PLEASE HELP ME ANSWER ALL OF THESE (NOT PARTIAL!) • What is the reaction of amin

Question

PLEASE HELP ME ANSWER ALL OF THESE (NOT PARTIAL!)

• What is the reaction of amino-acyl tRNA synthetases

• What reaction does peptidyl tranferase catalyze? What is the nucleophile?

• What binds the Shine-Delgarno sequence and where is it located?

• What is the order for the basic steps of protein synthesis?

• What type of RNA contains introns?

• What factors (in E. coli) are required for the initiation of translation, but are not permanently associated with the ribosome?

• What is the direction of DNA replication, transcription and translation?

THANK YOU!

Explanation / Answer

1. An aminoacyl tRNA synthetase (aaRS) is an enzyme that attaches the appropriate amino acid onto its tRNA. It does so by catalyzing the esterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form anaminoacyl-tRNA.

The mechanism can be summarized in the following reaction series:

2. The site in the ribosome where peptide-bond formation occurs, its peptidyl transferase center, catalyzes the synthesis of peptide bonds in vitro using substrates much smaller than the aminoacyl and peptidyl tRNAs that are the ribosome’s normal fare (Traut and Monro 1964; Monro 1967). The lowest-molecular-weight aminoacyl tRNA-like substrate the ribosome will accept is puromycin, which is effectively an adenosine aminoacylated with tyrosine, and molecules as small as CCA aminoacylated with N-formyl methionine will serve in place of peptidyl tRNA. Because the peptidyl transferase center is entirely contained in the large subunit, it should be possible to learn a lot about the mechanism of peptide-bond formation from crystal structures of large subunits with substrates like these bound. Consistent with this expectation, the structures that have been obtained of the large subunit with low-molecular-weight substrates and products bound are highly suggestive regarding the events that occur in the peptidyl transferase center. A nucleophile is a chemical species that donates an electron pair to an electrophile to form a chemical bond in relation to a reaction. All molecules or ions with a free pair of electrons or at least one pi bond can act asnucleophiles. Because nucleophiles donate electrons, they are by definition Lewis bases

3. The Shine-Dalgarno (SD) sequence is a ribosomal binding site in prokaryotic messenger RNA, generally located around 8 bases upstream of the start codon AUG.[1] The RNA sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning the ribosome with the start codon.

The Shine-Dalgarno sequence exists both in bacteria and archaea. It is also present in some chloroplast and mitochondrial transcripts. The six-base consensus sequence isAGGAGG; in Escherichia coli, for example, the sequence is AGGAGGU, while subsequence GAGG dominates in E. coli virus T4 early genes.

4. The three basic steps of protein synthesis are: 1. Transcription 2. Transferal 3. Translation

5. The nascent RNA also contains transcribed introns that are removed during splicing. However, it is possible that these introns may be retained during processing of the RNA.

6. Initiation: The ribosome assembles around the target mRNA. The first tRNA is attached at the start codon

In bacteria, translation occurs in the cell's cytoplasm, where the large and small subunits of the ribosome bind to the mRNA. In eukaryotes, translation occurs in the cytosol or across the membrane of the endoplasmic reticulumin a process called vectorial synthesis. In many instances, the entire ribosome/mRNA complex binds to the outer membrane of the rough endoplasmic reticulum (ER); the newly created polypeptide is stored inside the ER for later vesicle transport and secretion outside of the cell.

7. DNA biosynthesis proceeds in the 5- to 3-direction

  Transcription takes place in two broad steps. First, pre-messenger RNA is formed, with the involvement of RNA polymerase enzymes. The process relies on Watson-Crick base pairing, and the resultant single strand of RNA is the reverse-complement of the original DNA sequence. The pre-messenger RNA is then "edited" to produce the desired mRNA molecule in a process calledRNA splicing.

Each amino acid has its own special tRNA (or set of tRNAs). For example, the tRNA for phenylalanine (tRNAPhe) is different from that for histidine (tRNAHis). Each amino acid is attached to its tRNA through the 3-OH group to form an ester which reacts with the -amino group of the terminal amino-acid of the growing protein chain to form a new amide bond (peptide bond) during protein synthesis The reaction of esters with amines is generally favourable but the rate of reaction is increased greatly in the ribosome.

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