10 things about replication

Overview:
1. The replication process is semiconservative.
2. Hydrogen bonds between complementary bases break.
3. DNA helix unzip. Replication bubbles are formed.

4. Each single-stranded DNA sequence acts as a guiding pattern for producing a complementary DNA strand (template).
5. Because the 2 strands in a double helix are antiparallel, one goes in the 5' to 3' direction while the other goes in the 3' to 5' direction.
6. However, DNA only elongates in the 5' to 3' direction.
7. The leading strand elongates in the 5' to 3' direction towards the replication fork.
8. Okazaki fragments are formed on the lagging strand. They elongate in the 5' to 3' direction, away from the replication fork.
9. THE TOP STRAND IS NOT NECESSARILY THE LEADING STRAND.

10. The stages are initiation, elongation, termination, and repair.

The stages:
i. Initiation - separating the DNA strands
Helicase unwinds the double-stranded DNA by breaking the hydrogen bonds.
Replication bubbles are formed.
Single-stranded binding proteins stabilize the single-stranded DNA.
Gyrase release tension brought by unwinding of DNA strands by cutting and resealing the strands.
RNA primase produce primers, which signal the release of DNA polymerase III.
RNA primers are recognized by DNA polymerase III. They anneal to the DNA template.

ii. Elongation - Building the complementary strands
RNA primers act as starting points of replication.
DNA polymerase III recognize the RNA primers. They add nucleotides to the template.
Nucleotides are continuously being added to the 3' end of the elongating strand. The strand elongates in the 5' to 3' direction.
The leading strand elongates towards the replication fork.
Okazaki fragments are formed on the lagging strand.


iii. Termination - Joining the DNA
DNA polymerase I replace RNA primers with DNA.
DNA ligase join the gaps in DNA.
Okazaki fragments are bonded by phosphodiester bonds.

iv. Repair - Proof-reading the DNA
DNA polymerase I and III act as exonuclease which proof-read the complenentary strand.
The strands automatically twist into a double helix.

Vocabs.

1. Cytosol
A semi-liquid found in the cytoplasm that contains microfillaments of the cytoskeleton (the supporting structure). It is where most cellular metabolism occurs.


2. Germ cells
Reproductive cells.

3. Diploid
A cell that contains 2 pairs of chromosomes (2n). For humans (under normal conditions), n=23, so 2n=46.

4. Hapoid
A cell that contains 1 complete set of chromosomes (n). For humans (under normal conditions), n=23.

5. Cytokinesis
A process in mitosis. It takes place in telophase. A cleavage furrow is formed at the center of the cell. The cell is then divided into 2 identical cells.
http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120073/bio14.swf::Mitosis%20and%20Cytokinesis

6. Histones
Proteins that are responsible for the structure of the chromotin and packaging of DNA into chromosomes.


7. Cell plates
A structure that is developed at the center of the cell during cytokinesis. It separates the chromosomes.


8. Chromatin
A mass that contains DNA and protein that will condense to form chromosomes during mitosis.


9. Sister chromatids
Single-stranded chromosomes that are identical and are connected by a centromere.


10. Homologs
One of a pair of chromosomes. In a pair of chromosomes, one homolog is from father and the other is from mother.

11. mRNA
Responsible for protein synthesis. It is attached to the DNA template during transcription. During translation, it binds to ribosome (sugar). At the same time, it serves as the binding site for tRNA. tRNA attaches 3 nucleotides to the corresponding sites on the mRNA.
http://www.youtube.com/watch?v=NJxobgkPEAo&feature=related

12. Prokaryotes
-ancient
-do not have cell nuclei
-do not have organelles surrounded by membranes
-DNA is concentrated in the nucleoid, but no membrane separates this part from the rest of the cell

13. Eukaryotes
-contains a cell nuclei
-have organelles surrounded by membranes
-some contains chloroplasts
-DNA is concentrated in the nucleus

Geneticists

1. T. H. Morgan
-observed eye colors of fruit flies

Cross	Outcome
	Expected Phenotypes	Observed Phenotypes
P1 Red ♀ × P1 White ♂	F1 = All Red	F1 = All Red*
F1 Red ♀ × F1 Red ♂	75% Red ♀ and ♂ 25% White ♀ and ♂	50% Red ♀ 25% Red ♂ 25% White ♂

Reference: http://www.nature.com/scitable/topicpage/thomas-hunt-morgan-and-sex-linkage-452
-all white-eyed flies were males
-the white-eye allele is recessive and is located on the X chromosome
-Males have white eyes because they only have 1 X chromosome. If the white-eye allele is inherited, it becomes dominant. (Well, not exactly dominant. But that's the only allele for eye color it has, right?)
Theories:
i. Genes are located on chromosomes
ii. Either protein or DNA codes for the genetic information

2. Hershey and Chase
The experiment:
Purpose: To illustrate the relation between DNA and heredity and to demonstrate that DNA is the genetic material
Procedure:
i. Allow phages to attack a bacterial cell. Their proteins are radioactively labelled.
ii. Allow a second group of phages to infect a bacterial cell. Their DNA is radioactively labelled.
Result:
i. Phages produced by the 1st cell were not radioactive.
ii. Phages produced by the 2nd cell were radioactive

Conclusion:
DNA is the genetic material that is passed from generation to generation.
check this out!!
http://highered.mcgraw-hill.com/olc/dl/120076/bio21.swf

3. Frederick Griffith
The experiment of transformation:
R strain --> rough --> harmless
S strain --> smooth --> fetal
Procedure:
Inject the strain(s) into mice
Trial 1: S strain is injected
Trial 2: R strain is injected
Trial 3: S strain is killed (by heat) and injected
Trial 4: Dead S strain and alive R strain are injected
Hypothesis:
Trial 1: The mouse would die.
Trial 2: The mouse would live.
Trial 3: The mouse would live.
*Trial 4: The mouse would live.
Results:
Trial 1: The mouse died.
Trial 2: The mouse lived.
Trial 3: The mouse lived.
*Trial 4: The mouse died.
Conclusion:
The injection caused a change in genotype and phenotype. This process is called transformation.


4. Erwin Chargaff
-discovered the 4 bases of DNA
Purines (double-ringed): adenine, guanine
Pyrimidines (single-ringed): thymine, cytosine
% T = % A
% G = % C
Each species has a distinct DNA composition.


5. Maurice Wilkins and Rosalind Franklin
-studied the structure of DNA according the diffraction pattern of X-ray


6. Watson and Crick

-studied Wilkins and Franklin's research
-DOUBLE HELIX
-Purine + Pyrimidine
 -A=T
 -G≡C
-diameter = 2 nm

New science fair idea

New idea for science fair!!
Expired chocolates :D

SUSANNE PLEASE DO NOT COPY MY IDEA.
THANK YOU FOR YOUR COOPERATION.



Just...ignore this stupid idea.
Here's a better one:
Caffeine and pea are SOMEHOW related.

Ideas for science fair

The human body
1. Brain surgery
2. Hereditary nonpolyposis colorectal cancer
3. Mutations
4. Heart disease
5. Ageing
6. Body-building
7. Emotions

Industries
8. Enzyme catalysts
9. Food additives
10. Alcohols

The environment
11. Corrosion
12. Adaptations of plants
13. Energy flow within an ecosystem
14. Industrial waste
15. Photosynthesis
16. Bacterial growth
17. Molds


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About the murder case...
"THOMAS SANDSTONE HAS AN AFFAIR WITH EVERYONE >_>" - Joanna Tsui.

It took me forever to finish the karyotype keys.
I really hate cutting and pasting stuff.