• BIO 375: Genetics and Molecular Biology
  • 1 - Chromosome Structure
  • 2 - Chromosome Compaction
  • 3 - Chromosome Variation
  • 4 - Gender Identity vs Biological Sex
  • 5 - Nucleic Acid Structure
  • 6 - DNA Replication
  • 7 - Mutations and DNA Repair
  • 8 - Polymerase Chain Reaction (PCR)
  • 9 - Transcription
  • 10 - RNA Modifications
  • 11 - Translation
  • 12 - Gene Cloning
  • 13 - The lac Operon
  • 14 - Gene Regulation in Eukaryotes
  • 15 - Epigenetics
  • 16 - Genome Editing
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  • Translations
  • 11 - Translation

    A. Introduction to Translation

    Translation is the cellular process that converts the language of nucleic acids contained within the mRNA molecule (A, U, G, C) into the language of amino acids in a synthesized protein (methionine, alanine, histidine, etc.). This translation process relies on a genetic code that converts nucleic acid sequence into amino acid sequence. Note that the genetic code that is translated into protein functions within the mRNA molecule, not in the DNA.

    The mRNA molecule is read by the ribosome during translation as a group of three nucleotides (triplet code). Each group of three nucleotides within the mRNA sequence is called a codon. In addition to the codons, the mRNA contains several sequence features that play a role in translation (figure 11.1). These sequence features are listed from 5’ to 3’ along the mRNA molecule, as follows:

    9.1_Features_of_Prokaryotic_and_Eukaryotic_mRNA.jpg
    Figure 11.1 - Prokaryotic and eukaryotic mRNA features. --- Image created by SL

    Key Questions

    • Identify one important sequence feature found in the 5’-UTR of bacterial mRNAs.
    • Identify two important sequence features found within the 5’-UTR of eukaryotic mRNAs.
    • What amino acid is encoded by 5’-AUG-3’ in bacteria?
    • What amino acid is encoded by 5’-AUG-3’ in eukaryotes?
    • What is the function of the coding region?
    • What is the function of the stop codon?
    • Does the stop codon encode an amino acid?
    • What is the function of the 3’-UTR?

    The Genetic Code

    There are 20 different types of amino acids typically incorporated in proteins; however, there are 64 possible combinations of four nucleotides (A, U, G, and C) in a triplet codon RNA sequence. As a result, there are more codons than amino acid possibilities (see figure 11.2). Thus, the genetic code is degenerate, meaning that more than one codon can encode a particular amino acid type.  For example, the amino acid valine (val) is encoded by four codons (5’-GUU-3’, 5’-GUC-3’, 5’-GUA-3’, and 5’-GUG-3’) that differ only in the 3’-most base (wobble base).  These four valine codons are called synonymous codons.

    The genetic code is also unambiguous, meaning that a particular codon sequence only encodes one type of amino acid. For example, the codon 5’-AAA-3’ always encodes the amino acid lysine (lys). Further, the genetic code is commaless, meaning that codons are read by the ribosome consecutively one after another as triplets, with no spacer nucleotides between the codons. The codons are also nonoverlapping, meaning each nucleotide in the coding region of the mRNA is a member of only one codon. Finally, the same genetic code is used in all organisms (in other words, the code is universal).

    9.2_The_Genetic_Code.jpg
    Figure 11.2 The genetic code. This representation of the genetic code is read from the center of the circle (the 5’-most base in the codon) to the periphery of the circle (the 3’- most base in the codon). Aminoacids Table was created by Mouagip and is used under CC0

    Key Questions

    • How do the words degenerate, unambiguous, commaless, nonoverlapping, and universal apply to the codons in a mRNA sequence?

    Directionality of Polypeptide Chains

    The polypeptide chains synthesized during translation have directionality (polarity); however, since the language of proteins is different than the language of nucleic acids, the labels 5' and 3' do not apply to the directionality of polypeptide chains.  Instead, the amino acid encoded by the start codon (closer to the 5’ end of the mRNA) contains a free amino (NH3+) chemical group and thus is said to be the amino or N-terminus of the polypeptide chain. As the polypeptide chain is synthesized, a peptide bond is formed between the carboxyl group (COO-) of the growing amino acid chain and the amino group of the incoming amino acid (see figure 11.3).  Peptide bond formation involves a condensation reaction that releases water as a product. The final amino acid added to a polypeptide contains a free carboxyl chemical group and is called the carboxyl terminal or C-terminal end of the polypeptide chain. The C-terminal end of the polypeptide corresponds to the codon immediately before the stop codon (closer to the 3’ end of the mRNA).

    9.3_Peptide_Bond_Formation.jpg
    Figure 11.3 Peptide bond formation --- Image Peptide Bond Formation was created by Yassine Mrabet and used under CC0

    Key Questions

    • How do the N- and C-terminal ends of a protein compare to the 5' and 3' ends of an mRNA molecule?

    tRNAs are Adaptor Molecules in Translation

    Transfer RNA molecules (tRNAs) act as adaptor molecules in translation. tRNAs function to:

    There are many different types of tRNA molecules in a cell. Each type is encoded by a different gene in the genome and has a unique nucleotide sequence. tRNA molecules are named according to the amino acid they carry.  For example, tRNAval carries the amino acid valine, while tRNAphe carries the amino acid phenylalanine.  tRNA molecules are example noncoding RNAs (ncRNAs).

    Key Questions

    • What are the two functions of a tRNA molecule?

    Features of tRNAs

    All tRNA molecules have similar structural features (figure 11.4):

    9.4_tRNA_Structure.jpg
    Figure 11.4 tRNA Structure.  tRNA molecules have three stem loop structures and an acceptor stem. --- Image used from OpenStax (access for free at https://openstax.org/books/biology-2e/pages/1-introduction)

    Key Questions

    • Where is the anticodon in a tRNA molecule?
    • Where is the amino acid attached to a tRNA molecule?

    Charging tRNAs

    The process of attaching an amino acid to the 3' end of a tRNA molecule is called charging. Charging tRNAs involves groups of enzymes that are collectively called aminoacyl-tRNA synthetases.  Aminoacyl-tRNA synthetases have the following features:

    The mechanism used by an aminoacyl-tRNA synthetase to charge a tRNA molecule has the following steps (see figure 11.5):

    1. The aminoacyl-tRNA synthetase binds to its preferred amino acid type and ATP.
    2. The ATP molecule is cleaved, PPi (pyrophosphate) is released, and the remaining AMP is covalently linked to the amino acid.  When AMP is linked to the amino acid, the aminoacyl-tRNA synthetase changes its conformation (shape) to produce the active form of the enzyme.  This new enzyme conformation allows the aminoacyl-tRNA synthetase to bind to a tRNA molecule.
    3. The aminoacyl-tRNA synthetase binds to a tRNA molecule that contains anticodon sequence specific for the amino acid carried by the aminoacyl-tRNA synthetase. If the anticodon on the incoming tRNA is incorrect, the tRNA is released from the aminoacyl-tRNA synthetase and a new tRNA binds to the enzyme.
    4. The aminoacyl-tRNA synthetase attaches the amino acid to the 3’ end of the tRNA.
    5. AMP is released.
    6. The charged tRNA (i.e., tRNA covalently linked to the correct amino acid) is released from the aminoacyl-tRNA synthetase.
      EDI_11.5_Charging_a_tRNA_Molecule-01_1.jpg
      Figure 11.5 Charging a tRNA Molecule --- Image by Dr. Frank Boumphrey used under license CC BY-SA 3.0

    Key Questions

    • Which molecule provides the energy for the tRNA charging reaction?
    • Explain the major events that occur during the tRNA charging reaction.

    Wobble

    Most synonymous codons (codons that encode the same amino acid) have identical bases at the first two nucleotide positions (the 5’-most base and the middle base of the codon). These first two bases obey the AU/GC base pairing rules when forming hydrogen bonds with the tRNA anticodon. Degeneracy in the genetic code typically occurs at the 3'-most base within the codon—the 3’-most base in the codon does not have to form conventional base pairing interactions with the 5’-most base of the anticodon, leading to “wobble.” The rules that govern codon-anticodon at this wobble position interactions are called the wobble rules (see Table 11.1).  For example, a U base in the wobble position of the codon (3'-most base) can form hydrogen bonds with A, G, or I in the wobble position of the anticodon (5'-most base).  Similarly, a U in the wobble position of the anticodon (5'-most base) can form hydrogen bonds with either A or G in the wobble position of the codon (3'-most base).

    9.1_Table_Wobble_Rules.jpg

    Table 11.1 Wobble Rules Table


    A group of tRNA molecules, with slightly different anticodon sequences, which recognize the same mRNA codon sequence are called isoacceptor tRNAs. For example, suppose we have the codon 5’-UUU-3’ in the mRNA. tRNA molecules containing either 3’-AAA-5’, 3’-AAG-5’, or 3’-AAI-5’ anticodons can recognize this mRNA codon, according to the wobble rules (see Table 11.1). Note that these isoacceptor tRNAs are charged by the same aminoacyl-tRNA synthetase and therefore, bear the same amino acid (phenylalanine). Alternatively, a tRNA with the 3’-GGU-5’ anticodon can recognize two codons: 5’-CCA-3’and 5’-CCG-3’ according to the wobble rules.  Both codons encode proline.

    Why is it advantageous to use this wobble phenomenon? Wobble gives the cell tremendous flexibility in codon:anticodon interactions.  A single mRNA codon can be recognized by more than one tRNA anticodon, and a single tRNA anticodon can bind to more than one mRNA codon.  This flexibility allows translation to occur at a reasonable rate and allows a cell to save energy in the synthesis of tRNA molecules. Instead of assembling 61 different types of tRNA molecules (one type for each possible sense codon, minus the three stop codons), a cell can get away with synthesizing only 30-40 types of tRNA molecules, with some tRNAs recognizing multiple codon sequences.

    Key Questions

    • What is meant by wobble?
    • What are isoacceptor tRNAs?
    • What is the advantage of wobble?

    Prokaryotic Ribosomes

    The multi-subunit ribosome is the central figure in the translation process. The ribosome binds to the mRNA, serves as a site for mRNA codon:tRNA anticodon recognition, breaks the covalent bond between the 3’ end of the tRNA and the amino acid, and synthesizes peptide bonds between amino acids. 

    A single bacterial cell is thought to contain approximately 10,000 ribosomes; these bacterial ribosomes are called 70S ribosomes. Note that the “S” designation of ribosomes correlates roughly with the overall three-dimensional shape of the ribosome component; the larger the molecule, the larger the “S” value.  The 70S ribosome consists of the following subunits (see figure 11.6):

    EDI_11.6_Prokaryotic_Ribosomes-01_1.jpg
    Figure 11.6 Prokaryotic Ribosomes --- Prokaryotic cell (Left) used from OpenStax (access for free at https://openstax.org/books/biology-2e/pages/1-introduction).Image created by SL

    Eukaryotic Ribosomes

    Eukaryotic cells have cytosolic ribosomes called 80S ribosomes. Mitochondrial and chloroplast ribosomes resemble prokaryotic 70S ribosomes.  The 80S ribosomes in the cytosol consist of the following subunits (see figure 11.7):

    EDI_11.7_Eukaryotic_ribosomes-01_1.jpg
    Figure 11.7 Eukaryotic ribosomes --- Image created by SL

    Key Questions

    • Compare and contrast the structural features of prokaryotic vs. eukaryotic ribosomes.
    • What is the name of the ribozyme within the 70S ribosome?
    • What is the name of the ribozyme within the 80S ribosome?

    Overview of Translation

    Translation in prokaryotes and eukaryotes occurs in three stages (see figure 11.8):

    1. During initiation, the large and small ribosomal subunits assemble near the mRNA start codon with an initiator tRNA molecule that has an anticodon sequence specific for the start codon sequence. Once all translation components have assembled correctly, the initiator tRNA is located at the P site (see below) within the ribosome.
    2. During elongation, the ribosome translocates (moves) along the mRNA in the 5’ to 3’ direction, reading triplet codons within the mRNA, converting the codon sequences into a chain of amino acids. During elongation, three tRNA binding sites within the ribosome are used. These tRNA binding sites are the:
      • Aminoacyl site (A site). Charged tRNAs that enter the ribosome at the A site.
      • Peptidyl site (P site). During a translation elongation cycle (see below), the polypeptide chain attached to the tRNA molecule in the P site is transferred to the tRNA in the A site as peptide bonds are formed.
      • Exit site (E site). The E site allows uncharged tRNA molecules to exit the ribosome.
    3. When the ribosome reaches a stop codon, translation terminates. The mRNA and the polypeptide chain are released from the ribosome, and the large and small subunits of the ribosome dissociate from each other.  The ribosome subunits and the mRNA can be recycled to synthesize another copy of the protein.
    EDI_11.8_Overview_of_Translation-01_1.jpg
    Figure 11.8 Overview of Translation --- image used from OpenStax (access for free at https://openstax.org/books/biology-2e/pages/1-introduction), modified by SL

    Key Questions

    • What major events are occurring during the initiation, elongation, and termination stages of translation?
    • What are the functions of the A, P, and E sites?

    Shine-Dalgarno Sequence

    The 5’-untranslated region (5’-UTR) of prokaryotic mRNAs plays a critical role in translation, as the 5’-UTR contains the ribosome-binding site. Specifically, the 5’-UTR contains a recognition sequence (5’-AGGAGGU-3’) called the Shine-Dalgarno sequence that forms hydrogen bonds with a complementary sequence within the 16S rRNA of the small ribosomal subunit (30S) (see figure 11.9). Hydrogen bond formation between the Shine-Dalgarno sequence and the 16S rRNA promotes ribosome assembly. Further, the Shine-Dalgarno sequence positions the P site of the ribosome properly at the start codon to initiate polypeptide synthesis.

    EDI_11.9_the_Shine-Dalgarno_Sequence-01_1.jpg
    Figure 11.9 The Shine-Dalgarno Sequence --- image created by Alejandro Porto and modified by SL. Used under license CC BY-SA 3.0

    Key Questions

    • What is the function of the Shine-Dalgarno sequence?

    Translation Initiation in Bacteria

    Translation initiation in the bacterium E. coli includes the following steps (see figure 11.10):

    1. The mRNA binds to the small ribosomal subunit (30S) via the Shine-Dalgarno sequence. An initiation factor protein called IF3 promotes the formation of hydrogen bonds between the 16S rRNA (ribosome) and the Shine-Dalgarno sequence (mRNA).
    2. The initiator tRNA (tRNAfmet) recognizes the start codon within the P site of the ribosome. The initiator tRNA anticodon forms hydrogen bonds with the mRNA start codon in the P site. In bacteria, this initiator tRNA is covalently attached to a modified form of methionine called N-formylmethionine (fmet). Thus, the N-terminal amino acid in all newly synthesized prokaryotic proteins is fmet. Binding of the tRNAfmet to the start codon requires the initiation factor protein IF2.  IF2 cleaves GTP to load the tRNAfmet into the ribosome P site. The complex of the 30S subunit, the mRNA, IF3, and IF2 is called the initiation complex.
    3. The 50S subunit of the ribosome is added to the initiation complex. The addition of the 50S ribosome subunit requires the release of IF2 and IF3.
    9.10_Translation_Initiation_in_Bacteria.jpg
    Figure 11.10 Translation initiation in bacteria --- Image created by JET

    Key Questions

    • How do IF2 and IF3 function in translation initiation in bacteria?
    • What molecule provides the energy for translation initiation in bacteria?

    Translation Initiation in Eukaryotes

    Translation initiation is more complex in eukaryotes than in prokaryotes. Key differences between eukaryotic and prokaryotic translation initiation include (see figure 11.11):

    The process of translation initiation in eukaryotes is as follows:

    1. The eIF2 protein binds to tRNAmet and guides it to the 40S ribosomal subunit. eIF2 cleaves GTP to deliver tRNAmet to the 40S ribosomal subunit.
    2. Assembly of a multi-protein initiation complex on the 7-methylguanosine (7-mG) cap at the 5’ end of the mRNA. This initiation complex includes:
      • the 40S ribosome subunit
      • A complex composed of eIF2 and tRNAmet
      • An eIF4 protein complex
      • Cap-binding protein 1 (CBP1). CBP1 is the protein responsible for recognizing the 7-mG structure on eukaryotic mature mRNAs.
    3. Identification of the start codon. The 40S ribosomal subunit and associated proteins factors move from the 7-mG cap 5’ to 3’ along the mRNA looking for a start codon. This scanning process requires the cleavage of ATP. Not all possible start codons (5’-AUG-3’) are chosen to initiate translation. The 5’-AUG-3’ that is chosen is within the Kozak sequence: 5’-GCC (A or G)CCAUGG-3’. When the tRNAmet forms hydrogen bonds with the start codon, tRNAmet is in the P site of the ribosome.
    4. Addition of the 60S ribosomal subunit to form the active 80S ribosome.

    9.11_Eukaryotic_Translation_Initiation.jpg


    Figure 9.11 - Translation initiation in eukaryotes.

    Key Questions

    • How do eIF2 and CBP1 function in translation initiation in eukaryotes?
    • What is the function of the Kozak sequence?
    • Which two nucleotides provide the energy for translation initiation in eukaryotes?

    Translation Elongation

    Translation elongation in bacteria involves a series of cycles, one cycle per sense codon in the mRNA. At the beginning of each cycle, the tRNA molecule located within the P site of the ribosome is either attached to single amino acid (beginning of elongation cycle one) or a chain of amino acids (later elongation cycles; see figure 11.12). The A and E sites of the ribosome are empty. Each elongation cycle then proceeds as follows:

    1. A charged tRNA is delivered to the ribosome A site. The prokaryotic elongation factor protein EF-Tu is responsible for loading a charged tRNA into the A site of the ribosome. This loading of a charged tRNA into the A site requires the cleavage of GTP.
    2. The codon and anticodon hydrogen bonds are checked. Of course, the anticodon within the newly delivered tRNA must form complementary hydrogen bonds with the mRNA codon according to the wobble rules. An incorrect tRNA bound to the A site is recognized by the 16S rRNA. When an incorrect anticodon is encountered, polypeptide synthesis is halted until the mismatched tRNA is released from the ribosome. This editing function of the 16S rRNA molecule allows for high fidelity in protein synthesis; it is estimated that only one mistake is made per 10,000 incorporated amino acids, or about one time in every 20 proteins synthesized by the ribosome.
    3. The formation of a peptide bond. The amino acid or amino acid chain bound to the tRNA in the P site is transferred to the tRNA in the A site via the formation of a new peptide bond. This enzyme reaction is catalyzed by the 23S rRNA component of the 50S ribosomeal subunit; the 23S rRNA is an example of a ribozyme (RNA enzyme). The 23S rRNA ribozyme is also called peptidyl transferase.
    4. Ribosome translocation. The ribosome translocates (moves) in the 5’ to 3’ direction one codon along the mRNA. The tRNA (with the attached polypeptide chain) that was in the A site moves to the P site. The uncharged tRNA that was in the P site moves to the E site and exits the ribosome. A bacterial elongation factor protein called EF-G cleaves GTP to translocate the ribosome to the next sense codon in the mRNA.
    5. Steps 14 are repeated for each sense codon in the mRNA. The rate of protein synthesis is 15–18 cycles (i.e., 15-18 amino acids) per second in prokaryotes.

    Translation elongation works similarly in eukaryotes; however, below are some minor differences to keep in mind for eukaryotic translation:

    EDI_11.12_Translation_elongation_in_bacteria-01_1.jpg
    Figure 11.12 A translation elongation cycle in bacteria -- The beginning of the translation cycle is shown at the top of the image.  Image used from OpenStax (access for free at https://openstax.org/books/biology-2e/pages/1-introduction), modified by SL

    Key Questions

    • Describe the events involved in one translation elongation cycle.
    • Explain when GTP is used during the elongation cycle.
    • What is the eukaryotic equivalent of 23S rRNA, EF-Tu, and EF-G?

    Translation Termination

    Translation termination in bacteria occurs as follows (see figure 11.13):

    1. As the ribosome approaches the 3’ end of the mRNA, a stop codon (5’-UGA-3’, 5’-UAG-3’, or 5’-UAA-3’) moves into the A site of the ribosome.
    2. The stop codon is recognized by a release factor protein. The release factor protein mimics the three-dimensional structures of a tRNA molecule. In bacteria, the release factor 1 (RF1) protein recognizes the stop codons 5’-UAA-3’ and 5’-UAG-3’. The release factor 2 (RF2) protein recognizes 5’-UAA-3’ and 5’-UGA-3’.
    3. The release factor protein cleaves the covalent bond between the tRNA and the polypeptide chain in the ribosome P site. As a result, the tRNA and the polypeptide chain are released from the ribosome. This step requires the release factor protein to cleave GTP.
    4. The ribosomal subunits, mRNA, and release factor protein dissociate, terminating translation.  The ribosome subunits and the mRNA can be recycled to begin translation again.

    Translation termination works essentially the same way in eukaryotes. One minor diference is the use of a single eukaryotic release factor (eRF) protein that recognizes all three possible stop codons. eRF cleaves GTP to terminate translation in eukaryotes.

    EDI_11.13_Translation_termination-01_1.jpg
    Figure 11.13 Translation termination  --- Image used from OpenStax (access for free at https://openstax.org/books/biology-2e/pages/1-introduction), modified by SL

    Key Questions

    • What is the difference between RF1 and RF2?
    • What molecule provides the energy to terminate translation?
    • Are some of the molecules involved in translation recycled? If so, which ones?

    Polysomes and Coupled Transcription and Translation

    In the electron microscope, multiple ribosomes (polyribosomes or polysomes) are often observed attached to a single mRNA transcript (see figure 11.14). Polysomes have been observed attached to both prokaryotic mRNA and eukaryotic mature mRNA transcripts.

    Since prokaryotic cells lack nuclei, transcription and translation are coupled, meaning that translation can begin before transcription is completed. In eukaryotes, transcription and translation are uncoupled. Transcription and RNA modifications occur within the nucleus; translation occurs later, in the cytoplasm.

    9.14_Polyribosomes.jpg
    Figure 11.14 Polyribosomes and coupled transcription/translation in bacteria --- Image used from OpenStax (access for free at https://openstax.org/books/biology-2e/pages/1-introduction)

    Key Questions

    • Why is it advantageous to have multiple ribosomes working simultaneously?
    • Why is prokaryotic transcription and translation coupled?
    • Why is eukaryotic transcription and translation uncoupled?

    Review Questions

    Fill in the blanks:

    1. The ______________ portion of a eukaryotic mature mRNA contains the polyadenylation signal sequences.
    2. The genetic code is said to be __________________, which means that each codon only specifies one type of amino acid. (For example, 5’-UUU-3’ always encodes phenylalanine)
    3. The cloverleaf structure of the tRNA is such that the ____________________________ is a single-stranded loop that forms hydrogen bonds with the mRNA codon, and the ___________________________ is the single-stranded region where an amino acid is attached via a covalent linkage.
    4. ____________________________ is an enzyme that links the amino acid to a tRNA molecule.
    5. The 30S and 50S ribosomal subunits in a prokaryotic cell combine to form a final size of _________ while in eukaryotes the _________ and __________ ribosomal subunits combine to form a final size of ______________.
    6. The initiator tRNA binds to the __________ site of the ribosome, whereas the remaining charged tRNAs bind to the ___________ site of the ribosome.
    7. An E. coli protein called _______________ delivers charged tRNAs to the ribosome during translation elongation.
    8. The ribosome moves along the mRNA in the _______to _______ direction.
    9. _______________ is a eukaryotic translation factor protein that delivers charged tRNAs to the ribosome during elongation.
    10. ___________ is a eukaryotic translation factor that helps the ribosome move one codon in the 3’ direction along the mRNA.
    11. The _________________ protein in bacteria mimics the structure of a tRNA and recognizes 5’-UGA-3’ in the A site of the ribosome.
    12. An E. coli protein called __________ delivers tRNAfmet to the ribosome during translation.

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