Translation2 Flashcards
Why is translation important?
Because proteins are necessary for life as we know it, translation is essential. It must be rapid and precise. In some ways, one might think of translation as being “harder” than transcription because the nucleotide code must be read and then expressed as an amino acid sequence. Cells devote a lot of energy to it. Four high-energy bonds are used for each peptide bond that is made, and the translation machinery can make up a substantial percentage of the material in the cell. Also, many pathways exist to regulate translation which again speaks to how important it is for translation to occur correctly and efficiently. The basic processes of translation differ only a little across life, they are fundamental and conserved.
What makes up the machinery of protein synthesis?
The key players are: messengerRNA(mRNA), Transfer RNAs (tRNA), Aminoacyl tRNA synthetases, ribosome, Initiation factors, Elongation factors and their partners, and Termination/recycling factors
messengerRNA(mRNA)
contains the nucleotide sequence that encodes the protein. The protein that is encoded in each mRNA is written in three-nucleotide “codons.” The codons do not overlap. There are 43=64 possible codons, all are used. AUG is used as the “start” codon, and there are several used as “stop” codons. Several different codons can encode the same amino acid, but the frequency by which codons are used is not random and can vary between organisms.
Transfer RNAs (tRNA)
adapters that “read” the message and deliver the right amino acid. tRNAs base-pair directly to the codons in the mRNA though the the tRNA’s anticodon loop. Thus, each codon is recognized by a specific type of tRNA. At the other end of the tRNA in the acceptor stem that has the amino acid attached that matches the anticodon. Some tRNAs can recognize more than one codon, due to wobble-pairing at the third location in the codon. The amount of each type of tRNA in the cell varies, usually matching codon frequency. The function of tRNA is dictated by its three-dimensional folded structure.
Aminoacyl tRNA synthetases
protein enzymes that put the right amino acid on the right tRNA. These enzymes are very important in that each identifies the right tRNA and puts on the correct amino acid. Each amino acid/tRNA has its own synthetase associated with it (e.g. valyl-tRNA synthetase puts a valine on a val-tRNA).
ribosome
the platform that brings it all together and contains the catalytic center. The ribosome is a massive machine containing both RNA and many proteins. The bulk of it is RNA. In all of life, it contains two subunits: in bacteria these are the 30S and 50S, and in eukaryotic these are the 40S and 60S. In a fully assembled ribosome, the mRNA and tRNA pass between the two subunits; there are three tRNA binding sites: the A, P, and E sites. The small subunit has the decoding groove through which the mRNA passes and the tRNAs read the message. The large subunit contains the catalytic center (the peptidyl transferase center, PTC), which appears to be made entirely of RNA and thus the ribosome is a ribozyme (uses RNA to perform catalysis). Many antibiotics target the ribosome.
Initiation factors
proteins that bring the ribosome to the message RNA and assist in getting the machinery assembled. There are three of these in bacteria, over a dozen in eukaryotes.
Elongation factors and their partners
proteins that deliver tRNAs and move the ribosome down the message.
Termination/recycling factors
proteins that deliver tRNAs and move the ribosome down the message.
Initiation
getting the machinery assembled in the right place and thus setting the reading frame. Initiation is the step that differs the most between bacteria and eukaryotes. However, in both the goal is the same: assemble a ribosome with the start codon (AUG) and initiator methionine tRNA in the P-site, ready to receive the next aa-tRNA in the A-site.
initiator methionine tRNA
initiates translation in eukaryotes, homologous to N-Formylmethionine (fMet)
N-Formylmethionine (fMet)
a derivative of the amino acid methionine in which a formyl group has been added to the amino group. It is specifically used for initiation of protein synthesis for bacterial and organellar genes, and may be removed post-translationally. It is located at the N-terminus of the growing polypeptide. fMet is delivered to the ribosome (30S) - mRNA complex by a specialized tRNA (tRNAfMet) which has a 3’-UAC-5’ anticodon that is capable of binding with the 5’-AUG-3’ start codon located on the mRNA.
Shine- Dalgarno sequence
a ribosomal binding site in prokaryotic mRNA, generally located around 8 bases upstream of the start codon AUG.[1] The RNA sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning the ribosome with the start codon. The ribosome recognises a purine-rich sequence (AGGAGGU) in the region upstream of the correct initiator AUG found in the ribosome binding sites
untranslated region
refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the 5’ side, it is called the 5’ UTR (or leader sequence), or if it is found on the 3’ side, it is called the 3’ UTR (or trailer sequence).
5’ untranslated region (5′ UTR)
The region of an mRNA that is directly upstream from the initiation codon. The elements of a eukaryotic and prokaryotic 5′ UTR differ greatly. The prokaryotic 5′ UTR contains a ribosome binding site (RBS), also known as the Shine Dalgarno sequence (AGGAGGU) which is usually 3-10 base pairs upstream from the initiation codon. Meanwhile the eukaryotic 5′ UTR contains the Kozak consensus sequence (ACCAUGG), which contains the initiation codon. The eukaryotic 5′ UTR also contains cis-acting regulatory elements called upstream open reading frames (uORFs) and upstream AUGs and termination codons (uAUGs), which have a great impact on the regulation of translation.
three prime untranslated region (3’-UTR)
Regulatory regions within the 3’-untranslated region can influence polyadenylation, translation efficiency, localization, and stability of the mRNA. The 3’-UTR contains both binding sites for regulatory proteins as well as microRNAs (miRNAs). The 3’-UTR also has silencer regions which bind to repressor proteins and will inhibit the expression of the mRNA. Furthermore, the 3’-UTR contains the sequence AAUAAA that directs addition of several hundred adenine residues called the poly(A) tail to the end of the mRNA transcript.
Translation in bacteria
in bacteria, there is no cap, no poly-A tail, and generally no UTRs. Several proteins can be encoded on a single mRNA (polycistronic). 1) Initiation factor proteins IF1 and IF3 bind the 30S subunit. The mRNA binds the 30S subunit using the Shine-Dalgaro sequence. This places the start AUG codon in the subunit’s P-site. 2) IF2 delivers a special “initiator” formylmethionine tRNA to the P-site to pair with the AUG codon. 3) GTP hydrolysis on IF2 leads to release of all the initiation factors and binding of the 50S subunit. This results in a 70S ribosome with the next codon to be read placed in the A-site.
Implication of the mechanism of initiation in bacteria
Initiation can occur at internal AUG codons in prokaryotic mRNA, so messages can be polycistronic (many messages strung together on a single RNA). Bacterial genes are often expressed in groups as an operon. Example: The lac operon in E. coli contains many AUGs, but only those with an associated SD sequence are sites of translation initiation.
translation in eukaryotes
initiation factor (eIF) 4E is required to bind to the 7-methyl guanosine cap on the 5’ end of the mRNA. This leads to binding of many other eIFs (4G, 4A, 4B, etc.) and eventually to binding of the small ribosomal subunit, which itself is bound by several factors (eIF3, eIF1A, eIF1, eIF2, etc.). The ribosome then scans down the message to find the AUG start codon. At that point, the large subunit can join the small, the factors are released, and the goal of initiation has been achieved. In addition to the canonical cap-dependent process, there is a cap-independent process in eukaryotes that is driven by specific RNA sequences and structures called internal ribosome entry sites. The majority of eukaryotic mRNAs are translated by a cap-dependent, scanning mechanism. The greater complexity allows for regulation of the process in many ways.
initiation factor (eIF) 4E
EIF4E is a eukaryotic translation initiation factor involved in directing ribosomes to the cap structure of mRNAs. The EIF4E polypeptide is the rate-limiting component of the eukaryotic translation apparatus and is involved in the mRNA-ribosome binding step of eukaryotic protein synthesis. eIF4E binds the first nucleotide on the 5’ end of an mRNA molecule (known as the cap): a 7 methyl guanosine (m7G),
7-methyl guanosine cap
The 5′ cap is found on the 5′ end of an mRNA molecule and consists of a guanine nucleotide connected to the mRNA via an unusual 5′ to 5′ triphosphate linkage. This guanosine is methylated on the 7 position directly after capping in vivo by a methyl transferase. This structure is involved in several cellular processes including enhanced translational efficiency, splicing, mRNA stability, and RNA nuclear export.
eIF4G
a protein involved in bringing mRNA to the ribosome for translation, eIF4G strongly associates with the protein that directly binds the mRNA cap: eIF4E. It is a scaffolding protein that also directly associates with eIF3
eIF4A
The mRNA cap is bound by eIF4E, eIF4G acts as a scaffold for the complex whilst the ATP-dependent RNA helicase eIF4A processes the secondary structure of the mRNA 5’ UTR to render it more conducive to ribosomal binding and subsequent translation. Together these three proteins are referred to as eIF4F.
eIF4B
Required for the binding of mRNA to ribosomes. Functions in close association with EIF4-F and EIF4-A. Binds near the 5’-terminal cap of mRNA in presence of EIF-4F and ATP. Promotes the ATPase activity and the ATP-dependent RNA unwinding activity of both EIF4-A and EIF4-F
eIF3
is associated with the small ribosomal subunit, and plays a role in keeping the large ribosomal subunit from prematurely binding. eIF3 also interacts with the eIF4F complex
eIF1A
Binds to the small ribosomal subunit, is essential for transfer of the initiator Met-tRNAf to 40 S ribosomal subunits in the absence of mRNA to form the 40 S preinitiation complex
eIF1
Binds to the small ribosomal subunit
eIF2
eIF2 is a GTP-binding protein responsible for bringing the initiator tRNA to the P-site of the pre-initiation complex. It has specificity for the methionine-charged initiator tRNA, which is distinct from other methionine-charged tRNAs specific for elongation of the polypeptide chain. Once it has placed the initiator tRNA on the AUG start codon in the P-site, it hydrolyzes GTP into GDP, and dissociates. This hydrolysis, also signals for the dissociation of eIF3, eIF1, and eIF1A, and allows the large subunit to bind. This signals the beginning of elongation. When large numbers of eIF2 are phosphorylated, protein synthesis is inhibited. This would occur if there is amino acid starvation or there has been a virus infection.