The four most common cancers are:
Cancers of Blood and Lymphatic Systems:
Skin cancers:
Cancers of Digestive Systems:
Cancers of Urinary system:
Cancers in women:
Miscellaneous cancers:
Saturday, January 22, 2011
The Twenty Amino Acids of Proteins
Based on the physical and chemical properties of R groups, the 20 amino acids of proteins may be classified as follows.
1. Acidic: including aspartic acid (aspartate) and glutamatic acid (glutamate). In a neutral solution, the R group of an acidic amino acid may lose a proton and become negatively charged.
2. Basic: including lysine, arginine and histidine. In a neutral solution, the R group of a basic amino acid may gain a proton and become positively charged. Interaction between positive and negative R groups may form a salt bridge, which is an important stabilizing force in proteins.
3. Aromatic: including tyrosine, tryptophan and phenylalanine. Their R groups contain an aromatic ring.
4. Sulfur: including cysteine and methionine. Their R groups contain a sulfur atom (S). The disulfide bond formed between two cysteine residues provides a strong force for stabilizing the globular structure. A unique feature about methionine is that the synthesis of all peptide chains starts from methionine (Chapter 5 Section C).
5. Uncharged hydrophilic: including serine, threonine, asparagine and glutamine. Their R groups are hydrophilic and capable of forming hydrogen bonds.
6. Inactive hydrophobic: including glycine, alanine, valine, leucine and isoleucine. These amino acids are more likely to be buried in the protein interior. Their R groups do not form hydrogen bonds and rarely participate in chemical reactions.
7. Special structure: including proline. In most amino acids, the R group and the amino group are not directly connected. Proline is the only exception among 20 amino acids found in protein. Due to this special feature, proline is often located at the turn of a peptide chain in the three-dimensional structure of a protein.
Figure 2-A-2. Names, symbols, chemical structures and hydrophobicity indices of the 20 amino acids found in proteins. They are arranged in the order as discussed above.
1. Acidic: including aspartic acid (aspartate) and glutamatic acid (glutamate). In a neutral solution, the R group of an acidic amino acid may lose a proton and become negatively charged.
2. Basic: including lysine, arginine and histidine. In a neutral solution, the R group of a basic amino acid may gain a proton and become positively charged. Interaction between positive and negative R groups may form a salt bridge, which is an important stabilizing force in proteins.
3. Aromatic: including tyrosine, tryptophan and phenylalanine. Their R groups contain an aromatic ring.
4. Sulfur: including cysteine and methionine. Their R groups contain a sulfur atom (S). The disulfide bond formed between two cysteine residues provides a strong force for stabilizing the globular structure. A unique feature about methionine is that the synthesis of all peptide chains starts from methionine (Chapter 5 Section C).
5. Uncharged hydrophilic: including serine, threonine, asparagine and glutamine. Their R groups are hydrophilic and capable of forming hydrogen bonds.
6. Inactive hydrophobic: including glycine, alanine, valine, leucine and isoleucine. These amino acids are more likely to be buried in the protein interior. Their R groups do not form hydrogen bonds and rarely participate in chemical reactions.
7. Special structure: including proline. In most amino acids, the R group and the amino group are not directly connected. Proline is the only exception among 20 amino acids found in protein. Due to this special feature, proline is often located at the turn of a peptide chain in the three-dimensional structure of a protein.
Figure 2-A-2. Names, symbols, chemical structures and hydrophobicity indices of the 20 amino acids found in proteins. They are arranged in the order as discussed above.
DNA's B Form, A Form and Z Form
In a DNA molecule, the two strands are not parallel, but intertwined with each other. Each strand looks like a helix. The two strands form a "double helix" structure, which was first discovered by James D. Watson and Francis Crick in 1953. In this structure, also known as the B form, the helix makes a turn every 3.4 nm, and the distance between two neighboring base pairs is 0.34 nm. Hence, there are about 10 pairs per turn. The intertwined strands make two grooves of different widths, referred to as the major groove and the minor groove, which may facilitate binding with specific proteins.
Figure 3-B-3. The normal right-handed "double helix" structure of DNA, also known as the B form.
In a solution with higher salt concentrations or with alcohol added, the DNA structure may change to an A form, which is still right-handed, but every 2.3 nm makes a turn and there are 11 base pairs per turn.
Another DNA structure is called the Z form, because its bases seem to zigzag. Z DNA is left-handed. One turn spans 4.6 nm, comprising 12 base pairs. The DNA molecule with alternating G-C sequences in alcohol or high salt solution tends to have such structure.
Figure 3-B-4. Comparison between B form and Z form.
In a solution with higher salt concentrations or with alcohol added, the DNA structure may change to an A form, which is still right-handed, but every 2.3 nm makes a turn and there are 11 base pairs per turn.
Another DNA structure is called the Z form, because its bases seem to zigzag. Z DNA is left-handed. One turn spans 4.6 nm, comprising 12 base pairs. The DNA molecule with alternating G-C sequences in alcohol or high salt solution tends to have such structure.
DNA Cloning
DNA cloning is a technique to reproduce DNA fragments. It can be achieved by two different approaches: (1) cell based, and (2) using polymerase chain reaction (PCR). In the cell-based approach, a vector is required to carry the DNA fragment of interest into the host cell. The following figure shows a typical procedure by using plasmids as the cloning vector.
Figure 9-A-1. The essential steps in DNA cloning using plasmids as vectors.
(a) DNA recombination. The DNA fragment to be cloned is inserted into a vector (more information). The recombinant vector must also contain an antibiotic-resistance gene (not shown).
(b) Transformation. The recombinant DNA enters into the host cell and proliferates. It is called "transformation" because the function of the host cell may be altered. Normal E. coli cells are difficult to take up plasmid DNA from the medium. If they are treated with CaCl2, the transformation efficiency can be significantly enhanced. Even so, only one cell in about 10,000 cells may take up a plasmid DNA molecule.
(c) Selective amplification. A specific antibiotic is added to kill E. coli without any protection. The transformed E. coli is protected by the antibiotic-resistance gene whose product can inactivate the specific antibiotic. In this figure, the numbers of vectors in each E. coli cell are not the same, because they may also reproduce independently.
(d) Isolation of desired DNA clones.
(a) DNA recombination. The DNA fragment to be cloned is inserted into a vector (more information). The recombinant vector must also contain an antibiotic-resistance gene (not shown).
(b) Transformation. The recombinant DNA enters into the host cell and proliferates. It is called "transformation" because the function of the host cell may be altered. Normal E. coli cells are difficult to take up plasmid DNA from the medium. If they are treated with CaCl2, the transformation efficiency can be significantly enhanced. Even so, only one cell in about 10,000 cells may take up a plasmid DNA molecule.
(c) Selective amplification. A specific antibiotic is added to kill E. coli without any protection. The transformed E. coli is protected by the antibiotic-resistance gene whose product can inactivate the specific antibiotic. In this figure, the numbers of vectors in each E. coli cell are not the same, because they may also reproduce independently.
(d) Isolation of desired DNA clones.
Problems With DNA Fingerprinting
Like nearly everything else in the scientific world, nothing about DNA fingerprinting is 100% assured. The term DNA fingerprint is, in one sense, a misnomer: it implies that, like a fingerprint, the VNTR pattern for a given person is utterly and completely unique to that person. Actually, all that a VNTR pattern can do is present a probability that the person in question is indeed the person to whom the VNTR pattern (of the child, the criminal evidence, or whatever else) belongs. Given, that probability might be 1 in 20 billion, which would indicate that the person can be reasonably matched with the DNA fingerprint; then again, that probability might only be 1 in 20, leaving a large amount of doubt regarding the specific identity of the VNTR pattern's owner.
1. Generating a High Probability
The probability of a DNA fingerprint belonging to a specific person needs to be reasonably high--especially in criminal cases, where the association helps establish a suspect's guilt or innocence. Using certain rare VNTRs or combinations of VNTRs to create the VNTR pattern increases the probability that the two DNA samples do indeed match (as opposed to look alike, but not actually come from the same person) or correlate (in the case of parents and children).
2. Problems with Determining Probability
A. Population Genetics
VNTRs, because they are results of genetic inheritance, are not distributed evenly across all of human population. A given VNTR cannot, therefore, have a stable probability of occurrence; it will vary depending on an individual's genetic background. The difference in probabilities is particularly visible across racial lines. Some VNTRs that occur very frequently among Hispanics will occur very rarely among Caucasians or African-Americans. Currently, not enough is known about the VNTR frequency distributions among ethnic groups to determine accurate probabilities for individuals within those groups; the heterogeneous genetic composition of interracial individuals, who are growing in number, presents an entirely new set of questions. Further experimentation in this area, known as population genetics, has been surrounded with and hindered by controversy, because the idea of identifying people through genetic anomalies along racial lines comes alarmingly close to the eugenics and ethnic purification movements of the recent past, and, some argue, could provide a scientific basis for racial discrimination.
B. Technical Difficulties
Errors in the hybridization and probing process must also be figured into the probability, and often the idea of error is simply not acceptable. Most people will agree that an innocent person should not be sent to jail, a guilty person allowed to walk free, or a biological mother denied her legal right to custody of her children, simply because a lab technician did not conduct an experiment accurately. When the DNA sample available is minuscule, this is an important consideration, because there is not much room for error, especially if the analysis of the DNA sample involves amplification of the sample (creating a much larger sample of genetically identical DNA from what little material is available), because if the wrong DNA is amplified (i.e. a skin cell from the lab technician) the consequences can be profoundly detrimental. Until recently, the standards for determining DNA fingerprinting matches, and for laboratory security and accuracy which would minimize error, were neither stringent nor universally codified, causing a great deal of public outcry.
1. Generating a High Probability
The probability of a DNA fingerprint belonging to a specific person needs to be reasonably high--especially in criminal cases, where the association helps establish a suspect's guilt or innocence. Using certain rare VNTRs or combinations of VNTRs to create the VNTR pattern increases the probability that the two DNA samples do indeed match (as opposed to look alike, but not actually come from the same person) or correlate (in the case of parents and children).
2. Problems with Determining Probability
A. Population Genetics
VNTRs, because they are results of genetic inheritance, are not distributed evenly across all of human population. A given VNTR cannot, therefore, have a stable probability of occurrence; it will vary depending on an individual's genetic background. The difference in probabilities is particularly visible across racial lines. Some VNTRs that occur very frequently among Hispanics will occur very rarely among Caucasians or African-Americans. Currently, not enough is known about the VNTR frequency distributions among ethnic groups to determine accurate probabilities for individuals within those groups; the heterogeneous genetic composition of interracial individuals, who are growing in number, presents an entirely new set of questions. Further experimentation in this area, known as population genetics, has been surrounded with and hindered by controversy, because the idea of identifying people through genetic anomalies along racial lines comes alarmingly close to the eugenics and ethnic purification movements of the recent past, and, some argue, could provide a scientific basis for racial discrimination.
B. Technical Difficulties
Errors in the hybridization and probing process must also be figured into the probability, and often the idea of error is simply not acceptable. Most people will agree that an innocent person should not be sent to jail, a guilty person allowed to walk free, or a biological mother denied her legal right to custody of her children, simply because a lab technician did not conduct an experiment accurately. When the DNA sample available is minuscule, this is an important consideration, because there is not much room for error, especially if the analysis of the DNA sample involves amplification of the sample (creating a much larger sample of genetically identical DNA from what little material is available), because if the wrong DNA is amplified (i.e. a skin cell from the lab technician) the consequences can be profoundly detrimental. Until recently, the standards for determining DNA fingerprinting matches, and for laboratory security and accuracy which would minimize error, were neither stringent nor universally codified, causing a great deal of public outcry.
Practical Applications of DNA Fingerprinting
1. Paternity and Maternity
Because a person inherits his or her VNTRs from his or her parents, VNTR patterns can be used to establish paternity and maternity. The patterns are so specific that a parental VNTR pattern can be reconstructed even if only the children's VNTR patterns are known (the more children produced, the more reliable the reconstruction). Parent-child VNTR pattern analysis has been used to solve standard father-identification cases as well as more complicated cases of confirming legal nationality and, in instances of adoption, biological parenthood.
2. Criminal Identification and Forensics
DNA isolated from blood, hair, skin cells, or other genetic evidence left at the scene of a crime can be compared, through VNTR patterns, with the DNA of a criminal suspect to determine guilt or innocence. VNTR patterns are also useful in establishing the identity of a homicide victim, either from DNA found as evidence or from the body itself.
3. Personal Identification
The notion of using DNA fingerprints as a sort of genetic bar code to identify individuals has been discussed, but this is not likely to happen anytime in the foreseeable future. The technology required to isolate, keep on file, and then analyze millions of very specified VNTR patterns is both expensive and impractical. Social security numbers, picture ID, and other more mundane methods are much more likely to remain the prevalent ways to establish personal identification.
Because a person inherits his or her VNTRs from his or her parents, VNTR patterns can be used to establish paternity and maternity. The patterns are so specific that a parental VNTR pattern can be reconstructed even if only the children's VNTR patterns are known (the more children produced, the more reliable the reconstruction). Parent-child VNTR pattern analysis has been used to solve standard father-identification cases as well as more complicated cases of confirming legal nationality and, in instances of adoption, biological parenthood.
2. Criminal Identification and Forensics
DNA isolated from blood, hair, skin cells, or other genetic evidence left at the scene of a crime can be compared, through VNTR patterns, with the DNA of a criminal suspect to determine guilt or innocence. VNTR patterns are also useful in establishing the identity of a homicide victim, either from DNA found as evidence or from the body itself.
3. Personal Identification
The notion of using DNA fingerprints as a sort of genetic bar code to identify individuals has been discussed, but this is not likely to happen anytime in the foreseeable future. The technology required to isolate, keep on file, and then analyze millions of very specified VNTR patterns is both expensive and impractical. Social security numbers, picture ID, and other more mundane methods are much more likely to remain the prevalent ways to establish personal identification.
Making a Radioactive Probe
1. Obtain some DNA polymerase [pink]. Put the DNA to be made radioactive (radiolabeled) into a tube.
2. Introduce nicks, or horizontal breaks along a strand, into the DNA you want to radiolabel. At the same time, add individual nucleotides to the nicked DNA, one of which, *C [light blue], is radioactive.
3. Add the DNA polymerase [pink] to the tube with the nicked DNA and the individual nucleotides. The DNA polymerase will become immediately attracted to the nicks in the DNA and attempt to repair the DNA, starting from the 5' end and moving toward the 3' end.
4. The DNA polymerase [pink] begins repairing the nicked DNA. It destroys all the existing bonds in front of it and places the new nucleotides, gathered from the individual nucleotides mixed in the tube, behind it. Whenever a G base is read in the lower strand, a radioactive *C [light blue] base is placed in the new strand. In this fashion, the nicked strand, as it is repaired by the DNA polymerase, is made radioactive by the inclusion of radioactive *C bases.
5. The nicked DNA is then heated, splitting the two strands of DNA apart. This creates single-stranded radioactive and non-radioactive pieces. The radioactive DNA, now called a probe [light blue], is ready for use.
Southern Blotting
The Southern Blot is one way to analyze the genetic patterns which appear in a person's DNA. Performing a Southern Blot involves: 1. Isolating the DNA in question from the rest of the cellular material in the nucleus. This can be done either chemically, by using a detergent to wash the extra material from the DNA,or mechanically, by applying a large amount of pressure in order to "squeeze out" the DNA.
2. Cutting the DNA into several pieces of different sizes. This is done using one or more restriction enzymes.
3. Sorting the DNA pieces by size. The process by which the size separation, "size fractionation," is done is called gel electrophoresis. The DNA is poured into a gel, such as agarose, and an electrical charge is applied to the gel, with the positive charge at the bottom and the negative charge at the top. Because DNA has a slightly negative charge, the pieces of DNA will be attracted towards the bottom of the gel; the smaller pieces, however, will be able to move more quickly and thus further towards the bottom than the larger pieces. The different-sized pieces of DNA will therefore be separated by size, with the smaller pieces towards the bottom and the larger pieces towards the top.
4. Denaturing the DNA, so that all of the DNA is rendered single-stranded. This can be done either by heating or chemically treating the DNA in the gel.
5. Blotting the DNA. The gel with the size-fractionated DNA is applied to a sheet of nitrocellulose paper, and then baked to permanently attach the DNA to the sheet. The Southern Blot is now ready to be analyzed.
In order to analyze a Southern Blot, a radioactive genetic probe is used in a hybridization reaction with the DNA in question (see next topics for more information). If an X-ray is taken of the Southern Blot after a radioactive probe has been allowed to bond with the denatured DNA on the paper, only the areas where the radioactive probe binds [red] will show up on the film. This allows researchers to identify, in a particular person's DNA, the occurrence and frequency of the particular genetic pattern contained in the probe.
2. Cutting the DNA into several pieces of different sizes. This is done using one or more restriction enzymes.
3. Sorting the DNA pieces by size. The process by which the size separation, "size fractionation," is done is called gel electrophoresis. The DNA is poured into a gel, such as agarose, and an electrical charge is applied to the gel, with the positive charge at the bottom and the negative charge at the top. Because DNA has a slightly negative charge, the pieces of DNA will be attracted towards the bottom of the gel; the smaller pieces, however, will be able to move more quickly and thus further towards the bottom than the larger pieces. The different-sized pieces of DNA will therefore be separated by size, with the smaller pieces towards the bottom and the larger pieces towards the top.
4. Denaturing the DNA, so that all of the DNA is rendered single-stranded. This can be done either by heating or chemically treating the DNA in the gel.
5. Blotting the DNA. The gel with the size-fractionated DNA is applied to a sheet of nitrocellulose paper, and then baked to permanently attach the DNA to the sheet. The Southern Blot is now ready to be analyzed.
In order to analyze a Southern Blot, a radioactive genetic probe is used in a hybridization reaction with the DNA in question (see next topics for more information). If an X-ray is taken of the Southern Blot after a radioactive probe has been allowed to bond with the denatured DNA on the paper, only the areas where the radioactive probe binds [red] will show up on the film. This allows researchers to identify, in a particular person's DNA, the occurrence and frequency of the particular genetic pattern contained in the probe.
What is DNA Fingerprinting?
The chemical structure of everyone's DNA is the same. The only difference between people (or any animal) is the order of the base pairs. There are so many millions of base pairs in each person's DNA that every person has a different sequence.
Using these sequences, every person could be identified solely by the sequence of their base pairs. However, because there are so many millions of base pairs, the task would be very time-consuming. Instead, scientists are able to use a shorter method, because of repeating patterns in DNA.
These patterns do not, however, give an individual "fingerprint," but they are able to determine whether two DNA samples are from the same person, related people, or non-related people. Scientists use a small number of sequences of DNA that are known to vary among individuals a great deal, and analyze those to get a certain
Using these sequences, every person could be identified solely by the sequence of their base pairs. However, because there are so many millions of base pairs, the task would be very time-consuming. Instead, scientists are able to use a shorter method, because of repeating patterns in DNA.
These patterns do not, however, give an individual "fingerprint," but they are able to determine whether two DNA samples are from the same person, related people, or non-related people. Scientists use a small number of sequences of DNA that are known to vary among individuals a great deal, and analyze those to get a certain
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