Cell Bio Test 4

Chapters 15, 16 and 20

isolating and organizing methods for chemical reactions in cells

1. grouping enzymes required to catalyze a sequence of reactions into large multicomponent complexes
-Ex: DNA replication and protein synthesis
2. confine metabolic processes within the organelles
-each organelle has a unique set of proteins that are selectively transferred from cytosol to compartment they are used

Prokaryotic cells consist of a ________ compartment enclosed by the plasma membrane

single
-have no other membrane-enclosed organelles/structures

Eukaryotic cells are ____-________ by internal membranes

sub-divided
-includes multiple small membrane-enclosed sacs, tubes, spheres, and irregularly shaped structures.
-all distinct with unique sets of large and small molecules that determine its specialized function

cytosol

contains many metabolic pathways; protein synthesis; cytoskeleton

nucleus

contains main genome; DNA and RNA synthesis

endoplasmic reticulum

synthesis of most lipids; synthesis of proteins for distribution to many organelles and to the plasma membrane

golgi apparatus

modification, sorting, and packaging of proteins and lipids for either secretion or delivery to another organelle

lysosomes

intracellular degradation

endosomes

sorting of endocytosed material

mitochondria

ATP synthesis by oxidative phosphorylation

chloroplasts

ATP synthesis and carbon fixation by photosynthesis

peroxisomes

oxidative breakdown of toxic molecules

proteins must accurately be delivered to their appropriate _______________ to perform their function

organelle
-some proteins will be secreted from the cell or replace organelle proteins that have been degraded
-necessary for cells to grow, divide, and function properly

protein sorting

process of transporting a protein to its destination where it will function.
-part of amino acid sequence acts as signal and involved in directing the protein to a particular organelle/location.
-synthesis of most proteins in cell begins at ribosomes

protein sorting routes

-for nucleus, mitochondria, chloroplasts, peroxisomes, and ER, proteins are delivered directly from the cytosol.
-for the ER, most proteins are transported by vesicles to the Golgi and then to plasma membrane
-for the Golgi, lysosomes, and inner nuclear membrane proteins and lipids are delivered indirectly via the smooth and rough ER.

proteins are transported into organelles by three mechanisms

1. transport from cytosol into the interior of the nucleus through nuclear pores
2. transport across organelle membranes through protein translocators
3. transport from one organelle to another by transport vesicles

transport through nuclear pores

-transport into nucleus
-pores act as selective gates that actively transport specific macromolecules, but also allow free diffusion of smaller molecules
-proteins are completely synthesized in cytosol and correctly folded into its three dimensional structure before import

transport through protein translocators

-translocator proteins form translocator channels through the membrane.
-protein is transported across organelle membrane through the channel in an UNfolded state.
-protein transported from the cytosol into the ER, mitochondria, chloroplasts, or peroxisomes.

transport through transport vesicles

-transport of proteins synthesized in the ER move by vesicular transport through the secretory pathway.
ER-->Golgi-->cell surface/lysosomes
-vesicles become loaded with proteins from internal space of appropriate organelle; pinch off from the membrane and fuse with the membrane of another organelle
-membrane lipids and proteins are also delivered to other organelles similarly

sorting signal sequences

direct movement of/sorts proteins
-comprised of continuous stretch of 15-60 amino acids
-removed from finished protein once sorted
-proteins that lack sorting signal remain in the cytosol

cytosilic protein

protein that gets transformed from an ER protein after the removal of signal sequence

ER protein

protein that is transformed after an addition of signal sequence to a cytosilic protein

signal patches

form of targeting proteins to specific locations
-made up of amino acids that are far apart but come closer together in the tertiary structure of the folded protein
-visible after protein has been folded and is not evident until that folding occurs
-never removed
-commonly used for directing proteins to nucleus

the nuclear envelope has how many membrane?

2
-inner nuclear membrane: contains proteins that act as anchoring sites for chromosomes; nuclear lamina provides structural support for envelope
-outer nuclear membrane: closely resembles the membrane of the ER

nuclear pores

physical holes in the membrane that act as gates for molecules to travel through
-made up of large protein complexes which results in a water-filled channel that allows small, water soluble molecules to pass freely between the nucleus and cytosol.
-noncovalent interactions/bonds
-transport proteins in FULLY FOLDED conformation into/out of the nucleus

traffic flow of molecules through nuclear pores

Into the nucleus: newly made proteins enter from the cytosol
Out of nucleus: RNA molecules synthesized in the nucleus and ribosomal subunits assembled in the nucleus

nuclear localization signal

consist of one or two short sequences containing several positively charged amino acids
-acts as sorting signal sequence that directs protein from cytosol into the nucleus

nuclear import receptors

recognize the nuclear localization signal and bind to signal.
-helps direct the protein from the cytosol to nuclear pore

nuclear exports receptors

transport materials out of the nucleus and into the cytosol. similar to nuclear import receptors

Proteins ________ to enter mitochondria and chloroplasts

Unfold
-different from nuclear pore transport since nuclear pores transport proteins fully folded.
-M and C have inner and outer membranes and both contain their own DNA to make some of their own proteins

Process which proteins enter mitochondria and chloroplasts
(Protein Translocator process)

-proteins have signal sequence at N-terminus which contains hydrophobic and positively charged amino acids
-sequence recognized by import receptors
-specificity between this interaction is what directs protein from the cytosol to the given organelle
-import recpetor associates with in the membrane
-proteins translocated SIMUTANEOUSLY across inner and outer membranes
-each protein is UNFOLDED and once inside organelles SS is removed and protein gets folded back through chaperone proteins

import receptors

protein attached to the organelle membrane
-associates with signal sequence, then protein translocator

protein translocator

type of channel embedded in an organelle membrane

chaperone proteins

aid in transport of the protein across the two membranes and help fold protein back into its tertiary structure

Lipid transportation into mitochondria and chloroplast

mechanisms not fully understood; most of their membrane phospholipids are thought to be imported from smooth ER
-transported to organelles by lipid-carrying proteins that extract a phospholipid molecule from one membrane and deliver it into another.
-believed to occur at specific junctions where mitochondrial and smooth ER membranes are held in close proximity

general process of protein transport to peroxisomes

get most of their proteins from ribosomes in cytosol
-involves short sequence of amino acids that serve as import signal, recognized nu recpetor proteins and will transport proteins to peroxisome.
-peroxisomal membrane contains translocator that aids in transport
-full mechanism still unknown

Proteins enter ER while being ______________

synthesized
-ER has most complex membrane system
-serves as entry point for proteins destined for other organelles as well as ER itself
-most ER proteins are translocated as they are translated
-elongation of each polypeptide provides the push needed to push the growing chain through the ER membrane
-once protein is through translocation channel, protein is released into the ER lumen

two kinds of proteins transferred from the cytosol to ER

1.water soluble proteins: completely translocated across membrane and enter ER lumen
2. prospective transmembrane proteins: partly translocated across the ER membrane and become embedded in it

two protein components help guide ER signal sequences to the ER membrane

1. A signal-recognition particle (SRP): binds to ribosome and ER signal sequence of polypeptide when it emerges from ribosome
2. SRP receptor: embedded in the ER membrane, recognizes the ERP
-SRP-ribosome complex binds to the SRP receptor in the ER membrane and docks with a protein translocator channel; SRP released and protein synthesis resumes

N-terminus

start of polypeptide chain and location of signal sequence.
opens the channel in the protein translocator
-remains bound to channel while polpeptide chain is threaded through the membrane

transmembrane signal peptidase

removes signaling sequence
-cleaved sequence released from translocation channel and degraded in lipid bilayer

__________ determine the arrangement of a transmembrane protein

start and stop signals
-along polypeptide chain is a stop-transfer sequence which causes the translocation channel to release growing polypeptide into lipid bilayer
-stop-transfer sequence remains in the bilayer, where it forms a transmembrane segment that anchors the protein in the membrane
-can also have start-transfer sequences for multi-spanning proteins

proteins that stay in the ER___________

are retained in the ER by a C-terminal sequence called ER retention signal
-recognized by a membrane-bound receptor protein in the ER

exit of proteins out of ER

contain additional signaling amino acid sequence that utilized to get the protein to its final destination

vesicular transport

transport vesicles will transport protein from ER to the Golgi and then to onto other compartments
-proteins undergo protein folding and addition of carbohydrates (glycosylation)
-vesicle membranes and the soluble proteins contained within vesicles are transported

Vesicular transport in eukaryotic cells depends on____________

specific sets of proteins involved in steps of vesicle budding, uncoating, tethering to target membrane, membrane fusion, and cargo release
-involved in production, transport, and delivery of vesicles that bud off of the ER and Golgi and fuse with the membrane of the target compartment
-contain specific transport signals that are recognized by a cargo receptor in Golgi or plasma membrane

vesicle budding

formation of vesicles from membranes of ER, Golgi, and plasma membrane.
-each bud has coated vesicles
-bud captures the specific molecules for outward transport

coated vesicles

distinctive coat protein on the cytosolic surface of vesicle buds
-helps shape membrane into bud
-removed after budding (uncoating)

Over short distances, the movement of vesicles is by

diffusion

Over longer distances, the movement of vesicles is dependent on

cytoskeleton-based motor proteins

Tethering/capturing of vesicle to its target membrane is specific and involves

specific proteins
-Rab proteins on the surface of the vesicle are recognized by corresponding tethering proteins on the cytosolic surface of the target membrane
-SNARES

vesicle-SNAREs

proteins in vesicle membrane that are complimentary to specific proteins called target SNAREs in the target membrane
-binding/interaction is specific between the v-SNARE and t-SNARE

vesicle fusion

once vesicle and target membranes are dock, other proteins join to form a fusion complex and results in the fusion of the vesicle with the target membrane and release of the vesicles molecules

cell signaling

the molecular mechanisms by which cells detect and respond to external stimuli and send messages to other cells
-critical for survival of cell to be able to adapt, respond, grow, divide, and repair.
-allows cells to be able to communicate with one another

cells most often communicate by ________ signals

chemical
-can take other forms
-can be in the form of proteins, amino acids, nucleotides, steroids, fatty acids, and gases
-can be in the form of a physical/environmental signal such as light, temperature, and pressure (but usually converted to chemical signals)

signal transduction pathways

comprised of a series of molecules in which one acts upon another, which in turn acts upon another, and so on.
-cell is able to convert one kind of signal or stimulus into another
-starts with a physical/environmental signal that produces a type of extracellular signal molecule

signal molecules

act upon another cell called the target cell by binding to special proteins embedded within their cell membranes called receptors
-found in extracellular fluid and extracellular matrix, or bound to surface of cells
-binding the signal molecule to the receptor then begins a specific signal transduction pathway
MUST HAVE RECEPTOR

three stages to signal transduction

1. reception: extracellular signal molecule binds to receptor
2. signal transduction: transfer of signal from outside of cell to inside of cell
3. cellular response: response is initiated and/or occurs entirely within receiving cell

different types of signaling mechanisms

endocrine signaling, paracrine signaling, autocrine signaling, neuronal signaling, and contact-dependent signaling.

endocrine signaling

long distance signaling that is able to signal the whole body
-often occurs through the systemic circulation
-hormones are released into the blood stream and bind to receptors on target cells located far away from the signaling cell
Ex: pancreas producing insulin, which regulates glucose uptake in cells found at different locations all over the body

paracrine signaling

a certain type of cell will release the signal and a different type of cell will respond to the signal
-signal does not affect originating cell, but does influence nearby cells
-short distance signaling: signals in neighborhood or communication to neighboring cells. local mediators
Ex: Epithelial cell communicating with a smooth muscle cell

autocrine signaling

form of paracrine signaling
-a certain type of cell will release the signal and the same cell will respond to the signal
-short distance signaling: signals in neighborhood or communication to neighboring cells. local mediators
Ex: epithelial cell communicating with itself

neuronal signaling

involves neurons delivering messages across long distances; delivery is quick and specific for individual target cells,
-able to convert electrical impulses to chemical and vice versa through neurotransmitters
-cell junctions allow signaling molecules to pass from one cell to another
SUPER FAST

contact-dependent signaling

occurs between cells that are in direct contact with each other; signal is never released into extracellular space
-the two cells in a sense, hold hands; they must be adjacent and in direct contact with one another
Ex: White blood cells leave circulation and enter site of injury

receptor

protein molecule usually found on the surface of a cell or inside it, that receives chemical signals
-activated by only one type of signal
-signal from receptor is conveyed into the target cell interior to change cell behavior

the ______ signal molecule can induce different responses in different target cells.

same

cells have many different types of receptors and ___________________________

have multiple copies of each one
-signals can then act together to have a larger effect
-allows cells to be sensitive to many signals

receptors relay signals from the outside to the inside via _____________________________

intracellular signaling pathways
-extracellular signal sent from a cell
-receptor protein receives the external signal and generates a new intracellular response
-intracellular signaling molecules pass the intracellular signal "down" a chain of intracellular signaling molecules
CASCADE until response or until desired effect is reached

functions of intracellular signaling pathway

-transforms the signal into an intracellular molecular form
-relays the signal from the signal entry site to the response site
-can amplify the signal received, making it stronger and resulting in a larger intracellular response
-integrates them before relaying and/or distributes the intracellular signal to various other signaling proteins
-modulates the other factors like other external signals to make many different types of effects; feedback regulation can also occur

reasons why there is a relay system

1. multiple steps in the relay can either make the signal stronger/louder or softer/quieter in a quick manner
2. provides more accurate and specific control (like a light dimmer)
3. more variability in response from cell to fell

Three types of cell-surface receptors

1. ion-channel-coupled receptors: change permeability of cell membrane to certain ions; signaling molecule regulates opening of ion transport channel
2. G-protein-couples receptors: activate membrane-bound (interior) proteins that then trigger intracellular signaling pathway
3. enzyme-coupled receptors: receptor has enzymatic capabilities or receptor activates/associates with an enzyme inside the cell

G-protein-coupled receptors (GPCRs)

transmit signals to intracellular targets via the intermediary action of guanine nucleotide-binding proteins called G proteins
-G proteins act as physiological switches that regulate the activities of a variety of intracellular targets in response to extracellular signals
-largest family of cell surface receptors
-large number of receptors responsible for a variety of cell process, in addition to physiological processes such as smell, sight, and taste

GPCR structure

characterized by 7 membrane-spanning helices
-binding of ligands to extracellular domain of these receptors induces a conformational change that allows the cytosolic domain of the receptor to bind to a G protein associated with the inner face of the plasma membrane; activates the G protein which dissociates from the receptor and carries the signal to an intracellular target
consist of three subunits

subunits of G proteins

alpha (a), beta (B), and gamma (Y)
-many different a, B and T subunits, as well as several which have splice variants, further increasing their variability

a subunit

binds guanine nucleotides (guanosine triphosphate and guanine diphosphate) which regulates G protein activity; different G proteins associate with different receptors so that these G proteins link receptors to distinct intracellular targets

stimulation of GPCRs activates ________________

G protein subunits
-signal molecule binding induces a conformational change in the receptor so that the receptor interacts with the G protein and stimulates the release of bound GDP and its exchange GDP
-activated GTP-bound a subunit dissociates from B and Y, which remain together and function as a BY complex
-both the active GTP-bound a subunit and the BY complex then interact with their targets to elicit an intracellular response

the activity of the a subunit is terminated by __________

hydrolysis of the bound GTP, and the inactive a subunit (now with GDP bound) then re-associates with the BY complex, so they cycle can start again
-the a subunit has intrinsic (built-in) GTPase activity that will eventually hydrolyze the GTP to GDP, returning the whole G protein to its original inactive conformation
-inactive G protein can now be reactivated again by another activated receptor event
-overall activation/inactivation of G protein is a few seconds long

receptor tyrosine kinases (RTKs)

enzyme coupled receptor that phosphorylate their substrate proteins on tyrosine residues
-receptors for most polypeptide growth factors
-protein-tyrosine phosphorylation mechanism (crossphosphorylation)

protein-tyrosine phosphorylation

key signaling mechanism involved in the control of cell growth, proliferation, differentiation, survival and migration

RTK structure

-an extracellular ligand-binding domain, a single transmembrane helix, and a cytosolic domain with protein-tyrosine kinase activity
-most consist of single polypeptides
-the binding of growth factors to the extracellular domain of these types of receptors activates their intracellular kinase domain
-different RTKs recruit different collections of intracellular signaling proteins, producing different effects

steps in signaling from RTKs

1. ligand-induced receptor dimerization
2.autophosphorylation of the receptor

ligand-induced receptor dimerization

-some growth factors are dimers consisting of two identical polypeptide chains which directly induce dimerization by simultaneously binding to two different receptor molecules
-other signaling molecules are monomers but have two distinct receptor binding sites that serve to cross-link the RTKs

autophosphorylation of the receptor

occurs as the dimerized polypeptide chain cross-phosphorylate one another
occurs at specific tyrosine residues found in the intracellular domain

key roles of autophosphorylation in signaling

1. phosphorylation of tyrosines within the catalytic domain may play a regulatory role by increasing RTK activity
2. phosphorylation of tyrosines outside of the catalytic domain creates specific binding sites for additional proteins that transmit intracellular signals downstream of the activated receptors

The association of downstream signaling molecules with RTKs is mediated by _________________

protein domains that bind to specific phosphotyrosine-containing peptides
-an adaptor protein is involved that recognizes the phosphorylated RTK and also the intracellular signaling protein

How to inactivate RTK

a tyrosine phosphatase enzyme removes the phosphates from the tyrosines on the activated receptor

examples of ion channel receptors

skeletal muscle cells have receptors for acetylcholine, which is the primary neurotransmitter released by motor neurons
-when acetylcholine binds to the receptors on a skeletal muscle cell, the ion channels open, causing sodium and potassium ions to enter the cell and subsequently launches a sequence of events that results in contraction of the cell

examples of GPCR signaling pathway

G protein-->adenylyl cyclase-->cyclic AMP-->PKA=
-involved in regulating glycogen, sugar, and lipid metabolism
G protein-->IP3-->Ca2+-->calmodulin-->CaM-kinase=
-involved in nervous system, such as nerve cell protection, and learning and memory processes

examples of RTK signaling pathways

PLC-->diacylglycerol (DAG)-->PKC=
-involved in regulating receptor desensitization, modulating membrane structure events, gene transcription, immune responses, cell growth, and learning and memory processes
PI 3-kinase-->PK1-->Akt kinase=
-regulates multiple biological processes including cell survival, proliferation, growth, and glycogen metabolism

cancer

disease caused by abnormal and uncontrolled cell proliferation followed by invasion and colonization of body sites normally reserved for other cells
-general name for a group of more than 100 diseases in which cells in a part of the body begin to grow out of control
-many types of cancer, but all start the same way

the origin of the word cancer is credited to

Hippocrates
-used terms carcinos and carcinoma to describe non-ulcer forming and ulcer-forming tumors

leading sites of cancer in men

1. prostate
2. lung and bronchus

leading sites of cancer in women

1. breast
2. lung and bronchus

two heritable properties of cancer cells

1. divide/proliferate out of control
2.cells can colonize and invade territories throughout the body

benign tumor

cells that proliferate excessively but remain clustered together in a single mass

when is a tumor cell cancerous?

when the cells have the ability to invade surrounding tissue, which causes a malignant tumor.

metastasized

cancer's ability to spread throughout the body

metastases

secondary tumors that have form after cancer cells have metastasized

mutation

any permanent alteration in the nucleotide sequence of DNA
-can have effect on protein function and phenotype
-not all mutations cause a change or significant effect on a protein

2 types of mutations

1. point mutations: mutation that alters the bases of a sequence
2. chromosomal mutations: mutations of large regions of DNA effecting the normal chromosome structure