text:
Proteomics/Protein Sample Preparation/Contaminant Elimination

Contaminant Elimination
In almost any biological experiment, eliminating contamination is of utmost importance. This is especially true when dealing with proteins, as human subjects can contaminate the sample with their own proteins, leading to unexpected results. Dialysis, Desalting, Protein Precipitation and Ultrafiltration are all methods that may be used to prevent unwanted molecules, assuring accurate and reliable results.

Dialysis
Dialysis is a common protocol for isolating proteins in a sample based on size exclusion. Semi-permeable membranes are manufactured with varying pore sizes such that a dialysis bag can be selected specific to a particular experiment's needs. The protein sample, in solution, is sealed in the bag which is then placed in a large volume of buffer, normally 200 – 500 times the volume of the sample [3]. Due to the gradient between the sample and the buffer, the molecules in the sample attempt to flow from the dialysis bag where only those smaller than the pore size actually leave the sample [2]. The power of dialysis lies in its ability to cleanse a sample of a number of contaminants at once, including small proteins, and small contaminating molecules such as salt.

The key to a successful separation based on dialysis is the selection of an optimal pore size. Membrane pore sizes are typically measured in Daltons such that pores measuring 1,000 Daltons will retain molecules a molecular mass of 1,000 Daltons. More information on preparing a dialysis tube based separation can be found here.

Desalting
Another method for removing foreign molecules from protein samples, desalting provides us with the ability to remove detergents, DNA or RNA, lipids and salts. Oftentimes, this method is known as gel filtration, or molecular exclusion. The premise behind desalting is that the molecules in the sample are passed through a porous resin. The smaller molecules pass into the pores and get stuck, whereas the larger molecules do not fit and simply flow around and out of the resin. In doing so, the larger molecules are separated away from the other molecules in the solution, which remain stuck in the pores.

Protein Precipitation
Similar to the other methods already discussed, precipitation involves removing unwanted substances from our protein sample prior to analysis. In this case, it is the protein that is precipitated, allowing for the remaining solution to be poured off. Most often, precipitation is achieved using salts.

At low salt concentrations, proteins are generally observed to be more soluble than at high concentrations. Using this information, a technique known as salting out is often used which involves increasing the salt concentration until the proteins precipitate out. Although this is the most common form of protein precipitation, similar results can be obtained by changing the pH of the solution or through the introduction of metal ions.

Ultrafiltration
Ultrafiltration is a process similar to gel filtration or molecular exclusion, but also relies on pressure in separating the molecules. Due to the pressurized samples, a much smaller pore size may be used (around 250 nanometers)[4]. The smaller molecules are then forced through the pores while the larger proteins are retained.


text:
Proteomics/Protein Sample Preparation/Prepts for Chromatography

Preps for Chromatography
For High Performance LC (HPLC), it is very important that the sample solution (mobile phase) be free of particulate matter. Due to the sensitive nature of a HPLC column and the extreme pressures involved, such contaminants can be extremely damaging and Protein_Sample_Preparation|Contaminant_Elimination#Contaminant_Elimination is very important.
 * Solubilization and Solution Preparation

 * Recombinant techniques for affinity chromatography

Affinity chromatography is a protein separation technique where substrates with affinities for specific proteins are used in the solid phase of a chromatography column. One highly specific technique is to use recombinant technology to isolate proteins expressed from recombinant DNA. If a gene is inserted into a cloning vector for the purpose of fermenting large amounts of a protein, the gene can be altered to include additional amino acids in the protein. This subsequence can then be utilized as a binding site for the stationary phase substrate. Two examples of this are the additions of histidine residues that bind covalently to certain metal ions and the addition of glutathione-S-transferase protein that will bind with glutathione. http://en.wikipedia.org/wiki/Affinity_chromatography

Single-step purification of bacterially expressed polypeptides containing an oligo-histidine domain. Gene. 1992 Feb 1;111(1):99-104.

Solubilization and purification of enzymatically active glutathione S-transferase (pGEX) fusion proteins. Anal Biochem. 1993 Apr;210(1):179-87.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Proteomics/Protein Sample Preparation/Sample Preparation for Electrophoresis

Sample Preparation for Electrophoresis
Polyacrylamide Gel Electrophoresis (PAGE), described in detail in Chapter 4.2, is a process by which molecules, typically proteins, are separated by their mass. By assuming the speed at which a protein travels through a gel matrix is directly related to its mass, that is, the total matter in the protein, it is crucial to ensure the shape of the protein is not affecting its speed. As such, a number of sample preparation techniques have been refined to confer similar shapes on all proteins in a sample. Furthermore, protocols have been refined to maximize the consistency of mass related characteristics. This section aims to confer the purpose and procedures of a number of these techniques involved in preparing a sample for gel electrophoresis.

SDS Treatment:
Sodium dodecyl sulfate (SDS) is an anionic detergent used to denature proteins prior to gel electrophoresis. As stated above, it is necessary to denature all proteins in a sample in order to separate them solely on their mass in a gel matrix. SDS efficiently breaks down secondary structures like alpha-helices and beta-sheets (both primarily comprised of hydrogen bonds) as well as many tertiary structures. However, SDS does not break down any of the disulfide bonds that participate in many tertiary structures; treatment with DTT, described below, is often necessary to break down disulfide bonds. SDS is found to be particularly useful in 2-dimensional electrophoresis (2DE). As mentioned in Chapter 4.2, 2DE involves an initial stage of Isoelectric Focusing (IEF) which results in all proteins finding their pI on the IEF strip resulting in all proteins having a net charge of zero. Due to the nature of PAGE, a negative charge is necessary to induce movement of the proteins through the gel matrix. Fortuitously, treatment of a protein sample with SDS not only denatures all proteins in the sample, it also binds all proteins and confers its negative charge to the bound proteins. It is seen that SDS binds a protein in a manner proportional to the mass of that protein which results in a negative charge directly related to the protein’s mass; further supporting a separation based on mass alone.

DTT Treatment:
Dithiothreitol (DTT) is a reducing agent typically used to break down the disulfide bonds contributing to tertiary structure which SDS was unable to affect, further denaturing the protein to deemphasize the role of protein shape in PAGE. DTT reduces a disulfide bond by two sequential thiol-disulfide exchange reactions resulting in DTT becoming a six-member ring structure. 2-mercaptoethanol (ME), another disulfide reducing agent, is commonly used in lieu of DTT. Furthermore, it should be noted that while both DTT and ME sufficiently reduce disulfide bridges in proteins, there is a propensity for them to reform. Thus the protein sample is commonly treated with 2-Iodoacetamide, an alkylating sulfhydryl reagent, which binds covalently to free sulfides and prevents disulfide bridges from reforming.

 * Dithiothreitol (DTT):

 * 2-mercaptoethanol (ME):

Protein Extraction from Yeasts
To extract proteins from yeast, the collected yeast cells are resuspended in a buffer containing NaOH, 2-mercaptoethanol, and SDS and immediately heated to 90oC. Then the sample is neutralized using a Tris-HCl buffer. Glycerol and bromophenol blue is then added so that the final sample is contained in a standard SDS-PAGE buffer. The combination of both the heat and the buffer in effect destroys all cell walls and at the same time makes soluble the proteins needed to be extracted.

Varying the concentration of SDS, boiling time, and the addition of solubilizing reagents can change and optimize the extraction of yeast proteins. The addition of deoxycholate or urea to the above protocol was found to optimize the extraction of certain proteins but decreased the optimization of others. The above parameters are optimal for the extraction of most of the proteins expressed in S. cerevisiae, but not for all proteins. To this date, there is no one universal buffer or protocol that can yield all expressed protein from the yeast cell.

Optimized Protein Extraction for Quantitative Proteomics of Yeasts
von der Haar T PLoS One 2(10):1-8 (2007)

Main Focus

The main focus of this article is to find the optimal extraction technique for yeast proteins. The von der Haar group has found an optimal technique for most of the yeast proteins but not all expressed proteins.

Summary

The abundance data that come out of published papers for any protein can vary from group to group. This is due to the varying efficiencies of the extraction procedures that they use. The von der Haar group has found a protein extraction procedure that can extract most of the proteins in the yeast S. cerevisiae. The original protocol that they found to be the best calls for the use of 0.1N NaOH as the resuspension buffer, incubate for several minutes, then boiled in standard SDS-PAGE sample buffer. The problem with this procedure is that when yeast is suspended and incubated in 0.1N NaOH not all the cell walls are destroyed. Many yeasts cells are still intact. This can lead to the yeast cells to express proteins not normally expressed solely under the environment of study but due to the NaOH environment. The von der Haar group has devised a new protocol that fixes this problem.

The new protocol calls for the extracted yeast cells to be resuspended in a buffer containing NaOH, 2-mercaptoethanol, and SDS and immediately heated to 90oC. Then the sample is neutralized using a Tris-HCl buffer and glycerol and bromophenol blue is then added so that the final sample is contained in a standard SDS-PAGE buffer. The combination of both the heat and the new buffer in effect destroys all cell walls and at the same time makes soluble the proteins needed to be extracted.

The von der Haar group has also found that varying the concentration of SDS, boiling time, and the addition of solubilizing reagents can change the optimization of protein extraction. The optimal concentration of SDS that they have found was 2%. The optimal time of boiling is 10 minutes at 90oC. These parameters are optimal for the extraction of most of the proteins expressed in S. cerevisiae, but not for all proteins. The addition of 1% deoxycholate increased the efficiency of the extraction of Sup45p and Rpl25p, but decreased the efficiency of Sup35p. The addition of 8M Urea increased the efficiency of extraction of Sup35p but decreased the efficiency of all the other proteins.

The von der Haal group did find the optimal protocol to extract most of the proteins expressed in S. cerevisiae, but not for all proteins. The addition of other solubilizing agents can be optimal for certain proteins but can significantly decrease the solubilization of others. It is clear that there can be no one universal buffer or protocol that can yield all expressed protein for the yeast cell.

For more descriptive steps, refer to Figure 1 of the article.

New Terms

 * proteome: The set of proteins expressed by the genetic material of an organism under a given set of environmental conditions ( http://www.answers.com/topic/proteome-2 )
 * cell density: The number of cells per unit volume ( http://www.oilgae.com/ref/glos/cell_density.html )
 * YPD (Yeast Peptone Dextrose): The media that contains peptone, dextrose and other material used to grow S. cerevisiae (http://www.clontech.com/products/detail.asp?tabno=2&catalog_id=630409&page=all)
 * Stationary Phase: Also known as the G0 phase, is a response to the lack of nutrients or starvation. The yeast cell can prolong its life by altering its structure and it metabolism. (http://www.rose.brandeis.edu/PRLab/projects/yeast/yeast.html)
 * alkaline lysis: a protocol using NaOH to break open cells in order to isolate DNA or proteins (http://bitesizebio.com/2007/11/07/the-basics-how-alkaline-lysis-works/)

Course Relevance

 * In the proteomics class we have learned how the analysis of protein expression under certain conditions could be quantified by experiments such as Mass Spectrometry or gel electrophoresis. But in order to correctly analyze the proteins expressed there must be a technique which will extract all if not most of the proteins.  This paper describes the optimal way to extract most proteins specifically for yeast.

Yeast Cell Lysates
The Gottschling Laboratory at Fred Hutchinson Cancer Research Center

http://labs.fhcrc.org/gottschling/Yeast%20Protocols/pprep.html (03/29/09)

Main Focus

The main focus of the website is to provide protocols and other information about the Gottschling Lab, a laboratory focused on cancer research.

Summary

The Gottschling laboratory is interested in studying yeast, specifically S. cerevisiae, because of its link to cancer. When yeast cells enter the middle to late stage of their lifespan, they experience genomic instability. This genomic instability can also be seen in humans due to increased age and cancer. The Gottschling group believe that there is a link between the transition experienced by yeast and the increased age and occurrence of cancer in humans.

The website provides many different protocols along with a protocol for extracting yeast proteins. They list three different ways to prepare yeast proteins for direct gel electrophoresis. The first uses a SUMEB buffer along with a protease inhibitor in order to extract yeast protein. The website provides the ingredients needed to make the SUMEB buffer. The second protocol uses only sample buffer and the website also provides the recipe for the sample buffer. The third protocol that they have listed is the use of glass beads along with sample buffer.

Refer to the website link for a more detailed description of the steps for rapid protein preparation.

Course Relevance

 * In the proteomics class we have learned how the analysis of protein expression under certain conditions could be quantified by experiments such as Mass Spectrometry or gel electrophoresis. But in order to correctly analyze the proteins expressed there must be a technique which will extract all if not most of the proteins. This website gives several different protocols in order to extract yeast proteins as a sample for gel electrophoresis.


text:
Wikijunior talk:Languages/German

Eszett?
If I'm not correct, but wasn't the eszett removed officially from German in 1999. 84.12.12.120 17:16, 23 April 2006 (UTC)Anon

No, it was not I think you're think of the spelling reform, where some not all lost the eszett. --German Men92 01:54, 27 April 2006 (UTC)

Bold text== Umlaute? ==

Isn't it umlaut? Umlaut. Kellen T 13:31, 18 June 2006 (UTC)

Ask the person who edited it, it is Umlaut, so I guess I'll change it back. --Je suis 02:58, 21 June 2006 (UTC) It is "umlaut", trust me, i took german lessons:)

Number of speakers?
Is it really 120 million second language speakers? Or is that supposed to say 120 million total? 139.133.7.37 (talk) 00:52, 11 March 2010 (UTC)

I think it's supposed to be 120 million total, because i know for a fact more people speak it as a mother tounge than people who learn it later on in life.Abby101leigh (discuss • contribs) 22:44, 5 February 2012 (UTC)

ill/sick, krank/übel
More sure about German than English here. Mir ist übel or mir ist schlecht means I am going to throw up (nausea). Ich bin krank means I am suffering from an illness (generally, with or without nausea). The English translations seem reversed to me (i.e. sick sounds more nauseous than ill to me). (I am a German living in England.) --86.166.39.171 (discuss) 20:13, 23 May 2013 (UTC)

title: Wikijunior talk:Languages/German


text:
AvernumScript/Appendix/Item, Special Item and Gold Calls

void change_coins(short coin_amount)

 * Changes the number of coins the party has by coin_amount (which can be negative). If the number is negative, then coins are taken away. If the party doesn't have enough coins, no coins are taken.

void change_spec_item(short which_item,short how_many)

 * Changes the amount of special item which_item the party has by how_many. If how_many is negative, the number of special item which_item will be reduced by how_many. If you try to take away more of the item than the party has, the party is left with 0 of the item.

void char_give_item(short which_char_or_group,short which_item)

 * Tries to give to which_char_or_group an item of type which_item. If you call char_give_item for a group, gives one of the item to each group member. The item will not automatically be identified. If the character doesn’t have enough space to take the item, nothing happens and the game gives a “can’t take the item” message.

Note: This call was added for Scenario Format Version 2, only use it with Mac version 1.1 or later or Windows version 1.0 or later.

short char_has_item(short which_char,short which_item)
Returns:

short char_has_item_of_class_equip(char char_num,short which_class,short take_item)
Returns:

Values for take item are:

Note: This call was added for Scenario Format Version 2, only use it with Mac version 1.1 or later or Windows version 1.0 or later.

void char_take_item(short which_char_or_group,short which_item)

 * Tries to take from which_char_or_group one item of type which_item. (If the item has charges, it will take 1 charge instead).

short coins_amount

 * Returns the number of coins the party has.

short has_item(short which_item)
Returns:

short has_item_of_class(short which_class,short take_item)
Returns:

Values for take item are:

short has_num_of_item(short which_item)

 * Returns how many of item which_item the party has. If the party doesn't have any items of type which_item, returns 0. If the items in question have charges, this call returns the total number of charges.

short has_special_item(short which_item)

 * Returns the number of the special item which_item the party has, 0 if they don’t have any.

short item_of_class_on_spot(short loc_x,short loc_y,short what_class)
Returns:

Note: If what_class is -1, returns 1 if any item is on the space, 0 otherwise.

void move_item_on_spot(short loc_x,short loc_y,short dest_x,short dest_y)

 * Takes all items sitting on town spot {loc_x,loc_y} and moves them to {dest_x,'dest_y}.

Note: If dest_x is a negative value, the items on the space are simply destroyed.

short pay_coins(short coin_amount)

 * Tries to take coin_amount coins from the party.

Returns:

void put_item_on_spot(short loc_x,short loc_y,short what_item)

 * Places an item of type what_item on town space {loc_x,loc_y}. If that spot is a container, the item won’t be contained inside it.

short reward_give(short which_item)

 * Tries to give item of number which_item to party. If the party can’t hold it, tries to place the item at their feet. (Placing the item at their feet will only work indoors.)

Returns:

short take_all_of_item(short which_item)

 * Takes all of item which_item from party, and returns the number of items taken. If the item given has charges, returns the total number of charges taken.

short take_all_of_item_class(short which_class,short gold_to_pay)

 * Takes from the party all items of special class which_class and, for each item taken, gives the party gold_to_pay gold.

Returns:

Note: If the item taken has charges, gives the amount of gold for each charge taken.

void take_item(short which_item)

 * Searches through the party’s inventory until it finds an item of type which_item and takes it. (If the item has charges, it will take one charge instead.)

short take_item_of_class_on_spot(short loc_x,short loc_y,short what_class)

 * Returns 1 if there is an item of special class what_class on town space {loc_x,loc_y}, 0 otherwise.

 * If there was an item of that type on the spot, destroys one of it. (If the item has charges, it will take one charge instead.)
 * If what_class is -1, destroys all items on town space {loc_x,loc_y} and returns TRUE if an is item destroyed.

void take_num_of_item(short which_item,short num_to_take)

 * Takes num_to_take items of type which_type from the party.

void take_special_item(short which_item)

 * Takes 1 of special item which_item from party. If the party has none of that special item, the call does nothing.


text:
Proteomics/Protein Sample Preparation/References

1. Patnaik, S. (2004) Protein Handling. obtained from http://stanxterm.aecom.yu.edu/wiki/index.php?page=Protein_handling in April, 2006

2. Ion Exchange Chromatography. Obtained from http://www.rit.edu/~pac8612/webionex/website/html/ione6eyb.html in April, 2006

3. Blaber, M. (1998) Protein Purification: Column Chromatography - Ion exchange; Dialysis and Concentration. obtained from http://wine1.sb.fsu.edu/bch5425/lect30/lect30.htm in April, 2006

4. Sample Preparation. Obtained from http://www.piercenet.com/Proteomics/browse.cfm?fldID=7FAD146E-B43B-4110-9F71-7F749D41BEC5#samp%20hand in April, 2006

5. Young, D. Protein Precipitation. Obtained from http://www.rpi.edu/dept/chem-eng/Biotech-Environ/PRECIP/precpintro.html in April, 2006

6. http://en.wikipedia.org/wiki/Affinity_chromatography

7. Single-step purification of bacterially expressed polypeptides containing an oligo-histidine domain. Gene. 1992 Feb 1;111(1):99-104.

8. Solubilization and purification of enzymatically active glutathione S-transferase (pGEX) fusion proteins. Anal Biochem. 1993 Apr;210(1):179-87.

9. Glaser, V. (2006) Sample Prep Upstream of Mass Spectrometry: Advances Focus on Sample Clean-Up, Fractionation, and Separation. Genetic Engineering & biotechnology News (Vol. 26, No. 10). Obtained from http://www.genengnews.com/articles/chitem.aspx?aid=1667&chid=1


text:
User:Agari

Wikipedia:user:Agari

Agari Agari

title: User:Agari


text:
Proteomics/Protein Sample Preparation/Sample Preparation for Chromatography

Solubilization and Solution Preparation
For High Performance Liquid Chromatography (HPLC), it is important that the sample solution (mobile phase) be free of particulate matter. Due to the sensitive nature of a HPLC column and the extreme pressures involved, such contaminants can be extremely damaging and contaminant elimination is very important. Each specific liquid chromatography technique requires specialized solutions. Reversed-phase chromatography requires polar organic solvents, while normal phase chromatography can use inorganic solvents such as water. One of the most common organic solvents is acetonitrile. This polarity gives the solvent the ability to elute proteins out of a reversed phase column, and it is also easily coupled to mass spectrometry. Also, solution buffers must contain high quality pH stabilizers such as acetic acid (acid) and sodium acetate (base). Salt buffers such as Potassium Chloride are used to produce elution conditions in ion-exchange chromatography, and also must be of very high purity. A list is given below of common chromatography reagents:
 * Buffer reagents
 * Acetic Acid
 * Phosphoric Acid
 * Triethylamine
 * Sodium Acetate
 * Ammonium Acetate
 * Potassium Phosphate
 * Sodium Bicarbonate
 * Sodium Chloride

RIPA is radio immunoprecipitation Assay the buffer can be used to solubilize proteins in a cell. Analysis shows that RIPA dissolves some membrane-bound proteins and most intracellular proteins. RIPA is not to be used to find protein-protein interactions because this buffer breaks the bonds of the protein-protein formations.

Recombinant Techniques for Affinity Chromatography
Affinity chromatography is a protein separation technique where substrates with affinities for specific proteins are used in the solid phase of a chromatography column. One highly specific technique is to use recombinant technology to isolate proteins expressed from recombinant DNA. If a gene is inserted into a cloning vector for the purpose of fermenting large amounts of a protein, the gene can be altered to include additional amino acids in the protein. This subsequence can then be utilized as a binding site for the stationary phase substrate. Two examples of this are the additions of histidine residues that bind covalently to certain metal ions and the addition of glutathione S-transferase|Glutathione-S-transferase protein that will bind with glutathione.

Sample prep for proteomics of breast cancer: proteomics and gene ontology reveal dramatic differences in protein solubilization preferences of radioimmunoprecipitation assay and urea lysis buffers
[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2600628&tool=pmcentrez Ngoka, Lambert CM; Proteome Science 6: 30. pg 1-21; Published online 2008]

The focus of this paper is to prepare a protein sample from cancer cells using the widely established RIPA method. RIPA buffer does this by taking proteins from there native insoluble state and solubilizing them into a separable sample. It also separates the proteins from salts and other contaminants making it a reliable sample prep tool. A problem with using just one sample buffer is that the buffer may not have solubilized all the proteins from the sample cell. This experiment, in addition to RIPA, also uses urea to extract proteins missed by RIPA. Tumor cells with varying origin characteristics were subjected to RIPA analysis and urea analysis. It was concluded that using the different methods each cell yielded some of the same proteins and many unique proteins. With the RIPA analysis many intracellular proteins and proteins with small molecular weights were readily soluble. Some Other Proteins would bind weakly to the buffer following for solubility. The results for the urea analysis proved somewhat opposite, this test would solubilize extracellular matrix proteins and proteins with high molecular weights. This is not to say that neither protein yielded the same results, from the paper it can be witnessed there is a big overlap of the same proteins found with different analysis. When making a protein sample or finding novel proteins experimenters should use multiple isolation techniques to obtain the greatest population of proteins available.

New Terms

plasmogen activators- molecule used to disassociate blood clots.

angiogenesis - blood vessel genesis and progression. (dictionary.com)

In the extraction process of proteomics it is useful to use more than one extraction buffer to obtain different libraries of proteins.

Immunoprecipitation
Summary

Immunoprecipitation has several steps, the first is to lysis the cell and obtain a protein mixture. It is then a good idea to clean the cell of all non-specific proteins. Following this cleaning you want to add the anti-bodies to precipitate the targets. Then you can isolate your sample for further analysis. Some lysis buffers are RIPA and NP-40, RIPA disrupts protein-protein interactions and NP-40 is used to identify protein-protein interactions. Success of this technique depends on the affinty binding of the protein-antibody formation.

Immunoprecipitation is a method of protein extraction, usually radio-labeled this technique can obtain the molecular weights and quantity of protein samples. Samples are extracted using anti-body- protein complexes. Immunoprecipitation can also be used to determine protein- protein interactions, rate of synthesis of a protein, and can concentrate small levels of proteins.

New Terms

pre-clearing - A step in imuunoprecipitation that lowers non-specific proteins.

mono-clonal antibodies - antibodies cloned to produce high volume populations of themselves. (dictionary.com)

Immunoprecipitation is widely used in sample preparation of proteins, it yields samples with acceptable concentrations and accurately targets specific proteins.


text:
User:Hojarasca.mx

My name is Juan Antonio Sánchez Scott, I am a mexican Industrial Design student and I live in Mexico City. I love electronic music and design. I love Wikipedia and I am very interested in computer science, engeneering and 3D computer graphics.

title: User:Hojarasca.mx


text:
Water Resources Directory/U.S. Army Corps of Engineers

Financial Assistance
Grant programs for water resources improvements:

Planning Assistance to States
(Section 22)
 * Water resource, watershed and ecosystem planning assistance ($500,000 per state)
 * Local sponsor match is 50%

Remedial Action Plans
(Section 401)
 * General assistance for RAP development and implementation
 * Local sponsor match is 50%, but may include in-kind services

Expedited Reconnaissance Study
(Section 905(b))
 * Conduct a reconnaissance study of local watershed problems to determine applicability to Corps programs ($100,000 per study)
 * Local sponsor match = none required

Beneficial Use of Dredged Material
(Section 204)
 * Protect, restore and enhance aquatic habitat using dredged material from Federal navigation projects
 * Local sponsor match is 25% (with credit for lands, easements, rights-of-way, and relocations)

Aquatic Ecosystem Restoration
(Section 206)
 * Plan, design and construct aquatic ecosystem restoration and protection projects ($5,000,000 per project)
 * Local sponsor match is 35% (with credits for lands, easements, rights-of-way, and relocations)

Restoration of Environmental Quality
(Section 1135) ($5,000,000 per project)
 * Modify Corps structures or their operations to restore environmental quality. Restoration may be away from Corps project
 * Local sponsor match is 25% (with credit for lands, easements, rights-of-way and relocations)

Flood Mitigation & Riverine Restoration
(Section 212) ($30,000,000 per project)
 * Develop flood protection projects that restore natural functions of floodplain and enhance habitat
 * Local sponsor match is 35% (with credit for lands, easements, rights-of-way and relocations)

Environmental Dredging
(Section 312)
 * Provide for the removal of contaminated bottom sediments in waterways outside Federal navigation Channels
 * Local sponsor match is 35% (with credit for lands, easements, rights-of-way and relocations)

Environmental Infrastructure
(Various authorities )
 * Support development or restoration of environmental infrastructure, including water supply, wastewater, combined sewer overflows
 * Local sponsor match is (variable).

River Basin Studies
(Section 729)
 * Study water resources needs of river basins and regions
 * Local sponsor match = none required.


text:
Talk:Issue Guide/Human Rights/Vietnam

Un-wikiness
Is it just me or does this article seem INCREADIBLY biased? Also author is refering to him/herself within the article. N1person 18:53, 23 April 2006 (UTC)

title: Talk:Issue Guide/Human Rights/Vietnam


text: French/Texts/National anthems/O Canada

title: French/Texts/National anthems/O Canada


text:
User talk:80.232.117.78

Please stop. If you continue to blank pages, you will be blocked from editing.

title: User talk:80.232.117.78


text:
Organic Chemistry/Carboxylic acid derivatives

The carboxyl group (abbreviated -CO2H or -COOH) is one of the most widely occurring functional groups in chemistry as well as biochemistry. The carboxyl group of a large family of related compounds called Acyl compounds or Carboxylic Acid Derivatives.

All the reactions and compounds covered in this section will yield Carboxylic Acids on hydrolysis, and thus are known as Carboxylic Acid Derivatives. Hydrolysis is one example of Nucleophilic Acyl Substitution, which is a very important two step mechanism that is common in all reactions that will be covered here.

Structure
This group of compounds also contains a carbonyl group, but now there is an electronegative atom (oxygen, nitrogen, or a halogen) attached to the carbonyl carbon. This difference in structure leads to a major change in reactivity.

Nomenclature
The systematic IUPAC nomenclature for carboxylic acid derivatives is different for the various compounds which are in this vast category, but each is based upon the name of the carboxylic acid closest to the derivative in structure. Each type is discussed individually below.

Acyl Groups
Acyl groups are named by stripping the -ic acid of the corresponding carboxylic acid and replacing it with -yl.

EXAMPLE: CH3COOH = acetic acid CH3CO-R = acetyl-R

Acyl Halides
Simply add the name of the attached halide to the end of the acyl group.

EXAMPLE: CH3COOH = acetic acid CH3COBr = acetyl bromide

Carboxylic Acid Anhydrides
A carboxylic acid anhydride ([RC=O]O[O=CR]) is a carboxylic acid (COOH) that has an acyl group (RC=O) attached to its oxygen instead of a hydrogen. If both acyl groups are the same, then it is simply the name of the carboxylic acid with the word acid replaced with anhydride. If the acyl groups are different, then they are named in alphabetical order in the same way, with anhydride replacing acid.

EXAMPLE: CH3COOH = acetic acid CH3CO-O-OCCH3 = Ethanoic Anhydride

Esters
Esters are created when the hydrogen on a carboxylic acid is replaced by an alkyl group. Esters are known for their pleseant, fruity smell and taste, and they are often found in both natural and artificial flavors. Esters (RCOOR1) are named as alkyl alkanoates. The alkyl group directly attached to the oxygen is named first, followed by the acyl group, with -ate replacing -yl of the acyl group.

EXAMPLE: CH3COOH = acetic acid CH3COOCH2CH2CH2CH3 = acetyl butanoate cooh 1 cooh 1 2-ethan oic acid

Amides
Amides which have an amino group (-NH2) attached to a carbonyl group (RC=O) are named by replacing the -oic acid or -ic acid of the corresponding carboxylic acid with -amide. EXAMPLE: CH3COOH = acetic acid CH3CONH2 = acetamide

Nitriles
Nitriles (RCN) can be viewed a nitrogen analogue of a carbonyl and are known for their strong electron withdrawing nature and toxicity. Nitriles are named by adding the suffix -nitrile to the longest hydrocarbon chain (including the carbon of the cyano group). It can also be named by replacing the -ic acid or -oic acid of their corresponding carboxylic acids with -onitrile. Functional class IUPAC nomenclature may also be used in the form of alkyl cyanides.

EXAMPLE: CH3CH2CH2CH2CN = pentanenitrile or butyl cyanide

Structure and Reactivity
Stability and reactivity have an inverse relationship, which means that the more stable a compound, generally the less reactive - and vice versa. Since acyl halides are the least stable group listed above, it makes sense that they can be chemically changed to the other types. Since the amides are the most stable type listed above, it should logically follow that they cannot easily changed into the other molecule types, and this is indeed the case.

The stability of any type of carboxylic acid derivative is generally determined by the ability of its functional group to donate electrons to the rest of the molecule. In essence, the more electronegative the atom or group attached to carbonyl group, the less stable the molecule. This readily explains the fact that the acyl halides are the most reactive, because halides are generally quite electronegative. It also explains why acid anhydrides are unstable; with two carbonyl groups so close together the oxygen in between them cannot stabilize both by resonance - it can't loan electrons to both carbonyls.

The following derivative types are ordered in decreasing reactivity (the first is the most reactive):

Acyl Halides (CO-X) > Acyl Anhydrides (-CO-O-OCR) > Acyl Thioester (-CO-SR) > Acyl Esters (-CO-OR) > Acyl Amides (-CO-NR2)

As mentioned before, any substance in the preceding list can be readily transformed into a substance to its right; that is, the more reactive derivative types (acyl halides) can be directly transformed into less reactive derivative types (esters and amides). Every type can be made directly from carboxylic acid (hence the name of this subsection) but carboxylic acid can also be made from any of these types.

Carboxylic Acids
1) As acids:

RCO2H + NaOH > RCO2-Na+ + H2O RCO2H + NaHCO3 > RCO2-Na+ + H2O + CO2

2) Reduction:  RCO2H + LiAlH4 --- (1) Et2O -- (2) H2O > RCH2OH

2a) Fukyama reduction: Pd and Et3SiH COOH->CHO

3) Conversion to acyl chlorides:

RCO2H -SOCl2 or PCl5 > RCOCl

4) Conversion to esters (Fischer esterfication):

RCOOH + R'-OH <--- HA --->  RCOOR' + H2O

5) Conversion to amides:

RCO2H -SOCl2 or PCl5 > RCOCl + NH3 <--> RCOO-NH4+ --- heat ---> R-CONH2 + H2O

6) Decarboxylation: (Note: you need a doubly-bonded oxygen (carbonyl) two carbons away or two carboxylic acid groups attached to a same carbon atom for this reaction to work)   Note: Decarboxylation by heating can only occur for ẞ-keto acids or 1,1-dicarboxylic acids   RCOCH2COOH  --- heat ---> R-COCH3 + CO2   HOCOCH2COOH --- heat ---> CH3COOH + CO2 7)R-COOH + R-OH -R-COOR + H2O

Acyl Chlorides
1) Conversion to acids:

R-COCl + H2O > R-COOH + HCl

2) Conversion to anhydrides:

R-COCl + R'COO- > R-CO-O-COR' + Cl-

3) Conversion to esters:

R-COCl + R'-OH --- pyridine ---> R-COOR' + Cl- + pyr-H+

4) Conversion to amides:

R-COCl + R'NHR" (excess) ---> R-CONR'R" + R'NH2R"Cl R' and/or R" may be H

5) Conversion to ketones:

Friedel-Crafts acylation R-COCl + C6H6 --- AlCl3 ---> C6H5-COR

Reaction of Dialkylcuprates (also known as a Gilman reagent) R-COCl + R'2CuLi > R-CO-R'

6) Conversion to aldehydes:

R-COCl + LiAlH[OC(CH3)3]3 --- (1) Et2O (2) H2O ---> R-CHO

Acid Anhydrides
1) Conversion to acids:

(R-CO)2-O + H2O > 2 R-COOH

2) Conversion to esters:

(R-CO)2-O + R'OH > R-COOR' + R-COOH

3) Conversion to amides:

(R-CO)2-O + H-N-(R'R") > R-CON-(R'R") + R-COOH R' and/or R" may be H.

4) Conversion to aryl ketones (Friedel-Crafts acylation):

(R-CO)2-O + C6H6 --- AlCl3 C6H5-COR + R-COOH

Esters
1) Hydrolysis:

R-COOR' + H2O <--- HA ---> R-COOH + R'-OH R-COOR' + OH- > RCOO- + R'-OH

2) Transesterification (conversion to other esters):

R-COOR' + R"-OH <--- HA ---> R-COO-R" + R'-OH

3) Conversion to amides:

R-COOR' + HN-(R"R"') > R-CON-(R"R"') + R'-OH R" and/or R"' may be H

4) Reaction with Grignard reagents:

R-COOR' + 2 R"MgX --- Et2O ---> R-C-R"2OMgX + R'OMgX ---> H3O+ R-C-R"2OH The intermediate and final product is a tetrahedral carbon with two R" attached directly to the carbon along with R and OH/OMgX

X = halogen.

5) Reduction:

R-COOR' + LiAlH4 --- (1) Et2O (2) H2O ---> R-CH2OH + R'-OH

Amides
1) Hydrolysis:

R-CON(R'R") + H3O+ --- H2O ---> R-COOH + R'-N+H2R" R-CON(R'R") + OH- --- H2O ---> R-COO- + R'-NHR" R,R' and/or R" may be H.

2) Dehydration (conversion to nitriles):

R-CONH2 --- P4O10, heat, (-H2O) ---> R-CN

Nitriles
1) Hydrolysis:

R-CN --- H3O+,heat ---> RCOOH R-CN --- OH-,H2O,heat ---> RCOO-

2) Reduction to aldehyde:

R-CN --- (1) (i-Bu)2AlH (2) H2O ---> R-COH (i-Bu)2AlH = DIBAL-H

3) Conversion to ketone (by Grignard or organolithium reagents):

R-CN + R"-M --- (1) Et2O (2) H3O+ ---> R-COR" M = MgBr (Grignard reagent) or Li (organolithium reagent)

Mechanisms
A common motif in reactions dealing with carboxylic acid derivatives is the tetrahedral intermediate. The carbonyl group is highly polar, with the carbon having a low electron density, and the oxygen having a high electron density. With an acid catalyst, a H+ is added to the oxygen of the carbonyl group, increasing the positive charge at the carbon atom. A nucleophile can then attack the carbonyl, creating a tetrahedral intermediate.

For example, in Fischer esterification, the mechanism can be outlined thus: 1) H+ is added to carbonyl oxygen 2) Oxygen atom of the alcohol adds to the carbonyl carbon 3) Proton transfer from alcohol oxygen to carboxyl oxygen 4) Water molecule ejected from tetrahedral intermediate, double bond forms, recreating the carbonyl 5) H+ is removed from carbonyl oxygen(very important for the base reduction of acids)


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Talk:World History/Exam Prep

maybe there should be some sample questions, or a link to a practice test

title: Talk:World History/Exam Prep


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User:Jeff Armstrong

I'm currently teaching the Data Structures course.

Feel free to contact me about the course at cruzer24816@hotmail.com

title: User:Jeff Armstrong


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User talk:81.211.116.115

Welcome!
A Caribean Poker book does not exist. If you would like to create it, click on Caribean Poker. If you have created the book, you can add it to the top of New. Otherwise, please do not blank the template. --Hagindaz 23:33, 23 April 2006 (UTC)

title: User talk:81.211.116.115


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Category:Recipes by expense

Recipes listed by expense.

title: Category:Recipes by expense


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Category:Very inexpensive recipes

Recipes that are rated "Very Inexpensive" (1 out of 5). Remember to consider the amount of servings the recipe will make. If the recipe costs $10, it is not expensive if it makes 400 servings (under 3 cents per person).

title: Category:Very inexpensive recipes


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Category:Inexpensive recipes

Recipes that are rated "inexpensive" (2 out of 5).

title: Category:Inexpensive recipes


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Category:Medium expensive recipes

Recipes that are rated "Medium Expensive" (3 out of 5).

title: Category:Medium expensive recipes


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Category:Expensive recipes

Recipes that are rated "Expensive" (4 out of 5).

title: Category:Expensive recipes


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Cookbook:Coleslaw I

| Salads

Ingredients

 * 4 tablespoons mayonnaise or 2 dL olive oil
 * ¼–½ cup (about 50–100ml) cider vinegar (optional)
 * 1 head white cabbage
 * 1 medium red onion, thinly sliced

Procedure

 * 1) If adding cider vinegar, add it to the mayonnaise and mix together well.
 * 2) Slice or shred the cabbage, as coarsely or finely as desired.
 * 3) In a large bowl, mix cabbage and onion together with mayonnaise.
 * 4) Set aside to allow the flavours to merge at least 20 minutes but preferably for a couple of hours.

Notes, tips and variations

 * Savoy cabbage can be used instead of white cabbage
 * Other vegetables can be added to the coleslaw for greater variety, including:
 * Sliced bell peppers (red, yellow, and orange)
 * Grated carrots
 * Chopped nuts (e.g. almonds, walnuts)
 * Some people prefer to sweeten the dressing by adding up to 2 tablespoons of sugar to the mayonnaise and vinegar
 * Spices can be added to the dressing to "liven it up" (e.g. ground black pepper, celery seeds)

title: Cookbook:Coleslaw I


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User talk:M2s17

estonian page
Thank you for your interesting page on Estonian. It does need a bit of cleaning up and improvement.

--EuropracBHIT 04:25, 24 April 2006 (UTC).

title: User talk:M2s17


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User talk:NicholasMorg~enwikibooks

Hi... I dont know what this is... anyway... umm... Greenday, RuneScape and Pokemon Crater Rock!

NicholasMorg 05:59, 24 April 2006 (UTC)Nick

Your account will be renamed
Hello,

The developer team at Wikimedia is making some changes to how accounts work, as part of our on-going efforts to provide new and better tools for our users like cross-wiki notifications. These changes will mean you have the same account name everywhere. This will let us give you new features that will help you edit and discuss better, and allow more flexible user permissions for tools. One of the side-effects of this is that user accounts will now have to be unique across all 900 Wikimedia wikis. See the announcement for more information.

Unfortunately, your account clashes with another account also called NicholasMorg. To make sure that both of you can use all Wikimedia projects in future, we have reserved the name NicholasMorg~enwikibooks that only you will have. If you like it, you don't have to do anything. If you do not like it, you can pick out a different name.

Your account will still work as before, and you will be credited for all your edits made so far, but you will have to use the new account name when you log in.

Sorry for the inconvenience.

Yours, Keegan Peterzell Community Liaison, Wikimedia Foundation 23:32, 17 March 2015 (UTC)

Renamed
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title: User talk:NicholasMorg~enwikibooks


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IB Biology/Cells

2.1 Cell Theory
2.1.1 Outline the Cell Theory
 * Living cells are composed of one or more cells
 * Cells are the smallest unit of life
 * All organisms come from pre-existing cells

2.1.2 Discuss the evidence for the cell theory

The cell theory has amassed tremendous credibility through the use of the microscope in the following:
 * Robert Hooke- studied cork and found little tiny compartments that he called cells
 * Antonie van Leeuwenhoek- observed the first living cells, called them 'animalcules' meaning little animals
 * Schleiden- stated that plants are made of 'independent, separate beings' called cells
 * Schwann- made a similar statement to Schleiden about animals
 * Rudolf Virchow- discovered that all organisms come from pre-existing cells

2.1.3 State that unicellular organisms carry out all of the functions of life
 * Metabolism; chemical reactions inside the cell, including cell respiration to release energy
 * Response; perceiving and responding to changes in the environment
 * Homeostasis; keeping conditions inside the organism within tolerable limits
 * Growth; an irreversible increase in size
 * Reproduction; producing offspring either sexually or asexually
 * Nutrition; obtaining food, to provide energy and the materials needed for growth
 * Defense; protection against enemies

Amoeba would be an example of an unicellular organism.

2.1.4 Compare the relative sizes of molecules, cell membrane thickness, viruses, bacteria, organelles and cells, using the appropriate SI unit

nm = nanometer µm = micrometer

 * Molecules - 1 nm
 * Thickness of membrane - 10 nm
 * Viruses - 100 nm
 * Bacteria - 1 µm
 * Organelles - up to 10 µm
 * Most cells - up to 100 µm (three dimensional nature/shape)

2.1.5 Calculate the linear magnification of drawings and the actual size of specimens in images of known magnifications
 * :Drawings should show cells and cell ultrastructure.
 * Include:
 * A scale bar: |--| = 1 µm
 * Magnification: ×250

 * To calculate magnification:
 * ''Magnification = Measured Size of Diagram ÷ Actual Size of Object

but before this, both magnifications must be in the same measuremente, either in mm, cm etc..

2.1.6 - Explain the importance of the surface area to volume ratio as a factor limiting cell size.
 * A cell needs a large surface area in order to carry out metabolic functions (as chemical reactions require a surface). As a cell grows, it needs to carry out more and more reactions. Therefore, since a cell has to maintain a certain surface area to volume ratio, its size is limited.
 * The rate of exchange of materials (nutrients/waste) and energy (heat) is a function of its surface area.
 * Thus: As a cell grows in size (volume), the distance increases between the cytoplasm at the center of the cell and the cell membrane. The rate of chemical exchange with the surrounding environment may hence become too low to maintain the cell. It is not able to excrete waste quickly enough or take in important minerals.
 * Volume of a cell determines requirements while surface area determines supply.

 2.1.7 - State that multicelluar organisms show emergent properties
 * Emergent properties arise from the interaction of component parts: the whole is greater than the sum of its parts

 2.1.8 - Explain how cells in multicellular organisms differentiate to carry out specialized functions by expressing some of their genes but not others.
 * During the early development stages of multicellular organisms, cells undergo differentiation, becoming specialized in structure and function. These cells are then organized into tissues and organs. Cells of multicellular eukaryotes express only a small fraction of their genes, allowing them to perform highly specialized functions. Cells, such as those of muscle or nervous tissue, express only a tiny fraction of their genes.

 2.1.9 - State that stem cells retain the capacity to divide and have the ability to differentiate along different pathways.
 * Unspecialised cells that can become any type of cells.
 * Embryo cells are "totipotent", meaning they can become any cells; after divisions, when the zygote became a ball of cells of blastocyst, which is "pluripotent", meaning capable of being almost any type of tissue. Stem cells can also come from umbilical cord of new baby, which are "multipotent", meaning they can be limited number of tissues.
 * Stem cells are self-sustaining: they can divide for many times.
 * They differentiate into specific tissue based on a chemical signal

 2.1.10 - Outline one use of therapeutic stem cells .
 * Bone marrow transplants. They only work because what you are actually transplanting is the hematopoetic stem cells in the marrow. And peripheral blood stem cells, as well as cord blood stem cells, can be used in lieu of bone marrow, making being a donor FAR easier today than in decades past.

http://www.marrow.org

Random Stuff that Doesn't fit or is old syllabus material

State that a virus is a non-cellular structure consisting of DNA or RNA surrounded by a protein coat.
 * Viruses are not cells. They are simple particles consisting of DNA and RNA wrapped in a protein coat. Viruses are not considered alive because they have no metabolism and they require a host to live. Viruses do not carry out all the functions of life, therefore they are not living.

Explain three advantages of using light microscopes.
 * Light microscopes
 * Display color instead of monochrome (black and white) images.
 * Provide a large field of view.
 * Facilitate preparation of sample material.
 * Allow for the examination of living material and the observation of movement.
 * Cheap in comparison to electron microscopes

Outline the advantages of using electron microscopes.
 * Electron microscopes:
 * Provide images of higher resolution and magnification than light microscopes.
 * Resolution refers to the ability to distinguish two objects as separate entities.
 * Magnification refers to the ability to increase the size of a viewed object.
 * Scanning Electron Microscopes (SEM) provide images of the specimen's surface while Transmission Electron Microscopes (TEM) provide images of a sample's interior. The resolution of an SEM is approximately half that of a TEM.
 * May provide a three dimensional view.

Define organelle.
 * An organelle is a discrete structure within a cell, and has a specific function. A mitochondrion would be an example of an organelle.

Organelle List:

mitochondrion

golgi body

endoplasmic reticulum

vacuole

lysosome

ribosome In contrast to the other organelles, they are not surrounded by a membrane.

centriole (Unique to animal cells)

chloroplast (Unique to plant cells)

Define tissue, organ and organ system.
 * Tissue: An integrated group of cells that share structure and are adapted to perform a similar function.
 * Organ: A combination of two or more tissues which function as an integrated unit, performing one or more specific functions.
 * Organ system: A group of organs that specialize in a certain function together.

2.2 Prokaryotic Cells
2.2.1 Draw and label a diagram of the ultrastructure of Escherichia (E. coli) as an example of a prokaryote
 * The Diagram Should show cell wall, plasma membrane, cytoplasm, pili, flagella, ribosomes and nuceloid (region containing naked DNA)

Two Good Pictures
 * http://www.the-simple-homeschool.com/image-files/prokaryote_cell_.gif
 * http://web.archive.org/web/20110718134337/http://www.ecoliblog.com/cell-ecoli.gif

2.2.2 Annotate the diagram from 2.2.1 with the functions of each of the named structures
 * Cell Wall: Maintains the cell's shape and gives protection.
 * Plasma Membrane: Regulates the flow of materials (nutrients, waste, oxygen, etc.) into and out of the cell.
 * Cytoplasm: Holds and suspends the cell's specialized organelles and enzymes.
 * Pili: The function of the pili is attachment to solid surfaces, apparatus for use in transfer of DNA from one cell to another, twitching motility, and cell-cell adhesion.
 * Flagella: Flagella are whip like tails that are used to propel the organism forward.
 * Ribosome: Protein synthesis.
 * Nucleoid: Nucleoid is the area in the cytoplasm where the strands of DNA are present.

2.2.3 Identify structures from 2.2.1 in electron micrographs of E. coli

http://www.ucmp.berkeley.edu/bacteria/bacteriatem.gif http://www.exploratorium.edu/traits/images/ecoli_micro.jpg

2.2.4 State that prokaryotes divide by binary fission.
 * Prokaryotes divide by binary fission.
 * The process starts with DNA replication, then separation of the two circular strands to either side of the cell. Then cytokenesis occurs: division into two.
 * Each new cell has about half of the cytoplasm.
 * Growth restores the original size.

Old Stuff not in syllabus or misplaced

State that prokaryotes show a wide range of metabolic activity including fermentation, photosynthesis and nitrogen fixation.
 * Prokaryotes demonstrate a range of metabolic activity
 * Cyanobacteria (often referred to as blue-green algae although they are not algae) obtain their energy through photosynthesis.
 * Bacteria can convert organic substances into other organic substances. (i.e., glucose to lactic acid during anaerobic respiration)
 * Some bacteria can fix nitrogen from the air, converting it into ammonia (which is biologically available).

2.3 Eukaryotic Cells
2.3.1 Draw and label a diagram of the ultrastructure of a liver cell as an example of an animal cell
 * Should include free ribosomes, the rough endoplasmic reticulum (rER), lysosome, Golgi apparatus, mitochondrion, and nucleus.

2.3.2 Annotate the diagram from 2.3.1 with the functions of each of the named structures.
 * Ribosomes: Main site of protein synthesis.
 * Rough endoplasmic reticulum (rER): Packages the proteins synthesized in the ribosomes.
 * Lysosome: Digests macromolecules and contain digestive enzymes.
 * Golgi apparatus: Modifies, stores and routes products of the endoplasmic reticulum.
 * Mitochondrion: Serves as the site of cellular respiration.
 * Nucleus: Contains a cell's genetic material

2.3.4 Compare prokaryotic and eukaryotic cells.
 * Differences should include
 * Contain naked DNA vs. DNA associated with proteins (DNA wrapped around histones, a protein molecule, creating units called nucleosomes)
 * DNA in cytoplasm vs. DNA enclosed in a nuclear envelope - Prokaryotes have naked DNA in cytoplasm, Eukaryotes have a nuclear membrane surrounding it in a nucelus.
 * No membrane-enclosed organelles vs. membrane-enclosed organelles (e.g., mitochondria, chloroplasts) - Prokaryotes have no mitchondria, thousands of reactions occur in cytoplasm.
 * 70S vs. 80S ribosomes - Prokaryotes = 70S, Eukaryotes = 80S.
 * Eukaryotic cells have internal membranes that compartmentalize their functions
 * prokaryotic is usually smaller in size, Eukaryotic is larger
 * both have cytoplasm
 * prokaryotic has no nucleus, Eukaryotic has a membrane-bound nucleus
 * prokaryotic has one chromosome / circular, Eukaryotic has two or more chromosomes
 * prokaryotic has DNA only, Eukaryotic has DNA with histones to bind together
 * prokaryotic has no membrane-bound organelles, E has some membrane-bound organelles
 * Eukaryotic has mitochondria, prokaryotic does not
 * Eukaryotic has other example of organelle, prokaryotic does not
 * both can have a flagellum
 * if flagella then E has 9+2 fibrils, prokaryotic does not
 * prokaryotic can have plasmids, Eukaryotic does not
 * both have ribosomes
 * prokaryotic has small ribosomes, Eukaryotic has larger ones
 * both have cell membrane
 * Eukaryotic has centriole, prokaryotic has no centriole

2.3.5 State three differences between plant and animal cells.
 * Only plant cells have:
 * Cell walls
 * Chloroplasts
 * Vacuole - more specificially central vacuole
 * Plasmodesmata

2.3.6 Outline two roles of Extracellular components
 * The plant wall maintains shape, prevents excess water uptake, and holds the whole plant up against the force of gravity.
 * Animal cells secrete glycoproteins that form the extracellular matrix (ECM). This functions in support, adhesion and movement.

Stuff not in syllabus or not relevant or misplaced

 * Starch granules for storage of carbohydrates
 * Centrioles
 * Cholesterol in the plasma membrane
 * Glycogen for storage of carbohydrate

State the composition and function of the plant cell wall
 * The main component of plant cell walls is cellulose. Cellulose molecules are arranged in bundles called microfibrils. These give the cell wall great tensile strength and allow high pressures to develop inside the cell.
 * extra:The cellulose cell wall consists of three layers: middle lamella, primary cell wall, and secondary cell wall. The overall functions the cell wall preforms are: structure, support, protection.

2.4 Membranes
2.4.1 Draw and label a diagram to show the structure of membranes.
 * Diagram should show the phospholipid bilayer, cholesterol, glycoproteins, and integral and peripheral proteins. Use the term plasma membrane not cell surface membrane for the membrane surrounding the cytoplasm.

'''2.4.2 Explain how the hydrophobic and hydrophilic properties of phospholipids help to maintain the structure of cell membranes. '''
 * Hydrophilic molecules are attracted to water. Hydrophobic molecules are not attracted to water, but are attracted to each other. The phosphate head is hydrophilic and the two hydrocarbon tails are hydrophobic. In water, phospholipids form double layers with the hydrophilic heads in contact with water on both sides and the hydrophobic tails away from the centre. The attraction between the heads and the surrounding water makes membranes very stable.

In your answer you should:
 * — First discuss PHOSPHOLIPID STRUCTURE
 * hydrophobic tail/hydrophillic head
 * head made from glycerol and phosphate
 * tail made from two fatty acids
 * —Then discuss the ARRANGEMENT IN MEMBRANE
 * form a bilayer
 * heads face outside the membrane/ tails face inside the membrane
 * there is a hydrophobic interior and a hydrophillic exterior
 * —DRAW A DIAGRAM
 * —STATE ADDITIONAL INFORMATION
 * phospholipids are held together by hydrophobic interactions
 * stabilized by interaction of hydrophillic heads with surrounding water
 * fluidity helps the membrane to be stable
 * the fluidity allows for breaking and remaking of the membranes
 * allows for endo/exocytosis
 * the hydrophyllic/hydrophobic layers restrict movement
 * phospholipids can move about horizontally.

'''2.4.3 List the functions of membrane proteins. '''
 * hormone binding sites
 * enzymes
 * electron carriers
 * Channels for passive transport
 * Pumps for active transport
 * cell to cell recognition
 * receptors for neurotransmitters

'2.4.4 Define diffusion and osmosis''. '''
 * Diffusion: is the passive movement of particles from a region of higher concentration to a region of lower concentration, as a result of the random motion of particles.
 * Osmosis: the passive movement of water molecules, across a partially permeable membrane, from a region of lower solute concentration to a region of higher solute concentration.

2.4.5 Explain passive transport across membranes by simple diffusion and facilitated diffusion. Mention channels for facilitated diffusion. A molecule or ion that crosses the membrane by moving down a concentration or electrochemical gradient and without expenditure of metabolic energy is said to be transported passively/diffused. All molecules and ions are in constant motion and it is the energy of motion - kinetic energy - that drives passive transport. Transport of uncharged species across a membrane is dictated by differences in concentration of that species across the membrane - that is, by the prevailing concentration gradient. For ions and charged molecules, the electrical potential across the membrane also becomes critically important. Together, gradients in concentration and electric potential across the cell membrane constitute the electrochemical gradient that governs passive transport mechanisms. 1. Carrier proteins (also known as permeases or transporters) bind a specific type of solute and are thereby induced to undergo a series of conformational changes which has the effect of carrying the solute to the other side of the membrane. The carrier then discharges the solute and, through another conformational change, reorients in the membrane to its original state. Typically, a given carrier will transport only a small group of related molecules.
 * Facilitated diffusion is diffusion that is "facilitated" by proteins that span the membrane and provide an alternative route or bypass. It is similar to simple diffusion in the sense that it does not require expenditure of metabolic energy and transport is again down an electrochemical gradient.  Two major groups of integral membrane proteins are involved in facilitated diffusion:

2. Ion Channels do not really bind the solute, but are like hydrophilic pores through the membrane that open and allow certain types of solutes, usually inorganic ions, to pass through. In general, channels are quite specific for the type of solute they will transport and transport through channels is quite a bit faster than by carrier proteins. Additionally, many channels contain a "gate" which is functions to control the channel's permeability. When the gate is open, the channel transports, and when the gate is closed, the channel is closed. Such gates can be controlled either by voltage across the membrane (voltage-gated channels) or have a binding site for a ligand which, when bound, causes the channels to open (ligand-gated channels). Ion channels allow currents to be carried across the membrane and are thus of particular importance in the physiology of excitable cells like neurons and muscle cells.

 * —BROKEN DOWN
 * passive transport requires no energy
 * molecules move down a concentration gradient
 * water moves by osmosis
 * moves from higher solute concentration to lower solute concentration
 * small uncharged molecules move by diffusion
 * charged molecules move by facilitated diffusion
 * facilitated diffusion requires protein channels

'''2.4.6 Explain the role of protein pumps and ATP in active transport across membranes. '''
 * Active transport is the movement of substances across membranes using energy from ATP. Active transport can move substances against a concentration gradient. Protein pumps in the membrane are used for active transport. Each pump only transports particular substances so cells can control what is absorbed and what is expelled.
 * goes against concentration gradient
 * requires a protein in the cell membrane /pump/carrier protein
 * hydrolysis of ATP / ATP → ADP + phosphate;
 * involves a conformational change in the pump / protein

'''2.4.7 Explain how vesicles are used to transport materials within a cell between the rough endoplasmic reticulum, Golgi apparatus, and plasma membrane. '''
 * vesicle is made by pinching off a piece of membrane
 * fluidity of membrane allows this
 * vesicles can be used to transport material around inside cells
 * proteins are transported in vesicles
 * from the rough endoplasmic reticulum to the Golgi apparatus
 * from the Golgi apparatus to the plasma membrane
 * formation of vesicle from plasma membrane allows material to be taken in
 * endocytosis/pinocytosis/phagocytosis is absorption of material using a vesicle
 * fusion of vesicle with plasma membrane allows material to be secreted / passed out
 * exocytosis is secretion of material using a vesicle

2.4.8 Describe how the fluidity of the membrane allows it to change shape, break and re-form during endocytosis and exocytosis
 * In endocytosis part of the plasma membrane is pulled inwards. A droplet of fluid becomes enclosed when a vesicle is pinched off. Vesicles can then move through the cytoplasm carrying its contents.
 * In exocytosis vesicles fuse with the plasma membrane. The contents of the vesicles are then expelled. The membrane flattens out again.

2.1 Cell Theory
(Yet to be fully updated)

2.5.1 Outline the stages in the cell cycle, including interphase (G1, S, G2, mitosis and cytokenisis)
 * Interphase: Divided into 3 phases; Gap Phase 1 (Cell grows larger), Synthesis (Genome is replicated), Gap Phase 2 (separates the newly replicated genome).
 * Mitosis: Includes four stages--prophase, metaphase, anaphase, and telophase. Spindle fibers attach to the chromosomes and pull sister chromatids apart. It separates two daughter genomes.
 * Cytokinesis: Division of the cytoplasm to form two new cells.

2.5.2 State that tumours (cancers) are the result of uncontrolled cell division and that these can occur in any organ or tissue
 * Tumors are formed when cell division goes wrong and is no longer controlled. This can happen in any organ or tissue.

2.5.3 State that interphase is an active period in life of a cell when many metabolic reactions occur, including protein synthesis, DNA replication and an increase in the number of mitochondria and/or chloroplasts.\

 * Interphase is an active period in the life of a cell during which many metabolic reactions occur such as protein synthesis, DNA replication and an increase in the number of mitochondria and/or chloroplast.

2.5.4 Describe the events that occur in the four phases of mitosis (prophase, metaphase, anaphase and telophase)
 * Prophase: The spindle microtubules are extended from each pole to the equator.
 * Metaphase: Chromatids move to the equator and the spindle microtubules from each pole attach to each centromere on opposite sides.
 * Anaphase: spindle microtubules pull sister chromatids apart making the centromeres to split. This brings the sister chromatids apart, splitting them into chromosomes. Each identical chromosome is pulled to opposite poles.
 * Telophase: Spindle microtubules break down, while chromosomes uncoil and therefore are no longer individually visible. The nuclear membrane now reforms. The cell then is divided by cytokinesis to form two daughter cells with identical genetic nuclei.

2.5.5 Explain how mitosis produces two genetically identical nuclei.

 * During prophase, chromosomes become visible under a light microscope as they super coil and therefore they get shorter and becomes more bulky. The nuclear envelope disintegrates and the spindle microtubules grow, moves towards each pole, towards the equator. At metaphase the chromatids move to the equator. The sister chromatids are two DNA identical molecules as they were replicated during DNA replication. These sister chromatids are then separated in anaphase as the spindle microtubules attaches to the centromere, it pulls the sister chromatids to opposite poles. Now that sister chromatids are separated, they are known as chromosomes. This means that each pole has the same chromosomes. Finally the microtubules break down, the chromosomes uncoil and the nuclear membrane reforms. The cell then divides into two daughter cells with genetically identical nuclei.

'''2.5.6 State that growth, embryonic development, tissue repair and asexual reproduction involve mitosis. '''

 * Growth, embryonic development, tissue repair and asexual reproduction involve mitosis.

title: IB Biology/Cells


text:
IB Biology/The Chemistry of Life

Chemical Elements and Water
''' State that the most frequently occurring chemical elements in living things are carbon, hydrogen, oxygen, and nitrogen. '''

''' State that a variety of other elements are needed by living organisms, including sulphur, calcium, phosphorus, iron and sodium. '''

 State one role for each of the elements mentioned above
 * Nitrogen: Required by proteins. (Remember, nitrogen is included in the amino acid structure) Essential to enzymes required for plant function.
 * Calcium: The mineral that strengthens bone and teeth uses calcium. Also important in nerve synaptic transmission of nerve impulses and muscle contraction. Regulates the cell wall construction in plants.
 * Phosphorus: Part of the phosphate groups in ATP and DNA molecules. In plants it is needed for cell reproduction and division. It is part of the cell membrane.
 * Iron: found in the structure of hemoglobin and essential for the production of red blood cells. It is involved in the light energy transferring compounds involved in photosynthesis in plants.
 * Sodium: Major ion associated with the propagation of a nerve impulse. Can replace potassium in some plants in membrane function.
 * Sulfur: It is a component of amino acids.

Outline the difference between an atom and an ion and a polypeptide
 * An atom is a single particle of a chemical element. When an atom either gains or loses an electron it then becomes an ion. Ions are charged, while atoms are uncharged. An Ion has either a negative or positive charge depending if it gained or lost an electron. On the other hand a polypepetide chain is a chain of amino acids joined through peptide bonds, the amino acids are molecules that are formed through the combination of ions.

'''Outline the properties of water that are significant to living organisms, including transparency, cohesion, solvent properties and thermal properties. Refer to the polarity of water molecules and hydrogen bonding when relevant.'''
 * Water is transparent which allows light to filter into aquatic environments, and thus aquatic plants can absorb light and perform photosynthesis. Since the ancestor of all plants originated in the ocean, the transparency of water has had an immeasurable influence on life as we know it.
 * Water is also cohesive, that is it binds to itself, due to the polarity of the water molecule. The positive, hydrogen side of the molecule binds to the negative, oxygen side of another water molecule. This bond is called a hydrogen bond. Water is also adhesive, that is it binds to other things around it. This property allows for transport of water against gravity in plants. The water adheres to the xylem tube of plants and is able to be drawn up in long columns up the stem due to its strong cohesive force
 * Water's solvent properties allows molecules to dissolve in it. This means that water can transport minerals up the xylem tube and sugars up the phloem tubes in plants. Blood in animals consists largely of water, allowing the transportation of oxygen, urea and glucose throughout the body. Water also is the site of metabolic reactions because reactions can occur between dissolved compounds.
 * Water's polarity also inhibits movement of its molecules. Since all the molecules are connected, they cannot freely move about as other, non-polar molecules do. Heat, the kinetic energy of molecules, is thus restricted and so water has a high specific heat (it must absorb large amounts of energy in order to change states). This means that water can serve as a temperature insulator, and does so in organisms of all kinds.
 * Water's high latent heat of vaporization is due to strong hydrogen bonds existing between water molecules. A large amount of heat is released when water in the liquid state vaporizes into the gaseous state.

Explain the significance to organisms of water as a coolant, transport medium and habitat in terms of its properties
 * 'Coolant: Allows us to perform homeostasis. (We sweat to cool ourselves down). Additionally, water's high heat of vaporization allows water molecules to absorb large amounts of energy from the body before evaporating - thus, the sweating individual loses heat.
 * Transport medium: Digestion, also important to help transport blood. Phloem in plants transport nutrients dissolved in water using the cohesive and adhesive properties.
 * Habitat: Organisms need water; the ready availability of it is essential in the choosing of a habitat. Water's high heat capacity (the amount of energy needed to increase the temperature of 1gm of water by 1 Degrees Celcius) and high heat of vapourization (amount of energy absorbed by 1gm of liquid to be converted to the gaseous form) prevents from plants and animals from overheating and dying.

Carbohydrates, Lipids, and Proteins.
Define organic
 * Organic compounds are defined as compounds containing carbon that are found in living organisms.
 * Compounds are considered inorganic when they contain carbon but are widely found in the environment (carbon dioxide and hydrogen).

Draw the basic structure of a generalized amino acid

Draw the structure of glycerol and a generalized fatty acid click link for picture

Outline the role of condensation and hydrolysis in the relationship between monosaccharides, disaccharides, and polysaccharides; fatty acids, glycerol and glycerides; amino acids, dipeptides, and polypeptides.
 * In a condensation reaction, two molecules work together and form one big molecule along with water, because water is released during this reaction. So, two amino acids could join together and form a dipeptide and this would be a condensation reaction. Same applies for monosaccharides becoming disaccharides, you get the drift.
 * Now in a hydrolysis reaction, water molecules are used up to make a large molecule into a small molecule. Think about it- "hydro" means water and "lysis" means splitting. So, water is used up to split a disaccharide into a monosaccharide.

Draw the structure of a generalized dipeptide showing peptide linkage http://homepages.ius.edu/GKIRCHNE/peptide.jpg

List three examples for each of monosaccharides, disaccharides, and polysaccharides
 * Monosaccharide: Glucose, Fructose and ribose
 * Disaccharide: Maltose (Glucose + Glucose) and Sucrose (Glucose + Fructose), and lactose.
 * Polysaccharide: Starch (made of glucose subunits) and Glycogen (made of glucose subunits, but linked differently from starch). (Plants use mostly starch, humans use mostly glycogen) and cellulose.

State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants.
 * Animals
 * Glucose: metabolized for energy.
 * Lactose: provides energy to mammalian young.
 * Glycogen: longer term energy in muscles and liver.
 * Plants
 * Fructose: sweetens fruit to disperse seeds
 * Sucrose: energy storage
 * Cellulose: cell wall structure

State three functions of lipids
 * Energy storage: Fat in humans. Oil in plants.
 * Heat insulation: A layer of fat under the skin reduces heat loss.
 * Buoyancy: Lipids are less dense than water.

Discuss the use of carbohydrates and lipids in energy storage.
 * Lipids and carbohydrates are excellent for storing energy in living organisms. Carbohydrates are usually used to store energy in the short-term while lipids are used for the long-run.
 * Advantages of Lipids
 * Contain more energy per gram. Therefore lighter to store.
 * Lipids are insoluble in water; do not interfere with osmosis.
 * Advantages of Carbohydrates
 * More easily digested, so energy is released more easily from them.
 * Carbohydrates are soluble in water, so easier to transport.

Explain the four levels of protein structure Primary structure
 * A linear sequence of amino acids joined by peptide linkages. There are about 20 different amino acids.

Secondary structure
 * α -Helix is maintained by hydrogen bonds. The helix makes up keratin (skin, nails, hair).

 * β -Pleated Sheet: flat zig-zag amino acid chain. The sheets make up fibroin (silk.

 * Both structures are fibrous and form structural proteins

Tertiary structure
 * Folded polypeptide chains into specific shapes. This means that tertiary proteins are globular (hormones, enzymes, membrane proteins).

Quaternary structure
 * Two or more polypeptide chains joined (e.g. haemoglobin).

Outline the difference between fibrous and globular proteins, with references to two examples of each protein type
 * Fibrous proteins (such as keratin, collagen)
 * Chain extended
 * Insoluble
 * Resistance to pH/temperature changes
 * Structural material

 * Globular proteins (such as haemoglobin, amylase)
 * Chain folded
 * Soluble/colloidal
 * Susceptible to pH/temperature changes
 * Compact, rounded molecules

Enzymes
Define Enzyme and Active Site
 * Enzyme: Globular proteins used to catalyze chemical reactions.
 * Active site: The binding site on the surface of an enzyme where catalysis occurs.

Explain enzyme-substrate specificity
 * The active site for an enzyme is very specific in shape, with very precise chemical properties. Active sites match the shape of their substrates. Other molecules do not fit or do not have the same chemical properties. Therefore the enzyme is substrate specific. This enzyme is a lock, and the substrate is the key which can open it.

Explain the effects of temperature, pH and substrate concentration on enzyme activity
 * Temperature, pH and substrate concentration all affect the rate at which enzymes catalyse chemical reactions.

Substrate concentration: At low s.c. the enzyme activity is proportional to the substrate concentration, because of random collision between substrate and enzyme. Thus the more substrate the higher the rate. However at a high substrate concentration, at some point all active sites are occupied so raising the substrate concentration has no effect.

Temperature: Enzyme activity increases as temperature increases, often doubling with each 10°C. This is because collision between the substrate and active site happen more frequently at higher temperatures, due to fast molecular movement. However, at high temperatures enzymes are denatured and stop working. This is because heat causes vibrations inside the enzyme, which break bonds needed to maintain the structure.

pH: There is an optimum at which enzyme activity is fastest ( mostly pH 7), and as pH increases or decreases from its optimum, enzyme activity is reduced. (acids and alkali denature enzymes)

Define Denaturation
 * Denaturation: A structural change in a protein that results in a loss of its biological properties. This can be caused by pH or by temperature.

Explain the use of lactase in the production of lactose free milk Lactose- The sugar present in milk. Lactase is obtained from Kluveromyces and lactis, a type of yeast that grows naturally in milk. Lactose can be converted to glucose and galactose using the enzyme lactase (di-saccarharide). Biotechnology companies culture the yeast and extract the enzyme in order to produce lactose free milk.

 * Advantages: Pectinase makes juice more fluid and easy to separate from pulp.

 * Fructose is widely used in food manufacturing because it is much sweeter than glucose. It is made from starch, usually found in maize. Amylase is needed to break down the starch into glucose.
 * 'Source of Enzyme: Amylase is obtained from fungi.
 * Use: Used to break Starch into glucose, which is then converted into fructose using the enzyme glucose isomerase.

DNA Structure
Outline DNA nucleotide structure in terms of sugar (deoxyribose), base, and phosphate.
 * A DNA is composed of a deoxyribose, a phosphate group and a nitrogen base (Adenine, Cytosine, Thymine, and Guanine). The phosphate group is covalently bonded to the carbon of the deoxyribose and then the nitrogenous base is attached to the deoxyribose.

State the four names of the bases of DNA
 * Adenine, Cytosine, Guanine, and Thymine.

Outline how the DNA nucleotides are linked together by covalent bonds into a single strand.
 * Two DNA nucleotides can be linked together by a covalent bond between the sugar of one nucleotide and the phosphate of another. More nucleotides can be added to form a single strand.

Explain how the DNA double helix is formed using complementary base pairing and hydrogen bonds.
 * DNA molecules consist of two strands of nucleotides which are then wound together to form a double helix. These are formed between the bases of two strands. However, it is formed by complementary base pairing because Adenine only forms hydrogen bonds with Thymine and Cytosine only forms hydrogen bonds with Guanine.

Draw a simple diagram of the molecular structure of DNA.

URL of a suitable picture: http://www.cem.msu.edu/~reusch/VirtTxtJml/Images3/dblhelx1.gif

DNA Replication
State that DNA replication is semi-conservative.
 * DNA replication copies DNA to produce new molecules with the same base sequence. It is semi-conservative because each new molecule formed by replication uses one new strand and one old strand which is conserved from the parent DNA molecule.

Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by the formation of the new complementary strands by DNA polymerase.
 * Stage 1: The DNA double helix is unwound and separated into strands by helicase breaking the hydrogen bonds holding the strands together and creating a replication bubble.
 * Stage 2: The single strands act as blueprints for new strands. Free nucleotides are present in large numbers. The enzyme primase places primers on the new strand, allowing DNA Polymerase III to add to the strand in a 5-carbon to 3-carbon direction. Several small strands are made within the replication bubble formed by helicase that are known as Okazaki fragments. DNA Polymerase III is then removed, and DNA polymerase I replaces primers with corresponding base pairs.  The enzyme ligase then binds these new base pairs to the rest of the strand. The bases of these nucleotides form hydrogen bonds with the bases of the parent strand. The nucleotides are connected to form a new strand.
 * Stage 3: The daughter DNA molecules each rewind into a double helix.

The two daughter DNA molecules are identical in base sequence to each other and to the parent molecule, because of complementary base pairing (Adenine pairs with Thymine and Cytosine with Guanine). Each of the new strand is complementary to the template on which it was made and identical to the other template.

Explain the significance of complementary base pairing in the conservation of the base sequence of DNA.
 * Because the nitrogenous bases that compose DNA can only pair with complementary bases, any two linked strands of DNA are complementary. This ensures that the old base sequence is conserved.

Transcription and Translation
Compare the structure of RNA and DNA
 * 1. The number of strands.
 * DNA has two strands forming a double helix.
 * RNA has one strand.
 * 2. The type of sugar.
 * DNA has deoxyribose.
 * RNA has a Ribose.
 * 3. The Nucleotides.
 * DNA has A,C,G,T
 * RNA has A,C,G,U, (Uracil replaces Thymine)

Outline DNA transcription in terms of the formation of the RNA strand complementary to the DNA strand by RNA polymerase.
 * Transcription: The copying of the base sequence of a gene by making an RNA molecule.
 * The DNA double helix uncoils and the two strands separate.
 * RNA Polymerase attaches to promoter regions of the DNA strand
 * RNA polymerase binds free RNA nucleotides to create mRNA that are a copied template of the corresponding DNA strand.
 * The mRNA separates from the DNA.
 * The DNA strands reforms into a double helix.

Describe the genetic code in terms of codons composed of triplets and bases. The genetic code is a triplet code- three bases code for one amino acid. A group of three bases is called a codon.

Explain the process of translation, leading to polypeptide formation
 * Before the mRNA strand is translated, it must be processed. A cap and tail are added to the mRNA strand to allow the mRNA strand out of the nucleus.
 * There are intron and exon segments of the strand. The introns are removed by the introduction of a splicesome.  The splicesome pushes out the introns and binds the exons together.
 * The mRNA then passes through the nuclear pore and enters the cytoplasm.
 * The two subunits of a ribosome (60s and 40s) lock onto the mRNA at the ribosome-binding site.
 * Transfer RNA (tRNA) are clover-leafed shaped molecules that have a specific amino acid attached.
 * Each tRNA also has three bases called the anticodon that binds to the mRNA. The anticodon determines which amino acid the tRNA carries.
 * The tRNA can only bind to the mRNA in the presence of a ribosome. In each ribosome there are two tRNA binding sites (Aminoacyl tRNA binding site or A site and Peptidinal tRNA binding site or P site) and a tRNA exit site (E site).
 * The mRNA is divided into groups of three bases each called a codon. The anticodon on the tRNA binds to the complementary codon on the mRNA. In so doing it brings the amino acid into position.
 * The mRNA is fed between the small and large subunits of the ribosome. The first tRNA molecule with the attached start amino acid, methanine, attaches at the A site and is transferred to the P site.  The next tRNA binds to the mRNA and contains an amino acid.
 * When two tRNA molecules are bound to the mRNA at the ribosome a ribosomal enzyme forms a peptide bond between the two amino acids.
 * The first tRNA becomes detached from its amino acid and moves off from the ribosome after it slides into the exit site.
 * The ribosome moves a distance of one codon and a new tRNA binds bringing in another amino acid to be joined to the polypeptide chain.
 * The first codon translated on any mRNA is always AUG. This is called the initiation codon and it sets the reading frame of the mRNA.
 * There are also three codons that signal the end of the mRNA and stop translation. They are the stop codons UAG, UAA and UGA.
 * Several ribosomes may all be translating the same mRNA at the same time. This is called a polysome.

Define the terms degenerate, and universal as they relate to the genetic code
 * Degenerate: Having more than one base triplet to code for one amino acid.
 * Universal: Found in all living organisms.

Discuss the relationship between one gene and one polypeptide
 * Polypeptides are long chains of amino acids.
 * Amino acids must be linked up in a precise sequence to make a polypeptide.
 * Genes store the information needed to make a polypeptide in a coded form.
 * The sequence of bases in a gene codes for the sequence of amino acids in a polypeptide.
 * The information in the gene is decoded during the making of the polypeptide.
 * This process is conducted in two stages known as transcription and translation.

Cell Respiration
Define Cell-Respiration
 * Cell Respiration: controlled release of energy in the form of ATP from organic compounds in cells.

In cell respiration, glucose in the cytoplasm is broken down into pyruvate with a small yield of ATP
 * Glucose is an organic compound that is sometimes used in cell respiration. Chemical reactions break Glucose into a simpler compound called pyruvate. A small amount of ATP (2 ATP) is produced by using energy released from glucose.

In anaerobic cell respiration pyruvate is converted into lactate or ethanol dioxide in the cytoplasm with no further yield of ATP
 * Lactic fermentation: In the process of glycolysis glucose is transferred into two pyruvate. Since no oxygen is available, the Krebs cycle cannot run which therefore also stops the process of the electron transport chain. Too much pyruvate is built up in the cytoplasm and we need to get rid of it. Therefore, it is transferred into the waste product - lactate - that can be removed from the cell. No ATP is produced.
 * Alcohol fermentation: since there is no oxygen, pyruvate is transferred into ethanol/alcohol and carbon dioxide is created as a bi-product. This is how one-celled organisms overcome oxygen deficiency.

In aerobic respiration pyruvate is broken down in the mitochondrion into carbon dioxide and water with a large yield of ATP If oxygen is available, the pyruvate is absorbed by mitochondrion. The pyruvate is then broken down into carbon dioxide and water. A large amount of ATP is produced.

 * Note: How to remember the difference! Aerobic sounds healthy- so something good comes out of it! Anaerobic sounds like unaerobic and that sounds unhealthy! Easy to remember, right? Also, think of doing aerobics, which is healthy as well and makes you breathe a lot!

Photosynthesis
State that photosynthesis involves the conversion of light energy into chemical energy.
 * Photosynthesis involves energy conversion. Light energy, usually sunlight, is converted into chemical energy.

State that white light from the sun is composed of a range of wavelengths.
 * Sunlight is called white light, but it is actually made up of a range of wavelengths including red, blue, and green.

State that chlorophyll is the main photosynthetic pigment
 * The structure of chlorophyll allows it to absorb some colors of wavelength better than others.

Outline the differences in absorption of red, blue and green light by chlorophyll
 * Red and blue light are absorbed more than green. The green light that cannot be absorbed is reflected giving plants (and the pigment chlorophyll) their green color.

State that light energy is used to split water molecules (photolysis) to give oxygen and hydrogen and to produce ATP

 * Some of the energy absorbed by chlorophyll is used to produce ATP
 * Some of the energy absorbed by chlorophyll is used to split water molecules. This is called photolysis of water
 * Photolysis of water results in the formation of oxygen and hydrogen. The oxygen is released as a waste product

State that ATP and hydrogen (derived from photolysis of water) are used to fix carbon dioxide to make organic molecules.
 * Carbon dioxide is absorbed for use in photosynthesis
 * The carbon from it is used to make a wide range of organic substances
 * The conversion of carbon in gas to carbon in solid compounds is called carbon fixation
 * Carbon fixation involves the use of hydrogen from photolysis and energy from ATP.

Explain that the rate of photosynthesis can be measured directly by the production of oxygen or the uptake of carbon dioxide, or indirectly by the increase of biomass
 * Uptake of carbon dioxide: Since carbon dioxide is important in the light-independent reactions of photosynthesis, its consumption by plants can be measured as a means to determine the rate of ATP and electron carriers used for carbon fixation.
 * Production of oxygen: Aquatic plants release bubbles of oxygen when they carry photosynthesis. e.g. these bubbles are collected; their volume can be measured.
 * Increase in Biomass: If batches of plants are harvested at a series of times and their biomass determined, then the rate of photosynthesis can be determined by an increase in biomass.

Outline the effects of temperature, light intensity, and carbon dioxide concentration on the rate of photosynthesis:
 * Light - At low medium light intensities the rate is directly proportional to light intensity. At high light intensities the rate reaches a plateau.
 * Carbon Dioxide - No photosynthesis at very low CO2 concentrations. At low to fairly high CO2 concentrations the rate is positively correlated with CO2 concentration. At very high CO2 concentrations the rate reaches a plateau.
 * Temperature - As temperature increases the rate increases more and more steeply. If the temperature increases with 10¤C it roughly doubles the rate. When it reaches it maximum point it is said to be its Optimum Temperature which is around 40¤C. Above the optimum temperature the rate slows down rapidly and then stops. This happens because the excessive heat destroys the enzymes which are responsible for catalyzing chemical reactions.

title: IB Biology/The Chemistry of Life