ch7 pt 3 w/o questions

What does initiation of protein synthesis in eukaryotes require?

Initiation of protein synthesis in eukaryotes requires translation initiation factors and a special initiator tRNA

What is first loaded into the P site of the small ribosomal subunit in eukaryotes?

In eukaryotes, an initiator tRNA, charged with methionine, is first loaded into the P site of the small ribosomal subunit, along with additional proteins called translation initiation factors.

What kind of tRNA molecule is capable of binding tightly to the P site in the absence of the large ribosomal subunit?

Only a charged initiator tRNA molecule is capable of binding tightly to the P site in the absence of the large ribosomal subunit.

What does the small ribosomal subunit loaded with the initiator tRNA bind to?

Next, the small ribosomal subunit loaded with the initiator tRNA binds to the 5′ end of an mRNA molecule, which is marked by the 5′ cap.

In what direction does the small ribosomal subunit move along the mRNA?

The small ribosomal subunit then moves forward (5′ to 3′) along the mRNA searching for the first AUG.

What happens when the first AUG is encountered and recognized by the initiator tRNA?

When this AUG is encountered and recognized by the initiator tRNA, several initiation factors dissociate from the small ribosomal subunit and the large ribosomal subunit binds and completes ribosomal assembly.

Why is protein synthesis ready to begin with the addition of the next charged tRNA to the A site?

Because the initiator tRNA is bound to the P site, protein synthesis is ready to begin with the addition of the next charged tRNA to the A site.

What signals the end of translation in both prokaryotes and eukaryotes?

The end of translation in both prokaryotes and eukaryotes is signaled by stop codons in the mRNA .

Which stop codons signal the ribosome to stop translation?

The stop codons—UAA, UAG, and UGA—are not recognized by a tRNA and do not specify an amino acid, but instead signal to the ribosome to stop translation.

What happens when a stop codon reaches the A site on the ribosome?

Proteins known as release factors bind to any stop codon that reaches the A site on the ribosome.

What does binding of a release factor do to peptidyl transferase?

This binding alters the activity of the peptidyl transferase in the ribosome, causing it to catalyze the addition of a water molecule instead of an amino acid to the peptidyl-tRNA.

What does the addition of a water molecule do?

This reaction frees the carboxyl end of the polypeptide chain from its attachment to a tRNA molecule

Why is the completed protein chain immediately released?

Because this is the only attachment that holds the growing polypeptide to the ribosome, the completed protein chain is immediately released.

What happens to the ribosome after the completed protein chain is released?

At this point, the ribosome also releases the mRNA and dissociates into its two separate subunits, which can then assemble on another mRNA molecule.

What is a polyribosome?

A series of ribosomes can simultaneously translate the same mRNA molecule.

What does a series of ribosomes do to the same mRNA molecule?

A series of ribosomes can simultaneously translate the same mRNA molecule.

What is shown in the electron micrograph?

Electron micrograph of a polyribosome from a eukaryotic cell.

What can a single prokaryotic mRNA molecule encode?

A single prokaryotic mRNA molecule can encode several different proteins

How are genes directing different steps in a process often organized in prokaryotes?

In prokaryotes, genes directing the different steps in a process are often organized into clusters (operons) that are transcribed together into a single mRNA.

How do prokaryotic ribosomes initiate translation compared with eukaryotic ribosomes?

Unlike eukaryotic ribosomes, which recognize a 5’ cap, prokaryotic ribosomes initiate translation at ribosome-binding sites (dark blue), which can be located in the interior of an mRNA molecule.

What does the location of ribosome-binding sites enable prokaryotes to do?

This feature enables prokaryotes to synthesize several separate proteins from a single mRNA molecule (polycistronic).

What do many effective antibiotics inhibit?

Many of our most effective antibiotics are compounds that act by inhibiting bacterial, but not eukaryotic protein or RNA, synthesis.

How do some antibiotics preferentially interfere with bacterial protein synthesis?

Some of these drugs exploit the small structural and functional differences between bacterial and eukaryotic ribosomes to interfere preferentially with bacterial protein synthesis.

Why can these compounds be taken in high doses without being toxic to humans?

These compounds can thus be taken in high doses without being toxic to humans.

What helps regulate the amount of each protein in a cell?

Controlled protein breakdown helps regulate the amount of each protein in a cell

How much can proteins vary in their life-span?

Proteins vary enormously in their life-span.

How long may structural proteins in a relatively stable tissue last?

Structural proteins that become part of a relatively stable tissue such as bone or muscle may last for months or even years

How long may metabolic enzymes and proteins that regulate cell growth and division last?

Other proteins, such as metabolic enzymes and those that regulate cell growth and division, last only for days, hours, or even seconds.

What do specialized cellular pathways do to proteins?

Cells possess specialized pathways that enzymatically break proteins down into amino acids (proteolysis).

What are proteases?

Proteases are enzymes that degrade proteins, first to short peptides and then to individual amino acids .

How do proteases act?

Proteases act by cutting (hydrolyzing) the peptide bonds between amino acids.

What is one function of proteolytic pathways?

To rapidly degrade proteins whose lifetimes must be kept short.

What is another function of proteolytic pathways?

To recognize and remove proteins that are damaged or misfolded to prevent protein aggregation.

What eventually happens to all proteins?

Eventually, all proteins accumulate damage and are degraded by proteolysis.

What does a proteasome degrade?

A proteasome degrades short-lived and misfolded proteins.

Where are proteasomes present in eukaryotic cells?

In eukaryotic cells, proteins are broken down by large protein machines called proteasomes, present in both the cytosol and the nucleus.

What forms the central cylinder of a proteasome?

A proteasome contains a central cylinder formed from proteases whose active sites face into an inner chamber.

What stoppered each end of the proteasome cylinder?

Each end of the cylinder is stoppered by a large protein complex formed from at least 10 types of protein subunits.

What do the protein stoppers bind?

The protein stoppers bind the proteins destined for degradation

What do the protein stoppers do using ATP hydrolysis?

The protein stoppers bind the proteins destined for degradation and then—using ATP hydrolysis—unfold the proteins and thread them into the inner chamber of the cylinder.

What happens to proteins once they are inside the proteasome?

Once inside, proteases chop the proteins into short peptides, which are then jettisoned from either end of the proteasome.

Why does housing proteases inside the proteasome make sense?

Housing proteases inside the proteasome makes sense, as it prevents the enzymes from running rampant in the cell.

How are proteins marked for destruction in eukaryotes?

In eukaryotes, proteasomes act on proteins that have been marked for destruction by the covalent attachment of a small protein called ubiquitin.

What do specialized enzymes do to selected proteins?

Specialized enzymes tag selected proteins with a short chain of ubiquitin molecules.

What happens to ubiquitylated proteins?

These ubiquitylated proteins are then recognized, unfolded, and fed into proteasomes by proteins in the stopper.

What sequence do short-lived proteins often contain?

Short-lived proteins often contain a short amino acid sequence that marks them to be ubiquitylated and degraded in proteasomes.

Which proteins are also recognized and degraded by the ubiquitin dependent proteolytic system?

Damaged or misfolded proteins, as well as proteins containing oxidized or abnormal amino acids, are also recognized and degraded by this ubiquitin dependent proteolytic system.

What do the enzymes that add polyubiquitin chains recognize?

The enzymes that add the polyubiquitin chains recognize signals that are exposed on targeted proteins as a result of misfolding or chemical damage.

What does protein production in a eukaryotic cell require?

Protein production in a eukaryotic cell requires many steps.

What determines the final concentration of each protein?

The final concentration of each protein depends on the rate of each step depicted.

How can protein and mRNA concentrations be regulated after they have been produced?

Even after an mRNA and its corresponding protein have been produced, their concentrations can be regulated by degradation.

How can the activity of a protein be regulated?

The activity of the protein can also be regulated by post-translational modifications or the binding of small molecules (see next slide).

What do many proteins require to become fully functional?

Many proteins require various modifications to become fully functional.

What must a completed polypeptide do to be useful to the cell?

To be useful to the cell, a completed polypeptide must fold correctly into its three-dimensional conformation and then bind any required cofactors (red) and protein partners—all via noncovalent bonding.

What do many proteins require to become active or be recruited to specific membranes or organelles?

Many proteins also require one or more covalent modifications to become active—or to be recruited to specific membranes or organelles (not shown).

What are the most common post-translational covalent modifications?

Although phosphorylation and glycosylation are the most common, more than 100 types of post-translational covalent modifications of proteins are known.

How many types of post-translational covalent modifications of proteins are known?

more than 100 types of post-translational covalent modifications of proteins are known.