exam 2 PTM

Question 1

what can protein function be regulated by

Answer 1

ligand binding (non-covalent interactions) and covalent interactions

Question 2

what do post-translational modifications do broadly

Answer 2

change protein structure and function

Question 3

what does proteolytic cleavage do

Answer 3

removes amino acids from the original translated sequence

Question 4

what do covalent modifications of an amino side chain do

Answer 4

change their chemical properties

Question 5

what can proteolytic cleavage specifically do

Answer 5

take off N-terminal methionine, remove signal sequence, and cut out sequences from inside protein

Question 6

what does a protein having multiple potential modification sites do

Answer 6

allows you to change function of polypeptide over time

sum total of modifications can change function of protein

Question 7

what is phosphorylation an addition of and to where

Answer 7

addition of a negatively charged phosphate to the R-group of serine, threonine, or tyrosine to their hydroxyl groups

Question 8

what does phosphorylation do

Answer 8

coverts neutral amino acid to a negatively charged amino acid

Question 9

what can bacterial cells phosphorylate

Answer 9

histidine residues - changes positively charged to negatively

Question 10

where does a phosphate come from

Answer 10

ATP, forming the phosphorylated amino acid residue + ADP

Question 11

what is phosphorylation catalyzed by

Answer 11

enzymes called protein kinases

Question 12

what is phosphate removal catalyzed by

Answer 12

protein phosphatases

Question 13

what adds phosphates

Answer 13

kinases

Question 14

what removes phosphates

Answer 14

phosphatases

Question 15

what does each phosphate group add to a protein

Answer 15

two negative charges

Question 16

what does phosphorylation cause

Answer 16

structural, activity, and solubility changes

Question 17

what can an added phosphate group create

Answer 17

a new recognition site

Question 18

what does a new recognition site allow for

Answer 18

other proteins to bind to the phosphorylated protein

Question 19

what is the SH2 domain

Answer 19

phosphotyrosine-binding motif

Question 20

what happens to the SH2 domain when a protein is phosphorylated

Answer 20

SH2 domain can bind

Question 21

what happens to the SH2 domain when a protein is not phosphorylated

Answer 21

SH2 domain cannot bind

Question 22

what is ubiquitylation

Answer 22

the addition of ubiquitin - a small cytosolic protein

Question 23

what is the structure of ubiquitin

Answer 23

compact with alpha helix and beta sheets, covalently attached to lysines of other proteins

Question 24

what does ubiquitylation serve as

Answer 24

a tag - it’s a binding site for other cellular machinery

Question 25

what does the tag of ubiquitylation mark proteins for and how

Answer 25

degradation by attaching a string of ubiquitin, which is recognized by proteasome to be degraded

Question 26

what does the tag of ubiquitylation direct proteins to do

Answer 26

to go to specific locations in the cell - single ubiquitin attached to protein is a localization signal

Question 27

is the cleavage of peptide bonds energetically favorable

Answer 27

yes - you get energy from cleaving

Question 28

why is ubiquitin an important regulatory function

Answer 28

it marks proteins for specific degradation at specific times

Question 29

does making ubiquitin and attaching it to proteins require energy

Answer 29

yes

Question 30

what are ligands

Answer 30

molecules proteins bind to, which interact to regulate the function of protein

Question 31

what determines a protein's biological properties

Answer 31

a protein's physical intereaction with other molecules

Question 32

why is ligand binding reversible

Answer 32

it's achieved by non-covalent bonds

Question 33

is ubiquitylation a covalent or non-covalent modification

Answer 33

covalent

Question 34

is phosphorylation a covalent or non-covalent modification

Answer 34

covalent

Question 35

why must protein binding be strong

Answer 35

to withstand the jolting of molecules bumping into one another and instead adhere to each other

Question 36

what is ligand binding strength achieved through

Answer 36

3D complementarity of binding or the formation of several non-covalent bonds

Question 37

what occurs when the shapes of two molecules fit like puzzle pieces

Answer 37

they will be able to interact for a longer time than non-3D complementarity molecules

Question 38

what occurs when having more non-covalent bonds

Answer 38

the more interactions, the better the interaction stability will be - strength in numbers

Question 39

what dimension are ligand binding sites

Answer 39

3D

Question 40

what comes together when a protein folds

Answer 40

amino acids that contribute to binding a ligand that are often far apart on protein's primary sequence

Question 41

what is how long two molecules take to come together classified by

Answer 41

k(on)

Question 42

what is how quickly molecules separate once complex is formed classified by

Answer 42

k(off)

Question 43

what contributes to strong binding

Answer 43

if molecules stay together for a long time

Question 44

what happens if on rate is slow and off rate is fast

Answer 44

molecules will quickly fall apart from weak binding

Question 45

what are k(on) and k(off)

Answer 45

the rates of the forward (association) and back-rate (dissociation) reactions that create or breakdown the protein-ligand complex

Question 46

what is K(a)

Answer 46

the association constant: k(on) divided by k(off)

Question 47

what is K(d)

Answer 47

the dissociation constant: 1/K(a)

Question 48

what occurs with a bigger association constant

Answer 48

the stronger the binding is

Question 49

what occurs with a smaller dissociation constant

Answer 49

the stronger the binding is

Question 50

what is ATP

Answer 50

the source of phosphate groups

Question 51

how can adding a phosphate to a protein change its structure

Answer 51

it turns it on or off

Question 52

what is GTP

Answer 52

activated energy carrier

Question 53

what does hydrolysis of GTP do

Answer 53

regulates protein function by changing non-covalent interactions

Question 54

what happens if a protein is bound to GTP

Answer 54

protein is on

Question 55

what happens if a protein is bound to GDP

Answer 55

protein is off

Question 56

how does GDP become GTP become GDP

Answer 56

remove GDP and replace it with GTP to turn protein on, then hydrolyze it to form GDP, releasing the phosphate and turning it off

Question 57

what occurs with a switch helix

Answer 57

hydrolyzing phosphates causes movement of the alpha helix, switching the protein from on to off

Question 58

what is GEF

Answer 58

a regulatory protein which facilitates the exchange of GDP for GTP

Question 59

what occurs very slowly

Answer 59

the exchange of GDP for GTP, along with the hydrolysis of GTP

Question 60

what is the function of GAP

Answer 60

speed up proteins hydrolyzing GTP

Question 61

how can proteins act as molecular integrators

Answer 61

by having multiple modification/interaction sites

Question 62

what are cyclin dependent kinases

Answer 62

they're involved in cell cycle regulation and their activity is regulated by - phosphorylation at one site - dephosphorylation at another

Question 63

what activates a kinase

Answer 63

binding to another protein, cyclin

Question 64

what are the three inputs needed to activate kinase

Answer 64

presence of cyclin, a signal to remove inhibitory phosphate, adding activating phosphate