A protein's activity can be regulated in a number of ways.  The first and most obvious is to control the total number of protein molecules present within the system.  

Let us assume that once synthesized, a protein is fully active.  With this simplifying assumption, the total concentration protein in a system [P_sys] is proportional to the

(the rate of protein synthesis) - (the rate of protein degradation). 

What controls the rate of protein synthesis?  Clear this is primarily a function of the number of mRNAs encoding the protein present in the cell. 

It is generally the case that once translation begins, it continues at more or less a constant rate. 

In the bacterium E. coli, the rate of translation at 37ºC is about 15 amino acids per second; translation of a polypeptide of 1500 amino acids would then take 100 seconds. 

After translation, folding and, in multisubunit proteins, assembly, the protein will function until it is degraded. 

Protein degradation often begins when the protein is specifically marked for degradation. 

This is an active process, involving ATP hydrolysis and a multisubunit complex known as the proteosome.

The proteosome degrades the polypeptide into small peptides and amino acids, that can be recycled.

• A cell is starved for amino acids - what will happen to protein synthesis rate and why?
• Why might a cell want a specific protein to have a short half-life?

A second and reversible form of regulation is known as allosteric regulation

In allosteric regulation, regulatory molecules bind reversibly to the protein, altering its confirmation, which in turn alters its activity.   Such allosteric effectors are not covalently attached to the protein.

Here, the activity of a protein is positively regulated by the binding of a factor.

This factor could be a small molecule or another protein.

What is important is that allosteric binding site is distinct from the enzyme's catalytic site.

That is what allosteric means, other site.

An allosteric effector can also act negatively, inhibiting enzyme activity.

Because allosteric regulators do not bind to the same site on the protein as the substrate, changing [substrate] generally does not alter their effects.

Of course there are other types of regulation as well.

Active site inhibitors:   An inhibitory factor may bind to and block the active site.

If this binding is reversible, then increasing the amount of substrate can over-come the inhibition.   An inhibitor of this type is known as a competitive inhibitor.

In some cases, the inhibitor chemically reacts with the enzyme, forming a covalent bond.  

Because this type of inhibitor is essentially irreversible, increasing substrate concentration can not overcome inhibition. These are therefore known as a non-competitive inhibitors. 

Allosteric effectors are also non-competitive, since they do not compete with substrate for binding to the active site.

• A protein binds an allosteric regulator - what happens to the protein?
• Why are allosteric regulators not "competitive"?
• What makes an inhibitor that binds to the active site of an enzyme "non-competitive" ?  

Post-translational regulation: Proteins may be modified after synthesis – this process is known as post-translational modification.

A number of post-translational modifications have been found to occur within cells. 

The first type involve the covalent addition of specific groups to the protein – these groups can range from phosphate groups (phosphorylation), an acetate group (acetylation), the attachment of lipid/hydrophobic groups (lipid modification), or carbohydrates (glycosylation) . 

Often post-translationally modifications are reversible, one enzyme adds the modifying group, and another can act to remove it.   For example, proteins are phosphorylated by enzymes known as a protein kinases, while protein phosphatases remove phosphate groups. 

Post-translational modifications act in much the same way as do allosteric effectors, they modify the activity of the polypeptide to which they are attached.   They can also modify a proteins interactions with other proteins, the protein's localization within  the cell, or its stability. 

Proteolytic processing:  Another method for regulating protein activity involves the cleavage of the polypeptide chain. 

Many proteins are originally synthesized in a longer, and inactive "pro-form". 

To become active the pro-peptide must be removed – it is cut by a protease. 

This proteolytic processing activates the protein.  Proteolytic processing is itself often regulated. 

• A protein is normally found free in the cytoplasm; where would you expect to be found following addition of a lipid group?
• What are the advantages/disadvantages of using proteolytic activation, compared to allosteric activation of a protein?
• Why are enzymes required for post-translational modification?
• Do you think it requires energy?

Telling proteins where to go:  Translation of proteins occurs in the cytoplasm, where mature ribosomes are located.   If no information is added, a newly synthesized polypeptide will remain in the cytoplasm, that is its default location.

Yet even in the structurally simplest of a cells, the prokaryotes (bacteria and archaea), there is more than one place that a protein may end up: it can remain in the cytoplasm, it can be inserted in the plasma membrane or it may be secreted from the cell. 

Both membrane and secrete polypeptides must be inserted into, or pass through, the plasma membrane.

Polypeptides destined for the membrane or for secretion are generally marked by a specific tag, known as a signal sequence.   The signal sequence consists of a stretch of hydrophobic amino acids, often at the N-terminus of the polypeptide. 

As the signal sequence emerges from the ribosome it interacts with a signal recognition particle or SRP - a complex of polypeptides and a structural RNA.

The binding of SRP to the signal sequence causes translation to pause.

The mRNA/ribosome/nascent polypeptide/SRP complex will find (by diffusion), and attach to, a ribosome/SRP receptor complex on the cytoplasmic surface of the plasma membrane.

This ribosome/SRP receptor is associated with a polypeptide pore. When the ribosome/SRP complex docks with the receptor, translation resumes and the nascent polypeptide passes through pore and so through the membrane.

As the polypeptide emerges on the extracytoplasmic side of the membrane, the signal sequence is generally removed by an enzyme, signal sequence peptidase.

If the polypeptide is a membrane protein, it will remain within the membrane. If it is a secreted polypeptide, it will be released into the periplasmic space.

• Is the signal sequence added post-translationally? 
• What is the difference, in terms of translation, between a protein with and one without a signaling sequence?  
• What would happen if you somehow put a signaling sequence at the beginning of a normally cytoplasmic polypeptide?

Eukaryotic cells are structurally more complex than prokaryotic cells; there are many more places for a newly synthesized protein to end up. 

While we will not discuss the details of that process, one rule of thumb is worth keeping in mind. 

Generally, in the absence of added information, a newly synthesized polypeptide will end up in the cytoplasm.

As in prokaryotes, polypeptides destined for secretion or insertion into internal membrane systems are directed to their final location by the signal sequence/SRP system.

Proteins that must function in the nucleus generally get there because they have a nuclear localization sequence or NLS.  

On the other hand, proteins can be excluded from the nucleus using a nuclear exclusion sequence or NES.

Likewise, other localization signals and sequences are used to direct proteins to other intracellular compartments. 

• There is a mutation in a gene that destroys the signaling sequence of polypeptide that is normally secreted; where is the mutant polypeptide in the cell?
• There is a mutation in a gene that destroys the NLS of a polypeptide; where is the mutant polypeptide in the cell?