mRNA in Prokaryotic and Eukaryotic cell

RIBONUCLEIC ACID - mRNA (Prokaryotic and Eukaryotic)

• mRNA accounts for 5% of the total RNA. A ribose nucleotide in the chain of RNA consists of a ribose sugar, phosphate group, and a base. 
• In each ribose sugar, one of the four bases is added: Adenine (A), Guanine (G), Cytosine (C), and Uracil (U).
• The base is attached to a ribose sugar with the help of a phosphodiester bond. As RNA comprises many ribose nucleotides, the length of the chains of nucleotides can vary according to their types or their functions.
• RNA thus differs from DNA, on the type of sugar used to make the molecule and replacement of base Thymine in DNA with Uracil in RNA. Additionally, DNA is a double-stranded molecule whereas RNA is a single-stranded molecule.
• ·   It carries genetic information in the form of triplet codon.
• START CODON - AUG  
• STOP CODON   - UAA, UGA, UAG.

 

 

 

PROKARYOTIC mRNA

 

·   mRNA is a single-stranded RNA molecule running from 5’ to 3’ direction.

·   It has sort lifespan and less stable.

·   In a prokaryotic cell, there is a lack of a distinct nucleus, thus the mRNA synthesized contained a copy of DNA sequences with a terminal 5’- triphosphate group and 3’ hydroxyl group. Prokaryotic mRNA at its 5’ end has a Shine Dalgarno sequence which is rich in purine nucleotide and is essential for facilitating the binding of mRNA to ribosome.

·   Prokaryotic mRNA starts at 5’ with a triphosphate group, followed by Shine Dalgarno sequences (untranslated region) and as we move along to the 3’ direction, the coding regions begin. The coding regions begin with a start codon and end when it reaches a stop codon, after encountering a stop codon, protein-coding regions come to an end, after which there is another untranslated region that terminates at the end of 3’.

·   This prokaryotic mRNA is polycistronic in nature.

·   It has Operon (Cluster of genes).

·   Translation and transcription take place in cytoplasm.

·   mRNA processing is not seen in prokaryotes.

 

EUKARYOTIC mRNA

• However, in a eukaryotic cell, the nucleus is distinct and has numerous enzymes in it that make the synthesized mRNA molecule go through modification at their terminals 5’ and 3’ to maintain the integrity and stability of the mRNA molecule (post-transcriptional modification).
• The 5’ triphosphate group of eukaryotic mRNAs is esterified forming a cap structure. This process is referred to as 5’ capping, which happens when a 7-methylguanosine cap is added to a 5’ free triphosphate group via 5’-5’ phosphate linkage with the help of an enzyme called guanyl transferase.
• The 5’ capping is important for the recognition of mRNA by the Ribosomes during protein synthesis. 
• And likewise, the 3’ hydroxyl group is cleaved to give a free hydroxyl group to which numerous adenine monophosphates are added to make the mRNA molecule more stable and prevent it from degradation. This tail of numerous adenine nucleotides is referred to as Poly-A-tail.
• The Poly-A-tail added to the 3’ end of eukaryotic mRNA are usually 100-200 bases long; the addition is catalyzed by an enzyme poly(A) polymerase that recognizes the sequence AAUAAA as a single for addition.
• The poly-A-tail is vital during transporting mRNA from the nucleus to the cytoplasm for proteins synthesis.
• Eukaryotic mRNA starts at 5’ with a cap followed by untranslated regions (5’ UTR), and as we move along 3’ direction, the coding regions begin with the start codon and continue till it reaches the stop codon, which marks the termination of coding regions, after which there is another untranslated region (3’ UTR) that terminate when Poly-A-tail begins, which further terminates at the end of 3’.

• UTR – Untranslated region sis mRNA domain, it contains regulatory elements which have two types, Cis regulatory elements, Trans – regulatory elements. The CRE elements present I the nearby location of the genes that are going to regulate the genes by acting as a Promotor (initiating transcript), Enhancer (Enhance the transcriptase), Silencer (Inhibit the Transcript).   &   The Trans Elements located at different location of the genome to the gene that they regulate. They are regulating by the repressor molecule.

• The 3′-untranslated region plays a crucial role in gene expression by influencing the localization, stability, export, and translation efficiency of an mRNA. It contains various sequences that are involved in gene expression, including microRNA response elements (MREs), AU-rich elements (AREs), and the poly(A) tail. In addition, the structural characteristics of the 3′-UTR as well as its use of alternative polyadenylation play a role in gene expression.

ABOUT DNA AND ITS STRUCTURE

                                              STRUCTURE OF THE DNA 

DEFINITION 

     DNA, or deoxyribonucleic acid, is the hereditary material in humans and almost all other organisms. Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus (where it is called nuclear DNA), but a small amount of DNA can also be found in the mitochondria and Chloroplast. The information in DNA is stored as a code made up of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). Human DNA consists of about 3 billion bases, and more than 99 percent of those bases are the same in all people.  The genome of the organism consists of Introns(Non coding genes)  and Exons (coding region). And only 2% of the total genome codes for protein, and others are intron (which is non - coding genes). 

HISTORY

     In the 1950s, Francis Crick and James Watson worked together at the University of Cambridge, England, to determine the structure of DNA.   In Wilkins’ lab, researcher Rosalind Franklin was using X-ray crystallography to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule using Franklin’s data.  Watson and Crick also had key pieces of information available from other researchers such as Chargaff’s rules. Chargaff had shown that of the four kinds of monomers (nucleotides) present in a DNA molecule, two types were always present in equal amounts and the remaining two types were also always present in equal amounts. This meant they were always paired in some way.

STRUCTURE OF THE DNA

  

a)   The building blocks of DNA are nucleotides, which are made up of three parts: a deoxyribose (5-carbon sugar), a phosphate group, and a nitrogenous base. 

* Deoxyribose Sugar Structure 

* N2 Bases Structure 

* Bonds: Hydrogen Bond, Phosphodiester bond

b) KEY POINTS: 

⦁ DNA is made of two helical chains that intertwine with each other to form a double helix. The most widely accepted structure of DNA is right-handed helix DNA also known as the B-form of DNA, which is 1.9 nm in diameter.

⦁ These helical chains run anti-parallel to each other, one polynucleotide chain runs from 5’ to 3’ and the other polynucleotide chain runs from 3’ to 5’. These chains are connected to each other via nitrogen bases through hydrogen bonding.

⦁ Hydrogen bonding contributes to the specificity of base pairing. Adenine preferentially pairs with Thymine through 2 hydrogen bonds. Similarly, Cytosine preferentially pairs with Guanine through 3 hydrogen bonds. 

⦁ We can even say, that the base pairing happens when Pyrimidines pair with Purines because Pyrimidines refers to the single ring structure of Thymine and Cytosine and Purines refers to double-ring structures, Adenine and Thymine.

⦁ The base pairs A = T and G ≡ C are known as complementary base pairs. Hence, the amount of Adenine is equal to the amount of Thymine, and the amount of Guanine is equal to the amount of Cytosine.

⦁ The geometry of the DNA is influenced by the distance between the backbones and the angle at which the nitrogenous bases are attached to the backbone.

⦁ The major groove occurs when the backbones are far apart from each other and the minor groove occurs when they are close.

⦁ The regularity of the helical structure forms two repeating and alternating spaces: Major and Minor grooves.

⦁ These groves act on base-pair recognition and binding sites for protein, the major groove contains base pair specific information while the minor groove is largely base-pair nonspecific, caused by protein interactions in the grooves

⦁ The double-helical structure of DNA is highly regular, each turn of the helix measures approximately 10 base pairs. In addition to hydrogen bonding in between the bases, the staging of bases also stabilizes the structure, there are pi-pi interactions between staged aromatic rings of the bases.

⦁ The distance between each turn is 3.4 nm.

⦁ The major groove is 2.2 nm wide and the minor groove is 1.1 nm wide.

⦁ Chargaff's Rule: Chargaff's rules state that DNA from any cell of all organisms should have a 1:1 ratio (base Pair Rule) of pyrimidine and purine bases and, more specifically, that the amount of guanine is equal to cytosine and the amount of adenine is equal to thymine.