epitope

portion of a molecule to which an antibody binds

a tag that you can put on a protein that an antibody will recognize

post-translational protein modification

what type of bonds

covalent modification of side chains in proteins after they are translated

target residues for phosphorylation

tyr

ser

thr

his

target residues for acetylation

lys,N-terminus

target residues for methylation

lys

p53

functions as tumor suppressor

18 phosphorylation sights

active when phosphorylated

transcription factor which regulates cell cycle

Rb protein

tumor suppressor protein

inactive when phosphorylated

inhibits cell cycle progression

binds E2F factor and keeps it from promoting mitosis

Rb protein induces growth arrest and cellular differentiation

src protein

(active and inactive)

protein participates in pathways that regulate cell growth

active:

Tyr 527 (C-terminus) unphosphorylated

Tyr 416 phosphorylated

inactive:

Tyr 527 (C-terminus) phosphorylated (clamps SH2)

Tyr 416 unphosphorylated

histone octomer

two each of :

H2A

H2B

H3

H4

Acetyl group

added to N terminal residue

phosphorylated amino acids

methyl group

heterochromatin methylated at

K9 of H3

also K27 of H3

euchromatin is methylated at

K4 of H3

Acetylation and Phosphorylation typically lead to ___ of gene expression

activation

how does methylation affect gene expression

can activate or silence

arabinogalactanproteins (AGPs)

major component of cell wall

helps stabilize the cell wall make it rigid

provide bulk around which cross-linking occurs

gets modified with O-linked glycans

and API anchors

SCF complex

skip 1

cullin

f-box

proteasome

26S

degrades proteins that have been polyubiquitilized

role of AAA ATPase in ubiquitin protein degradation pathway

ATPase recognizes marked protein and takes it to the 26S proteasome

APC^Cdc20

plays key role in euk cell cycle

targets mitotic cyclins for degradation, promoting exit from mitosis

E3 ligase

Cdc20 binds securin (recognizes its deadbox sequence)

and E3 ligase marks for degradation

separase

held inactive by securin which APC^Cdc20

marks for degradation

once securin is out of the picture, separase degrades scaffold protein that holds the two sister chromatids together and anaphase occurs

AXR6 mutant

resistant to auxin

cullin is mutated

AUX/IAA

transcriptional repressor

blocks auxin transcription factors

ARFs

auxin response factors

O-linked glycosylation

attach to hydroxy O of mainly Ser and Thr side chains

nuclear and cyoplasmic proteins can carry these modifications

GPI anchor

what does it do to the charge of the protein it's attached to?

glycosyl phospatidylinositol

carbohydrate post-tranl modification

links prots to lipids

glycolipid

important cell-cell signal

part of lipid rafts in plant & animal membranes

polarizes proteins

N-linked glycans

attach to amide N of asparagine side chains

plasma membrane proteins can carry these modifications

role of GPIs in AGPs and cell wall

help in assembly outside of the cell wall

help orient the cellulose microfibril cables (made of cellulose synthase)

in root, auxin ___ cell elongation

inhibits

in shoot, auxin ___ cell elongation

promotes

arrangement of histones in nucleosome

Trypsin

a serine protease

hydrolyzes proteins

predominantly cleaves peptide chains at carboxyl sides of arginine and lysine (except when either is followed by proline)

generally creates peptides of 20 residues or so

SH domain

domains in src family of cytoplasmic tyrosine kinases

SH1 is catalytic domain

SH2 and SH3 are protein binding domains

SH2 usually binds phosphotyrosine-containing proteins

SH2 in src protein

 phosphorylated Tyrosine 527 on C terminal of src protein binds SH2 domain, forming inactive clamp

acetylation of histones typically does what in terms of its lifespan?

protect against degradation

phosphorylated sites on histone 3

S28 and S10

glycolsylation

enzymatic process

links saccharides to produce glycans that are attached to proteins

majority of prots synthesized in the rough ER undergo glycosylation--perhaps 50%

ensure proper folding; stability of secreted prots

myristoylation

lipid modification

that helps direct proteins to membranes

common on glycine

prenylation

(farnesylation and genarylation)

addition of hydrophobic molecules to a protein

facilitate attachment to cell membrane

involves transfer of

farnesyl or geranyl moieties to C-term of cysteines

ubiquitin targets what residue?

lysine, via an isopeptide bond

glycosylhydrolase-47 family (GH47)

protein in ER that recognizes misfolded proteins (appears to bind glycan mofications)

securin deadbox sequence

E3 ligase recognizes deadbox sequence and adds ubiquitin chain

Cdc20

gives APC its specificity

binds securin

% of humans proteins that have been phosphorylated at some point

30%