The Genome:
A genome is the complete collection of hereditary information for an individual organism. In cellular life forms, the hereditary information exists as DNA. There are two fundamentally distinct types of cells in the living world, prokaryotic and eukaryotic, and the organization of genomes differs in these two types of cells.
Types:
Most biological entities that are more complex than a virus sometimes or always carry additional genetic material besides that which resides in their chromosomes. In some contexts, such as sequencing the genome of a pathogenic microbe, "genome" is meant to include information stored on this auxiliary material, which is carried in plasmids. In such circumstances then, "genome" describes all of the genes and information on non-coding DNA that have the potential to be present.
In eukaryotes such as plants, protozoa and animals, however, "genome" carries the typical connotation of only information on chromosomal DNA. So although these organisms contain chloroplasts and/or mitochondria that have their own DNA, the genetic information contained by DNA within these organelles is not considered part of the genome. In fact, mitochondria are sometimes said to have their own genome often referred to as the "mitochondrial genome". The DNA found within the chloroplast may be referred to as the "plastome".
Genome Size or C Value:
The C value is the amount of DNA in a haploid complement. Currently, the amount is reported as the total number of base pairs. Generally, more complex organisms have more DNA. For example, the haploid complement of Homo sapiens DNA contains between 3.12 and 3.2 gigabases (the prefix "giga" denotes billions), while the haploid complement of yeast (Saccharomyces cerevisiae) DNA contains 12,057,500 base pairs.
Unexpected genomic sizes occur, however, in a condition called the C value paradox. Two closely related species can have widely divergent amounts of DNA. For example, Paramecium caudatum has a C value of 8,600,000 kilobases (where the prefix "kilo" denotes thousands) while its near relative P. aurelia has a C value of just 190,000 kilobases. Another paradoxical circumstance occurs when a simpler organism has a C value higher than a more complex organism. For example, Amphiuma means (a newt) and Amoeba dubia (an amoeba) have, respectively, C values that are 26 and 209 times the C value of humans.
Friday, April 23, 2010
Sunday, April 11, 2010
change-your-biochemistry-to-get-bigger penis
Are you unhappy with the size of your manhood and would desperately like to know what you can do about it? If so, you've come to the right place because I can help you to add inches to your penis in a matter of weeks. There's nothing to buy, so it wont cost you a penny and the whole process is exactly the same one that your body followed during puberty, meaning that it is 100% safe too. So, how do you make your manhood grow? The answer is simple - you just have to use natural enlargement...
Is natural enlargement a tried and tested approach? Does it really work?
The answer to both of these questions is yes - I have personally added 4 inches to my penis this way! Also, it has been proven to work by various scientists all around the world, and this makes it truely unique. I would never have believed that getting a larger member could be done so effortlessly, but with natural enlargement it couldn't have been simpler! The key is to get your body to do the work - once you do that, natural growth becomes much easier.
What is the process that it follows?
Like I've already mentioned, to grow, you need to follow the same process that caused a change in your size during puberty. And that means, you will need to put back any biochemicals that were originally around at that time. By changing your biochemistry, you can unlock your body's true potential to grow - and the results are amazing.
Is there anything you can do to grow even faster?
The best thing to accelerate growth is exercise. By using a natural enlargement scheme, you will learn how to change your biochemistry and how to exercise - and these are the two key parts to your success. This is your way to finally get the manhood you deserve - you'd be fool to miss out!
After only 4 weeks, I doubled in size and I have to say it feels great! I'm more confident and my life is on the up - you could feel this way too.
Is natural enlargement a tried and tested approach? Does it really work?
The answer to both of these questions is yes - I have personally added 4 inches to my penis this way! Also, it has been proven to work by various scientists all around the world, and this makes it truely unique. I would never have believed that getting a larger member could be done so effortlessly, but with natural enlargement it couldn't have been simpler! The key is to get your body to do the work - once you do that, natural growth becomes much easier.
What is the process that it follows?
Like I've already mentioned, to grow, you need to follow the same process that caused a change in your size during puberty. And that means, you will need to put back any biochemicals that were originally around at that time. By changing your biochemistry, you can unlock your body's true potential to grow - and the results are amazing.
Is there anything you can do to grow even faster?
The best thing to accelerate growth is exercise. By using a natural enlargement scheme, you will learn how to change your biochemistry and how to exercise - and these are the two key parts to your success. This is your way to finally get the manhood you deserve - you'd be fool to miss out!
After only 4 weeks, I doubled in size and I have to say it feels great! I'm more confident and my life is on the up - you could feel this way too.
How to Study Biochemistry
Biochemistry is a notorious course for demanding a high-volume of information in a short amount of time. However, there are studying methods to assist students in learning efficiently and effectively. I have studied and interviewed groups of medical and science students that have mastered their course work. It is true that there are specific and detailed guidelines that these students adhere to and credit for their academic success. The successful student must excel in visualizing relationships, memorizing facts, and reciting complex metabolic reactions of the human body. With some time and applying these strategies and tips from past honor students of Biochemistry, you will greatly improve your academic performance.Study Skill #1 - Do NOT procrastinate. The most obvious, and yet least followed advice by students. Biochemistry is a high-volume course that progresses and builds its concepts on the fundamentals. Moreover, many pathways and reactions require memorization and must be acquired over time. The last thing you want to do is cram for this course.Study Skill #2 - Know the terminology and nomenclature, it will make things much easier down the road. An enzyme or protein will often have its function built into its name. Take Protein Kinase A for example. As a member of the Kinases, it will almost always add a phosphate group to its substrate. Or, take Alcohol Dehydrogenase, structures that are Dehydrogenases always oxidize a substrate. In this case, it oxidizes alcohols into aldehydes and ketones. Once you get this down, you will begin to recognize names and automatically correlate them with a specific function.Study Skill #3 - Start with the big picture. There is no doubt that you will have to memorize multi-step metabolic pathways. The best way to do this is to start with the easy steps and understand the overall flow of the reaction. First, write only the substrates and products in order. Do this repeatedly, until it is memorized. Then add the enzymes. Then continue to add co-factors and by-products. If necessary, label each as an exer- or endergonic reaction. Use the nomenclature to help you remember what is going on in each step. For example, Phosphofructokinase-1 - adds a phosphate group (phospho-kinase) to the molecule fructose (-fructo-) at the first position (-1). By breaking down the pathways and focusing on the terminology it will greatly speed up your ability to memorize them.Study Skill #4 - Buy a dry erase board. Use this to memorize the pathways and any other reactions you have to know. There are no short-cuts, but writing things out reinforces them in your memory. It tends to be much more efficient than staring and reciting from your textbook.Study Skill #5 - Know the purpose of a reaction. Take the Bohr Effect for example. An increase in (decrease in pH), temperature, and 2,3-BPG all occur in active skeletal muscle. They also all encourage release from hemoglobin. This makes sense if you think that working muscle is metabolic tissue and needs oxygen to survive. Incorporating the larger concept will also allow you to predict the flow of reactions in other situations throughout the body.Study Skill #6 - Stare at the graphs and plots. These questions are virtually freebies on exams because all the information you need to solve them is included. Know what the x- and y-intercept, the slope, and the area under the graph represent. Know what makes the graphed line move to the right or left. You will absolutely be asked about the Michaelis-Menten graph and the Hemoglobin dissociation curve - these are staples of biochemistry.Study Skill #7 - Seek to understand first, and then memorize. Like many other courses, biochemistry can be overwhelming at first. There is no easy way to memorize every amino acid or metabolic reaction. But students always claim that if they take the time to first get the concept down, the memorizing is not as difficult as it once seemed. Stay focused, break it down into small steps, and practice.Jordan Castle is a medical student in Detroit, Michigan. His work spans many different aspects of the learning process and aims to help students excel in their individual courses.
Saturday, March 27, 2010
A Shifting Drug Industry Means New Opportunities in Translational Research
New opportunities
Despite all the changes, pharmaceutical companies are maintaining a strong internal development program in areas with large markets such as oncology, neuroscience, and diabetes/obesity; and they are hiring people whose skills fit with their drug-development programs. Furthermore, the shifts in the industry may herald a new, more fluid division of labor where nontraditional partnerships take on the earliest stages of drug development. "I think it may be up to smaller biotech companies and academia to come up with new drugs," Littman says. "And smaller biotech companies are very interested in generating biomarkers, working on proof of concept, and testing in smaller patient populations."
It's a modular approach to drug discovery and translational research that both FitzGerald and others believe will become prevalent. They also think this will necessitate changes in the way industry and academia handle things such as intellectual property. People choosing industry careers should be prepared and adaptable.
"I think there is a lot of uncertainty out there in the world right now," says Will West, chief executive at CellCentric, a biotechnology company in Cambridge, United Kingdom. "If you are a young graduate, I can see how basing a career in industry may seem like a difficult choice to make. I see the opposite. I think in a changing model, there is opportunity for bright people to take advantage of that change and be drivers for the solutions.
Despite all the changes, pharmaceutical companies are maintaining a strong internal development program in areas with large markets such as oncology, neuroscience, and diabetes/obesity; and they are hiring people whose skills fit with their drug-development programs. Furthermore, the shifts in the industry may herald a new, more fluid division of labor where nontraditional partnerships take on the earliest stages of drug development. "I think it may be up to smaller biotech companies and academia to come up with new drugs," Littman says. "And smaller biotech companies are very interested in generating biomarkers, working on proof of concept, and testing in smaller patient populations."
It's a modular approach to drug discovery and translational research that both FitzGerald and others believe will become prevalent. They also think this will necessitate changes in the way industry and academia handle things such as intellectual property. People choosing industry careers should be prepared and adaptable.
"I think there is a lot of uncertainty out there in the world right now," says Will West, chief executive at CellCentric, a biotechnology company in Cambridge, United Kingdom. "If you are a young graduate, I can see how basing a career in industry may seem like a difficult choice to make. I see the opposite. I think in a changing model, there is opportunity for bright people to take advantage of that change and be drivers for the solutions.
Sunday, March 7, 2010
Recombinant DNA Technology Has Revolutionized All Aspects of Biology
recombinant DNA technology, which has permitted biology to move from an exclusively analytical science to a
synthetic one. New combinations of unrelated genes can be constructed in the laboratory by applying recombinant DNA
techniques. These novel combinations can be cloned amplified manyfold by introducing them into suitable cells,
where they are replicated by the DNA-synthesizing machinery of the host. The inserted genes are often transcribed and
translated in their new setting. What is most striking is that the genetic endowment of the host can be permanently
altered in a designed way.
Restriction Enzymes and DNA Ligase Are Key Tools in Forming Recombinant
DNA Molecules
Let us begin by seeing how novel DNA molecules can be constructed in the laboratory. A DNA fragment of interest is
covalently joined to a DNA vector. The essential feature of a vector is that it can replicate autonomously in an
appropriate host. Plasmids (naturally occurring circles of DNA that act as accessory chromosomes in bacteria) and
bacteriophage l , a virus, are choice vectors for cloning in E. coli. The vector can be prepared for accepting a new DNA
fragment by cleaving it at a single specific site with a restriction enzyme. For example, the plasmid pSC101, a 9.9-kb
double-helical circular DNA molecule, is split at a unique site by the EcoRI restriction enzyme. The staggered cuts made
by this enzyme produce complementary single-stranded ends, which have specific affinity for each other and hence are
known as cohesive or sticky ends. Any DNA fragment can be inserted into this plasmid if it has the same cohesive ends.
Such a fragment can be prepared from a larger piece of DNA by using the same restriction enzyme as was used to open
the plasmid DNA
The single-stranded ends of the fragment are then complementary to those of the cut plasmid. The DNA fragment and
the cut plasmid can be annealed and then joined by DNA ligase, which catalyzes the formation of a phosphodiester bond
at a break in a DNA chain. DNA ligase requires a free 3 -hydroxyl group and a 5 -phosphoryl group. Furthermore, the
chains joined by ligase must be in a double helix. An energy source such as ATP or NAD+ is required for the joining
reaction,
This cohesive-end method for joining DNA molecules can be made general by using a short, chemically synthesized
DNA linker that can be cleaved by restriction enzymes. First, the linker is covalently joined to the ends of a DNA
fragment or vector. For example, the 5 ends of a decameric linker and a DNA molecule are phosphorylated by
polynucleotide kinase and then joined by the ligase from T4 phage . This ligase can form a covalent bond
between blunt-ended (flush-ended) double-helical DNA molecules. Cohesive ends are produced when these terminal
extensions are cut by an appropriate restriction enzyme. Thus, cohesive ends corresponding to a particular restriction
enzyme can be added to virtually any DNA molecule. We see here the fruits of combining enzymatic and synthetic chemical approaches in crafting new DNA molecules.
synthetic one. New combinations of unrelated genes can be constructed in the laboratory by applying recombinant DNA
techniques. These novel combinations can be cloned amplified manyfold by introducing them into suitable cells,
where they are replicated by the DNA-synthesizing machinery of the host. The inserted genes are often transcribed and
translated in their new setting. What is most striking is that the genetic endowment of the host can be permanently
altered in a designed way.
Restriction Enzymes and DNA Ligase Are Key Tools in Forming Recombinant
DNA Molecules
Let us begin by seeing how novel DNA molecules can be constructed in the laboratory. A DNA fragment of interest is
covalently joined to a DNA vector. The essential feature of a vector is that it can replicate autonomously in an
appropriate host. Plasmids (naturally occurring circles of DNA that act as accessory chromosomes in bacteria) and
bacteriophage l , a virus, are choice vectors for cloning in E. coli. The vector can be prepared for accepting a new DNA
fragment by cleaving it at a single specific site with a restriction enzyme. For example, the plasmid pSC101, a 9.9-kb
double-helical circular DNA molecule, is split at a unique site by the EcoRI restriction enzyme. The staggered cuts made
by this enzyme produce complementary single-stranded ends, which have specific affinity for each other and hence are
known as cohesive or sticky ends. Any DNA fragment can be inserted into this plasmid if it has the same cohesive ends.
Such a fragment can be prepared from a larger piece of DNA by using the same restriction enzyme as was used to open
the plasmid DNA
The single-stranded ends of the fragment are then complementary to those of the cut plasmid. The DNA fragment and
the cut plasmid can be annealed and then joined by DNA ligase, which catalyzes the formation of a phosphodiester bond
at a break in a DNA chain. DNA ligase requires a free 3 -hydroxyl group and a 5 -phosphoryl group. Furthermore, the
chains joined by ligase must be in a double helix. An energy source such as ATP or NAD+ is required for the joining
reaction,
This cohesive-end method for joining DNA molecules can be made general by using a short, chemically synthesized
DNA linker that can be cleaved by restriction enzymes. First, the linker is covalently joined to the ends of a DNA
fragment or vector. For example, the 5 ends of a decameric linker and a DNA molecule are phosphorylated by
polynucleotide kinase and then joined by the ligase from T4 phage . This ligase can form a covalent bond
between blunt-ended (flush-ended) double-helical DNA molecules. Cohesive ends are produced when these terminal
extensions are cut by an appropriate restriction enzyme. Thus, cohesive ends corresponding to a particular restriction
enzyme can be added to virtually any DNA molecule. We see here the fruits of combining enzymatic and synthetic chemical approaches in crafting new DNA molecules.
PCR Is a Powerful Technique in Medical Diagnostics, Forensics, and Molecular
In 1984, Kary Mullis devised an ingenious method called the polymerase chain reaction (PCR) for amplifying specific
DNA sequences. Consider a DNA duplex consisting of a target sequence surrounded by nontarget DNA. Millions of the
target sequences can be readily obtained by PCR if the flanking sequences of the target are known. PCR is carried out by
adding the following components to a solution containing the target sequence: (1) a pair of primers that hybridize with
the flanking sequences of the target, (2) all four deoxyribonucleoside triphosphates (dNTPs), and (3) a heat-stable DNA
polymerase. A PCR cycle consists of three steps (Figure 6.8).
1. Strand separation. The two strands of the parent DNA molecule are separated by heating the solution to 95°C for 15 s.
2. Hybridization of primers. The solution is then abruptly cooled to 54°C to allow each primer to hybridize to a DNA
strand. One primer hybridizes to the 3 -end of the target on one strand, and the other primer hybridizes to the 3 end on
the complementary target strand. Parent DNA duplexes do not form, because the primers are present in large excess.
Primers are typically from 20 to 30 nucleotides long.
3. DNA synthesis. The solution is then heated to 72°C, the optimal temperature for Taq DNA polymerase. This heatstable
polymerase comes from T hermus aq uaticus, a thermophilic bacterium that lives in hot springs. The polymerase
elongates both primers in the direction of the target sequence because DNA synthesis is in the 5 -to-3 direction. DNA
synthesis takes place on both strands but extends beyond the target sequence.
These three steps strand separation, hybridization of primers, and DNA synthesis constitute one cycle of the PCR
amplification and can be carried out repetitively just by changing the temperature of the reaction mixture. The
thermostability of the polymerase makes it feasible to carry out PCR in a closed container; no reagents are added after
the first cycle. The duplexes are heated to begin the second cycle, which produces four duplexes, and then the third cycle
is initiated . At the end of the third cycle, two short strands appear that constitute only the target
sequence the sequence including and bounded by the primers. Subsequent cycles will amplify the target sequence
exponentially. The larger strands increase in number arithmetically and serve as a source for the synthesis of more short
strands. Ideally, after n cycles, this sequence is amplified 2 n -fold. The amplification is a millionfold after 20 cycles and
a billionfold after 30 cycles, which can be carried out in less than an hour.
Several features of this remarkable method for amplifying DNA are noteworthy. First, the sequence of the target need
not be known. All that is required is knowledge of the flanking sequences. Second, the target can be much larger than the
primers. Targets larger than 10 kb have been amplified by PCR. Third, primers do not have to be perfectly matched to
flanking sequences to amplify targets. With the use of primers derived from a gene of known sequence, it is possible to
search for variations on the theme. In this way, families of genes are being discovered by PCR. Fourth, PCR is highly
specific because of the stringency of hybridization at high temperature (54°C). Stringency is the required closeness of the
match between primer and target, which can be controlled by temperature and salt. At high temperatures, the only DNA
that is amplified is that situated between primers that have hybridized. A gene constituting less than a millionth of the
total DNA of a higher organism is accessible by PCR. Fifth, PCR is exquisitely sensitive. A single DNA molecule can be
amplified and detected.
PCR can provide valuable diagnostic information in medicine. Bacteria and viruses can be readily detected with the use
of specific primers. For example, PCR can reveal the presence of human immunodeficiency virus in people who have
not mounted an immune response to this pathogen and would therefore be missed with an antibody assay. Finding
Mycobacterium tuberculosis bacilli in tissue specimens is slow and laborious. With PCR, as few as 10 tubercle bacilli
per million human cells can be readily detected. PCR is a promising method for the early detection of certain cancers.
This technique can identify mutations of certain growth-control genes, such as the ras genes (Section 15.4.2). The
capacity to greatly amplify selected regions of DNA can also be highly informative in monitoring cancer chemotherapy.
Tests using PCR can detect when cancerous cells have been eliminated and treatment can be stopped; they can also
detect a relapse and the need to immediately resume treatment. PCR is ideal for detecting leukemias caused by
chromosomal rearrangements.
PCR is also having an effect in forensics and legal medicine. An individual DNA profile is highly distinctive because
many genetic loci are highly variable within a population. For example, variations at a specific one of these locations
determines a person's HLA type (human leukocyte antigen type); organ transplants are rejected when the HLA types of
the donor and recipient are not sufficiently matched. PCR amplification of multiple genes is being used to establish
biological parentage in disputed paternity and immigration cases. Analyses of blood stains and semen samples by PCR
have implicated guilt or innocence in numerous assault and rape cases. The root of a single shed hair found at a crime
scene contains enough DNA for typing by PCR
DNA is a remarkably stable molecule, particularly when relatively shielded from air, light, and water. Under such
circumstances, large fragments of DNA can remain intact for thousands of years or longer. PCR provides an ideal
method for amplifying such ancient DNA molecules so that they can be detected and characterized (Section 7.5.1). PCR
can also be used to amplify DNA from microorganisms that have not yet been isolated and cultured. As will be discussed
in the next chapter, sequences from these PCR products can be sources of considerable insight into evolutionary
relationships between organisms.
DNA sequences. Consider a DNA duplex consisting of a target sequence surrounded by nontarget DNA. Millions of the
target sequences can be readily obtained by PCR if the flanking sequences of the target are known. PCR is carried out by
adding the following components to a solution containing the target sequence: (1) a pair of primers that hybridize with
the flanking sequences of the target, (2) all four deoxyribonucleoside triphosphates (dNTPs), and (3) a heat-stable DNA
polymerase. A PCR cycle consists of three steps (Figure 6.8).
1. Strand separation. The two strands of the parent DNA molecule are separated by heating the solution to 95°C for 15 s.
2. Hybridization of primers. The solution is then abruptly cooled to 54°C to allow each primer to hybridize to a DNA
strand. One primer hybridizes to the 3 -end of the target on one strand, and the other primer hybridizes to the 3 end on
the complementary target strand. Parent DNA duplexes do not form, because the primers are present in large excess.
Primers are typically from 20 to 30 nucleotides long.
3. DNA synthesis. The solution is then heated to 72°C, the optimal temperature for Taq DNA polymerase. This heatstable
polymerase comes from T hermus aq uaticus, a thermophilic bacterium that lives in hot springs. The polymerase
elongates both primers in the direction of the target sequence because DNA synthesis is in the 5 -to-3 direction. DNA
synthesis takes place on both strands but extends beyond the target sequence.
These three steps strand separation, hybridization of primers, and DNA synthesis constitute one cycle of the PCR
amplification and can be carried out repetitively just by changing the temperature of the reaction mixture. The
thermostability of the polymerase makes it feasible to carry out PCR in a closed container; no reagents are added after
the first cycle. The duplexes are heated to begin the second cycle, which produces four duplexes, and then the third cycle
is initiated . At the end of the third cycle, two short strands appear that constitute only the target
sequence the sequence including and bounded by the primers. Subsequent cycles will amplify the target sequence
exponentially. The larger strands increase in number arithmetically and serve as a source for the synthesis of more short
strands. Ideally, after n cycles, this sequence is amplified 2 n -fold. The amplification is a millionfold after 20 cycles and
a billionfold after 30 cycles, which can be carried out in less than an hour.
Several features of this remarkable method for amplifying DNA are noteworthy. First, the sequence of the target need
not be known. All that is required is knowledge of the flanking sequences. Second, the target can be much larger than the
primers. Targets larger than 10 kb have been amplified by PCR. Third, primers do not have to be perfectly matched to
flanking sequences to amplify targets. With the use of primers derived from a gene of known sequence, it is possible to
search for variations on the theme. In this way, families of genes are being discovered by PCR. Fourth, PCR is highly
specific because of the stringency of hybridization at high temperature (54°C). Stringency is the required closeness of the
match between primer and target, which can be controlled by temperature and salt. At high temperatures, the only DNA
that is amplified is that situated between primers that have hybridized. A gene constituting less than a millionth of the
total DNA of a higher organism is accessible by PCR. Fifth, PCR is exquisitely sensitive. A single DNA molecule can be
amplified and detected.
PCR can provide valuable diagnostic information in medicine. Bacteria and viruses can be readily detected with the use
of specific primers. For example, PCR can reveal the presence of human immunodeficiency virus in people who have
not mounted an immune response to this pathogen and would therefore be missed with an antibody assay. Finding
Mycobacterium tuberculosis bacilli in tissue specimens is slow and laborious. With PCR, as few as 10 tubercle bacilli
per million human cells can be readily detected. PCR is a promising method for the early detection of certain cancers.
This technique can identify mutations of certain growth-control genes, such as the ras genes (Section 15.4.2). The
capacity to greatly amplify selected regions of DNA can also be highly informative in monitoring cancer chemotherapy.
Tests using PCR can detect when cancerous cells have been eliminated and treatment can be stopped; they can also
detect a relapse and the need to immediately resume treatment. PCR is ideal for detecting leukemias caused by
chromosomal rearrangements.
PCR is also having an effect in forensics and legal medicine. An individual DNA profile is highly distinctive because
many genetic loci are highly variable within a population. For example, variations at a specific one of these locations
determines a person's HLA type (human leukocyte antigen type); organ transplants are rejected when the HLA types of
the donor and recipient are not sufficiently matched. PCR amplification of multiple genes is being used to establish
biological parentage in disputed paternity and immigration cases. Analyses of blood stains and semen samples by PCR
have implicated guilt or innocence in numerous assault and rape cases. The root of a single shed hair found at a crime
scene contains enough DNA for typing by PCR
DNA is a remarkably stable molecule, particularly when relatively shielded from air, light, and water. Under such
circumstances, large fragments of DNA can remain intact for thousands of years or longer. PCR provides an ideal
method for amplifying such ancient DNA molecules so that they can be detected and characterized (Section 7.5.1). PCR
can also be used to amplify DNA from microorganisms that have not yet been isolated and cultured. As will be discussed
in the next chapter, sequences from these PCR products can be sources of considerable insight into evolutionary
relationships between organisms.
Exploring Genes
Recombinant DNA technology has revolutionized biochemistry since it came into being in the 1970s. The genetic
endowment of organisms can now be precisely changed in designed ways. Recombinant DNA technology is a fruit of
several decades of basic research on DNA, RNA, and viruses. It depends, first, on having enzymes that can cut, join, and
replicate DNA and reverse transcribe RNA. Restriction enzymes cut very long DNA molecules into specific fragments
that can be manipulated; DNA ligases join the fragments together. The availability of many kinds of restriction enzymes
and DNA ligases makes it feasible to treat DNA sequences as modules that can be moved at will from one DNA
molecule to another. Thus, recombinant DNA technology is based on nucleic acid enzymology.
A second foundation is the base-pairing language that allows complementary sequences to recognize and bind to each
other. Hybridization with complementary DNA or RNA probes is a sensitive and powerful means of detecting specific
nucleotide sequences. In recombinant DNA technology, base-pairing is used to construct new combinations of DNA as
well as to detect and amplify particular sequences. This revolutionary technology is also critically dependent on our
understanding of viruses, the ultimate parasites. Viruses efficiently deliver their own DNA (or RNA) into hosts,
subverting them either to replicate the viral genome and produce viral proteins or to incorporate viral DNA into the host
genome. Likewise, plasmids, which are accessory chromosomes found in bacteria, have been indispensable in
recombinant DNA technology.
These new methods have wide-ranging benefits. Entire genomes, including the human genome, are being deciphered.
New insights are emerging, for example, into the regulation of gene expression in cancer and development and the
evolutionary history of proteins as well as organisms. New proteins can be created by altering genes in specific ways to
provide detailed views into protein function. Clinically useful proteins, such as hormones, are now synthesized by
recombinant DNA techniques. Crops are being generated to resist pests and harsh conditions. The new opportunities
opened by recombinant DNA technology promise to have broad effects.
The Basic Tools of Gene Exploration
The rapid progress in biotechnology indeed its very existence is a result of a relatively few techniques.
1. Restriction-enzyme analysis. Restriction enzymes are precise, molecular scalpels that allow the investigator to
manipulate DNA segments.
2. Blotting techniques. The Southern and Northern blots are used to separate and characterize DNA and RNA,
respectively. The Western blot, which uses antibodies to characterize proteins, was described in Section 4.3.4.
3. DNA sequencing. The precise nucleotide sequence of a molecule of DNA can be determined. Sequencing has yielded a
wealth of information concerning gene architecture, the control of gene expression, and protein structure.
4. Solid-phase synthesis of nucleic acids. Precise sequences of nucleic acids can be synthesized de novo and used to
identify or amplify other nucleic acids.
5. The polymerase chain reaction (PCR). The polymerase chain reaction leads to a billionfold amplification of a segment
of DNA. One molecule of DNA can be amplified to quantities that permit characterization and manipulation. This
powerful technique is being used to detect pathogens and genetic diseases, to determine the source of a hair left at the
scene of a crime, and to resurrect genes from fossils.
A final tool, the use of which will be highlighted in the next chapter, is the computer. Without the computer, it would be
impossible to catalog, access, and characterize the abundant information, especially DNA sequence information, that the techniques just outlined are rapidly generating.
endowment of organisms can now be precisely changed in designed ways. Recombinant DNA technology is a fruit of
several decades of basic research on DNA, RNA, and viruses. It depends, first, on having enzymes that can cut, join, and
replicate DNA and reverse transcribe RNA. Restriction enzymes cut very long DNA molecules into specific fragments
that can be manipulated; DNA ligases join the fragments together. The availability of many kinds of restriction enzymes
and DNA ligases makes it feasible to treat DNA sequences as modules that can be moved at will from one DNA
molecule to another. Thus, recombinant DNA technology is based on nucleic acid enzymology.
A second foundation is the base-pairing language that allows complementary sequences to recognize and bind to each
other. Hybridization with complementary DNA or RNA probes is a sensitive and powerful means of detecting specific
nucleotide sequences. In recombinant DNA technology, base-pairing is used to construct new combinations of DNA as
well as to detect and amplify particular sequences. This revolutionary technology is also critically dependent on our
understanding of viruses, the ultimate parasites. Viruses efficiently deliver their own DNA (or RNA) into hosts,
subverting them either to replicate the viral genome and produce viral proteins or to incorporate viral DNA into the host
genome. Likewise, plasmids, which are accessory chromosomes found in bacteria, have been indispensable in
recombinant DNA technology.
These new methods have wide-ranging benefits. Entire genomes, including the human genome, are being deciphered.
New insights are emerging, for example, into the regulation of gene expression in cancer and development and the
evolutionary history of proteins as well as organisms. New proteins can be created by altering genes in specific ways to
provide detailed views into protein function. Clinically useful proteins, such as hormones, are now synthesized by
recombinant DNA techniques. Crops are being generated to resist pests and harsh conditions. The new opportunities
opened by recombinant DNA technology promise to have broad effects.
The Basic Tools of Gene Exploration
The rapid progress in biotechnology indeed its very existence is a result of a relatively few techniques.
1. Restriction-enzyme analysis. Restriction enzymes are precise, molecular scalpels that allow the investigator to
manipulate DNA segments.
2. Blotting techniques. The Southern and Northern blots are used to separate and characterize DNA and RNA,
respectively. The Western blot, which uses antibodies to characterize proteins, was described in Section 4.3.4.
3. DNA sequencing. The precise nucleotide sequence of a molecule of DNA can be determined. Sequencing has yielded a
wealth of information concerning gene architecture, the control of gene expression, and protein structure.
4. Solid-phase synthesis of nucleic acids. Precise sequences of nucleic acids can be synthesized de novo and used to
identify or amplify other nucleic acids.
5. The polymerase chain reaction (PCR). The polymerase chain reaction leads to a billionfold amplification of a segment
of DNA. One molecule of DNA can be amplified to quantities that permit characterization and manipulation. This
powerful technique is being used to detect pathogens and genetic diseases, to determine the source of a hair left at the
scene of a crime, and to resurrect genes from fossils.
A final tool, the use of which will be highlighted in the next chapter, is the computer. Without the computer, it would be
impossible to catalog, access, and characterize the abundant information, especially DNA sequence information, that the techniques just outlined are rapidly generating.
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