Neurotransmitters

Acetylcholine:

• it is a chemical transmitter in the central/parasympathetic nervous system
• it is the first neurotransmitter discovered
• it is a deliverer of sodium ions
• people who have Alzheimer's Disease have a shortage of acetylcholine
• it is an ester of acetic acid and choline
• too much acetylcholine can decrease heart rate, while a shortage causes motor dysfunction
• can be used in cataract surgery to constrict the pupil

Seratonin:

• a neurotransmitter involved in the transmission of nerve signals
• it is made by the amino acid tryptophan
• it maintains our happiness, and keeps emotions under control
• seratonin is used in depression medications
• in the nerve cell, it is released from the end of the presynaptic cell, and then binds to the postsynaptic cell

Endorphins:

• it works with sedative receptors to relieve pain
• it produces a natural "high" feeling, but it's not addicting
• leads to pleasure; good feelings
• high levels of endorphins lead to less pain and stress
• meditation can increase endorphin amounts

Norepinephrine:

• is a hormone and a neurotransmitter
• as it hormone it gives the body quick energy when stressed
• as a neurotransmitter is transmits nerve impluses from one neuron to the next
• its main function is a stress hormone; the brain releases it in times of stress

Photosynthesis

                                          Electron Transport Chain

Non Cyclic

- Light dependant reaction takes place inside the thylakoid in the chloroplast of a plant cell

1. Light hits PSII (photosystem 2) which absorbs the wavelength of 680 in light. This causes a photon to bounce on thePSII until it hits a reaction centre, where an electron is released.

2. This causes the the splitting of water by a Z protein to acculmulate free electrons, protons (H+) and an oxygen molecule. This process is called "photolysis".

3. The electron then moves to the PQ. While this is happening, a hydrogen proton from the chloroplast stroma is pumped through the PQ and makes PQH2.

4. The electron then moves to b6f, while the hydrogen proton is pumped out to the thylakoid lumen.

5. the electron then enters the PC, then through PSI (photosystem 1, with p700) where light hits again to excit the electron.

6. Electron then moves to Fd, to FNR where the electron turns NADP to NADPH with a H+ floating in the stroma.

Cyclic

1. When there is insufficent amounts of light, the electron is passed from PSI to fd to b6f where a hydrogen proton is pumped through to the thylakoid. The electron continues to the PC then back to the PSI.

2. This process generates ATP from the transition of the proton to the thylakoid, but does not make NADPH, since there is not enough light and ATP carries more energy.

Generating ATP

1. Since there is a high concentration of H+ protons in the thylakoid lumen, the pH level is high and unbalanced compared to the stroma.

2. The H+ are pumped through ATPase, and ADP is turned into ATP.

                                                           Calvin Cycle

Phase #1- carbon fixation

1. 3 RuBP (3 p-c-c-c-c-c-p) [15 carbons] combine with 3 CO2 from the outside with the help of the enzyme rubisco to make 3(p-c-c-c-c-c-c-p) [18 carbons]

Phase #2-reduction

2. This stucture is unstable so it breaks in half to make six 3-phosphateglyercate or 3PGA. (6 c-c-c-p) [18 carbons] Since there is only one phosphate at the end, this stucture is very polar.

3. Thus another phosphate is added to the other end. ATPs give 6 phosphates, and makes ADPs. Now the structure is stable and is called 1,3-bipohsophateglycerate. (6 p-c-c-c-p) [18 carbons]

4. Next NADPH comes and takes a phosphate away to makes NADP+. The phosphate left with the H in NADPH. Now the product is glyceraldehyde-3-phosphate or G3P or PGAL (6 c-c-c-p) [18 carbons]

5. One G3P comes out so 5 G3Ps left. [15 carbons]

       *This G3P is later made into glucose. Since there is only 3 carbons in a G3P, the calvin cycle must be run twice.*

Phase #3-regeneration of CO2 acceptor RuBP

6. Through a series of reactions and using 3 ATPs, the 5 G3Ps (5 c-c-c-p) are turned into 3 RuBPs (3 p-c-c-c-c-c-p) [15 carbons] and the cycle is complete. 

Hydrogen Peroxide and Liver Reaction Lab

Procedure:
1. A 10mL graduated cylinder was acquired. 2mL of hydrogen peroxide and 8mL of water to create a diluted hydrogen peroxide solution of 20%.
2. Step one was repeated for solutions of 30%, 40%, 50% and 60% concentrations of hydrogen peroxide.
3. An overflow pan was filled with water, and a 1L graduated cylinder filled with water was inverted into the pan. The amount of air in the graduated cylinder at the beginning was recorded.
4. 5 disks of liver was placed in a 20mL Erlenmeyer flask. A rubber stopper with a funnel and tubing that extends into the inverted 1L graduated cylinder.
5. The rubber stopper was placed in the flask, and the 20% hydrogen peroxide solution was poured into the funnel. The funnel was capped immediately, and the flask was shaken.
6. The amount of water that the oxygen gas displaced was recorded, and was subtracted from the original amount of air in the graduated cylinder to find the total amount of oxygen produced.
7. Steps 3-6 were repeated for the 30%, 40%, 50% and 60% solutions of hydrogen peroxide.
8. Station was cleaned, and equipment was put back.

Data Table:

Conclusion:
As the amount of substrate (hydrogen peroxide) increases in the diluted solution; the amount of oxygen gas produced in the reaction with the liver increases.


Sources of Errors:

• not immediately shaking the flask with the liver disks and the hydrogen peroxide
• different disks (sizes) of enzymes; some pieces were bigger/ with liver pieces stuck on it
• leftover water in the flask due to rinsing after each trial

The 3 Laws of Thermodynamics

Law 1: (also called Law of Conservation of Matter) states that matter or energy cannot be created or destroyed. In a reaction, the amount of matter in the reactants equal the amount of matter in the products. Same with energy. The amount of energy required for the reaction, is the same as the amount of energy exposed after the reaction (ex. in the form of heat)
Since some energy goes into the outside world, this energy contributes to the second law.

Law 2: (also called Law of Increased Entropy) states that as energy is lost, it increases randomness and chaos in an environment.

Law 3: states that as temperatures approach absolute zero, matter will no longer move; thus no more energy. At this point there will no longer be any matter. Since there is no movement, electrons ceases to make bonds, molecules fall apart, and everything disappears.

Law of Entropy (2nd Law):
- the 'loss' of energy into the outside world creates more chaos. This can suggest that the universe is losing energy, not gaining it. However this 'lost' energy contributes to more randomness in the world.
- example, the universe is constantly expanding (getting more random/chaotic). Whatever happens in the universe will lead to more randomness/chaos.
this law talks about how in nature things are irreversable. An example being evolution; organisms become more and more complicated, the organism does not go back to being simpler.
-For some situations it appears that things are getting simpler (ex. water freezing into ice), but since energy is required to freeze the ice, the situation is acutally more complicated.

The 4 Macromolecules

Macromolecule DNA:

- Are made up of monomers of nucleotides (adenine, guanine, cytosine, thymine), has a sugar phosphate backbone
-Bonding within the monomers are hydrogen bonds, whilst bonding between the monomers are phosphodiester bonds.

- Functions: for inheritence, coding for the production of proteins (protein synthesis), and genetics.

                                 - Shape is a double helix

Macromolecule Proteins:

- Its monomers are amino acids
- an amino group and a carboxyl group make a protein

- Bonding within the monomers are peptide bonds

- Functions: for signaling within a cell, to make cell parts

- Shape is different every time; different shape means different function for the protein
- amino group + carbonyl group makes a protein (the bond between them is called peptide linkage)
- has 4 structures: primary (sequence of AA's)
                               secondary (helix, or pleaded sheet)
                               tertiary (bending of a AA chain due to attraction of other AA)
                               quaternary: packings of chains together
- two types of protein :
 essential (amino acids that animals cannot synthesize,  usually dietary)
  nonessential (made by animal body, usually non dietary)

Macromolecule Lipid:

- It's monomers are glycerol and fatty acids

- It's hydrophillic (water-loving) and hydrophobic (water-fearing)

- Bonds with ester bonds (hydroxyl +carboxyl)

- Function: for energy storage, membrane structure (example in a cell, the phospholipid bilayer), hormones and vitamins.

- Example: a triglyceride, it had a hydrophillic head, and 3 tails that are hydrophobic.
- lipids can be saturated (maximum # of hydrogens bonded to the carbon chains) or unsaturated (has 1+ double bonds, less stable, not the maximum # of hydrogen bonds)


Macromolecule Carbohydrates:

- Monomers are monosaccharides (ex. gluctose, fructose) can be a triose, terose, pentose or hexose. Usually hexose.
- glucose is a hexsose that makes a 6 carbon ring, while fructose is a hexose that makes a 5 carbon ring.
- 2 monosaccharides bonded covalently makes a disaccharide , ex. maltose, lactose
- many monosaccharides makes a polysccharide, ex. Amylose, amylopectin.
- Bonds with glycosidic bond
- in the process called "condensation", glucose+ glucose = water+ maltose (2 monosaccharides make a disaccharide and water)
- in "hydrolysis" sucrose and water come together to make fructose and glucose. (disaccharide and water, makes 2 monosaccharides)
- function: primarily as an energy source

DNA Replication

*DNA replication is called semiconservative replication since there is one old strand and one new strand in the daughter DNA;DNA replicates in the form of a bubble
*the point where the DNA strands begin to be split apart is called the replcation fork
*DNA grows 5' to 3'

1.  DNA helicase unwinds and unzips the double stranded DNA into single strands for replication by breaking the hydrogen bond between the nucleotides.
2.  DNA gyrase helps to relieve the tension in the DNA as it is unwinding, by cutting both DNA strands then gluing them back together.
3.  Since single stranded DNA is very unstable, single-stranded binding proteins (SSBs) help to keep the two single stranded DNA seperated. Once the DNA unzips, it immediately starts to replicate.
4.  The 2 strands are seperated into two types of strands :
      - Leading strand--> the strand which grows 5' to 3' into the replication fork.
    - Lagging strand--> the strand that grow 5' to 3' away from the replication   fork, thus can only replicate in short segments called Okazaki Fragments.

5.  RNA Primase attaches itself to the DNA once it has unzipped and creates a primer (approx. 10-60 RNA segments that are complimentary to the parent DNA strand).
6.  With the primer on, DNA polymerase III attaches itself to the primer and begins to add nucleotides to the parent DNA strand.
7.  However on the lagging strand, the DNA must grow in short segements (Okazaki fragments) because it cannot wait for the whole DNA to unzip first then replicate, or else the DNA will degrade.
8.  DNA polymerase I removes the primers once the polymerase III has finished replicating a section. it replaces the primers with the correct DNA sequences. polymerase I also checks for mistakes in the replication and replaces it with the correct sequences.
9.  Finally DNA ligase glues the gaps between the okazaki segments with a phosphodiester bond.

a link that shows the process of DNA replication: http://www.youtube.com/watch?v=Yl754_TtJ_M

5 Famous Geneticists

James Dewey Watson

Birth: Watson was born on April 6th, 1928 in Chicago,United States .
Year they became famous: In 1953 he and Francis Crick discovered that DNA was a double helix structure.
Publications that made him famous: he published "the Double Helix" which included his findings on DNA in 1968.
Contributions to the world of genetics: Watson's discovery of the double helix structure of DNA help scientists better understand how DNA functions and other categories on DNA such as cloning, hereditary traits,and genes.

Thomas Hunt Morgan


Birth: September 25th, 1866 in Kentucky, USA.
Death: December 4th, 1945
Year they became famous: He began his research on the fruit fly in 1909, and he recieved his Nobel Prize in 1933 for his research on heredity.
Publications that made him famous: He published many books, one of his first being "Mechanisms of Mendelian Heredity" in 1915.
Contributions to the world of genetics: his intensive study of the fruit fly, which teachs scientist about heredity of traits and genes.



Dr. Kary Banks Mullis

Birth: December 28, 1944 in North Carolina, United States.
Year they became famous: In 1983 he developed the Polymeraise chain reaction.
Publications that made him famous: He recieved the Nobel Prize in chemistry in 1993 for his discovery of PCR.
Contributions to the world of genetics: His discovery of PCR made a great contribution to the world of genetics; now one molecule (usually DNA) can be amplifide to billions more molecules for  detailed research to be conducted.

Barbara McClintock

Birth: June 6th, 1902 in Hartford, Connecticut.
Death: September 2nd, 1992

Year they became famous: in 1930 she was the first person to explain the details of crossing over in meiosis.
Publications that made her famous: in 1931 she published the first genetic makeup of her research on maize. Also in 1950 she published a paper on how genes can change their loci on a chromosome, her paper was called "The origin and behavior of mutable loci in maize."
Contributions to the world of genetics: Her studies on genetic transposition told scientists alot about genes and how they can behave, such as "jumping" from one area of a chromosome to another area. McClintock proved that some genes don't always stay in a fixed spot on a chromosome.

Roaslind Franklin

Birth: July 25, 1920 in London, England.
Death: April 16, 1958 in London, England.

Year they became famous: 1952 when she made the first photograph of the DNA's X shape, which later paved the way to prove that DNA's structure is a double helix.
Publications that made her famous: in 1953 Roaslind Franklin published an article in Nature on the DNA which included her famous DNA x-ray.
Contributions to the world of genetics: Rosalind Franklin developed the basis of what DNA's structure is (the double helix), with her x-ray of DNA, which showed an X formation.