Population dynamic activity

Last week, we played a deer simulation game to observe how various factors would affect the deer population. The whole full class took a role either as a deer or a type of resource, and of course this role was not permanent.
In our first simulation, we started off with just few deers and abundant resources. Through generations, the change in the deer population was predictable: As resources were gradually being used up, the deer population flourished and reproduced. But as their population grew larger and resources became unavailable, competition between species begin to take place, known as intraspecfic competition. Subsequently, the depleting resources could not support the growing deer population. As they died, their body decomposed and eventually recycles back into the system to become resources. This accurately showed that there's a carrying capacity for populations, once it reaches its carrying capacity, its number would start to decrease.
In our next simulation, we introduced density-dependent and density-independent factors. These are things like flood, forest fire, drought (density independant), predation (density dependent) and etc. After several generations, the deer population decreased drastically, and was on the verge of extinction. This goes to explain as for why many species are in danger of extinction, for majority of the factors affecting its population are not density dependent.
Overall, this simulation was lots of fun, and it also accurately portrayed the behaviour of a species population in general. In a bigger picture, this simulation also reflect greatly about the human population.  In the near future, when our population reaches its carrying capacity, it really makes us worry for what would happen then. I guess this activity was a great way gets us to think about these things and become aware of them. On top of that, the "juvenile" play was insanely fun, just like back in summer camp. :)

Photosynthesis and Cellular Respiration

20 Facts about the Krebs cycle

• Proposed by Hans. A Kreb in 1937
• Occurs in the mitochondria, the power plant of cells
• Takes place after glycolysis, the pyruvates produced travel into the mitochondria of the cell from the cytoplasm
• carbon dioxide is enzymatically removed from each three-carbon pyruvic acid molecule to form acetic acid.  The enzyme then combines the acetic acid with an enzyme, coenzyme A, to produce acetyl coenzyme A, also known as acetyl CoA.
• Acetyl CoA initiates the 8 steps cycle of Krebs cycle
• Acetyl CoA combines with oxaloacetate to form citrate, coenzyme A is ditched and used as a temporary transport.
• An isomerization reaction takes place, forming isocitrate
• NAD oxidizes the isocitrate molecule, forming alpha-ketoglutarate, also releasing CO2 in the process.
• coenzyme A oxidizes the alpha-ketoglutarate molecule to form succinyl-coenzyme A complex.  A molecule of NAD is reduced to form NADH and hydrogen. 
• Coenzyme A is displaced by a free floating phosphate group. The phosphate is transferred to a molecule of ADP to form ATP, leaving behind succinate.
• succinate is oxidized to form fumarate.
• Water is added to the fumarate molecule to form malate.  
• the malate molecule is oxidized to form oxaloacetate, and the Krebs cycle can start all over again.
• For each cycle (1 glucose molecule), 2 molecules of ATP, 6 molecules of NADH, and 2 molecules of FADH2 are produced.
• The NADH and FADH2 molecules will be used to produce ATP in the next step – electron transport chain.
• Hans A. Kreb was awarded the nobel prize for his work
• The availability of oxygen is critical to the ability of the Krebs cycle to function
• The cycle occurs in nearly all aerobic cells, not just in animals.
• The pathway is amphibolic.
• Regulation is provided by substrate availability and product inhibition.

Thermodynamics and Metabolism

The laws of thermodynamics govern the nature of heat and thermal energy. There are 3 laws of thermodynamics:

·         First Law: In a closed system, the amount of input energy equals total output, thus energy cannot be created nor destroyed.

·         Entropy: Entropy is the measure of chaos and disorder in a system. More disorder implies for higher entropy and vice versa. The law of entropy states that entropy will increase for any process because various forms of waste energy, such as heat will be generated. Thus, the entropy of the universe can never decrease.

·         Third Law: At 0 Kelvins (-273 C), all motions will stop. Therefore, it is the lowest possible temperature and is impossible to reach.

How does the law of entropy relate to metabolism?

Essentially, every process in nature drifts away from order, and towards chaos. Organisms die and decay, stars burn out and this is no difference for metabolic processes. Exergonic reaction release energy, thus increases entropy, while endergonic requires energy and decreases entropy. However, when everything is considered as a big closed system, the entropy will always be increasing. Evidently, metabolism without an exception, also obeys the laws of thermodynamics.

Many Facts about Carbohydrates

• Carbohydrates provide energy for the body.
• Carbohydrates contain carbon, oxygen, and hydrogen atoms in a 1:1:2 ratio respectively
• Its empirical formula is (CH2O)
• Simple sugar (glucose), also known as monosaccharide is the building block of complex carbohydrates. They are named according the number of carbons in the structure. (i.e hexose – 6)
• Monosaccharide can be distinguished by the functional group they possess – either aldehyde group (aldoses) or ketone group (ketoses).
• Pentose and Hexose can cyclize through the reaction between the double bonded O with the OH.
• Because of the nature of carbon bonds, the shape of the cyclic glucose can either be in the shape of a “boat” or chair.
• The shape of the chair is much more stable because the two reactive ends are more further apart.
• Monosaccharides are joined together by a glycosidic bond to form a disaccharide.
• This occurs through a condensation reaction, in which a water molecule is formed.
• The glycosidic bond can be either alpha (below the ring) or beta (above the ring), characterized by the location of the OH group.
• For example, Maltose has an alpha glycosidic link between the hydroxyl on the first carbon and the hydroxyl of the fourth carbon of the 2 glucoses. Therefore, the bond is called a(C1 – 4) glycosidic link.
• A Hydrolysis reaction is basically the opposite of a condensation reaction, in which a disaccharide reacts with water to break down into 2 monosacchrides.
• Oligosaccharides: few monosacchrides bonded together
• Polysaccharides eventually form as more and more small molecular bond together.
• Plants store glucose as amylose or amylopectin
• Amylose is a glucose polymer with an a(1-4) glycosidic link.
• Amylopectin is also a glucose polymer with an a(1-4) glycosidic link, but it also has branches formed by a(1 – 6) linkages.
• In animals, glycogen stores the glucose, and it has even more branches and thus a(1 – 6) linkages.
• The highly branched structure allows faster release of glucose, which is more essential in animals than plants.
• In cell walls of plants, cellulose consists of long chain of glucose with B(1 – 4) linkages.
• The beta links flip over every other glucose, which promotes intra-chain and inter-chain hydrogen bonds.

Biotech Notes

 

Plasmids

·         Small, circular double stranded DNA molecules in the cytoplasm of many strains of bacteria

·         Plasmid and bacteria have a mutual arrangement: Plasmid uses the enzymes and ribosome of the bacterial cell, while bacterial cells benefit from the genes carried and expressed by plasmids to confer antibiotic resistance. The relationship between bacteria and plasmids is endosymbiotic.

·         Higher copy number means for more copies of a plasmid existing in a host bacterial cell, thus more protein will be synthesized to strengthen the resistance to antibiotics.

·         Multiple cloning is a region in an artificial plasmid where it has been engineered to contain many recognition sites of various restriction endonucleases.

·         If the foreign gene has been excised using the same restriction enzyme, it will anneal and permanently become part of the plasmid. DNA ligase then reforms the phophodiester bonds, and now the plasmid is recombinant DNA. As this plasmid replicates, copies of the recombinant DNA are produced, and this gene is said to be cloned.

Transformation:

·         Introducing DNA from another source is called transformation, and vectors such as plasmid, carry a desired gene into a host cell.

·         Competent cells readily take up foreign DNA. Cells that are not naturally competent can be chemically induced with the aid of calcium chloride. As the positive calcium ions stabilize the negative charges of the phosphates (membrane), the solution is quickly heated that creates a draft. This draft sweeps the plasmids into the cell through the membrane.

·         It is possible that the bacteria exhibit antibiotic resistance by taking up the plasmid that has failed to transform. Therefore, it is necessary to check that the gene exists in the transformed bacteria. This is again accomplished by using a restriction enzyme to release the cloned fragment from the vector after colonies of growth.

·         Selective plating isolates the cells with recombinant DNA. If transformation is successful, the bacteria will be able to resist the antibiotic.

·         Today, electroporators are also used, which subject the bacteria to an electric shock that loosens the structure of the cell membrane to allow foreign DNA to enter.