Oh, DEER!

Prancing on a grass field pretending to be a wild animal during class time is what every learning environment should be like! Not only is it entertaining, but it's memorable.

As two deer approached the plentiful number of resources from a distance, it was easy to see that this would be the ideal environment. Unlimited resources such as food, water and shelter sounds like a magical place. However, the deer unsurprisingly mate and boost the population which will ultimately increase the competition for the resources.

 As competition gets worse and worse, some deer will die off and decompose. It is simply the survival of the fittest as exemplified by the other students. As some sprinted to the other side to get the resources, compared to those who simply walked over, they were less likely to survive. Those who could run faster had the advantage over those who did not; the faster runners were more likely to outrun the predators. These different factors and advantages would be dependent factors of density.

 However, there are simply just some factors that cannot be controlled. Fit or not, the deer will not be able to fend off a forest fire, a drought, or a floods. These density independent factors could also lead to the declination of a population in the wild.

In summary, everything must be in equilibrium. There cannot be too many deer in contrast to resources and vice versa, there cannot be too many predators and there cannot be back-to-back natural disasters. All of these different factors leads to the changes in the population and is are key factors in the extinction of any species.

Kreb's Cycle.

- discovered by Sir Hans Krebs (1900-81) in 1937

- takes place in the mitochrondial matrix
- part of cellular respiration

- is an eight-step process with each step catalyzed by a specific enzyme

- the original glucose molecule is entirely consumed at the end of the cycle

 Steps of the Kreb's Cycle:

1. acetyl group (2C) condenses with oxaloacetate (4C) and forms citrate (6C)
2. citrate (6C) is rearranged to isocitrate (6C)
3. carbon dioxide is lost, NAD+ is reduced to NADH, isocitrate becomes alpha-ketoglutarate (5C)
4. carbon dioxide is lost, coenzyme A is added, two hydrogen atoms reduce to NAD+ to NADH, and it becomes succinyl-CoA. (4C)
5. ATP is formed by substrate level phosphorylation, coenzyme A is released and succinate (4C) is formed.
6. two hydrogen atmos reduce from NAD to NADH2 and is converted into fumerate (4C)
7. fumerate to maltate (4C)
8. two hydrogen atoms reduce NAD+ to NADH, and is converted into oxaloacetate (4C)

- cyclic process because the oxaloacetate is a product and soon becomes a reactant

- energy is harvested in steps 3, 4, 5, 6, 8.

- NADH and FADH2 molecules will eventually be transferred to ATP to the last stage of cellular respiration

- all six carbon atoms of glucose have been oxidized and released as metabolic waste as carbon dioxide

Our Creation!

The outcome of what was the most creative quiz I have ever 'written' was evidently very appealing and educational. For those who are visual learners, such as myself, it was a very good learning trick.

Metabolism and the Law of Thermodynamics.

DEFINITIONS:

Catabolic Reactions: reactions that result in the breakdown of complex substances.
Anabolic Reactions: cells build complex substances from simpler subunits e.g: DNA from nucleotidessum of all anabolic and catabolic processes in a cell or organism
Metabolism: sum of all anabolic and catabolic processes in a cell or organism

First Law of Thermodynamics/Law of Conservation Energy: states that energy can neither be created nor destroyed. It may change from one form to another, but the energy in a closed system remains constant.

Second Law of Thermodynamics/Law of Entropy: states that when energy is transferred, there will be less energy available at the end of the transfer process than at the beginning. Due to entropy, which is the measure of disorder in a closed system, all of the available energy will not be useful to the organism. Entropy increases as energy is transferred.

Third Law of Thermodynamics/Absolute Zero: theoretical temperature (0K) at which entropy reaches its minimum value.

CONNECTIONS:

 It is important to keep in mind that the human body does not consume energy, it merely changes it from one form to another, in reference to the first law, where it can be concluded that energy is conserved. The Law of Entropy states that a highly ordered system, such as life, tends to become more and more disordered. The increase in entropy in the surroundings produced by the living system is always greater than the decrease in entropy obtained in the living system itself. For example, if one were to drop mass, its potential energy is transformed into kinetic energy, and then into heat, sound and light. As a result, the entropy of the surroundings (the universe) will increase. The change in entropy is a function of the energy transformed in the body. In other words, an exergonic reaction releases energy which would increase entropy while endergonic reactions would decrease entropy. Looking at it from a 'big picture' perspective, where the planet is considered a closed system, the entropy will always be increasing. Additionally, if the world reached a temperature of absolute zero, humans would cease to exist for all the bonds would be broken. Humans are nothing but bonds being held together... therefore, is there really a point in referring the third law to metabolism? If I must, it would be the point where all molecular motions would cease and the high temperature would render the enzyme useless, for they would not be able to function. Ultimately, this is how I think metabolism obeys the three Laws of Thermodynamics.

Carbohydrates - twenty points to keep in mind.

1. among the most common organic material on Earth

2. used by organisms as sources of energy, as building materials, and as cell surface markers for cell-to-cell identification and communication

3. composed of carbon, hydrogen and oxygen in a 1:2:1 ratio

4. emperical formula:

where n represents the number of carbon atoms

5. the simplest carbohydrates are monosaccharides which contain a single chain of carbon atoms which hydroxyl groups are attatched, additionally the two simplest forms of monosaccharides are dihydroxyacetone and glyceraldehyde.

6. monosaccharides can be distinguished by the carbonyl group they possess, whether it be aldehyde of ketone, as well as the number of atoms in their carbon backbone

7. sugar with three carbons is called a triose, four carbons - tetrose, five carbons - pentose and six carbons - hexose

8. when two monosaccharides come together, it is called a disaccharide

9. when a few of the disaccharides form a covalent bond, it is called oligosaccharides

10. polymers consisting of chains of monosaccharide of disaccharide units are called polysaccharides

11. due to the tetrahedral nature of carbon bonds, and depending on the sugar, pyranose sugars form a 'chair' or 'boat' configuration

12. glycosidic bonds forms when the anomeric hydroxyl and a hydroxly of another sugar or some other compound that can join together which results in the splitting water and ultimately forming the glycosidic bond

13. plants store glucose as amylose of amylopectin, glucose polymers collectively called 'starch'

14. glucose storage in polymeric form minimizes osmotic effects

15. amylose if a glucose polymer withlinkages and adopts a helical conformation

16. the 'twin sister' named amylopectin is uglier, with a glucose polymer mainly  linkages, but it also has branches formed by linkages

17. amylopectin has a friend named glycogen with a similar structure with more  branches where the highly branched structure permits rapid release of glucose from glycogen stores

18. cellulose is a major component of plant cell walls for strength and rigidity, and it consists of long linear chains of glucose with  linkages

19. lectins are glycoproteins that recognize and bind to specific oligosaccharides

20. selectins are integral proteins of the plasma membrane with lectin-like domains that protrude on the outer surface of mammalian cells

Biotechnological Tools and Techniques.

Restriction Endonucleases (Restriction Enzymes)
- molecular scissors that can cut double-stranded DNA at a specific base-pair sequence
- each restricion endonucleases regonize a characteristic sequence of nucleotides known as 'recognition sites,' which are typically four to eight base pairs long
- palindromic because both strands have the same base sequence when read in the 5' to 3' direction
- ends of DNA fragments produced by a cut by different restriction endonucleases differ, depending on where the phosphodiester bonds are broken in the recognition sites
- the decrease in occurence of longer recognition sites results in fewer cuts - an important factor for molecular biolgoists who want to excise a piece of DNA that includes a whole gene.
- isolated and purified soely from bacteria
- provide a crude immune system
- around 200 of these restrictions endonucleases are avaliable commercially to molecular biologists

Gel Electrophoresis
- through taking advantage of the chemical and physical properties of DNA, gel electrophoresis seperates the unwanted fragments from the desired gene
- DNA fragments migrate through the gel at a rate that is inversely proportional to the logarithm of their size
- usually a square or rectangular slab and consists of a buffer containing electrolytes and agarose (gel-forming polysaccharide found in some types of seaweed that is used to form a gel meshwork for electrophoresis) or possibly polyacrylamide (aritifical polymer used to form a gel meshwork for electrophoresis)
- the DNA solutioon containing fragements to be seperated is mixed with a loading dye containing glycerol - a loading dye which allows visualization.
- using direct current, a negative charge is placed at one end of the gel where the wells are, and a positive charge is placed at the opposite end of the gel. The electrolyte solution conveys the charged electrode, with the shorter fragments migrating faster than the longer fragments, acheiving sepeartion
- small molecules can be visualized (they migrate ahead of all the DNA fragments) the electric current can be turned off before they reach the end of the gel.
- gel electrophoresis is not limited to the sepeartion of nucleic acids but is also commonly applied to proteins

Plasmids
- small, circular, double stranded DNA molecules lacking a protein coat that naturally exists in the cytoplasm of many starins of bacteria
- independent of the chromosome of the bacterial cell and range in size from 1000 to 200 000 base pairs
- carry genes that express proteins able to confer antibiotic resistance
- protect bacteria by carrying genes for resistance to toxic heavy metals, such as mercury, lead, or cadmium
- some bacteria carry plasmids possessing genes that enable the bacteria to break down herbicides, certain industeial chemicals or the components of petroleum
- relationship between bacteria and plasmids are endosymbiotic - both benefit from this mutual arrangement
- copy number: number of copies of a particular plasmid found in a bacterial cell
- engineered to contain a unique region that can be cut by many restriction enzymes
- after becoming recombinant DNA, a combination of the original plasmid DNA and the foreign DNA may now be introduced into a bacterial cell where it will be replicated to form many copies within the cell

Transformation
- the introduction of DNA from another source
- bacterium that has taken in a foreign plasmid is referred to as being transformed
- calcium ions neutralize the negative charge from the phosphate group on the plasmid DNA and on the phospholipids found in the cell membrane, minimizing the repelling effect of like charges, DNA can then enter the bacterial cell more easily
- ekectrioiratirs, chambers that subject the bacteria to an electric shock are also used to loosen the structure of the cell walls and allows foreign DNA to enter.

The story of replication, transcription and translation.

	Replication	Transcription	Translation
Initiation	- helicase - single stranded binding protein keep template strands apart - gyrase releases tension from the unwinding DNA - primase (A to U, C to G)	- All in the initiation complex found in the promoter region - transcription factors (proteins) - TATA box on DNA - RNA II (protein and template)	- tRNA, mRNA, the first amino acid and two ribosomal subunits are brought together - MET, the start codon - read 5’ AUG 3’
Elongation	- DNA polymerase III elongates from 5’ to 3’ and reads 3’ to 5’	- Known as the Transcription Unit - RNA polymerase II reads DNA 3’ to 5’, ultimately creating RNA 5’ to 3’ that is similar to the coding strand	- read mRNA from 5’ to 3’ - codon recognition occurs at the A-site with the bonding of mRNA with the anticodon - peptide bond formation with amino acids from A site and polypeptide at P site - ribosome move tRNA with polypeptide from A to P site for translocation.
Termination	- DNA polymerase I proofreads and replaces RNA primers with DNA nucleotides - ligase ‘glues’ the gaps	- AAUAAA sequence (RNA) stops the production of RNA - pre mRNA is created	- stops upon reaching a stop codon: UAA, UAG, UGA