RNA and Protein Synthesis
- Shivani Kanjerla
- Aug 6, 2021
- 7 min read
By: Shivani Kanjerla
07/27/2021
By: Shivani Kanjerla
Hello and welcome to the second episode of The Secrets of Science! Within today's episode, we will be covering the definition of RNA, comparing DNA to RNA, discussing the creation of RNA, and finally, the process of protein synthesis. To access the transcript version along with images, make sure to check out my recent blog post on my website. Within the blog post, there will be links to videos, textbook information, and other resources for aiding guided learning. Overall, it can be noticed that the “world of biology” is commonly defined by DNA from its definition of genetic information all the way down to its keyboard emoji (RNA does not have one). Previously, RNA was commonly overlooked within the world of genome analysis by the use of DNA. However, it is truly essential to learn about, because RNA plays a crucial role in many cell processes such as cell division, life span, and growth. Additionally, while DNA may provide the instructions on how a protein should be made, it is the responsibility of RNA to actually go ahead and provide this information to the ribosomes.
RNA: Stands for Ribonucleic Acid
Comparing and contrasting DNA AND RNA:
RNA has a variety of similarities to DNA such as the fact that it is also made from nucleotides.
3 essential differences between DNA and RNA:
One major difference to note is that RNA uses the nucleotide uracil in the place of thymine. As a result, the uracil will pair to the adenine but cytosine will still pair with guanine.
The difference between thymine and uracil is the methyl group that is placed in thymine within the C-5 location. As a result, the molecular formula for thymine is C5H6N2O2 and the molecular formula of uracil is C4H4N2O2.
RNA is single stranded and as already mentioned, DNA is double stranded.
RNA nucleotides are composed of the sugar molecule ribose instead of deoxyribose like DNA. (Hence the name ribonucleic acid).
Image source: https://www.thoughtco.com/dna-versus-rna-608191
Creation of RNA: done through a process known as transcription with 3 major steps
Initiation: During this phase, RNA polymerase will bind to the DNA molecule and unwind the double helix leaving two strands of exposed DNA. Similarly to the process of DNA replication, there is one template and one non-template strand present.
Like DNA polymerase, RNA polymerase develops RNA in the 5 prime to 3 prime direction.
RNA polymerase links itself to the section of the DNA which is referred to as the promoter. The promoters are composed of specific base pair sequences. In this case, the promoter signals the start and end site for the transcription process.
Elongation: The RNA polymerase begins attaching nucleotides to the template strand in the 5 prime to 3 prime direction resulting in a complementary RNA strand.
RNA uses uracil to adenine pair instead of thymine to adenine like DNA.
Termination: Once the RNA polymerase reaches the ending promoter sequence it stops adding the nucleotides. The RNA molecule then isolates and separates itself from the DNA molecule. Afterwards, the DNA then rebinds to its original double helix form.
Image source:
Translation/Protein synthesis:
I am sure that you have heard about 3 primary types of RNA, messenger RNA, transfer RNA, and ribosomal RNA. All of these play a role in the process of protein synthesis, also known as translation.
First, let's start with the basics:
A protein is a polymer made up of the monomer amino acids which are linked together through peptide bonds.
A polymer is: a group of small molecules linked together in a chain to create a large molecule.
The 4 main macromolecules are proteins, carbohydrates, lipids, and nucleic acids.
A monomer is: atoms/small molecules that link together through peptide bonds in order to form larger molecules such as the polymers mentioned previously.
The 4 main types of monomers include fatty acids, amino acids, sugars, and nucleotides.
The process in which monomers combine to form polymers is referred to as “polymerization.”
The amino acids comprise the proteins.
Carbohydrates are composed of sugars.
Lipids are made of fatty acids.
Nucleic acids are composed of DNA and RNA as well as their respective nucleotides.
Image source: By OpenStax CC BY 4.0, via Wikimedia Commons
There are 20 different amino acids, the way a protein functions and its definition is determined by their order of arrangement.
Codons are 3 nucleotides in a row which code for amino acids.
In order to tell which amino acid a codon codes for, a codon chart can be used. There are two types of charts, one is in a spherical shape which is defined as “Genetic Code.” The other is in a table form and is known as a “Codon Table.”
Image source https://www.genomenon.com/codon-chart/
As mentioned previously there are 3 main types of RNA, messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). HOWEVER, THERE ARE MORE THAN THESE 3: for example, small nuclear RNA (snRNA) and transfer-messenger RNA (tmRNA).
mRNA: mRNA contains information for the order of amino acids in order to develop the protein. It is known as the overall blueprint as it is responsible for the identity of the protein.
The nucleotides on the mRNA strand are in codon groups
(The use of mRNA within vaccines: In this case, the mRNA within the vaccine forces the body to produce a protein as an immune response).
tRNA: tRNA is known as Transfer RNA and folds into a T like shape.
On the top of the T shape, there is an attachment site for the amino acids. On the bottom end 3 nucleotides are present; these are called the anticodon. The bottom end is the site which attaches to the mRNA codons.
tRNA has the responsibility of bringing the amino acid to the protein, attaching it mRNA, and then adding the amino acids to the developing protein.
It decodes the sequences of codons provided by the mRNA to match the anticodon.
Image source: https://www.genome.gov/genetics-glossary/Transfer-RNA
rRNA: Ribosomal RNA
Similarly to the name rRNA, is the structure of ribosomes as well as the location for the process of protein synthesis.
Ribosomes are developed in the nucleolus of a cell which is located inside of the nucleus. They later come out to the rough endoplasmic reticulum.
It is important to note that the rough endoplasmic reticulum is different from the smooth endoplasmic reticulum.
The smooth ER is known as a storage area and stores polymers such as lipids and proteins. It is also a crucial site for lipid synthesis and hormones. Furthermore, it detoxifies harmful byproducts and stores as well as maintains the calcium ion concentration of the cell. Also, as per the name it has a smooth surface due to the lack of ribosomes and looks like a tube located near the cell membrane. The tubular structure is referred to as cisternae.
The rough ER plays a crucial role in protein synthesis and folding/molding. Moreover, they are involved with protein transportation after synthesis to locations such as the cellular membrane. The rough ER has a rigid exterior caused by ribosomal attachments. It is located around the nuclear membrane.
There are two parts to each ribosome:
A large subunit: This is where three attachment sites for tRNA are located (the A site(aminoacyl-tRNA), the P site (peptidyl-tRNA), and the E site (exit)). From left to right, the ribosome displays the E site on the left hand side, P site in the middle, and A site on the right hand side.
A small subunit: The small unit contains an attachment site for the mRNA strand.
The smaller subunit fits right under the large subunit.
Steps in protein synthesis: A summarized six step process:
Step 1: The mRNA slides in and attaches itself to the small subunit with the start codon located directly below the P site. There is only one start codon which is AUG (methionine) and three stop codons which are UGA, UAG, and UAA. The start codon signals the location in which the protein begins and the stop codon signals the end of the translation process.
Step 2: The tRNA comes into the P site and attaches the anticodon to AUG (UAG) to the AUG codon on the mRNA. (The anticodon is the opposite of matching nucleotides to the codon). Along with this, the tRNA is carrying the methionine amino acid.
Step 3: A tRNA enters the A site located on the right hand side and carries an anticodon which corresponds to the codon below the A site. Along with this, the tRNA is also bringing along the respective amino acid.
Step 4: In order to join the developed amino acids together, a peptide bond is used. Furthermore, after the next amino acid is added to the chain, the original methionine amino acid is released from its tRNA molecule.
Step 5: The ribosome continues to move down the mRNA strand every three bases (one codon) which shifts the polypeptide chain and the second tRNA to the P binding site. This leaves the A binding site open and the empty tRNA is then located in the E binding site.
Step 6: A new tRNA enters the A site once the empty tRNA in the E site is released from the ribosome.
This process continues and the amino acids continue to be added to the peptide chain while the mRNA moves through the ribosome. The new tRNA’s will enter from the A site and then proceed to leave by the means of the E site once they provided the corresponding amino acid.
Protein synthesis terminates when the stop codons (UGA, UAG, and UAA) are present. Unlike the other codons, these codons do not code for any amino acid. Once the stop codon enters the A site, a “release factor” will fill the A site ending the translation process.
Once this happens:
The mRNA leaves the ribosome
The protein is then released from the last used tRNA
The ribosome subunits (small and large) then proceed to separate.
This concludes this week's episode regarding RNA, the creation of RNA, the types of RNA, and the process of protein synthesis. In order to access the transcribed version, make sure to check out my blog post (link in the description). Additionally, within the blog posts, there will be links to resources such as textbook pages, websites, and videos which can all be used for aided learning. Furthermore, there will be images along with the post so that it is easier to follow along, especially for the process of protein synthesis.
Thanks for your time,
Shivani Kanjerla
Resources:
Smooth Endoplasmic Reticulum: Definition, Function & Structure
Designer Genes - Wiki (Scioly)
Heredity - Wiki (Scioly)
Difference Between rRNA and Ribosomes | Compare the Difference Between Similar Terms
Textbook:
AP Edition Biology Seventh Edition by: Campbell Reece
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