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BSCI330 SPRING > exam 2 PTM > Flashcards

exam 2 PTM Flashcards

1
Q

what can protein function be regulated by

A

ligand binding (non-covalent interactions) and covalent interactions

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2
Q

what do post-translational modifications do broadly

A

change protein structure and function

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3
Q

what does proteolytic cleavage do

A

removes amino acids from the original translated sequence

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4
Q

what do covalent modifications of an amino side chain do

A

change their chemical properties

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5
Q

what can proteolytic cleavage specifically do

A

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

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6
Q

what does a protein having multiple potential modification sites do

A

allows you to change function of polypeptide over time

sum total of modifications can change function of protein

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7
Q

what is phosphorylation an addition of and to where

A

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

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8
Q

what does phosphorylation do

A

coverts neutral amino acid to a negatively charged amino acid

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9
Q

what can bacterial cells phosphorylate

A

histidine residues - changes positively charged to negatively

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10
Q

where does a phosphate come from

A

ATP, forming the phosphorylated amino acid residue + ADP

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11
Q

what is phosphorylation catalyzed by

A

enzymes called protein kinases

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12
Q

what is phosphate removal catalyzed by

A

protein phosphatases

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13
Q

what adds phosphates

A

kinases

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14
Q

what removes phosphates

A

phosphatases

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15
Q

what does each phosphate group add to a protein

A

two negative charges

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16
Q

what does phosphorylation cause

A

structural, activity, and solubility changes

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17
Q

what can an added phosphate group create

A

a new recognition site

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18
Q

what does a new recognition site allow for

A

other proteins to bind to the phosphorylated protein

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19
Q

what is the SH2 domain

A

phosphotyrosine-binding motif

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20
Q

what happens to the SH2 domain when a protein is phosphorylated

A

SH2 domain can bind

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21
Q

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

A

SH2 domain cannot bind

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22
Q

what is ubiquitylation

A

the addition of ubiquitin - a small cytosolic protein

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23
Q

what is the structure of ubiquitin

A

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

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24
Q

what does ubiquitylation serve as

A

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

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25
Q

what does the tag of ubiquitylation mark proteins for and how

A

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

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26
Q

what does the tag of ubiquitylation direct proteins to do

A

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

27
Q

is the cleavage of peptide bonds energetically favorable

A

yes - you get energy from cleaving

28
Q

why is ubiquitin an important regulatory function

A

it marks proteins for specific degradation at specific times

29
Q

does making ubiquitin and attaching it to proteins require energy

A

yes

30
Q

what are ligands

A

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

31
Q

what determines a protein’s biological properties

A

a protein’s physical intereaction with other molecules

32
Q

why is ligand binding reversible

A

it’s achieved by non-covalent bonds

33
Q

is ubiquitylation a covalent or non-covalent modification

A

covalent

34
Q

is phosphorylation a covalent or non-covalent modification

A

covalent

35
Q

why must protein binding be strong

A

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

36
Q

what is ligand binding strength achieved through

A

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

37
Q

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

A

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

38
Q

what occurs when having more non-covalent bonds

A

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

39
Q

what dimension are ligand binding sites

A

3D

40
Q

what comes together when a protein folds

A

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

41
Q

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

A

k(on)

42
Q

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

A

k(off)

43
Q

what contributes to strong binding

A

if molecules stay together for a long time

44
Q

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

A

molecules will quickly fall apart from weak binding

45
Q

what are k(on) and k(off)

A

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

46
Q

what is K(a)

A

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

47
Q

what is K(d)

A

the dissociation constant: 1/K(a)

48
Q

what occurs with a bigger association constant

A

the stronger the binding is

49
Q

what occurs with a smaller dissociation constant

A

the stronger the binding is

50
Q

what is ATP

A

the source of phosphate groups

51
Q

how can adding a phosphate to a protein change its structure

A

it turns it on or off

52
Q

what is GTP

A

activated energy carrier

53
Q

what does hydrolysis of GTP do

A

regulates protein function by changing non-covalent interactions

54
Q

what happens if a protein is bound to GTP

A

protein is on

55
Q

what happens if a protein is bound to GDP

A

protein is off

56
Q

how does GDP become GTP become GDP

A

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

57
Q

what occurs with a switch helix

A

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

58
Q

what is GEF

A

a regulatory protein which facilitates the exchange of GDP for GTP

59
Q

what occurs very slowly

A

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

60
Q

what is the function of GAP

A

speed up proteins hydrolyzing GTP

61
Q

how can proteins act as molecular integrators

A

by having multiple modification/interaction sites

62
Q

what are cyclin dependent kinases

A

they’re involved in cell cycle regulation and their activity is regulated by

  • phosphorylation at one site
  • dephosphorylation at another
63
Q

what activates a kinase

A

binding to another protein, cyclin

64
Q

what are the three inputs needed to activate kinase

A

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

BSCI330 SPRING (24 decks)

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