Neurotransmitters

Acetylcholine

• It is a chemical transmitter found in the central and parasympathetic nervous system
• It effectively transports sodium ions, allowing muscle to contract and excite nerves. 
• Increasing acetylcholine results in a decreased heart rate, increased amount of saliva, and prepares the muscles for work. 
• With high doses, it can cause convulsions and tremors.
• When levels are low, it can help create to motor dysfunction. 
• Botulin suppresses the release of acetylcoline

Serotonin

• synthesized from the protein tryptophin
• a type of chemical that helps move signals from one area of the brain to another.
• Since it helps in moving signals, it affects many aspects of the brain with regards to mood, sexual desire and function, appetite, sleep, memory and learning, temperature regulation, and some social behavior.
• It can also affect the functioning of the cardiovascular system, muscles and other parts of the endocrine system. 
• nicotine increases serotonin levels 
• foods that increase serotonin levels: dark chocolate, whey protein, flax seeds, banana

Endorphins

• It is found in the  pituitary gland but is given throughout the nervous system
• stress and pain are the two common factors release endorphins
• the body creates endorphin during continuous exercise 
• endorphins give feelings of euphoria, release of sex hormones, modulation in appetite, decreased feelings of pain, and enhanced immune response
• foods such as chili and chocolate can enhance the release of endorphins

Norepinephrine

• a stress hormone, released by the brain 
• release energy from fat, increase heart rate, increase muscle readiness
• can be used to treat life-threatening low blood pressure 

Photosynthesis

Non-Cyclic Electron Flow: (light reaction)

• Photosystem II begins the reaction once the photons hit the reaction centre where it causes H20 to split into its elements (photolysis – by z protein) 
• H+ remains while the electrons travel to PQ in the process of a redox reaction;
• PQ  pumps in protons into the lumen
• Electrons then go to b6f, whereby more protons are pumped into lumen 
• Electrons then go to PC before going to Photosystem I
• Photosystem I  excites the electron before passing it on to Ferredoxin (Fd) 
• At Fd the electrons reduce NADP to become NADPH, before attaching to FNR (ferredoxin-NADP reductase)
•  Since a large number of protons are present in the thylakoid lumen, chemiosmosis, must take place in order to move the protons to the chloroplast stroma – a process in which ATP is synthesized form ADP.

Cyclic Electron Flow

• Occurs when there is not enough light
• It starts at PSI and when light hits it electrons travel through to Fd, B6F, PC, and then back to PSI
• ATP is made in this process

Calvin Cycle: (dark reaction)

• The production of glucose in the production of carbon fixation.
• RuBP (Rubulose Biphosphate), a 5-carbon sugar, gets CO2 from the atmosphere to form a 6-carbon sugar 
• Thereafter the 6-carbon sugar divides to form a 3-carbon sugar also known as 3-Phosphoglycerate.
• The 3-Phosphoglycerate is reduced, as an ATP molecule loses a phosphate to form 1,3 -Biphosphoglycerate 
• 1,3 Biphosphoglycerate is oxidized by an NADPH to for G3P (Glyceraidehyde-3-phosphate) 
•  One G3P leaves cycle in order to form glucose (2 G3P needed per glucose molecule)
• The remaining 5 G3P continue along the cycle in order to RuBP which is the initial molecule in this cycle

Catalase Lab

Materials

• timer
• filter paper
• 100 mL graduated cylinder
• water bath
• 10 mL graduated cylinder
• cork/funnel with tube
• hydrogen peroxide (3% solution)
• liver 
• Erlenmeyer Flask

Procedure

1. The liver was ground up and mixed with the number of filter discs. 
2. One disc was taken placed in an Erlenmeyer flask.The opening of the flask was covered with the cork/funnel attached to a tube. The other end of the tube was placed into the water bath container.
3. The water bath was setup and the 100 mL graduated cylinder was filled to the rim with water and was flipped into the water bath. The opening of the graduated cylinder covered the tube.
4. A 10 mL graduated cylinder to measure 5.0 mL of hydrogen peroxide. 
5. The peroxide was put into the flask and the hole in the funnel was blocked.
6. Swirl/shake the flask until the gas stops displacing the water. 
7. Record the amount of gas produced
8. Discard the products down the sink and wash out the flask.
9. Repeat steps 2-8 for multiple trials with a variable number of filter discs

Qualitative Observations

Before	During	After
H2O2 - colourless solution	- bubbling alot	- white bubbles
liver discs - reddish paper	- water being displaced by gas	- very light brownish translucent solution with lighter red paper discs

 

Quantitative Observations

H2O2 (aq) used (mL)	[enzyme] (# discs)	O2 (g) produced (mL)
5.0	1	55.0
5.0	3	52.0
5.0	5	50.0
5.0	7	48.0

The Second Law of Thermodynamics

The second law of thermodynamics also known as the law of entropy is a measure of disorder in the universe and the availability of the energy in a system to do work. Although, these two ideas may not visually have anything to do with one another, they actually are to be explained simultaneously in order to fully grasp the idea of the law of entropy. It has been stated that the more disordered a closed system is, the closer it is to equilibrium. Equilibrium is reached when the energy inputted is equal to the energy outputted. For example, if one was to take an elastic band, when it is stretched its entropy is zero, but when it is loose the entropy is said to be higher. Although this may not make sense to the naked eye, if one were to analyze a rubber band, it would make sense. When an elastic band is stretched, the crystals are lined up (ordered). When an elastic band is in its loose positions, the crystals go all over the place (disorder). Hence this shows that entropy is higher when the elastic band is loose (disordered).

Entropy is a measure of the amount of energy that is not available for work, or the distribution of energy in a system. An example of when entropy increases is as heat moves from a hot area to a cold area, there is a more even distribution of heat (energy) in the surrounding (system). It is also legitimate to stay that the heat become more disordered, as it was dispersed over a larger areas. 

Macromolecules

Macromolecules are made up of polymers which have subunits bonded together known as monomers. Our bodies are composed of these chains of subunits which in turn allows us to function. Subunits are covalently bonded through condensation reactions where water is a product of that specific reaction. The functionality of macromolecules is determined by its shape. There are four main types of macromolecules: carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates play a significant role in the body as they are the source that provides energy and structural protection in cell walls. In addition they are one of the most common organic molecules. Carbohydrates can be identified as monosaccharides, disaccharides, oligosaccharides, and polysaccharides. Monosaccharides are simple sugars such as Glucose and Fructose. Glucose contains an aldehyde group also known as an Aldses. Fructose is a ketone also known as an Keytoses. Both of these are Hexoses as they contain 6 carbons. However, the difference is that Glucose forms a 6 carbon ring with Fructose forms a 5 carbon ring. Carbohydrates are formed through Glycosidic bonds where : R-OH + HO-R' ---> R-O-R' + H2O. A glycosidic bonds allows a monosaccharide to become a disaccharide. Examples of a disaccharides include: maltose which is made of two glucose monomers, lactose which is made of one glucose and one galactose molecule, sucrose which is made up of one glucose and one fructose. Multiple glycosidic bonds make polysaccharides which are polymers of carbohydrates. Examples include amylose or multiple maltose molecules, and glycogen which is multiple glucose molecules.

Lipids are macromolecules which help the body in digestion, insulation, energy storage, control with hormones, structure with body composition, and vitamins. In addition, lipids are hydrophobic molecules. Some types of molecules include triglycerides, fatty acids, phospholipids and steroids. Triglycerides are made of three fatty acid chains and a glycerol. Triglycerides are formed through ester linkages where an carboxyl group and hydroxyl group react to create the triglyceride and three H2O. Lipids can either be saturated or unsaturated. Saturated lipids are more stable, packable, do not react, have single covalent bonds between carbons, and are solid at room temperature. Unsaturated lipids are less stable, have more room for reactions, can be monounsaturated or polyunsaturated, have kink which make them less packable and are healthier. Phospholipids form a phospholipid bilayer called micelle which includes a fatty acid and phosphate where there is a hydrophillic head and hydrophobic tail. Finally, steroids are lipids with a four carbon ring frame. There are four types of steroids which include cholesterol, vitamin D, cortisol, and testosterone. It is mainly used to increase muscle size.

Proteins polymers of amino acids which are formed through peptide linkage where an amino group and carboxyl group react. Its function is to provide the structure for the body, energy, enzymes and cell cycle regulation. The structure for proteins are primary, secondary, tertiary and quaternary. Primary is a straight sequence of amino acids. Secondary is where forces are generated and closely bind. Teritary is where the amino acid bends and quaternary is where multiple tertiary attach together. Amino acids are non-polar through London forces, symmetrical. Essential amino acids are ones the body cannot produces while non-essential are ones that the body can produce. The main important point for a protein is that is that its shape is what allows it to function. Denaturation is where the protein loses its shape whereas renaturation is where the denatured protein forms its original shape but loses function.

Nucleic Acids are best known for being polymers of nucleotides which include the phosphate group, sugar and nitrogenous base. Its function allows for inheritance, genetics and genes, and protein synthesis. They are formed through hydrogen bonds between complementary bases. It is a weak bond that is able to break apart when necessary for example DNA replication. It also contains phosphodiester bonds is a covalent between the sugar and phosphate group (backbone of DNA strands)

DNA Replication

DNA replication is the process where the double helix containing the DNA unwinds, separates and replicates in order to form two individual copies of the the original double helix. Each new copy contains one parent strand and one daughter stand through the method of semi-conservative replication. Due to the fact that is only one old strand and one new strand, DNA must replicate in the form of a bubble. Replication fork (the edge of the bubble where the two sides meet) is the area where the DNA strand has not unwound itself protecting the sequence from being attacked by enzymes. 

The following is an explanation on the process of DNA Replication:

1. DNA Helicase unwinds and unzips the double helix containing the DNA into single strands for replication through breaking apart the hydrogen bonds between the nucleotides. Simultaneously, DNA Gyrase helps to relieve the tension in the DNA while it unwind by relaxing it (Cutting both DNA strands then gluing them back together).

2. Single stranded DNA is very unstable. If left unraveled for too long, the DNA could degenerate. As the DNA strands are separated they continuously want to reconnect back into their original positions. Single-stranded binding proteins (SSBs) help to keep the two single stranded DNA separated. This is also why once the DNA unzips, it immediately starts to replicate.

3. As the 2 strands are separated they each undergo different methods of achieving a replicated DNA stand in relation to a replication fork:

- The Leading strand grows 5' to 3' into the replication fork.

- The Lagging strand grow 5' to 3' away from the replication fork, thus allowing it to only replicate in short segments called Okazaki Fragments.

4. RNA Primase attaches itself to the DNA once it has unzipped and creates a primer

5. Thereafter, DNA polymerase 3 attaches itself to the primer and begins to add the appropriate Deoxyribonucleoside Triphosphates to the 3' end of the new strand using the template strand as a guide. On the lagging strand, DNA must replicate in short segments because it cannot wait for the whole DNA to unzip then replicate as the DNA will degrade. Okazaki Fragments are created by adding Primase every so often to lagging strand. The Polymerase 3 will then add a few nucleosides. This process will continue until it reaches the replication fork 

6. DNA polymerase 1 removes the primer once the polymerase 3 has replicated a section. It replaces the primer areas with the correct DNA sequences. In addition, Polymerase 1 checks for mistakes in the replicated strand and replaces them with the correct sequences. 

7. Finally DNA Ligase glues the gaps between the Okazaki segments with a Phosphodiester bond.

List of Enzymes 

Helicase

DNA Ligase

Primase

Gyrase

DNA Polymerase 1

DNA Polymerase 3

http://www.johnkyrk.com/DNAreplication.html

5 Famous Geneticists

Rosalind Franklin

Date of Birth: July 25th, 1920 – April 16th 1958

Year of Fame: 1958 (For creating Photograph 51 in 1952 -- after her death)

Contributions: Dr. Franklin, had a significant impact on the study of genetics. She created Photograph 51 through X-ray crystallography (a technique used to determine a molecules three-dimensional structure) in order to show the structure of DNA. At the time the discovery of the structure of DNA was largest advancement in science, for it allowed James Watson and Francis Crick to develop the model of the double helix (using Photograph 51). In addition,  Rosalind Franklin's discovery gave Geneticist's the key to understand the way in which life has passed down for many generations. However, she was unable to publish this discovery.

Publications: Her main discovery was never published but was mentioned in Watson and Crick's article on the DNA. She also wrote four other articles for Nature on Tobacco Mosaic Virus

Arthur Kornberg

Date of Birth: March 3, 1918 – October 26, 2007

Year of Fame: 1959 (Nobel Prize in Physiology or Medicine for isolating the first DNA polymerizing enzyme) 

Contributions: Arthur Kornberg along with his partner Severo Ochoa spent years isolating and purifying enzymes that run cells.  Soon thereafter, they were able to identify the enzyme involved in the creation of DNA -- Polymerase I. This was an important concept in understanding the molecular biology of cells. Kornberg's greatest synthesis was of the virus PhiX174. It was the first time a biochemist had produced a virus in a lab.

Publications: Germ Stories. New York: University Science Books, 2007; The Golden Helix: Inside Biotech Ventures. Sausalito, CA: University Science Books, 1995; DNA Replication. 2nd ed. New York: W. H. Freeman and Co., 1992; Genetic Chemistry and the Future of Medicine. San Diego: University of San Diego Press, 1990;  For the Love of Enzymes: The Odyssey of a Biochemist. Cambridge, MA: Harvard University Press, 1989;  DNA Replication. San Francisco: W. H. Freeman and Co., 1980; DNA Synthesis. San Francisco: W. H. Freeman and Co., 1974; Enzymatic Synthesis of DNA. Hoboken, NJ: John Wiley and Sons, 1961; "Biologic Synthesis of Deoxyribonucleic Acid." Science 131, no. 3412 (20 May 1960): 1503-1508; "Enzymatic Replication of E. coli Chromosomal Origin is Bidirectional." Nature 296, no. 5858 (15 April 1982): 623-627; Kornberg, Arthur. "Science is Great, But Scientists are Still People." Science 257, no. 5072 (14 August 1992): 859; " Nature 366, no. 6454 (2 December 1993): 408; "Wrong Move." Nature 373, no. 6511 (19 January 1995): 184. 

Fredrick Sanger

Date of Birth: August 13, 1918 -

Year of Fame: 1958 (Finding the complete sequence of insulin giving him the Nobel Prize in Chemistry in 1958)

Contributions: In 1943, Fredrick Sanger joined Chibnall's research group at the Cambridge University where they worked on proteins but more importantly insulin. At the time protein chemistry was considered of significant importance and new techniques like fractionation were being put in place. It was believed that there was a real possibility of determining the chemical structure of fundamental components that making up matter. Sanger was able to replicate amino acid sequencing which lead to coming up with a sequence for insulin.

Publication: DNA Sequencing with Chain-Terminating Inhibitors, PNAS, vol. 74, no. 12, p. 5463-5467 (1977);

Barbara McClintock

Date of Birth: June 16 1902 -  September 2 1992

Year of Fame: 1983 (Nobel Prize for Physiology or Medicine due to her discovery in genetic transposition)

Contributions: Barbara McClintock is a highly esteemed geneticist in today's times. She work dealt with cyto-genetics which led her to hypothesize that genes are transportable meaning that they can move around in on the chromosome, and between chromosomes. Her theory was lead from the many colour variations found on kernels after many generations of crossing over. Her proposal was well ahead of what scientists knew about genes at the time, however her hypothesis was proved correct in the 1970s and 1980s when new techniques were established. She was awarded the Nobel Prize in Physiology or Medicine in 1983. 

Publication(s):  "A cytological and genetical study of triploid maize". Genetics 14:180–222; "A Correlation of Cytological and Genetical Crossing-Over in Zea Mays". Proceedings of the National Academy of Sciences 17:492–497; "The order of the genes C, Sh, and Wx in Zea Mays with reference to a cytologically known point in the chromosome". Proceedings of the National Academy of Sciences 17:485–91; "The stability of broken ends of chromosomes in Zea Mays". Genetics 26:234–82; "Neurospora: preliminary observations of the chromosomes of Neurospora crassa". American Journal of Botany. 32:671–78; "The origin and behavior of mutable loci in maize". Proceedings of the National Academy of Sciences. 36:344–55; "Induction of instability at selected loci in maize". Genetics 38:579–99; "Some parallels between gene control systems in maize and in bacteria". American Naturalist 95:265–77

Paul Berg

Date of Birth: June 30, 1926 -

Year of Fame: 1980 (He was awarded the Nobel Prize in Chemistry in 1980 for introducing recombinant DNA)

Contributions: When Paul Berg returned to Stanford, he began to use SV40 as a hypothesis to try and insert new new genes into  cells similar to that of  bacteriophage induces DNA into infected cells. Soon thereafter, he was able to develop a way to join two DNA's together. This led

Publication: "Moments of Discovery: My Favorite Experiments." Journal of Biological Chemistry 278, no. 42;  "Enzymatic Phosphorylation of Nucleoside Diphosphates." Journal of Biological Chemistry 210; "Potential Biohazards of Recombinant DNA Molecules." Science 185; "Asilomar Conference on Recombinant DNA Molecules." Science 188; Exploring Genetic Mechanisms, University Science Books, 1997; Dealing with Genes: The Language of Heredity, University Science Books, 1992; Genes and Genomes: A Changing Perspective, University Science Books, 1991.