5. Translation – Essentials of Molecular Biology

5

Translation

CONCEPT OUTLINE
  • Introduction
  • Genetic Code
    • Codons

       

  • Deciphering the Genetic Code
    • Nirenberg and Khorana experiment

       

  • Characteristic Features of the Genetic Code
    • The mitochondrial genetic code

       

  • Wobble Hypothesis
    • Codon—anticodon interactions
    • Wobble hypothesis
  • Ribosome Structure
    • Prokaryotic ribosome—70S ribosome
    • Self-assembly of ribosomes
    • Eukaryotic ribosome—80S ribosome
  • Protein Synthesis in Prokaryotes
    • Activation of the amino acids
    • The two classes of aminoacyl-tRNA synthetases
    • Aminoacyl-tRNA synthetases and proof reading
    • tRNA molecule acts as adaptors
    • The interaction between aminoacyl-tRNA synthetases and tRNA constitutes a second genetic code
    • Polypeptide synthesis begins at the amino-terminal end
    • The process of translation
    • Polyribosomes are the active structures of protein synthesis
  • Protein Synthesis in Eukaryotes
    • Initiation of translation in eukaryotes
    • Elongation
    • Termination
    • Regulation of translation
  • Post-translational Modifications
    • proteolytic cleavage
    • Acylation
    • Myristoylation
    • Methylation
    • Phosphorylation
    • Acetylation
    • Formylation
    • Sulphation
    • Prenylation
  • Summary
  • References
INTRODUCTION

Proteins are the end products of most information pathways. A cell requires about thousands of different proteins. Translation is the process of the synthesis of proteins in the cell. Translation is a complex biosynthetic process that involves several proteins, enzymes and RNA molecules. The genetic information stored in the DNA is transcribed into a messenger RNA (mRNA), which takes the message to the cytosol and is translated into a protein. In prokaryotes, transcription and translation are coupled processes, as they do not have a well-defined nucleus. In eukaryotes, transcription and translation are not coupled because there is compartmentalization of these events; transcription takes place in the nucleus and translation takes place in the cytosol of the cell. Prokaryotic mRNAs are ‘monocistronic’ that is they code for only one protein, whereas eukaryotic mRNAs are ‘polycistronic’ that is they code for many proteins.

GENETIC CODE

Codons

DNA specifies protein through an mRNA. Hidden within the mRNA lies the ‘triplet code’, a series of three nucleotides, called codons that code for a single amino acid. There are only 20 amino acids that occur in naturally derived proteins. The mRNA contains four different nucleotides namely: adenine (A), uracil (U), guanine (G) and cytosine (C). Thus, 20 amino acids are coded by only four unique bases in mRNA. The codons of the mRNA read from 5′ → 3′ direction corresponds to the amino acid sequence of the protein read from its N-terminus to C-terminus.

The variation in the number of nucleic acid bases and the number of amino acids proves that there cannot be a code of one base per amino acid. Even if two nucleotides code an amino acid (a doublet code), it could not account for 20 amino acids. As with four bases and a doublet code, there would only be 16 possible combinations (42 = 16) and thus, they could not encode all 20 amino acids. However, a triplet code produces 64 (43 = 64) possible combinations or codons and thus could satisfactorily code all the 20 amino acids but a triplet code introduces the problem of there being more than three times the number of codons than amino acids.

DECIPHERING THE GENETIC CODE

Nirenberg and Khorana Experiment

Marshall W. Nirenberg and Heinrich J. Matthaei (1962) made their own simple and artificial mRNA and identified the polypeptide product that was encoded by it. They used the enzyme polynucleotide phosphorylase, which randomly polymerizes any RNA nucleotides that it finds. They began with the simplest codes possible. Polynucleotide phosphorylase was added to a solution of pure uracil(U). Poly(U) polymer was created. These molecules were known as poly(U) RNAs. These poly(U) RNAs were added to 20 tubes containing all the components required for protein synthesis such as ribosomes, activating enzymes, tRNAs and other factors. Each tube contained one of the 20 amino acids, which were radioactively labelled. Of the 20 tubes, 19 tubes did not form the protein. Only one tube, the one that had been loaded with the labelled amino acid phenylalanine, yielded a product. Assuming triplet code, Nirenberg and Matthaei, therefore, found that the UUU codon could codes for the amino acid phenylalanine. Similar experiments conducted using poly(C) and poly(A) RNAs revealed that CCC encodes the amino acid proline and lysine was encoded by the AAA codon.

In an effort to decode the other codons, Nirenberg et al. made artificial RNAs containing two or three different bases. As previously mentioned, polynucleotide phosphorylase joins nucleotides randomly; as a result, these artificial RNAs contained random mixtures of the bases in proportion to the amounts of bases mixed. For example, when A and C were mixed with polynucleotide phosphorylase, the resulting RNA molecules contained eight different triplet codons: AAA, AAC, ACC, ACA, CAA, CCA, CAC and CCC. These eight random poly(AC) RNAs produced proteins containing only six amino acids: asparagine, glutamine, histidine, lysine, proline and threonine. Previous experiments had already revealed that CCC and AAA code for proline and lysine, respectively. Thus, it was concluded that the four newly incorporated amino acids could only be encoded by AAC, ACC, ACA, CAA, CCA and/or CAC.

In 1965, H. Gobind Khorana and his colleagues used another method to further decipher the genetic code. These researchers used chemically synthesized RNA molecules of known repeating sequences rather than random sequences. For example, an artificial mRNA of alternating guanine and uracil nucleotides (GUGUGUGUGUGU). This mRNA upon translation is read as two alternating codons, GUG and UGU, and encodes a protein of two alternating amino acids, cysteine and valine respectively. However, this technique could not determine whether GUG or UGU encoded cysteine.

 

 

Nirenberg and Philip Leder developed a technique using ribosome-bound transfer RNAs (tRNAs). They showed that a short mRNA sequence—even a single codon (three bases)—could still bind to a ribosome, even if this short sequence was incapable of directing protein synthesis. The ribosome-bound codon could then base pair with a particular tRNA that carried the amino acid specified by the codon. They synthesized many short mRNAs with known codons. The mRNAs were then added one by one to a mix of ribosomes and aminoacyl-tRNAs with one amino acid radioactively labelled. For each reaction, they determined whether the aminoacyl-tRNA was bound to the short mRNA sequence and to the ribosome. By this method, they identified the particular aminoacyl-tRNA that was bound to each mRNA codon.

CHARACTERISTIC FEATURES OF THE GENETIC CODE

The genetic dictionary of the mRNA codons reveals the following important features of triplet codons:

  1. Degeneracy: There are 64 different triplet codons but only 20 amino acids. This proves that some amino acids must be specified by more than one codon. For example, the three amino acids arginine, serine and leucine, each have six synonymous codons. The first two bases of the synonym codons are constant, whereas the third can vary; for example, all codons starting with CC specify proline (CCU, CCC, CCA and CCG) and all codons starting with AC specify threonine. This third position is known as the ‘wobble’ position of the codon. This is because though the identity of the base at the third position can wobble, the same amino acid will still be specified. This wobbling offers some protection against mutation—if a mutation occurs at the third position of a codon, there is a good chance that the same amino acid can be specified and the encoded protein does not change.
  2. Non-overlapping: The code is non-overlapping, meaning that no single base can take part in the formation of more than one codon. The genetic code is read in groups of three nucleotides. After reading one triplet, the ‘reading frame’ shifts over the next three letters and not just one or two. In the following example, the code would not be read GAC, ACU, CUG, UGA…

     

     

    Rather, the code would be read GAC, UGA, CUG, ACU…

     

     

  3. Reading Frames: The triplet-based genetic code can be read in three possible ways. For example, the following code can be read in three different ways as:

     

     

    Each way of reading would yield completely different results. Hence, the correct way of reading the genetic code becomes a must. The genetic code is read continuously from the 5′ → 3′ direction.

  4. Ambiguity: The genetic code is non-ambiguous, that is, each codon specifies a particular amino acid, and only one amino acid. In other words, the codon ACG codes for the amino acid threonine, and only threonine.
  5. Commaless: The genetic code is commaless, which means that no codon is reserved for punctuations.
  6. Starting codons: AUG codon is called starting or chain initiation codon, because, it initiates the synthesis of polypeptide chain. AUG also codes for the amino acid methionine. The first AUG in the mRNA signals for translation to begin. The subsequent codons are read in the same reading frame. Translation continues until a stop codon is encountered.
  7. Stop codons: There are three stop codons: ‘UAA’, ‘UAG’ and ‘UGA’. The UAA is also called ochre and UAG is also called amber. These codons do not specify any amino acid and hence they are also called ‘non-sense codons’. They are also called termination codons. A reading frame between a start codon and an in-frame stop codon is called an ‘open reading frame’ (ORF).

    For example, consider the following sequence:

     

    5′-GUCCCGUGAUGCCGAGUUGGAGUCGAUAACUCAGAAU-3′

     

    The code is read in the 5′ → 3′ direction. The first AUG read in that direction sets the reading frame, subsequent codons are read in frame, until the stop codon, UAA, is reached.

     

     

    It is an absolute requirement that the codes are read in frame. In the above example, the three nucleotides marked with asterisk would specify the stop codon UAG if not read in frame.

    In the above sequence, there are nucleotides at either end that are outside of the ORF. Because they are outside of the ORF, these nucleotides are not used to code for amino acids and are called untranslated regions. The region at the 5′-end that is not translated is called the 5′ untranslated region or 5′-UTR. The region at the 3′-end is called the 3′-UTR. These sequences contain regulatory sequences that can regulate the gene expression.

  8. Universality: The genetic code has been found to be universal, because the same code applies in all kinds of living systems.

The Mitochondrial Genetic Code

Human mitochondrial DNA encodes only 22 tRNA that are used for the translation of mitochondrial mRNAs. The U of the anticodon in tRNA can pair with any of the four bases in the third codon position of the mRNA. This enables four codons to be recognized by a single tRNA. Moreover, some codons specify different amino acids in mitochondria than in the universal code.

Differences between the universal and mitochondrial genetic codes

The genomes of prokaryotic and eukaryotic cells have less genetic code variations. Among the lower eukaryotes, certain ciliated protozoans (Tetrahymena and Paramecium) use UAA and UGA as glutamine codons rather than stop codons (Table 5.1). Mycoplasma, for example, uses the stop codon UGA to specify Trp. Some UGA codons in both prokaryotes and eukaryotes (including humans) are used to specify selenocysteine. In several species of Archaea and bacteria, pyrrolysine amino acid is encoded by UAG. How the translation machinery knows when it encounters UAG whether to insert a tRNA with pyr-rolysine or to stop translation is not yet known.

 

Table 5.1 Universal and mitochondrial genetic codes

Codon Universal code Human mitochondrial code
UGA Stop Trp
AGA Arg Stop
AGG Arg Stop
AUA Ile Met
WOBBLE HYPOTHESIS

Codon-anticodon Interactions

The genetic code is read in the 5′ → 3′ direction along the mRNA by sequential binding of the codons to the complementary anticodons of specific tRNA molecules. Each codon of the mRNA can be hydrogen bonded to a tRNA anticodon (present in the tRNA anticodon loop) consisting of complementary base sequence. The tRNA is oriented anti-parallel to the mRNA. The 1st, 2nd and 3rd bases of the mRNA codons pair respectively with the 3rd, 2nd and 1st bases of the tRNA anticodons obeying Watson-Crick base pairing rule. Thus, this codon-anticodon interaction enables the genetic code to be translated into specific amino acid sequence of the protein to be synthesized (Figure 5.1).

Wobble Hypothesis

It is a hypothesis given by Crick to explain how one tRNA molecule can accommodate more than one codons of amino acid. In order to explain the above anomaly, Crick proposed a word ‘wobble’ which according to him is the relative lose base pairing between base at the 3′-end of the codon and the complementary base at the 5′-end of the anticodon in the tRNA. The hypothesis proposes the following relationships:

  1. The first two bases of a codon always form strong Watson-crick base pair with the corresponding bases of anticodon and this confers most of the coding specificity.
  2. The first base of anticodon [5′ → 3′ direction] or the 3rd base [3′ → 5′ direction] called the wobble base allows the single tRNA to bind with more than one codon. The 3rd base [3′ → 5′ direction] of the codon which leads to lose base pairing is termed as ‘wobble’. The wobble permits tRNA to read more than one codon with the maximum limits of three codons.

     

    Figure 5.1 Codon-anticodon interaction

     

  3. If the ‘wobble’ base is ‘C’ or ‘A’ in the anticodon, then it recognize only one codon which mostly contain ‘G’ or ‘U’ respectively in its 3′ position. Here, ‘C’ and ‘A’ form Watson-Crick base pair with ‘G’ and ‘U’ respectively.

     

     

  4. When the first base in the 5′-end in the anticodon is ‘U’, then third base in codon can be either ‘A’ or ‘G’. The ‘U’ forms strong Watson-Crick base pair with ‘A’ and wobble pairing with ‘G’. Similarly, if ‘G’ is present at 5′-ends of anticodon, then ‘G’ forms Watson-Crick base pair with ‘C’ and wobble base pair with ‘U’.

     

     

  5. When ‘I’ or some other modified base is present at 5′-end of anticodon, then tRNA can recognize three different codons, all of which form a wobble base pairing at 3′ position of codon. The bases that can pair in this case are ‘A’, ‘U’ and ‘C’.

     

     

For example, the IGC anticodon of yeast alanine tRNA can pair with any of the codons GCU, GCC and GCA.

Thus, a part of degeneracy of the genetic code arises from wobble in the pairing of the third base of the codon. A minimum of 32 tRNAs are required to translate all 61 different codons for the amino acids.

RIBOSOME STRUCTURE

Ribosomes are compact ribonucleoprotein particles found in the cytosol of all cells, as well as in the matrix of mitochondria and the stroma of chloroplasts. Ribosomes are mechano-chemical systems that move along mRNA templates, co-ordinates the interactions between successive codons and the corresponding anticodons of the aminoacyl-tRNAs. Ribosomes also catalyse the formation of peptide bonds between adjacent amino acid residues. Prokaryotes and eukaryotes have similar ribosomes that are quite similar in both structure and function.

Prokaryotic Ribosome—70S Ribosome

The bacterial ribosomes contain 65 per cent RNA and 35 per cent protein. They have a diameter of about 18 nm and are composed of two unequal subunits with a sedimentation coefficient of 70S (Figure 5.2). The 50S subunit comprises of 34 proteins (L-proteins) and 23S and 5S rRNAs. The 23S rRNA is made up of 2,904 nucleotide residues and 5S rRNA of 120 nucleotide residues. The 30S subunit consists of 21 ribosomal proteins (S-proteins) and 16S rRNA molecule which contain 1,532 nucleotide residues (Figure 5.3 (a)).

Most ribosomal proteins are low molecular weight basic protein. The basic charge enables them to interact with negatively charged RNA. The RNA molecules within the ribosome have well-defined secondary structure and can interact with the ribosomal protein in precise manner. Prokaryotic ribosome can be split into RNA and protein components and then reassembled into active functional ribosome. Ribosomal proteins are present as single copy except L-7 and L-12 proteins.

Self-assembly of Ribosomes

Ribosomal subunits are capable of self-assembly from their macromolecular components. If the individual proteins and rRNAs composing ribosomal subunits that are mixed together in vitro under appropriate conditions of pH and ionic strength, spontaneous self-assembly into functionally competent subunits takes place without the intervention of any additional factors or chaperones. The rRNA acts as a scaffold upon which the various ribosomal proteins are attached. Ribosomal proteins bind in a specified order. Assembly of 30S subunits begins even as the rRNA precursor is being transcribed. The 5′-region of the 16S rRNA possesses a cluster of the strongest protein-binding sites.

Eukaryotic Ribosome—80S Ribosome

Eukaryotic cells have ribosomes in their mitochondria (and chloroplasts) as well as in the cytosol. The mitochondrial and chloroplastic ribosomes resemble prokaryotic ribosomes in size, organization, structure and function. This fact reflects the prokaryotic origins of these organelles. Eukaryotic cytosolic ribosomes are larger and considerably more complex.

 

Figure 5.2 Prokaryotic 70S ribosome

 

Figure 5.3 Prokaryotic and eukaryotic ribosome composition

 

Eukaryotic ribosomes are made up of two subunits namely large 60S subunit and smaller 40S subunit. 60S subunit contains about 40–5 polypeptides and three rRNA components [28S rRNA, 5.8S rRNA and 5S rRNA] and 40S subunit contains about 30 polypeptides and 18S rRNA components (Figure 5.3(b) and Figure 5.4).

 

Figure 5.4 Eukaryotic 80S ribosome

 

Figure 5.5 Ribosomal sites

 

X-ray diffraction studies have revealed that ribosomes have some sites which are discussed in the following sections (Figure 5.5)

P-site (Peptide site)

It is located on 30S subunit and can also extent to 50S subunit. It is the site to which the initiating tRNA, i.e., N-formyl methionine-tRNAfmet binds. During translation, the peptide containing tRNA is present in this site and hence the name peptide site.

A-site (Amino acid site)

It lies closely to P-site. The incoming aminoacyl-tRNA binds to this site.

mRNA-binding site

It is located on 30S subunit. It is associated with 16S rRNA and carries the Shine-Dalgarno sequence which plays a key role in the mRNA binding.

Peptidyl transferase site

It lies somewhere between A-site and P-sites. 23S rRNA and some of the L-proteins are needed for their activity.

5S rRNA site

It is located near peptidyl transferase site.

E-site

It is the excision site which is located on 50S subunit. Empty tRNA after releasing their amino acids is freed from this site.

PROTEIN SYNTHESIS IN PROKARYOTES

Protein biosynthesis in all cells is characterized by three distinct phases: initiation, elongation and termination. At each stage, the energy required for the process is provided by GTP hydrolysis. Specific soluble protein factors participate in the events.

Activation of the Amino Acids

Amino acid activation takes place in the cytosol and not on the ribosomes. Each of the 20 amino acids is covalently attached to a specific tRNA. ATP provides the energy required. These reactions are catalysed by a group of Mg2+-dependent activating enzymes called ‘aminoacyl-tRNA synthetases’, each specific for one amino acid and its corresponding tRNAs.

When two or more tRNAs exist for a given amino acid, one aminoacyl-tRNA synthetase generally aminoacylates all of them. Aminoacylated tRNAs are referred to as being ‘charged’. Only the L amino acids take part in protein synthesis. Thus, a second genetic code is constituted by the aminoacyl-tRNA synthetases. That is each aminoacyl-tRNA synthetase discriminates between the 20 amino acids and the many tRNAs and uniquely picks out its proper substrates—one specific amino acid and the tRNA(s) appropriate to it—from among the more than 400 possible combinations.

Many of the other common amino acids which are not used in protein synthesis, e.g. citrulline, β alanine, etc. are also rejected. The activation of amino acids takes place through their carboxyl groups.

Amino acid + tRNA + ATP + Mg2+ → aminoacyl-tRNA +AMP + PPi

The activation reaction occurs in two steps. In the first step, an enzyme-bound intermediate, aminoacyl-adenylate (aminoacyl-AMP) is formed by reaction of ATP and the amino acid. In this reaction, the carboxyl group of the amino acid is bound in anhydride linkage with the 5′-phosphate group of AMP, with the displacement of pyrophosphate. In the second step, the aminoacyl group is transferred from the enzyme-bound aminoacyl-AMP to its corresponding specific tRNA (Figure 5.6).

The Two Classes of Aminoacyl-tRNA Synthetases

Aminoacyl-tRNA synthetases are a diverse group of proteins in terms of size, amino acid sequence and oligomeric structure. The aminoacyl-tRNA synthetases are classified into two fundamental classes based on similar amino acid sequence motifs, oligomeric state and acylation function, namely: class I enzymes, which are chiefly monomeric and class II aminoacyl-tRNA synthetases, which are always oligomeric (usually homodimers). Furthermore, first, class I aminoacyl-tRNA synthetases add the amino acid to the 2′-OH of the terminal adenylate residue of tRNA before shifting it to the 3′-OH; then, class II enzymes add it directly to the 3′-OH (Figure 5.7).

 

Figure 5.6 Amino acylation of tRNA by amino acyl tRNA synthetases

 

Figure 5.7 (a) t-RNA amino acylation (b) Steps in amino acylation by the two classes of amino acyl tRNA synthetases.

  1. activation of the amino acid.
  2. attachment of activated aminoacid to be tRNA

Aminoacyl-tRNA Synthetases and Proof Reading

While selecting an amino acid, aminoacyl-tRNA synthetases hardly make mistakes 1 in 10,000–100,000; however, while selecting tRNA, they may make a mistake 1 in 1,000,000. If a mistake has occurred, it is corrected by cognate tRNA binding; it also performs what is called chemical proof reading, i.e., after charging, if found wrong, it is hydrolysed and removed.

tRNA Molecule Acts as Adaptors

The fidelity of protein synthesis requires the accurate recognition of three-base codons on mRNA. An amino acid cannot itself recognize a codon. Consequently, an amino acid is attached to a specific tRNA molecule that can recognize the codon by Watson-Crick base pairing, that is tRNA serves as the adaptor molecule that binds to a specific codon and brings with it an amino acidfor incorporation into the polypeptide chain (Figure 5.8). Apart from tRNA molecules, the aminoacyl-tRNA synthetase enzymes are also adaptors of equal importance to the decoding process. Thus, the genetic code is translated by two sets of adaptors that act sequentially. Each of the adaptors match one molecular surface to another with great specificity and their combined action that associates, each codon with its particular amino acid.

 

Figure 5.8 Aminoacylated tRNA (a) Secondary structure of tRNA, before and after amino acid attachment (b) Tertiary structure of tRNA

 

The Interaction Between Aminoacyl-tRNA Synthetases and tRNA Constitutes a Second Genetic Code

An individual aminoacyl-tRNA synthetase must be specific not only for a single amino acid but for tRNA as well. Discriminating among several tRNAs is important for the overall fidelity of protein biosynthesis. The interaction between amino acyl-tRNA synthetases and tRNA has been referred to as ‘second genetic code’ to reflect its critical role in maintaining the accuracy of protein synthesis.

Polypeptide Synthesis Begins at the Amino-Terminal End

Polypeptide synthesis begins at the amino-terminal end and is elongated by sequential addition of residues to the carboxy-terminal end. This pattern has been confirmed by numerous researches and applies to all proteins in all cells.

The Process of Translation

Initiation

Initiation involves the reactions that precede the formation of the peptide bond between the first two amino acids of the protein. It requires the ribosome to bind to the mRNA. This is relatively slow step in translation and usually determines the rate at which an mRNA is translated. Initiation of translation is not a function of intact ribosomes, but is undertaken by the separate subunits, which re-associate during the initiation reaction.

The initiation codon in an mRNA is AUG, which codes for the amino acid methionine. There are two tRNAs for methionine in all organisms. One tRNA is used exclusively when AUG represents the initiation codon for protein synthesis. The second is used when methionine is added at an internal position in a polypeptide. In bacteria, two separate classes of tRNA specific for methionine are designated as tRNAMet and tRNAfMet. The starting amino acid at the amino-terminal end is N-formyl methionine. It enters the ribosome as N-formyl methionyl-tRNAfMet, which is formed in two successive reactions catalysed by the enzyme Met-tRNA synthetase.

Methionine + tRNAfMet + ATP → Met-tRNAfMet + AMP + PPi

Second, a formyl group is transferred to the amino group of methionine residue from N10-formyl tetrahydrofolate by a transformylase enzyme.

N10-formyl tetrahydrofolate + Met-tRNAfMet → tetrahydrofolate + fMet-tRNAfMet

This transformylase enzyme is more selective than the Met-tRNA synthetase and it cannot formylate free methionine residues or methionine residues attached to tRNAMet. Instead, it is specific for tRNAfMet.

 

 

The initiation of polypeptide synthesis in bacteria requires:

  • the 30S ribosomal subunit, which contains the 16S rRNA,
  • the mRNA coding for the polypeptide to be made,
  • the initiating fMet-tRNAfMet,
  • a set of three proteins called initiation factors (IF-1, IF-2 and IF-3),
  • GTP,
  • the 50S ribosomal subunit and
  • Mg2+.

The formation of the initiation complex takes place in three steps:

  1. The 30S ribosomal subunit binds initiation factor 3(IF-3), which prevents the 30S and 50S subunits from combining prematurely. Binding of the mRNA to the 30S subunit then takes place in such a way that the initiation codon AUG binds to a precise location on the 30S subunit. The initiating AUG is guided to its precise position on the 30S subunit by an initiating signal called the Shine-Dalgarno sequence in the mRNA, centred 8–13 base pairs to the 5′ side of the initiating codon. Generally consisting of four-nine purine residues, the Shine-Dalgarno sequence is recognized by and base pairs with a complementary pyrimidine-rich sequence near the 3′-end of the 16S rRNA of the 30S subunit. This mRNA-rRNA interaction fixes the mRNA, so that the AUG is correctly positioned for initiation of translation.

     

     

    Ribosomes have two sites that bind aminoacyl-tRNAs, the aminoacyl or A-site and the Peptidyl or P-site. Both 30S and 50S subunits contribute to the characteristic of each site. The initiating AUG is positioned in the P-site, which is the only site to which fMet-tRNAfMet can bind. During subsequent elongation stage, all other aminoacyl-tRNAs bind to the A-site.

  2. In the second step of the initiation process, the complex consisting of the 30S subunit, IF-3 and mRNA now forms a still larger complex by binding IF-2, which is already bound to GTP and the initiating fMet-tRNAfMet. The anticodon of this tRNA pairs correctly with the initiation codon.
  3. In the third step, this large complex combines with the 50S ribosomal subunit; simultaneously, the GTP molecule bound to IF-2 is hydrolysed to GDP and Pi (which are released). IF-3 and IF-2 also depart from the ribosome (Figure 5.9).

Elongation

Elongation involves the stepwise addition of amino acids to the polypeptide chain. Elongation requires:

  1. The initiation complex described above,
  2. The next aminoacyl-tRNA, specified by the next codon in the mRNA,
  3. A set of soluble cytosolic proteins called elongation factors (EFs) (EF-Tu, EF-Ts and EF-G)
  4. GTP.

 

Figure 5.9 Initiation of translation in prokaryotes

 

Elongation comprises three steps:

  1. In the first step of elongation, the next aminoacyl-tRNA is first bound to a complex of EF-Tu containing a molecule of GTP. The resulting aminoacyl-tRNA-EF-Tu-GTP complex is then bound to the A-site of the 70S initiation complex. The GTP is hydrolysed, an EF-Tu-GDP complex is released from the 70S ribosome and EF-Tu-GTP is regenerated. The guanine nucleotide exchange factor (GEF) EF-Ts mediates the regeneration of used form EF-Tu-GDP into the active form EF-Tu-GTP. First, EF-Ts displaces the GDP from EF-Tu, forming EF-Tu-EF-Ts. Then, GTP displaces EF-Ts reforming EF-Tu-GTP. This active complex binds aminoacyl-tRNA and the released EF-Ts can recycle. The hydrolysis of EF-Tu-GTP is relatively slow; it takes longer time for an incorrect aminoacyl-tRNA to dissociate from the A-site; therefore, ribosome checks the codon-anticodon interactions and most incorrect species are removed at this stage. Proof reading by the ribosome is made possible by the GTPase activity of Ef-Tu and thus makes an important contribution to the rate and fidelity of the overall biosynthetic process.
  2. In the second step, a new peptide bond is formed between the amino acids bound by their tRNAs to the A-site and P-site on the ribosome (Figure 5.10). This occurs by the transfer of the initiating formylmethionine group from its tRNA to the amino group of the amino acid now in the A-site. The α amino group of the amino acid in the A-site acts as a nucleophile, get attacks the carboxyl group of the amino acid in the P-site to form the peptide bond. This reaction produces a dipeptidyl-tRNAfMet in the A-site and now ‘uncharged’ (deacylated) tRNAfMet remains bound to the P-site. The activity responsible for the synthesis of peptide bond is called peptidyl transferase. Peptidyl transferase is a function of the large ribosomal subunit. The 23S rRNA has peptidyl transferase activity.
  3. The 3 step of elongation is called ‘translocation’ (Figure 5.11).The ribosome advances by three nucleotides along the mRNA towards the 3′-end. This movement of the ribosome shifts the dipeptidyl-tRNA from the A-site to P-site and the deacylated tRNA is released from the exit-site or E-site. The third codon of the mRNA will now be in the A-site and the second codon in the P-site. This shift of the ribosome along mRNA requires EF-G (also called translocase). The energy for the process is provided by the hydrolysis of GTP. The ribosome that switches between alternative and discrete co-formations results in the changes in rRNA base pairing, breaking many of its contact with the tRNA and allows the movement of the ribosome. EF-G is released following ribosome movement. Hydrolysis of GTP is needed to release EF-G.

 

Figure 5.10 Peptide bond formation

 

Figure 5.11 Elongation of the peptide chain

 

Termination

Elongation continues until the ribosome adds the last amino acid, completing the polypeptide coded by the mRNA. Termination is signalled by termination or stop codons in the mRNA (UAA, UAG and UGA), immediately following the last amino acid codon (Figure 5.12).

 

Figure 5.12 Termination of translation

 

Figure 5.13 Polysomes (a) An mRNA molecule is generally translated simultaneously by several ribosomes in clusters called polyribosomes (b) This micrograph shows a large polyribo-some in a prokaryotic cell (TEM)

 

In bacterial genes, UAA is the most commonly used termination codon. UGA is used more frequently than UAG. The termination codons are recognized by release factors, namely RF1 and RF2 (class 1 release factors) and RF3 (class 2 release factors). RF1 recognizes UAA and UAG. RF2 recognizes UGA and UAA. The factors act at the ribosomal A-site and require peptidyl-tRNA at the P-site. The class 1 release factors are assisted by class 2 release factors, which are not codon-specific. The class 2 factors are GTP-binding proteins. In E. coli, the role of class 2 factor is to release class 1 factor from the ribosome. The class 1 factors recognize the termination codons and activate the ribosome to hydrolyse the peptidyl-tRNA. The peptidyl-tRNA transfers the growing peptide chain to a water molecule rather than to another amino acid. At this point, RF1 and RF2 are released by class 2 RF3 followed by the dissociation of the 70S ribosome into 50S and 30S ribosomes.

Polyribosomes are the Active Structures of Protein Synthesis

Active protein-synthesizing units consist of an mRNA with several ribosomes attached to it. Such structures are polyribosomes or simply called polysomes (Figure 5.13). All protein synthesis occurs on polysomes. In the polysome, each ribosome is traversing the mRNA and independently translating it into polypeptide. The farther a ribosome has moved along the mRNA, the greater the length of its associated polypeptide product. In prokaryotes, as many as 10 ribosomes may be found in a polysome. Ultimately, as many as 300 ribosomes may translate an mRNA, so as many as 300 enzyme molecules may be produced from a single transcript. Eukaryotic polysomes typically contain fewer than 10 ribosomes.

PROTEIN SYNTHESIS IN EUKARYOTES

Eukaryotic mRNAs are characterized by two post-transcriptional modifications: the 5′-7-methyl-GTP cap and the poly(A) tail. The 7-methyl-GTP cap is essential for ribosomal binding of mRNAs in eukaryotes and also enhances the stability of these mRNAs by preventing their degradation by 5′-exonucleases (Figure 5.14). The poly(A) tail enhances both the stability and translational efficiency of eukaryotic mRNAs. The Shine-Dalgarno sequences found at the 5′-end of prokaryotic mRNAs are absent in eukaryotic mRNAs.

 

Figure 5.14 Capped and tailed eukaryotic mRNA

 

Initiation of Translation in Eukaryotes

The eukaryotic initiator tRNA is a unique tRNA functioning only in initiation. Like the prokaryotic initiator tRNA, the eukaryotic version carries only Met. However, unlike prokaryotic f-Met-tRNAfMet, the Met on this tRNA is not formylated. Hence, the eukaryotic initiator tRNA is usually designated tRNAiMet, with the ‘i’ indicating ‘initiation.’

Eukaryotic initiation can be divided into four fundamental steps.

  1. A ribosome must dissociate into its 40S and 60S subunits.
  2. A ternary complex termed the preinitiation complex is formed consisting of the initiator, GTP, eIF-2 and the 40S subunit.
  3. The mRNA is bound to the preinitiation complex.
  4. The 60S subunit associates with the preinitiation complex to form the 80S initiation complex.

The initiation factors eIF-1 and eIF-3 bind to the 40S ribosomal subunit favouring anti-association to the 60S subunit. The prevention of subunit re-association allows the preinitiation complex to form.

The first step in the formation of the preinitiation complex involves the binding of GTP to eIF-2 to form a binary complex. eIF-2 is composed of three subunits— α, β and γ. The binary complex then binds to the activated initiator tRNA; met-tRNAmet forming a ternary complex that then binds to the 40S subunit forming the 43S preinitiation complex. The preinitiation complex is stabilized by the earlier association of eIF-3 and eIF-1 to the 40S subunit (Table 5.2).

The cap structure of eukaryotic mRNAs is bound by specific eIFs prior to association with the preinitiation complex. Cap binding is accomplished by the initiation factor eIF-4F. This factor is actually a complex of three proteins—eIF-4E, A and G. The protein eIF-4E is a 24-kDa protein which physically recognizes and binds to the cap structure. eIF-4A is a 46-kDa protein which binds and hydrolyses ATP and exhibits RNA helicase activity. Unwinding of mRNA secondary structure is necessary to allow access of the ribosomal subunits. eIF-4G aids in binding of the mRNA to the 43 S preinitiation complex.

Once the mRNA is properly aligned onto the preinitiation complex and the initiator met-tRNAmet is bound to the initiator AUG codon (a process facilitated by eIF-1) the 60S subunit associates with the complex. The association of the 60S subunit requires the activity of eIF-5 which has first bound to the preinitiation complex. The energy needed to stimulate the formation of the 80S initiation complex comes from the hydrolysis of the GTP bound to eIF-2. The GDP-bound form of eIF-2 then binds to eIF-2B which stimulates the exchange of GTP for GDP on eIF-2. When GTP is exchanged, eIF-2B dissociates from eIF-2. This is termed as the eIF-2 cycle (see Figure 5.15). This cycle is absolutely required in order for eukaryotic translational initiation to occur. The GTP exchange reaction can be affected by phosphorylation of the α-subunit of eIF-2.

 

Table 5.2 Eukaryotic initiation factors and their functions

Initiation factor Activity
eIF-1 Repositioning of met-tRNA to facilitate mRNA binding
eIF-2 Ternary complex formation
eIF-2A AUG-dependent met-tRNAmeti binding to 40S ribosome
eIF-2B (also called GEF) GTP/GDP exchange during eIF-2 recycling
eIF-3, composed of 13 subunits Ribosome subunit anti-association by binding to 40S subunit; eIF-3e and eIF-3i subunits transform normal cells when overexpressed; eIF-3A (also called eIF3 p170) overexpression has been shown to be associated with several human cancers
Initiation factor complex often referred to as eIF-4F composed of three primary subunits: eIF-4E, eIF-4A and eIF-4G and at least two additional factors: PABP and Mnk1 (or Mnk2) mRNA binding to 40S subunit, ATPase-dependent RNA helicase activity, interaction between poly(A) tail and cap structure
PABP: poly(A)-binding protein Binds to the poly(A) tail of mRNAs and provides a link to eIF-4G
Mnk1 and Mnk2 eIF-4E kinases Phosphorylate eIF-4E increasing association with cap structure
eIF-4A ATPase-dependent RNA helicase
eIF-4E 5′-cap recognition; frequently found overexpressed in human cancers, inhibition of eIF4E is currently a target for anti-cancer therapies
4E-BP (also called PHAS) three known forms When de-phosphorylated, 4E-BP binds eIF-4E and represses its activity, phosphorylation of 4E-BP occurs in response to many growth stimuli leading to the release of eIF-4E and increased translational initiation
eIF-4G Acts as a scaffold for the assembly of eIF-4E and eIF-4A in the eIF-4F complex, interaction with PABP allows 5′-end and 3′-ends of mRNAs to interact
eIF-4B Stimulates helicase, binds simultaneously with eIF-4F
eIF-5 Release of eIF-2 and eIF-3, ribosome-dependent GTPase
eIF-6 Ribosome subunit anti-association

 

Figure 5.15 Eukaryotic translation initiation

 

The eIF-2 cycle involves the regeneration of GTP-bound eIF-2 following the hydrolysis of GTP during translational initiation. When the 40S preinitiation complex is engaged with the 60S ribosome to form the 80S initiation complex, the GTP bound to eIF-2 is hydrolysed providing energy for the process. In order for additional rounds of translational initiation to occur, the GDP bound to eIF-2 must be exchanged for GTP. This is the function of eIF-2B which is also called GEF.

At this stage, the initiator met-tRNAmet is bound to the mRNA within the ribosome P-site. The incoming charged tRNAs binds to the A-site.

Elongation

The process of elongation, like that of initiation, requires specific non-ribosomal proteins namely EFs in prokaryotes; moreover, in eukaryotes, these are eEFs. Elongation of polypeptides occurs in a cyclic manner such that at the end of one complete round of amino acid addition, the A-site will be empty and ready to accept the incoming aminoacyl-tRNA dictated by the next codon of the mRNA. The process is accompanied by the movement of the ribosome to the next codon in the mRNA. Each incoming aminoacyl-tRNA is brought to the ribosome by an eEF-1 α-GTP complex. After the correct tRNA is deposited into the A-site, the GTP is hydrolysed and the eEF-1α-GDP complex dissociates. The GDP must be exchanged for GTP for additional translocation events. This is carried out by eEF-1βγ similarly to the GTP exchange that occurs with eIF-2 catalysed by eIF-2B.

The peptide attached to the tRNA in the P-site is transferred to the amino group at the amino-acyl-tRNA in the A-site. This reaction is catalysed by peptidyl transferase. This process is termed transpeptidation. The elongated peptide now resides on a tRNA in the A-site. The A-site needs to be freed in order to accept the next aminoacyl-tRNA. The process of moving the peptidyl-tRNA from the A-site to the P-site is termed as translocation. Translocation is catalysed by eEF-2 coupled to GTP hydrolysis. In the process of translocation, the ribosome is moved along the mRNA such that the next codon of the mRNA resides under the A-site. Following translocation, eEF-2 is released from the ribosome. The cycle can now begin again.

The ability of eEF-2 to carry out translocation is regulated by the state of phosphorylation of the enzyme, when phosphorylated the enzyme is inhibited. Phosphorylation of eEF-2 is catalysed by the enzyme eEF2 kinase (eEF2K). Regulation of eEF2K activity is normally under the control of insulin and Ca2+ fluxes. The Ca2+-mediated effects are the result of calmodulin interaction with eEF2K. Activation of eEF2K in skeletal muscle by Ca2+ is important to reduce consumption of ATP in the process of protein synthesis during periods of exertion which will lead to release of intracellular Ca2+ stores. eEF2K itself is also regulated by phosphorylation and one of the kinases that phosphorylates the enzyme is regulated by mTOR In addition, the master metabolic regulatory kinase, AMP-activated protein kinase, will phosphorylate and activate eEF2K leading to inhibition of eEF-2 activity.

Termination

Translational termination requires specific protein factors identified as releasing factors, known as eRFs in eukaryotes. There are two RFs in E. coli and one in eukaryotes. The termination signals are the same in both prokaryotes and eukaryotes. There are three termination codons, which are UAG, UAA and UGA.

The eRF binds to the A-site of the ribosome in conjunction with GTP. The binding of eRF to the ribosome stimulates the peptidyl transferase activity to transfer the peptidyl group to water instead of an aminoacyl-tRNA. The resulting uncharged tRNA left in the P-site is expelled with concomitant hydrolysis of GTP. The inactive ribosome then releases its mRNA and the 80S complex dissociates into the 40S and 60S subunits, ready for another round of translation.

Regulation of Translation

The expression of most genes is controlled at the level of their transcription. Transcription factors (proteins) bind to promoters and enhancers turning on (or off) the genes they control.

However, gene expression can also be controlled at the level of translation.

By general RNA-degradation machinery

P-Bodies

The cytosol of eukaryotes contains protein complexes that compete with ribosomes for access to mRNAs. As these increase their activity, they sequester mRNAs in larger aggregates called ‘P-bodies’.

These protein complexes break down the mRNA by:

  • removing its ‘cap’,
  • removing its poly(A) tail and
  • degrading the remaining message (Degrading in the 5′ → 3′ direction).

What controls the dynamic balance between ribosomes and P-bodies for access to mRNAs remains to be learned. However, this mechanism provides for destruction of ‘bad’ mRNAs (e.g., those with premature STOP codons thus increasing the flexibility of gene expression in the cell.

Exosomes

These are hollow macromolecular complexes with two openings. They take in unfolded RNA molecules and degrade them in the 3′ → 5′ direction.

By MicroRNAs (miRNAs)

Here, small RNA molecules bind to a complementary portion in the 3′-UTR of the mRNA and prevent it from being translated by ribosomes and/or trigger its destruction. Both these activities take place in P-bodies.

By Riboswitches

The regulation of the level of certain metabolites is controlled by riboswitches. A riboswitch is a part of a molecule of mRNA with a specific binding site for the metabolite (or a close relative).

Examples:

  • If thiamine pyrophosphate (the active form of thiamine [vitamin B1]) is available in the culture medium of E. coli,
    • it binds to an mRNA whose protein product is an enzyme that is needed to synthesize thiamine from the ingredients in minimal medium.
    • binding induces an allosteric shift in the structure of the mRNA, so that it can no longer bind to a ribosome and thus cannot be translated into the enzyme.
    • E. coli no longer wastes resources on synthesizing a vitamin that is available preformed.

By gene-specific proteins

Translation of mRNA in humans is repressed by aminoacyl-tRNA synthetase in response to the inflammatory cytokine interferon-gamma [IFN-γ]. In presence of IFN-γ, the synthetase abandons its normal function (adding Glu and Pro to their respective tRNAs) and instead binds to the mRNA blocking its translation.

In some bacteria, a protein product may inhibit the further translation of its own mRNA (a kind of feedback inhibition). It does so by binding to a site which blocks the mRNA from further association with a ribosome.

POST-TRANSLATIONAL MODIFICATIONS

Most of the proteins that are translated from mRNA undergo chemical modifications before becoming functional in different body cells. The modifications collectively are known as post-translational modifications (Figure 5.16). The protein post-translational modifications (PTMs) play a crucial role in generating the heterogeneity in proteins and also help in utilizing identical proteins for different cellular functions in different cell types.

PTM increases the functional diversity of the proteome by the covalent addition of functional groups or proteins, proteolytic cleavage of regulatory subunits or degradation of entire proteins. These modifications include phosphorylation, glycosylation, ubiquitination, nitrosylation, methylation, acetylation, lipidation and proteolysis and influence almost all aspects of normal cell biology and pathogenesis. Therefore, identifying and understanding PTMs is critical in the study of cell biology and disease treatment and prevention.

Proteolytic cleavage

Following translation, most proteins undergo proteolytic cleavage. The simplest form of this is the removal of the initiation methionine. Many proteins are synthesized as inactive precursors that are activated under proper physiological conditions by limited proteolysis. Pancreatic enzymes and enzymes involved in clotting are examples of the enzymes that are activated by proteolytic cleavage. Inactive precursor proteins that are activated by the removal of polypeptides are termed as proproteins.

An example of a preproprotein is insulin. Since insulin is secreted from the pancreas, it has a prepeptide. Following the cleavage of the 24-amino acid signal peptide, the protein folds into proin-sulin. Proinsulin is further cleaved yielding active insulin which is composed of two peptide chains linked together through disulphide bonds.

Still other proteins (of the enzyme class) are synthesized as inactive precursors called zymogens. Zymogens are activated by proteolytic cleavage such as the proteins of the blood clotting cascade.

Acylation

Many proteins are modified at their N-termini following synthesis. In most cases, the initiator methionine is hydrolysed and an acetyl group is added to the new N-terminal amino acid. Acetyl-CoA is the acetyl donor for these reactions.

Myristoylation

N-myristoylation is also an acylation process found to be specific to N-terminal amino acid. Some proteins have the 14-carbon myristoyl group added to their N-termini. The donor for this modification is myristoyl-CoA. The latter modification allows the association of the modified protein with membranes.

 

Figure 5.16 Post-translational modifications

 

The catalytic subunit of cyclicAMP-dependent protein kinase (PKA) is myristoylated.The cytosolic enzyme A-myristoyltransferase (NMT) catalyses myristoylation.Myristoylation plays a vital role in the secondary cellular signalling, in the infectivity of retroviruses and oncogenesis in eukaryotes.

Methylation

Post-translational methylation of proteins occurs on nitrogen and oxygen. The activated methyl donor is S-adenosylmethionine (SAM). The most common methylations are on the ε-amine of lysine residues. Additional nitrogen methylations are found on the imidazole ring of histidine, the guanidino moiety of arginine and the R-group amides of glutamate and aspartate. Methylation of the oxygen of the R-group carboxylates glutamate and aspartate and forms methyl esters. Proteins can also be methylated on the thiol R-group of cysteine.

 

 

Methylation in the proteins increases the hydrophobicity of the protein. Methylation on carboxylate side chains cover up negative charge and adds hydrophobicity.

For example, N-methylation of lysines does not alter the cationic charge but does increase hydrophobicity.

Phosphorylation

Post-translational phosphorylation is one of the most common protein modifications that occur in animal cells. Phosphorylations regulate the biological activity of a protein and as such are transient. In other words, a phosphate (or more than one in many cases) is added and later removed.

For example, proteins such as glycogen synthase and glycogen phosphorylase in hepatocytes are phosphorylated in response to glucagon release from the pancreas. Phosphorylation of synthase inhib its its activity, whereas the activity of phosphorylase is increased. These two events lead to increased hepatic glucose delivery to the blood.

The enzymes that phosphorylate proteins are termed as kinases and those that remove phosphates are termed as phosphatases. Protein kinases catalyse reactions of the following type:

ATP + protein ↔ phosphoprotein + ADP

In animal cells, serine, threonine and tyrosine are the amino acids that subject to phosphorylation. The largest group of kinases are those that phosphorylate either serines or threonines and as such are termed as serine/threonine kinases. The ratio of phosphorylation of the three different amino acids is approximately 1,000/100/1 for serine/threonine/tyrosine.

Although the level of tyrosine phosphorylation is minor, the importance of phosphorylation of this amino acid is profound.

Acetylation

The acetylation and deacetylation take place on lysine residues in the A-terminal tail in histone acetylation and deacetylation. These reactions take place in the presence of the enzymes histone acetyltransferase (HAT) or histone deacetylase (HDAC).

 

Formylation

Formylation is one of the post-translational modifications of the protein, in which a protein is modified by the attachment of formyl group. The most commonly studied mechanism is the N6-formylation of lysine. Histone and other nuclear proteins are modified by formylation. The post-translational modification of histone and other chromatin proteins regulates gene expression.

Sulphation

Sulphate modification of proteins occurs at tyrosine residues such as in fibrinogen and in some secreted proteins (e.g., gastrin). The universal sulphate donor is 3′-phosphoadenosyl-5′-phosphosulphate (PAPS).

 

Prenylation

Prenylation refers to the addition of the 15-carbon farnesyl group or the 20-carbon geranyl group to acceptor proteins, both of which are isoprenoid compounds derived from the cholesterol bioszynthetic pathway. The isoprenoid groups are attached to cysteine residues at the carboxy terminus of proteins in a thioether linkage (C-S-C). A common consensus sequence at the C-terminus of prenylated proteins has been identified and is composed of CAAX, where C is cysteine, A is any aliphatic amino acid (except alanine) and X is the C-terminal amino acid. In order for the prenylation reaction to occur, the three C-terminal amino acids (AAX) are first removed. Following attachment of the prenyl group, the carboxylate of the cysteine is methylated in a reaction utilizing SAM as the methyl donor.

 

 

Many proteins are modified at their C-terminus by prenylation near a cysteine residue in the consensus CAAX. Following the prenylation reaction, the protein is cleaved at the peptide bond of the cysteine and the carboxylate residue is methylated by a prenylated protein methyltransferase. One such protein that undergoes this type of modification is the proto-oncogene RAS.

Some of the most important proteins whose functions depend upon prenylation are those that modulate immune responses. These include proteins involved in leukocyte motility, activation and proliferation and endothelial cell immune functions. These immune modulatory roles of many prenylated proteins are the basis for a portion of the anti-inflammatory actions of the statin class of cholesterol synthesis-inhibiting drugs due to a reduction in the synthesis of farnesyl pyrophosphate and geranyl pyrophosphate and thus reduced the extent of inflammatory events. Other important examples of prenylated proteins include the oncogenic GTP-binding and -hydrolysing protein RAS and the γ-subunit of the visual protein transducin, both of which are farnesylated. In addition, numerous GTP-binding and -hydrolysing proteins (termed as G-proteins) of signal transduction cascades have γ-subunits modified by geranylgeranylation.

  • In eukaryotes, the processes of transcription and translation are separated both spatially and in time. Transcription of DNA into mRNA occurs in the nucleus. Translation of mRNA into polypeptides occurs on polysomes in the cytoplasm.
  • In bacteria (which have no nucleus), both these steps of gene expression occur simultaneously: the nascent mRNA molecule begins to be translated even before its transcription from DNA is complete.
  • The genetic code is a triplet code, with codons of three bases coding for specific amino acids. Each triplet codon speciies only one amino acid, but an individual amino acid may be speciied by more than one codon.
  • A start codon, AUG, sets the reading frame and signals the start of translation of the genetic code. Translation continues in a non-overlapping fashion until a stop codon (UAA, UAG or UGA) is encountered in frame. The nucleotides between the start and stop codons comprise an ORF.
  • Prokaryotic mRNAs are monocistronic that is they code for only one protein, whereas eukaryotic mRNAs are polycistronic that is they code for many proteins.
  • Protein synthesis requires the translation of nucleotide sequences into amino acid sequences. AminoacyltRNA synthetases read the genetic code.
  • The codons of mRNA recognize the anticodons of tRNAs rather than the amino acids attached to the tRNAs. A codon on mRNA forms base pairs with the anticodon of the tRNA. Some tRNAs are recognized by more than one codon, because pairing of the third base of a codon is less crucial than that of the other two (the wobble mechanism).
  • The basic plan of protein synthesis in eukaryotes is similar to that of prokaryotes, but there are some significant differences between them. Eukaryotic ribosomes (80S) consist of a 40S small subunit and a 60S large subunit. The initiating amino acid is again methionine, but it is not formylated. The initiation of protein synthesis is more complex in eukaryotes than in prokaryotes.
  1. Define codons. Explain the signiicance of Nirenberg and Khorana experiment in deciphering the genetic code.

  2. What do you mean by non overlapping of genetic codes.

  3. Enumerate the characteristic features of genetic code.

  4. Describe wobble hypothesis with suitable examples.

  5. Explain the structure of ribosomes supported with neat illustrations.

  6. Discuss in detail about the process of translation in eukaryotes.

  7. Differentiate betweent the translation process taking place in prokaryotes and eukaryotes.

  8. Enlist atleast 5 eukaryotic initiation factors along with their functions.

  9. What is meant by the term post translational modiications?

  10. Explain the process of methylation and sulfation with respect to post translational modiications with suitable examples.

MULTIPLE-CHOICE QUESTIONS
  1. r Proteins are

    1. RNA proteins
    2. Ribozomal protein
    3. restriction proteins
    4. none of the given options
  2. The incoming amino acyl t RNA binds to

    1. A site
    2. P site
    3. E site
    4. all of the given options
  3. The Shine-Dalgarno sequence helps in——— of translation

    1. initiation
    2. elongation
    3. termination
    4. all of the given options
  4. The Ochre codon is

    1. UAG
    2. UAA
    3. UGA
    4. AUG
  5. The initiation codon is

    1. AUG
    2. UAG
    3. UGA
    4. AGU
  6. The peptidyl transferase activity resides in

    1. 18 S rRNA
    2. 23S rRNA
    3. 16S r RNA
    4. none of the given options
  7. The component of 43S pre initiation complex in eukaryotic translation are

    1. e IF2
    2. e IF3
    3. Met- tRNA
    4. all of the given options
  8. The r RNA of the 60 S ribosomal subunit are

    1. 28S rRNA
    2. 5.8S r RNA
    3. 5S rRNA
    4. all of the given options
  9. ——— is a component of the 50S ribosomal subunit

    1. 28S rRNA
    2. 5.8S r RNA
    3. 23S rRNA
    4. 16S r RNA
  10. ——— is the cofactor used in translation

    1. Vit B12
    2. TPP
    3. THF
    4. formyl THF

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Fox, T. D. 1987. ‘Natural Variation in the Genetic Code’, Annual Review of Genetics, 21:67–91.

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Lipmann, Fritz, Hülsmann, W. C., Hartmann, G., Boman, Hans G. and Acs, George. 1959. ‘Amino Acid Activation and Protein Synthesis’, Journal of Cellular and Comparative Physiology, Supplement: Symposium on Enzyme Reaction Mechanisms, 54(S1): 75–88.

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