DNA and Protein Synthesis

Structure, Replication, Transcription and Translation    

 

  

1.1 Structure of DNA

            Deoxyribonucleic acid or DNA is the basic genetic component of a living organism that stores information in the form of codes (Alberts et al., 2002). This code is made up of four main chemical bases namely- Adenine (A), Guanine (G), Cytosine (C) and Thymine (T). The DNA bases are usually present in paired forms, A with T and C with G and are called base pairs (Medicine, 2017). Each of these four bases is attached to a phosphate molecule and a sugar molecule.

Figure 1: DNA double helix structure (Original unlabelled diagram taken from t2.gstatic.com)

 

The base, sugar and the phosphate molecules are collectively known as “nucleotide”.  The nucleotides are present as two long strands in the form of a spiral. This structure is known as “double helix” (Medicine, 2017). It resembles a ladder, where the base pairs form the rungs of the ladder and the sugar-phosphate backbone form the vertical pieces. Hydrogen bonds are present at the basal portions of the nucleotides that hold the polynucleotide chains together.

A wide gap is observed in the DNA helix. It is known as the “major groove” (Watson, 2004). It arises from the geometrical configuration of the base pair. Normally the angle at which the two sugar molecules project out from the base pairs is nearly 120o (narrow angle) or 240o (wide angle) (Watson, 2004). The narrower angle between the sugars one side of the base pairs thereby form a minor groove. The large angle on the other edge generates the major groove (Watson, 2004).

It is observed that the bases normally face inwards. This has been explained by Watson and Crick’s theory (1953). Based on the mutual repulsion of the negative charges of the phosphate molecules, Watson & Crick (1953) placed the ribose-phosphate backbone on the outer side. This necessarily implies the inward orientation of the bases. 

1.2 Relationship between structure of DNA and the process of DNA replication

            DNA replication is the mechanism of generation of two identical DNA molecules from a double stranded parent DNA molecule. DNA replication is semi-conservative in nature (KhanAcademy, 2007). This implies that the individual strands in the DNA double helix act as basic templates for the generation of new complementary strands.

            The DNA replication process starts with breaking of the hydrogen bonds between the base pairs. In the next step, the sequence of bases on the segregated strands facilitates the insertion of complementary set of bases (Kyrk, 2015). These new strands are formed from deoxynucleoside triphosphates. Each arriving nucleotide is linked via covalent bond to the 3-carbon atom on the pentose molecule. The second and third phosphates are separated in a combined manner as a molecule of the Pyrophosphate. The sequence of the nucleotides should match the sequence of the bases (templates) on the original strand (Kyrk, 2015).

            The enzymes typically involved in the DNA replication process are- DNA Polymerase, Topoisomerase, Primase, Helicase and Ligase. The DNA Polymerase elongates the DNA chain being synthesized, by integrating complementary nucleotides (KhanAcademy, 2007). The Polymerase actively eliminates the wrongly inserted nucleotides and adds only the complementary nucleotides to the 3’ end of the DNA strand.

            Helicase is an important replication enzyme that attaches itself to the origin of replication, that has a length of 245 base pairs. Helicase is responsible for breaking the hydrogen bonds between the nitrogenous base pairs. In this way it helps the replication fork (Y-shaped structures formed by opening of the DNA) to move forward (KhanAcademy, 2007).

            The Primase enzyme along with the DNA polymerase attaches the first nucleotide to a new replication fork. The Primase synthesizes a RNA primer, which is a short chain of nucleic acid that is complementary to the template. It provides a 3’ end to the DNA polymerase. The DNA polymerase can continuously synthesize the new DNA strand in the 5’ to 3’ direction, towards the replication fork. This is called a “leading strand” (KhanAcademy, 2007). The other DNA strand that progresses 5’ to 3’ away from the replication fork is normally formed in small fragments. This is called the “lagging strand” and the fragments are called the “Okazaki fragments”. As the fork progresses forward, the DNA polymerase detaches itself and again gets attached to the newly opened DNA (KhanAcademy, 2007). An essential protein called the “sliding clamp” prevents the DNA polymerase of the lagging strand from drifting away when it re-attaches itself to a new Okazaki fragment. The sliding clamp is loaded onto the DNA by a particular enzyme called “clamp loaders” (KhanAcademy, 2007).

            The Topoisomerase enzyme prevents the DNA double helix at the front of the replication fork from getting tightly wound. It forms temporary “nicks” in the process. The residual nicks at the end of the process are sealed by the enzyme DNA ligase (Kyrk, 2015).           

2.1 Transcription of DNA to mRNA

            DNA transcription to mRNA marks the beginning step of gene expression. In this process, a portion of the DNA is copied into the RNA with the help of the RNA polymerase enzyme. The primary enzyme involved in DNA transcription is the RNA polymerase. This enzyme elongates a pre-existing RNA strand in the 5’ to 3’ direction (Clancy, 2008).

            DNA transcription occurs in three main stages. These are given below-

  1. Initiation: In this stage, the RNA polymerase binds to a specific sequence of the DNA called “promoter” located at the beginning of the gene (KhanAcademy, 2007). The RNA polymerase then separates the individual DNA strands. The single strands then act as the templates for transcription.
  2. Elongation: In this stage, the RNA polymerase appends the complementary nucleotides and synthesizes an RNA molecule that grows in the 5’ to 3’ direction (KhanAcademy, 2007). The RNA transcript contains information identical to that of the “coding strand” of DNA. But instead of Thymine (T) it contains the base Uracil (U).
  3. Termination: In this stage, certain sequences known as “terminators” send out signals that the RNA transcript is complete. Henceforth, the RNA polymerase releases the transcripts (KhanAcademy, 2007).

In bacteria, the transcript RNA can directly act as a messenger RNA or mRNA. But in Eukaryotes, a pre-mRNA forms first. This pre-mRNA transforms into an actual mRNA by appending a 5’ cap to the beginning and a poly-A tail to the end of the RNA. The 5’ cap (modified guanine nucleotide) is attached to the first nucleotide in the transcript. It facilitates the attachment of the ribosome to the mRNA and “reads” it base-by-base, before starting the protein synthesis (Clancy, 2008). A particular sequence called the polyadenylation signal occurs in an RNA molecule during transcription. On receiving this signal, the enzyme chops the RNA into two and another enzyme inserts around 100-200 adenine (A) nucleotides to the chopped end. This forms a poly-A tail, which increases the stability of the transcript (Clancy, 2008). 

2.2 Translation of mRNA into protein

Translation is the mechanism of conversion of the genetic codes into amino acid chains (Clancy & Brown, 2008). Translation occurs in three main steps-

  1. Initiation: In this stage, the Transfer RNA (tRNA) carrying methionine attaches itself to the ribosomal subunit. This combined unit then binds to the 5’ end of the mRNA and gradually progress towards the 3’ end (Clancy & Brown, 2008).
  2. Elongation: When the tRNA detaches itself from the ribosome, a fresh codon becomes visible at a separate site called “A site”. This “A site” acts as the binding site for the next tRNA (Koch, 1996). The transfer of methionine from the first tRNA to the amino acid of the second tRNA makes the elongation of the polypeptide chain possible.
  3. Termination: The termination stage begins when a stop codon in the mRNA enters the “A site”. The stop codons are identified by proteins called “release factors”. Addition of a water molecule to the last amino acid of the chain isolates the tRNA from the chain (KhanAcademy, 2007). The newly synthesized protein is released thereafter.

The resulting polypeptides containing all the amino acids undergo some transformations and are ready to carry out the necessary functions within the cell (Brown & Brown, 2006).

 

References

Alberts, B. et al., 2002. Molecular Biology of the Cell. 5th ed. New York: Garland Science.

Brown, T. & Brown, D., 2006. Transcription, Translation and Replication. [Online] Available at: http://www.atdbio.com [Accessed 4 January 2017].

Clancy, S., 2008. DNA transcription. Nature Education, 1(1), p.41.

Clancy, S. & Brown, W., 2008. Translation: DNA to mRNA to Protein. Nature Education , 1(1), p.101.

KhanAcademy, 2007. Molecular mechanism of DNA replication. [Online] Available at: https://www.khanacademy.org [Accessed 4 January 2017].

KhanAcademy, 2007. Stages of transcription. [Online] Available at: https://www.khanacademy.org [Accessed 4 January 2017].

KhanAcademy, 2007. Stages of translation. [Online] Available at: https://www.khanacademy.org [Accessed 4 January 2017].

Koch, A., 1996. Translation of mRNA to Protein: Initiation, Elongation & Termination Steps. [Online] Available at: https://www.study.com/ [Accessed 4 January 2017].

Kyrk, J., 2015. DNA Replication. [Online] Available at: http://www.biology-pages.info/ [Accessed 4 January 2017].

Medicine, U.S.N.L.o., 2017. Your guide to understanding genetic conditions. [Online] Available at: https://ghr.nlm.nih.gov [Accessed 4 January 2017].

Watson, J.D., 2004. The Structures of DNA and RNA. In Molecular Biology of the Gene. 5th ed. New York: Cold Spring Harbor Laboratory Press. pp.1-33.

Watson, J.D. & Crick, F.H.C., 1953. The Structure of DNA. In Cold Spring Harbor Symposia on Quantitative Biology. New York , 1953. Cold Spring Harbor Laboratory Press.

 

 

 

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