All organisms are composed of cells
Caenorhabditis elegans (C. elegans) is an organism of exactly 959 cells. Two things are known about C. elegans: the complete sequence of its DNA, and what every one of its 959 cells does.
There are many things we don't know about C. elgans. One is the answer to the question: since all 959 cells come from one original cell, how does each of the 959 cells decide what sort of cell to become?
All cells have DNA and a cell membrane.
In bacterial cells the DNA is free in the cell, there is no nucleus and no internal membranes. These organisms are called prokaryotes.
The cells of C. elegans (and everything higher than a bacterium, including humans) have a nucleus containing DNA. There is both a cell membrane and internal membranes. These organisms are called eukaryotes.
All cells also have machinery for making proteins (called ribosomes). Only higher cells have special machinery (mitochondria) for supplying energy for the all the processes in the cell . Ribosomes are like protein factories, and mitochondria are like banks which distribute the currency (ATP) which all the different pieces of machinery in the cell use to pay their energy bills.
Bacteria always have cell walls outside their cell membranes. Plants and fungi and some one-celled organisms have cell walls, but animal cells do not.
|
Prokaryotes |
Eukaryotes |
| Bacteria | Animals, plants, fungi, one-celled organisms such as amoeba |
| Cell membrane, DNA free inside cell,
ribosomes (70s), no internal membranes |
Cell membrane, DNA in nucleus, ribosomes (80s), internal membranes, mitochondria, chloroplasts in plants |
| Cell wall outside cell membrane | No cell wall in animal cells Cell wall outside cell membrane in plants and fungi and some one-celled organisms |
The cell membrane is a barrier between the cell and the outside world.
The cell membrane controls everything which goes in and out of the cell.
The cell membrane has many different types of molecule. These include lipids (fats and oils), proteins and carbohydrates.
Lipids form the basic structure of the cell membrane. Lipids consist of a head and a tail. The membrane consists of two layers; in one layer the heads face the outside world. In the other layer the lipid molecules are turned around so the heads face the inside world. The lipid molecules in the two layers are then tail to tail. This bilipid layer (which has the consistencey of olive oil) creates a water-free zone between the cell and the outside world. Molecules which dissolve in water can't get through the lipid part of the membrane.
Proteins floating in the lipid create channels which allow water-soluble molecules to go in and out of the cell.
Carbohydrate molecules (sugars) which are attached to the part of the proteins which faces the outside world give information about the cell.
Cells continuously send messages to each other. Any type of molecule can be a message. Chemical messages are 'recognised' by special proteins sticking out of the membrane. These proteins span the membrane.
When a message from outside the cell is 'recognised' by a protein in the membrane, this causes a change in the bit of the protein which faces the cell on the inside of the membrane. This tells the inside of the cell what the message is. Other molecules carry the message to wherever it has to go inside the cell.
Messages can tell the cell what to do, or can tell the cell what to become.
Stem cells are cells which have not yet decided what to become. A human embryo has many stem cells. As the embryo grows and the body needs brain cells, liver cells, blood cells etc. these stem cells become 'committed' to one or other of these cell types.
Unlike C. elegans, where every cell becomes committed immediately, a few stem cells are still to be found even in an adult human hiding in the bone marrow and the brain.
Scientists are beginning to figure out how to turn these uncommitted stem cells into different types of cell. By sending them the right chemical message, they can make a stem cell become a nerve cell, a liver cell, a blood cell etc.
Biological organisms are made of atoms
All matter, including biological organisms, is composed of atoms (e.g. C, N, O, H). When atoms have been chemically combined, they are known as molecules.
Molecules can be made of the same type of atom (known as an element e.g. H2) or they can be composed of more than one type of atom (known as a compound e.g. H2O).
Atoms themselves are built from smaller particles. The nucleus of the atom is found in the center and contains the protons and the neutrons. Protons have a positive charge while neutrons are neutral and have no charge.
The atomic mass can be calculated using the number of protons and neutrons combined.
The nucleus is surrounded by electrons which are found in different electron shells. The space which an electron occupies is called its orbital. Electrons carry a negative charge.
In any atom, the number of positive charges (i.e. number of protons) is equal to the number of negative charges (i.e. number of electrons). However, atoms can undergo chemical changes whereby electrons are gained or lost. An atom that has gained or lost one or more electrons is known as an ion.
An atom that has lost one or more electrons acquires an overall positive charge. It is now a positive ion. e.g. Na+
An atom that has gained one or more electrons acquires an overall negative charge. It is now a negative ion. e.g. Cl-
Atoms combine to form molecules
The atoms in any molecule are joined by chemical bonds. Chemical bonds can be formed in several ways.
These chemical bonds are formed by chemical reactions that may involve the attraction between atoms, the transfer of electrons between atoms, or the sharing of electrons between atoms.
An atom may transfer electrons to another atom. When this happens, the donor atom acquires a positive charge while the recipient atom acquires a negative charge. These oppositely charged ions are now attracted to one another. This attractive force that joins these ions to each other is known as an ionic bond. A common example of a molecule that is held together by an ionic bond is table salt or NaCl.
Atoms may share two or more pairs of electrons. This type of bond is known as a covalent bond. This is a strong attractive force.
There are two type of covalent bonds. When the electrons are shared equally between the atoms, this is known as a nonpolar covalent bond. A common example of a molecule that is held together by a nonpolar covalent bond is O2.
However, the pairs of electrons can also be shared unequally between the atoms. This is known as a polar covalent bond. A common example of a molecule held together by a polar covalent bond is H2O. In any molecule that contains a polar covalent bond, one end of the molecule has a slight positive charge while the other end of the molecule has a slight negative charge. Such a molecule is known as a polar molecule.
Hydrogen bonds sometimes result between two polar molecules. This occurs when the slightly positively charged hydrogen of one molecule is attracted to the slightly negatively charged oxygen or nitrogen of a neighbouring molecule. A common example of this is seen in H2O. Although hydrogen bonds alone are weak attractive forces, billions of hydrogen bonds together can result in a strong cohesive force as observed in water.
The pH is determined by the number of hydrogen ions in a solution
The ionization of water occurs when water separates into its component ions. That is, one molecule of H2O separates into H+ (the hydrogen ion) and OH- (the hydroxyl ion). This occurs about one time in every billion water molecules.
The level of H+ and OH- ions in solution is measured on the pH scale.
The pH scale runs from 0 to 14.
A pH value less than 7 indicates acidity and reflects a larger concentration of H+ ions in solution (e.g. hydrochloric acid or HCl).
A pH value of exactly 7 indicates a neutral reading and reflects an equal number of H+ and OH- ions in solution. Water is considered a neutral substance with a pH reading of 7 because when water ionizes, there is an equal number of H+ and OH- ions. The pH of pure water is 7 because when pure water ionises there are 10-7 moles of hydrogen ions per litre of water.
A pH value greater than 7 indicates a basic reading and reflects a greater concentration of OH- ions in solution (e.g. sodium hydroxide or NaOH).
Buffers are substances that resist changes in pH despite the addition of acid or base. Buffers are found in living organisms. The pH in biological systems is tightly regulated as most chemical reactions in living organisms only take place within a narrow range of pH levels.
Biochemistry is the study of chemical reactions in living organisms
The biochemistry of living organisms involves a small number of inorganic molecules (Na+, K+, Ca2+, Cl-, PO43- etc.)and a large number of organic molecules. Organic molecules always contain carbon. Most organic molecules also contain hydrogen and oxygen, and many contain nitrogen, sulphur or phosphorous. All organisms are built out of these organic molecules (CHNOPS).
There are four major classes of organic compounds.
1. Proteins
2. Lipids
3. Carbohydrates
4. Nucleic acids
Some organic molecules consist of long chains, called polymers. Each unit of the chain is called a monomer. These monomers are joined together to form polymers by a process known as dehydration synthesis. This chemical reaction involves the loss of water molecules.
Proteins play specialized roles in the biological organisms. They can act as structural elements (e.g. keratin found in hair and nails), receptors (e.g. antibodies to detect foreign invaders) or enzymes (e.g. amylase to speed the process of digestion).
The monomer for the protein is the amino acid. Proteins or polypeptides are essentially composed of long chains of amino acids. These amino acids are linked by peptide bonds (a type of covalent bond).
There are at least 20 different amino acids. They all share the same general structure but differ in the chemical group found at the variable R-position. All amino acids contain a carboxylic acid group (-COOH) and an amino group (-NH2) attached to a central carbon.
e.g. NH2.CH2.COOH glycine, NH2.CH(CH3).COOH alanine.
Proteins are distinguished from each other by the number, type and position of the amino acids found in the polypeptide chain. The primary structure for a protein refers to the linear sequence of amino acids found in a polypeptide chain.
The secondary structure for a protein occurs when the chain of amino acids fold to form either an alpha helix or beta pleated sheet. Examples of secondary structure are found in keratin and silk. The secondary structure is held by hydrogen bonds between amino acids.
The tertiary structure for a protein occurs when the secondary structure further folds to form a globular form. The tertiary structure is held together by hydrogen, ionic and disulphide bonds between amino acids. Examples of tertiary structure include enzymes.
The quaternary structure for a protein occurs when two or more globular or tertiary structures come together to form a larger structure. This quaternary structure is held together by ionic, hydrogen and disulfide bonds between amino acids. An example of a protein with quaternary structure is haemoglobin.
In biological organisms, lipids are the most important component of the cell membrane. They are also important for long term storage of energy in the body. In some organisms they are important for insulation against cold. Lipids are also known commonly as fats and oils.
The building blocks for lipids are fatty acids and glycerol. Fatty acids can be saturated or unsaturated. A saturated fatty acid contains no double bonds between its carbon atoms whereas an unsaturated fatty acid does contain at least one double bond between its component carbons. A fatty acid is unsaturated if it is possible to add more hydrogen atoms to it. When no more can be added, it is saturated.
CH2=CH_CH=CH_COOH unsaturated
CH3_CH2_CH2_CH2_COOH saturated
It is generally thought that an excess consumption of saturated fats (those that contain saturated fatty acids, such as butter and margarine) is a health risk.
2. Carbohydrates
Carbohydrates function primarily as an energy source or structural component within living organisms. For example, glycogen is a short term energy reserve within the human body and cellulose is a component of the plant cell wall.
The monomer for carbohydrates is known as a monosaccharide. Examples of monosaccharides are glucose, fructose and galactose.
These carbohydrate monomers can recombine to form other molecules. Two monosaccharides linked together by a glycosidic bond are known as disaccharides. Examples of disaccharides include maltose (glucose + glucose), sucrose (glucose + fructose) and lactose (glucose + galactose).
Large polymers of monosaccharides also exist. The most common example is starch which consists of a long chain of glucose molecules. Other examples are glycogen and cellulose. The differences between these molecules lie primarily in the way their glucose molecules are linked in the glycosidic bond.
Enzymes are a very important class of proteins
In a biological organism, chemical reactions can only occur efficiently at everyday temperatures in the presence of specialized proteins known as enzymes.
Enzymes are usually proteins found in their tertiary structure. Their presence serves to speed up or catalyze chemical reactions.
Enzymes are not used up in a chemical reaction. They can be used over and over again.
Many different enzymes exist. Usually, enzymes are only capable of catalyzing a single specific reaction.
This specificity is dictated by the presence of a specific region on the enzyme known as the active site. This active site can attract and hold onto molecules which are complementary in shape and charge.
The molecules that the enzymes attract and hold onto are known as the substrate for that particular enzyme. For example, starch is the substrate for the enzyme amylase but maltose is the substrate for the enzyme maltase. Both of these enzymes are important for digestion.
Enzymes can catalyze the breakdown of larger macromolecules into smaller building blocks (known as a catabolic reaction) as beautifully demonstrated during digestion but they are equally important in catalyzing the joining together of building blocks into larger macromolecules (known as an anabolic reaction).
Enzymes usually work within certain limits. Because enzymes are proteins, they are pH- and temperature-dependent.
Most enzymes are sensitive to changes in pH. For example, pepsin works best at a pH of 2 while lipase works best at a pH of 9. The pH at which an enzyme works bests is called the optimum Ph for that enzyme.
Enzymes are also sensitive to temperature changes. For example, all enzymes found in the human body function optimally at 37oC, while some bacteria found living in hot springs have enzymes that function optimally at temperatures approaching 90oC. Most chemical reactions speed up at higher temperatures, but if the temperature gets too high, the enzymes are denatured.
How Do Enzymes Bind To Their Substrates?
In the lock and key model model the substrate's molecular shape is complementary in shape and charge to the molecular shape of the enzyme's active site.
In this model the substrate fits into the enzyme's active site in much the same way that a key fits into a lock. Just as only one key fits a particular lock so, in most cases, only one substrate fits a particular enzyme.
In the induced fit model, as the substrate binds to the enzyme's active site, the enzyme changes shape to fit and hold the substrate. It is now thought that all enzymes change shape slightly when they bind to the substrate.
Nucleic acids encode the genetic information which dictate most basic life processes. The monomer for nucleic acids is the nucleotide.
Nucleotides contain three major components: a nitrogen base attached to a pentose sugar (a monosaccharide with 5 carbons), attached to one or more phosphate groups.
Nucleic acid polymers are long chains of nucleotides linked by covalent bonds. If the nucleotides contain the pentose sugar deoxyribose, then the nucleic acid is called DNA (DeoxyriboNucleic Acid ). If the nucleotides contain the pentose sugar ribose, then the nucleic acid is called RNA (RiboNucleic Acid).
DNA mostly occurs as double stranded structure (two molecules twisted around each other), called a double helix. RNA is mostly a single stranded structure (which can sometimes double back on itself to form a partially double stranded single molecule).
The structure of DNA was first figured out by James Watson and Francis Crick in 1953, based on X-Ray crystallographs of DNA made by Rosalind Franklin. They determined that DNA molecules are composed of two long chains of DNA. Each chain of DNA is connected lengthwise by covalent bonds between the sugar and phosphate groups. The two chains run next to each other but in opposite directions (antiparallel). The chains are held together by hydrogen bonds between nitrogen bases in opposite chains.
There are four different types of nucleotide found in DNA. Each nucleotide contains one of four possible nitrogen bases A, T, C or G, a deoxyribose sugar, and a phosphate group. The four nucleotides are known as adenine (A), guanine (G), cytosine (C) and thymine (T).
Between the two chains of DNA, the nitrogen bases form specific pairs. The bases are complementary to each other. Using data obtained by the scientist, Edwin Chargaff, it was determined that A pairs with T and G pairs with C. That is, if one chain contains an A at a particular point, then on the opposing chain, there will be the complementary T.
A . . . T
C . . . G
The specificity of complementary base pairing is dictated by the numbers of hydrogen bonds that can form between the bases. There are two hydrogen bonds between A and T while there are three hydrogen bonds between G and C.
In RNA the sugar is ribose instead of deoxyribose, and the four nucleotides are adenine (A), guanine (G), cytosine (C) and uracil(U). Uracil behaves just like Thymine in DNA. The base paring between DNA and RNA becomes:
A . . . U
C . . . G
DNA encodes all the information needed for an organism to produce another organism similar to itself
DNA is long chain of nucleotides that contains all the hereditary information in an organism. Every cell in that organism starts out with a complete set of this information. The order in which the bases come (i.e. the sequence of bases) is unique for each organism. This order encodes the information.
This complete set of informations, encoded in the organism's DNA is called the organism's genome. The genomes of certain organisms have been completely sequenced. This includes our closest evolutionary relative, the chimpanzee, C. elegans and the fruit fly Drosophila melanogaster.
The Human Genome Project (HGP) was a collaborative effort between scientists from around the world to identify the complete sequence of bases in the human genome. After thirteen years, the HGP was completed in April 2003.
The lengths of the DNA strands (or number of nucleotides) varies between species. For example, humans contain approximately 3 billion base pairs in the nucleus of every cell (with the exception of the sperm and egg). A comparison of genomes from different species has helped evolutionary scientists further understand the interrelationships between humans and other species and how they evolved.
DNA forms the genes. Genes are the units of genetic information that are transmitted from parent to offspring. Each gene is a unique sequence of DNA of a specific length. Scientists are now attempting to locate and identify the estimated 20,000-25,000 genes that are scattered along the human DNA.
DNA is found in the cell in packages known as the chromosomes. In all animals above bacteria these chromosomes are made up of DNA wrapped around a series of protein beads. Humans (with normal genetic content) contain 23 pairs of chromosomes (=46 chromosomes) within the average cell (again with the exception of sperm and egg).
A mechanism exists to accurately copy the DNA from a cell of one generation to the next. This process, known as DNA replication, ensures that each new generation of cells contains the complete DNA sequence (and all the genes) of that individual.
Watson and Crick were the first to suggest that complementary base pairing is the key to DNA replication.
DNA replication is semi-conservative. That is, when the parent DNA is copied, the daughter DNA products each contain one strand of original DNA and one newly synthesized complementary DNA strand.
A series of enzymes are needed for the synthesis of DNA.
DNA helicase unwinds the two strands of the DNA double helix and breaks the hydrogen bonds between them.
The site at which the DNA helicase unwinds the double helix is known as the replication fork.
As DNA helicase unwinds the double helix it provides access to the DNA sequence on the separated chains so they can be copied.
DNA polymerase uses the two separated parent DNA strands as templates and builds new complementary strands. That is, if a G appears on the template, then DNA polymerase will incorporate a C on the growing complementary strand.
The nucleotides that DNA polymerase III uses for synthesis of the new strands are produced during metabolism and are stored in the cell.
DNA polymerase III can only work in one direction. That is, the enzyme can only add new nucleotides to one of the two ends of each growing complementary chain of DNA.
Since the parental DNA strands run in opposite directions, the DNA polymerase III must also extend the two new DNA strands in opposite directions. This gives rise to leading strand and lagging strand synthesis. Leading is going in the same direction as the replication fork, lagging is going away from the replication fork.
The lagging strand is synthesized one short length of DNA at a time, separated by small gaps. These short lengths of DNA are known as Okazaki fragments.
The Okazaki fragments on the lagging strand are eventually joined together by covalent bonds. This is accomplished with the enzyme DNA ligase.
Every human being has a unique sequence of DNA
The length of the human genome is approximately 3 billion base pairs. Every cell of that organism starts out with a complete set of that information.
The exact sequence of DNA nucleotides varies between individuals (except identical twins).
Although the DNA sequence varies between individuals of the same species, greater variation exists between species. An analysis of DNA sequence similarities between species is an indicator of evolutionary relationships. For example, humans and chimps are very closely related in evolutionary terms and 96% of their DNA sequence is identical.
Subtle differences between the DNA of different people can be identified by DNA profiling/DNA fingerprinting. This information can be important to resolve forensic or paternity questions.
DNA fingerprinting relies on the fact that every individual (with the exception of identical twins) has a unique DNA sequence. This implies that every individual has a unique DNA 'fingerprint'. This permits a comparison between DNA samples.
Restriction enzymes recognize and cleave DNA only at specific palindromic sequences. There are hundreds of different restriction enzymes, all of which recognize and cut at different DNA sequences. For example, the restriction enzyme EcoR1 cleaves at the recognition sequence GAATTC.
If two DNA samples are identical, the same restriction enzyme will find the same palindromic recognition sequcence and cleave these DNA samples at all the same places along the DNA strand thus generating fragments of the same size.
In DNA samples from different people, some of these palindromic recognition sequences may be absent in one person's DNA and present in another. Where palindromic recognition sequences are absent, the restriction enzyme will chop the DNA into fewer, but larger fragments.
DNA gel electrophoresis allows scientists to analyze and compare these DNA fragments.
Larger fragments will end up at different places on the gel after DNA electrophoresis.
The fragmented DNA samples are loaded into the wells of an agarose gel. The agarose gel is initially prepared in a casting tray. Each DNA sample is loaded into a separate well.
The agarose gel is then placed into an electrophoresis chamber. The gel is covered with electrophoresis buffer which helps to maintain the pH and carries an electric current.
The electrophoresis chamber has a positive pole and a negative pole. The agarose gel is positioned in the chamber such that the wells containing the DNA samples are next to the negative pole.
As DNA has an overall negative charge (due to the negatively charged phosphate groups of the DNA backbone), it is repelled by the negative pole and attracted to the positive pole.
The agarose gel acts as a molecular sieve. The smaller DNA fragments will migrate quickly through the porous agarose gel while the larger fragments will migrate slowly. Due to these differences, the DNA fragments are separated on the basis of size and charge.
After running the gel for a specified period of time, the electricity is turned off.
The DNA fragments are then visualized by staining with a dye that binds specifically to DNA.
If two DNA samples are from the same individual, the DNA fragment patterns that results should be identical. If the two DNA samples are from different individuals, the DNA fragment patterns that result should be different.
This allows forensic scientists to use DNA profiling/fingerprinting as a reliable method of identification. Errors are rare and DNA fingerprinting is often used to settle many criminal cases.