Studying Expressions

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Part 2 - Studying Expression and Function of Gene

Procedures: Gel Electrophoresis, Southern Blotting, Microarrays

Gel Electrophoresis


Describe It

Clear liquid(DNA and Restriction Enzyme), Chambered plastic (wells), Sticky globs (gel)

Analyze It

Parts: Gel, Test tubes, Glass plates, Power source, DNA samples, Restriction Enzyme
  • Gel electrophoresis separates macromolecules on the basis of their rate of movement through a gel in an electric feild. How far a DNA molecule travels while the current is on is inversely proportional to its length.
  1. Each sample, a mixture of DNA molecules, is placed in a separate well near one end of a thin slab of gel, The gel is supported by glass plates, bathed in an water solution, and has electrodes attached to each end.
  2. When the current is turned on, the negatively charged DNA molecules move toward the positive electrode, with shorter molecules moving faster than the longer ones.
  3. After the current is turned off, a DNA- binding dye is added
  4. This dye attaches to the DNA.
  5. Then wash the gel, removing all the dye that isn't bonded to the DNA, and place the remaining under a light and the DNA will glow.

Apply It

  • Gel electrophoresis is used for separating nucleic acids or proteins that differ in size, electrical charge, or other physical properties.
  1. This is very helpful for scientists to learn about the physical properties of DNA.
  2. Helps determine size/length of strand.

Synthesize It

  • This makes me think of a bus going through the forest vs. a running person because they can go faster through the trees.

Argue for or Against it

I am for this because I believe that it is a very useful way to help scientists with their research. This is something that can be important in many different types of experiments.

Southern Blotting Southern_Blot.jpg


Describe It

tall, sticky glob, colorful (after probe is attached)

Analyze It


Parts: DNA samples, tubes, gel, probe, restriction enzyme, sponge, weight, sponge, paper towels, alkaline solution,film

  • Developed by British biochemist Edwin Southern, combines gel electrophoresis and nucleic acid hybridization, allows us to detect just hose bands that include parts of a certain globin gene.

  1. Prepare the restriction fragments: Each DNA sample is mixed with the same restriction enzyme. Digestion of each sample yields a mixture of thousands of restriction enzymes.
  2. Gel electrophoresis: The restriction fragments in each sample are separated by electrophoresis, forming a characteristic patter of bands.
  3. Blotting: With the gel arranged over a sponge in alkaline solution and under paper towels and weight, capillary action pulls the alkaline solution upward through the gel, transferring the DNA to a nitrocellulose membrane, producing the blot; the DNA is denatured in the process. The single strands of DNA struck to the nitrocellulose are positioned in bands corresponding to those on the gel.
  4. Hybridization with radioactive probe: The nitrocellulose blot is exposed to a solution containing a radioactively labeled probe. Probe molecules attach by base-pairing to any restriction fragments containing a part of a gene.
  5. Probe detection: A sheet of photographic film is laid over the blot. The radioactivity in the bound probe exposes the film to form an image corresponding to those bands containing DNA that base-paired with the probe.

Apply It


  • Researchers can detect specific nucleotide sequences within a complex DNA sample.
  • Southern Blotting is useful for comparing the restriction fragments produced from different samples of genomic DNA.

  1. Can be used to identify heterozygous carries of the sickle-cell allele.
  2. Can be used to identify those who have sickle-cell disease.
  3. Can be used to determine individuals who have who don't carry the trait.

Synthesize It


  • This makes me think of punnet squares. This is a way to find out what the alleles of individuals are that can be put into the squares.

Argue for or Against it

I am for this because it is very helpful to geneticists who are trying to determine the genotypes of individuals. This is also helpful for parents who want to know the probability of passing a disease onto their child.


Microarrays

microarray.jpg

Describe It

Tube, clear liquid

Analyze It


Parts: Sample in which to isolate mRNA, cDNA, Microscope, Slide

  1. Isolate mRNA
  2. Make cDNA by reverse transcription, using fluorescently labeled nucleotides.
  3. Apply the cDNA mixture to a microarray, a microscope slide on which copies of single-stranded DNA fragments from the organism's genes are fixed, a different gene in each spot. The cDNA hybridizes with any complementary DNA on the microarray.

Apply It


  • Makes genome-wide expression studies possible

  1. Scientists can then use microarrays to assess gene expression in a single sample or to compare gene expression in two different types of samples, such as two different tissue samples.
  2. This is also useful to be able to look at the expression of thousands of genes at once, which causes scientists to be able to easily examine gene expression

Synthesize It


  • Microarrays make me think of charts. Scientists use microarrays to compare and contrast different genes.

Argue for or Against it

I am for this because it is very helpful for scientists to be able to use to easily compare and contrast gene expressions.