Chapter 17 (4)

In the process of __, a cell interprets a genetic message and builds a polypeptide accordingly. The message is a series of __along an mRNA molecule, and the interpreter is __.

What is the function of tRNA?
--A cell keeps its cytoplasm stacked with 20 amino acids, either by synthesizing them from other compounds or by taking them up from the surrounding solution

The __adds each amino acid brought to it by __to the growing end of a polypeptide chain.

Molecules of __are not all identical. The key to translating a genetic message into a specific __is that each type of tRNA molecule translates a particular __into a particular amino acid.

As a __molecule arrives at a ribosome, it bears a specific __at one end. At the other end of the tRNA is a nucleotide triplet called an __, which base-pairs with a complementary codon on mRNA.

As an mRNA molecule is moved through a ribosome, __ will be added to the polypeptide chain whenever the __ is presented for __.

Codon by codon, the genetic message is translated as __deposit amino acids in the order prescribed, and the __joins the amino acids into a chain.

Each __is used repeatedly, picking up its designated amino acid in the cytosol, depositing this cargo onto a polypeptide chain at the ribosome, and then leaving the ribosome, ready to pick up another amino acid.
A __ molecule consists of a single RNA strand that is only about __ nucleotides long (compared to hundreds in mRNA).
Because of the presence of complementary stretches of bases that can __to each other, this single strand can fold back upon itself and form a molecule with a three-dimensional structure.

Flattened into one plane to reveal this base pairing, a tRNA molecule actually twists and folds into a compact three-dimensional structure that is roughly __-shaped.
· The loop extending from one end of the __ includes the __, the particular base triplet that base-pairs to a specific __.
· From the other end of the __-shaped tRNA molecule protrudes its 3’ end, which is the attachment site for an __. Thus, the structure of a tRNA molecule fits its function.

The accurate translation of a genetic message requires two processes that involve molecular recognition.
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· First, a __that binds to an mRNA codon specifying a particular amino acid must carry that __, and no other, to the ribosome. The correct matching up of tRNA and amino acid is carried out by a family of related enzymes called __. The active site of each type of each type of __ fits only a specific combination of amino acid and tRNA. There are __ different synthetases, one for each amino acid; each synthetase is able to bind all the different tRNAs that code for its particular amino acid. The synthetase catalyzes the __attachment of the amino acid to its tRNA in a process driven by the __of ATP. The resulting aminoacyl tRNA also called a__tRNA, is released from the enzyme and is then available to deliver its amino acid to a growing polypeptide chain on a ribosome.

The accurate translation of a genetic message requires two processes that involve molecular recognition.

· The second recognition process involves matching up a __ with the appropriate mRNA codon. If one tRNA variety existed for each mRNA codon that specifies an amino acid, there would be __ tRNAs. In fact, there are only about __, signifying that some tRNAs must be able to bind to more than one codon. Such versatility is possible because the rules for __ between the third base of a codon and the corresponding base of a tRNA anticodon are relaxed compared to those at other codon positions.

For example, the base __ at the 5’ end of a tRNA anticodon can pair with either A or G in the third position (at the 3’ end) of an mRNA codon. The flexible base pairing at this codon position is called __.
§ __explains why the synonymous codons for a given amino acid can differ in their third base, but usually not in their other bases.

__facilitate the specific coupling of tRNA anticodons with mRNA codons during __. A ribosome is made up of a small and a large subunits; they are constructed of proteins and RNA molecules named __.
· In eukaryotes, these are made in the nucleolus.

A functional ribosome, in both bacteria and eukarya, are formed ONLY when they attach to an __. About 2/3 of the mass of a ribosome consists of __, either three molecules (bacteria) or four (eukarya). Because most cells contain thousands of ribosomes, __is the most abundant type of cellular RNA.

Although the ribosomes of bac. and euk. are very similar in structure and function, those of eukaryotes are slightly larger and differ somewhat from bacterial ribosomes in their __. The differences are medically significant.
Certain antibiotic drugs can activate bacterial ribosomes without inhibiting the ability of eukaryotic ribosomes to make proteins. (for bacterial infections.)

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 biding sites for tRNA: __, __, __

· The __(peptidyl-tRNA) holds the tRNA carrying the growing polypeptide chain, while the __(aminoacyl-tRNA site) holds the tRNA carrying the next amino acid to be added to the chain.
· Discharged tRNAs leave the ribosome from the __(exit site).

· The ribosome holds the __ and __ in close proximity and positions the new amino acid for addition to the __end of the growing polypeptide. It then catalyzes the formation of the __. As the polypeptide becomes longer, it passes through an __in the ribosome’s large subunit.
· When the polypeptide is complete, it is released to the cytosol through the __.

True or False
Hypothesis: that rRNA, not protein, is primarily responsible for both the structure and the function of the ribosome.
True False

The __, which are largely on the exterior, support the shape changes of the __molecules as they carry catalysis during __. __ is the main constituent of the interface between the two subunits and of the __ and __ sites, and it is the catalyst of peptide bond formation. Thus, a ribosome can be regarded as one colossal __.

__(synthesis of a polypeptide) is divided into three stages: __, __, and __. All three stages require protein “factors” that aid in the translation process.
For certain aspects of __, energy is also required. It is provided by the hydrolysis of __.

The initiation stage of __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 __.

o In bacteria, the small subunit can bind these two in either order; it binds the mRNA at a specific RNA sequence, just __of the start codon, __.
o In eukaryotes, the small subunit, with the __already bound, binds to the 5’ cap of the mRNA and then moves, or scans, __along the mRNA until it reaches the start codon, and the initiator tRNA __to it.
o In either case, the start codon signals the start of __; this is important because it establishes the __for the mRNA.

The union of mRNA, initiator tRNA, and a small ribosomal subunit is followed by the attachment of a large ribosomal subunit, completing the __.
Proteins called __are required to bring all the components together. The cell also expends energy in the form of a __molecule to form the __.

At the completion of the __, the initiator tRNA sits in the __ site of the ribosome, and the vacant __ site is ready for the next __.
A polypeptide is always synthesized in one direction, from the initial __at the amino end, also called the __, toward the final amino acid at the carboxyl end (__).

In the __ stage of translation, amino acids are added one by one to the preceding amino acid.
Each addition involves the participation of several proteins called __ and occurs in a __-step cycle. Energy expenditure occurs in the first and third steps.
Codon recognition requires hydrolysis of one molecule of __, which increases the accuracy and efficiency of this step. One more __ is hydrolyzed to provide energy for the __ step.

The mRNA is moved through the ribosome in one direction only, __’ end first; this is the same as a ribosome moving 5'--> 3’ on the mRNA.
· Important point: ribosome and the mRNA move relative to each other, unidirectionally, codon by codon. The __takes less than a tenth of a second in bacteria and is repeated as each amino acid is added to the chain until the polypeptide is completed.

The final stage of translation is __.
___ continues until a stop codon in the mRNA reaches the __ site of the ribosome. The base triplets __, __, and __ do not code for amino acids but instead acts as signals to stop translation.

A protein called a __binds directly to the stop codon in the __ site. The __causes the addition of a water molecule instead of an amino acid to the polypeptide chain. This reaction breaks (__) the bond between the completed polypeptide and the tRNA in the __ site, releasing the polypeptide through the __ of the ribosome’s large subunit.

The remainder of the __ then comes apart in a multistep process, aided by other protein factors. Breakdown of the translation assembly requires the hydrolysis of two more __molecules.
A single ribosome can make an avg-sized polypeptide in less than a minute.
Typically, however, multiple ribosomes translate an __at the same time; that is, a single mRNA is used to make many copies of a polypeptide simultaneously.

Once a ribosome moves past the start codon, a second ribosome can attach to the mRNA, eventually resulting in a number of ribosomes trailing along the mRNA. Such strings of ribosomes, called __(or __), can be seen with an electron microscope.
__are found in both bacterial and eukaryotic cells. They enable a cell to make many copies of a polypeptide very quickly.

The process of __is often not sufficient to make a functional protein.
During its synthesis, a polypeptide chain begins to coil and fold spontaneously as a consequence of its amino acid sequence (__), forming a protein with a specific shape: a 3D molecule with secondary and tertiary structure.
· Thus, a __determines primary structure, and primary structure in turn determines shape. In many cases, a __ helps the polypeptide fold correctly.

Additional steps- __-may be required before the protein can being doing its particular job in the cell.
Certain amino acids may be chemically modified by the attachment of __, __, __ or other additions. __may remove one or more amino acids from the leading (amino) end of the polypeptide chain.
In some cases, a polypeptide chain may be enzymatically cleaved into two or more pieces.

There are two types of ribosomes (and polyribosomes): __ and __.
· __make proteins that stay in the cytosol and function there.
· __make proteins of the endomembrane system as well as proteins secreted from the cell.

The __are themselves are identical and can switch their status from free to bound.

What determines whether a ribosome will be free in the cytosol or bound to rough ER at any given time?
· __always begins in the cytosol, when a __ ribosome starts to translate an mRNA molecule. There the process continues to completion- unless the growing polypeptide itself cues the ribosome to attach to the ER.
· The polypeptides of proteins destined for the endomembrane system or for secretion are marked by a signal peptide, which targets the protein to the ER.

The __, a sequence of about 20 amino acids at or near the leading (amino) end of the polypeptide, is recognized as it emerges from the ribosome by a protein- RNA complex called a __.

The __ functions as an adapter that brings the ribosome to a receptor protein built into the ER membrane. This receptor is part of a __. Polypeptide synthesis continues there, and the growing polypeptide snakes across the membrane into the ER lumen via a __.

§ The __ usually removed by an enzyme. The rest of the completed polypeptide, if it is to be secreted from the cell, is released into solution within the ER lumen.
§ Alternatively, if the polypeptide is to be a __, it remains partially embedded in the ER membrane.

§ Other kinds of __are used to target polypeptides to mitochondria, chloroplasts, the nucleus interior, and other organelles not part of the endomembrane system.

True or False
The critical difference in these cases is that translation is completed in the cytosol before the polypeptide is imported into the organelle.
True False

The mechanisms of __also vary, but in all cases studied to date, the “zip codes” that address proteins for secretion or to cellular locations are __of some sort. Bacteria also employ signal peptides to target proteins for secretion.