Prokaryotes vs. Eukaryotes

A few differences:

Prokaryotes:
-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

Eukaryotes:
-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

THINGS TO REMEMBER:
- 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:

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

2)Elongation:
-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.

3)Termination:
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.

DNA: Structure – People and History

RECALL:

-DNA is a polymer of nucleotides linked together by phosphodiester linkages
-A nucleotide consists of a five carbon sugar (ribose) with a phosphate group attached to carbon number 5, and a nitrogen base attached to carbon number 1 using a glycosyl bond.
-There are 4 base pairs (2 purines: 2 rings, and 2 pyramidines: 1 ring).
-They are grouped together as complimentary base pairs:
Cytosine (pyramidine) with Guanine (purine)
Thymine (pyramidine) with Adenine (purine)
-DNA consists of two anti-parallel strands in a double helical structure connected by hydrogen bonds.


1949—Erwin Chargaff

-analysed data from chemical analysis of DNA
-found Adenine and Thymine, Cytosine and Guanine, Purines and Pyramidines existed in equal proportions

1953—Rosalin Franklin, Maurice Wilkins
-used x-ray diffraction to analyse DNA structure
-suggested double helical structure (2nm diameter, 3.4nm helical twist)
-Wilkinson presented data to Watson and Crick before it was published

1953—Watson, Crick
-presented DNA structure based on Chargaff, Franklin and Wilkin’s observations

DNA: Hereditary Material – People and History

1869—Friedrich Miescher

-extracted white substance (DNA) from nucleus and called it nuclein
-found that its properties differed from those of proteins

1908—T.H. Morgan

-experimented with Drosophilia (fruit flies) and associated phenotype with a specific chromosome
-concluded that genes are found on chromosomes

1920’s—Frederick Griffith

-used mice and two strands of pneumococcus bacteria (virulent/non-virulent)
-found that when heat treated virulent bacteria (denatured proteins) was mixed with healthy non-virulent bacteria and was injected into mice, these mice died
-caused people to suspect that DNA, not proteins in chromosomes, is responsible for inheritance
-discovered process of transcription

1930’s—Joachim Hammerling

-used Acetabularia (A. crenulata and A. medittarnea: long cells with nucleus located at the base) to prove that material in nucleus is responsible for heredity
-chopped off top, regenerated
-chopped off bottom, no regeneration

1944—Avery, McCarty, MacLeod
-separated DNA and proteins from chromosomes of streptococcus pneumonia bacteria
-injected DNA and proteins into separate bacteria
-bacteria with DNA injected became virulent
-more support that DNA contains genetic information

Photosynthesis: Environmental Factors

Rate of photosynthesis:
Measured by the net CO2 uptake: photosynthetic uptake – photorespiratory evolution – respiratory evolution

There are 4 main factors affecting the rate of photosynthesis in plants:

1) Light Intensity

Generally, as light intensity increases, the rate of photosynthesis also increases.
When there is no light, net CO2 production is negative due to cellular respiration.
Light-compensation point - when the amount of CO2 used is equal to the CO2 produced: net CO2=0
Light Limited phase - For sometime, the rate of photosynthesis increases in direct proportion to light (the relationship is linear). The reaction is speeding up as substrate concentration is increasing until the enzymes are working at full potential.
Light Saturation point - carbon fixation has reached maximum rate: enzyme concentration in limiting.

2) Temperature

Between 10-30 degrees: rate increases with temperature.
40 + degrees: the enzymes which catalyze the reactions within photo synthesis become denatured and are no longer able to function. This causes the rate to decrease after this point.

3) Carbon dioxide Concentration

Generally, the higher the concentration of CO2 in the atmosphere, the higher the rate of photosynthesis.
The enzyme rubisco involved in the Calvin Cycle also has a high affinity for oxygen. The greater the carbon dioxide concentration, the less chance RuBP will oxidized.
Once again, this increase in rate of photosynthesis is only until the enzymes involved are working at full potential.

4) Water Concentration
Water is another reactant in photosynthesis, and therefore causes an increase in reaction rate also until the enzymes are working at their full potential.

Can a plant get too much water?

Yes, in large plants, root cells are responsible for carrying water to upper cells for photosynthesis. They, themselves, perform cellular respiration to survive which requires oxygen which they absorb from air pockets in the soil. If the soil is completely saturated with water, no oxygen will be absorbed by these cells, and they will die. This may eventually lead to the death of the entire plant.