Saturday, November 29, 2014

The Replication of Old Man DNA

Note: Cast

Act I: Initiation:
Once upon a time, there was a DNA that felt that it was time to replicate. He was very old so he enlisted the help of the younger generation.
First, a replication fork is to be formed to separate the strands. This is done by Helicase. He untwistes a section of DNA, then he pulls apart the strands easily because of the weak hydrogen bonds. But he realized that he could not hold the strand apart by himself, so he called upon his buddy, Single-strand binding proteins, who specializes in this job.
While this was happening Old man DNA complained that other parts of his structure became too tight. So Gyrase comes in to release the tension.
Then finally, the synthesis of the daughter strands can begin.
Act II: Elongation:
Since the DNA has been split into 2 strands and each runs anti-parallel to each other. And the new daughter strand is to be synthesised in a 5'-> 3' direction. The 2 daughter strands needs to be formed, each one in the opposite direction of the Old man DNA stand, or template. And depending on whether it is forming towards the fork or away, it is a different process.
Leading strand (towards the fork):
First, RNA primase builds a small RNA segment called RNA primer. Then DNA polymerase III adds nucleotides to the RNA primer continuously.
Things are not so easy for the Lagging strand (away from the direction of fork opening):
The daughter strand is synthesized discontinuously, in sections, where it also starts with a RNA primase, RNA primer, and DNA polymerase III. This is called an Okazaki fragment.
But that's not all, when the Okazaki fragment runs into the RNA primer of another Okazaki fragment in front of it, in comes DNA polymerase I to replace the RNA neucleotides with DNA.
Act III: Termination:
And finally DNA ligase, AKA the Glue man, who's been called in by the youngsters and waiting while this is all taking place, can join the Okazaki fragments. As well Polymerase I & DNA Polymerase II proofreads and repair errors.

Saturday, November 8, 2014

Metabolism: Anabolism/Catabolism

In order to visualize Metabolism (biochemical reactions that occur in living organisms),we made 3D posters to model the reactions that takes place.

Anabolism (photosynthesis)- synthesizing molecules from smaller components in order to store energy, requires energy in the process. (Photons ---> Glucose)

Noncyclic Photophosphorylation (light-dependent):
- P680 absorbs a photon, the excited electron goes to b6-f complex, then to P700 where electrons get excited by photons, then they are used by NADP reductase to reduce NADP+
- Oxygen and NADPH are formed
- can produce ATP






Cyclic Photophosphorylation (light-dependent):
- electron in P700 is excited by a photon, instead of being used to reduce NADP+ like in noncyclic photophosphorylation, electrons from Fd is passed to b6-f complex and back to P700
- no NADPH or oxygen is formed
- can produce more ATP the little NADP is available.






Calvin Cycle (light-independent):
- rubisco fixs CO2 and RuBP (5C) to become 2 PGA (3C)---> 2BPG (3C)---> 2 G3P (3C)
- some G3P are used to make glucose, others recycled (G3Px2---> 1 glucose)
- uses ATP and NADPH













Catabolism (celluar respiration)- breaking down complex molecules into smaller units, releasing energy in the process. (Glucose ---> ATP)

Glycolysis:
- Glucose---> Glucose 6-phosphate---> Fructose 6-phosphate---> Fructose 1,6-phosphate ---> Dihydroxyacetone/G3P---> 2 BPG---> 3PG---> 2PG---> 2 PEP---> 2 pyruvate
- 2 ATP consumes, 4 ATP produced, 2 H2O produced













Kreb's Cycle:
- OXAL (4C)+Acetyl-CoA (2C)---> CIT(6C)---> ISO (6C)---> alphaKG (5C)---> Succinyl-CoA (4C)---> SUC (4C)---> FUM (4C)---> MAL (4C)---> OXAL (4C)
- produces 2 ATP, 6 NADH, 2 FADH2













Electron Transport Chain:
- 2H+---> 1 ATP
- NADH passes 2 electrons to NADH dehydrogenase---> bc1 complex---> Cytochrome oxidase complex => 6 H+
1 NADP---> 3 ATP, 24 ATP (2 NADP from glycolysis behaves like FADH2)
- FADH2 passes 2 electrons to bc1 complex---> Cytochrome oxidase complex => 4 H+
1 FADH2---> 2ATP, 8 ATP





Sources:
  • Nordqvist, Christian. "What Is Metabolism? How Do Anabolism and Catabolism Affect Body Weight?" Medical News Today. MediLexicon International, 26 Sept. 2014. Web. 10 Nov. 2014.
  • Carter-Edwards, Trent. Biology 12. Toronto: McGraw-Hill Ryerson, 2011. Print.