Cell Bio Test Ii

Front 1

alpha6beta4

Back 1

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

a laminin binding integrin

Front 2

Ser-Lys-Leu (SKL)

Back 2

- a tri-peptide targeting signal at the C-terminal that marks the protein for import into peroxisomes.

Front 3

protein import into peroxisomes requires ...

Back 3

ATP hydrolysis, because there is NO electrochemical gradient across the peroxisomal membrane

Front 4

PTSIR

Back 4

Peroxisomal targeting signal receptor - binds sequence and directs the catalyse tetramer to be imported.

Front 5

Mechalis Menten

Back 5

Vmax*[s]
Km + [s]

Front 6

Kdiss =

Back 6

Kdiss = 1/Kassoc =
(F*(Bmax-B))/B

Front 7

What are the x and y axis of a scatchard? And what is the scattchard equation

Back 7

Y axis = B/F
X axis = B

B/F = (-1/Kd)x + Bmax/Kd

Front 8

What can you get off a scatchard?

Back 8

* you can get Kd and Bmax

slope = -1/Kd
X intercept = Bmax

think of it as a lineweaver burke for affinity

Front 9

For a hormone binding plot, what are the x and y axis?

Back 9

x axis is [F] (concentration of free hormone)

y axis is B is bound hormone or bound receptor

Front 10

Compare the rate of transport between the two general classes of membrane transport proteins

Back 10

- carrier : 100 molecules/sec (slow)

-channel: 10,000,000 molecules/sec (fast)

Front 11

What are the three different ways to drive active transport?

Back 11

- coupled carrier (symport or antiport)
- ATP driven pump (primary active transport)
-light driven pump (secondary active transport)

Front 12

What is the rate of simple diffusion determined by?

Back 12

The rate of simple diffusion is proportional to the concentration gradient of the solute across the bilayer.

Front 13

another word for facillitated diffusion?

Back 13

passive transport

Front 14

facillitated diffusion vs. facillitated transport?

Back 14

Facillitated transport refers to ionophores, while facillitated difusion revers to passive transport

Front 15

What are the types of primary active transport proteins?

Back 15

- 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

Front 16

describe secondary active transport

Back 16

- 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

Front 17

SGLT2 -

Back 17

think sodium glucose transporter
an example of ion driven active transport

Front 18

oubain

Back 18

blocks the sodium/potassium transporter

Front 19

What types of molecules can pass between gap junctions?

Back 19

-Ca++
-cAMP

Front 20

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

Back 20

- production of inhibitory protein

Reasons to become desensitized -
-too many signalling proteins
-adjust the sensitivity of the signal.

Front 21

The main places that sorting signals will direct a protein are:

Back 21

-nucleus
-mitochondria
-peroxosome
-ER (endoplasmic reticulum)

Front 22

Where are phospholipids synthesized

Back 22

SER

Front 23

Three functions of the SER

Back 23

-site of PHOSPHOLIPID synthesis
-detoxification of lipid soluble drugs
-storage site of Ca++

Front 24

Four important chaperone proteins found in the ER that are involved in quality control

Back 24

-BIP
-calreticulin
-calnexin
-Protein disulfide isomerase

Front 25

BIP

Back 25

HSP70!!
a chaperons prtoein found in the ER that is involved in quality control

BIP sees hydrophobic ares on misfolded proteins and binds to them

Front 26

protien disulfide isomerase

Back 26

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

Front 27

The lipids and proteins for the membranes of which cellular components are synthesized in the ER?

Back 27

For the ER, the golgi, the lysosome, and the plasma membrane

Front 28

Where do proteins and lipids from the golgi go?

Back 28

1) plasma membrane
2) lysosome
3) the cell surface to be secreted.

Front 29

Leydig cells

Granulosa cells

Back 29

LC - in testes, secrete hormones

GC - in ovaries secrete hormones

Front 30

SRP, where is it found?

Back 30

SRP - signal recognition peptide
for cotranslational translocation

for bringing peptides into the ENDOPLASMIC RETICULUM

Front 31

signal peptidase

Back 31

cleaves off the signal sequence of a protein that is being translocated into the ER lumen

Front 32

What is the difference in signal sequence between a soluble ER protein, a transmembrane ER protein and a resident ER protein?

Back 32

- 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

Front 33

What end is the KDEL sequence on?

Back 33

THe C TERMINAL END ONLY !!!

Front 34

What are the types of post-translational modifications that can occur in the RER?

Back 34

1) glycosylation
2) cleavage of peptide signal
3) addition of oligosaccharide, dimerization
4) HYDROXYLATION OF PROLINE AND LYSINE FOR COLLAGEN
5) Conformational changes

Front 35

calnexin...

Back 35

chaperone that binds N-glycoproteins with GlcNac

-A LECTIN Chaperone
-is a membrane protein

Front 36

calreticulin binds

Back 36

calcium?

-A LECTIN Chaperone
-is in the ER lumen

Front 37

positive inside rule

Back 37

determines the orientation of transmembrane proteins in the ER - basically the + charge wants to be on the cytostolic (inside) side

Front 38

ER resident signals

Back 38

-KDEL
-LysLys or ArgArg (these can bind and interact with COPI and therefore be in vesicles going retrograde

Front 39

What is the difference in type between nucleoside analog drugs (like AZT, didanosine), Nevirapine, and indinavir?

Back 39

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)

Front 40

cholera (as an example)

Back 40

inhibits GTPase activity causing the G protein alpha unit to remain activated

Front 41

Explain how the system of second messengers can provide an amplkification of the hormone signal

Back 41

- 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

Front 42

PKA

Back 42

think G protein & cAMP. Basically how gene transcription is activated by a rise in cAMP

Front 43

CREB

Back 43

activated by PKA due to a rise in cAMP, can effect gene transcription

- a response element found in genes activated by cAMP

Front 44

PKC

Back 44

found in the inositol phospholipid pathway

Front 45

ERbB2

Back 45

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

Front 46

Ras

Back 46

- 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

Front 47

Gef

Back 47

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

Front 48

What type of kinase is MAP kinase?

Back 48

- serine threonine phosphorylaters

Front 49

What's the slope on a lineweaver burke plot?

Back 49

- km/Vmax

Front 50

What two adhesins do H.pylori have? What do they do?

Back 50

-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

Front 51

BabA

Back 51

Adhesin found on H. pylori that(binds LeB in gi

Front 52

SabA

Back 52

- adhesin found on H. pylori that (binds sLex), s is for sialyl

Front 53

LeB

Back 53

receptor in gi, that is the site of attachement of H. pylori (BabA adhesin on H. pylori)

this stimulates bacterial growth

Front 54

sLex

Back 54

receptor in gi, that is the site of attachement of H. pylori (SabA adhesin on H. pylori)

Front 55

What unusual substance can prevent H. pylori growth in stomach? How does it prevent bacterial proliferation?

Back 55

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.

Front 56

alpha-GlcNac

Back 56

terminal sugar in a mucin secreted by the mucusoal gland that prevents proliferation of H. pylori

Front 57

What is the terminal sugar in a mucin secreted by the mucusoal gland that prevents proliferation of H. pylori

Back 57

alpha-GlcNac

Front 58

where does glycosylation occur?

Back 58

In the golgi!!! (outside of the cell!!)

Front 59

glyco as in glycosyltransferase means ...

Back 59

transfer of carbohydrate

Front 60

What enzyme removes sugars and which enzyme adds sugars?

Back 60

Glycosyltransferase: Enzyme which adds sugars (transfers
from sugar nucleotide to protein/lipid)

Glycosidase: Enzyme which removes sugars

Front 61

describe/ draw the glycosyltransferase reaction

Back 61

-sugars are added as nucleotide sugars
- the glycosyltransferase transfers only the sugar leaving behind the nucleotide diphosphate

Front 62

What is the one exception to glycosyltransferase transfering only the sugar and leaving behind the nucleotide diphosphate?

Back 62

- M-6-P glycosylation - a sugar and a phosphate is added, and a UMP instead of the normal UDP is released.

Front 63

What does galactosyltransferase do?

Back 63

-it ONLY transfers galactose to the protein
-it is specific in terms of whether an alpha or beta bond is formed.

Front 64

why glycosylate

Back 64

-shock absorbers
-helps proteins fold correctly
-cell-cell recognition (think leukocytes in extravasation)
-MAY PROTECT FROM DEGREDATION
-TARGETING (like M-6-P)

Front 65

sialyl transferase is added in the

Back 65

golgi !

Front 66

what amino acid is involved in your n-linked sugar

Back 66

- asparagine

Front 67

what amino acid is involved in your o-linked sugars?

Back 67

-serine or threonine

Front 68

Glycophorin

Back 68

A Glycophorin is a sialoglycoprotein of the membrane of a red blood cell.

Front 69

GalNAc T’ase - where?

Back 69

GalNAc T’ase is localized in
rough ER

Front 70

SA - what is it and where?

Back 70

NANA (or sialic acid) T’ase is
localized in trans golgi
network (TGN)

Front 71

Gal T’ase - where?

Back 71

Gal T’ase is in trans golgi

Front 72

sialyltransferase

Back 72

transferase sialic acid - in the TGN, is the terminal sugar in O linked

Front 73

what sugar is never found in an N linked sugar?

Back 73

GalNAc (N-linked has a gluNac)

Front 74

what kind of sugar linkages do proteoglycans have?

Back 74

O-linkages

Front 75

What is unusual about proteoglycans?

Back 75

they have a high carbohydrate to protein ratio?

Front 76

What are the subunits of a GAG?

Back 76

Repeating disaccharide containing an acid
sugar (Glucuronic or iduronic acid) and an
amino sugar (GlcNAc or GalNac)

Front 77

Asn-X-Ser/Thr

Back 77

Consensus sequence for Nglycosylation

Front 78

dolipol

Back 78

- 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

Front 79

composition of the N-linked 14 en bloc carbohydrate

Back 79

added outside ER
-2 glcNac
-5 mannose

added on ER lumen
-4 mannose
-3 glc

Front 80

What are the two types of N-linked sugards?

Back 80

- complex
-high mannose

Front 81

what is the major signalling molecule for getitng rid of senescent cells

Back 81

galactose
-marker of old cells

Front 82

What enzymes are involved in synthesis of mannose-6-phosphate recognition sequences on proteins?
What is special about it?

Back 82

- 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?

Front 83

blocked phosphate

Back 83

- 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

Front 84

o-linked examples

Back 84

-h. pylori recognition
-blood cell types
-proteoglycans - o-linked GAG chains

Front 85

n-linked examples

Back 85

-carbohydrate recognition in germ cells - sperm recognize sertoli cells
-M6p recognition sequence

Front 86

In a proteoglycan, what attaches the GAG chain to the core protein?

Back 86

- a tetrasaccharide attaches the GAG chain ot the core protein

Front 87

homotropic effect

Back 87

think cooperativity - it means that the molecule causing the cooperativeity is the one that will be affected by it

Front 88

What is K0.5

Back 88

K0.5 is a measrue of cooperativity

K0.5>1 have + cooperativity
K0.5 <1 have - cooperativity

Front 89

Allosteric modification

Back 89

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

Front 90

Tyr-X-X-φ

Back 90

CLATHRIN COATED

Tyr-X-X-φ or Leu-Leu
bind to μ2 subunit of AP2
(LDLR, TfR, M6PR have
sequence)
AP 2 PM --> endosome (Receptor-mediated endocytosis)

Front 91

Leu-Leu

Back 91

Tyr-X-X-φ or Leu-Leu
bind to μ2 subunit of AP2
(LDLR, TfR, M6PR have
sequence)
AP 2 PM --> endosome (Receptor-mediated endocytosis)

Front 92

Assembly particle/adaptor proteins,

Back 92

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

Front 93

Dynamin:

Back 93

ONLY FOR CLATHRIN COATED
Cytosolic G protein
• Subunits polymerize around
neck of vesicle
• Binds GTP
• Hydrolyzes GTP to promote
fusion of membranes
and vesicle formation

Front 94

ADP-ribosylation factor
(ARF):

Back 94

assembly of COP-I
(no GDI)

Front 95

Sar 1

Back 95

assembly COP-II
(no GDI)

binds G-protein

Front 96

Rab:

Back 96

targeting of vesicles
(bound to GDI in cytosol)

Front 97

uncoating ATPase

Back 97

a chaperone protein of the heat shock
protein 70 family (hsp70)
Relase of clathrin requires the action of an uncoating
ATPase

Front 98

Auxillin,

Back 98

a vesicle associated protein, is thought to
activate the ATPase

Front 99

Coatamer

Back 99

consists of 7 polypeptides (α,β,β’,
γ, δ, ε, and ζ COP)

-like clathrin

Front 100

β COP

Back 100

β COP is similar to adaptor
proteins of clathrin

Front 101

Asp-X-Glu

Back 101

Controls movement of vesicles from ER to cis golgi
transmembrane proteins with cytosolic

COP II-dependent transport

Front 102

V-SNARE

Back 102

used for targeting
found on the vesicle

Front 103

SNAP 25/ TSNARE

Back 103

used for targeting
found on the target membrane

Front 104

sec 23/24

Back 104

think COP II

Front 105

sec 12

Back 105

guanine nucleoside exchange factor for COP II

Front 106

Rab protein

Back 106

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

Front 107

complexin

Back 107

a clamping mechanism involved in SNARE exocytosis

Front 108

SNAPs

Back 108

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

Front 109

what can drive selective aggregation of a subset of soluble secretory proteins?

Back 109

intrinsic physical properties,

it also helps if ph is low and ca ++ is high

Front 110

granins

Back 110

acdic Ca++ binding proteins that foster aggregation of Secretory granual contents

Front 111

proprotein convertases

Back 111

proteases that cleave secretory proteins

Front 112

furin

Back 112

in the constitutive pathway, cleaves at a partiicular sequence

Front 113

what is found in some apically directed membrane proteins (think polarized cell sorting)

Back 113

- a GPI anchor

Front 114

where in the transferrin cycle is Fe+3 released?

Back 114

In the late endosome.