Part Two ~ Studying Expression and Function of Gene
Gel Electrophoresis
Describe it- Gel Electrophoresis is a process used to separate nucleic acids or proteins by size or charge. The molecules are first placed in a porous gel, then an electric field is sent through the gel. Nucleic acids have negative charges, which cause them to move towards the positive electrode in the electric field. Larger DNA molecules are impeded more then the shorter ones, which creates separate bands of same sized DNA molecules. A dye is added to make the DNA visible.
Analyze it- The gel is made in a special way to allow concentration of different sizes of DNA molecules. It is made out of different concentrations of acrylamide and a cross-linker. This creates different sized mesh networks of polyacrylamide. If the DNA molecules are considerably larger, then agarose is used instead of acrylamide. An electromotive force is added to the gel, causing negatively charged molecules to move towards the anode side and positively charged molecules to move towards the cathode side. Because of the different size of pores in the gel, smaller molecules are able to move at a faster rate.
Apply it- This method can be used to distinguish genetic mutations such as sickle-cell anemia.
As you can see above, the sickle-cell allele lacks a sequence recognized by restriction enzymes. This causes the sickle-cell allele to be cut into larger fragments, while the normal allele is cut into smaller fragments. When the two alleles are sent through Gel Electrophoresis, the fragments of the normal allele travel farther then the mutant allele fragments. The normal allele also creates more bands because the fragments have more variation in size then with the mutant allele, since the mutant allele wasn't cut in all the places it should've been.
Synthesize it- This procedure reminds me of removing salt from salt water. Because the DNA molecules are so small you cannot pick out different sizes yourself, just as you cannot pick the salt out of the water. Instead you have to use Gel Electrophoresis to separate the different sizes of DNA, just like you would evaporate the water to uncover the salt.
Argue it- I don't see any reason this process shouldn't be used. Nothing can really go wrong with. It helps scientists with their research which in turn could lead to a cure in many genetic diseases.
Describe it- Southern Blot is a process used to find specific nucleotide sequences. Transferring the bands of DNA from the gel to a nitrocellulose sheet (or the blot) and then adding radioactive probes will allow you to see the specific genes you are looking for.
Analyze it- First the bands of DNA are transfered from the gel to a nitrocellulose sheet. This can be done simply by setting the nitrocellulose sheet on the gel and adding a heavyweight on top of that. After that is finished, probes, which are radioactive strands of DNA complementary to the desired gene, are added to the nitrocellulose sheet. The probes attach to the gene of interest, which allows us to see the radioactivity by taking an x-ray photograph.
Apply it- It has been applied to detect Restriction Fragment Length Polymorphism and Variable Number of Tandem Repeat Polymorphism. The latter is the basis of DNA fingerprinting.
Synthesize it- Southern Blotting is like taking a machine that isn't working and then finding what needs to be fixed. With a machine a mechanic will take the the machine apart, piece by piece, like separating DNA fragments. Once the machine is taken apart the mechanic will now what parts need to be replaced like how the DNA with the required gene is exposed to radioactive probe to tell which was contain the gene.
Argue it- Using this method is safe and easy. The scientist will clearly be able to see what DNA strands have the gene they are looking for in fast efficient way.
Describe it- Microarrays consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles of a specific DNA sequence, known as probes. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample under high-stringency conditions.
Analyze it- In standard microarrays, the probes are attached via surface engineering to a solid surface by a covalent bond to a chemical matrix. The solid surface can be glass or a silicon chip, in which case they are colloquially known as an Affy chip when an Affymetrix chip is used. Other microarray platforms, such as Illumina, use microscopic beads, instead of the large solid support. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system.
Apply it-DNA microarrays can be used to detect DNA, or detect RNA that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling.
Synthesize it-Microarrays work like a CD player. A CD player must detect information from a disk and translated it to play a certain type of music. The way that CD player detects for songs is exactly like how microarray detect wither RNA or DNA so that it can be furthered processed into proteins.
Argue it- I wouldn't see why this process wouldn't be used. It gives a nice visual on what genes are being expressed either by the affected or non-affected cells. The chip also gives the ration of genes being expressed to make this process easier for the operator.
Part Two ~ Studying Expression and Function of Gene
Gel Electrophoresis
Describe it- Gel Electrophoresis is a process used to separate nucleic acids or proteins by size or charge. The molecules are first placed in a porous gel, then an electric field is sent through the gel. Nucleic acids have negative charges, which cause them to move towards the positive electrode in the electric field. Larger DNA molecules are impeded more then the shorter ones, which creates separate bands of same sized DNA molecules. A dye is added to make the DNA visible.Analyze it- The gel is made in a special way to allow concentration of different sizes of DNA molecules. It is made out of different concentrations of acrylamide and a cross-linker. This creates different sized mesh networks of polyacrylamide. If the DNA molecules are considerably larger, then agarose is used instead of acrylamide. An electromotive force is added to the gel, causing negatively charged molecules to move towards the anode side and positively charged molecules to move towards the cathode side. Because of the different size of pores in the gel, smaller molecules are able to move at a faster rate.
Apply it- This method can be used to distinguish genetic mutations such as sickle-cell anemia.
Synthesize it- This procedure reminds me of removing salt from salt water. Because the DNA molecules are so small you cannot pick out different sizes yourself, just as you cannot pick the salt out of the water. Instead you have to use Gel Electrophoresis to separate the different sizes of DNA, just like you would evaporate the water to uncover the salt.
Argue it- I don't see any reason this process shouldn't be used. Nothing can really go wrong with. It helps scientists with their research which in turn could lead to a cure in many genetic diseases.
Here is a great animation of the process.
Source
Southern Blotting
Describe it- Southern Blot is a process used to find specific nucleotide sequences. Transferring the bands of DNA from the gel to a nitrocellulose sheet (or the blot) and then adding radioactive probes will allow you to see the specific genes you are looking for.
Analyze it- First the bands of DNA are transfered from the gel to a nitrocellulose sheet. This can be done simply by setting the nitrocellulose sheet on the gel and adding a heavyweight on top of that. After that is finished, probes, which are radioactive strands of DNA complementary to the desired gene, are added to the nitrocellulose sheet. The probes attach to the gene of interest, which allows us to see the radioactivity by taking an x-ray photograph.
Apply it- It has been applied to detect Restriction Fragment Length Polymorphism and Variable Number of Tandem Repeat Polymorphism. The latter is the basis of DNA fingerprinting.
Synthesize it- Southern Blotting is like taking a machine that isn't working and then finding what needs to be fixed. With a machine a mechanic will take the the machine apart, piece by piece, like separating DNA fragments. Once the machine is taken apart the mechanic will now what parts need to be replaced like how the DNA with the required gene is exposed to radioactive probe to tell which was contain the gene.
Argue it- Using this method is safe and easy. The scientist will clearly be able to see what DNA strands have the gene they are looking for in fast efficient way.
Here is a great animation of the process.
Source
Microarrays
Describe it- Microarrays consists of an arrayed series of thousands of microscopic spots of DNA oligonucleotides, called features, each containing picomoles of a specific DNA sequence, known as probes. These can be a short section of a gene or other DNA element that are used to hybridize a cDNA or cRNA sample under high-stringency conditions.
Analyze it- In standard microarrays, the probes are attached via surface engineering to a solid surface by a covalent bond to a chemical matrix. The solid surface can be glass or a silicon chip, in which case they are colloquially known as an Affy chip when an Affymetrix chip is used. Other microarray platforms, such as Illumina, use microscopic beads, instead of the large solid support. DNA arrays are different from other types of microarray only in that they either measure DNA or use DNA as part of its detection system.
Apply it-DNA microarrays can be used to detect DNA, or detect RNA that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling.
Synthesize it-Microarrays work like a CD player. A CD player must detect information from a disk and translated it to play a certain type of music. The way that CD player detects for songs is exactly like how microarray detect wither RNA or DNA so that it can be furthered processed into proteins.
Argue it- I wouldn't see why this process wouldn't be used. It gives a nice visual on what genes are being expressed either by the affected or non-affected cells. The chip also gives the ration of genes being expressed to make this process easier for the operator.
Here is a great animation of the process
Source