Nucleic acid, DNA replication and Protein Synthesis

As the two DNA strands separate (unzip) and the bases are , the enzyme DNA polymerase moves into position at the point where synthesis will begin.

The start point for DNA polymerase is a short segment of RNA known as an RNA primer. The term "primer" is indicative of its role, which is to "prime" or start DNA synthesis at certain points. The primer is "laid down" complementary to the DNA template by an enzyme known as RNA polymerase or Primase.

The DNA polymerase then adds nucleotides one by one in an exactly complementary manner, A to T and G to C.

DNA polymerase is described as being "template dependent" in that it will "read" the sequence of bases on the template strand and then "synthesize" the complementary strand. The template strand is always read in the 3' to 5' direction. The new DNA strand must be synthesized in the 5' to 3' direction. DNA polymerase catalyzes the formation of the hydrogen bonds between each arriving nucleotide and the nucleotides on the template strand.

In addition to catalyzing the formation of Hydrogen bonds between complementary bases on the template and newly synthesized strands, DNA polymerase also catalyzes the reaction between the 5' phosphate on an incoming nucleotide and the free 3' OH on the growing polynucleotide. As a result, the new DNA strands can grow only in the 5' to 3' direction, and strand growth must begin at the 3' end of the template.

Because the original DNA strands are complementary and run antiparallel, only one new strand can begin at the 3' end of the template DNA and grow continuously as the point of replication (the replication fork) moves along the template DNA. The other strand must grow in the opposite direction because it is complementary, not identical to the template strand. The result of this side's discontiguous replication is the production of a series of short sections of new DNA called Okazaki fragments. To make sure that this new strand of short segments is made into a continuous strand, the sections are joined by the action of an enzyme called DNA ligase, which ligates the pieces together by forming the missing .

The last step is for an enzyme to come along and remove the existing RNA primers and then fill in the gaps with DNA. This is the job of yet another type of DNA polymerase, which has the ability to chew up the primers and replace them with the deoxynucleotides that make up DNA.

This form of replication has been refered to as semi-consravtive replication, because each newly formed double helix contains one of the polynucelotide chains of the original double helix.

 

Each sugar molecule in the strand also binds to one of four different nucleotide bases.  These bases: Adenine (A), Guanine (G), Cytosine (C) and Thymine (T).  Each sugar molecule in the DNA strand will bind to one nucleotide base.  Thus, as our description of DNA unfolds, we see that a single strand of the molecule looks more like this:

Each strand of DNA contains millions or even billions (in the case of human DNA) of nucleotide bases.  These bases are arranged in a specific order according to our genetic ancestry.  The order of these base units makes up the code for specific characteristics in the body, such as eye colour or nose-hair length.  Just as we use 26 letters in various sequences to code for the words you are now reading, our body's DNA uses 4 letters (which is known as the 4 nucleotide bases) to code for millions of different characteristics.
        Each molecule of DNA is actually made up of 2 strands of DNA cross-linked together.  Each nucleotide base in the DNA strand will cross-link (via hydrogen bonds) with a nucleotide base in a second strand of DNA forming a structure that resembles a ladder.  These bases cross-link in a very specific order: A will only link with T (and vice-versa), and C will only link with G (and vice-versa).  Thus a picture of DNA now looks like this:

 

 

      

  The specific base-pairing of DNA aids in reproduction of the double helix when more genetic material is needed (such as during reproduction, to pass on characteristics from parent to offspring).  When DNA reproduces, the 2 strands unzip from each other and enzymes add new bases to each, thus forming two new strands. 
        Within this coil of DNA lies all the information needed to produce everything in the human body.  A strand of DNA may be millions, or billions, of base-pairs long.  Different segments of the DNA molecule code for different characteristics in the body.  A Gene is a relatively small segment of DNA that codes for the synthesis of a specific protein.  This protein then will play a structural or functional role in the body.  A chromosome is a larger collection of DNA that contains many genes and the support proteins needed to control these genes.

PROTEIN SYNTHESIS

Protein synthesis involves the transfer of the coded information from the nucleus to the cytoplasm (transcription) and the conversion of that information into polypeptides on the ribosome’s (translation).

Transcription

Transcription occurs in the nucleus. The enzyme RNA-polymerase becomes attached to the double helix of the DNA in the region of the gene that is being expressed. This usually occurs at a codon for the amino acid methionine, which acts as a start signal. The hydrogen bonds on this region of the double helix are broken and the DNA unwinds. One of the strands of the DNA, the coding strand acts as a template and is copied by base pairing of nucleotides. A complementary polynucleotide strand of mRNA is built up from a pool of nucleotides in the nucleus. The formation of the strand is catalysed by RNA-polymerase. As it forms, the strand of mRNA detaches from the coding strand of DNA and, when complete, it leaves the nucleus through a pore in the nuclear envelope. Once in the cytoplasm, it becomes attached to a ribosome.  

• Translation: After the mRNA is manufactured, it leaves the cell nucleus and travels to a cellular organelle called the ribosome. In the ribosome, the mRNA code is translated into a transfer RNA (tRNA) code which, in turn, is transfered into a protein sequence.  In this process, each set of 3 mRNA bases will pair with a complimentary tRNA base triplet (called an anticodon).  Each tRNA is specific to an amino acid, as tRNA's are added to the sequence, amino acids are linked together by , eventually forming a protein that is later released by the tRNA.  Using the mRNA strand we obtained above, you can generate the complimentary tRNA/amino acid .

After the processes of transcription and translation are complete, we are left with a protein that consists of the chain:

Although our 'protein' is only 2 amino acids in length, proteins normally consist of hundreds or thousands of amino acids.

Two big differences between DNA and RNA:

1. The sugar in DNA is deoxyribose; in RNA it is

2. The nitrogenous base  is used in RNA in place of T (they are very similar bases; in RNA U= A just like T = A.)

The RNA molecule that is sent into the cytoplasm is basically just a copy of one particular gene; RNA carries instructions to make whatever proteins the cell needs at that particular time. It is also a single stranded molecule, not a double helix.

Chemical differences between DNA & RNA

Both RNA and DNA are composed of repeated units. The repeating units of RNA are ribonucleotide monophosphates and of DNA are 2'-deoxyribonucleotide monophosphates.

Both RNA and DNA form long, unbranched polynucleotide chains in which different purine or pyrimidine bases are joined by N-glycosidic bonds to a repeating sugar-phosphate backbone.

The chains have a polarity. The sequence of a nucleic acid is customarily read from 5' to 3'. For example the sequence of the RNA molecule is AUGC and of the DNA molecule is ATGC

The base sequence carries the information, i.e. the sequence ATGC has different information that AGCT even though the same bases are involved

DNA and RNA structure in brief

• DNA and RNA belong to a class of macromolecules called nucleic acids.
• Nucleic acids are polynucleotides which means they contain many nucleotides joined together.
• A nucleotide consists of:

• One cyclic five-carbon sugar (The carbons found in this sugar are numbered 1' through to 5')
• One phosphate
• One nitrogenous base

• The sugar is deoxyribose in DNA and ribose in RNA. The only difference between the sugars is that ribose has a hydroxyl group (OH) on the 2' carbon and deoxyribose does not. This makes deoxyribose more stable than ribose.
• The phosphate is linked to the 5' carbon of the sugar in both RNA and DNA.
• The nitrogenous bases are adenine(A), guanine(G), cytosine(C), thymine(T), and uracil(U).

• Adenine and guanine are purines (contains a six membered ring of carbon and nitrogen fused to a five membered ring).
• Adenine and guanine are both found in DNA and RNA.
• Cytosine, thymine and uracil are pyrmidines (contains a six membered ring of carbon and nitrogen).
• Cytosine is found in both DNA and RNA, but thymine is only found in DNA and uracil is only found in RNA.

• A nucleotide is formed when a phosphate attahes to the 5' carbon of the sugar and one of the nitrogenous baseses attaches to the 1' carbon of the sugar.
• A strand of DNA or RNA consists of nucleotides linked together by phosphodiester bonds.

• A phosphodiester bond exists between the phosphate of one nucleotide and the sugar 3' carbon of the the next nucleotide.
• This forms a backbone of alternating sugar and phosphate molecules known as the "sugar-phosphate backbone".

• RNA, in most cases, consists of one strand of nucleic acids linked together by phosphodiester bonds.
• A DNA molecule consists of two strands of nucleotides twisted together to form a double helix.

• The sugar-phosphate backbone is found on the outside of this helix and the bases are found braching towards the middle.

References:

• Letts, Revise Biology.
• Molecules and Cells, John Adds, Erica Larcom, Ruth Miller
• Advanced Biology, W R Pickering
• Cambridge Coordinated Science, Jones and Jones
• Various internet  sites, including yahoo search