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ANAT 212 > Lecture 4 > Flashcards

Lecture 4 Flashcards

1
Q

describe ptm

A

post translational modifications
proteins can be chemically modified after translation to get new functions

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2
Q

why are post translational modifications important

A

important contribution to proteomic diversity and complexity and are essential for regulation of protein function and cellular signalling
like switch - allows new functions

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3
Q

name diff types of modifications

A

phosphorylation
cleaved into smaller proteins by peptidases - transmembrane proteins
covalent modifications of N terminus - co translational, not talked about much
covalent modification of side chains = introduce functional groups to proteins

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4
Q

what are side chain modifications used for

A

various cellular functions

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5
Q

name and describe cellular functions side chain modifications are used for

A

can change surface of conformation of protein
can create or block a binding site (active site) for other proteins
many modifications are regulated and reversible
Modifications are fast and useful as switches, active/inactive, on/off, functions

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6
Q

what are all ptms mediated by

A

enzymes
follow rules of ochem

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7
Q

name main types of modifications

A

phosphorylation
methylation
acetylation
glycosylation, sumoylation, ubiquitination

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8
Q

describe phosphorylation

A

major regulatory mechanism
phosphorylation on hydroxyl groups - S,T,Y
adding a phosphoryl group changes the charge and size
30% of proteins in cells

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9
Q

describe serine phosphorylation

A

serine –> phopshoserine = larger, polar, neg charge, ionic and electrostatic interactions now

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10
Q

describe kinases - phosphorylation

A

transfer phosphates from atp
500 diff ones
specific for side chain and the surrounding peptide sequence

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11
Q

describe phosphatases - phosphorylation

A

remove phosphates
reversible

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12
Q

describe ptm - phosphorylation of s,t,y - kinase families

A

ser/thr kinases
tyr kinases - add to these
dual specificity - ser/thr and tyr
tyrosine has diff structure

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13
Q

describe ptm - phosphorylation of s,t,y - phosphatase families

A

ser/thr phosphatases
protein tyr phosphatases
dual specificity - ser/thr and tyr

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14
Q

describe the role of phosphorylation in protein function

A

phosphomimic - S by D = sub serine by aspartic acid, phosphoserine synthesized in lab, similar structure - size use trick
de-phosphorylated - S by A = serine by alanine, never get neg charge with alanine, substitution

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15
Q

describe phosphopeptide binding

A

specialized domains bind p-ser, p-thr or p-tyr
phosphorylation is required for binding
surrounding polypeptide sequence also contributes

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16
Q

explain example of phosphopeptide binding = WD40 domain of Cdc4 with the Sic1 CPD peptide with pThr

A

high turnover of proteins during cell cycle
Cdc4 is present in mitosis then degraded
sic1 CPD peptide = present in cell, in certain states of cell cycle and then degraded in others
pThr has to be phosphorylated for degradation and is neg charged and can interact with arginine
positive charge then can engage in interactions, gives time for it to be ubiquitinated and therefore degraded ON arg534

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17
Q

describe what phosphorylation does

A

Determines stability
signal to degrade proteins
only phosphorylated proteins are ubiquitinated

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18
Q

describe acetylation of lysine

A

acetylation of lys amine changes polarity - isopeptide bond
lysine - k - acetyltransferases = KATs and deacetylases KDACs, originally histone acetyltransferases = recognize specific sequences
signalling and metabolic effects

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19
Q

what changes can lysine go through after being acetylated

A

increase in size
change in charge = no more electrostatic interactions

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20
Q

describe histone acetylation - gen

A

active transcription
HATs- important for transcription

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21
Q

describe histone acetylation - detailed

A

lysine - pos charge = ionic or electrostatic interactions, compact chromatin since dna neg, no transcription
compact chromatin since dna neg and hides dna, mark unaccessible regions
weaker interaction with dna, now = accesible and can induce translation

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22
Q

what does acetyl coa do

A

gives acetyl group

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23
Q

describe methylation of arginine

A

methylation of arginine = involves addition of 1 or 2 methyl groups to guanidino group= mono or di
methylarginines = not well understood how methylated
add size to k and r

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24
Q

how many methyls can lysine have - describe methylation of lysine

A

mono, di, or trimethylated

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25
Q

what are KMTs and KDMs

A

lysine methyltransferases = KMTs
lysine demethylases = KDMs

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26
Q

describe PTM binding

A

consequences for transcription and dna repair mechanisms
like phosphorylation, acetylation and methylation provide new binding sites for proteins
Specific domains bind Ac-Lys, Me-lys, Me-arg and surrounding sequences
play an important role in transcription regulation

27
Q

what are methylations and acetylations important for

A

regulation of transcription
chromatin and dna repair

28
Q

when do ptms happen

A

when protein folded

29
Q

describe protein folding - depends on

A

folded structure depends on hydrophobic interactions in the interior of the structure
polar side chains found on outer surface

30
Q

what is the native state

A

completely folded conformation of a protein
functional conformation of a protein

31
Q

when do side chain modifications take place

A

usually after folding is complete

32
Q

name and describe interactions important for folding

A

polar = can bond with other proteins and make soluble, far away comes together

hydrophobic interactions = many, strong
h bonds = many, moderate
van der waals interactions = many, weak
ionic bonds = few, v strong, since only 5 aas
disulfide bonds = few, very strong covalent, since only 1 aa

33
Q

what do H bonds do - for folding

A

stabilize secondary structures – involve peptide bond= backbone

34
Q

what do hydrophobic interactions do - for folding

A

hydrophobic interactions between secondary structures form the tertiary structures –> involve side chains

35
Q

what is native structure determined by

A

primary sequence of aa

36
Q

what is state of native structure

A

state of minimal energy - folding is thermodynamically favoured = ΔG neg, free energy, lower than that 0, that of primary structure, see if active

37
Q

is folding spontaneous

A

can be spontaneous in principle but assisted by diff biological mechanisms

38
Q

describe the folding process

A

complex process - diff free energy conformations
unfolded (denatured) domains have extended conformations with no secondary or tertiary structure
folding proceeds through intermediates that have increasing structure to native state

39
Q

describe flexibility of protein structures

A

primary = very flexible, moves a lot, flexibility of alpha carbons
secondary = less flexible
native state = one structure usually, folding goes through intermediate states

40
Q

what is the native state - stability

A

native state is most stable conformation of protein
native state can be in eq with near native folding intermediates

41
Q

what is native state stabilized by

A

hydrophobic contacts - exclusion of water
faces interior of protein

42
Q

are all domains of native state stable

A

NOOO
some domains need a ligand partner to be stable
cofactor (haem, steroid, etc) or another protein subunit

43
Q

describe folding of native state - gen

A

get closer together in structure
native state can be in eq - stabilized with an intermediate state

44
Q

describe folding intermediates

A

have some secondary structure, but tertiary structure incomplete
some hydrophobic side chains exposed instead of buried
more of the polypeptide is flexible and disordered

45
Q

describe folding intermediates - risk of aggregation

A

hydrophobic regions prefer to be in contact with others
Interaction between diff unfolded proteins leads to insolubility
fried egg

46
Q

describe intermediate vs native state

A

intermediate - some regions hydrophobic residues face water = high risk aggregation, salvation cages, makes protein v unstable, if other proteins close = aggregates and misfolded proteins
when native state = all in right state, not as risky for misfolding

47
Q

describe protein misfolding

A

leads to incompletely folded proteins
immediately after protein synthesis = needs time to fold
if require ligand not available - like cofactor = hydrophobic residues visible

48
Q

name reasons for protein misfolding

A

genetic mutations
harmful environmental conditions
aging
also the require ligand thing

49
Q

explain genetic mutation - protein misfolding

A

leads to misfolded proteins and disease
eg - sickle cell anemia and cystic fibrosis

50
Q

explain harmful environmental conditions - protein misfolding

A

eg heat, like global warming too
leads to unfolding and misfolding of properly folded proteins

51
Q

describe aging - protein misfolding

A

descrease efficiency of protein quality control mechanisms –> loss of protein homeostasis –> harmful aggregates of a misfolded protein eg amyloid –> neurodegeneration (Alzheimer, parkinsons, als, dementia)

52
Q

describe types of genetic mutations

A

can lead to changes in polypeptide sequences = aa substitution, indels, premature stop (cannot achieve native state)
allelic variations sometimes cause genetic disease

53
Q

what happens if aa similars or divergent for genetic mutations

A

sub to similar aa = may have little or not effect
sub that greatly changes aa properties = can disrupt folding or function of protein

similar = maybe nothing
divergent = maybe cannot fold, so bad

ex =
phe to ser and ser to leu = both pathogenic
asp to asn = not pathogenic

54
Q

describe pressure to fold for proteins

A

crowded environments= 10^5 - 10^6 total mrnas and 10^10 total proteins
so lots of pressure to fold properly
have help with chaperones = hold them and helps them fold

55
Q

what is protein homeostasis

A

proteostasis
refers to an extensive network of components that acts to maintain proteins in the correct concentration, conformation, and subcellular location, to cooperatively achieve the stability and functional features of the proteome

56
Q

what are chaperones

A

center of protein quality control network
not part of native state tho
molecular chaperones assist folding and prevent aggregation

57
Q

describe chaperones - gen

A

hydrophobic residues showing so chaperones protect and once full protein is out = folds, maybe with help
if aggregates = chap can help refold
sometimes only way is to degrade protein= proteasome

58
Q

what do chaperones recognize

A

exposed hydrophobic regions of folding intermediates, since should be on inside

59
Q

when are chaperones expressed

A

Constitutively expressed
essential under non stress conditions

60
Q

what are many chaperones

A

heat shock proteins = HSPs
temp goes ip and need more proteins to stop aggregates
high expressed after stress
eg = HSP70 is the 70kda HSP

61
Q

describe ptms - summary

A

covalently add a functional group to a side chain modifying the functional interactions of a protein are important for several cell functions like signalling and metabolism
reversible and used as a switch

62
Q

describe protein folding - summary

A

Determined by aa sequence and their hydrophobic and noncovalent interactions
polypeptide chains transition over several intermediate folding structures before acquiring native stage = stage of minimal energy, protein folding is spontaneous

63
Q

describe chaperones - summary

A

families of proteins
assist in cellular protein folding and provide protein quality mechanisms to ensure homeostasis and avoid protein misfolding/aggregation
Constitutively expressed and essential under non stress conditions

ANAT 212 (34 decks)

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