Sunday, April 24, 2011

Prokaryotes vs. Eukaryotes

A few differences:

-circular genetic information
-all extrons (no introns)
-DNA in cytosol
-naked DNA
-RNA needs no protection due to constant environment
-transcription and translation occur simultaneously

-linear genetic information
-both extrons and introns
-DNA in nucleus
-DNA wrapped around histones (proteins)
-mRNA needs protection
-transcription and translation occur seperately

Genetics: Protein Synthesis: Translation

Translation: the process by which mRNA is used to code for proteins.

Location: Ribosome/Cytoplasm

- 3 nucleotides code for one amino acid
- these groups of 3 nucleotides are called codons (there are 64)
- UAA UGA UAG are all stop codons
- AUG is the start codon
- the third base wobble: sometimes, more than one codon codes for the same amino acid. The third nucleotide may differ. This allows for less tRNA (which we will learn about shortly).
- translation occurs from 5 prime to 3 prime also
- amino acids have anticodons complimentary base pairs to those on the mRNA

tRNA: tRNA is known as transfer RNA. It is composed of a string of nucleotides in the shape of a clover. Its shape is secured by hydrogen bonds. It possesses an anticodon on the leaf side where mRNA can bind using hydrogen bonds and a 3 prime end where amino acids can bind by a unstable covalent bond. The third nucleic acid on the anticodon is angled inwards resulting in the third base wobble.

Ribosome: Ribosomes are manufactured in the nucleolus. Their structure helps to form the peptide bind between amino acids. They are made of rRNA and proteins. They are composed of a large and small sub unit. They also have 3 sections: E, P and A.

The steps:

mRNA, ribosomal subunits and initiator tRNA (for AUG) are brought together by initiation factors.

-An enzyme called aminoacyl-trna synthetase attaches amino acid to tRNA.
-tRNA brings the amino acid to the ribosome and binds to the A site. The tRNA containing the polypeptide chain is on the P site. The tRNA from the A site moves to the P site adding its amino acid to the chain and the tRNA that used to be on the P site is now empty and moves to the E site where it will exit.

The end codon codes for a release factor, and the polypeptide chain is complete!

Here is an animation of the process, enjoy!

Genetics: Protein Synthesis: Transcription (2)

RNA Polymerase is the enzyme responsible for transcription.
There are 3 types of RNA Polymerase:
1)RNA Polymerase 1: makes ribosomes (transcribes rRNA) (non-structural)
2)RNA Polymerase 2: transcribes mRNA (structural)
3)RNA Polymerase 3: transcribes tRNA(non-structural)

The steps:

1) Initiation:
Transcription factors first bind to the promoter region of the gene. Transcription factors are groups of proteins that bind to a gene turning off/on transcription according to the bodies needs. The promoter region is a sequence of nucleotides that come before the gene. It includes the TATA box. The RNA Polymerase then also bonds to the location and the initiation complex is formed.

2) Elongation:
RNA Polymerase adds complimentary base pairs to one strand (the template strand) making a copy of the coding strand (with the exception of thymine which is replaced by uracil). Synthesized 5 prime to 3 prime.

3) Termination:
New RNA strand is completely released from template strand. DNA finishes recoiling.

4) Post Transcriptional Processing:
Splisosomes cut out unnecessary info (introns) and remaining useful info (extrons) are rejoined. Now the pre-RNA becomes mRNA through the addition of some features for protection. A modified guanine cap on the 5 prime side and a poly-A tail on the 3 prime end.

The mRNA now passes through the nuclear membrane and into the cytoplasm where it prepares for translation!

Genetics: Protein Synthesis: Transcription (1)

Transcription: The process by which DNA is copied into mRNA.

Location: Nucleus

Why? There are a number of advantages to having this process:
- DNA is sacred, and better left protected in the nucleus
- It is large, it is more convenient to move small pieces around in the cytoplasm.
- Not all the DNA codes for the same protein; it is better to only take what is needed into the cytoplasm
- There is only one copy of DNA per cell; mRNA allows for protein synthesis to occur at many different ribosomes at once to satisfy the needs of the cell
-It can penetrate the pores of the nuclear membrane

Its structure?
It is very much like DNA except the sugar used is Ribose instead of Deoxyribose, Uracil is used instead of Thymine and it is single stranded as opposed to the double helical structure of DNA.

Genetics: Telomeres

What is a telomere?

A telomere is a repeated non-coding portion of DNA found on the ENDS of the chromosome as illustrated above.

What's its role?

Protection. After ever replication, a single nucleotide at the end of the DNA is lost. Telomeres prevent any important information from being lost. Of course, it has its limits. The deterioration of the telomere is linked to the process of aging!

So, what is telomerase?

Telomerase is an enzyme found in some cells that seems to add on to the 5 prime end of DNA (extends telomeres). These enzymes are only found in germ cells and even cancer cells!

Scientists hope that with the knowledge of telomeres, we can find cures for things such as aging and cancer!

HERE is some more information on telomeres!

This VIDEO will also give you a better understanding!

Genetics: DNA Replication (2)

To remember: DNA has direction (a 5 prime end, where the phosphate group is attached, and a 3 prime end where a hydroxyl group is attached)

Replications begin at many points along the DNA called points of origin:

Here are a summary of the basic steps involved in DNA replication:

1) Unwind DNA: Helicase is the enzyme responsible for unwinding the DNA and breaking the hydrogen bonds between the nitrogen bases. Gyrase is the enzyme which relieves tension during this process. To prevent the DNA from recoiling, Single-stranded Binding Proteins bind to the individual chains of nucleic acids.

2) Primer is added: RNA Primase adds a RNA primer to the DNA chain so that DNA polymerase can function.

NOTE: DNA polymerase has two restrictions: It cannot add to the the 5 prime end, and it needs an RNA primer to start it off.

3) Daughter strand is built: DNA Polymerase 3 is the enzyme responsible adds nucleotides to the 3 prime end of the new chain forming polydiester bonds.

NOTE: The new strand must grow from 5 prime to 3 prime due to energy needs.
Forming a new DNA chain is a analytic reaction which is endergonic.
The energy comes from the phosphate groups attached to nuclosides (which are basically nucleotides with 2 additional phosphate groups attached)

Ex. ATP (nucleoside shown below) turns to AMP (the nucleotide used in DNA). During this process, 2 phosphate groups are released in addition to energy which is used to synthesize the new DNA.
The nucleotide must add to the 3 prime side so that the bond may be broken to produce energy.

NOTE: Because of the need for nucleotides to grow from 5 prime to 3 prime, one strand of DNA is produced continuously (the leading strand), where as the other is produced in pieces (the lagging strand). The pieces are called Okazaki Fragments.

4) Primer is removed, segments produced on lagging strand are connected: The enzyme ligase is responsible for sealing the holes between the segments. DNA polymerase serves as a proof reader; it removes RNA primer and replaces it with DNA, it also checks for errors. Once again, ligase seals the holes.

Here is a link to a helpful youtube video that may help you better visualize the process: CLICK HERE!

Genetics: DNA Replication (1)

Why bother with DNA replication?
It is essential to allow for daughter cells to have identical and complete copies of the genetic information. If it weren't for replication, the amount of genetic material present in cells would decrease and necessary information would go missing not allowing the cell to function.

Initially, there were three basic theories regarding how genetic information is replicated:
1) Dispersive: Where the new DNA was composed of patches of the old DNA and newly assembled DNA
2) Conservative: Where the old DNA strand was kept in tact and a completely new and separate strand was assembled
3) Semi-conservative: Where one strand of DNA served as a template strand. So the resulting DNA strands would have one on strand of nucleotides from the parent and one new strand.

These theories are illustrated in the above diagram.

The semi-conservative theory was proven to be correct by Meselson and Stahl through an experiment:
In short, DNA marked with a radioactive isotope of Nitrogen (Nitrogen-15) was left to replicate.
After one replication, all the DNA seemed to have both Nitrogen-15 from the parent DNA and Nitrogen-14 (normal Nitrogen) from there environment in equal share.
After the second generation, half of the Genetic information was still a mix of N-14 and N-15, however the other half was purely N-14.
These observations were indicative of semi-conservative replication.