4.2 Protein Synthesis

How does insulin make it to the rest of the body?

-specialized cells in the pancreas secrete insulin -these cells have many secretory vesicles filled with insulin -they release insulin via exocytosis

Enzymatic catalysis of the peptide bond between the growing polypeptide and the next incoming amino acid takes place in which binding site? A) E site B) A site C) P Site D) combined A and P sites

B) A site

Change the first base in the simulation back to adenine by clicking on the letter three more times. Click on other bases in the sequence and run the simulation to see what peptide is created. How many codons in this sequence can be altered at a single position to result in a prematurely terminated peptide? A) 3 B) 0 C) 2 D) 4 E) 1

E) 1

Is the Shine Dalgarno translated?

No

A) 3'CUU5'

Referring to the figure, what is the anticodon of the next tRNA to enter the A site? A) 3'CUU5' B) 5'GAA3' C) 5'CUU3' D) 3'GAA5' E) 3'UGG5'

What are the three "stop" codons?

UAA, UAG, or UGA

Reading Frames

following a start codon, a consecutive sequence of codons for amino acids

Where does translation take place in eukaryotes?

in the cytoplasm

What happens in the A site?

polypeptide chains (with the exception of Met) are added to the amino acid sitting in the A site

What helps a vesicle detach from the ER?

the binding of coat proteins, which are then shed once the vesicle is released

What is the process of tRNA obtaining the amino acid and attaching to the mRNA?

the tRNA covalently binds with the corresponding amino acid via the aminoacyl tRNA synthetase, becoming charged. once charged, the tRNA brings the amino acid to the mRNA by finding the corresponding antiparallel mRNA with the matching base sequence. The ribosome then takes the amino acid to form the polypeptide chain.

How do v-snares know where they're supposed to bind?

via specific v-snare and t-snare interactions

How do vesicles bind to the target membrane?

via v-snare and t-snare interactions that promote diffusion

What is wobble?

when different base sequences can create the same amino acid

Initiation codon

where translation begins and is coded by AUG, specifying methionine

how many codons code for 20 amino acids?

64 codons, but only 61 codons are translated and 3 are for stop codons which aren't translated into an amino acid

What are the three binding sites for molecules of transfer RNA of the large subunit of the ribosome?

A (aminoacyl site) P (peptidyl site) E (exit site)

Translation occurs in which large ribosomal subunit? A, P, or E?

A site

Assuming A-U and G-C pairing between the anticodon and the codon, what anticodon in tRNA Met would pair with the codon 5'-AUG-3'? A) 5'-CAU-3' B) 5'-GIU-3' C) 5'-AUG-3' D) 5'-UAC-3' E) 5'-ATC-3'

A) 5'-CAU-3'

Which step occurs in the A site of the ribosome during translation? A) an incoming charged tRNA binds to this site B) an uncharged tRNA is ejected from this site as the ribosome slides to the next codon C) the tRNA carrying the growing polypeptide moves tot his site as the ribosome slides to the next codon D) none of the answer options is correct

A) an incoming charged tRNA binds to this site

Which statements about the simulation are TRUE? Select all that apply. A) changing the guanine in the sixth codon of the original sequence to an adenine will not change the outcome of the simulation B) by changing zero, one, or two bases from each of the labeled codons, it is possible to create a tetrapeptide (four amino acids) of all methionines C) changing the adenines at the 3' end of the mRNA will result in a nonfunctional protein because it is critical that every protein possesses a tail of lysine amino acids at the C-terminus D) every amino acid in a synthesized polypeptide enters the ribosome at the A site E) changing the uracil in the first codon of the original sequence to a cytosine will not change the outcome of the simulation

A) changing the guanine in the sixth codon of the original sequence to an adenine will not change the outcome of the simulation B) by changing zero, one, or two bases from each of the labeled codons, it is possible to create a tetrapeptide (four amino acids) of all methionines

How is the amino acid held on the charged tRNA? A) covalent bond B) it can be a combination of all bond types C) hydrogen bonds

A) covalent bond

The ribosome ___ subunit has ___ binding sites for tRNA molecules. A) large; three B) large; four C) small; two D) small; three E) large; two

A) large; three

Binding sites for tRNA are located in: A) the large ribosomal subunit B) the small ribosomal subunit C) neither ribosomal subunit D) both ribosomal subunits

A) the large ribosomal subunit

What feature or structure in the simulation indicates that this is eukaryotic translation? A) the small ribosomal subunit binds to the 5' end of the mRNA and scans to the nearest AUG codon B) the first incorporated amino acid is methionine C) the small ribosomal subunit binds to a Shrine-Dalgarno sequence in the mRNA and locates a nearby AUG codon

A) the small ribosomal subunit binds to the 5' end of the mRNA and scans to the nearest AUG codon

Which of the answer choices occurs in the E site of the ribosome during translation? A) an incoming charged tRNA binds to this site B) an uncharged tRNA is ejected from this site as the ribosome slides to the next codon C) the tRNA carrying the growing polypeptide moves tot his site as the ribosome slides to the next codon D) none of the answer options is correct

B) an uncharged tRNA is ejected from this site as the ribosome slides to the next codon

Which of the following is the actual event that translates the language of nucleic acids (the sequence of bases, A, T (U), C, and G) to the language of proteins (determining which amino acid will be added to the polypeptide)? A) establishing the correct reading frame by the ribosome B) attachment of the appropriate amino acid to the tRNA by aminoacyl tRNA synthetase C) release of the finished polypeptide at the stop codon D) binding of charged tRNA to the ribosome A site E) catalysis of a new peptide bond from the growing polypeptide to the next amino acid

B) attachment of the appropriate amino acid to the tRNA by aminoacyl tRNA synthetase

The simulation demonstrates translation in: A) both bacteria and eukaryotes B) eukaryotes C) bacteria

B) eukaryotes

When a charged tRNA is about to bind to the vacant A site of a ribosome, where is the growing polypeptide? A) in the E site B) in the P site C) in the A site D) the polypeptide is equally likely to be in any of the three sites

B) in the P site

The nonmutant version of the simulated stretch of DNA (the sequence shown when the simulation first loads) depicts synthesis of a peptide that is how many amino acids in length? A) 6 B) 7 C) 5 D) 3 E) 4

C) 5

Change the first base in the simulation from an adenine to a uracil (change bases by clicking on them in the simulation), then re-run the simulation. This change results in: A) the peptide not being terminated at the appropriate stop codon B) an identical peptide being synthesized C) no peptide being synthesized D) a peptide of identical length for the wild type peptide, but with one amino acid difference E) the peptide being prematurely terminated after one amino acid

C) no peptide being synthesized

Which step occurs in the P site of the ribosome during translation? A) an incoming charged tRNA binds to this site B) an uncharged tRNA is ejected from this site as the ribosome slides to the next codon C) the tRNA carrying the growing polypeptide moves tot his site as the ribosome slides to the next codon D) none of the answer options is correct

C) the tRNA carrying the growing polypeptide moves tot his site as the ribosome slides to the next codon

How many aminoacyl-tRNA synthetase enzymes must be present in cells to properly synthesize proteins? A) 3, one for each base in a codon B) 4, one for each base in the mRNA C) 64, one for each possible codon D) 20, one for each amino acid

D) 20, one for each amino acid

Ribosomes in prokaryotes and eukaryotes are: A) similar in structure and translate using different genetic code B) identical in structure but translate using different genetic codes C) identical in structure and translate using the same genetic code D) similar in structure and translate using the same genetic codes

D) similar in structure and translate using the same genetic codes

What provides the energy for ribosome movement along the mRNA and formation of the peptide bonds?

Elongation Factors are bound to GTP molecules, and break their high-energy bonds to provide energy for the elongation of the polypeptide

What are the potential causes for a frameshift mutation?

In Frame Deletion or In Frame Insertion that shifts the reading frame and subsequently, potentially all the amino acids it reads; 1 or 2 nucleotides can be removed/added.

In which direction do codon charts show the mRNA codon sequence?

In the 5' to 3' direction

C) box C

In the figure, which box encloses the anticodon currently at the A site of the ribosome? A) box A B) box B C) box C D) box D

B) box B

In the figure, which box encloses the codon currently at the P site of the ribosome? A) box A B) box B C) box C D) box D

Where does translation coding begin?

It begins at and downstream of AUG (methionine)

What are the needed components for translation?

1) ribosomes 2) charged tRNA 3) amino acids 4) aminoacyl tRNA synthetase

What are the three steps of translation?

1. Initiation 2. Elongation 3. Termination

Explain the process of translation.

1. initiation factors bind to the 5' cap of the mRNA in the cytoplasm 2. initiation factors attract a small ribosomal subunit and a tRNA charged with Met (separate attractions) 3. the small ribosomal subunit and initiation factors travel along the mRNA in the 5' to 3' direction until AUG (start codon) is reached on the mRNA 4. when the start codon is reached, a large ribosomal subunit joins the small ribosomal subunit (P site onto the tRNA Met) and the initiation factors are released 5. an additional tRNA complementary to the next codon binds to the A site 6. a reaction transfers the Met to the amino acid on the tRNA in the A site, forming a peptide bond, and making the tRNA that was containing the Met, uncharged in the P site 7. the ribosome moves down one codon so that the uncharged tRNA sits in the E site and is ejected, and the tRNA carrying the polypeptide is in the P site. a new tRNA complementary to the next codon binds to the A site 8. the polypeptide transfers to the amino acid on the tRNA in the A site. the polypeptide continues to be elongated and repeating the process until a stop codon is reached.

What direction does the ribosome move along the mRNA in translation?

5' to 3'

A) C; mRNA

Once the molecule here is "charged," the outlined region labeled ___ will form complementary base pairs with the codon in the ___ in the A site of the ribosome. A) C; mRNA B) A; mRNA C) A; amino acid D) B; amino acid

D) AGA

Referring to the figure, what is the codon (5'>3') that specifies the addition of Arg (amino acid argenine) to the polypeptide? A) UCU B) CUU C) GAA D) AGA E) UGG

How is translation initiated in prokaryotes?

Shine-Dalgarno sequence in the mRNA (5'-AGGAGGU-3') and the start codon AUG is 8 nucleotides downstream

What are the relationships among the template strand of DNA, the codons in mRNA, anticodons in tRNA, and amino acids?

The codons of mRNA are groups of three nucleotides that code for a particular amino acid. Each is transcribes from the template strand of DNA according to the normal rules of base pairing (but in RNA, U replaces T). The sequence of the codons in the mRNA gives rise to the order of the resulting amino acid polypeptide chain. The codons are translated by tRNAs. The sequence of each tRNA includes a group of three nucleotides called an anticodon that is complementary in sequence and, therefore, can recognized and bind to a specific codon in the mRNA. Because of the complementary and antiparallel nature of nucleic acid structures, an anticodon in a tRNA has the same 3' to 5' sequence as the template DNA, except with U's instead of T's. Each tRNA is also bound to a specific amino acid, affiliated with a particular anticodon/codon pair, on the 3' end of the molecule. When the mRNA is being "read" through the ribosome, the order of the amino acids in the polypeptide chain is dependent upon the sequential interaction of the mRNA codon with the correct tRNA anticodon/amino acid pair. See Figure 4.15.

Which polypeptide sequences would you expect to result from a synthetic mRNA with the repeating sequence 5'-UUUGGGUUUGGGUUUGGG-3'?

The three readings are as follows: i. UUU GGG UUU GGG..., which codes for repeating Phe-Gly-Phe-Gly... ii. UUG, GGU, UUG GGU..., which codes for repeating Leu-Gly-Leu-Gly... iii. UGG GUU UGG GUU..., which codes for repeating Trp-Val-Trp-Val...

D) a tRNA; an amino acid; A

This image represents ___ and ___ is attached at the outlined region labeled ___. A) an aminoacyl tRNA synthase; an amino acid; A B) a tRNA; an amino acid; C C) an minoacyl tRNA synthase; an anticodon; C D) a tRNA; an amino acid; A E) a folded protein; an amino acid; A

What is the major role of the ribosome?

To ensure that when the mRNA is in place on the ribosome, the sequence in the mRNA coding for amino acids is read in successive, non-overlapping groups of three nucleotides; establish the correct reading frame for the codons

What direction does translation occur?

Translation occurs in a 5' to 3' direction. The start codon (AUG) is on the 5' end of all mRNA molecules, therefore translation works in a 5' to 3' direction. The ribosome also moves in this direction and the mRNA is read 3' to 5'

How many units are there in a ribosome?

Two -- one large subunit that contains the three binding sties for tRNAs and one small subunit

How are vesicles transported?

Via motor proteins that move them along tubulents and are directed by the proteins bound to the exterior of the vesicle

Bacterial DNA containing an operon encoding three enzymes is introduced into chromosomal DNA in yeast (a eukaryote) in such a way that it is properly flanked by a promoter and a transcriptional terminator. The bacterial DNA is transcribed and the RNA correctly processed, but only the protein nearest the promoter is produced. Why?

With proper eukaryotic processing, the RNA transcript from the bacterial DNA will be capped at the 5' end. The initiation complex will form at the 5' cap and move along the mRNA until the first AUG codon is encountered. At that point, then translation begins. When one of the termination codons is encountered, the polypeptide is released. Translation of the downstream polypeptides cannot take place because the Shrine-Dalgarno sequences preceding them are not recognized by the eukaryotic translational machinery.

Can an RNA molecule behave like a protein?

Yes, nucleotides can interact like amino acids and form secondary and tertiary "like" structures. Ex. tRNA

Silent Mutation

a change in a nucleotide in the mRNA strand, but no change in resulting amino acid/translation

Nonsense Mutation

a change in a nucleotide on the mRNA strand that results in a stop codon; premature ending and a shorter protein/polypeptide sequence. usually results in a nonfunctional protein.

Missense Mutation

a change in a nucleotide that changes the amino acid

Ribosomes

a complex structure of RNA and protein, bound to the cytosolic face of the RER in the cytoplasm, on which proteins are synthesized

Operon

a group of functionally related genes located in tandem along the DNA and transcribed as a single unit from one promoter; the region of DNA consisting of the promoter, the operator, and the coding sequence for the structural genes

Codon

a group of three adjacent nucleotides in RNA that specifies an amino acid in a protein or that terminates polypeptide synthesis

What defines the structure of tRNA?

a nucleotide sequence CCA at its 3' end and the 3' hydroxyl of the A is the attachment site for the amino acid corresponding to the anticodon

Initiation Factors

a protein that binds to mRNA to initiation translation

Elongation Factors

a protein that breaks the high-energy bonds of the molecule GTP to provide energy for ribosome movement and elongation of a growing polypeptide chain

Release Factor

a protein that causes a finished polypeptide chain to be freed from the ribosome

Polycistronic mRNA

a single molecule of messenger RNA that is formed by the transcription of a group of functionally related genes located next to one another along bacterial DNA

How do most codons specify an amino acid?

according to a genetic code (sometimes called the "standard" genetic code because some minor differences are found in a few organisms as well as in mitochondria

What is the catalyst for the Met or polypeptide chain transferring to the A site to form a peptide bond and elongate the polypeptide chain?

an RNA in the large ribosomal subunit

Aminoacyl tRNA Synthetase

an enzyme that attaches a specific amino acid to a specific tRNA molecule

When does translation begin in prokaryotes?

as soon as the mRNA comes off the DNA template while transcription is still occurring

What is the purpose of aminoacyl tRNA synthetase?

connects specific amino acids to specific tRNA molecules--they're directly responsible for actually translating the codon sequence in a nucleic acid to a specific amino acid in a polypeptide chain

What direction is a polypeptide synthesized?

from the amino end to the carboxyl end, so Methionine forms at the amino end and new amino acids are added to the carboxyl end

What are the steps of translation? Name and describe each one.

i. Initiation: Initiation factors bind to the 5' cap of the mRNA (in eukaryotic cells) or at the Shrine-Dalgarno sequence (for prokaryotes) and recruit the small subunit of the ribosome and a tRNA charged with methionine. This complex then moves along the mRNA until it finds a start codon (AUG, coding for methionine). The large ribosomal subunit then joins the complex and causes the initiation factors to be released. The tRNAMet is then bound in the P site of the ribosome. The next tRNA, determined by the codon of the mRNA, binds in the A site of the ribosome. This elicits a coupled reaction in which the bond between the Met and its tRNA is broken and a new bond is formed between the carboxyl group of the Met and the amino group of the next amino acid (a peptide bond). The ribosome complex then slides to the next codon on the mRNA, shifting the now-uncharged tRNAMet to the E site, where it is released from the ribosome complex, and moving the peptide-bearing tRNA to the P site. The A site is now free for the next charged tRNA. ii. Elongation: The ribosome continues in this fashion, shifting down the mRNA one codon at a time, adding amino acids to the growing peptide chain. Elongation factors provide the energy needed for these reactions to happen. iii. Termination: When the ribosome complex comes across a stop codon (UAA, UAG, or UGA), a protein release factor binds in the A site for the ribosome and causes the bond between the polypeptide chain and the last tRNA to break. Once the polypeptide chain is released, the ribosomal subunits disassociate from the mRNA and each other, and translation is complete. See Figures 4.17 and 4.18.

Termination

in protein translation, the time at which the addition of amino acids stops and the completed polypeptide chain is released from the ribosome. in cell communication, the stopping of a signal.

What are the initiation factors that bind to the mRNA in translation?

initiation factor binds to the 5' cap of the mRNA strand that is added to the mRNA during posttranscriptional processing; these factors recruit a small ribosomal subunit of the ribosome, and other initiation factors bring up a transfer RNA charged with Met

What happens when the large ribosomal subunit joins the small ribosomal subunit?

initiation factors are released, it attaches the tRNA Met at the P site and the tRNA complementary to the next codon site bids to the A site

How many aminoacyl tRNA molecules are there?

most organisms have one aminoacyl tRNA synthetase for each amino acid

Wild Type

normal phenotype (no mutation)

A (aminoacyl) site

one of three binding sites for tRNA on the large subunit of a ribosome

E (exit) site

one of three binding sites for tRNA on the large subunit of a ribosome

P (peptidyl) site

one of three binding sties for tRNA on the large subunit of a ribosome

What is a charged tRNA?

one with an amino acid attached

What is an uncharged tRNA?

one without an amino acid attached

Translation

synthesis of a polypeptide chain corresponding to the coding sequence present in a molecule of messenger RNA

What are other words for stop codons?

termination codons nonsense codons

What happens in the P site?

the Met (first step) or polypeptide (elongation) gets transferred to the A site of the amino acid to make a peptide bond and elongate the polypeptide chain

messenger RNA

the RNA molecule that combines with a ribosome to direct protein synthesis; it carries the genetic "message" from the DNA to the ribosome

What is one thing that is unique about translation in prokaryotes?

the ability to initiate translation internally and code for more than one protein (polycistronic mRNA)

A new amino acid is added to what end of the polypeptide chain?

the amino end of the amino acid is attached to the carboxyl end

Genetic Code

the correspondence between codons and amino acids, in which 20 amino acids are specified by 64 codons

Elongation

the process in protein translation in which successive amino acids are added one by one to the growing polypeptide chain

Anticodon

the sequence of three nucleotides in a tRNA molecule that base pairs with the corresponding codon in an mRNA molecule

Initiation

the stage of translation in which methionine is established as the first amino acid in a new polypeptide chain

What happens in the E site?

the uncharged tRNA that donated its amino acid/growing polypeptide chain from the P site to the A site is ejected

What is a v-snare?

they bind to complementary target membrane t-snares before membranes can fuse; they act an address label on the vesicle

Why are polycistronic mRNA strands useful?

they often code for successive steps in the synthesis of an essential small molecule such as an amino acid or for successive steps in the breakdown of a source of energy

What do stop codons do?

they trigger the end of translation, where the polypeptide is released into the cytosol. they are not translated.

What is the importance of the sequence of bases in an RNA molecule (messenger RNA) that are obtained from transcription?

they're used to specify the order in which successive amino acids are added to a newly synthesized polypeptide chain

What is the purpose of the tRNA?

translates each codon in the mRNA into one amino acid in the polypeptide

What is a UTR?

untranslated region of the mature mRNA that will not be translated; located before the start codon and may include the 5' cap, and can also be located after the stop codon and include the poly(A) tail

How do release factors terminate translation?

when a stop codon is encountered (UAA, UAG, or UGA), a protein release factor binds to the A site, which releases the polypeptide chain by breaking the bond connecting the polypeptide to the tRNA. This creates the carboxyl terminus of the polypeptide and completes the chain. once the finished polypeptide is released, the small and large ribosomal subunits disassociated both from the mRNA and from each other.

When does the large ribosomal subunit join the translation process?

when the small ribosomal subunit containing the tRNA Met attached by initiation factors reaches the AUG on the mRNA

Is methionine cleaved off by an enzyme after synthesis is complete?

yes