Neurotransmitters

Serotonin

- is a neurotransmitterthat is found naturally in the human brain

- is important in transmitting nerve impulses

- produced amino acid tryptophan 

- can be considered a "happy" hormone

- helps to regulate moods, temper anxiety, and relieve depression and plays an important role in regulating such

things as aggression, appetite, and sexuality

Endorphins

- a natural pain reliever produced by the body in response to a number of factors.

- transmit signals throughout the nervous system and are found in the brain

- releases varies according to the individual

- the primary activity of endorphins is to relieve pain, they can also trigger feelings of euphoria

Acetylcholine

- the first substance proven to be a neurotransmitter

- produced by neurons referred to as cholinergic neurons

- as a chemical transmitter find in both the peripheral nervous system (PNS) and central nervous system (CNS) 

- a deliverer of sodium ions 

- increase acetylcholine can cause heart rate decrease, however, decrease acetylcholine can cause motor 

dysfuntion

Norepinephrine

- a chemical responsible for moving nerve impulses between neurons

- acting as neurotransmitter and stress hormone

- has a role to play in a person’s fight-or-flight response, working in conjunction with epinephrine

- does not function properly, depression and attention disorder may occur

Photosynthesis

Non-Cyclic Electron Flow

-Photosynthesis is the process of converting light energy to chemical energy and storing it in the bonds of sugar.

-It takes place in the chloroplasts, specifically using chlorophyll, the green pigment involved in photosynthesis.

-It occurs when the electrons from water are excited by the light in the presence of P680.

-Light energy causes the removal of an electron from a molecule of P680 that is part of Photosystem II.
-The P680 requires an electron, which is taken from a water molecule, breaking the water into H⁺ ions and O^-2 ions. These O^-2 ions combine to form the diatomic O² that is released.

-Through a series of redox reactions, the electron is transferred to an electron carrier PQ (as long as electron arrived PQ, protons are pumped in from stroma)

-Then the electron is transferred to B6F, more protons are pumped in from stroma.

-The electrons then move through PC and eventually attaching it to a molecule in Photosystem I.

- Light acts on a molecule of P700 in Photosystem I, causing an electron to be "boosted" to a still higher potential.

-The electron continues to pass through FD and FRN and eventually being attached to NADP⁺ and H⁺ to form NADPH, an energy carrier needed in the Light Independent Reaction.

-In Photosystem II, the pumping to H⁺ into the thylakoid and the conversion of ADP into ATP is driven by electron gradients established in the thylakoid membrane.

 

Cyclic Electron Flow

- Light acts on a molecule of P700 in Photosystem I, causing an electron to be "boosted" to a still higher potential.

- The electron continues to pass through FD, instead of going to FRN the electron is transferred to B6F.

-The electrons then move through PC and eventually back to a molecule in Photosystem I.

Calvin Cycle

- Glucose and other carbohydrates are synthesized in the carbon-fixing reaction of photosynthesis, often called the Calvin cycle.

- The carbon dioxide is attached to a five-carbon compound called RuBP, ribulose diphosphate, with an enzyme called rubisco.
- After carbon dioxide has been joined to ribulose diphosphate, a six-carbon product forms, which immediately breaks into two three-carbon molecules called 3-phosphoglycerate.
- ATP and NADPH₂ from the light reactions are used to convert 3-phosphoglycerate to 1, 3-phosphoglycerate to glyceraldehydes 3-phosphate, G3P, the three-carbon carbohydrate precursor to glucose and other sugars.

-One of the G3P leaves the cycle.

-The remaining 5G3P go through a series of steps to become the original RuBP.

-The cycle runs twice for make 1 glucose.

Enzyme Lab

Procedure:

1.       Line up three dry test tubes and label them 1, 2 and 3.

2.       Using a 10.00ml graduated cylinder and pipette, add 3.00ml of hydrogen peroxide into first test tube. This test tube will be used as the standard.

3.       3.00ml of hydrogen peroxide and 3.00ml of water are added into the same 10.00ml cylinder. Pour the solution into a clean, dry test tube to mix it. Using the same 10.00ml graduated cylinder and pipette measure 3.00ml of this solution, and pour it into test tube2.

4.       3.00ml of hydrogen peroxide and 6.00ml of water are added into the same 10.00ml cylinder. Pour the solution into a clean, dry test tube to mix it. Using the same 10.00ml graduated cylinder and pipette measure 3.00ml of this solution, and pour it into test tube3.

5.       Overflow pan is filled with water.

6.       Add water to fill the 1L graduated cylinder to the top and invert it into the pan. Record the volume of gas in the cylinder.

7.       Put 5 disks of liver in a 20.00ml Erlenmeyer flask. A rubber stopper with a funnel and tubing that extends into the 1L cylinder.

8.       Put the rubber stopper on the flask and pour the first test tube’s solution into the funnel. Cap the funnel with finger immediately and shake the flask.

9.       Record the time as long as the gas produced.

10.   Record the new volume of gas in the cylinder.

11.   Repeat step 6 -10 for test tube2 and test tube3.

12.   Clean up

Result:

	Test tube1	Test tube2	Test tube3
Volume of H2O2	3.00ml	3.00ml	3.00ml
Volume of H2O	0.00ml	3.00ml	6.00ml
Volume of the solution add into test-tube	3.00ml	3.00ml	3.00ml
Original volume of gas in the cylinder	75.00ml	66.00ml	67.00ml
Amount of gas after reaction in the cylinder	59.00ml	55.00ml	63.00ml
Total amount of gas produced	16.00ml	11.00ml	5.00ml
The time it used	11.60seconds	15.31seconds	13.52seconds

Thermodynamics

The first law of thermodynamics suggests that energy can be transferred from one system to another in many forms. Also, it can not be created or destroyed. Thus, the total amount of energy available in the Universe is constant.

The second law of thermodynamics also knows as the Law of Increased Entropy. Entropy is the measure of the randomness or disorder of a system. A more random or disordered system will have a higher entropy. Heat is a random form of energy, so adding heat energy to a system will increase its entropy. The second law states that nay process will generate some waste heat energy. This heat energy is random and increases the entropy ( or disorder) of a system.

The energy from the sun allows living organisms on earth to temporarily decrease entropy, but organized systems require an overall input of energy (provided by the sun) otherwise will break down. The second law also says that closed systems become more disorganized over time. Often this is expressed by the saying "entropy tends to increase".

The third law of thermodynamics states that if all the thermal motion of molecules (kinetic energy)could be removed, a state called absolute zeor would occur. Absolute zero results in a temperature of 0 Kelvins or -273.15° Celsius.

4 Macromolecule

Carbonhydrates 

• Structures: C_m(H₂O)_n
• Three main functions: energy for cells, structural support, cell-cell communication

1. Monosaccharides

Three common sugars share the same molecular formula: C₆H₁₂O₆. Because of their six carbon atoms, each is a hexose:

      Glucose: grape sugar, corn sugar, dextrose

      Fructose: honey

      Galactose: part of milk sugar (lactose)

Three common disaccharides:

      Lactose = glucose - galactose (milk sugar) 2. Polysaccharides

      Sucrose = glucose - fructose (table sugar)
      Maltose = glucose - glucose (brewing beer)

  Starches are polymers of glucose. Two types are found:

• amylose consists of linear, unbranched chains of several hundred glucose residues (units). The glucose residues are linked by a glycosidic bond between their #1 and #4 carbon atoms.
• amylopectin differs from amylose in being highly branched. At approximately every thirtieth residue along the chain, a short side chain is attached by a glycosidic bond to the #6 carbon atom (the carbon above the ring). The total number of glucose residues in a molecule of amylopectin is several thousand.

Glycogen

Animals store excess glucose by polymerizing it to form glycogen. The structure of glycogen is similar to that of amylopectin, although the branches in glycogen tend to be shorter and more frequent.
Glycogen is broken back down into glucose when energy is needed

Lipids
Triacylglycerols  (store energy)
Three main categories: fats, steroids, and phospholipids

• A fat is composed of a glycerol molecule (a short hydrocarbon) bonded to three fatty acids through dehydration synthesis. Saturated fats are solids at room temperature and are found mostly in animals, while unsaturated fats are liquids (oils) at room temperature and occur chiefly in plants.
• Steroids are made of four interconnecting carbon rings and cholesterol is the most common steroid.
• Phospholipids are composed of a glycerol molecule bonded to two fatty acids and a phosphate group.This phosphate group is polar although the rest of the molecule is hydrophobic.

Proteins

    They are constructed from one or more unbranched chains of amino acids( polymers) linked together by peptide .

    Functions: structure, support, movement, energy transfer, and defense

    Proteins have many levels of structure.

• Primary level of structure is the sequence of amino acids linked together in a peptide chain.There are only 20 amino acids, each with a hydrogen, an amino group (NH2 -), a carboxyl group (COO -), and an R group. This R group is known as a side chain and is composed of varying molecules.
• The secondary level of structure in proteins is the bending of this peptide chain into either an alpha helix (coil) or a beta sheet (plaited sheet) as a result of hydrogen bonding.
• The tertiary structure is based on the folding of the secondary structure caused by interactions between amino acid side chains. These include ionic and covalent bonds, disulphide bonds, and hydrophobic interactions.
• A protein's quaternary structure is based on the interaction between many peptide chains.

Deoxyribonucleic Acids

• Nucleic acids
• is composed of a nitrogenous base, a fvie-carbon sugar (a pentose), and a phosphate group.
• Five nitrogenous bases: Adnine, Guanine, Thymine and Cytosine. Cytosine will only bond with Guanine and that Adnine will only bond with Thymine.
• A phosphate group is linked to the sugar via a phosphodiester bond and the three nucleotides have become a nucleic acid.
• holds the generic information necessary for protein synthesis

DNA Replication

Initiation:

            The initiation point where the splitting starts is called "origin of replication". The structure that is created is known as "Replication Fork".

            A helicase is the enzyme that splits the two strands. Thereafter, single-strand binding proteins (SSB) swiftly bind to the separated DNA, thus preventing the strands from reuniting. A primase, which generates an RNA primer to be used in DNA replication. RNA Primase can attract RNA nucleotides which bind to the DNA nucleotides of the 3'-5' strand due to the hydrogen bonds between the bases.

Elongation:

            The elongation process is different for the 5'-3' and 3'-5' template. The leading strand is synthesized continuously in the 5'-3' direction by DNA polymeraseIII. The lagging strand is synthesized discontinuously Primase synthesizes a short RNA primer, which is extended by DNA polymeraseIII to form an Okazaki fragment.In the lagging strand the DNA Polymerase I  reads the fragments and removes the RNA Primers. DNA Ligase joins in the Okazaki fragment to growing the strand.

            Each new double helix is consisted of one old and one new chain. This is what we call semiconservative replication.

Termination:

            The last step of DNA Replication is the Termination. This process happens when the DNA Polymerase reaches to an end of the strands. We can easily understand that in the last section of the lagging strand, when the RNA primer is removed, it is not possible for the DNA Polymerase to seal the gap (because there is no primer). So, the end of the parental strand where the last primer binds isn't replicated. These ends of linear (chromosomal) DNA consists of noncoding DNA that contains repeat sequences and are called telomeres. As a result, a part of the telomere is removed in every cycle of DNA Replication.

            The DNA Replication is not completed before a mechanism of repair fixes possible errors caused during the replication. Enzymes like nucleases remove the wrong nucleotides and the DNA Polymerase fills the gaps.


Role of enzymes:

           The enzyme helicase seperates the DNA helix so the DNA can be replicated. The enzyme polymerase matches up the new nucleotide bases to the original bases (during replication) and the enzyme ligase "mends" or "glues" the phosphate "backbone" into place with the new nucleotide bases forming a replication of the original DNA strand. (Whichever strand was replicated at the time).

DNA Replication video&review question

5 Famous Geneticists

Name: Edward B. Lewis
Birth: May 20, 1918 – July 21, 2004
Year of Fame: 1995 (Nobel Prize in Physiology or Medicine)

Contributions:  During the 1950s, Dr. Lewis studied the effects of radiation from X-rays, nuclear fallout and other sources as possible causes of cancer. His Nobel Prize winning studies with Drosophila, founded the field of developmental genetics and laid the groundwork for our current understanding of the universal, evolutionarily conserved strategies controlling animal development.

Publications: Lewis' key publications  in the fields of genetics, developmental biology, radiation and cancer are presented in the book Genes.

Name:Carolyn Widney "Carol" Greider

Birth: April 15, 1961-

Year of Fame:2009( Nobel Prize in Physiology or Medicine)

Contributions: Together with Elizabeth Blackburn and Jack W. Szostak, they discover  how chromosomes are protected by telomeres and the enzyme telomerase.

Publications: Blackburn and Greider  published their findings in the journal Cell in December, 1985.

Name:Barbara McClintock
Birth: June 16, 1902 – September 2, 1992
Year of Fame:1983(unshared Nobel Prize in Physiology or Medicine)

Contributions:McClintock studied chromosomes and how they change during reproduction in maize.  She developed the technique for visualizing maize chromosomes and used microscopic analysis to demonstrate many fundamental genetic ideas, including genetic recombination by crossing-over during meiosis—a mechanism by which chromosomes exchange information.

Publications:McClintock's key  publications are presented in the book: Genetics,Proceedings of the National Academy of Sciences, American Journal of Botany, and American Naturalist.  




 

Name: Arthur Kornberg

Birth: March 3, 1918 – October 26, 2007

Year of Fame: 1959(The Nobel Prize in Physiology or Medicine )

Contributions: Kornberg's primary research interests were in biochemistry, especially enzyme chemistry, deoxyribonucleic acid synthesis (DNA replication) and studying the nucleic acids which control heredity in animals, plants, bacteria and viruses. He discovery of "the mechanisms in the biological synthesis of deoxyribonucleic acid (DNA)" together with Dr. Severo Ochoa of New York University.

Publications: two Books,For the Love of Enzymes: The Odyssey of a Biochemist (1989) and The Golden Helix: Inside Biotech Ventures (2002)

Name: Hermann Joseph Muller

Birth: December 21, 1890 – April 5, 1967

Year of Fame: 1946(unshared Nobel Prize in Physiology or Medicine )

Contributions: Muller discovers the production of mutations by means of X-ray irradiation".

Publications: The Mechanism of Mendelian Heredity(1915)