Protein synthesis and types of RNA

What is the RNA?

Ribonucleic acid (RNA) is an essential molecule for life that is present in all living organisms. This molecule is similar to DNA in its chemical structure, but has some unique characteristics that make it very important for the functioning of cells.

RNA is composed of a chain of nucleotides that contain a nitrogenous base, a sugar, and a phosphate group. The nitrogenous bases are adenine, guanine, cytosine, and uracil, and the sequence of these bases determines the genetic information contained in the RNA.

RNA is synthesized from a DNA strand during the process of transcription and is then used as a template for protein synthesis during the process of translation. Additionally, RNA also has regulatory and structural functions within the cell.

There are various types of RNA involved in protein biosynthesis in cells. Messenger RNA (mRNA) carries genetic information from DNA to ribosomes, where it is translated into protein. Transfer RNA (tRNA) brings amino acids to the ribosome, where they are assembled into a polypeptide chain according to the instructions carried by the mRNA. Ribosomal RNA (rRNA) is a component of the ribosome itself and helps catalyze the formation of peptide bonds between amino acids.

Types of RNA

Messenger RNA (mRNA)

The mRNA i is a long single-stranded molecule that contains the codons (a triplet of nucleotide bases) that will be translated into a sequence of amino acids for a protein. Its synthesis takes place in the nucleus and it enters the cytoplasm through the pores of the nuclear envelope. In the cytoplasm, messenger RNA (mRNA) binds to ribosomes, where its codons are translated into the language of amino acids contained in proteins. (One can imagine mRNA as a “molecular photocopy” of the DNA gene.)

Ribosomal RNA (rRNA)

Ribosomes are composed of ribosomal RNA and a large number of proteins. Each ribosome is composed of two subunits: a larger one and a smaller one. The smaller subunit recognizes and binds to messenger RNA and a portion of transfer RNA. The larger subunit consists of three molecules of messenger RNA and several proteins. It contains an enzymatic region that catalyzes the addition of amino acids to the growing protein chain and two catalytic sites (designated P and A) that bind to transfer RNA.

The function of ribosomal RNA is to recognize messenger RNA and catalyze the formation of peptide bonds between the amino acids of the protein.

Transfer RNA (tRNA)

Transfer RNA molecules bind amino acids and deliver them to the ribosome, where they are incorporated into protein chains. There are many types of transfer RNA, at least one type for each amino acid. Their function is to decipher the codons of messenger RNA and translate them into the amino acids of proteins. Transfer RNA molecules have a clover-like structure with a stem.

The outer part of the central leaf contains three exposed bases, called an anticodon, which decipher the code of messenger RNA and is complementary to the codon of messenger RNA that specifies the amino acid to which the transfer RNA is bound. For example, the GUA codon of messenger RNA is complementary to the CAU anticodon of a transfer RNA molecule that carries the amino acid Valine. All of these processes require energy that is provided by the ATP molecule.

Protein synthesis

Stages of protein synthesis.

Protein synthesis occurs in two stages. First, during transcription, messenger RNA is transcribed from the DNA template of the genes in the nucleus. The mRNA travels to a ribosome in the cytoplasm. Second, during translation, the ribosome attaches to the mRNA and the appropriate transfer RNAs.

protein biosynthesis is a fundamental process in the cell that is carried out by translating the genetic information contained in DNA into the language of amino acids. The process of protein synthesis consists of three main stages: initiation, elongation, and termination. The process is explained step by step below:

1. DNA Transcription: First, DNA is transcribed into messenger RNA (mRNA). This process involves the synthesis of an mRNA molecule that is complementary to one of the two DNA strands. The mRNA contains genetic information that will be used for protein biosynthesis. The genetic code is the set of rules that determine how genetic information is translated into sequences of amino acids. In this code, each group of three nucleotides (known as a codon) codes for a specific amino acid. For example, the codon AUG codes for the amino acid methionine.
2. Initiation: The process of protein synthesis begins with initiation. The ribosome binds to the 5′ end of the mRNA, recognizing the AUG initiation codon. A tRNA loaded with the amino acid methionine binds to the initiation codon.
3. Elongation: The next stage is elongation, in which amino acids are added to the growing chain. The ribosome moves along the mRNA, reading each codon and bringing the corresponding tRNA. The amino acid carried by the tRNA is added to the growing chain through a peptide bond. The ribosome iteratively moves along the mRNA, adding one amino acid after another, until it reaches a stop codon.
4. Termination: When the ribosome reaches a stop codon, protein synthesis ends. At this point, the chain of amino acids is released from the ribosome and folds into a functional protein.

In summary, RNA is a key molecule in cell biology, with essential functions in protein synthesis and gene regulation. Its unique characteristics, such as the presence of uracil instead of thymine and the ability to fold into complex three-dimensional structures, make it a very versatile and adaptable molecule to the needs of the cell.

Synthesis of proteins is a complex process that involves the translation of genetic information from mRNA into the language of amino acids, following the genetic code. Initiation, elongation, and termination are the three main stages of the process. During elongation, the ribosome reads each codon of the mRNA and adds the corresponding amino acid to the growing chain. When the ribosome reaches a stop codon, protein synthesis ends and the chain of amino acids is released to form a functional protein.

The genetic code

Example of protein biosynthesis from a given gene.

Given the following nucleotide sequence in DNA:

TAC CGG AAA CTT AGG GCT ACA CTG CTA TTA

…we will carry out protein biosynthesis.

To obtain the complementary RNA sequence to a DNA sequence, it must be taken into account that the nitrogenous bases adenine (A) pairs with uracil (U) and cytosine (C) pairs with guanine (G).

So, the complementary RNA sequence to the given DNA sequence would be:

AUG GCC UUU GAA UCC CGA UGU GAC GAU UAA

This gene contains 10 codons of three nucleotides each, which are the basic units that the ribosome reads to synthesize the corresponding protein. To simplify the example, let’s assume that this gene codes for a 10 amino acid protein.

The transcription of this gene would result in a complementary mRNA molecule of 30 nucleotides that would bind to the ribosome to begin protein synthesis. Next, a polypeptide chain of 10 amino acids would be assembled from the mRNA codons.

The translation of this gene would follow the following sequence of codons and amino acids:

As can be seen, the sequence of codons in the mRNA dictates the sequence of amino acids in the resulting protein. In this case, the protein contains Methionine, Alanine, Phenylalanine, Glutamic acid, Serine, Arginine, Cysteine, Aspartic acid, Aspartic acid, and a stop codon. Once protein biosynthesis is complete, the polypeptide chain would be released from the ribosome and folded to form a functional three-dimensional protein.

Activities

1. The following sentences describe the processes of INITIATION, ELONGATION, and TERMINATION. Which one corresponds to which?

In the ________________________________, DNA unwinds and is transcribed into a messenger RNA (mRNA) molecule, which contains a copy of the gene’s base sequence. This mRNA is processed and transported from the nucleus to the cytoplasm, where it will bind to the ribosome to begin the synthesis of the protein.

In the ________________________________, the ribosome reaches a termination codon in the mRNA, indicating that the synthesis of the protein is complete. The polypeptide chain is released from the ribosome and folds into a functional three-dimensional protein.

In the ________________________________, the ribosome moves along the mRNA, reading its base sequence and assembling a chain of amino acids in the correct sequence to form the protein. Amino acids are transported by transfer RNA (tRNA) molecules, which bind to the corresponding codons on the mRNA. The binding of amino acids forms peptide bonds, which create the polypeptide chain of the protein.

2. Indicate the protein formed from the following nucleotide sequence of an RNA:

AUG GCU CAG UUC AAG UGG AAU UAC AGC UCC AGU GAA UAA

Extend to see the answer key. [expand]

This gene contains 13 codons of three nucleotides each, and it can be assumed to code for a protein of approximately 13 amino acids. The transcription of this gene would result in a complementary mRNA molecule of 40 nucleotides that would bind to the ribosome to begin the synthesis of the protein. The translation of this gene would follow the sequence of codons and amino acids:

As it can be observed, the sequence of codons in the mRNA dictates the sequence of amino acids in the resulting protein. In this case, the protein contains Methionine, Alanine, Glutamine, Phenylalanine, Lysine, Tryptophan, Asparagine, Tyrosine, Serine, Serine, Serine, Glutamic acid, and a termination codon.

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3. Given the following DNA nucleotide sequence, obtain the RNA sequence and then carry out the synthesis of the protein

TAC CCT GTT ATA ACG ACT

Extend to see the answer key. [expand]

To obtain the complementary DNA sequence to an RNA sequence, it should be considered that the nitrogenous bases adenine (A) in RNA pairs with thymine (T) in DNA, while guanine (G) in RNA pairs with cytosine (C) in DNA. In addition, uracil (U) in RNA is replaced by thymine (T) in DNA.

Therefore, the complementary DNA sequence to the given RNA sequence would be:

TAC CCT GTT ATG ACG ACT

This gene contains 6 codons of three nucleotides each and it can be assumed to code for a protein of around 6 amino acids. The transcription of this gene would result in a complementary mRNA molecule of 18 nucleotides that would bind to the ribosome to start the synthesis of the protein. The translation of this gene would follow the sequence of codons and amino acids:

AUG GGA CAA UAC UGC UGA

(Methionine, Glycine, Glutamine, Tyrosine, Cysteine, Stop codon)

Teaching resources

There are several sources of simulation and videos about protein synthesis. Here are some suggestions:

1. The Virtual Cell Animation Collection by North Dakota State University: This website provides a variety of interactive animations and simulations related to cell biology, including protein synthesis. The animations can be accessed for free at https://vcell.ndsu.edu/animations/.

2. HHMI BioInteractive Protein Synthesis Video: This video, produced by the Howard Hughes Medical Institute, provides a detailed explanation of protein synthesis, including transcription and translation. It can be viewed for free at https://www.biointeractive.org/classroom-resources/protein-synthesis.

3. Protein Synthesis Simulation by PhET: This simulation allows users to explore the process of protein synthesis by assembling a protein from amino acids and following the steps of transcription and translation. It can be accessed for free at https://phet.colorado.edu/en/simulation/protein-synthesis.

4. Amoeba Sisters Protein Synthesis Video: This video, produced by the Amoeba Sisters, provides a simplified explanation of protein synthesis, including the role of DNA, RNA, and ribosomes. It can be viewed for free at https://www.youtube.com/watch?v=4SQDyb1nCfo.

5. Molecular Workbench Protein Synthesis Simulation: This simulation allows users to interactively explore the process of protein synthesis, including the role of mRNA, tRNA, and ribosomes. It can be accessed for free at https://mw.concord.org/modeler/index.html#model=/mw/models/biology/protein-synthesis.xml.

These are just a few examples of the many resources available online for learning about protein synthesis.

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