Nucleic+Acids+(HL)

=Nucleic Acids (HL)=

Task

 * ===== A page must include valid, original information that will help your fellow classmates learn, understand, and study for this subtopic. You should include diagrams, videos, practical explanations and practice IB type questions. =====
 * ===== You will be graded your page presentation and information (check objectives) of your subtopics. =====
 * ===== A file with questions covering each topic will then be posted that you will answer using the wiki pages. =====

Deadlines:

 * ===== February 1 Pages built per subtopic =====
 * February 7 Answer questions in GoogleDoc


 * Objectives**

=__**What are Nucleic Acids?**__= Nucleic acids are large biological molecules made up of monomers called nucleotides.These nucleotides combine to form the building blocks of living organisms, which are DNA and RNA.

__**B.8.1 Structure of Nucleotides and Nucleic Acids**__
 * All cells in a human body contain DNA except for red blood cells
 * Deoxyribonucleic Acid (DNA) and Ribonucleic Acid (RNA) are made up of repeating base-sugar-phosphate units called __nucleotides__


 * Nucleotides are monomers consisting of either a deoxyribose sugar or a ribose sugar covalently bonded to a phosphate group, and one of the one or two ring nitrogen base (A,T,C,G in DNA or A,U,C,G in RNA)


 * Nucleotides condense to form a polynucleotides where each nucleotide is joined by a phosphodiester bond between C3 of the sugar and the neighbouring phosphate group
 * Polynucleotides form the backbone of the nucleic acid with the repeating pattern of -sugar-phosphate-sugar-phosphate
 * The nitrogenous bases are attached to the first carbon atom in the sugar of the backbone
 * Polynucleotides (multiple nucleotides) are put into a helical shape in DNA
 * Two helices are held together by H bonds between bases
 * Bases have specific complementary bases that they only bond to: thymine (T) forms two bonds with adenine (A), and cytosine (C) forms three bonds with guanine (G)
 * Thymine (T) is replaced by uracil (U) in RNA
 * C, T and U are called pyrimidines and each has a single nitrogen-containing ring
 * A and G are purines and each has two nitrogen-containing rings



Overview:

__**B.8.2 Distinguish between the structures of DNA and RNA**__ DNA and RNA are very similar because they are both nucleic acids with sugar-phosphate backbones, that are attached to nitrogenous bases. However, t here are 3 major differences between their structures.
 * 1) The first, and most commonly known is the type of sugar. ** RNA has ribose as it's pentose sugar group ** whereas ** DNA have deoxyribose, ** which means it has one oxygen atom less than RNA.
 * 2) The second, as visible clearly in the picture above, is the difference in the type of strand. ** RNA is a single strand, ** whereas ** DNA is in a double helix form, ** where two complimentary strands are connected by hydrogen bonds from the bases.
 * 3) The third and final major difference between the two is the type of bases that are found on RNA or DNA. ** RNA could have Cytosine, Guanine, Adenine or Uracil, ** whereas ** DNA may have Cytosine, Guanine, Adenine or Thymine. ** Therefore, in ** RNA, Cytosine and Guanine form a base pair, and Adenine and Uracil form another. In DNA, Cytosine and Guanine form a base pair too, however Adenine pairs with Thymine. **

__**B.8.3 Explain the double helical structure of DNA**__
 * DNA has a double helical structure that is formed by the hydrogen bonding of nucleotides on one nucleic acid, with corresponding nucleotides on a second nucleic acid. The nucleotides provide each nucleic acid with a sugar phosphate backbone, and the bases pair together to link the two and form the DNA secondary structure. The hydrogen bonding can only occur between certain bases, and thus form base pairs. As explained above, Cytosine bonds with Guanine, and Adenine bonds with Thymine, because these nucleobases naturally occur opposite one another.
 * What holds the double stranded DNA molecule together is the intermolecular hydrogen bonding that takes place between the bases. This is also the primary reason as to why Cytosine can only bond with Guanine and Adenine only with Thymine. Cytosine and Guanine form 3 hydrogen bonds between each other, and the latter two form two hydrogen bonds. If Cytosine were to combine with Thymine, or any other out-of-the-ordinary combination were to occur, they would not form a strong enough hydrogen bond to hold the double helix together. Other forces such as dipole-dipole hydrophobic interactions and Van der Waals' forces between the base pairs also help maintain the DNA structure.
 * The sugar phosphate backbone gives DNA it's helical structure in order to minimize electrostatic repulsions between the negatively charged phosphate residues.

__**B.8.4 Describe the role of DNA as the repository of genetic information, and explain its role in protein synthesis**__

__**B.8.5 Outline the steps involved in DNA profiling and state its uses**__ DNA profiling is generally conducted through a process known as gel electrophoresis. This process separates DNA fragments by sizes with the use of an electric field.
 * Initially, a sample of DNA is taken from the subject and amplified through the polymerase chain reaction (PCR).
 * This DNA is then cut at various points using specific restriction enzymes, hence generating a number of fragments, each with a unique length.
 * These fragments are then used for DNA profiling, through gel electrophoresis.

__The steps involved in gel electrophoresis:__
 * 1) The fragmented DNA is taken and placed in agarose gel. This gel is ideal for the procedure because it has a physical setting and can be moved in a certain direction easily.
 * 2) The gel is put into a buffering solution and an electrical current is passed through the gel.
 * 3) Due to the phosphate in DNA, it is negatively charged and is therefore attracted towards the positive anode.
 * 4) The smaller fragments aren't as obstructed by the gel matrix as the larger ones are, and therefore mover faster through it.
 * 5) Hence, the fragments are separated according to their sizes.

__The uses of DNA profiling__ There are 2 main uses for DNA profiling which are for paternity tests and forensic investigations. In both cases, a comparison of two or more sets of DNA that have been profiled through gel electrophoresis is made.
 * Paternity tests: Children inherit one half of their alleles from the father, and the other from the mother. Therefore, they possess the alleles of both, which should be visible in the profiled DNA because some of the alleles of the child would match his/her mothers, and the others should match his/her fathers.
 * Forensic investigations: A DNA sample collected from a crime scene can be profiled, and compared with the profiled DNA of potential suspects in order to find matches and prove individuals innocent or guilty of crimes.



__**Bibliography**__ IB Study Guide Chemistry for the IB Diploma http://www.ib.bioninja.com.au/standard-level/topic-4-genetics/44-genetic-engineering-and.html

__Pictures & Diagrams:__ http://science.halleyhosting.com/sci/ibbio/chem/notes/chpt14/chpt14.htm http://chemwiki.ucdavis.edu/?title=Under_Construction/Schaller/Part_I:__Structure_in_Organic,_Biological_%26_Inorganic_Chemistry/IB._Introduction_to_Biomolecules/IB3._Nucleic_Acids http://www.ncbi.nlm.nih.gov/Class/MLACourse/Original8Hour/Genetics/nucleotide.html http://staff.jccc.net/pdecell/biochemistry/nucleotides.html http://openstudy.com/updates/51efa293e4b00daf471a9a04 http://commons.wikimedia.org/wiki/File:Difference_DNA_RNA-EN.svg