Lesson 17. Genetic code and protein synthesis

Lesson 17. Genetic code and protein synthesis

Qestions: What are the building blocks of nucleic acids? What is the difference between DAN and RNA? Which cell component is responsible for synthesis of proteins?

Task 1. Read the text, listen to your instructure explanations and make a scheme of genetic information flow inside the cell.

Genes provide the instructions for making specific proteins. There are only four nucleotide bases to specify 20 amino acids. How many nucleotides, then, correspond to an amino acid? Triplets of nucleotide bases are the smallest units of uniform length that can code for all the amino acids. If each arrangement of three consecutive nucleotide bases specifies an amino acid, there can be 64 (that is, 4³) possible code words—more than enough to specify all the amino acids. Experiments have verified that the flow of information from gene to protein is based on a triplet code: The genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words. The series of words in a gene is transcribed into a complementary series of nonoverlapping, three-nucleotide words in messenger-RNA (mRNA), which is then translated into a chain of amino acids. The mRNA nucleotide triplets are called codons, and they are customarily written in the 5’ -> 3’ direction.

The flow of genetic information inside the cell

Task 2. Read the text, listen to your instructor’s explanation and make a scheme of transcription. Mark the main three stages and provide their short description.

Transcription is the synthesis of RNA using information in the DNA. Transcription occurs in the cell nucleus, where the DNA is held. During transcription, the gene determines the sequence of nucleotide bases along the length of the RNA molecule that is being synthesized. Messenger RNA, the carrier of information from DNA to the cell’s protein-synthesizing machinery, is transcribed from the template strand of a gene. For each gene, only one of the two DNA strands is transcribed. This strand is called the template strand because it provides the pattern, or template, for the sequence of nucleotides in an RNA transcript. For any given gene, the same strand is used as the template every time the gene is transcribed. For other genes on the same DNA molecule, however, the opposite strand may be the one that always functions as the template.

Transcription can be divided into three stages: initiation, elongation, and termination. At the stage of initiation, an enzyme called an RNA polymerase binds to a specific sequence of nucleotides along DNA called promoter. This enzymes pairs the two strands of DNA apart and joins together the RNA nucleotides as their pair along the DNA template. During elongation, the polymerase moves downstream, unwinding the DNA and elongating the RNA transcript 5’ -> 3’. After transcription, the DNA strands reform a double helix. At the termination stage, the RNA polymerase is released and the polymerase is detached from the DNA.

The stages of transcription: initiation, elongation and termination.

Problem: The template strand of a gene contains the sequence 3’-TTCAGTCGT-5’. Draw the nontemplate sequence and the mRNA sequence, indicating 5’ and 3’ ends of each. Compare the two sequences.

Task 3. Read the text, listen to your instructor’s explanation and make a scheme of tRNA, a ribosome and translation. Mark the main three stages of translation and provide their short description.

Translationis the synthesis of a polypeptide using the information in the mRNA. During translation, the sequence of codons along an mRNA molecule is decoded, or translated, into a sequence of amino acids making up a polypeptide chain. The sites of translation are ribosomes, complex particles that facilitate the orderly linking of amino acids into polypeptide chains. The physical link between the nucleotide sequence of nucleic acids (DNA and mRNA) and the amino acid sequence of proteins is a transfer RNA (tRNA). It does this by carrying an amino acid from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome. A cell keeps its cytoplasm stocked with all 20 amino acids, either by synthesizing them from other compounds or by taking them up from the surrounding solution.

Molecules of tRNA are not all identical, and each type of tRNA molecule translates a particular mRNA codon into a particular amino acid. A tRNA molecule arrives at a ribosome bearing a specific amino acid at one end. At the other end of the tRNA is a nucleotide triplet called an anticodon, which base-pairs with a complementary codon on mRNA.

Two-dimensional structure of tRNA Schematic model of a ribosome

Ribosomes facilitate the specific coupling of tRNA anticodones with mRNA codones during the protein synthesis. A ribosome, which is large enough to be seen with an electron microscope, is made of two subunits, called the large and small subunits. The ribosomal subunits are constructed of proteins and RNA molecules names ribosomal RNA, or rRNA. The structure of a ribosome reflects its function of bringing mRNA together with tRNAs carrying amino acids. In addition to a binding site for mRNA, each ribosome has three binding sites for tRNA. The P site (peptidyl-tRNA binding site) holds the tRNA carrying the growing polypeptide chain, while the A site (aminoacyl-tRNA binding site) holds the tRNA carrying the next amino acid to be added to the chain. Discharged tRNAs leave the ribosome from the E site (exit site).

Translation can be divided into three stages (analogous to those of transcription): initiation, elongation and termination.

The initiation stage of translation brings together mRNA, a tRNA bearing the first amino acid of the polypeptide, and the two subunits of a ribosome. First, a small ribosomal subunit binds to both mRNA and a specific initiator tRNA, which carries the amino acid methionine. The union of mRNA, initiator tRNA, and a small ribosomal subunit is followed by the attachment of a large ribosomal subunit, completing the translation initiation complex. The cell also expends energy obtained by hydrolysis of a GTP molecule to form the initiation complex. At the completion of the initiation process, the initiator tRNA sits in the P site of the ribosome, and the vacant A site is ready for the next aminoacyl tRNA. Note that a polypeptide is always synthesized in one direction, from the initial methionine at the amino end, also called the N-terminus, toward the final amino acid at the carboxyl end, also called the C-terminus.

In the elongation stage of translation, amino acids are added one by one to the previous amino acid at the C-terminus of the growing chain. Elongation occurs in a three-step cycle. 1) Codon recognition. The anticodon of an incoming aminoacyl tRNA base-pairs with the complementary mRNA codon in the A site. Hydrolysis of GTP increases the accuracy and efficiency of this step. 2) Peptide bond formation. An rRNA molecule of the large ribosomal subunit catalyzes the formation of a peptide bond between the amino group of the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site. This step removes the polypeptide from the tRNA in the P site and attaches it to the amino acid on the tRNA in the A site. 3) Translocation. The ribosome translocates the tRNA in the A site to the P site. At the same time, the empty tRNA in the P site is moved to the E site, where it is released. The mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site.

The final stage of translation is termination. Elongation continues until a stop codon in the mRNA reaches the A site of the ribosome. The nucleotide base triplets UAG, UAA, and UGA do not code for amino acids but instead act as signals to stop translation. A release factor, a protein shaped like an aminoacyl tRNA, binds directly to the stop codon in the A site.

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