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Demystifying SDS Page

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Summary of Article or Video THAT INCLUDES FUNCTION OF THE TOOL.

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Summary of Article or Video THAT INCLUDES FUNCTION OF THE TOOL.

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This video describes why how SDS is used to coat proteins for protein electrophoresis that can be used to ensure purity or identity of the protein.  It does an excellent job of demonstrating the equipment that is used and acting out what occurs on the molecular level.

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A picture I found that helps me remember key points of the video or article

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A picture I found that helps me remember key points of the video or article

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Gene editing tools.
Clustered Regularly Interspaced Short Palindromic Repeats

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How CRISPR lets you edit DNA - Andrea M. Henle

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Summary of Video (Includes function of CRISPR)

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Summary of Video (Includes function of CRISPR)

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Scientists can now change an organism's features with genetic editing tools. CRISPR has worked as a bacterial immune system. It uses two components:
- Short repetitive DNA sequences (aka CRISPR's)
- Cas (CRISPR associated proteins): They cut DNA, like molecular scissors.

This was usually used to kill any viruses that tried to kill the bacteria. Now scientists use it not only to make Cas target viral DNA but almost any DNA.
By injecting Cas 9 bound to a short piece of RNA scientists can edit almost any gene, altering DNA and changing specific genes through homology directed repair which guides the rebuilding process, making it easier to insert a completely new gene or for the cells to repair a gene.

ABILITY TO FIX ERRORS IN THE GENOME! (AKA AMAZING)

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(Cas 9 targeting a specific gene and killing it)

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Gel electrophoresis is a widely used technique in life science laboratories to separate macromolecules such as DNA, RNA, and proteins. In this technique, molecules are separated based on their size and electric charge. Gel electrophoresis is usually performed in labs to analyze DNA, RNA, or protein samples from various sources.

Principles of gel electrophoresis

The gel electrophoresis technique exploits the difference in size and charge of different molecules in a sample. The DNA or protein sample to be separated is loaded on to a porous gel placed in an ionic buffer medium. On application of electric charge, each molecule having different size and charge will move through the gel at different speeds.

The porous gel used in this technique acts as a molecular sieve that separates bigger molecules from the smaller ones. Smaller molecules move faster across the gel while the bulkier ones are left behind. The mobility of the particles is also controlled by their individual electric charge. Two oppositely charged electrodes that are part of the system pull molecules of towards them on the basis of their charge.

How does it work?

The gel used in gel electrophoresis is usually made of a material called agarose, which is a gelatinous substance extracted from seaweed. This porous gel could be used to separate macromolecules of many different sizes. The gel is submerged in a salt buffer solution in an electrophoresis chamber. Tris-borate-EDTA (TBE) is commonly used as the buffer. Its main function is to control the pH of the system. The chamber has two electrodes - one positive and another negative - at its two ends.

Samples that need to be analyzed are then loaded into tiny wells in the gel with the help of a pipette. Once loading is complete, an electrical current of 50-150 V is applied. Now, charged molecules present in the sample start migrating through the gel towards the electrodes. Negatively charged molecules move towards the positive electrode and positively charged molecules migrate towards the negative electrode.

The speed at which each molecule travels through the gel is called its electrophoretic mobility and is determined mainly by its net charge and size. Strongly charged molecules move faster than weakly charged ones. Smaller molecules run faster leaving behind the larger ones. Thus, strong charge and small size increases a molecule's electrophoretic mobility, while weak charge and large size decreases the mobility of a molecule. When all molecules in a sample are of the same size, the separation will solely be based on their size.

Once the separation is complete, the gel is stained with a dye to reveal the separation bands. Ethidium bromide is a fluorescent dye commonly used in gel electrophoresis. The gel is soaked in a diluted ethidium bromide solution and then placed on a UV transilluminator to visualize the separation bands.

The bands are immediately examined or photographed for future reference, as they will diffuse into the gel over time. The dye can also be loaded into the gel well in advance to track the migration of the molecules as it happens.

Applications of gel electrophoresis

Gel electrophoresis is widely used in the molecular biology and biochemistry labs in areas such as forensic science, conservational biology, and medicine.

Some key applications of the technique are listed below:

In the separation of DNA fragments for DNA fingerprinting to investigate crime scenes

To analyze results of polymerase chain reaction

To analyze genes associated with a particular illness

In DNA profiling for taxonomy studies to distinguish different species

In paternity testing using DNA fingerprinting

In the study of structure and function of proteins

In the analysis of antibiotic resistance

In blotting techniques for analysis of macromolecules

In the study of evolutionary relationships by analyzing genetic similarity among populations or species

References

Further Reading

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Gel electrophoresis is a widely used technique in life science laboratories to separate macromolecules such as DNA, RNA, and proteins. In this technique, molecules are separated based on their size and electric charge. Gel electrophoresis is usually performed in labs to analyze DNA, RNA, or protein samples from various sources.

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This video describes how gel Electrophoresis is used and the principles to it and it also included the application of gel Electrophoresis. It tells us what tools are used during gel Electrophoresis. The function of gel Electrophoresis is to separate either DNA, RNA, and proteins. This tool separates them based on size and electric charge.

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Technique used to separate segments of DNA based on their size using electric current

Targeting gene with a mutation

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The Deadliest Being on Planet Earth – The Bacteriophage

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The Deadliest Being on Planet Earth – The Bacteriophage

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The Deadliest Being on Planet Earth – The Bacteriophage

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The video describes how phages work to kill bacteria. It also describes how we are trying to use phages in place of antibiotics to fight bacteria as a result of superbugs (stemming from our misuse of antibiotics).
First, bacteriophages or phages attach to bacteria by attaching their tail fibers to receptors and using a syringe like structure to puncture the surface. It then squeezes its tail in and injects its genetic information. The bacteria is then forced to manufacture parts for new phages till its filled up with new phages. Lastly, it produces endolysin, which punctures holes into the bacteria. Eventually, the bacteria explodes and releases many new phages.

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Gel electrophoresis | Chemical processes | MCAT | Khan Academy

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Gel electrophoresis is a technique used to separate DNA fragments or other macromolecules, such as RNA and proteins based on their size and charge. Electrophoresis involves running a current through gel containing the molecules of interest. Based on their size and charge, the molecules will travel through the gel in different directions or at different speeds, allowing them to be separated from one another. All DNA molecules have the same amount of charge per mass because of that, gel electrophoresis of DNA fragments separates them based on size only. Using electrophoresis, we can see how many different DNA fragments are present in a sample and how large they are relative to one another. We can also determine the absolute size of a piece of DNA by examining it next to a standard "yardstick" made up of DNA fragments of known sizes

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Transfection is used to  create cells and animals model to for human clinical trials. In transfection there is a study of gene expression and the function of the proteins. Transfection is used to go through the cell membrane, it is procedure called Microinjection. This technique needs precision and experience. There is also electroporation uses high voltage electric shots to bring in nucleic acid to open spaces. Another example is viral infection. There is also chemical based DNA transfection mechanism when there is genetically modified positive charge polymer this lets in nanoparticles inside the cell. Then the nuclear enters the Nucleus. Chemical based transfection is the best option and less costly.

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The transplantation of living cells, tissues or organs from one species to another. This entails the transplantation of an animal's organ to the human body!

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Xenotransplantation: When People Get Animal Parts

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Xenotransplantation is utilizing the organs of an animal (most notable pigs) and transplanting them in human organs that are failing to function properly. Xenotransplantation is most used when the heart valve fails, so scientists replace it when pig valves. Why do scientists use organs of other species instead of human organs? The procedure to transplant human organs to another human is extremely convoluted, seeing as the body is more prone to reject foreign human organs due to the protein human leukocyte antigen. Thus, transplant rejection is likely. Xenotransplantation avoids transplant rejection. Further bioengineering advancements have allowed scientists to develop pigs that do not produce "alpha gal", the antigen responsible for triggering organ rejection, thus minimizing the risks of xenotransplantation.

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Illustration to help remember details in the video:

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Illustration to help remember details in the video:

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How the gene gun works to transform cells with new DNA.

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How the gene gun works to transform cells with new DNA. This is the sixth of a series of seven animations that detail the process of crop genetic engineering.

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The gene gun is a transformation method that uses microscopic gold particles to deliver new genes into a nucleus. Hundreds of gold particles are coated with thousands of copies of the new gene. A marker gene may also be added to aid in determining which cells have been transformed. The coated gold particles are shot at target cells on a petri dish using air pressure. If a gold particle lands in a nucleus, its genes separate from it and are incorporated into the chromosomes. The gene is now part of the cell's DNA. The same gene inserted into different nuclei may show differences in expression.

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Bacteriophage- A type of virus that infects bacteria. It attaches itself to a susceptible bacterium and infects the host cell
Phage therapy- Uses viruses that attack bacteria to treat pathogetic bacterial infection, so it selects certain bacteria to kill it without harming everything else.

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Fighting infection with Phages

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phages are viruses that are meant to kill bacteria. Their shape helps its function. The Phage consists of a head, a sheath and the tail fibers
-tail fiber-- mediates attachment to the bacteria that will be attacked.
sheath--DNA that is stored within a sheath is injected in the bad cell
the phage then makes copies of it self by taking over the DNA and changing it
The new phages then kind of pop from the bacterium that was taken over, which both kills, or resets the life cycle of the phage and also kills the bad cell... All this happens within the "bad or targeted" cell.
In this treatment,,
1. the identity of the pathogen would be identified
2. You would then select the phage, or screen for the phage,
3. This would be found in the phage depository, like a library foe phages

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Antibiotics are creating resistance, so phages are now more favorable

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Separate a single chemical compound from a mixture dissolved in a fluid.

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Column chromatography | Chemical processes | MCAT | Khan Academy

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Column chromatography is used to separate chemical compounds. Drug companies will often use column chromatography to produce large amounts of medicine by a purification process that can be done on a large scale. You can separate chemical compuds with column chromatography based on their polarity

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A way to inject a liquid substances into something at a microscopic level.

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https://www.youtube.com/watch?v=R2OVe1qx444

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For this video it is showing the process that is taken when doing a microinjection.

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DNA microinjection methods are used to transfer genes between animals and are a popular technique for creating transgenic organisms, particularly mammals.

An Explanation of DNA

DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. Nearly every cell in a person's body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can be found in the mitochondria, called mitochondrial DNA or mtDNA.

The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99% of those bases are the same in all people.

The sequence of these bases determines the information available for building and maintaining an organism. This system is similar to the way in which letters of the alphabet appear in a certain order to form words and sentences.

Nucleotides

DNA bases pair up with each other (i.e., A with T, and C with G) to form units called base pairs. Each base is attached to a sugar molecule and a phosphate molecule. When the three are put together (a base, a sugar, and a phosphate) it becomes a nucleotide.

Nucleotides are arranged in two long strands that form a spiral called a double helix. The structure of the double helix is somewhat like a ladder, with the base pairs forming the ladder's rungs and the sugar and phosphate molecules forming the vertical sidepieces of the ladder.

An important property of DNA is that it can replicate, or make copies of itself. Each strand of DNA in the double helix can serve as a pattern for duplicating the sequence of bases. This is critical when cells divide because each new cell needs to have an exact copy of the DNA from the old cell.

The Process of DNA Microinjection

In DNA microinjection, also known as pronuclear microinjection, a very fine glass pipette is used to manually inject DNA from one organism into the eggs of another.

The best time for injection is early after fertilization when the ova have two pronuclei. When the two pronuclei fuse to form a single nucleus, the injected DNA may or may not be taken up.

In mice, the fertilized eggs are harvested from a female. The DNA is then microinjected into the eggs, and the eggs are re-implanted into a pseudopregnant female mouse (the ovum is transferred into the oviduct of a recipient female, or foster mother, that has been induced by mating with a vasectomized male).

Results of Microinjection

The University of California (San Diego) Moore's Cancer Center Research and Training Center reports over 80% survival rate for transgenic mouse implants.

The Transgenic Mouse Facility at the University of California San Diego (Irvine) reports an estimated success rate of 10% to 15% based on experiments with mice testing positive for transgenes.

If the DNA is incorporated into the genome, it is done so randomly. Because of this, there is always a chance the gene insert will not be expressed (the cell won't produce the molecules it needs) by the GMO, or may even interfere with the expression of another gene on the chromosome.

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DNA Is Inserted into Cells Using Microinjections

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DNA microinjection methods are used to transfer genes between animals and are a popular technique for creating transgenic organisms, particularly mammals. DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. Nearly every cell in a person's body has the same DNA.

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In this article I learned that a microinjection is a very fine glass pipette used to inject DNA of an animal into another animals eggs. They usually inject the DNA when  the animal is early after fertilization, sometimes the DNA will be expressed but at other times it will not. DNA microinjection is used to transfer genes between animals also known as transgenic organisms which are mostly done on mammals .

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A picture I found that helps me remember the key points of the article

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A picture I found that helps me remember the key points of the article

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Gel electrophoresis is used to separate molecules based on how big they are in size. The machine has an electrical charge

running through a gel which is made of agarose. Agarose is a polysaccharide polymer. Agarose gel lets the DNA molecules travel within it. One end of the gel has  holes called wells, where the DNA is placed into the area of the gel where the wells are negatively charged, and the area of the gel is positively charged. If it's negatively charged, it's going to travel to the positive side.

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The process of transplanting organs or tissues between members of different species.

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Xenotransplantation is the procedure of transplanting organs, tissues, or cells from one species to another; in most cases animals to humans. The safest animal to take organs and cells from for humans is pigs. Their organs are the most similar in size and have the smallest risk of infecion after the transplant. The cells in pigs have actually helped people fight against diseases like parkinsons. Throughout the 1900's multiple attemps at xenotransplantation had started taking place starting with monkeys but all failed up until the 2000's after a ban was lifted from practicing this procedure due to a disease in pigs going around.

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Picture to keep in mind of the key points

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Picture to keep in mind of the key points

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PCR is like a printer for DNA. It provides more copies of little DNA segment. Why do we do this? It can be used to help solve a crime scene, and or even help diagnose a disease.cYou need a little segment of DNA, a buffer, primer, DNA polymerase, & nucleotides to do the PCR procedure. The first step is to denaturation. You can do this with heat. The heat will separate the two DNA strands. The next step is annealing, it's going to cool down the DNA strands to allow the primers to bind to the specific segment of DNA that are going to be copied (or amplify). The next step is making more copies of DNA, called DNA synthesis. That's when the DNA polymerase will work on both the DNA strands. You can repeat= this over and over again!!

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The Deadliest Being on Planet Earth – The Bacteriophage

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(Bacteriophage for short phage)Bacteriophage is a virus that is not alive or dead. The head of it contains the Phage DNA/virus this sits on a tail with legs. Phage kills bacteria. They need host to be able to survive. Antibiotics were created to kill virus then but as time passed bacteria became immune. now being called a super bug which is immune to antibiotics. But Phage is what can save us from those super bugs. Phage's will only attack bacteria. If bacteria became resist to Phages it would have to give up resist to antibiotics. Basiclly Phages could as millions of lives!

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Zinc-finger nucleases are artificial restriction enzymes generated by fusing a zinc finger DNA-binding domain to a DNA-cleavage domain. Zinc finger domains can be engineered to target specific desired DNA sequences and this enables zinc-finger nucleases to target unique sequences within complex genomes.  The results are also permanent and thus inheritable which bring up the usual ethical dilemma of "super babies" and "playing god".

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Zinc-finger nucleases are artificial restriction enzymes generated by fusing a zinc finger DNA-binding domain to a DNA-cleavage domain. Zinc finger domains can be engineered to target specific desired DNA sequences and this enables zinc-finger nucleases to target unique sequences within complex genomes.  The results are also permanent and thus inheritable which bring up the usual ethical dilemma of "super babies" and "playing god".

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This video goes through the procedure of prepping a microinjector,  using a microinjector (specifically injecting morpholino into embryos), and what Microinjection looks like through a microscope. Microinjection uses a micropipette to inject a substance into a cell or any other intracellular space. It can be used to inject embryos, deliver antibodies, etc.

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A picture I found that helps me remember key points of the video or article

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A picture I found that helps me remember key points of the video or article

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What is Gel Electrophoresis | Don't Memorise

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Gel electrophoresis is a technique used to separate DNA fragments or other macromolecules, such as RNA and proteins based on their size and charge. Electrophoresis involves running a current through gel containing the molecules of interest. Based on their size and charge, the molecules will travel through the gel in different directions or at different speeds, allowing them to be separated from one another. All DNA molecules have the same amount of charge per mass because of that, gel electrophoresis of DNA fragments separates them based on size only. Using electrophoresis, we can see how many different DNA fragments are present in a sample and how large they are relative to one another. We can also determine the absolute size of a piece of DNA by examining it next to a standard "yardstick" made up of DNA fragments of known sizes

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Gel electrophoresis is a technique used to separate DNA fragments or other macromolecules, such as RNA and proteins based on their size and charge. Electrophoresis involves running a current through gel containing the molecules of interest. Based on their size and charge, the molecules will travel through the gel in different directions or at different speeds, allowing them to be separated from one another. All DNA molecules have the same amount of charge per mass because of that, gel electrophoresis of DNA fragments separates them based on size only. Using electrophoresis, we can see how many different DNA fragments are present in a sample and how large they are relative to one another. We can also determine the absolute size of a piece of DNA by examining it next to a standard "yardstick" made up of DNA fragments of known sizes

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Gel electrophoresis is used to separate the same DNA fragments as RNA. Electrophoresis involves passing an electric current through a gel that contains a target molecule. Based on the size and charge of the molecules, the molecules pass through the gel in different directions or at different speeds and separate from each other. Since all DNA molecules have the same mass and charge, gel electrophoresis of DNA fragments is only size-separated. You can use electrophoresis to determine the number of DNA fragments present in a sample and the size between them. We are also composed of DNA fragments of known sizes and can confirm the absolute size of standard DNA fragments.

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Gel electrophoresis is used to separate the same DNA fragments as RNA. Electrophoresis involves passing an electric current through a gel that contains a target molecule. Based on the size and charge of the molecules, the molecules pass through the gel in different directions or at different speeds and separate from each other. Since all DNA molecules have the same mass and charge, gel electrophoresis of DNA fragments is only size-separated. You can use electrophoresis to determine the number of DNA fragments present in a sample and the size between them. We are also composed of DNA fragments of known sizes and can confirm the absolute size of standard DNA fragments.

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Pcr is a technique for producing millions, if not billions, of copies of DNA samples. This is done by taking a little piece of DNA and amplifying it in order to examine it.

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Flow Cytometry is a technique which is used in order to measure the physical and chemical properties of a population of particular cells. Within this process, a sample of cells is injected into a flow cytometer instrument in order to undergo analysis.