Cell Bio ch 4-16

Enzyme Rate of Disassociation and Association “Turnover Rate”

Bond strength

How tightly packed the molecules are

How often they collide

How much substrate exists in the cell

Enzyme activity

Quantity of enzyme

Highly Regulated !!!

Accessibility of enzyme/substrate

Subcellular location

Scaffolding proteins

Feedback Inhibition

An enzyme acting early in a reaction is stopped by a late product in the pathway

Often acts allosterically

Negative Feedback

Ex: When an amino acid is synthesized, it inhibits the reaction. When the amino acid is used up, the cell stops the inhibition to remake the amino acids.

Positive Feedback

What does Ligand Bonding do?

It stabilizes conformation in order to increase enzyme activity

Allosteric Feedback inhibition

Many proteins are allosteric

They can adopt 2+ slightly different conformations

Allosteric binding shifts protein from one form to another ( active v inactive )

Can regulate activity

binding sites for ligands are altered when protein changes shape

Chemical Modifications

Can act as an on/off switch

Phosphorylation is the most common form of this. The addition of a PO4 group can “flip” polarity

Also known as Post Translational Modification

Covalent Modifications

Control location + assembling of proteins

Post translational Modification

Forms “Regulatory Protein Code” aka the protein to do list

20 Modifications = a lot of combos = the behavior of the proteins can be altered in MANY different ways

Protein Machines

Large complexes

Individual proteins which collaborate for a specific task (Quaternary)

Ex: Unwinding DNA in a damaged area

GTP Binding Proteins

Regulated by the cycle of the phosphate group being gained and lost

Protein whose conformation + activity is determined by its association with GTP or GDP

Resetting the switch requires the tightly bound GDP to dissociate, a slow step that is greatly accelerated by specific signals

Active and Inactive formation fall under this

Active Formation

GTP bound

Inactive Action

Protein hydrolyzes GTP to GDP → Releases phosphate and flips to inactive conformation

Nucleotide Hydrolysis

Conformational changes occur in response to it

Hydrolysis of GTP causes a small shift in structure (0.1 nm), but this gets exaggerated due to the shape of the protein allowing the complex to open and release the tRNA

GTP hydrolysis releases an intramolecular bond, like a ‘latch’ (red arrows), which allows domain 2 & 3 to rotate and release tRNA (from slides, unsure which parts we need to know)

Protein Movement

Proteins walk by using ATP Hydrolysis

Signaling Cascade

Cells send signals and it ends with making proteins which can function in various ways

Endocrine

Hormonal

Long distance, goes in bloodstream

Ex) Epinephrine

Paracrine

Localized

Within 1 organ

Neuronal

Neurons

Very fast

Electrical signaling

Contact Dependent

Must be touching