RNA to Protein ??!!

Hi everyone, before this, we had discussed regarding of transcription of DNA and how DNA can be transformed into RNA. Now, we shall talk about translation of RNA into protein and yes, this is the continuation from transcription of DNA. 

As we can see on the picture above, translation occurs after transcription of DNA into RNA is done. After that, RNA will further modify into mRNA, rRNA, and tRNA. Then, mRNA will be transported into the cytoplasm. At cytoplasm, mRNA will be translated into amino acid sequences based on the genetic code that was carried by mRNA. Within a gene, information for the amino acid sequence of a protein is encoded in a triplet code or also called as codon. This triplet code must not be overlapping and continuous throughout the strand. The genetic code in form of codon is shown below.

       Based on the codon shown above, each of them will be translated into amino acid before bonded to form protein. Before that, we need to know the requirement and the steps needed in order for mRNA to be translated into protein. The requirements are mRNA as codons, tRNA as anti-codons, ribosomes and various protein factors. There were several steps that must be followed such as amino acid activation, chain initiation, chain elongation and chain termination. 
       The first step is amino acid activation. In this step, amino acid must be activated by tRNA and aminoacyl-tRNA synthetases to form aminoacyl-tRNA before being incorporated into growing protein chain. 
       Then, chain initiation will take place. It requires tRNA, initiation codon, 30S and 50S ribosomal units, initiation factors, GTP and Mg2+. In initiation steps, all ribosomes, tRNA and the first amino acid will assemble at mRNA specifically at the start codon which is AUG. tRNA will carry the anticodon which is AUC which complements to its codon. Before tRNA attach to mRNA, first amino acid, methionine will bind with tRNA and move with tRNA toward the ribosomes. After that, chain elongation takes place. In this stage, the chain of amino acids will be elongated via formation of peptide bonds. After the first aminoacyl- tRNA is attached to P site, the second aminoacyl-tRNA will bound at A site of the ribosome. Then, peptide bond will be formed between these two amino acids on the both side. The old aminoacyl-tRNA will exit from the ribosome through E site and the new one will shift into the P site allowing another aminoacyl-tRNA to bound on A site. The formation of peptide bond is a continuous process thus it will be forming a chain of amino acids or known as polypeptide. 
           Lastly, chain termination will take place. After a long continuous process of formation of peptide bonds, eventually, the ribosomes reaching a point called as a stop codon. Stop codons does not have any tRNA thus there will be no aminoacyl-tRNA will be attached to its codon causing a disruption in the process. Formation of peptide bonds will stop and the old aminoacyl-tRNA will exit from the ribosome through E site. After that, all the ribosomal units will dissociate with the aid of release factors thus setting the polypeptide free to go. The newly synthesized polypeptide undergo posttranslational modification thus they will be modified before they reach their final form. The video below shows the whole process of translation.

Process Of Transcription

Transcription has three phase of process that we know for the general knowledge as a biochemistry student. The three phase of transcription are:

• Chain Initiation (First Phase)
• Chain Elongation (Second Phase)
• Chain Termination (Third Phase)

Chain Initiation

Chain initiation is the first phase of transcription. This phase will begin when RNA polymerase binds to the promoter and forms closed complex. What is a promoter? A promoter is a DNA sequence that provides direction for DNA polymerase. Promoters can be about 100–1000 base pairs long. After that, DNA unwinds at promoter to form an open complex, which is required for the chain initiation.

After the first bond is synthesis, the RNA polymerase must escape the promoter. The process of the promoter escape is called as DNA scrunching, providing the energy needed to break interactions between RNA polymerase holoenzyme and the promoter.

Chain Elongation

The second phase of transcription is chain elongation. After the strands have been separated, transcription bubbles move down the DNA sequence to be transcribed. RNA polymerase catalyzes the formation of phosphodiester bond between the incrorp. ribonucleotides. Topoisomerases relax supercoils in front and behind the transcription bubble.

Chain Termination

Chain Termination is the last phase of the transcription. There are two types of termination mechanisms which are:

Intrinsic Termination: controlled by specific sequences
Termination involves "rho" protein: Rho-dependent sequences cause hairpin loop to form.
When the hairpin forms, the mechanical stress breaks the weak rU-dA bonds, now filling the DNA–RNA hybrid. This pulls the poly-U transcript out of the active site of the RNA polymerase, terminating transcription. In the "Rho-dependent" type of termination, a protein factor called "Rho" destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex

Transcription Of Nucleic Acid

Assalammulaikum and a very good day to everyone. I hope all the readers in a pink for today. Today, I would like to share about the next stage of nucleic acid which is transcription. Before this, we will discuss about the DNA, RNA and DNA replication. 

So, what is transcription of nucleic acid? Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (especially mRNA) by the enzyme RNA polymerase. The mechanisms by which information is transferred in the cell is based on the "Central Dogma"

There are two keywords that we must know in this process. First is CODING STRAND and TEMPLATE STRAND.

• Coding Strand : The DNA strand of a DNA molecule which has the same base sequences as the RNA transcript. For the RNA strand, T is replaced to U. 
• Template Strand : The DNA strand of a DNA molecule that is used as a template for RNA synthesis.

For the example, the coding strand of a DNA contains bases 5'-TAGGCA-3'. So that, the template strand of the DNA is 3'-ATCCGT-5'. How about the mRNA strand? Hmm. The mRNA strand is 5'-UAGGCA-3'.

Okay guys. It all for today. I hope my information will help you all to discover about the nucleic acid. Thank You.

Replication of DNA

        Assalamualaikum and hi everyone. Today, we will discuss how DNA can replicate themselves to form a new strand. Basically, DNA replication is a process of copying DNA molecules. During replication, the original strands serve as templates for synthesis the new DNA. Although this process will create new DNA strands, it is considered as semiconservative because one of the original strands is present in each new DNA helix. Each daughter DNA molecule consists of one new chain of nucleotides and one from the parents DNA molecules. The new daughter DNA molecule will be identical to the parent molecule.

          The picture above shows steps in DNA replication. Basically, there are three main steps in DNA replication such as initiation, elongation, and termination. In the first step, it starts at a point called oriC which certain initiator protein bind and start to unwind the DNA double helix structure. Besides that, the presence of an enzyme called as helicase also helps in the process of unwinding the DNA structure. This process is important as they will prepare the DNA for the next steps.
          Next, for elongation, new DNA strands will be synthesised from 5' - 3' end based on the direction of template strand which is 3' - 5' end by an enzyme called DNA polymerase III.  On each old DNA strands, the DNA replication occurs differ with each other. For leading strand, it was synthesised continuously from 5' - 3' and moving toward the replication fork as the template strand starts from 3' - 5' end. Meanwhile, for lagging strand, it will be synthesised semi-discontinuously as small fragments from 5' - 3' end but moving away from the replication fork. These small fragments are called as Okazaki fragments. First, RNA primer will be synthesised by primase then extended into Okazaki fragments before being linked together by DNA ligase.
           After all of the bases are matched up (A with T, C with G), termination will take place. An enzyme called exonuclease will strips away the primers. The gaps where the primers had left will be filled by yet more complementary nucleotides. The new strand is proofread to make sure that there are no mistakes in the new DNA sequence.The result of DNA replication is two DNA molecules consisting of one new strand and one parent strand. This is the reason why DNA replication described as semi-conservative as half of the chain is part of the original DNA molecule, half is brand new strand. 

DNA versus RNA ! Which one is better ?

Assalamualaikum and hi everyone. We meet again today to discuss further regarding of DNA and RNA. In the previous post, I had mentioned about what is DNA and RNA and their characteristics. So for today, we will talk about the differences and similarities between DNA and RNA. First, let's talk about their similarities. First of all, lets see the similarities between  DNA and RNA on the picture below.

Although DNA and RNA are comprised of nucleotides and produced in the nucleus, there also many differences between them that make them significantly important on their own.

Here is a video for us to see the main differences between RNA and DNA and gain a thousand more info about both of those Nucleic Acids. Hope you enjoy it..

That's all for today, stay tuned for more information about DNA and RNA

Two types of Nucleic Acids

 Assalamualaikum and hi everyone. We meet again for another round of our discussion about nucleic acids. Before this, we had discussed about what is nucleic acids and their history. Today, we will further discuss about two types of nucleic acids which are ribonucleic acids (RNA) and deoxyribonucleic acids (DNA). So, lets us begin!

What is Ribonucleic Acids?

     Ribonucleic acid or mostly called as RNA is a molecule that is single-stranded nucleic acids composed of nucleotides. RNA plays a major role in protein synthesis as it is involved in the transcription, decoding, and translation of the genetic code to produce proteins. RNA nucleotides contain three major components.  

• A nitrogenous base 
• A five-carbon sugar
• A phosphate group

     RNA nitrogenous bases include adenine(A), guanine(G), cytosine(C) and uracil(U). The five-carbon (pentose) sugar in RNA is ribose. RNA molecules are polymers of nucleotides joined to one another by the covalent bond between the phosphate of one nucleotide and the sugar of another. These linkages are called phosphodiester linkages.
Although single-stranded, RNA is not always linear. It has the ability to fold into complex 3-D shape and form hairpin loops. When this occurs, the nitrogenous bases bond to one another. Adenine pairs with uracil(A-U) and guanine pairs with cytosine (G-C). Hairpin loops are commonly observed in RNA molecules such as messenger RNA (mRNA) and transfer RNA (tRNA).

      There are many types of RNA present in the cells. As we all know, RNA was produced in the nucleus of our cells and can also be found in the cytoplasm. The three primary types of RNA include messenger RNA, transfer RNA and ribosomal RNA.

1. Messenger RNA (mRNA) plays and important role in the transcription of DNA.
2. Transfer RNA (tRNA) plays and important role in the translation portion of protein synthesis.
3. Ribosomal RNA (rRNA) is a component of cell organelles called ribosomes.

What is Deoxyribonucleic Acids?

        Deoxyribonucleic acids or also known as DNA is one of the nucleic acids present in our body cells. DNA mainly important to give instructions for organism needs to develop, live and reproduce. These instructions are found inside every cell and are passed down from parents to their offspring through fertilization. Without DNA, variation does not occur hence there is no variety of the species.

      DNA sequences form genes, which is the language of the cell that gives instructions how to make proteins. The structure of DNA is double helix formed by the nucleotides that attached together to form two long strands. The structure of DNA is mostly being compared with ladder which the phosphate and sugar molecules would be the sides while the bases would be the rungs.The structure of DNA actually has its own base pairing and it is complimentary. A major factor stabilizing the double helix is base pairing by hydrogen bonding between T-A and G-C.

     DNA molecules are so long to a point where they cannot fit into cells without the right packaging. In order to fit inside the cells, DNA is coiled tightly to form structures that we called as chromosomes. This process is shown on the picture above. Each chromosome contains a single DNA molecule. and each living organisms have specific value pairs of chromosomes that will determine the physical traits of the living organism. For example, each human being must have 23 pairs of chromosomes meanwhile a cat must 19 pairs of chromosomes.

LEVELS OF STRUCTURE OF DNA

• 1^o STRUCTURE - the polynucleotide sequence
• 2^o STRUCTURE - the three-dimensional  conformation of the polynucleotide                                               backbone
• 3^o STRUCTURE - supercoiling
• 4^o STRUCTURE - interaction between DNA and proteins

DNA (1^o STRUCTURE)

• the sequence of bases along the pentose-phosphodiester backbone of DNA molecule
• the sequence that produced is read from the 5' end to the 3' end
• it involves certain letter which represents bases which are A, T, G, and C.

DNA (2^o STRUCTURE)

• the order arrangement of nucleic acid strand which is the double helix model the double helix model DNA 2^o Structure
• DOUBLE HELIX MODEL: two anti-parallel polynucleotide strands coiled in a right-handed manner about the same axis

DNA (3^o STRUCTURE)

• the 3-D arrangement of all atoms of a nucleic acid (super-coiling) which is the further coiling and twisting of DNA helix
• CIRCULAR DNA: a type of double-stranded DNA in which the 5' ends and 3'ends of each strand are joined by phosphodiester bond

DNA (4^o STRUCTURE)

• the structure of chromatin
• each 'bead' is actually a nucleosome and it consists of DNA wrapped around the histone core
• HISTONE: a protein. found associated with eukaryotic DNA
• CHROMATIN: DNA molecules wound around particles of histones in a bead-like structure

     DNA is a very unique protein in terms of its own structure as it has its own level to produce the complete red blood cells that we know today. Can you imagine how a very tiny cell has its own level of structure to produce a complete one? It must be a really complicated process for a red blood cell to be completed.

Introduction of Nucleic Acid

Assalamualaikum and hi everyone. As you can see from the title, our blog will mainly discuss nucleic acid as a part of our assignment. So, before that, we must know the history of nucleic acid. How they were found? Who was responsible for finding nucleic acid? First of all, what is nucleic acid? Nucleic acid is a part of biomolecules that comprises in our body. Nucleic acid are essential in all living organism either plants or animals.

Sir Johannes Friedrich Miescher

Nucleic acid were first found as nuclein by Sir Johannes Friedrich Miescher. He has isolated various phosphate-rich chemicals from the nuclei of white blood cells in 1869. His finding helps to determine hereditary was carried by the structure of DNA. Then, in 1889, Sir Richard Altmann had introduced the "nucleic acid" term to replaced nuclein as he found that it has acidic properties. After that, Rosalind Franklin had use X-ray crystallography to study the structure of DNA during 1950 until 1953 throughout her time at King's College. Based on her experiment, she suggested that the structure of DNA is a helical shape.

 

    Rosalind Franklin and her famous image, Photo 51 captured during her experiment that leads into a conclusion regarding DNA structure.

Finally, James Watson and Francis Crick had developed a complete model of DNA structure in 1953 with the help from Rosalind Franklin and Maurice Walkins experiment regarding of X-ray crystallography of DNA structure. Their DNA model had been used widely since then.

Watson and Crick double helix DNA model structure

This amazing scientific breakthrough in genetics and life science helps scientists to better understand how inheritance among organism occur. Stay tuned for more information about nucleic acids as there are many more facts that we can learn about nucleic acid. See all of you in another time. Bye