exam 2 PTM Flashcards
what can protein function be regulated by
ligand binding (non-covalent interactions) and covalent interactions
what do post-translational modifications do broadly
change protein structure and function
what does proteolytic cleavage do
removes amino acids from the original translated sequence
what do covalent modifications of an amino side chain do
change their chemical properties
what can proteolytic cleavage specifically do
take off N-terminal methionine, remove signal sequence, and cut out sequences from inside protein
what does a protein having multiple potential modification sites do
allows you to change function of polypeptide over time
sum total of modifications can change function of protein
what is phosphorylation an addition of and to where
addition of a negatively charged phosphate to the R-group of serine, threonine, or tyrosine to their hydroxyl groups
what does phosphorylation do
coverts neutral amino acid to a negatively charged amino acid
what can bacterial cells phosphorylate
histidine residues - changes positively charged to negatively
where does a phosphate come from
ATP, forming the phosphorylated amino acid residue + ADP
what is phosphorylation catalyzed by
enzymes called protein kinases
what is phosphate removal catalyzed by
protein phosphatases
what adds phosphates
kinases
what removes phosphates
phosphatases
what does each phosphate group add to a protein
two negative charges
what does phosphorylation cause
structural, activity, and solubility changes
what can an added phosphate group create
a new recognition site
what does a new recognition site allow for
other proteins to bind to the phosphorylated protein
what is the SH2 domain
phosphotyrosine-binding motif
what happens to the SH2 domain when a protein is phosphorylated
SH2 domain can bind
what happens to the SH2 domain when a protein is not phosphorylated
SH2 domain cannot bind
what is ubiquitylation
the addition of ubiquitin - a small cytosolic protein
what is the structure of ubiquitin
compact with alpha helix and beta sheets, covalently attached to lysines of other proteins
what does ubiquitylation serve as
a tag - it’s a binding site for other cellular machinery
what does the tag of ubiquitylation mark proteins for and how
degradation by attaching a string of ubiquitin, which is recognized by proteasome to be degraded
what does the tag of ubiquitylation direct proteins to do
to go to specific locations in the cell - single ubiquitin attached to protein is a localization signal
is the cleavage of peptide bonds energetically favorable
yes - you get energy from cleaving
why is ubiquitin an important regulatory function
it marks proteins for specific degradation at specific times
does making ubiquitin and attaching it to proteins require energy
yes
what are ligands
molecules proteins bind to, which interact to regulate the function of protein
what determines a protein’s biological properties
a protein’s physical intereaction with other molecules
why is ligand binding reversible
it’s achieved by non-covalent bonds
is ubiquitylation a covalent or non-covalent modification
covalent
is phosphorylation a covalent or non-covalent modification
covalent
why must protein binding be strong
to withstand the jolting of molecules bumping into one another and instead adhere to each other
what is ligand binding strength achieved through
3D complementarity of binding or the formation of several non-covalent bonds
what occurs when the shapes of two molecules fit like puzzle pieces
they will be able to interact for a longer time than non-3D complementarity molecules
what occurs when having more non-covalent bonds
the more interactions, the better the interaction stability will be - strength in numbers
what dimension are ligand binding sites
3D
what comes together when a protein folds
amino acids that contribute to binding a ligand that are often far apart on protein’s primary sequence
what is how long two molecules take to come together classified by
k(on)
what is how quickly molecules separate once complex is formed classified by
k(off)
what contributes to strong binding
if molecules stay together for a long time
what happens if on rate is slow and off rate is fast
molecules will quickly fall apart from weak binding
what are k(on) and k(off)
the rates of the forward (association) and back-rate (dissociation) reactions that create or breakdown the protein-ligand complex
what is K(a)
the association constant: k(on) divided by k(off)
what is K(d)
the dissociation constant: 1/K(a)
what occurs with a bigger association constant
the stronger the binding is
what occurs with a smaller dissociation constant
the stronger the binding is
what is ATP
the source of phosphate groups
how can adding a phosphate to a protein change its structure
it turns it on or off
what is GTP
activated energy carrier
what does hydrolysis of GTP do
regulates protein function by changing non-covalent interactions
what happens if a protein is bound to GTP
protein is on
what happens if a protein is bound to GDP
protein is off
how does GDP become GTP become GDP
remove GDP and replace it with GTP to turn protein on, then hydrolyze it to form GDP, releasing the phosphate and turning it off
what occurs with a switch helix
hydrolyzing phosphates causes movement of the alpha helix, switching the protein from on to off
what is GEF
a regulatory protein which facilitates the exchange of GDP for GTP
what occurs very slowly
the exchange of GDP for GTP, along with the hydrolysis of GTP
what is the function of GAP
speed up proteins hydrolyzing GTP
how can proteins act as molecular integrators
by having multiple modification/interaction sites
what are cyclin dependent kinases
they’re involved in cell cycle regulation and their activity is regulated by
- phosphorylation at one site
- dephosphorylation at another
what activates a kinase
binding to another protein, cyclin
what are the three inputs needed to activate kinase
presence of cyclin, a signal to remove inhibitory phosphate, adding activating phosphate
