Drug Effects

Acetylcholine
A neurotransmitter in both the peripheral nervous system (PNS) and central nervous system (CNS) in many organisms. It is presented in autonomic nervous system (ANS) and in the motor division of the somatic nervous system. It is believed to be involved in memory, mood and learning.

There are two main types of cholinergic receptors, 1)nicotinic and 2)muscarinic.
1.Nicotinic receptors are located at synapses between two neurons and at synapses between neurons and skeletal muscle cells. Upon activation a nicotinic receptor acts as a channel for the movement of ions into and out of the neuron, directly resulting in depolarization of the neuron.
2.Muscarinic receptors, located at the synapses of nerves with smooth or cardiac muscle, trigger a chain of chemical events referred to as signal transduction.
 

Seretoin
A monoamine neurotransmitter presented in pineal gland, blood platelets, the digestive tract, and certral nervous system of human (CNS). It is used to alter mood of a person or treat depression.  Also refered to as Happiness Hormone.

Endorphins (endogenous morrphine)
A neurotransmitter produced by pituitary gland and hypothalamus in vertebrates during exercise, excitement, pain, love, etc.
It act as a pain killer. Immediately after injury, endorphins allow animals to feel a sense of power and control over themselves that allows them to persist with activity for an extended time.

Norepinephrine
A nerotransmitter affect part of the brain where attention and responding actions are controlled. The brain also increases its stimulation on norepinephrine when stress is signaled.

Photosynthesis

Non-cyclic Electron Flow (yield ATP & NADPH)

 

-Light is radiated to plants' leaves and reaches chloroplast where most of the photosynthetic reactions take place. The photons strike PSII (photosystem two) consisting antenna complex and a reaction centre.

-Antenna absorbs photons and transfer the energy from one to another, until it reach to reaction centre-chlorophyll a.

-The energy is used to excite an electron at chlorophyll P680. The electron is captured by electron acceptor, pheophytin.  Through redox reactions, the electron is transferred to plastoquinone (PQ).

- When the electron is missing at PS 680,  Z protein would splits 2H₂O à O₂ + 4H⁺+ 4e^-, the electrons produced will be use to replace the missing one; the oxygen get released as a byproduct; and the hydrogen ions are kept inside in the thylakoid lumen. The process of splitting water is called, photolysis.   

-The electron carrier PQ transfer the electron to b₆-f cytochrome complex while this is happening, hydrogen ions from the chloroplast stroma are being pumped into the thylakoid lumen.

-The electron gets carried away by plastocyanin (Pc) to PSI (photosystem one) replacing the missing electron excited by the last photon energy.

-The electron in PSI excited by photon energy and transferred to FNR (ferredoxin NADP reductase) by ferredoxin the electron carrier.

-The transferred 2e^- +H⁺ floating in the stroma to convert NADP⁺ into NADPH for use of Calvin Cycle.

-The hydrogen ions accumulated through the reaction increases the electrochemical gradient. To balance the pH level between the thylakoid lumen and stroma, H⁺ is pumped out though a complex called, ATP synthase.  By doing so, ADP can be converted into ATP by adding Pi in the process of photophosphorylation.

Cyclic Electron Flow (yield only ATP)                  

-Happens when not enough light or water is presented in the plant cell.

-Photon energy excites the electron at PSI, the electron is transferred through ferredoxin to b6-f cytochrome and back to PSI.

-H+ is being pumped into the lumen adding gradient for chemiosmosis which will produce ATP same as non-cyclic electron flow.    

pH level affecting the rate of enzyme activity Lab

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} 

Title: pH level affecting the rate of enzyme activity Lab 

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

Theromodymamic Laws

I. the total amount of energy in the universe is constant. Energy cannot be created or destroyed vut only converted from one form into another. If an object or process gains an amount of energy, it does so at the expense of a loss in energy somewhere elesin the universe


II. the entropy of the universe increases with any change that occurs.  DS_universe  > 0

III. absolute zero is removal of all thermal molecular motion

In any chemical reactions, the output of energy will exceed the input of energy. Just like investing money into an account, a portion of money is used to make more money as in chemcial reactions the energy is put into something that will yield more energy in the end as a result. 
For example, cellular respiration shown in the diagram. The first part of the reaction is an anatabolic process which energy is used as activaion. Free energy is put into to break glucose and later combined with oxygen to produce carbon dioxide, water and ATP for body function.  The second part of the reaction is a catabolic process. Through the process, the reaction yields greater free energy than the free energy used for synthesis them. More energy means more entorpy. While the reaction is in progress the energy is released and result in the total free engergy less than 0.  Thus, DG< 0.

 
ex. glucose+ oxygen = carbon dioxide + water

4 Macromolecues

Carbohydrate

-Amylopectin

-Monomer: glucose

-1° Bonding: glycosidic
-Function: energy source

 

-contains carbon, hydrogen, oxygen atoms in 1:2:1 ratio

-contain an aldehyde (functional group at the end) or a ketone (functional group inside)group and one or more hydorxyl group

-simplest carbohydrates are monosaccharides

            Examples: galactose, glucose, fructose 

            -glucose is an energy source

            -sugars are linear with five or more carbons but are readily to form cyclic structures when           dissolved in water

-disaccarides have two covalently linked monosaccharides

         Example: sucrose (glucose and fructose), Lactose (galactose and glucose), Maltose (glucose+ glucose)

-polysaccharides are composed of thousands of monosaccharide subunits held together by glycosidic linkages

           Examples: amulopectin, amylose

          -some are straight chains, others are branched

          -two important functions are energy storage and structural support

             Cellulose (polymer b-glucose)top holding hands; Starch (polymer a-glucose) bottom holding hands

Lipids

-Triglycerid

-Monomer: glycerol + fatty acid

-Hydrophilic vs. Hydrophobic(tail)

-1°  Bonding: ester

-Function: energy storage, membrane structure, hormones, vitamins

-hydophobic molecules composed of carbon, hydrogen, and oxygen

-insoluable in water but soluble in other nonpolar substances

-used for energy storage, building membranes, and other cell parts, chemical signalling molecules

-fatty acids with many carbon-carbon double bonds are called polyunsaturated fatty acids        

Divided into four families:

 fats

-most common fat in plants and animals are triglycerides

               -contans three fatty acids and a molecule of glycerol

-saturated fatty acids have single bonds – more stable

-unsaturated fatty acids have one ore more double bond – less stable – break more easily 

  phospholipids

-composed of a glycerol molecule attached to two fatty acid (hydrophobic), and a highly polar phosphate group (hydrophilic)

-tail and head, respectively

- form spheres, micelles, when added to watter (heads dissolve in watter, tails mix with one another in the center)

Steroids

-compact hydrophobic molecules, four hydrocarbon rings, several functional roups

Eg. Cholestrol, testosterone, estrogens

Protein

-Four-stranded parallel  ß-sheet (gold), for a helicaes (red) and a single 316 helix (purple)

-Low molecular wight

-Monomer: 157 amino acid

-1°  Bonding: peptide

-Function: signal transduction, cell cycle regulation, differenciation

-variety of roles, strctural building blocks, involved in almost everything the cell do

-amino acid polymers folded into specific 3-D shapes

-contains carboxyl and amino group 

-proteins have four levels of structure

Primary structure

-the sequence of amino acidss in the polypeptide strand

Secondary Structure

-portions of polypeptide chain forms coil due to hydrogen bond between oxygen of the carboxyl group and hyrogen of an amino group  

-Beta sheets – two parts of the polypeptide chain lie parallel to one another

Tertiary Structure

-contains both beta sheets and helix

Quaternary Structure

-composed of more that one tertiary protein

A change in 3-D shape of proteins caused by changes in temperature, pH, ionic concentration, or other environmental factors is called denaturation (cannot carry out is biological functions)

 

 

Nucleic Acid

-deoxyribonuleic acid

-Monomer: nucleotides

-N-Base: A, T, G, C

-1°  Bonding: phosphodiester

-Function: inheritance, genetic, protein synthesis

 

DNA

-contains sugar deoxyribose, phosphate group, nucleotides (A,C,G,T)

-hydrogen bond between the two strands between nitrogenous bases

-phosphodiester linkage between phosphate group of one nucleotide and the sugar of the next

RNA  

-contains ribose instead of deoxyribose, nucleotide U instead of T

Replication

DNA Replication
-DNA replicate semi-conservatively. During DNA replication, base pairing enables existing DNA strands to serve as templates for new complementary base pairs.
-On each of the upper and lower strand will have many lagging and leading strand. To be more specific at each replication bubble there is one lagging and one leading strand on the DNA itself. 

Replication Enzymes
       DNA Helicase           Primase-RNA Primer    DNA polymerase I     Single Stranded Binding Protein   
 DNA Polymerase III             DNA Ligase                   DNA Gyrase


1) DNA Helicase- Unwind the double helix by breaking the hydrogen bonds between complenmentary base pairs that hold DNA strand together.

2) Gyrase- Massage the unwinding DNA to release any tension.

3) Single Stranded Binding Protein- Bind to exposed single stranded DNA and block hydrogen bonding to prevent the two strand of DNA anneal back.

4) Primase- is an enzyme synthesis RNA Primer, which is the initiation sequence for replication.

5) Polymersase III- build complementary strand using the template strand/ catalyze the elongation of new DNA at a replication fork/grab deoxyribonucleoside trisophate as new strand building up using the template strand. As it is add from the 3' to 5' the leading strand will replicate continuously and the lagging strand will replicate along with the unzipping process of DNA. On the lagging strand there are many different fragments of replicated DNA, Okazaki  fragments, from 3's to 5's due to the prevention of degration of DNA.

6) Polymerase I- remove the RNA Primer from the replicated DNA of the leading and lagging strand.  And replace these RNA Primers with appropriate deoxyribonucleotides.

7) Ligase- act as glue to join the Okazaki fragments of the lagging strands and gaps between pieces of DNA at the end of replication fork.

8) Polymerase I & Polymerase III- proofread the finish replicated DNA.

Francois Jacob

Francois Jacob (1920- )

Background Info---

- Borned in Nancy, France on June 17, 1920.

-Abandoned Medical School due to the out break of WWII and moved to work in London.

-He then enlisted in Franch army as an army doctor and wounded in Normandy battle.

-He was honored with the highest Croix de la Libération.

-Due to his wounded hand he was precluded being a surgon, thus, he became a research biologist.

Year Became Famous---

In 1965, he was granted with The Nobel Prize in Physiology or Medicine along with two other scientists.

Publication Made Him Famous---

- E. coli bacterium represses production of enzymes involved in lactose metabolism when lactose is not available.

-controling of enzyme levels in all cells happens through feedback on transcription.

Contribution to World Genetics---

 Jacob and Monod made key experimental and theoretical discoveries that demonstrated that in the case of the lactose system outlined above (in the bacterium E. coli), there are specific proteins that are devoted to repressing the transcription of the DNA to its product (RNA, which in turn is decoded into protein).

Works Cited

2010. Francois Jacob.  September 18, 2010  http://www.nndb.com/people/157/000129767/

François Jacob-Bioraphy. Nobelprize.org. September 18, 2010 http://nobelprize.org/nobel_prizes/medicine/laureates/1965/jacob-bio.html

Crick Francis

Francis Harry Compton Crick (1916- 2004)
Background Info---
-Graduated in 1937, studied physics at University College, London.
-While obtainign his Ph.D. the outbreak war interrupted him.  Thus, he workded as a scientist for the British Admiralty. (Associated with magnetic and acoustic)
-In 1947, he left Admiralty to study biology
 -He was graduated with a Ph.D  in 1954 on a thesis entitled "X-ray diffraction: polypeptides and proteins"

Year Became Famous---

1962, he won the Nobel Prize in Physiology or Medicine with critical influence of J.D. Waston.

Publication Made Him Famous---
From 1951 to 1953 Watson (as a 23 year old young man) along with Crick leading to the proposal of the double-helical structure for DNA and the replication schemein.

Contribution to World Genetic---
 The double helical structure of DNA solved the question existed and put together the knowledge they found at the time.

Works Cited
The Nobel Prize in Physiology or Medicinne 1962 Francis Crick, james Watson, Maurice Wilkins. September 18, 2010 http://nobelprize.org/nobel_prizes/medicine/laureates/1962/crick-bio.html
James Watson, Francis Crick, Maurice Wilkins, and Rosalind Franklin. September 18, 2010
http://www.chemheritage.org/discover/chemistry-in-history/themes/biomolecules/dna/watson-crick-wilkins-franklin.aspx

Arthur Kornberg

Arthur Kornberg (1918- 2007)------------

Background Info----                                                                          -Graduated from College of New York in 1937                                   -Obtained M.D. degree from University of Rochester in 1941             -Served as a commissioned officer in the U.S. Public Health Service, first assigned to the Navy as a ship's doctor, then research scientist at the National Institutes of Health from 1942 to 1953.                             -In 1946, he was training in enzymology at New York University and in 1947, he was at Washi9ngton University School of Medicine.        

Year Became Famous------

In 1959, he recieved Nobel Prize for Physiology or Medicine

Publication Made Him Famous-----

- The basic mechanisms of DNA replication through isolating and purifying the enzymes that run the machinery of the cell.

-Elucidating key steps in the pathways of pyrimidine and purine nucleotide synthesis, including the discovery of PRPP as an intermediate, he found the enzyme that assembles the building blocks into DNA, named DNA polymerase. This ubiquitous class of enzymes make genetically precise DNA and are essential in the replication, repair and rearrangements of DNA. Many other enzymes of DNA metabolism were discovered responsible for the start and elongation of DNA chains and chromosomes

-Identify the enzyme catalyzing the synthesis of DNA, polymerase I.

Contribution to World Genetic
- He had comprehended a key component of molecular genetics
- Kornberg's approach - isolating enzymes in the chemist's lab and analyzing them within their biological context - was a crucial component in understanding the molecular biology of the cell.
-Kornberg's successful synthesis of the biologically active PhiX174 virus in 1967. For the first time, a biochemist produced an active virus in the lab.
-Enzymes he discoverd were the basis of discovery of recombinant DNA which helped ignite the biotechnology revolution.

Works Cited
Jochen Kumin. Aruther Kornberg (1918-2007).  September 17, 2010.
http://www.accessexcellence.org/RC/AB/BC/Arthur_Kornberg.php

 

Lawrence K Altman. October 28, 2007. September 17, 2010.
http://www.nytimes.com/2007/10/28/science/28kornberg.html

Corn Lady--- Barbara McClintock

Barbara McClintock(1902-1992)
Background Info
-Born in Hartford, Connecticut, US, June 16, 1902.  Died at age of 90 in 1992.
-Barbara's father is a doctor and mother is a piano teacher.
-Went to Cornell University in 1918 due to the effect of her family under such a time period.
-As a student she identified all ten maize.
-Recieved her doctor degree in 1927 in Cornell. While teaching at Cornell she helped in laboratory experiments-determining (genetic) information is transferred between chromosomes in the crossing-over stage of cell division.
-She was unable to obtain a position in Cornell University due to the role as a woman.
-She joined Cold Spring Harbour Laboratory and started her significan contribution there.

Year Became Fame
1983- When she won an unshared Nobel Prize of Physiology or Medicine.

Publication that Made Her Fame
In 1948 published the "Jumping Gene" in corn, the process of transposition in corn chromosomes.
Transposition: the ability of genes to change position on second site in the DNA. Genetic transposition was the first type of genetic instability to be discovered. 

Contibution to World Genetics
This contribution significantly increased the knowledge of genetic function and organization.

Interesting Facts
-She loved playing sports, vollyball, swimming and swimming but most of all tennis.
- black walnut is her favourite flavor


Works Cited
Barbara McClintock. Sept 15, 2010
http://www.nobel-winners.com/Medicine/barbara_mcClintock.html
Cold Spring Harbour Laborat. oryBarbara McClintock's World. Sept 15, 2010 http://www.weedtowonder.org/mcclintock/gallery/gallery15.html

Rosalind Elsie Franklin

Rosalind Elsie Frankin (1910-1958)--------            
Background Info---
-Rosalind was born in England on July 25, 1910. She died at the same place on April 16, 1958.

-Graduated from Cambridge University in 1941as a Ph.D.. Later worked in a labatory in Paris, France, studying x-ray diffraction.

-1951, She began to focus on DNA research at Medical Research Council

Year Became Famous---

Four years after her death, in 1962 after Watson and Crick won their nobel prize. 

Publication that Made Her Famous---

-Publication in 1953 of her own work, however, the structure of DNA had not been discoverd or completed yet.

-The photograph Watson and Crick use as a resource now known to be photograph 51

-Her real fame came when Francis Crick admitted in Nature magazine while their work had been published that Rosalind "is only 2 steps away from the solution" and the discoery contain a portion of  her contribution.

Contribution to the World of Genetic--- 

Her discovery of the molecular structure of deoxyribonucleic acid (DNA) by using the technique of x-ray diffraction solved the puzzle and colaborated the knowlegde of DNA at the time.


Works Cited
Encyclopedia of World Biography on Rosalind Elsie Franklin. September 15, 2010
http://www.bookrags.com/biography/rosalind-elsie-franklin/
Ardell, David. October 25, 2006. Rosalind Franklin(1920-1958). Septmeber 15, 2010
http://www.accessexcellence.org/RC/AB/BC/Rosalind_Franklin.php
Michon, Scott. June 20, 2010. Rosalind Franklin. Septmeber 15, 2010 www.strangescience.net/rfranklin.htm

Bio Blog Entry

AH... DUNT FEEL LIKE DOING IT HERE
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NO! I GOTTA GO TO SLEEP >.<