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203 Cards in this Set

  • Front
  • Back
Eucaryotic cells contain protein fibers that are involved in what?
-establishing cell shape
-providing mechanical strength
- cell movement
- chromosome separation
- intracellular transport of organelles
Protein fibers form the cytoskeleton and there are 3 types ..
- Actin filaments (also called microfilaments)
- Intermediate filaments
- Microtubules
Some functions of actin filaments are:
- to provide mechanical strength to the cell by forming a band under the plasma membrane
- link transmembrane proteins to cytoplasmic proteins
form contractile ring during cytokinesis in animal cells
cytoplasmic streaming
- generate locomotion in cells such as white blood cells and amoeba
- Interact with myosin to provide force of muscular contraction
What type of activities do Microtubules participate in through out the cell?
Most involve motion that
is provided by protein “motors” that use ATP. They determine the positions of
membrane-enclosed organelles and direct intracellular transport. The migration of
chromosomes during mitosis and meiosis takes place on microtubules that make up
the spindle fibers.
What do intermediate filaments do?
provide mechanical strength and resistance to shear stress.
What are the different filaments and their functions?
-Keratins: are found in epithelial cells, hair and nails
-Nuclear lamins: form a meshwork that stabilizes the inner nuclear membrane
-Neurofilaments: strengthen the long axons of neurons
-Vimentins: provide mechanical strength to muscle and other cells
Defective keratins lead to what?
epidermolysis bullosa simplex disorder
The tubulin and actin subunits assemble head-to-tail to create what?
polar filaments
What is the limiting step in the formation of a cytoskeletal polymer?
Nucleation
Microtubules and actin filaments have two distinct ends that do what?
grow at different rates
What are consequences of nucleotide hydrolysis by tubulin and actin?
Filament treadmilling and dynamic instability
What occurs at intermediate concentrations of free subunits?
Treadmilling
Nucleation is catalyzed by a complex of proteins that includes what?
actin-related proteins (ARPs
The ARP complex nucleates actin filament growth how?
-from the (-) end, allowing rapid elongation at the (+) end
-The ARP complex can also attach to the side of another actin filament while remaining bound to the (-) end of the filament that it has nucleated
When is the ARP complex nucleated filaments more efficiently?
when it is bound to the side of a preexisting actin filament resulting in a filament branch that grows at a 70° angle relative to the original filament
How is actin elongation mediated?
formins
How is Filament elongation is modified?
by proteins that bind to the free subunits
What is a special protein that binds to actin?
Thymosin
- Actin monomers bound
to thymosin are locked where they cannot associate with either the (+) end
or (-) end of the actin filament.
How do cells recruit actin monomers from this sequestered pool and use them for polymerization?
Recruitment depends on another monomer-binding protein profilin.
What is profilin?
Profilin binds to the face of actin opposite the ATP-binding cleft.
What is Actin-profilin?
Actin-profilin can bind to the plus end of the actin filament but is unable to bind to the minus end.
Proteins that bind to the sides of actin filaments can either ..
stabilize or destabilize them
Tropomyosin stabilizes actin filaments by binding simultaneously to what?
seven adjacent actin subunits in one protofilament This prevents other proteins from binding to actin
What destabilizes actin filaments by forcing it to twist a little more tightly?
Cofilin
What organizes assemblies of actin filaments?
Cross-linking proteins
Polymerization of tubulin nucleated by what?
g-tubulin ring complexes
Actin-based motor proteins are members of what super family?
myosin
What Are Two Types of Microtubule Motor Proteins?
Kinesins and Dyneins
The Structural Similarity of Myosin and Kinesin Indicates what?
a common evolutionary origin
Motor Proteins Generate Force by what?
Coupling ATP Hydrolysis to Conformational Changes
Motor Proteins Mediate what?
the Intracellular Transport of Membraneenclosed Organelles
The Cytoskeleton Localizes what?
Specific RNA Molecules
Cells regulate what?
motor protein function
The cytoskeleton and cell behavior causes what to happen in muscles?
muscle contraction is a burst of calcium while Sliding of Myosin II and Actin Filaments Causes Muscles to Contract
Cilia and Flagella Are Motile Structures Built from what?
Microtubules and Dyneins
Construction of the Mitotic Spindle Requires
Microtubule
Actin Polymerization Drives
Plasma Membrane Protrusion
Cell Adhesion and Traction Allow Cells to move how?
Pull Themselves Forward (sticking to wall of vessel and exiting areas of infection or inflammation)
Which family causes Major Rearrangements of the Actin Cytoskeleton?
Rho protein family
Extracellular Signals Can Activate how many Rho Protein Family Members?
3!
What Can Dictate the Direction of Cell Migration?
External signals
Dyneins are a family of
minus-end directed microtubule motors
Two major families of dyneins
cytoplasmic dyneins and axonemal dyneins
Cytoplasmic dyneins are found in all eucaryotic cells and are important for what?
vesicle trafficking and localization of the Golgi apparatus near the center of the cell
Axonemal dyneins are highly specialized for what?
rapid and efficient sliding movement of microtubules that drive the beating of cilia and flagella and negatively charged
What do dyneins require to associate with membrane-enclosed organells?
a large number of accessory proteins
Ion concentration differences across the lipid bilayer are useful for 4 things:
1) Driving various transport processes
2) Conveying electrical signals in electrically excitable cells
3) Making most of the cell’s ATP
4) Cell signaling
The rate at which a molecule diffuses across a synthetic lipid bilayer depend on its ..
size and solubility
Complete the statement:

The smaller the molecule and the less polar it is, the ...
the more rapidly it diffuses across the
bilayer
What are the 2 main classes of membrane transport proteins?
Transporters and channels
What do transporters do?
bind to a specific solute and undergo a series of conformational changes
What does a channel do?
interact with the solute much more weakly
form aqueous pores
transport at a faster rate
How do solutes cross membranes?
either active or passive transport
AcActive transport goes against...
the concentration gradient
Electrochemical gradients do what 2 thing?
combines membrane potential & the concentration gradient
A conformational change in a transporter could mediate
the passive transport of a solute
Cells carry out active transport in three main ways:
(1) Coupled transporters couple the uphill transport of one solute
across the membrane to the downhill transport of another.

(2) ATP-driven pumps couple uphill transport to the hydrolysis of ATP.

(3) Light-driven pumps, found mainly in bacteria and archaea,
couple uphill transport to an input of energy from light.
ion-driven transporters mediate
secondary active transport
ATP-driven transporters mediate
primary active transport
Three types of transporter-mediated transport
1) Uniports
2) symports
3) antiports
are all used for both passive and active transport
Coupled transport involves...
either the simultaneous
transfer of a second solute in the same direction (symporters) or the transfer of a second solute in the opposite direction (antiporters)
The glucose-Na+ symport protein uses the electrochemical Na+ gradient to drive what?
the import of glucose
The active transport of many sugars and amino acids into bacterial cells is driven by what?
the electrochemical H+ gradient across the
plasma membrane
During the transport cycle, some of the helices undergo what kind of motion?
sliding motions causing them to tilt
An asymmetric distribution of carrier proteins underlies the transcellular transport of solutes... meaning what?
You don’t have an equal number of proteins in the cell which allows the gradient to exist, if equal gradient wouldn’t be forcing ion drive. Asymmetrical allows transcellular transport.
what are the 3 classes of ATP-driven pumps?
P-type pump
F-type pump
ABC transporter
what does the p-type pump do?
relies on the hydrogen, potassium, sodium or calcium can be outside causing the gradient getting a phosphorous attachment or attachment. ATP converting to ADP with phosphorous converting to the pump.
What does the F-type pump do?
allows the phosphorous to drive the hydrogen into the pump itself. These require the phosphorous to change the shape of the pump allowing for hydrogen to flow totally driven by phosphorous
What does the ABC transporter do?
requires two ATP molecules pushing the molecule out against the gradient and the abc transporters are forcing the gradient in the opposite direction
where does the p-class pump occur?
-plasma membrane of plants, fungi, bacteria (H+ pump)
-plasma membrane of higher eukaryotes (Na+/K+pump)
-Apical plasma membrane of mammalian stomach (H+/K+ pump)
-plasma membrane of all eukaryotic cells (Ca2+ pump)
-Sarcoplasmic reticulum membrane in muscle cells (Ca2+ pump)
Where does the F-class proton pump occur?
-Bacterial plasma membrane
-Inner mitochondrial membrane
-Thlakoid membrane of chlorplast
(similar to the mitochondria that drives the oxidative phosphorylation Hydrogen ions that drive the motor in the F-pump to ADP to ATP)
V-Class proton pump occurs where?
-Vacuolar membranes in plants, yeast and other fungi
-Endosomal and lysosomal membranes in animal cells
-Plasma membrane of osteoclasts and some kidney tubule cells
Where does the ABC superfamily occur?
-Bacterial plasma membranes
(amino acid, sugar and peptide transporters)
-Mammalian plasma membranes
(transporters of phospholipids, cholesterol and other small molecules)
How have structures of the Ca2+ pump been determined?
x-ray crystallography
What is the structure and function of Ca2+ pump?
Without the release of calcium you wont have muscle movement or immune response. A burst of calcium allows for the release of inflammatory mediators into tissue. Calcium is the last ion that has to move into or out of the cell for a muscle contraction to take place. 10-20years of work to figure out all this information.
What kind of pump is the Na+-K+ pump?
P-type transport ATPase
What and how many ions go in and out of the Na+-K+ pump?
3 ions of sodium going into the pocket and 2 potassium's going out
The Na+ - K+ pump is required to maintain what?
osmotic balance and stabilize cell volume
Where does the ATPases belong to?
ABC transporter superfamily
A typical ABC transporter consists of four domains
two highly hydrophobic domains and two ATP-binding catalytic domains
ATP binding leads to dimerization of ...
the two ATP-binding domains and ATP
hydrolysis leads to their dissociation.
How fast can Ion Channels transport?
100 million ions per second
greater than that mediated by a carrier protein
What are some of the ion channel functions?
-control the pace of the heart
-regulate the secretion of hormones into the bloodstream
-generate the electrical impulses underlying information transfer in the nervous system
Ion channels are..
Ion selectivity
Ions fluctuate between ...
open and closed states (gated)
What are the Ion channels specific substrates?
potassium
sodium
calcium
chloride channels
permit only their namesake ions to diffuse through their pores
The ability of channels to discriminate among ions is called
Ion selectivity
What is the atomic radius of potassium compared to Sodium?
The atomic radius of K+ is 1.33 Å and that of Na+ is 0.95 Å

With only this difference to work with. K+ channels manage to select for the K+ ion over the Na+ ion by a factor of more than 1000.
What is Ion channel Gating?
Ion channel gating refers to opening and closing of the ion conduction pore in response to a specific stimulus.
What are the different ion gating channels?
ligand-gated channels (intracellular & extracellular)
voltage-gated channels
mechanically gated channels
Define membrane potential
difference in electrical charge on the two sides of a membrane as a result of active electrogenic pumping and passive ion diffusion
The equilibrium condition, in which there is no net flow of ions across the plasma membrane defines the
resting membrane potential
What equation expresses the equilibrium condition quantitatively about resting membrane potential?
Nernst equation
What amino acids are responsible for potassium selectivity?
Potassium channels are tetramers of identical subunits in which specific "signature sequences" are the amino acids responsible
The signature sequence is conserved in all potassium channels throughout nature and forms a structural unit
called the ..
selectivity filter
In the vestibule (talking about K+ specificity of the selectivity filter in a K+ channel) ions are...
hydrated
Dehydration of the K+ ions require..
energy

which is precisely balanced by the energy regained by the interaction of the ion with the carbonyl oxygens that serve as surrogate water molecules
Who won the chemistry nobel prize in 2003?
Roderick MacKinnon for discoveries concerning channels in the cell membrane
Shape of the channels mimics what?
the shape of the ion (ex: potassium ion for potassium channel)
A marvelous electrostatic feature of the potassium channel is a cavity of...
water half way across the membrane with specifically oriented a helices.
The cavity of water design reduces what and causing what to happen?
This design reduces the dielectric barrier, that is, the energetic cost of moving an ion from the high-dielectric environment of water to the low-dielectric membrane, and thereby supports a high ion throughput
What is voltage sensing?
Conformational changes underlying voltage sensing in KvAP are large and involve movements of arginine residues through the membrane, near the protein lipid interface
Aquaporins are permeable to ..
water but impermeable to ions
Aquaporins play a key role in...
in cellular water homeostasis in humans, animals, and plants. These water channel proteins associate as tetramers. Each aquaporin contains a single 28-Å-long cylindrical pore that supports a string of nine hydrogen-bonded water molecules in single file.
The structure of aquaporins needs what?
more alpha than beta sheets to protect the structure
How many and what type of atoms are lined in the aquaporin?
a row of 8 carbonyl oxygen atoms that can accept hydrogen bonds from the queue of water molecules
because the rest of the pore is lined with mostly hydrophobic amino acids, "water-pore interactions are kept to a minimum," allowing water to rush through each pore at a rate of...
3 x 10 (raised) 9 molecules per second.
a pair of asparagine residues as well as the dipole moments of short a-helices would force water to do what?
to flip near the pore's center. This forced reorientation breaks the continuous chain of hydrogen-bonded waters and prevents protons from "hopping" along the hydrogen-bond network.
What does a proton block do?
keeps hydrogen from moving across the membrane
Unlike gramicidin A, an antibiotic peptide that kills bacteria by forming pores in their cell membranes, aquaporins must not leak protons. Doing so would disturb what?
the delicate balance of charge across cell membranes that underlies cellular function
how do aquaporins manage to do what gramicidin A can't?
Near the center of the aquaporin pore, hydrogen bonds from a pair of asparagine residues (as well as the pull of nearby a-helix dipoles) reorient the central water molecule, preventing it from accepting a proton from nearby water molecules.
Recent results indicate that the main barrier to proton transfer is not caused by interruption of the hydrogen-bonded water chain, as had previously been speculated, but rather ....
by an electrostatic field created by the a-helix dipoles in the NPA region.
Voltage-gated cation channels generate action potentials in electrically excitable cells which are what 4?
- neurons
- muscle cells
- endocrine cells
- egg cells
Action potentials are the direct consequence of ...
the properties of voltage-gated cation channels
Invention of patch-clamp allowed us to understand what?
if you don’t hit thresh hold you wont get an action potential, you need enough energy to open up the gate
transmitter-gated ion channels convert chemical signals into ...
electrical signals at chemical synapses
Three conformations of the acetylcholine receptor
occupied and open
occupied and closed (inactive)
unoccupied and closed
What do genes code for?
MRNA and eventually amino acids and those amino acids become proteins
How are cells and bodies made from the instructions in DNA?
DNA to Proteins to Cells to an organism
The Central Dogma of DNA to protein is:
DNA, transcription to RNA, translation to Protein to get the trait
To get from the chemical language of DNA to the chemical language of proteins requires 2 major stages:
transcription and translation
Each disease (phenotype) is caused by non-functional gene product, some diseases are:
lack of an enzyme
Tay sachs
PKU
albinism
Who discovered that genes act by regulating definite chemical events?
George Beadle and Edward Tatum
(1941:1958)
what is made in nucleus?
replication of DNA
ribosomes
RNA, TRNA, SRNA in addition to the reading of genes
when making mRNA the transcribed DNA strand =...
template strand
when making mRNA UNtranscribed DNA strand=..
coding strand
Transcription requires what enzyme?
RNA polymerase making the bubble which creates the strand 5'to 3'
How many RNA polymerases are there?
3!
what does RNA polymerase 1 do?
-only transcribes rRNA genes
-makes ribosomes
What does RNA polymerase 2 do?
transcribes genes into mRNA
what does RNA polymerase 3 do?
only transcribes tRNA genes
DNA to protein we are actually using what?
RP2
What is the promoter region?
binding site before beginning of gene
in promoter region is what?
TATA box
-thymine and adenine sequence that tells the binding proteins that this is the promoter region
TATA bos does what?
binding site for RNA polymerase & transcription factors
what is the enhancer region?
binding site far upstream of gene
-turns transcription on high
What does the initiation complex include?
transcription factors that bind to the promoter region
-trigger the binding of RNA polymerase to DNA
exons=
the real gene
expressed/coding DNA
introns=
the junk
in between sequence
What does mRNA spicing do?
edit out introns
primary transcript in mRNA splicing = what?
pre-mRNA
When and by who were the discovery of introns/exons?
1977 & 1993
Richard Roberts
Philip Sharp
If an error occurs in splicing what happens?
a single base added or lost throws off the reading fram
What are snRNPs?
small nuclear RNA
What is a spliceosome?
several snRNPs
recognizes splice site sequence which can cut and paste genes
How does mRNA code for proteins?
it reads in sets of 3 (Codon then translated into amino acid)
What code is a start codon?
AUG
what codes is/ are a stop codon?
UGA
UAA
UAG
What aids in the loading tRNA bond?
Aminoacyl tRNA synthetase
Are ribosomes an organelle or enzyme?
Ribosomes are both an organelle and enzyme: not surrounded by membranes, function like an organelle but act like a protein.
What are the different Ribosome sites?
A-site
P-site
E-site
What does the A-site do?
aminoacyl-tRNA site
what does the P-site do?
peptidyl-tRNA site
What does the E-site do
exit site
What 3 steps are needed to build a polypeptide?
Initiation
Elongation
Termination
What is the purpose of protein targeting?
signal peptide (address label)
What do prokaryotic genes contain?
DNA in cytoplasm
circular chromosomes
naked DNA
NO introns
What do eukaryotic genes contain?
DNA in nucleus
linear chromosomes
DNA wound on histone proteins
introns vs. exons
Transcription and translation are what in bacteria?
simultaneous!
- while ribosomes read mRNA as its transcribed
What is the difference between prokaryotes & eukaryotes in translation?
Time and physical separation between processes
(Eukaryotes takes ~1hr from DNA to protein)
What are the modes of cell signaling?
Direct cell-cell signaling
Signaling by secreted molecules
signaling molecules
What are the signals secreted by molecules?
Endocrine:
- distant signaling ex: estrogen
Paracrine:
-act on neighboring target cells ex: neurotransmitters
Autocrine:
-self signaling molecules ex: T cells
What are the classes of signaling molecules?
Hydrophobic
neurotransmitters
peptide signaling molecules
eicosanoids
which signaling molecules are use membrane receptors?
Neurotransmitters
peptide signaling molecuels
eicosanoids
What do hydrophobic signaling molecules do?
passively diffuse across the cell membrane
ex: vitamin D3, steroid hormones thyroid hormone etc.
- use intracellular receptors & function as activators or repressors of genes
How do neurotransmitters carry signals?
between neurons to other target signals
-they are hydrophilic and bind to surface receptors
What are 3 peptide signaling molecules?
peptide hormones
neuropeptides
polypeptide growth factors
Eicosanoids lipid signaling molecules include what?
prostagiandins
prostacyclin
throboxanes
leukotrienes
Peptide signaling molecules have what kind of lifespan?
short lived
act in autocrine or paracrine pathways
What are the 2 types of signaling receptors?
Intracellular
membrane integral
what do kinases bond to ?
phosphate
Nuclear receptor superfamily has transcription factors that have domains for...
ligand binding
DNA binding
modulate transcription
Glucocorticoid receptors
What is the purpose of hormone binding?
replaces HDAC with HAT and may alter the activity of the receptor
How many membrane-spanning alpha helices are in membrane receptors?
7
What is a G protein?
important class of membrane bound receptors that have conformational change and trigger signal cascade inside the cell as well as other numerous activities inside the cell
What do kinases move?
phosphate
How many receptors do humans have?
59
What do receptor protein- tyrosine kinases help do?
ligand binding and autophosphorylation of receptors
What mediates binding/activation of downstream signaling molecules in tyrosine kinases?
SH2 domains
What are some non-receptor protein-tyrosine kinases?
Cytokine receptor superfamily
and non-receptor protein tyrosine kinases
ex: JAK
janus protein tyrosine kinases
What does ligand binding induce?
receptor dimerizaiton
What is intracellular signal transduction?
chain of reactions, transmits signals/cell surface --> intracellular targets
-First studied for epinephrine
What takes place first in intracellular signal transduction?
breakdown of glycogen
What is the purpose of cyclic AMP?
a secondary messenger leading to the breakdown of glycogen
Regulates genes and Metabolic regulation
cAMP signal transduction pathways:
- What are the 2 phophorylation downstream enzymes?
Glycogen synthase (inactivated)
Phosphorylase kinase (activated)
Where do cascading events end up?
promoter regions
What does CREB do?
neuronal development
memory
differentiation
proliferation
cognition
PLC stimulates hydrolysis of ...
pip2 to DAG and IP3 because DAG and IP3 are secondary messengers
what does IP3 regulate?
calcium
When is calmodulin activated?
When calcium is increased from an inactive state to an active state
What does calmodulin activate as it is phosphorylated?
protein kinases
metabolic enzymes
ion channels
transcription factors (CREB)
MLCK (myosin light chain kinase) is activated by what?
calmodulin which will activate muscle
Getting calcium into the cell does what?
brings more calcium for a cascading event to take place
PIP3 targets a protein-serine/threonine kinase called ..
Akt and also binds protein kinase PDK1
Akt phosphorylates several target proteins, transcription factors, and other protein kinases
Transcription factors include members of the
forkhead or FOXOX family which travel to the nucleus and then bind to the genes that inhibit cell proliferation
Conserved across eukarytoic cells are 3groups of MAP kinases which are..
Stimulus
Growth Factors
Inflammatory cytokines
(ERK, JNK and p38)
3 classes of signaling proteins are
cyclic AMP
pI3
MAP kinase
What does ERK regulate?
meiosis
mitosis
cell proliferation
and differentiation
What are ligands?
growth factors
cytokines and viral infections
carcinogenic chemicals
ERK activation leads to ...
RAS to RAF to MEK to ERK and goes into the nucleus and tells the cell todo something
ERK goes to the nucleus and phosphorylates
Elk-1
ERK tells the nucleus what?
To grow and divide
RAF MEK and ERK are held together by ...
KSR scaffold