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Welcome to the Biology 12 QE wiki page. We will be creating a collaborative bonus assignment for Unit 3. In order for you to receive credit you must contribute on this page. You must contribute 5 things to this wiki. **__Please read discussion before beginning__!**

1. Demonstrate an understanding of the following terms: metabolism, substrate, enzyme, coenzyme, activation energy. Metabolism-a chemical activities of a cell that are controlled by enzymes.** Substrate - the reactants in an enzymatic reaction Activation energy- http://www.youtube.com/watch?v=VbIaK6PLrRM Activation energy- is the initial amount of energy required for all chemical reactions to take place Enzyme- stabilizes the substrates so a reaction can occur with a lower activation energy. Enzymes are biological catalyst; they speed up the reaction, but actually are not part of the reaction. Coenzyme- an organic cofactor which helps create a more stable active site Apoenzyme- when a coenzyme such as a vitamin in needed to provide a more stable active site, the original enzyme is called the Apoenzyme
 * A. Enzymes:

-The enzyme has a an active site which __perfectly binds__ to substrate(s) - Has a General Equation of E+S -->ES -->E +P -The enzyme's shape does not change. -Refers to a perfect fit between the Enzyme and Substrate to form the ES complex. - when the __ES__ is formed, the __Ea__ is lowered for the reaction http://www.youtube.com/watch?v=z8lG8X9ZvxQ&feature=related
 * 2. Explain the 'lock and key" model of enzymatic action.**

-make part of coenzymes - vitamins are small organic molecules and are required for the formation of coenzymes that are important for health and physical fitness
 * 3. Describe the role of vitamins in biochemical reactions.**

-Enzyme acts as an organic catalyst which speeds up a chemical reaction and provides an active site for substrate(s) to attach. -Co-enzyme assists the enzyme and contribute atoms to the reaction -Co-enzyme is a organic co-factor that makes the active site on the original enzyme more stable by adding/removing atoms, molecules and electrons. for example: NAD can add/remove H+ form the active site of enzyme. -Co-enzymes are small organic molecules that are required for the catalytic function of certain enzymes. [|http://www.elmhurst.edu/~chm/vchembook/images/571NAD.gif] -Co-enzymes fucntion as intermediate carriers of electrons and many co-enzymes are derived from vitamins. -Enzymes are proteins that speeds up the reaction.Reactions can occur without the enzymes but the rate would be slow. http://www.biologyreference.com/images/biol_02_img0148.jpg - Enzymes lower the energy of activation.
 * 4. Differentiate between the roles of enzymes and co-enzymes in biochemical reactions.**

__Substrate Concentration__ -As the substrate concentration increases, the ROR (rate of reaction) increases - However,after a certain increase in [ ] of substrate, the ROR will stay constant as all enzymes will be saturated. __Enzyme Concentration__ - As the enzyme concentration increases the ROR also increases if there is adequate substrates present. - A reaction is able to take place without an enzyme, but without the enzyme it is likely that the reaction may not take place efficiently enough to sustain itself This graph should not start at 0. The reason is that reactions still occur without enzymes. __Competitive Inhibitors__ -looks identical to the substrates and binds to the active site to prevent substrates from binding. -Binds to the active site of an enzyme and prevent a substrate from binding to it, reducing enzyme activity. - Binding onto the active site can be reversible in some cases, and irreversible in others, such as Penicillin binding to certain bacterial enzymes. __Temperature__ - 37 degrees celsius is the "optimal temperature" for enzymes to function in humans - from 0 to 37 degrees, an increase in temperature will increase the ROR - after 37 degrees, an increase in temperature will cause the enzyme to change in shape, and at 50 degrees enzyme will not function due to being too denatured -as the temperature increases from 0-37 degrees celsius there is a increase in collisions, however after 37 degrees celsius the collisions end up denaturing the enzymes. __pH__ - Enzymes work effectively at optimum pH levels.Optimal pH levels vary depending on enzyme. A change in pH may affect the shape of an enzyme (denature) and cause it to be disfuctional towards any further activity.
 * 5. Apply knowledge of proteins to explain the effects on enzyme activity of pH, temperature, substrate concentration, enzymes concentration, competetive inhibitors, and heavy metals.**

__Heavy Metals__ - mercury, lead and other heavy metals bind irreversibly to enzymes and change the active site and effect ES complex formation.They are a type of non-competitive inhibitors. -They bind to another place of an enzyme besides active side. However, this causes a change in the active site, and effects the ES complex formation.

-The hormone Thyroxine regulates the metabolic rate - Thyroxine increases the rate of cellular respiration - less ATP energy is produced by individuals who have lower amounts of thyroxine in their body, therefore they gain more weight from the storage of more glucose - determines how fast or slow chemical reactions proceed in a person's body
 * 6. Explain the role of thyroxin(e) on metabolic rates.**


 * B. DNA:**

__Unzipping__ - Hydrogen bonds between nitrogen bases break. http://youtube.com/watch?v=hfZ8o9D1tus&feature=related __Complementary base pairing__ - unoccupied nucleotides from the nucleus attach to the complementary bases on the original DNA strands - the original DNA strands serve as templates for the free nucleotides to pair up with complementary bases - base pairings in DNA are adenine-thymine and cytosine-guanine -Bases are connected by hydrogen-bonds (yellow lines in above diagram) __Joining of Adjacent Nucleotides__ -Join together by the phosphate of one nucleotide binding to the sugar of another with the help of the enzyme DNA polymerase http://www.youtube.com/watch?v=rpwjZX_z5rg&feature=related
 * 7. Describe DNA replication with reference to three basic steps: unzipping, complementary base pairing and joining of adjacent nucleotides.**

- in a sense, it is "cutting and pasting" of DNA from different organisms http://www.youtube.com/watch?v=x2jUMG2E-ic - a form of artificial DNA that is created by a combination one or more DNA strands which wouldn't naturally fit together. - often also known as gene therapy, DNA from two separate sources is fit together to form a "hybrid" DNA, which can be used in various industries http://www.iptv.org/EXPLOREMORE/ge/what/recombinant.cfm eg. Human Insulin gene is injected into E Coli (host cell) where it is replicated to produce larger quantities.
 * 8. Define Recombinant DNA.**

-Genetherepy:replaces defective genes with healthy genes -Medical industry: insulin is made by combining DNA from a bacteria with the human insulin gene Food Industry: To obtain desirable traits for certain crops by using recombinant DNA
 * 9. Describe 3 uses for Recombinant DNA**

- DNA is a polynucleotide -DNA is a thick double stranded structure -DNA twists to form a double helix -RNA is straight and doesn't form a helix -RNA is a thin single stranded structure -Sugar for DNA is Deoxyribose -Sugar for RNA is Ribose -RNA is able to leave the nucleus in order to replicate genetic information since it is thinner than DNA and can fit through the nuclear pores -DNA contains the nitrogenous bases Adenine, Guanine, Thymine & Cytosine while RNA contains the same except instead of Thymine it contains Uracil -Both DNA and RNA have a backbone made from a sugar and a phosphate group, with rails made of nitrogen bases.
 * 10. Compare and contrast the general structural composition of DNA and RNA.**



- DNA unzips and mRNA makes a template which exits the nucleus through the nuclear pores . DNA holds the code for the production of amino acids and proteins. It is used as a template for mRNA in transcription. -After DNA unzips, RNA nucleotides will pair up with the nucleotides on the unzipped DNA, these RNA nucleotides are joined together by RNA polymerase to form mRNA -mRNA leaves the nucleus and attaches itself to the ribosomes -Ribosome is the site of protein synthesis -Ribosomes have a binding site for mRNA and for tRNA and helps the binding of codons and anticodons -then the tRNA which is free floating comes and reads the codons of mRNA. The tRNA has an anticodon that is complementary to the codons of mRNA. On the other end is the amino acid the codon is coding for. - the complimentary site on the tRNA that reads and matches the codon of mRNA is known as the anticodon. -another tRNA comes and will complementary pair with next codon and the chain will continue until stop codon is read bytRNA.
 * 11. Demonstrate a knowledge of the basic steps of protein synthesis, identifying the roles of DNA, mRNA, tRNA, and ribosomes in the processes of transcription and translation.**



http://www.youtube.com/watch?v=XS_Dky-s2-c

-DNA and mRNA strands are complementary ex. DNA- ATG GCT CCG mRNA- UAC CGA GGC Amino Acids- Tyrosine-Arginine- Glycine - Though DNA and mRNA are complementary, the nitrogenous base of Uracil replaces Thymine in mRNA
 * 12. Determine the sequence of amino acids coded for by a specific DNA sequence, given a table of mRNA codons.**


 * 13. Give examples of 2 environmental mutagens that can cause mutations in humans.**

-X-rays and Pesticides can cause mutations in humans.

-radiation and exposure to harmful chemical can cause the alteration in nucleotides.(mutation)

-Gene mutation is changes in the nucleotide sequences of a gene -when any types of mutation occurs (point mutation or frameshift mutations) it creates different codons, which will then code for different amino acids so, different protein is produced instead of the intended one. -example: in Sickle cell Anemia, the amino acid Glutamine is changed to Valine which causes red blood cells to become sickle-shaped. This affects the transport of oxygen by red blood cells.
 * 14. Use examples to explain how mutations in DNA affect protein synthesis and may lead to genetic disorders.**

Mutuation --> Different codons --> Different ammino acid -->Production of different protein --> Intended enzyme is not made (could cause a disorders)

http://www.youtube.com/watch?v=kp0esidDr-c