neurotransmitters

Acetylcholine

• first neurotransmitter identified
• chemical transmitter in both central and peripheral nervous system
• effective deliverer of sodium ions, which stimulate muscles and excite nerves
• an increase in acetylcholine causes decreased heart rate, increased saliva production, and makes the muscles ready for for work; when there is a high dose of it, it causes tremour and convulsions, when there's too little, it causes motor dysfunction
• Botox works by suppressing this neurotransimtter (inject Botulin, a toxin that suppresses the acetylcholine, muscles have no stimulation)

Serotonin

• synthesized from the protein tryptophin
• affects our mood and associated with biological processes or disorders such as depression, migrain headaches, anxiety, sleeping disorders etc
• nicotine increases serotonin levels (one of the reasons why a person who starts quitting smoking gains weight because he/she is trying to get their 'fix' of serotonin from food)
• foods that increase serotonin levels: dark chocolate, whey protein, flax seeds, banana

Endorphins

• can be found in the pituitary gland and also distributed throughout the nervous system
• stress and pain are the two most common factors that lead to release of endorphins
• the body produces endorphin after prolonged, continuous exercise (e.g. "runner's high")
• endorphins lead to feelings of euphoria, release of sex hormones, modulation in appetite, decreased feelings of pain, and enhanced immune response
• certain foods such as chili and chocolate can also enhance the sercretion of endorphins

Norepinephrine

• a stress hormone, secreted by the brain (adrenal glands during synaptic transmission)
• release energy from fat, increase heart rate, increase muscle readiness
• can be used to treat life-threatening low blood pressure (works by constricting the blood vessels and increasing the blood pressure and glucose levels)

photosynthesis

CO₂+ H₂O --> C₆H₁₂O₆ + O₂

_{Non-Cyclic Electron Flow}

• 1.       Light photon strikes PS II (P680), electron gets excited and goes to the reaction center.
  2.       Z protein splits H₂O into O₂ (leaves the cell) , H⁺ proton which goes into lumen, and releases 2 electrons (photolysis)
  3.       Electron passes to PQ, which passes to B₆F through redox reaction, and during this process, H⁺ ion gets pumped into the lumen from stroma ([H⁺] increases inside lumen, prepares for chemiosmosis)
  4.       The electron continues to pass to PC, then
  5.       At PS I (P700), when light photon strikes, the electron passes to Fd, then to FNR (or NADP reductase).
  6.       FNR uses the two electrons and H⁺ (from stroma) to reduce NADP⁺ to NADPH (which goes to Calvin Cycle).
  7.       At ATPase complex, because of the H⁺ ions that added up inside the lumen, this drives the chemiosmosis, in which the high [H⁺] would move from inside the lumen to outside (stroma).
  8.       As protons move through the ATPase to stroma, ATP is formed (photophosphorylation)
  
  
  Cyclic Electron Flow
  
  
  9.        When light is not sufficient, only PS I is involved in a cyclic electron flow: photons strike PSI, electron passed to Fd, then B₆F complex then to PC (an ATP is made in the process), then back to PSI
  
  
  Calvin Cycle 
  (C₃ Plants @ cool, moist environments) (e.g. soybean, wheat, rice)
  
  
  10.   Calvin cycle starts with 3 molecules of ribulose RuBP (1,5-biphosphate) in Phase 1: Carbon fixation where 3 CO₂ are added to the enzyme rubisco to make 6 molecules of PGA (3-phosphoglycerate), which is extremely polar and need an extra P
  11.   Phase 2: reduction reaction: Uses 6 ATP to add a phosphate to each of the PGA to make it into 1,3 BPG (1,3-biphosphoglycerate)
  12.   The first phosphate is attracted to NADPH’s H⁺, so 6 NADPH are used and becomes 6 NADP⁺ (6 P’s run away with 6 H⁺’s), resulting with 6 molecules of G3P (glyceraldehydes 3-phosphate)
  13.   1 molecule of G3P comes out of the cycle and combines with another G3P to form glucose/starch/sucrose {*need to run cycle twice to get a sugar since 2 G3P come to make a sugar}
  14.   Phase 3: regeneration of RuBP : RuBP is regenerated through a series of steps, and produces 3 molecules of RuBP again to continue the cycle
  
  
  C₄ Plants @ hot, dry environments (e.g. sugar cane, corn)
  (separate by location)
  
  
  15.   There are alternative mechanisms of carbon fixation evolved in hot, acid climates for C₄ plants (their stomata are clsed on hot, dry days, but there’s still light and O₂, so they need a carbon storage)
  16.   When stomata is open, they fix extra carbon, store extra carbon in mesophyll cells
  17.   They use an enzyme called PEP carboxylase and catalyzes the addition of a CO₂ molecule to a three-carbon molecule called PEP, which makes oxaloacetate (OAA) ßstore carbon
  
  
  
  
  CAM Plants @ hot, dry, desert environments
  (separate by time, same location) (e.g. pineapple)
  
  
  18. In dry environments, stomata has to be very carefully regulated
  19. Daytime: stomata shut tight, to preserve water, use the CO₂ stored in vacuoles from night time to use in Calvin cycle
  20. Night time: temperature is less hot, humidity is higher, stomata opens to get CO₂ 

enzyme lab (pH levels)

Purpose: To see the effects of varying pH on the enzyme activity and to find the optimal pH for catalase to work.

Procedure:

1. Dilute solutions of HCl and NaOH in different test tubes according to the table below, add 5 mL of H₂O_{2 to each test tube, swirl to mix}
2. _{Set up a water displacing station: fill a water trough and graduated cylinder with water (to the top), invert the graduated cylinder into the water trough carefully (do not let air in).  Place a beaker underneath the water trough to collect displaced water.}
3. Insert a rubber tube into the graduated cylinder that is connected to a rubber stopper (will be used to cover Erlenmeyer flask)
4. _{In an Erlenmeyer flask, add 5 pieces of filter paper (soaked in liver juice) to the bottom of the flask}
5. _{Add the first dilution into the flask, shake and cover the flask immediately, use a timer to record time needed for the reaction.}
6. _{Stop timer and record results when oxygen stops displacing water and when water stops overflowing from the water trough}
7. _{Repeat steps 2-6 for other dilutions}

Dilutions:

HCL	0ml	3ml	1ml
Water	0ml	2ml	4ml
time	39’	1:07’	1:45’
Amount water displaced	0 ml	0ml	5ml

NaOH		1ml	2ml	3ml	1ml *2nd trail
Water		4ml	3ml	2ml	4ml
time		2:10’	3:00’	2:40’	2:21’
Amount of displaced	gas	153ml	15ml	5ml	167ml
	water	115ml	11ml	2ml	220ml

lab partners: Ellen Zhou, Grace

entropy

Entropy is chaos, disorder, randomness.
According to the second law of thermodynamics, everything that happens in the universe leads to more disorder, everything increases in complexity over time.
Disorder puts energy in a usable form (free energy), sometimes a system may seem like it's getting more organized but more work is required, leading to even more chaos.

Law of Thermodynamics

The 3 Laws of Thermodynamics are:

1. Conservation of mass-energy: Energy can neither be created nor destroyed, they can only be converted from one form to another
2. Law of Entropy: all spontaneous events act to increase the total entropy (measurement of disorder/chaos)
3. Absolute Zero: absolute zero is removal of all thermal molecular motion

Second Law of Thermodynamics with reference to metabolic processes:

Living organisms constantly use anabolic processes to build highly ordered structures such as proteins, DNA, and membranes.  These are endergonic reactions which are not spontaneous and uses up energy.  This seems to violate the second law of thermodynamics by decreasing the amount of disorder and increasing the free energy.  However, in reality, every 'order' created by anabolic processes are actually followed by an even greater disorder caused as these catabolic processes release energy.  The overall (net) free energy is less than 0, more disorder is created, which supports the second law of thermodynamics.  

macromolecules

Deoxyribonucleic Acids

• It is a polymer made up of nucleotides (adenine, thymine, cytosine, guanine), ribose sugar, and phosphate.
• It contains phosphodiester bonds, hydrogen bonds, and glycosyl bonds.
• The functional groups in this macromolecule are carbonyl and hydroxyl groups.
• Functions: contains genetic material for inheritance and replication, protein synthesis, and reproduction
• Characteristics: it has a double helix shape with the two strands running antiparallel to each other.

Carbohydrates

(maltose)

• Empirical formula: (CH₂O)_n 
• Carbohydrates may be classified into three groups: monosaccharides, oligosaccharides, and polysaccharides.
• Simple sugars can have spatial arrangement of their atoms, forming isomers with different chemical properties (e.g. glucose, galactose, and fructose)
• Monosaccharides are monomers that can undergo condensation reaction to form dimers (e.g. maltose, sucrose), or polymers.  
• Bonding between the monomers are glycosidic linkage (covalent bonds), the condensation reaction also produces a biproduct of water
• Function: energy storage, structural support, building materials, cell surface markers for cell-to-cell identification and communication
• Characteristics of Carbohydrates (polymers): can be straight chain or branched
• Examples: fructose, glucose, sucrose maltose, lactose, amylose, amylopectin, cellulose, glycogen, chitin

Proteins

(keratin)

• Amino acid polymers folded into specific 3-D shapes.  Its structural characteristics determine its function.
• An amino acid is an organic molecule with a central carbon atom attached to an amino group, a carboxyl group, a hydrogen atom, and an R chain.
• Monomers of protein polypeptide bonds to form polypeptide chains into polymers through condensation reaction
• Functions: signal transduction, cell cycle regulation, differentiation, structural building blocks
• Characteristics: may be polar, nonpolar, or charged, low molecular weight
• Examples: keratin, fibrin, collagen

Lipids

(cholesterol)

• Hydrophobic molecules composed of carbon hydrogen, and oxygen.
• They are polar molecules
• Lipids can be divided into four families: fats, phospholipids, steroids, and waxes.
• Triglycerides are lipids containing three fatty acids attached to a single molecule of glycerol
• Glycerol reacts with fatty acids through a condensation reaction between the hydroxyl group of glycerol and the carboxyl group of a fatty acid.  The bond is called an ester linkage. (esterification)
• Functions: energy storage, membrane structure, hormones, vitamins
• Examples: cholesterol (steroids), testosterone, butter, cutin, beeswax

DNA Replication

• DNA replication is a semiconservative process, in which there is one parent strand and one daughter strand in the replicated DNA.
• Each parent strand is a template for ordering nucleotides to make a new complimentary strand
• There are many sites of replication on a strand of DNA called "replication bubbles", with replication forks on each ends.
• The strands in the double helix are antiparallel, so one strand runs in 5' -> 3' direction, while the other runs in 3'->5' direction
• A new DNA strand can only elongate in the 5'->3' direction

The process:

1. DNA helicase unwinds the double helix
2. DNA gyrase (bacterial enzyme) relieves the tension (produced from unwinding of DNA)
3. Single-stranded binding proteins (SSBs) keeps separated strands of DNA apart
4. Primase (RNA polymerase) makes primer, which signals Polymerase III to make complementary strand
5. DNA Polymerase III then grabs nucleotides to make complementary strands of DNA
6. One of the parental strand (3'->5' into the fork), the leading strand (growing towards the fork) can form a continuous complimentary strand (only need one single primer as the fork continues to separate and the new strand continues to elongate)
7. The lagging strand (5'->3' into the fork) has to be copied away from the fork in Okazaki fragments, in order to elongate in the 5'->3' direction (it also needs a new primer for each fragment)
8. DNA Polymerase I then replaces the RNA primer with DNA
9. DNA ligase join all the gaps that are present on the daughter strands

Five Famous Geneticists

Erwin Chargaff

(1905-2002)

Year of Fame: 1947

Publications that make him Famous: Chargaff's Rules

Contribution to the world of Genetics: His rules on the complimentary base pairs helped Watson and Crick to find the double helix structure of DNA.  His lab also researched on the metabolism of amino acids, lipids, etc.

Arthur Kornberg

(1918-2007)

Year of Fame: 1957

Publications that make him famous: In 1956, he isolated the first DNA polymerizing enzyme (now known as DNA polymerase I).  This won him the Nobel prize in 1959.

Contributions to the world of Genetics: His discovery of the DNA polymerizing enzyme later on became the crucial steps in gene splicing and other techniques in genetic engineering.  It also contributed to the drug-making to treat cancers, AIDS, and other viral infections.

In 1967, he and his team "created life in a test tube" - they produced the active inner core of a virus in a lab.

Rosalind Franklin

(1920-1958)


Year of Fame: 1958 (after her death)


Publications that make her famous: Her discovery that the sugar-phosphate backbone of DNA lies on the outside of the molecule, instead of inside.  She also found that the structure of DNA has two strands, not three.  These were published by her supervisor, Maurice, without her consent.  She also had publications on the structure of an entire virus, called the Tobacco Mosaic Virus.


Contributions to the world of Genetics: Her discovery about the DNA's structure using X-ray crystallography made it possible for Watson and Crick to make the DNA double helix structure.




Barbara McClintock

(1902-1992)


Year of Fame: 1983 (First woman to win the Nobel Prize, unshared!)


Publications that make her famous: Genetic structure of maize: "A cytological and genetical study of triploid maize", "A Correlation of Cytological and Genetical Crossing-Over in Zea Mays"...


Contributions to the world of Genetics: Her theory that genes are transportable on and between chromosomes have helped her proof that genes are responsible for turning physical characteristics on and off.  She also developed the technique for visualizing maize chromosomes and demonstrated many fundamental genetic ideas such as crossing-over during meiosis to exchange genetic information.


Kary Banks Mullis

(1944- )


Year of Fame: 1993


Publications that make him famous: The invention of the polymerase chain reaction (PCR), which won him the Nobel Prize.


Contributions to the world of Genetics: He invented a method (PCR) for amplifying DNA, which is used in medicine, biotechnology, forensics, and genetics.  He also developed a revolutionary approach cause the immune system to react instantly to fight invading toxins and pathogens (Altermune LLC).  It is currently focusing on Influenza A and drug resistant Staphylococcus aureus.