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Nucleic Acids

Nucleic acids are long polymers (repeating units) of nucleotides.  They have a five carbon sugar, one base (either A, C, G, or T), and a phosphate group.  There are two types, DNA or RNA.  

RNA

DNA

-phosphate -phosphate
-negative charge -negative charge
-ribose sugar -deoxyribose sugar
-G, C, A, U -G, C, A, T

There are two types of nitrogenous bases: purines and pyrimidines.  Purines have two rings and are either A or G.  Pyrimidines have one ring and are either T, C, or U.  

DNA forms a double helix of two complementary strands.  The base pairs join and forms hydrogen bonds.  The angles of the various bonds cause the helix to twist.  

Proteins

Proteins are made of amino acids.  They have one amino group, one carboxyl group, one central carbon, one hydrogen, and one functional group.  It is the functional group that distinguishes one amino acid from another.  A protein won't function properly if it doesn't have a 3D shape.  The 3D structure is ultimately dependent on the functional groups.  

Proteins are long strands of amino acids joined by peptide bonds.  The 3D structure of the proteins can be one of four ways.  The first way is the primary structure.  This is just the sequence of amino acids.  The second way is called the secondary structure.  It can form an alpha helix or beta pleated sheet.  This way is dependent on hydrogen bonds between the different amino acids.  The third way is the tertiary structure.  This is dependent on interaction of various functional groups.  The fourth way is called the quaternary structure.  This type is only in some proteins.  This occurs when two or more amino acid chains associate with one another.

Protein Synthesis

Protein synthesis is a process whereby DNA encodes for the production of amino acids and proteins.  Note that mRNA is messenger RNA, tRNA is transfer RNA, and rRNA is ribosomal RNA.  Protein synthesis can be divided into two parts: 

Transcription

In this stage, DNA goes to mRNA.  Transcription occurs in the nucleus.  The DNA is unraveled with the help of enzymes, and the two chains are broken apart.  The double helix is now separated.  RNA polymerase binds on to one strand of DNA.  Transcription begins at the start codon, which is TAC.  RNA polymerase reads DNA from 3' (prime) to 5', and builds RNA from 5' to 3'.  mRNA is build by adding one nucleotide onto the strand at a time, so that mRNA is complementary to the DNA template.  When RNA arrives at the stop codon of the gene, RNA disengages from the DNA.  The hydrogen bonds that were formed to ensure accurate transcription are now broken, and the mRNA is freed from the DNA template.  The two strands of DNA rejoin and coil.  mRNA leaves the nucleus and enters the cytoplasm.

Translation

Translation involves three stages: initiation, elongation, and termination.

Initiation

The methionine attaches to the free end of a tRNA, using the enzyme methioninyl - tRNA synthetase.  The tRNA binds to a small ribosomal subunit.  The ribosomal subunit and the tRNA help the ribosome find the initiation site on the mRNA.  Once the initiation site is found, the large ribosomal subunit attaches to the mRNA.  The complex is on the P side of the ribosome.

Elongation

At this point, the tRNA is on the P side of the ribosome.  There are two subunits to the ribosome.  The larger subunit has two sites that are used in protein synthesis: the P site and the A site.  With the help of elongation, the appropriate tRNA molecule and the associated amino acid enters the A site.  To make sure the proper tRNA molecule has entered the A site, the bases of the mRNA codon and tRNA anticodon bind.  Now, a peptide bond is formed between the amino group of the amino acid in the A site and the carboxyl group of the amino acid in the P site.  Enzymes help the tRNA and the amino acid complex in the A site move to the P site.  The tRNA that was in the P site is freed with the help of enzymes, and can now circulate throughout the cytoplasm looking for a new amino acid.  There is now a tRNA and polypeptide in the P site, so the next tRNA and amino acid complex can enter the A site.  There is a peptide bond formed between the amino acid in the P site and the amino acid in the A site.  The ribosome moves down the mRNA, three base pairs at a time.  The tRNA that was in the P site is released.  This process is continued until a stop codon is reached.

Termination

As soon as one of the three possible stop codons is reached, the stop codon attracts releasing factors instead of a tRNA molecule.  An OH molecule is added to the final amino acid of the new protein to form a carboxyl group.  The protein is released.  The ribosome separates back into its two subunits, and is free to start the process again.  

DNA Replication

DNA replication occurs during the interphase of mitosis or meiosis.  An enzyme unzips DNA at one end, and forms a replication fork.  Two separate DNA polymerase enzymes attach to the DNA, one on each strand.  DNA is replicated from 3' to 5' and is build from 5' to 3'.  DNA polymerase works only by reading DNA 3' to 5'.  Because of this, the two strands are replicated differently. 

3' to 5' Strand of DNA

5' to 3' Strand of DNA

-DNA replication occurs one nucleotide at a time, with a continuing motion.  Because of this, it is called continuous synthesis.

-The new strand of DNA is called the leading strand.

-DNA polymerase can't read this in order, therefore it jumps ahead about 1000-2000 nucleotides and replicates DNA in a direction away from the fork.

-Once complete, DNA ligase attaches adjacent DNA fragments

-DNA polymerase then jumps ahead and works backwards to fill in the gap.  This is called discontinuous synthesis, and the DNA strand is called the lagging strand.

Genetic Engineering

Genetic engineering means to go and change the DNA of an organism.  For examples, farmers breed a certain vegetable to get the best results.  In order to do genetic engineering, first, the gene that is going to be worked on is isolated.  The gene is cut out of the chromosome.  Next, the gene is inserted into a bacterial plasmid.  The plasmid is a piece of bacterial DNA, which isn't part of the main chromosome.  After, the plasmid is put back into a bacterium.