Tag: Protein Synthesis
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Protein Synthesis: Definition, Steps, and Diagram
Continue ReadingWhat is Protein Synthesis?
The process of creating polypeptide chains is called protein synthesis. The process completes with an implication of amino acid synthesis, transcription, translation, and post-translational events in a biological system.
The formation of amino acids from carbon sources like glucose is termed amino acid synthesis. It is a set of biochemical reactions. All organisms consist of several essential and non-essential amino acids. Some of the amino acids have been obtained from the diet whereas other amino acids are produced by the body.
Proteins are crucial biomolecules involved in various cellular functioning. These proteins are produced by the process of transcription and translation. The procedure of synthesizing mRNA templates from DNA molecules is called transcription. Later, these mRNA templates are used to translate them into amino acids.
The proteins or polypeptide chains are made by linking together these amino acids in a particular order based on the genetic code. After translation, these polypeptide chains undergo the process of post-translational modification, called protein folding.
Protein Synthesis Definition
The process of the creation of proteins is called protein synthesis. This process completes inside the cell in all organisms. In eukaryotic cells, the transcription takes place in the nucleus.
Later these mRNA templates move into the cytosol where it translated into polypeptides. The prokaryotic cells lack the nucleus since transcription completes in the cytoplasm of the cell.
Etymology
Protein synthesis is made up of two words, here the word protein is derived from the Greek word protos, meaning “first“. The word synthesis is derived from sunthesis, meaning “to put together“.
Prokaryotic Protein Synthesis vs Eukaryotic Protein Synthesis
All living organisms require several biomolecules to develop and proteins are one of the important biomolecules used by all cellular organisms. Numerous cellular activities in the cell need proteins in prokaryotic and eukaryotic cells.
These proteins are used in different biochemical reactions, act as a catalyst, and used for structural purposes. The mechanism of protein synthesis is different in prokaryotic and eukaryotic organisms.
Eukaryotes have a well-defined nucleus and the transcription completes in the nucleus of the cell whereas transcription in prokaryotes completes in the cytoplasm.
In a eukaryotic cell, the mRNA is transported into the cytoplasm where it is translated by ribosomes. Here the nucleotides are converted into amino acid chains.
Protein Synthesis and Genetic Code
A genetic code or codon is a trinucleotide sequence that identifies a particular amino acid. A codon is a group of three nucleotides so it is called a trinucleotide sequence. For example, a sequence GCC (guanine-cytosine- cytosine) codes for the particular amino acid alanine.
Similarly, 64 codons are present that encode different amino acids. These codons are present in the mRNA template that adjuncts to anticodons present in the tRNA molecule. These anticodons are also trinucleotide sequences.
mRNA, tRNA, and rRNA
There are three types of RNA involved in the process of protein synthesis. The first type is mRNA (messenger RNA) which carries codons that are converted into an amino acid chain. These mRNA molecules are produced by a DNA template in the nucleus of the cell.
However, in prokaryotes, it synthesizes in the cytoplasm. The mRNA is consists of a 5′ cap, 5′ UTR region, coding region, 3′ UTR region, and a poly (A) chain. The coding region of mRNA is responsible for gene expression which has a start codon at 5′ end and a stop codon at 3′ end.
Another type of RNA is the tRNA molecule, also called transfer RNA. The transfer of particular amino acid to the ribosome is completed by a tRNA molecule. It has a cloverleaf resembling structure that has two major sites, named as- anticodon arm and accepter stem.
The anticodons are present in the anticodon arm and the accepter stem specifies the particular amino acid that needs to be attached. Now the ribosome translates the mRNA template into a polypeptide chain.
This ribosome is composed of rRNA (ribosomal RNA) and some proteins. It is a cytoplasmic organelle present in both prokaryotic as well as in eukaryotic cells. However, the structure and composition of the ribosome can differ in both the cell. In prokaryotes, the ribosome is composed of 70S subunit whereas eukaryotic organisms consist of 80S ribosomes.
There are three binding sites present in rRNA, named as- A, P, and E sites. The aminoacyl tRNA docks at the A site and peptidyl- tRNA binds at the P site. The site where the tRNA leaves the ribosome is termed as E (exit) site.
Protein Synthesis Steps
i. Transcription
The process of producing an mRNA template from a DNA molecule is termed transcription. The mRNA has trinucleotide sequences (codons) that encode for particular amino acids and provide a template for the process of translation.
Transcription completes in four major steps-
(1) Initiation
(2) Promoter Escape
(3) Elongation
(4) Termination
In the initiation phase, the RNA polymerase binds to the promoter of DNA with the intervention of any transcription factor. After the binding, the DNA starts unwinding and form a transcription bubble which is also termed as transcription start site.
In the next step, the RNA polymerase escapes the promoter to step into the elongation phase. The RNA travel across the DNA template and base pairs with the nucleotides on the noncoding strand in the elongation phase.
The RNA polymerase forms the sugar-phosphate backbone and thymines are replaced by uracils. The termination step starts with the breaking of hydrogen bonds of RNA- DNA helix.
The mRNA script in eukaryotes goes through polyadenylation, capping, and splicing but the prokaryotic mRNA does not undergo these modifications.
ii. Translation
The process of producing amino acids from the mRNA script is called translation. These amino acids are linked together and form a polypeptide chain.
Protein Synthesis Diagram
Translation completes in the cytoplasm of the cell and consist of four phases-
(1) Activation
(2) Initiation
(3) Elongation
(4) Termination
The initiation starts with the binding of the ribosome to 5’end of mRNA. In elongation, the binding of aminoacyl-tRNA to the ribosome occurs. When the A site of ribosome faces a stop codon, the process terminates.
iii. Post-Translation
In eukaryotic translation, proteins undergo some post-translational modifications like protein folding, proteolysis. These modifications are termed as several enzymatic actions of a polypeptide chain that occur after the formation of a polypeptide chain.
For example- to ensure proper cellular localization, the ends may be modified. The folding of the polypeptide chain to conclude secondary and tertiary structures is termed as protein folding.
Protein Synthesis Citations
- Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae. Genetics . 2016 May;203(1):65-107.
- Bacterial Protein Synthesis as a Target for Antibiotic Inhibition. Cold Spring Harb Perspect Med . 2016 Sep 1;6(9):a025361.
- Branched-chain amino acids and muscle protein synthesis in humans: myth or reality? J Int Soc Sports Nutr . 2017 Aug 22;14:30.
- Protein synthesis and quality control in aging. Aging (Albany NY) . 2018 Dec 18;10(12):4269-4288.
- Protein Synthesis Initiation in Eukaryotic Cells. Cold Spring Harb Perspect Biol . 2018 Dec 3;10(12):a033092.
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Protein Synthesis: Definition, Steps, Site, and Diagram
Continue ReadingProtein Synthesis or Protein Translation
o Protein Translation is the process of protein synthesis directed by mRNA.
o mRNA is the template which carries the genetic code from the nucleus to the cytosol in the form of codons.
o The mRNA message is always written in the 5’ → 3’ direction, and the polypeptide chain is synthesized starting with its N-terminal residue.
o The mRNA is always read in groups of 3 nucleotides.
o Prokaryotic translation may occur simultaneously with transcription.
o tRNA contains a set of nucleotides that is complimentary to the codon called the anticodon.
o tRNA sequesters the amino acid that corresponds to its anticodon.
o The 5’ base of the anticodon is capable of a “wobble” in its position during translation, allowing it to make alternative hydrogen bonding arrangements with several different codon bases.
o Identity elements (not on the anticodon) as well as the anticodon determine which amino acid is bound to the tRNA by the aminoacyl-tRNA synthetases.
o rRNA with protein makes up the ribosome, which provides the site for translation to take place.
o The ribosome is composed of a small subunit and a large subunit made from rRNA and many separate proteins.
o The ribosome and its subunits are measured in terms of sedimentation coefficients given in Svedberg units (S).
o The sedimentation coefficient gives the speed of a particle in a centrifuge, and is proportional to mass, and related to shape and density.
Protein Synthesis Diagram
o Prokaryotic ribosomes are smaller than eukaryotic ribosomes.
o Prokaryotic ribosomes are made from a 30S and a 50S subunit and have a combined sedimentary coefficient of 70S.
o Eukaryotic ribosomes are made from a 40S and a 60S subunit and have a combined sedimentary coefficient of 80S.
o The complex structure of ribosomes requires a special organelle called the nucleolus in which to manufacture them.
o Prokaryotes don’t have a nucleolus, but synthesis of prokaryotic ribosomes is similar to that of eukaryotic ribosomes.
o Although the ribosome is assembled in the nucleolus, the small and large subunits are exported separately to the cytoplasm.
o rRNA is synthesized in the nucleolus.
o After posttranscriptional processing in a eukaryote, mRNA leaves the nucleus through the nuclear pores and enters the cytosol.
o With the help of initiation factors, the 5’ end attaches to the small subunit of a ribosome.
o A tRNA possessing the 5’-CAU-3’ anticodon sequesters the amino acid methionine and settles in the P site (peptidyl site).
o This is the signal for the large subunit to join and form the initiation complex.
o This process is called initiation. Now elongation of the polypeptide begins.
"Prokaryotic ribosomes are smaller than eukaryotic ribosomes"
o A tRNA with its corresponding amino acid attaches to the A site (aminoacyl site) at the expense of two GTPs.
o The C-terminal of the methionine attaches to the N-terminal of the incoming amino acid at the A site in a dehydration reaction catalyzed by peptidyl transferase, an activity possessed by the ribosome.
o In an elongation step known as translocation, the ribosome shifts 3 nucleotides along the mRNA toward the 3’ end.
o The tRNA that carried methionine is carried to the E site where it can exit the ribosome.
o Then the tRNA that is in the A site is moved to the P site.
o Translocation requires the expenditure of another GTP.
E ⇒ EXIT
P ⇒ PROCESS
A ⇒ ARRIVE
Protein Synthesis Steps
o Translation ends when a stop codon (UAA, UAG, UGA) is reached in a step called termination. When a stop (or nonsense) codon reaches the A site, proteins known as release factors bind to the A site allowing a water molecule to add to the end of the polypeptide chain.
o The protein is released and the rRNA breaks up into its subunits and waits for it to be used again in another round of translation Even as the polypeptide is being translated, it begins folding.
o The amino acid sequence determines the folding conformation and the folding process is assisted by proteins called chaperones.
o In post-translational modification, sugars, lipids, or phosphate groups may be added to the amino acids.
o The polypeptide may be cleaved in one or more places, or other polypeptides might join to form a quaternary structure.
o Translation may take place on a free floating ribosome in the cytosol producing proteins that function in the cytosol or a ribosome may attach itself to the rough ER during translation and inject the protein into the ER lumen.
o Proteins injected into the ER lumen are destined to become membrane bound proteins of the nuclear envelope, ER, Golgi, plasma membrane, or to be secreted from the cell.
o Free floating ribosomes are identical in structure to the ribosomes that attach to the ER.
o The growing polypeptide may or may not cause the ribosome to attach to the ER depending upon the polypeptide.
o A 20 amino acid sequence called a signal peptide near the front of the peptide is recognized by protein-RNA signal- recognition particles (SRPs) that carries the entire ribosome complex to a receptor on the ER.
o The peptide is actually pulled through the membrane through an ATP driven process.
o The signal peptide is also usually removed by an enzyme.
"Signal peptides may also be attached to polypeptides to target them to mitochondria, the nucleus, or other organelles"
Protein Synthesis Citations
- Protein synthesis. Annu Rev Biochem . 1966;35:723-58.
- A Quick Guide to Small-Molecule Inhibitors of Eukaryotic Protein Synthesis. Biochemistry (Mosc) . 2020 Nov;85(11):1389-1421.
- Protein synthesis. Annu Rev Biochem . 1973;42:397-438.
- Bacterial Protein Synthesis as a Target for Antibiotic Inhibition. Cold Spring Harb Perspect Med . 2016 Sep 1;6(9):a025361.
- Protein synthesis and quality control in aging. Aging (Albany NY) . 2018 Dec 18;10(12):4269-4288.
- Protein Synthesis Initiation in Eukaryotic Cells. Cold Spring Harb Perspect Biol . 2018 Dec 3;10(12):a033092.
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