OH! DEER! ( Factors Relate to Population Size)

   "OH! DEER!" is a simulation the class has played in order to understand the factors affecting population sizes. The simulation makes the knowledge " jumps out " of the textbook and teaches us as we play. Two most important factors that affects population size we have learned from "OH! DEER!" are density-dependent factor and density-independent factor.

    Density-dependent factors occur when the increasing population are facing a limited resources. This was introduced to us in the first part of the game, when the class was divided into two groups -- deer and resource. Individuals in both groups had to choose what they are (resource) or what they consume (deer) with options of water,shelter and food. As the game progress, the resource reduced as the deer consumed it. Soon enough the resource available was not able to meet the need of the deer. This was where it reached the carrying capacity.Consequently, dead deer will eventually turned back into resource as it decomposes by the fungi over the time. 

   Density-independent factors are factors such as flood, drought, forest fire or predators. This was presented during the second part of the game where factors of flood and such were inserted into the game in which gave a limitation on resources. As result, the deer population started to shrink due to a shortage of supply or the death from predator.Similarly to the predator who consume on the deer, they will face a density-dependent factor when their resource -- the deer is short.

Photosynthesis and Cellular Respiration

( Photo Credits to Elaine Li)




Cyclic Light -dependent reaction is an alternative pathway for non-cyclic pathway in a condition of the absence of  limited factor NADP+.




Alternative Pathway of CAM and C4 occurs when water or carbon dioxide are limited.
C4 --> different reactions take place in different part of the cell by the use of oxaloacetate (4C).
CAM --> different reactions occur in different time period of a day.










Fermutation occurs when oxygen is not available.

20 Points On Krebs Cycle

1. It was discovered by Hans Adolf Krebs in 1930s.
2. Hans Adolf Krebs was awarded Nobel Prize for his work of Krebs Cycle.
3. It is also known as the citric cycle since citric acid is the 6 carbon molecule that initiates the Krebs cycle.
4. It takes place in mitochondria which is the energy generator for the cell, specifically it occurs at the matrix of mitochondria. 
5. It has 8 steps and each step is catalyzed by a specific enzyme.
6.  Overall chemical equation for the Krebs cycle: oxaloacetate + acetyl-CoA + ADP + Pi + 3NAD⁺ + FAD → CoA + ATP + 3NADH + 3H⁺ + FADH2 + 2CO2 + oxaloacetate
7. Oxaloacetate is the final product of the Krebs cycle then it goes back and combine with acetyl-Coa again to start a new cycle.
8. Acetyl-CoA is formed from pyruvate oxidation where a pyruvate molecule releases one carbon and oxidase by NAD+ then combine with the enzyme CoA. 
9. Acetyl- CoA (2C) enters the cycle releases CoA and combine with oxaloacetate(4C) to form citric acid (6C)
10. Citric acid(6C) undergoes isomerization to form isocitric(6C).
11. Isocitric(6C) converts into α-ketoglutarate (5C), one carbon and two hydrogen atoms are lost during the process which reduces NAD+ into NADH.
12.  α-ketoglutarate (5C) converts into succinyl-CoA (4C). A Carbon is lost, enzyme CoA is added, and two hydrogen atoms has reduced NAD+ into NADH.
13.  succinyl-CoA (4C) converts into succinate (4C).  Enzyme CoA has been released, GDP has reduced from the process in which then later oxidased by ADP in order to produce ATP. 
14. FADH 2 through the reduction from FAD+ during the conversion from Succinate(4C) to Fumarate (4C).
15. Fumarate(4C) converts into Malate (4C) by an addition of water. 
16. NADH is produced from the conversion from Malate(4C) to Oxaloacetate(4C).
17. Krebs cycle will occur twice since glycolysis can generate two pyruvates. 
18. Energy is produced in step 3.4.5.6 and 8.
19. NADH & FADH2 produced from the cycle will move into Electron Transport Chain in order to convert into ATP.
20. The carbon dioxides formed from the cycle will move out of the cell as metabolism wastes.

3 Laws of Thermodynamics with Respect to Metabolism Process

The first law of thermodynamics: Energy can neither be created or destroyed.
This law is obeyed by the metabolism process since the carbohydrates consumed have not been lost but absorbed by the body as a source of energy or heat.
The second law of thermodynamics: All spontaneous events are increasing the total entropy in the system.
The second law has applied to the process of metabolism by which the carbohydrates have changed its original states as the progress carries on, in which it has created entropy.
The third law of thermodynamics: Absolute zero is removal of all movements.
First of all, with respect to recent science researching we have not yet reached to the point where absolute zero is at. Secondly,  human is not able to survive at such temperature.

Specifically to the second law of thermodynamics with respect to the metabolism process. The second law has stated that the entropy increases over time. Since all biological organism are undergoing  exergonic processes to maintain the internal order.  All exergonic processes are spontaneous and are creating entropy in which negative energy are produced from the activation energy used. More energy available for use after the process. However, with respect to the first law of energy, the energy are conserved within the process in a form of heat. Also the randomness created by the metabolism can be proven by the biological process such as photosynthesis or cellular respiration. Where final products are in  different states or energy forms from the initial inputs. ( photosynthesis uses heat as initial input, and produced ATP as the final products.) Therefore, as conclusion, the metabolism has obeyed the second law of thermodynamics in which randomness has been created.

20 Facts on Carbohydrat

1. Carbohydrate is one of the four macro-molecules .
2. The main function of carbohydrates is to store energy. They are the main energy source in living organisms.
3. Carbohydrates contain carbon, oxygen and hydrates only.
4. Monosaccharide can be divided into Aldoses and ketoses. Aldoses are the sugars that contain an aldehyde group at the end such as glucose. Differently, ketoses have a ketone group (most likely at C2) , one of the examples of ketoses is Fructose. 
5. Sugars are usually seen in pentatoses ( 5 carbons ) or hexoses (6 carbons ). In order to become stable, they generally would form a ring at where the carbonyl group is at. 
6. Fructose and glucose are both hexoses, even though fructose forms a ring of five carbons with one extra carbon attaches on the C5.
7. Sugars are not plain 2D diagrams but in real life it can be presented into two ways -- "chair" and "boat".However chair form is more stable.
8. Glycosidic bonds are formed when two sugars combine though a process of condensation (dehydration synthesis) . In which the water is produced in order to link two carbohydrates together. 
9. Opposite to condensation is the synthesis of hydrolysis. The process of separate two sugars by adding in the water.
10. Disaccharides means the molecule combined from two monosaccharides. Examples of disaccharides are : maltose,  a starch formed by two glucose (C1-4). Sucrose, commonly known as table sugar in which is formed by glucose and fructose. Lactose, it is found in the milk and formed from galactose with glucose.
11. The shape of α linkage looks like two molecules are "holding hands" and "pointing". Examples: Maltose, Sucrose.
12. The shape of β linkage is looks more similar as a straight line rather than α linkage. Example: Lactose.
13. Carbohydrate polymers ( such as starch, glycogen and cellulose ) are formed from many monosaccharides connected together with glycosidic linkages. 
14. Amylose is a glucose polymer with α(1-4) linkages. It normally presents in a single helix shape.
15. Amylopection is a glucose polymer with mainly α(1-4) linkage, but few of α(1-6) linkages in which is able to produce multiple chains. 
16. The polymer of energy storage in animals is called glycogen, in which is a glucose polymer with α(1-4) linkages and α(1-6) linkages. However, it contains more α(1-6) linkages than amylopectin so it is able to form more branches than amylopectin.
17. In order for the plant cells to keep its shape, the cell walls of plant cells contains cellulose. Cellulose has long chains of glucose with β(1-4) linkages in which stabilizes its shape. 
18. Humans are unable to digest cellulose in the plants ( such as grass or vegetables) due to the lack of the appreciate enzyme to breakdown the β linkages. Unlike humans, animals such as sheep or cow has the symbolic enzymes in the intestinal tract that allows them to digest the plants.
19. Oligosaccharides means few monosaccharides are joined together either in linear or branched chains. They covalently attached to proteins or to membrane lipids.
20. Selectins are integral proteins of the plasma membrane with lectin-like domain that protrude on the outer surface of mammalian cells. 

Notes on Restriction Endonuleases, Gel Electrophoresis, Plasmid and Transformation

Compare & Contrast : Replication, Transcription and Translation

Five of the Great Scientists in the Genetics Field

Hugo De Vries (February 16,1848 - May 21, 1935)
De Vries is one of the first geneticists. Both De Vries and Mendel had worked on the research of the discovery of the law of heredity with the unawareness of each other. He is also known suggesting the concept of the genes. In which himself called this particle contains inheritance traits as pangenes.  He introduced the theory of mutation, in which he believed species evolve one from another through sudden changes in traits. 

Thomas Hunt Morgan ( September 25, 1866 - December 4, 1945)

Morgan was initially again the theory of chromosomes contain inheritance traits. He worked with his students in Columbia University, together they studied the reproduction of the Drosophila melanogaster (a common seen type of fruit flies). He then became a big supporter of the idea of the chromosomes passes down the inheritance traits. Morgan and his students provided proofs for the chromosomal theory of inheritance. They also worked out the evidence for genetic linkage in which is the concept that there are more than one genes located on the same chromosome. Their research also include non-disjunction and chromosomal crossing over.

Walter S.Sutton (April 5, 1877 - November 10, 1916)

Sutton is an American scientist who applied Medal's Law of inheritance to the chromosomes and concluded the chromosomes are the basis of inheritance. He observed each chromosome in the grasshoppers' cell are clearly different. The chromosomes reduce the number of chromosomes in gametes. Sutton published his work in 1903. However, he never finished his research. He entered medical school and became a surgeon, then served in WWI as a doctor. He died at age of 39.

Rosalind Franklin (July, 25,1920-April 16,1958)
She is the first person who took a clear picture of the structure of DNA with X-ray diffraction technique. In which later it has helped Watson and Crick with the building the 3D molecular structure of DNA. Her picture of DNA has shown a clear "X" shape. This discovery prompted Watson and Crick that DNA is not a straight ladder but instead it is a twisted double helix. The Double Helix structure is "protecting" the hydrogen bonds in DNA from denaturing by the water. Unfortunately, she died 4 years earlier before the Nobel Prize in 1962 most likely due to the frequent exposure to X-ray.


Barbara McClintock (June 16, 1902 - September 2, 1992) 
McClintock awarded the Nobel Prize of 1983 in Physiology or Medicine for her discovery of the transposition of corn chromosomes. She realized the maize (corn) husks have different colors and the corn kernels have spots. She worked on her observation at the Cold Spring Harbor Laboratory. McClintock then found the existence of "jumping" genes, she is the first one who recognized this element. She concluded from her work that the small segment of DNA "jumps" between different chromosomes, and this action leads to activate or deactivate of certain traits.




Bibliography 

"Barbara McClintock." National-Academies.org | Where the Nation Turns for Independent, Expert Advice. Web. 12 Feb. 2012. <http://www.nas.edu/history/members/mcclintock.html>. 

"Hugo De Vries :: DNA from the Beginning." DNA from the Beginning - An Animated Primer of 75 Experiments That Made Modern Genetics. Web. 11 Feb. 2012. <http://www.dnaftb.org/6/bio.html>. 

"Rosalind Franklin Biography | Genius of Britain | Athena." Athena - Engage Your Mind | Expand Your World. Web. 10 Feb. 2012. <http://www.athenalearning.com/programs/genius-britain/rosalind-franklin-bio>. 

"Thomas Hunt Morgan :: DNA from the Beginning." DNA from the Beginning - An Animated Primer of 75 Experiments That Made Modern Genetics. Web. 12 Feb. 2012. <http://www.dnaftb.org/10/bio.html>. 

"Walter Stanborough Sutton :: DNA from the Beginning." DNA from the Beginning - An Animated Primer of 75 Experiments That Made Modern Genetics. Web. 11 Feb. 2012. <http://www.dnaftb.org/8/bio-2.html>.