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114 Cards in this Set

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  • Back
an integrin ONLY involved in hemidesmosomes - i.e. linking KERATIN to the ECM

a laminin binding integrin
Ser-Lys-Leu (SKL)
- a tri-peptide targeting signal at the C-terminal that marks the protein for import into peroxisomes.
protein import into peroxisomes requires ...
ATP hydrolysis, because there is NO electrochemical gradient across the peroxisomal membrane
Peroxisomal targeting signal receptor - binds sequence and directs the catalyse tetramer to be imported.
Mechalis Menten
Km + [s]
Kdiss =
Kdiss = 1/Kassoc =
What are the x and y axis of a scatchard? And what is the scattchard equation
Y axis = B/F
X axis = B

B/F = (-1/Kd)x + Bmax/Kd
What can you get off a scatchard?
* you can get Kd and Bmax

slope = -1/Kd
X intercept = Bmax

think of it as a lineweaver burke for affinity
For a hormone binding plot, what are the x and y axis?
x axis is [F] (concentration of free hormone)

y axis is B is bound hormone or bound receptor
Compare the rate of transport between the two general classes of membrane transport proteins
- carrier : 100 molecules/sec (slow)

-channel: 10,000,000 molecules/sec (fast)
What are the three different ways to drive active transport?
- coupled carrier (symport or antiport)
- ATP driven pump (primary active transport)
-light driven pump (secondary active transport)
What is the rate of simple diffusion determined by?
The rate of simple diffusion is proportional to the concentration gradient of the solute across the bilayer.
another word for facillitated diffusion?
passive transport
facillitated diffusion vs. facillitated transport?
Facillitated transport refers to ionophores, while facillitated difusion revers to passive transport
What are the types of primary active transport proteins?
- F-ATPase (mitochondria)
V-ATPase - vacuolar - ATP hydrolysis and proton movement

- P-ATPase -transport protein is reversibly phosphorylated during transport

-ABC binding casette - ATP hydrolysis causes mechanical pumping action
describe secondary active transport
- generally ATP hydrolysis establishes an electrochemical gradient of the co-transported molecule

i.e. ATP hydrolysis sets up the concentration gradient for Na+, then Na+ going down its concentration gradient can be coupled to glucose moving up its concentration gradient
think sodium glucose transporter
an example of ion driven active transport
blocks the sodium/potassium transporter
What types of molecules can pass between gap junctions?
What is the fifth way to desensitize a target cell (the one that you always forget)?

What is the point (2) of target cells becoming desensitized to signal molecules
- production of inhibitory protein

Reasons to become desensitized -
-too many signalling proteins
-adjust the sensitivity of the signal.
The main places that sorting signals will direct a protein are:
-ER (endoplasmic reticulum)
Where are phospholipids synthesized
Three functions of the SER
-site of PHOSPHOLIPID synthesis
-detoxification of lipid soluble drugs
-storage site of Ca++
Four important chaperone proteins found in the ER that are involved in quality control
-Protein disulfide isomerase
a chaperons prtoein found in the ER that is involved in quality control

BIP sees hydrophobic ares on misfolded proteins and binds to them
protien disulfide isomerase
a chaperons prtotein found in the ER that is involved in quality control

- catalyzes rearrangement of disulfide bonds, so that they can achieve the most thermodynamically stable configuration
The lipids and proteins for the membranes of which cellular components are synthesized in the ER?
For the ER, the golgi, the lysosome, and the plasma membrane
Where do proteins and lipids from the golgi go?
1) plasma membrane
2) lysosome
3) the cell surface to be secreted.
Leydig cells

Granulosa cells
LC - in testes, secrete hormones

GC - in ovaries secrete hormones
SRP, where is it found?
SRP - signal recognition peptide
for cotranslational translocation

for bringing peptides into the ENDOPLASMIC RETICULUM
signal peptidase
cleaves off the signal sequence of a protein that is being translocated into the ER lumen
What is the difference in signal sequence between a soluble ER protein, a transmembrane ER protein and a resident ER protein?
- soluble ER - just an ER signal sequence and a start sequenc e

- transmembrane ER - an ER signal sequence, a start sequence and a stop sequence

- resident ER protein - an ER signal sequence, a start sequence, and a KDEL sequence
What end is the KDEL sequence on?
What are the types of post-translational modifications that can occur in the RER?
1) glycosylation
2) cleavage of peptide signal
3) addition of oligosaccharide, dimerization
5) Conformational changes
chaperone that binds N-glycoproteins with GlcNac

-A LECTIN Chaperone
-is a membrane protein
calreticulin binds

-A LECTIN Chaperone
-is in the ER lumen
positive inside rule
determines the orientation of transmembrane proteins in the ER - basically the + charge wants to be on the cytostolic (inside) side
ER resident signals
-LysLys or ArgArg (these can bind and interact with COPI and therefore be in vesicles going retrograde
What is the difference in type between nucleoside analog drugs (like AZT, didanosine), Nevirapine, and indinavir?
NAD - competitive inhibitor of the substrate molecule (weird)

nevirapine - noncompetitive inhibitor of the enzyme reverse trancscriptase

indinavir - competive inhibitor of the viral protease (enzyme) (rather normal)
cholera (as an example)
inhibits GTPase activity causing the G protein alpha unit to remain activated
Explain how the system of second messengers can provide an amplkification of the hormone signal
- because a rise in a second messenger can effect gene transcription

-e.g. cAMP can bind PKA and activate it and cause it to go into the nucleus where it can effect gene transcription
think G protein & cAMP. Basically how gene transcription is activated by a rise in cAMP
activated by PKA due to a rise in cAMP, can effect gene transcription

- a response element found in genes activated by cAMP
found in the inositol phospholipid pathway
amplification of erbB2 is associated with breast cancer development
HER 2/neu (aka erbB2) is essentially an EGFR (epidermal growth factor receptor

to treat HER2/neu positive
- typically associated with the activation of tyrosine kinase receptors

-RAS is a monomeric GTP binding protein that activates downstream MAP-Kinases like ERK

involved in transmitting growth factor signals to the nucleus
Think Ras GEF -
Guanine nucleotide factor

this ia an adapter protein that helps activate RAS in the tyrosine kinase pathway by exchanging GDP for GTP
What type of kinase is MAP kinase?
- serine threonine phosphorylaters
What's the slope on a lineweaver burke plot?
- km/Vmax
What two adhesins do H.pylori have? What do they do?
-BabA (binds LeB)
-SabA (binds sLex), s is for sialyl

They are adhesins (A is for adhesin) that help H.pylori attach to the stomach lining
Adhesin found on H. pylori that(binds LeB in gi
- adhesin found on H. pylori that (binds sLex), s is for sialyl
receptor in gi, that is the site of attachement of H. pylori (BabA adhesin on H. pylori)

this stimulates bacterial growth
receptor in gi, that is the site of attachement of H. pylori (SabA adhesin on H. pylori)
What unusual substance can prevent H. pylori growth in stomach? How does it prevent bacterial proliferation?
the mucousal gland cells generate a mucin (terminal alpha-GlcNac) that is an antibiotic that prevents the proliferation of the H. pylori

It prevents glucosylation of the cholesterol in the H. pylori, without glucosylation the H. pylori cannot survive.
terminal sugar in a mucin secreted by the mucusoal gland that prevents proliferation of H. pylori
What is the terminal sugar in a mucin secreted by the mucusoal gland that prevents proliferation of H. pylori
where does glycosylation occur?
In the golgi!!! (outside of the cell!!)
glyco as in glycosyltransferase means ...
transfer of carbohydrate
What enzyme removes sugars and which enzyme adds sugars?
Glycosyltransferase: Enzyme which adds sugars (transfers
from sugar nucleotide to protein/lipid)

Glycosidase: Enzyme which removes sugars
describe/ draw the glycosyltransferase reaction
-sugars are added as nucleotide sugars
- the glycosyltransferase transfers only the sugar leaving behind the nucleotide diphosphate
What is the one exception to glycosyltransferase transfering only the sugar and leaving behind the nucleotide diphosphate?
- M-6-P glycosylation - a sugar and a phosphate is added, and a UMP instead of the normal UDP is released.
What does galactosyltransferase do?
-it ONLY transfers galactose to the protein
-it is specific in terms of whether an alpha or beta bond is formed.
why glycosylate
-shock absorbers
-helps proteins fold correctly
-cell-cell recognition (think leukocytes in extravasation)
-TARGETING (like M-6-P)
sialyl transferase is added in the
golgi !
what amino acid is involved in your n-linked sugar
- asparagine
what amino acid is involved in your o-linked sugars?
-serine or threonine
A Glycophorin is a sialoglycoprotein of the membrane of a red blood cell.
GalNAc T’ase - where?
GalNAc T’ase is localized in
rough ER
SA - what is it and where?
NANA (or sialic acid) T’ase is
localized in trans golgi
network (TGN)
Gal T’ase - where?
Gal T’ase is in trans golgi
transferase sialic acid - in the TGN, is the terminal sugar in O linked
what sugar is never found in an N linked sugar?
GalNAc (N-linked has a gluNac)
what kind of sugar linkages do proteoglycans have?
What is unusual about proteoglycans?
they have a high carbohydrate to protein ratio?
What are the subunits of a GAG?
Repeating disaccharide containing an acid
sugar (Glucuronic or iduronic acid) and an
amino sugar (GlcNAc or GalNac)
Consensus sequence for Nglycosylation
- dolipol serve as a structure on which an en bloc carbohydrate can be built, the whole carbohydrate can then be added en bloc from the dolipol to the target aa.

- the 14 sugar residue precursor that is added to proteins to make N-linked sugars
composition of the N-linked 14 en bloc carbohydrate
added outside ER
-2 glcNac
-5 mannose

added on ER lumen
-4 mannose
-3 glc
What are the two types of N-linked sugards?
- complex
-high mannose
what is the major signalling molecule for getitng rid of senescent cells
-marker of old cells
What enzymes are involved in synthesis of mannose-6-phosphate recognition sequences on proteins?
What is special about it?
- N-acetylglucosamine phosphyltransferase
- it is special because it transferase sugar-P instead of just sugar. UMP is cast of instead of UDP

-and N-acetylglucosamine phosphodiesterase?
blocked phosphate
- when adding a m-6-p recognition sequence, a sugar-P is added on, the sugar blocks the P and will be cleaved off in a subsequent step
o-linked examples
-h. pylori recognition
-blood cell types
-proteoglycans - o-linked GAG chains
n-linked examples
-carbohydrate recognition in germ cells - sperm recognize sertoli cells
-M6p recognition sequence
In a proteoglycan, what attaches the GAG chain to the core protein?
- a tetrasaccharide attaches the GAG chain ot the core protein
homotropic effect
think cooperativity - it means that the molecule causing the cooperativeity is the one that will be affected by it
What is K0.5
K0.5 is a measrue of cooperativity

K0.5>1 have + cooperativity
K0.5 <1 have - cooperativity
Allosteric modification
generally refers to regulation of a long metabolic pathway, think
1. feedback inhibition
2. blocking at the committed step

allosteric enzymes usually have a change in K0.5 but not a change in Vmax

Tyr-X-X-φ or Leu-Leu
bind to μ2 subunit of AP2
(LDLR, TfR, M6PR have
AP 2 PM --> endosome (Receptor-mediated endocytosis)
Tyr-X-X-φ or Leu-Leu
bind to μ2 subunit of AP2
(LDLR, TfR, M6PR have
AP 2 PM --> endosome (Receptor-mediated endocytosis)
Assembly particle/adaptor proteins,
Bind the globular head of clathrin heavy chain and the cytosolic tail
of receptors
Three classes mediate transport between different organelles:
AP 1 Trans golgi --> endosome (Man 6 P receptor)
AP 2 PM --> endosome (Receptor-mediated endocytosis)
AP 3 Trans golgi --> lysosomes
Cytosolic G protein
• Subunits polymerize around
neck of vesicle
• Binds GTP
• Hydrolyzes GTP to promote
fusion of membranes
and vesicle formation
ADP-ribosylation factor
assembly of COP-I
(no GDI)
Sar 1
assembly COP-II
(no GDI)

binds G-protein
targeting of vesicles
(bound to GDI in cytosol)
uncoating ATPase
a chaperone protein of the heat shock
protein 70 family (hsp70)
Relase of clathrin requires the action of an uncoating
a vesicle associated protein, is thought to
activate the ATPase
consists of 7 polypeptides (α,β,β’,
γ, δ, ε, and ζ COP)

-like clathrin
β COP is similar to adaptor
proteins of clathrin
Controls movement of vesicles from ER to cis golgi
transmembrane proteins with cytosolic

COP II-dependent transport
used for targeting
found on the vesicle
used for targeting
found on the target membrane
sec 23/24
think COP II
sec 12
guanine nucleoside exchange factor for COP II
Rab protein
a regulator of fusion - all you need for fusion is V-SNARE, T-SNARE, and Snap 25, but Rab protein makes it go faster.

- a g protein that catalyzes the fusion event
a clamping mechanism involved in SNARE exocytosis
along with NSF, ATP and SNAPs, they help DISSOCIATE SNARES, so that they are free to go around for another round of recognition and fusion
what can drive selective aggregation of a subset of soluble secretory proteins?
intrinsic physical properties,

it also helps if ph is low and ca ++ is high
acdic Ca++ binding proteins that foster aggregation of Secretory granual contents
proprotein convertases
proteases that cleave secretory proteins
in the constitutive pathway, cleaves at a partiicular sequence
what is found in some apically directed membrane proteins (think polarized cell sorting)
- a GPI anchor
where in the transferrin cycle is Fe+3 released?
In the late endosome.