10 Things you need to know about Replication

Watson and Crick published their hypothesis for how DNA replicates in a second paper in 1958. Then, Matthew Meselson and Franklin Stahl devised a clever experiment that suggested that DNA replication is semiconservative. This experiment was growing E. coli bacteria in a nutrient medium that was rich in heavy isopotes of nitrogen then changing this medium that was rich in light isotope of nitrogen. They used density gradient centrifugation to analyze the density of DNA (cesium chloride solution) and they found out that layer of intermediate DNA was kept as generations had passed. In other words, DNA replication is semiconservative, but not conservative.

Prokaryotic cells and eukaryotic cells have the same semiconservative pattern of DNA replication. The only difference is that prokaryotic cells usually have only one replication origin while eukaryotic cells have multiple origins of replication. 

Replication Fork: the region where the enzymes replication a DNA molecule are bound to untwisted (region where helicase is attached)

Replication Bubble: the region where two replication forks are in close proximity to each other, oriducing a bubble in the replicating DNA.

Steps of DNA Replication

Initiation:

1. DNA helicase: the enzyme that unwinds double-helical DNA by disrupting hydrogen bonds
2. SS binding protein or SSBs(Single-Stranded binding protein): a protein that keeps separated strands of DNA apart/ keeps away from annealing
3. DNA gyrase: the bacterial enzyme that relieves the tension produced by the unwinding of DNA during replication
4. DNA primase: produce primers(a sequence of 10 to 60 RNA bases) which signals the DNA polimerase 3 

Elongation:

1. DNA polymerase 3: 

• recognizes RNA primers
• elongate new DNA strand 5' to 3' direction
• leading strand towards the fork; lagging strand (or Okazaki fragments) away from the fork

Termination:

1. DNA polymerase 1: an enzyme that replaces RNA primers with appropriate deoxyribonucleotides; proof reads and cut out a mistaken nucleotides acting as exonuclease.
2. DNA ligase: an enzyme that joins DNA fragments together by catalyzing the formation of a bond between the 3' hydroxyl group and a 5' phosphate group on the sugar-phosphate backbones.

Important Facts to know

• Deoxyribonucleoside triphosphates are added by DNA polymerase 3 then two phosphates are removed and reclycled again.
• New strands are formed starting from the bubble.

Example Discussion

On Wednesdays each group has to present their thoughts about their article. Mr Chung showed us an example of how it should be like when we present it. His presentation started with an overview. It included: 

1) Itinerary
2) Questions
3) Hook in the form of an activity/game/media (he had both a video and an activity)
4) 5 minute quiz
5) 15-20 minute discussion on findings, its usefulness and future reserach

The molecule basis of Inheritance

1) The search for genetic material lead to DNA

Until 1940s, the great heterogeneity and specificity of function of proteins seemed to indicate that proteins were the genetic material. Then, T.H. Morgan showed that genes are located on chromosomes, the two constituents of chromosomes - proteins and DNA - were the candidates for the genetic material. However, it was not consistent with experiments with microorganisms like bacteria and viruses.T.H. Morgan arrived with this idea through the comparison of fruit flies' phenotypes and research done by Mendel.

The discovery of genetic role of DNA began with research by Frederick Griffth in 1928. He studied Treptococcus pnewmoniae, a bacterium that is responsible for pneumonia in mammals.In an experiment, he mixed heat-killed Smooth strain (harmful) with live Rough (harmless) strain bacteria and injected into a mouse. Logically, the mouse should live because harmful bacteria is removed and harmless bacteria is injected; however, the mouse is dead due to phenotype and genotype change due to the assimilation of a foreign substance (DNA). This phenomenon is called transformation.

Living S cells are found in blood sample from dead mouse after injected by heat-killed S cells mixed with living R cells.

Hershey and Chase did experiment on T2 Phage, a virus.  DNA and protein were stained respectively, and DNA of virus was confirmed to be found inside infected cell, not protein. A virus infects a host cell and takes over the cell's metabolic machinery to replicate itself. Viruses are not considered organisms.

By 1847, Erwin Chargaff had developed a seres of rules based on a survey of DNA composition in organisms. DNA consists of nitrogenous base, deoxyribose, and a phosphate group. The base could be adenine (A), thymine (T), guanine (G), or cytosine (C). Chargaff noted that DNA composition varies from species to species. 

Chargaff's rules: (%T=%A) & (%G=%C)

2) Watson and cRick discovered the double helix by building models to conform to X-ray data

Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study the structure of DNA. X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and diffracts into many specific directions. The diffraction pattern can be used to deduce the three-dimensional shape of molecules.Franklin did not receive proper recognition because she was female and was dead from cancer (overdose of X-Ray).

James Watson and Francis Crick learned from Franklin's study that DNA was helical in shape and he deduced the width of the helix and the spacing of bases. The nitrogenous bases are paired in specific combiantions: A and T & G and C. A and G are purine and C and T are pyrimidine. A purine-purine pair would be too wide and a pyrimidine-pyrimidine paring would be too narrow. Thus, Watson and Crick came up with a pyrimidine-purine paring which is consistent with X-ray data.There are minor groups and major groups in DNA.  Minor are shorter connections between bases, whereas major have longer connections between bases. Hydrogen bonds connected two strands together.  Adenine and thymine would only form double bonds, and guanine and cytosine would only form triple bonds. This explained Chargaff's rules. Watson and Crick began to work on a model of DNA with two strands, the double helix. The linear sequence of the four bases can be varied in countless ways.

Captain Relish's murder case project

I was supposed to write this yesterday but I was too busy working on this project.
So basically, Mr. Chung told us the day before that he would bring a professor from U of T and his name was Professor R... But the next day Mr. Chung said he was murdered on the way to this school...and then Mr. Chung wanted us to find out who the killer is... WOW a project already?!?! Anyway, it involved some grade 11 biology such as karyotypes, pedigrees, and chromosome disorders. And it also had DNA sequencing... I had no idea where to start from for this project but now I got it!

Ideas for the science fair ISP

I thought of some ideas...
1) How are tears formed?
2) Why do humans cough?
3) Why do people get dizzy after getting up?
4) Why do people close their eyes when sneezing?
5) When your throat is itching scratch the back part of your ear...
6) Why does the right ear has a better hearing than the left ear to the fast tempoed conversation?
7) Sexual imagination can delay men's urinary signal

... that's about it for now

First Day

It was our first day of the second semester and I am really looking forward to have a great learning time in Mr. Chung's Biology class.

Today's task was to sign up at moodle.ayjscience.ca, read and choose the article to present, and make a blog which I managed to finish :p

That is all