BSCI 330 Exam II - protein shape and structure II

post-translational modification

changes made to polypeptides following translation

- covalent mod of AA side changes chemical properties
- proteolytic cleavage removes AA from original translated sequence
- proteins may have multiple modification sites---not all of which are used at the same time

- reversible - can switch between states dynamically

phosphorylation

- addition of negatively charged phosphate group to the R group of: threonine, tyrosine, and serine (IN EUK)
- many changes in protein structure and activity are driven by phosphorylation

ex.
- serine R: -CH2-OH
- phosphoserine R: -CH2-O-PO3(-2)
- transient modification
- sequence protein will still be serine

phosphate

- comes from ATP
> phosphorylated AA residue
> ADP

- non spontaneous
- ATP hydrolysis is irreversable (except in mt)

protein kinases

- catalyzes phosphorylation
- each kinase phosphoralizes one kind of molecule (ex. carbokinase, lipid kinase, protein kinase)

- need 1 ATP (energenetically expensive)

protein phosphatases

- phosphate removal; reverses phosphorylation (ex. lipid phosphatase, carb phosphatase, protein phosphatase)

-2 charge

- per phosphate group

- drives major structural changes
- activity changes
- or changes to protein solubility

- added p group creaes new recognition site that allows other proteins to bind to phosphorylated protein

ex. SH2 domain is a phosphotyrosine binding motif (recognizes tyrosine in a specific sequence context

ubiquitin

- 76 amino acid protein; 8 kilodaltons (only modificaiton that is a protein itself)
- small cytosolic protein
- covalently attached to proteins (reversable; can recycle ubiquidin after degredation)

- 2 ATP per ubiquidin added
- localization can change

- acts as a large tag:

> chain marks protein for regulated degredatio by another multiprotein complex (protreasome)
> single directs proteins to specific locations in the cell (locamotion

small ubiquitin muyideen

- SUMO
- changes localization
- isn't involved in degredation

ligand binding

- proteins bind to other molecules
- every protein must interact with something

- protein's physical interactions with other molecules determines its biological properties
- reversible - LB is achieved by non-covalent bonds

ligand

the "other molecule"

receptor

what we are interested in describing function-wise

strength of LB

- what determines it?
- molecles are in constant motions- always bumping into one another
- binding must be strong enough to withstand jolting of molecular motions
- binding strength is achieved through:

1. 3D complementary binding (how tightly do the 2 pieces fit together, i.e ball/socket vs barely touching)
2. several non-covalent bonds (strength in numbers)

LB sites

- 3D
- amino acids that contribute to binding a ligand are far apart on a protein's primary sequence
- come together when protein folds (becomes 3D)

AB

- protein ligand complex
= A + B (protein + ligand)

Kon

forward/association

Koff

backward/dissassociation

Ka

= Kon/Koff

- association constant; measures the strength of binding

1/Ka

- dissociation constant
- affinity of binding
- concentration of how much ligand is needed ot achieve 50% saturation

more Kd

weaker AB bind

less Kd

stronger AB bind

antibody binding

- Kd of 10^-12 M
- needs to be really strong for its function
- one of the strongest in the cell

calmodulin binding

- Kd og 10^-6 M
- not as strong
- so we can let go when we want

GTP

- guanosine triphosphate
- activated energy carrier
- binds to protein to regulkate their activity

- costs 1 ATP to hydrolize (like hydrolizing ATP costs 1 ATP)
- hydrolysis rate is slower

- if protein binds to GTP, it says on until it receives help
- if protein binds to GDP, it stays off

multiple modification sites

allows proteins to act as molecular integrators

ex. cyclin dependent kinases
- cell cycle regulation
- regulated by:
1. phosphorylation at one site
2. dephosphorylation at another site
3. binding to another protein (cyclin) at another site