Structure: "The Lock and Key Model"

With the exception of a few enzymes that are made up of RNA, enzymes are proteins . Recall that a protein is composed of one or several long chains of amino acids attached together, and that each amino acid chain folds into a specific 3-dimensional shape based on the amino acid sequence and how the individual amino acids in the chain interact with each other and with the surrounding solution.

Enzymes are folded up in such a way so that they have an indentation, or a pocket on their surface. This pocket is called the active site. The Lock and Key Model postulates that the shapes of the reacting molecules (the substrates) and the enzyme's active site are such that they fit together much like a key fits into a specific lock. So the lactose molecule fits perfectly into the active site of the lactase enzyme, meaning that the lactase enzyme can only catalyze the breakdown of lactose.

Enzymes are important!

Enzymes carry out hundreds of chemical reactions that are essential for our survival. They carry out the reactions necessary for our digestion of foods, for the build-up and break down of DNA and RNA, as well as many other vital processes. A deficiency in the lactase enzyme, for example (which is rather common in humans) results in an inability to break down lactose, and a condition called lactose intolerance. Lactose intolerance can be overcome by swallowing tablets containing lactase enzymes before eating dairy products.

Protein Synthesis

The following is a brief overview of how a gene (a section of the DNA molecule ) serves as a template for the synthesis of a protein . The process can be split into two phases.Transcription occurs first, followed by translation.

Transcription:

Transcription is the process where a special piece of RNA - called messenger RNA (mRNA for short) - is constructed using a particular genetic sequence (DNA) as a template.

First, enzymes unravel a section of the double stranded DNA helix and break the bonds between the complementary base-pairs in the unravelled section. Next, a complementary mRNA strand is synthesized, using one of the strands of the unravelled DNA as a template. For example, if part of one strand of the unravelled DNA reads GATCAT, the complementary mRNA sequence will read CUAGUA. (Recall that Uracil (U) nucleotides take the place of Thymine in RNA). Finally, after the complementary mRNA is made, the section of DNA is rewound into its original double helix conformation.

The result of transcription is that an mRNA molecule, which is complementary to a given section of DNA (which constitutes a gene), is created.Unlike DNA molecules, mRNA molecules are free to float out of the nucleus through pores in the nuclear membrane into the rest of the cell (called the cytosol). It is in the cytosol that translation takes place.

Translation:

This is the process where a protein is made, based on the information contained in an mRNA molecule. We should first remember that like DNA and RNA, proteins are also chains of small pieces attached together. For DNA, these small pieces are called nucleotides and for proteins, these pieces are called amino acids. The sequence of nucleotides in the mRNA is simply converted to a sequence of amino acids, based on a consistent code.

Each sequence of 3 mRNA bases codes for a particular amino acid. For example, the mRNA sequence AUG codes for an amino acid called methionine. Ribosomes, the "machines" that carry out protein synthesis, attach themselves to the mRNA strand and move down it, reading' the sequence of nucleotides and putting together the appropriate protein as they move. The first set of 3 nucleotides the ribosome will read is always AUG. This is because the AUG sequence serves as a marker, telling the ribosome to "start reading here."

As the ribosome proceeds along the mRNA, it adds the appropriate amino acid to the growing chain corresponding to each set of three nucleotides. Each set of three nucleotides that codes for a specific amino acid is called a codon. All twenty amino acids used to make biological proteins have at least one corresponding codon. For example, the codon GCA codes for an amino acid called alanine. And the codon AAU codes for an amino acid called asparagine. Therefore, a portion of an mRNA sequence that reads: AUG GCA AAU will result in the following string of amino acids: methionine-alanine-asparagine.

By reading the entire mRNA sequence, the ribosome constructs a long chain of amino acids, which make up the protein.

Bacteria

Bacteria are unicellular organisms. Although some bacteria are the infectious agent in many human diseases, there are many strains that are harmless or even essential to humans. Many strains are very important in biotechnology labs! One important use of bacteria cultures is as producers of useful proteins. For example, a bacteria species called E. coli can be genetically altered so that it produces large amounts of human insulin, which can be administered to diabetics. The following is a brief overview of some of the characteristics of bacteria which make them ideal for many biotechnology applications.

Bacteria are prokaryotes, which means that they do not contain a cell nucleus. Prokaryotes are composed of single cells, although they often grow in groups where the bacteria adhere to each other. These groups of bacteria are called colonies. The bacterial genome consists of a large circular double-stranded DNA molecule, located in the cell cytoplasm. This large DNA molecule, the bacterial chromosome, contains most of the bacterial genes. In addition to this large DNA molecule, bacteria often have smaller circular DNA molecules called plasmids. These plasmids also contain genes, but unlike the large circular chromosome, they are highly mobile. They can be passed easily from one bacterium to another and in this way, genes are passed between bacteria. Plasmid molecules, once i n the recipient bacterial cell, can become permanently integrated into the large bacterial chromosome.

The capability of plasmids to enter bacterial cells and become integrated into those cells' chromosome makes them very useful tools for inserting a gene into a bacterial cell. Can you see how? We will explain how plasmids are used in this way in the Genetic Engineering section.

Viruses

What is a Virus?

Viruses are made up of genetic material (either DNA or RNA ), surrounded by a protective protein coat. Some animal viruses are also surrounded by a lipid (fatty) membrane. A virus is not an independently living organism. Viruses only exist to make more viruses, and unless a virus is inside a living cell, it is inactive and cannot make copies of itself. When a virus or part of a virus successfully penetrates a cell, we call this an infection.

Depending on the virus, either the entire virus enters the cell, or the genetic material alone is "injected" into the cell while the external coat remains outside. In the case of the T4 bacteriophage - a type of virus that infects certain bacteria - the inner DNA is injected into the cell to be infected.On the other hand, the entire AIDS virus (called HIV), enters human T-cells to infect them.

In either case, the result of viral infection is that the virus' genetic material gets into the cell cytoplasm, which contains all the necessary enzymes and other materials that are needed for the replication of the virus' genetic material and the synthesis of its proteins.

Why is a Viral Infection Harmful to a Cell?

A virus is harmful to the cell it infects, because it "hijacks" the cell's gene and protein-making machinery, causing the production of only virus parts. Once these are made, they assemble into tons of new viruses, which fill up the cell.

These new viruses either leave the cell a few at a time (budding) or by a process called lysis, where the cellular membrane breaks open and releases all the virus particles at once. The ultimate result is that the host cell is killed, while the released virus particles go on to infect other cells.

Retroviruses A Different Type of Infection

Sometimes, a virus doesn't hijack the cell machinery as soon as it infects the cell. Retroviruses, which possess RNA as their core genetic material carry with them a special enzyme that uses RNA to make a complementary double-stranded DNA molecule. The enzyme (known as reverse transcriptase), synthesizes DNA from the virus' RNA and that DNA can become incorporated into the host cell's genome located in the nucleus.

During a latency period, the viral genes lie dormant within the host cell's chromosomes. Many stretches of the human genome are believed to consist of endogenous retroviruses, which are ancient, defective retrovirus DNA which became incorporated thousands of years ago and which have been present, without causing any adverse effects, ever since. We might say that the "latency period" of these viruses is practically infinite! On the other hand, the HIV virus (a retrovirus) has a considerably shorter latency period (the average is about 8 years).

After the latency period, the virus genes will be turned on and by the usual process of protein synthesis , will hijack the cell's machinery, making viral RNA and proteins, causing virus particles to be produced.

Since retroviruses are very good at incorporating their own genetic material into their host cell's genome, they are often used as recombinant DNA vectors. That is, if we want to incorporate a specific gene that was isolated, developed or altered using genetic engineering (this is what is meant by recombinant), into a cell's genome, we add the gene into the DNA of a retrovirus, remove the harmful parts of the retrovirus DNA that cause cell hijacking', and use the retrovirus to carry the desired gene into the cell. When we allow the modified virus to infect the host cell, the viral DNA, along with the new gene, gets incorporated into the host cell genome. A more complete description of this process can be found in the Genetic Engineering and Gene Therapy sections.