Chapter 40-Mechanisms of protein synthesis

What are the simple steps of proteins synthesis?

1.) Initiation at 5' cap of mRNA 2.) elongation 3.) termination

How is protein synthesized in eukaryotes

1.) The ribosomes are larger-40s and 60s form 80s ribosome 2.) Protein synthesis begins with a methionine rather than formylmethionine. A special tRNA called met-tRNA is required. 3.) The initiator codon is always the first AUG form he 5' end of the mRNA. more protein initiation factors are required (NO DELGARNO-SEQUENCE 4.) The mRNA is circular because of interaction betwen proteins that bind the 5' cap and those that bind the poly A tail

What are the three steps in chain elongation

1.) positioning of the correct A.A. tRNA in A site 2.) Formation of peptide bond 3.) shifting mRNA by one codon 20-40 A.A./ sec 1000 nucleotides/sec in DNA synthesis

Why is proteins synthesis energetically expensive?

4 phosphoanhdride bonds are cleaved for each A.A. added to a polypeptide chain

What helps the correct A.A. tRNA insert into the A site? How does it do this?

Bacterial elongation factor EF-Tu helps the correct A.A. tRNA insert into A site. An EF-Tu-GTP complex binds to all AA-tRNA molecules except fmet-tRNAfmet (the initiator)

What does double stranded RNA bind?

DS RNA binds mRnA to the ribosome

How is the double stranded RNA cleaved? by what? What are the fragments bound to? what does this form? What does the complex do?

Dicer, a ribonuclease, cleaves double stranded RNA into small fragments called interfering RNA (siRNA) that are bound by a class of proteins called Argonaute to form the RnA inducer silencing complex (RISC) The complex locates mRNA complementary to the siRNA and degrades them to save the cell

How is elongation and termination similar and different between eukaryotes and prokaryotes

Elongation and termination are similar except that bacteria have 3 release factors while eukaryotes have one. Also eukaryotic protein synthesis occurs in the cytoplasm and utilizes large complexes associated with the cytoskeleton.

how is iron transport and storage carefully regulated?

Ferritin: an iron storage protein in the cell has translational regulation from its mRNA. A stem loop structure in the 5' UTR (iron response element =IRE) binds the IRE bind protein (IRE-BP) when iron is absent and prevents translocation. when present iron binds the IRE-BP causing it to dissociate from the IRE, allowing translocation

How many tRNA binding sites are in the Ribosome and what are they called and what the heck do they do?

It has 3 tRNA binding sites 1.) The A (aminoacyl) site binds the incoming tRNA 2.) the P (peptidyl) site bind the tRNA with the growing peptide chain 3.) The E (exit site) binds uncharged tRNA before it Leaves the ribosome

What is bacterial protein synthesis initiated by?

It is initiated by formylmetionyl tRNA. This is a modified form of methionine. Called N-formylmethionine (fmet). This is the initiator amino acid in most bacterial proteins

What does the f met attach to?

It will attach to the initiator tRnA (tRNAf). f-met-trnaf binds only to the initiation codon not to other AUGs

What catalyzes peptide bond formation?

Peptidyl transferase catalyzes peptide bond synthesis Peptidyl transferase is responsible for formation of peptide bond once AA-tRNAs are positioned in P and A sites. Activity is contained in P and A sites. Activity is contained with in the large ribosomal subunit Substrate biding site in 23S rRNA and 50S ribosomal proteins Catalytic activity from 23S rRNA

Where does protein synthesis all start?

Protein synthesis all starts at the Ribosome

What is protein synthesis carried out by? Where does complex assemble and dissassemble? What direction does complex move how is the protein synthesized?

Protein synthesis is carried out by a complex composed of the ribosome, initiation factors, mRNA, and charged tRNA molecules Initiation complex assembles at the first mRNA codon and disassembles at termination step. Ribosome complex moves 5' to 3' along template mRNA polypeptide synthesized in N terminus to C terminus direction

What are he e. coli release factor? How is translation terminated? What are the termination codon?

RF-1, RF-2, and RF-3 Translocation will eventually position one of the 3 termination codons in the A site. No tRNA molecules recognize these codons and protein synthesis stalls

WHAT can RNA interference cause What is this type of mechanism?

RNA interference (RNAi) leads to mRNA degradation induced by the presence of double stranded RNA. This is likely a protective mechanism against viruses since ds RNA can be present during certain viral infections.

What are ribosomes composed of? e. coli eukaryotic

Ribosome is composed of rRNA and protein. All ribosomes contain two subunits of unequal size. E.co.i is 70s ribosome with a 30S and a 50s subunits Eukaryotic is 80S with a 40S and 60S subunit both have multiple rRNA and proteins

What must the ribosome align? where are aminoacylated ends positioned What does ribosomes hold

Ribosome must align two charged tRNA molecules so that anticodons interact with correct codon of mRNA. Aminoacylated ends of the tRNA are positioned at the site of peptide bond formation. Ribosomes must hold mRNA and growing polypeptide chain

Where does the initiation site assemble? What does ribosome need to recognize?

Ribosome must recognize protein synthesis at the start codon which is usually AUG. In prokaryotes the Ribosome binds to the shine Delgarno sequence upstream of he initiation sequence. S-D sequence also binds to a complementary base sequence of the 3' end of the 16S rRNA

what are ribosomes bound to and what do they secret? What directs protein sorting in euks/ Where are proteins inserted during the secretory pathway? Where does protein synthesis in secretory pathway occur

Ribosomes bound to the endoplasmic reticulum manufacture secretory and membrane proteins. proteins sorting directs proteins disting organelles. in the secretory pathway, proteins are inserted into the ER membrane co translationally Protein synthesis in the secretory pathway occurs on ribosomes bound to the ER. ER+ribosomes=rough ER

When does bacterial translation begin?

Since transcription and translation both occur in the 5' to 3' direction, bacterial protein synthesis begins before transcription is complete Several ribosomes can translate an mRNA molecule at the same time, forming poly ribosomes or polyosomes. This will require multiple S-D sequences

What does the formation of the new peptide bond look like and where is the bond formed?

The A site attacks the P site to from the peptide bond. Peptide bond formed in the P site.

What does EF-Tu-GTP-AA-tRNA complex bind to? When is the complex stabilized?

The EF-Tu-GTP-AA-tRNA binds in the ribosomal A site. Complex is stabilize when the anticodon of the AA-tRNA correctly base pairs with mRNA codon.

What binds to the SRP ribosome complex and what happens after?

The SRP receptor that is an integral membrane with GTPase activity binds to SRP ribosome complex. The translocon which is a protein conducting channel accepts the ribosome from the SRP-SRP receptor complex and protein synthesis begins again with the protein now passing through the membrane in the translocon

How is translation initiated in prokaryotes?

The nucleotides between the 5' end of the mRNA and the first codon translated are called the untranslated region (UTR) The UTR contains a shine delgarno (S-D) sequence that directs protein synthesis machinery to the start site. The S-D sequence is purine rich about 10 bp up stream of the start site and interacts with the 16 S rRNA to correctly position AUG codon in the A site

What is the ribosome?

The ribosome is a complex of RNA and protein. This is the site where genetic information is translated into protein Gene transcribed left to right. Ribosome bind to the 5' end of the mRNA

How is stability of mRNA regulated?

Transferrin-receptor, which binds iron-rich transferrin and facilitates its entry into cells, also several IREs located in the 3' untranslated region. When iron is absent IRE-BP binds the IREs, allowing the mRNA to be translated. When iron is present it binds to the IRE, BP which dissociates from the transferrin receptor mRNA with out the IRE-BP, then the receptor mRNA is degraded

How is the ribosome moved? Where does the energy come from? Where is the peptidyl-tRNA when translocation occurs? how does the polypeptide chain grow?

Translocation moves the ribosome by one codon. Elongation factor G uses the energy of GTP hydrolysis to translocate the mRNA by one codon. peptidyl-tRNA is fully in the P site, the A site is now vacant, and uncharged tRNA is in the E site-disengaged from the mRNA. The polypeptide chain grow from the amino terminal to the carboxyl terminal.

What do micro RNA do?

micro RNA (miRNA)-21 nucleotides long) regulate gene expression post transcriptionally. These may regulate up to 60% of mammalian protein coding genes. some miRNA promote cleavage of specific mRNAs. Some miRNA promote translational repression or deadenylation of mRNAs

What does the release factor bind?

one of the release factors (RF) binds and cuases hydrolysis of peptidyl-tRNA to release the peptidyl-tRNA to release the polypeptide chain.

What antibiotics target the ribosome and how/why?

streptomycin changes the shape of 30S portion and causes code on mRNA to be read incorrectly. 30 only in bacteria and wont target eukaryotic. Erythomycin binds to 50s portion of Bacteria RNA and prevents translocation movement of ribosome along the mRnA

Where does the secretory pathway begin? What emerges from the ribosome? What binds to the signal sequence?

synthesis of proteins for the secretory begins on ribosomes that are free in the cytoplasm. A portion of the nascent protein that contains the signal peptide emerges from the ribosome. The sequence is 9-12 hydrophobic amino acids and ofen located at the N-terminal region of the primer structure. The signal recognition particle (SRP) binds the signal sequence as it exits the ribosome and directs the complex to the ER

What recognizes internal codons for methionine?

t-RNA-m will recognize internal codons for methionine

How is initiation of translation started?

the translation complex is assembled at the beginning of the mRNA coding sequence. This complex consists of Ribosomal subunits, mRNA template to be translated, Initiator tRNA molecule, protein initiation factors