Cell Bio exam 2

4 destinations in which proteins will be sent

signal peptides

organelle have receptors for signal sequences and translocators to move the proteins

the rough ER is composed of a network of flattened sacs called

is continuous with the outer mem of the nuclear envelope and has ribosomes on its cytosolic surface

the ribosomes attached to the ER are involved in the translation of mrna to protein

protein synthesis starts in the cytosol and the presence of a 16-30 AA sequence in the nascent protein directs the ribosome to the ER

protein synthesis starts in the cytosol and might go to the ER

n-terminal signal sequence targets proteins to the rough ER

cotranslation translocation

one or more positive AA next to a stretch of 6-12 hydrophobic AA

is a cytoplasmic ribonucleoprotein particle

functions of the signal recognition particle

this receptor is located in the ER membrane

srp will stop translation until it binds to its receptor

the interaction between srp and its receptor is strengthened by

the translocon in animals is composed of three proteins known as the sec 61 complex

sec61 alpha is an integral protein with 10 alpha helicles

energy from translocation comes from the elongation process

location of the translocon

post translational translocation has been found in yeast

some secretory proteins enter the lumen after being translated

all membrane proteins must be incorporated to the mem in the ER

mem proteins will be sent to diff organelles

topogenic sequences function

refers to the # of times that a polypep chain spans the mem and the orientation of the segments in the mem

3 sequences a single pass protein can present

signal sequence has 1 or more + AA besides the stretch of 6-12 hydrophobic AA

signal sequence is responsible for

these kinds of proteins present a signal sequence and a stop transfer anchor sequence

these 2 types of proteins lack the N-terminal ER signal sequence

type 2 & 3 posses an internal hydrophobic signal anchor sequence that works as both an ER signal sequence and a mem anchor sequence

the orientation of the type 1-3 proteins depends on the orientation of the signal anchor sequence in the translocon

tail anchored proteins are known as

in tail anchored proteins when is the hydrophobic c-terminal available for insertion

tail anchored proteins are recognized by specialized complex of proteins including these 2

Get 3 recognize tail anchored proteins when

when get1/2 recognizes the tail anchored proteins and bind, they

get3 binds to ATP and leaves get1/2

some proteins are attached to the mem by a covalently attached amphipathic molecule called

GPI are initially synthesized just like type 1 proteins

a short sequence of AA in the luminal domain is recognized by a

the function of the transamidase enyme

how do hydrophobicity plots work

proteins encoded by mito/chloro DNA are synthesized by ribosomes w/in the organelles and directed to the correct subcompartment immediately after synthesis

the majority of proteins located in mito and chloro are encoded by genes in the nucleus and are imported into organelles after their synthesis

for proteins to go to the right organelle they need to have signal sequences that are recognized by receptors in the organelles

additional sequences from the signal help to guide the protein to the right area of the organelles

when proteins are imported into the mito they are kept unfolded in the cytosol by

the mito sequence binds to an import receptor in the outer mit mem. The diff import receptors recognize diff signals

general import pore

the import receptor transfer the mito protein to an import channel in the outer mem known as the

the driving force for unidirectional transport of the protein into the mito is due to the mito itself

the general import pore of the mito is called

translocation requires 3 diff energy inputs

H+ electrochemical gradient aka

if the electrochemical gradient has dissipated then the proteins will bind the outer mem but will fail to translocate

mito proteins can be targeted to

single signaling in mito proteins occur in the

multiple signals in mito proteins occurs in these 3 areas

proteins can be targeted to diff areas in the chloro such as these 4

what kind of sequence is needed for the proteins to be targeted to the stroma of chloro

in order for a protein to enter the thylakoids it must go through the stroma using its N-terminal stromal import sequence. Then another sequence guides the protein into the thylakoids

the protein enters the thylakoid by what sequence

antibodies against supposed translocating proteins can be used to test whether they block translocation into the matrix

the movement of proteins and molecules in and out of the nucleus takes place

proteins that are destined to be in the nucleus and are found in the nucleus have

proteins enter through the nuclear pore in a folded state

NLS signal classical

how do we confirm the NLS signal targets proteins to the nucleus

how do chimeric proteins confirm NLS signals targets proteins to nucleus

a detergent that removes everything in a cell except for the nucleus an the mem

digitonin helps researchers to see what happenes to transport proteins when there are no cytosolic elements

2 additional cytosolic proteins required for nuclear protein translocation

monomeric g-proteins that exist in either GTP or GDP bound conformation

these 2 proteins are required for nuclear protein translocation

importin alpha function

importin beta function

importin beta can also bind some NLS sequences and translocate proteins alone

signal used for ran dependent nuclear export

2 proteins involved for ran dependent nuclear export

export 1 is used for

export t is used for

Membrane and soluble proteins synthetised in theER undergo four main modifications:

this is the covalent addition and processing of carbohydrates in the ER and golgi

only folded proteins are transported to the rough ER and golgi

carbohydrates chains may be added to the hydroxyl group in these 2 in protein glycosilation

2 carbo chains that may be added to the hydroxyl group in serine and threonine or asparagine

n-linked oligosaccharides contains these 3

these are preformed and are added to asparagine

what happens in protein glycosylation when the carbo chain n-linked oligo is attached to asparagine

n-linked oligo have 14 residues when added to asparagine, once added the 5 residue core always remains

the synthesis of oligosaccharides takes place in the

proteins cant fold back into their native shape if they can it takes hours

modifications of n-linked oligo are used to monitor folding and quality

important protein folding catalyst in the ER lumen are

these are enzymes that accelerate the rotation about peptidyl-prolyl bonds at proline residues

improper folding of proteins are retained in the ER and are seen bound to the ER chaperones bip and calnexin

the presence of unfolded proteins in the ER results in an increase in expression of ER chaperones and proteins, this is known as

proteins going from the ER to the golgi
proteins going from the Golgi to the ER

materials carried between compartments use

2 functions of protein coats

3 kinds of coated vessicles

the function of COPII vess

function of COPI

function of clathrin

if GTP hydrolysis is blocked, coated vesicles accumulate, this can only happen 2 ways

addition of COPII proteins to a cell free sys induces protein coated buds from ER derived vesicles

mechanism by which the vesicle coat selects proteins is by

this signal binds the luminal domains of certain cargo proteins

soluble proteins are taken by vesicles that have luminal sorting sig

mutations in the COPI proteins stops both retro and antero transport, ER s depleted of pro and mem necessary for sorting

most soluble ER resident proteins carry these 4 amino acid sequences at their c-terminal KDEL

KDEL signal sequence is the

KDEL signal is sufficient and necessary for

adding KDEL to a normally secreted protein causes

when KDEL is removed from an ER destined protein

KDEL receptor binding proteins are pH dependent

KDEL receptor is located in vesicles between ER and golgi

cystic fibrosis is caused by

common mutation in CFTR gene  is

function of mutated CFTR gene

3 sub comparts of golgi

movement of proteins in the Golgi takes place by cisternal maturation

uptake of cell surfaces receptors and bound extracellular ligands

uptake of particular matter

uptake of specific extracellular ligands following their binding to receptors

substances that enter through RME become bound to

clathrin regions invagimate into the cyto then pinch free of the cyto

clathrin contains 3 chains that form a triskelion

coated vesicles contain adaptors between clathrin and mem

this done by this is required for the final stages of vesicle budding during endo

in the endocytic pathway vesicle bound materials are transported in vesicles and tubules called

LDL cholesterol is bad for you

low density lipoproteins

LDL receptor are transported to the plasma mem and bound to a coated pit

function of LDL

transport cholesterol from tissue to the liver excretion

LDL increase cholest while HDL lower

deposition of LDL leads to plaque formation on the inner walls of blood vessels

major glycoprotein of the blood

function of transferrin

Transferrin with Fe
w/o Fe

cells need to sense their environment and respond to it

4 things cells sense for

4 things needed in order for cells to communicate

the signaler aka 
signal aka
detector aka

when signals in cell need to change physical state

distant sig from one cell to target cells by ligands secreted into the blood stream

short range sig by a cell to adjacent ones

special type of paracrine sig

signaling by neuron to another neuron of an effecter cell

sig by a cell to itself

cells have fast and slow responses to sig

sig molecules can bind a receptor in the cell mem or if lilophilic, one in the cyto

steroid hormone cortisol acts by

local sig molecule that can travel through the mem

function of NO

enzymes that add phos groups

2 types of kinases that undergo switching by phos

enzymes that remove phos groups

3 cell surface receptor classes

this receptor allows for the flow of ions

ions going in/out of cells results in changes in the mem potential and can produce an electrical current

first and second messengers in signaling from cell surface

function of 2nd messengers

the binding of the ligand to its receptors alters the conc of the second messengers inside the cell

advantages of second messengers

signals from cell surface reaches their targets through 2nd messengers

2 characteristics of the structure of g-protein coupled receptors

4 terminations of g protein coupled receptors

desensitization termination of the response of GPCR occurs

G protein couple receptor kinase GRK termination of the response of GPCR function

arrestins termination of the response of GPCR function

termination of the reponse of GPCR is accelerated by

FRET study the interaction between 2 protein

FRET

fret can be done to test to see how 2 known proteins interact and when in vitro and in vivo

FRET function It relies on 2 fluorescent proteins of different absorption andemission spectra, with the special design characteristic thatthe emission wavelength of the first one matching theabsorption wavelength of the second one

cAMP rises rapidly in response to an extracellular signal

binding of serotonin to neurons results in

cholera

function of the cholera toxin enzyme

alters the alpha subunit it so that it can no longer hydrolyze its bound GTP

when ADP ribosylation can no longer hydrolyze its bound GTP it causes it to

the prolonged elevation in cAMP levels w/in intestinal epithelial cells causes a large efflux of Cl- and H2O into the gut (causes symptoms of cholera)

is a protein-based toxinproduced by the bacterium Bordetella pertussis,which causes whooping cough.

pertussis toxin function

pertussis toxin effect prevents the subunit from interacting withreceptors; as a result, this α subunit retains itsbound GDP and is unable to regulate its targetproteins.

extracellular signals can induce long term responses

receptors can be located in the mem or cyto

3 affects that extracellular signals do to cell function

2 ways extracellular signals modulating gene transcription

2 functions of intracell domain

enzyme coupled receptors are

enzyme coupled receptors contain an extracell ligand binding domain

Ras proteins is a family of small GTP biding proteins

ras proteins structure

why are early response genes called this title

2 important early response genes

function of the 2 most important response genes

receptors do not have enzymatic activity

signal form unrelated receptors can ______ to activate a common effector

identical signals can ______ to activate a variety of effectors

signals can be passed back and fourth between pathways as a result of