BIOL 306-Gentics Notes
[A continuation of last week’s notes and this week’s notes. Includes chapter 10 and some of chapter 11 from the book and PowerPoints.]
Chapter 10 ppt notes 09/14/18
*important to note: the Hopi culture traditionally treated albinos with respect, they were looked at as being special and were awarded. The Hopi tribe traditionally did farm work, therefore, albino males did not have to work and spent most of their times in the village so they would not be harmed by the sun. By spending most of their time in the village, this gave them a mating advantage allowing them to reproduce more. Due to the way that the Hopi tribe viewed albinism, as a purity in the village, they allowed the increase in the allele frequency of the gene.
Hershey and Chase Experiment (slide image 11 and 12) We also discuss several other topics like What does convergence mean?
Question: does the DNA or Protein part of the Phage serve as the genetic material and is transmitted to the phage progeny?
1. Using T2 Phage, which contains both DNA and Protein, infect E.Coli that has been grown in the medium containing 35S. If you want to learn more check out What is an atomic orbital?
2. 35S is then taken up in the Phage protein section, which contains S but not P.
3. Phages with 35S then went on to infect unlabeled E.Coli 4. The mixture is then placed in a blender where the protein coats are sheared off.
5. The protein is then separated from the cells by centrifuging. 6. After being centrifuged, 35S is able to be recovered from the fluid containing the virus coats.
7. There was no radioactivity detected, this means that protein has not been transmitted to the progeny phages.
1. Using E. coli, they infect E.coli grown in medium containing 32P. 2. 32P is then taken up in the phage DNA, which contains P but not S in this circumstance.
3. Phages that have 32P will infect unlabeled E.coli.
4. Protein coats are then sheared off in the blender.
5. The proteins are then separated from the cells by centrifuging. 6. After being centrifuged, the infected bacteria form a pellet that contains 32P at the bottom of the tube.
7. There is radioactivity in the progeny phages, this means that DNA has been transmitted to the progeny phages.Don't forget about the age old question of Who did beowulf rescue?
Conclusion: DNA is the genetic material in bacteriophages, not protein. Three Competing Models of Replication (slide image 13) Don't forget about the age old question of How does marketing create value?
DNA is composed of a double helix/strands, a feature of having two strands is that DNA should be able to replicate or encode another strand.
1. Semiconservative Replication: produces two copies that each contain one of the original strands and one new strand.
2. Conservative Replication: this produces two original template DNA strands together in a double helix and would also produce a copy that is composed of two new strands that contain all of the new DNA base pairs.
3. Dispersive Replication: this form of replications uses the original DNA chain and breaks it into pieces that are then recombined in a random fashion with the new strands.
The Meselson-Stahl Experiment
∙ In 1958: Meselson and Stahl used cesium chloride (CsCl) centrifugation to test the “Three Competing Models of Replication” for DNA. ∙ Centrifugation: the process by which a mixture is separated through spinning REALLY FAST. This process is able to separate molecule with slightly different molecular weights. Don't forget about the age old question of Why is directly observing electrons impossible?
Don't forget about the age old question of What are the three categories of managerial roles according to mintzberg?
∙ Meselson and Stahl began their experiment by growing E.coli in a medium containing heavy nitrogen, also known as N15, for many generations.
∙ Once all of the bacterial cells in the culture had DNA that only contained heavy nitrogen, they transferred the bacteria to medium containing N14.
∙ After a single round of replication, the DNA of an aliquot of cells was isolated and centrifuged in order to determine its density.
∙ The same step was repeated after the successive replication cycles. ∙ IMAGE ON SLIDE 20 explains more and describes the results. ∙ Conservative replication is wrong because the results of the first cycle
contain two bands while the actual results from the Meselson-Stahl experiment prove that there should only be one band.
∙ Dispersive Replication is able to be eliminated because the random mixture of DNA sequences. If this was so, the Meselson-Stahl experiment would have shown a smear in the second cycle rather than clear bands.
∙ Semiconservative replication is the most probable method of DNA replication since the first and second cycle outcomes correlate with Meselson-Stahl experiment results.
Rolling Circle Replication slide image 22 : A process in which there is unidirectional nucleic acid replication, this can very quickly synthesize multiple copies of circular molecules of DNA or RNA. For example: plasmids, the genomes of bacteriophages, and the circular RNA genome of viroids.
*ALL genetic information is encoded in the structures of DNA or RNA
Image 10.7 Slide 24 : This is an X-ray diffraction image of DNA. 1. X-rays are aimed at crystals of a substance which are then diffracted. 2. The spacing of the atoms within the crystal enables us to determine
the diffraction pattern, this appears as spots on a photographic film. 3. The diffraction pattern provides information about the structure of the molecule.
*Watson and Crick used Rosalind Franklin’s X-ray image of DNA, as well as other means, to determine the three-dimensional structure of DNA.
*In most organism’s DNA carries the genetic information, while in some organism’s RNA carries the genetic information.
Tobacco Mosaic Virus image 10.9 slide 27
Question: What substances, RNA or Protein, carries the genetic material in tobacco mosaic virus (TMV)?
1. Type A TMV and Type B TMV are both degraded.
2. This allows them to yield RNA and coat proteins.
3. Then RNA of one type is mixed with the protein of the other type, for both.
4. This creates hybrid viruses.
5. Use the hybrid viruses to infect tobacco.
6. The type of RNA in the hybrid parent TMV determines the RNA and protein of progeny viruses.
Conclusion: RNA is the genetic material of TMV.
The Primary Structure of DNA
DNA consists of two complementary and antiparallel nucleotide strands that form a double helix. DNA- Deoxyribonucleic acid- has three parts: a phosphate, sugar, and a base. There are purine and pyrimidine bases.
Purine: adenine and guanine.
Pyrimidine: cytosine, thymine (present in DNA), and uracil (present in RNA). Phosphates are negatively charged, while histones are positively charged.
Table 10.2 Names of DNA bases, nucleotides, and nucleosides (image slide 33)
The Secondary Structure of DNA
Double Helix of DNA: two strands that wrap around each other, can be compared to a twisted ladder.
The backbone of DNA is formed through phosphodiester bonds.
Complementary bas pairing: Adenine pairs with thymine, while guanine pairs with cytosine.
The nucleotides in a base pair are complementary, therefore their shapes allow them to bond to each other with hydrogen bonds. Adenine and thymine pair forms two hydrogen bonds, while cytosine and guanine pair forms three hydrogen bonds.
Hydrogen bonding: the hydrogen bonding between complementary base pairs is what holds the two strands of DNA together.
The strands of DNA run in opposite directions meaning they are antiparallel.
The antiparallel nature of DNA refers to: the opposite direction of the two strands of nucleotides.
DNA Backbone: consists of deoxyribose sugar linked by phosphate Differences between RNA and DNA
*There are many differences but here are a few:
DNA consists of Deoxyribose sugar (no oxygen), while RNA consists of Ribose sugar (has oxygen, OH group).
In RNA uracil replaces thymine as the complementary base for adenine.
3-D structure identified by Watson and Crick image 10.15
B-DNA: is the most common double helical structure found in nature. The double helix is known to be right-handed and has about 10-10.5 base pairs per turn.
*important to note Professor skipped slides 41-49, still open to be reviewed online.
Chapter 10 Book notes
Carried out the experiment with the mouse testing with the smooth and rough strain of pneumococcus. (testing for pneumonia)
Chargaff’s rule: DNA from any cell should have a 1:1 ratio of pyrimidine and purine bases. A=T, G=C
Avery, Macleod, and McCarthy
Went off of Griffiths findings and conducted a mouse experiment of their own. Tested whether genetic material was contained in RNA, DNA, or Proteins. Concluded that genetic material is in DNA. (used enzymes)
A geo-biophysicist, one of the first to study DNA in a more detailed manner. First to take an X-ray image of DNA.
Watson and Crick
Used Rosalind Franklin’s X-ray image of DNA to determine that the 3D structure of DNA. Discovered that DNA has a double helix.
Hershey and Chase
Conducted an experiment to
determine whether DNA or Protein carries the genetic material. Used 35S and 32P, found 32P present concluding that DNA is the genetic material.
Fraenkal-Conrat and Singer
Conducted the Tobacco Mosaic Virus Experiment. Is RNA or Protein for genetic material? Switched the coats and the new generation went back to normal concluded that RNA is for
the genetic material.
Meselson and Stahl
They were testing the three
competing models of DNA
replication. Grew E.coli in N15 and N14. The first and second cycle canceled out conservative
replication and dispersive
replication. The results of the experiment correlated most with semi-conservative replication and that has been determined to be the way that DNA replicates.
∙ 10.1 Genetic Material Possesses Several Key Characteristics o Genetic material must contain complex information
Because it is capable of storing large amounts of
o Genetic material must replicate faithfully
To make an animal, a cell must undergo billions of cell
divisions, and the genetic instructions must be accurately
transmitted to descendant cells
Genetic instructions must be copied with fidelity
o Genetic material must encode the phenotype
Genetic material (genotype) must have the capacity to be expressed as a phenotype to code for traits
The product is often a protein or RNA molecule
o Genetic material must have the capacity to vary
Genetic info must have the ability to vary because different species, and even individual members of the same species, differ in the genetic makeup.
∙ 10.2 All Genetic Information is Encoded in the
Structure of DNA or RNA
o Johann Miescher established that the nuclear material contained a novel substance that was slightly acidic and high in phosphorus
Now know it was protein and DNA
He called it nuclein and later named nucleic acid by his students
o By 1887, researchers concluded that the basis of heredity lies in the nucleus
o Chromatin was shown to consist of nucleic acid and proteins but which was actually the genetic info, that wa not clear
o Kossel carried out an experiment and determined DNA contains four nitrogenous bases: adenine, cytosine, guanine, and thymine
o Phoebus Levene discovered that DNA consists of a large number of linked, repeating units, called nucleotides (consisting of a sugar, phosphate and a base)
But he thought that the bases were in a fixed order therefore not variable enough to make it the genetic material
o Erwin Chargaff found that the amount of A=T and C=G Also that A/T and C/G=1
o A huge step to labeling DNA as the genetic info was the discovery of transformation
Observed with Fred Griffith who studied the smooth and rough pneumoniae
o Avery, Colin MacLeod, and Maclyn McCarty isolated the transforming substance and matched it to DNA or Protein by using DNase, Protease, and RNase.
o Hershey-Chase then used phosphate and sulfur isotopes and figured out that the genetic material is DNA
o Watson and Crick used all these previous experiments and Franklin’s x-ray diffraction to back up that DNA was the genetic material
o BUT RNA also is genetic material for viruses.
Fraenkel-Conrat and Singer worked with tobacco mosaic virus (infected tobacco plants)
Found that the genetic material was in the RNA not the Protein
∙ 10.3 DNA Consists of Two Complementary and
Antiparallel Nucleotide Strands That Form a Double Helix
o DNA is a polymer, that is a chain made up of many repeating units linked together (repeated units of DNA= nucleotides)
o Sugar of nucleic acids=pentose sugars (five carbon atoms)
o The sugars of DNA is deoxyribose (does not have an OH on the 2 prime) and that of RNA is ribose (has an OH on the 2 prime)
o A sugar (ribose or deoxyribose) + a base (A,C,T,G,U) = nucleoside
Adenine and Guanine are purines (Pure As Gold) (two rings) Cytosine, Thymine, and Uracil are all pyrimidines (one ring)
o The nucleotides are connected by covalent bonds and these bonds are called phosphodiester linkages (strong covalent bonds)
A series of nucleotides linked this way gives a
The backbone is a sugar phosphate backbone
o DNA is a double helix, the strands are lined up in opposite direction therefore antiparallel, the two strands are also not identical but complementary DNA strands
∙ 10.4 Special Structures Can Form in DNA and RNA
o Single strands of nucleotides form a hairpin, they can form a stem shape or a secondary complex structure.
o Three stranded (triples) structures are called H-DNA, some of the DNA unwinds and a single polynucleotide strand from one part of the molecule pairs with double-stranded DNA from another part of the molecule
o DNA can be modified:
DNA methylation, the process of adding CH3 to certain positions on the nitrogenous bases
Bacterial DNA is often methylated to distinguish from
Example is 5-methylcytosine
Chapter 11 ppt Notes 9/18/18
*DNA IS NOT STIFF OR STATIC*
Some DNA is circular, linear, or has a somewhat U shape in it. DNA is located in the nucleus of the cell.
DNA is coiled together to form rope-like chromosomes.
In order to make RNA or carry out DNA replication the chromosomes must untie.
*When a person becomes sunburnt a: Mutation, repair, and restructure has occurred.
DNA must be tightly packed to fit into a cell.
Supercoiling: DNA supercoiling is when there is over- and or under- winding of a DNA strand.
1. Positive supercoiling: this occurs when the right-handed, double helical conformation of DNA is twisted very tightly until the helix starts to knot.
2. Negative supercoiling: this is the uncoiling of DNA strands performed in a left-handed direction.
3. Topoisomerase: this is the enzyme that adds coils in positive supercoiling while removing turns in negative supercoiling.
*Important note: early childhood stress is linked to shorter telomeres.
Telomeres, Aging, and Cancer: Telomeres have been known to be linked with aging and cancer.
Telomere: a telomere is the structure at the end of a chromosome. Telomeres shorten with age, the rate of telomere shortening may indicate the pace of age.
Telomere length is not only important when dealing with age, but is also important for chromosome stability, cell longevity, and reproductive success.
Telomerase: an enzyme that functions by adding nucleotides to telomeres. This is increased in cancer cells.
Telomerase inactivity tends to be associated with the normal aging of cells.
Telomerase is also active in germ-line cells and a few stem cells in eukaryotes.
A cell with no telomerase activity, consequently, has a limited life span (on average 30-50 cell divisions). Differentiated somatic cells and cells in culture are such cells.
Werner Syndrome: (aka adult progeria) is a rare, autosomal recessive disorder that is hereditary. Is characterized by premature aging and an increased risk of cancer as well as other diseases. Named after the German scientist Otto Werner, the first to describe it in his doctoral thesis.
Someone who has Werner Syndrome does not go through the usual growth spurt during their teenage years, they tend to be shorter than others.
Cause: a mutation in RECQL2 – a gene that encodes a helicase that is required for telomerase activity.
Damage to Mitochondrial DNA: also associated with aging
Tend to appear in middle age or later
Those with the mutations start life with decreased oxidative phosphorylation capacity.
Oxidative Phosphorylation Capacity: Is at its maximum when born, declines with age.
Mechanism of damage is unknown
As of now *September 2018: stress has been known to be correlated with increases mtDNA in circulating blood.