Anaerobic Respiration

This content is also copied from our biology textbook. Nelson Biology 12.

If the oxygen is not available, we wouldn't be able to continue glycolysis. One method involves transferring the hydrogen atoms of NADH to certain organic molecules instead of the electron transport chain. This process is called Fermentation.

Bacteria - Ethanol Fermentation


Fig. 1 Ethanol fermentation creates ehtnaol and carbon dioxide from glucose, In this process, NADH is oxidized to NAD+, allowing glycolysis to continue

Eukaryotes (Human, animal) - Lactate (Lactic acid) Fermentation.

Figure 2. Lactate fermentation produces lactic acid from glucose. inthe process, NADH is oxidized to NAD+, allowing glycolysis to continue.

This process is much more effective than ethanol fermentation because in this process, the pyruvate is directly converted into lactate whereas ethanol fermentation requires extra energy to covnert pyruvate into 2 Acetaldehyde. When the Lactate is accumlated in your muscle, it causes stiffness, soreness, and fatigue but once the enough oxygen is provided to blood, it is converted back into pyruvate then goes back through the kreb cycle.

C4 vs CAM plants

This content is all from grade 12 biology text book in A.Y Jackson S.S
Nelson biology 12

C4 vs CAM plants

C4 photosyntehsis - a photosynthetic pathway of carbon fixation that reduces the amount of photorespiration that takes place by continually pumping CO2 molecules (via malate) from mesophyll cells into bundel-sheat celss, where rubisco brings them into the C3 Calvin cycle

- Sugar cand and corn, member of grass faimly, are examples of C4 plants
- In this process, an enzyme called phosphenolpyruvate carboxylase first catalzyes the addition of a Co2 molecule to a three-carbon molecue called phosphenolpyrubvae (PEP), forming four-carbon molecue oxaloacetate (OAA). This is why hte process is called C4 photosynthesis or the C4 pathway.
-The C4 patheway uses almost twice as much ATP as the C3 pathway to produce glucose, but without this mechanism, photorespiration would reduce the glucose yield to less than half that produced by the C3 pathway.
-Key words to know ' Oxaloacetate/Plasmodesmata/PEP/

*This process is advantageous in hot tropical climates where photorespiration would otherwise convert more than half of the glucose prodcued back to CO2




Crassulacean acid metabolism (CAM) - a photosnythetic mechanism in which stomata open at night so that plants can take in CO2 and incorporate it into organic acids, and close during the day to allow the organic acids to release CO2 molecules that enter C3 Calvin cycle to be fixed into carbohydrates.

-Water-storing plants (known as succulents) such as cacti and pineaaples, are examples of CAM plants
-Closing stomamta during the day helps conserve water but prevents CO2 from entering the leaves. In the dark, when stomamta open, the plants take in CO2 and incoporate it into C4 organic acids using the enzymes PEP carboxylase.
-This occurs in a hot,dry and desert environment.

Comparison
1) In C4 plants, such as sugar cane, Co2 is first incoprated into C4 organic acids in mesophyll cells. The C4 organic acids enters bundle-sheath cells throguh cell-cell conncetions and then releases carbon dioxide, which is fixed via the Calvin cycle.
2) IN CAM plants, such as pineapples, carbon fixation into organic acids occurs at night, and the Clavin cycle occurs in the day.

Lab result :D

Control = 5 mL/run

Run 1 - 100% H2O2
Rapid bubbles inside beaker
75 mL of H2O displaced
34.2 seconds

Run 2 - 80% H2O2, 20% H2O
32 mL of H2O displaced
14 seconds

Run 3 - 60% H2O2, 40% H2O
34 mL of H2O displaced
13 seconds

Run 4 - 40% H2O2, 60% H2O
24 mL of H2O displaced
12.4 seconds

Run 5 - 20% H2O2, 80% H2O
18 mL of H2O displaced
10.8 seconds

Importance of Entropy

Importance of Entropy

If you have taken Chemistry or physics, you learned what Entropy is all about.

By definition, entropy is simply a measure of randomness (uncertainty) or disorder in a collection of objects or energy; symbolized by S.

Typical example would be when you place an ice cube on a table in room temperature, the ice cube

would melt due to the room temperature, and thus the randomness of the particles increase, because the heat

causes the particles to be free and moving into open space.

The importance of Entropy is because without this law (the spontaneity in our world), there is no single

reaction in our world therefore, nothing will occur.

#5 Vector Cloning VS PCR

Vector Cloning

- I don't think it is relatively cheaper than PCR because if you think about what you need; plasmid, gene of interest ,yeast, specific R.E etc. Thoes are not cheap.

- replicates entire DNA and once it is replicated, you are going to get the same targeted DNA over a long period of time.

- Depending on the purpose, it can produce protien.

PCR

- Takes less time than Vector Cloning.

- It only replicates DNA.

- one DNA strand can produce a billion strands of DNA in no time, but if the one DNA strand is contaminated, then the rest of the copied DNA is also contaminated.

- it is widely used in forensics. When they gather evidence, the first thing they do is PCR.

-If there is machine for PCR, everything is automated, so you can just leave it to machine and go for lunch.

*I'll edit more if i find more info regarding this topic :D

#4 10 Things to know about DNA replication!

10 Things I should know about DNA Replication

1.     Before I even take a look at what really happens, I should understand why DNA replicates!

è  DNA replication (Synthesis same term) is the process of copying a double helix DNA strand in a cell, before the cell divisions. This process happens during S phase of the cell cycle before, mitosis and meiosis. This is the key part. I know that human body constantly needs to get worn out old cells and produce new cells to form our body. The new cells produced must have a full set of genes in order to function normally. In order to do so, DNA must be replicated equally before the cell divisions.

2.     What allows existing DNA strands to serve as templates for new complimentary strands during DNA replication?

è  ‘Base pairing’ is the answer.

3.     Watson and Crick’s proposed models.

è  Watson and Crick's models. Here is the picture of the models. The picture itself pretty much explains everything. I remember Mr. Chung explaining this models with biology textbooks.

4.     What is ‘Enzyme’?

è  In chemistry, Mrs. Greenberg told me that the Enzymes are complex molecules that act as a catalyst for chemical change in living organisms. So I did a bit of research to find out what are enzymes in biology. In Biology, Enzymes are ‘any of a group of large catalytic proteins present in living organisms. Enzymes, like all catalysts, accelerate, but are not consumed by, a specific chemical reaction. In this way enzymes promote biochemical activities that would otherwise occur at a metabolically useless rate.’

If you want to know more about enzymes here Is the website I looked at.

 http://ea.grolier.com/article?id=0144250-00

5.     Enzymes in Initiation (Helicase, Single-strand binding proteins, Gyrase, RNA primase)

è  Enzymes are significantly important in DNA replication because a large number of enzymes and other proteins carry out DNA replication!! First of all, in the process of Initiation, There are 4 enzymes worked together. By the way, the timing is really important as well. So, firstly, Enzyme called ‘Helicase’ untwists DNA and breaks up hydrogen bonds. Then, Single-strand binding proteins come to stabilize the unpaired strands. After, an enzyme called ‘Gyraes’ releases the tension that was made when the DNA was separated. Lastly, RNA primase signals Polymerase 3 by producing a primer!!

6.     Enzymes in Elongation (DNA polymerase 3)

è  DNA Replication continues in this process. Only one enzyme is related in this process; DNA Polymerase 3. As RNA primase makes signal, Polymerase 3 recognize RNA Primer. Then it starts to elongate new DNA 5’ -> 3’ (Always) The strand towards the fork is called Leading strand and the strand away from the fork is called lagging strand (composed of many Okazaki fragments).

7.     Important term in Elongation : Leading strand

è  Say, Mr. Chung gives a test question that asks which strand is leading strand and lagging strand? And I’m like “OMG which one is lagging and leading strand?? I am so confused.” To make sure this does not happen during the test. Let’s make it clear what is the leading strand and lagging strand.

è  Leading strand is copied continuously into the fork from a single primer at the replication fork and it is always from 5’ -> 3’. Don’t forget this!!

8.     Lagging strand

è  What about Lagging strand then?

Lagging strand is copied away from the fork in short segments, (Okazaki fragments), each requiring a new primer. It is also from 5’ -> 3’ Remember, DNA strand is always from 5’ -> 3’

è  I get it now but … then what’s the difference??

9.     Differences between leading/lagging strand

è  There are some differences between leading and lagging strands but the biggest difference is that the lagging strands are joined by an enzyme called ‘ligase’ after the elongations process.

10.   Enzymes in Termination (DNA Polymerase 1, Ligase)

Final process of DNA replication, two enzymes finish off the termination. Firstly, DNA Polymerase 1 (Big brother) replaces RNA primers with DNA, and makes sure that there is no mistake made by DNA Polymerase 3 (Little brother). Then, if the strand is lagging strand, ‘Ligase’ joins the gaps in DNA (Okazaki fragments).

As I was writing the last one, I just came up with the question, does the leading strand continue all the way?? Or does it stop at some point? Or it is joined by Ligase like lagging strand at some point?

I should ask this question !!

#3 Grade 12 University Biology Review

Terms to study !!! I am a strong visual learner so I posted some picture to help understand it.

RNA – stands for ribonucleic acid. It performs a variety of functions in the living cell but its primary function is in protein synthesis.

DNA – stands for deoxyribonucleic acid. It is the genetic substance of all living cells and viruses. It contains hereditary information.

mRNA – stands for Messenger RNA (ribonucleic acid). It is a molecule of RNA that serves as a template for protein synthesis.

Cytosol – is also known as intracellular fluid or cytoplasmic matrix. It is the liquid found inside of the cells.

Histone

Histones – is a protein which helps compact DNA inside a cell.

Vand der Waals Force – named after Johannes Diderik van der Waals. It is the attractions between atoms, molecules, and surfaces. His force is different from covalent or ionic bonding because Van der Waals interaction is the sum of the attractive or repulsive forces between molecules other than those due to covalent bonds or to the electrostatic interaction.

London Forces – is part of the Vand der Waals Force. It is the weakest intermolecular interaction including gases such as O2, N2, Ch4 and alkanes.

Somatic cell – are all the cells that build up an organism except the germ cells.

Eukaryote – is any cell or organism that possesses a well-defined nucleus. (Unlike prokaryote)

Prokaryote – or known as prokaryote is any single celled organism that lacks cell a nucleus enclosed in a membrane.