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175 Cards in this Set

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Eukaryotes:
describe genetic material
linear double helix located in nucleus
Prokaryotes:
describe genetic material
"naked" circular molecule (in cytoplasm)

*no membrane bound organelles
layer that encloses all cells and lets sufficient amounts of oxygen and other nutrients to enter and leave the cell as needed?
plasma membrane
layer in prokaryotic cells and plant cells what contains cellulose micro-fibrils and maintains the shape of the cell?
cell wall
flagellum of prokaryotic cell is connected to __________.
rotary motor
"hairs" of prokaryotic capsule?
pili
The nucleus is contained in a lipid bilayer called ________.
nuclear envelope
Structural components within cells that are involved in many cellular processes including mitosis, cytokinesis, and vesicular transport.
microtubules
Components of the cytoskeleton which move under the influence of molecular motors.
microtubules
Microtubules are attached to the _________ with a pair of _________.
centrisome
centrioles (for mitosis)
An organelle that serves as the main microtubule organizing center (MTOC) of the animal cell as well as a regulator of cell-cycle (cell division) progression.
centrosome
what cell deposits extracellular matrix?
fibroblast cells
2 items in the cytoplasm of a prokaryote?
ribosomes and (circular) DNA
membrane bound nutrient storage area found in plants?
Vacuole
Ribosomal RNA (rRNA) is transcribed and assembled within the ________.
NucleOLus
non-membrane bound structure[1] composed of proteins and nucleic acids found within the nucleus.
nucleolus
The nucleus takes up ___% of a cell's volume.
10%
a small membrane-enclosed sack that can store or transport substances
vesicle
*look like white splotches
within the nucleus:
dark stained DNA vs light DNA....which part makes genes?
light.
Heterochromatin
dark splotches
dense DNA,not making proteins
what are the dark splotches in the nucleus?
heterochromatin
dense DNA, not making proteins
the light area in the nucleus....rich in genes.
euchromatin
describe euchromatin.
lightly packed form of chromatin (DNA, RNA and protein) that is rich in gene concentration, and is often (but not always) under active transcription.
*active portion of genome
nuclear and cytosolic fibrils that extend into the nucleoplasm and cytiplasm around nuclear pores... that mediates binding to nuclear transport protiens.
nuclear basket
nuclear envelope is composed of ...
double lipid bilayer:
inner and outer nuclear membranes.
nuclear pores form a _____.
rosette
An organized meshwork of fibrils on the internal face of the envelope, while less organized support is provided on the cytosolic face of the envelope, provides structure.
nuclear lamina
name for chemosensory neuron?
chemoreceptor
in C. elegans:
cluster of neurons in head?
amphid neurons
in C. elegans:
cluster of neurons in tail?
phasmid neurons
the ganglia around the pharynx of C. elegans?
Nerve ring
In C. elegans: chemotaxis using what mechanism?
Bind chemicals on CILIATED nerve endings which are exposed to the environment! Neurons identify using variation in cilia.
(I think)
what organelle synthesizes lipids and steroids, metabolizes carbohydrates and steroids

**Also regulates calcium concentration (with phosphorylipase C), drug detoxification, and attachment of receptors on cell membrane proteins
SMOOTH endoplasmic reticulum
which organelle synthesizes proteins (translation, transport & chaperones found here for protein folding)?
ROUGH endoplasmic reticulum
________ then read the information in this RNA and use it to create proteins.
Ribosomes

(Then they send it to the ER for folding.)
What are the internal compartments formed by the inner membrane of a mitochondrion?
Cristae
What makes the rough ER rough?
ribosomes
What does the rough ER do with proteins?
translate
fold (with chaperones)
sort
transport
composition of a ribosome?
base and large subunit
What are the 3 mentioned functional regions of the Golgi apparatus
& What are the functions of the golgi?
1) Cis Golgi (proximal to ER)
2) medial golgi
3) trans golgi

packages macromolecules, such as proteins and lipids
Stacks of membrane-bound structures that the golgi apparatus is composed of?
How many of these stacks in anaimal cells?
cisternae

4-7 stacks
what packages macromolecules, such as proteins and lipids?
golgi apparatus
what transports lipids and proteins from the golgi?
transport vesicles
a special kind of smooth ER that stores and releases CALCIUM ions to trigger MUSCLE contractions .
**found in both smooth AND striated muscle.
sarcoplasmic reticulum
which organelle is responsible for cellular respiration?
mitochondria
what organelle genertaes ATP?
mitochondria
membrane-bound compartment inside chloroplasts and cyanobacteria.
(hint: they compose stacks called grana)
thylakoids
Region that contains chlorophyll where light-dependent reactions of photosynthesis take place?
thylakoid membrane
The "Degradation center" of the cells. they digest and break down particles.

(the broken down particles can even be seen within these structures under magnification.)
Lysosomes
The "detox center" of the cell.
Contains oxidative enzymes.
They break down hydrogen peroxide and larger fatty molecules too.
light colored and usually smaller than lysosomes.
PEROXISOMES
This structure is composed of collagen which forms a regular banding pattern & supports the cell.

**looks like lines in long. section, looks like polka dots in cross section.
ECM
extra-cellular matrix
process by which cells absorb or secrete molecules (such as proteins) by engulfing them or secreting them. Uses VESICLES (w lipid bilayer).
endocytosis & exocytosis
______ & ______ are taken into the White blood cells and digested by its ________.
Antigens & antibodies

Lysosomes!
*in phagocytes
antibodies recognize specific _____.
antigens
shape of antibody?
Y shaped
what kind of cell produces anibodies?
A class of white blod cells called:
B lymphocytes
AKA
B cells
How is a b- cell triggered and what happens after it is triggered?
Triggered by an antigen binding to the specific receptor (antibody).

Then the B cell secretes a lot of those specific antibodies in a soluble form.
What are the (3) steps in fighting infection with antibodies?
1)foreign molecules, viruses and bacteria form aggregates with antibodies
2)phagocytes ingest antibodies and antigens
3)special proteins kill the antibody coated pathogens.
white blood cells that protect the body by ingesting (phagocytosing) harmful foreign particles
phagocytes
How do we raise antibodies in a lab using animals?
give a mouse (for example) 2 or 3 boosts of antibodies
then the blood will contain a variety of different anti-A antibodies that bind in different ways. Then we can take the blood and purify it using affinity chromatography!
How do we use immunoaffinity chromatography to collect pure antigen?
(antigen A)
-coat beads with A antibodies and pack the column with these beads
-wash mixture of molecules through beads and antibodies collect A's.
-rinse out excess contaminant
-Elute (chemically extract A's from antibodies) and collect pure antigen A!
what is the benefit of creating a b-cell - tumor cell hybrid?

(B cells taken from antigen A injected animal)
it can make antibodies and divide indefinitely- creating a large amount of antibodies!
2 ways to use antibodies to purify molecules.
immunoprecipitation
&
immunoaffinity column chromatography
How does immunoprecipitation work?
Add specific anti-A antibodies to a mixture of molecules
-antibodies (anti A) and antigens(A molecule) form aggregate and collected via centrifugation
Antibodies harvested from a b-cell- tumor cell hybrid are called _______.
monoclonal antibodies
How do molecular tags work with antibodies? (2 ways)
either:
1) tag antibody with gold or fluorescent dye, then fluorescent antibody binds to antigen and is viewed with microscope
2) molecules are separated by gel electrophoresis and incubated with fluorescent antibodies which will bind to the antigen and show it's position.
process of detecting & labeling antigens (e.g., proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues
immunohistochemistry
What are 2 examples of immunohistochemistry?
monoclonal antibodies and molecular tags (IMMUNOSTAINING)
what is immunostaining?
fluorescent antibody binds to specific site ("antigen" could be a specific organelle) and can be viewed with FLUORESCENT microscope
How is a fluorescent microscope different from a light microscope?
UV light is passed through 2 filters:
1st- FILTERS the light so that the only wavelenghts that pass through EXCITE specific fluorescent dyes.

2nd- blocks out the filtered light only letting the wavelengths emitted by the fluorescent dyes through.

**fluorescence is the only light that reaches your eye!
Which ions are in greater concentrations EXTRACELLULAR?
Calcium
Sodium
Chloride (anion)
Which ions are in greater concentrations INTRACELLULAR?
potassium
hydrogen
which is more acidic, intra or extra cellular?
extracellular
what 2 things determine the diffusion rate of molecules across a membrane?
size
solubility
Can this molecule get through a cell membrane easily?
small hydrophobic
yes
Can this molecule get through a cell membrane easily?
small uncharged polar molecules
yes

polar is bad, but if small, it will get through
Can this molecule get through a cell membrane easily?
larger uncharged polar molecules
NO

large molecules need help to get through, so do polar
Can this molecule get through a cell membrane easily?
IONS
NO

charged molecules need help to get through a membrane
membrane protein that opens and closes according to a molecules size and charge
channel protein
a membrane protein that develops a specific binding site for a ligand
transporter
what drives passive transport? What membrane proteins use passive transport?
Driven by CONCENTRATION GRADIENT. (diffusion)

All channel proteins and many transporter proteins use passive.
what drives active transport? What membrane proteins use active transport?
energy, like ATP to work against diffusion

Special carrier proteins use active transport.
what kind of transport protein do lysosomes use?
ACTIVE H+ pump to maintain acidity
Where is a glucose carrier located?
active or passive?
Liver cells & epithelial
passive (concentration gradient)

also:
12-dimer, and 2 conformations binding site in or binding site out. In liver glucose is turned into glycogen and stored.
Electrochemical gradient is comprised of what 2 factors?
concentration gradient + membrane potential (voltage across membrane)

**weak when they work in opposite directions, strong when they work in the same direction.
membrane potential?
voltage difference across a membrane (interior vs exterior) of a cell
what are the three ways of active transport?
1) COUPLED TRANSPORTER (one uphill one downhill- "recoil")
2) ATP DRIVEN PUMP (one uphill = ATP hydrolysis)
3) LIGHT DRIVEN PUMP (like the cell membrane of our eyes, or bacteria)
3 types of coupled transporters?
UNIPORT- one molecule
SYMPORT- a molecule and an ion go in same direction
ANTIPORT- an ion and a molecule go in opposite directions
30% ATP is consumed by _______.
carrier/transport proteins
another name for Na+ pump?

How does it work?
sodium potassium ATPase

It pumps sodium out (active, against charge concentration) and potassium in.
It uses ATP to keep the negative potential in cytosol.
zero driving force for K+ influx.
describe the cyclic action of the sodium pump AKA "sodium potassium ATPase"
In original conformation Na+ binds to pump
-Harvest energy from ATP in form of 1 phosphate- this triggers conformation change-->Na+ ejected while K binds
-when pump is dephosphorylated it returns to original conformation and ejects the K+
Then it can cycle again.
How does the Glucose- Na+ Symport protein function?
Glucose + sodium go INTO the cell, (same direction)
-Electrochemical energy from sodium is the driving force
-glucose hitchhikes!
-ACTIVE, AGAINST GRADIENT!
How does glucose -Na+ symport work in gut cells?
The glucose is taken into high glucose concentration intestinal epithelial cells using Na+ ENERGY(NA gradient), then it is passed out of the high concentration PASSIVELY. (glucose carrier)
*intestinal and kidney cells
2 THINGS ION CHANNEL SELECTIVITY DEPENDS ON?
1. Diameter and shape of the ion channel
2. Distribution of charged amino acids in the lining
ion channels are mainly for which ions?
Ion channels are _____ pores.
Ions: Na+, K+, Cl-, Ca +2

AQUEOUS!
In order for K+ to travel through an ion channel the lining must be _____.
negative

specifically (for K+), negative carbonyl ions!
How many configurations for ion channel?
How is influx controlled?
How many ion can pass through/second?
2: open and closed.

"ID" "gated" ion channel requires specific signal from other protein

1 million per second!
What are the effects caused by the influx of ions through an ion channel?
1-Change membrane potential.
2-Forces other ion channels to open or close in msec.
3-Generate electric signal across membrane.(Mechanism for neural function!)
what items are needed for patch clamp recording?
1 GLASS MICROELECTRODE (1 micro-m in diameter)
- attach to cell membrane
2. detached PATCH (contains a few ion channel)
3 METAL WIRES connected to oscilloscope & glass microelectrode
- apply voltage using current through electrode, through membrane, up the microelectrode to the wire!
4 record the current with OSCILLISCOPE
- test effects of chemicals or membrane conditions
What are the 4 kinds of stimuli for Ion channels?
a. voltage- gated -- voltage sensor on the channel proteins (like Na+ channel in neurons)

b. ligand- gated (extracellular ligand)-- neurotransmitter-gated ion channel, e.g. glutamate

c. ligand-gated (intracellular ligand) -- chemical ligand-gated ion channel

d. mechanically gated --like ion channels on auditory hair cells
How are auditory nerves regulated?
STRESS ACTIVATED ION CHANNELS!
Fluid responds to sound waves mechanical force (stress) touches cilia (on auditory hair cells) and ion channel on hair surfaces send the signal to the axons and then the BRAIN!!
How many different K+ channels can C. elegans genes encode?
68 different K+ channels!
What kid of stimuli does a venus fly trap (ion channel) use?
mechanically gated ion channel
(like our auditory cells!)
what drives the Na+-H+ pump?
function of this pump?
Na+ gradient

export of H+ for pH regulation
what drives the H+ pump and what is it's function?
H+-ATPase....ATP driven

Active export of H+ ions out of cytosol into either extracellular, lysosome or vacuole.
Sequence that signal travels through a nerve cell?
1. branching DENDRTITES to receive signals
2. CELL BODY
3. a long AXON, which ends in branches of
4. NERVE TERMINALS, to conduct signals away from cell body
______ of the neurons decide which type of signal to send and where to (to which terminal)
dendrites
the decision makers!
what are the conformations of the Na+ channel and what is their polarization state?
polarized membrane:
CLOSED (this is normal level)

membrane depolarized:
OPEN
or INACTIVATED (not completely closed yet, but unable to reopen, so signal can only travel in 1 direction)
what is the membrane potential of a closed polarized Na+ channel(neural)?
-60 mV
when the Na+ channel (neural) is opened and the membrane becomes depolarized , the membrane potential goes from _____ to _____.
-60 mV to +40 mV
At what voltage does the Na+ channel (neural) becomes inactivated?
+40 mV

closes and tapers off back to -60 mV
What is action potential numerically and qualitatively?
+40 mV

This is the peak of the Na+ influx.
At this point the open channel becomes inactivated.
What is threshold potential numerically and qualitatively?
-40 mV

depolarizing stimulus must be strong enough to get the voltage from -60 mV to -40 mV to TRIGGER INFLUX of Na+
What is resting membrane potential numerically and qualitatively?
-60 mV

This is the normal polarized state of the membrane. Channels are closed.
How does the propogation of action potentials work/ flow?
UNIDIRECTIONAL
-backward flow prevented by inactivated channels
-depolarization from one channel spreads across membrane in a chair reaction.
The specialized junctions between the transmitting and receiving neurons are called ____.
synapses
In neurons the electrical signal is converted into a chemical signal in the form of a small signaling molecule known as _________.
a neurotransmitter
In a neuron, ________ store various neurotransmitters that are released at the synapse.
synaptic vesicles (or neurotransmitter vesicles)

(lots of these in nerve terminals!)
In the synapses you will find a lot of _______.
ECM extracellular matrix!
The neuron that sends the message is the _____ and the one that receives is the ______.
Presynaptic nerve (terminal)

Postsynaptic nerve (dendrite)
the surfaces between the nerve terminals and the dendrites receiving the messages are called _________ and ________.
presynaptic and postsynaptic membranes
The release of neurotransmitter is triggered by ______-gated ________ channels
VOLTAGE gated

Ca+2 channels
what neurotransmitter is unique to muscle fiber?
acetylcholine
What opens the Ca+ channel in a neuron?
What does the influx of calcium trigger?
electrical impulse= depolarization

triggers: release of neurotransmitters from vesicle
How does the postsynaptic cell receive neurotransmitters?
The neurotransmitter diffuses across the synaptic cleft, then binds to NEUROTRANSMITTER RECPEPTOR (transmitter gated ion channel) concentrated in the postsynaptic membrane.
Between the pre- and postsynaptic cells is a gap about 20 nm wide called the __________.
synaptic cleft
What happens after a neurotransmitter (ligand) has been bound to the neurotransmitter receptor?
The receptor, a gated ion channel, is opened and and there is an influx of ions (which depolarize or polarize the membrane)
What are the 3 common excitatory neurotransmitters?
Acetylcholine
serotonin
glutamate
What are the 2 common inhibitory (like tranquilizers) neurotransmitters and what ion do they channel?
GABA
Glycine

both bind to Cl- channels (negative!!)
the neurotransmitter Acetylcholine uses ______ion channels.
Na+
the neurotransmitter GLUTAMATE uses ______ion channels.
Ca +2
Acetylcholine gated ion channel:
How many transmembrane subunits in dimer?
5
Mechanism behind PROZAC?
This antidepressant blocks the reuptake of the excitatory serotonin.

What other drug works like this?
COCAINE!!
Psychoactive drugs target _____________.
neurotransmitter-gated ion channels
Which excitatory toxin causes muscle spasms by blocking inhibitory signals?
strychnine
Which inhibitory toxin relaxes muscle by blocking excitatory signals?
curare
How many nerve terminals send signals to one neuron (cell body & dendrites)?
Can be thousands!
Four Ways of Cell Communication?
What are their corresponding signals?
1) ENDOCRINE via hormone
2) PARACRINE via local mediator
3) NEURONAL via neurotransmitter
4) CONTACT DEPENDENT via membrane bound signal molecule
Endocrine signaling: What are the signaling molecules and how are they transported?
1. signal molecules are HORMONES... are long lived & affect cells very distant from the releasing cells
2. long distance through circulatory system (unlike paracrine which travels short distances)
Paracrine signaling: What are the signaling molecules and how are the transported?
1. LOCAL MEDIATORS (eg. growth factor) are usually short-lived and have LOCAL effects
2. coordinate the activities of clusters of neighboring cells
3. might influence back to the signaling cell (autocrine)
a form of paracrine signaling in which a cell secretes a hormone or chemical messenger that binds to receptors on the same cell.
Autocrine signaling
neuronal signaling: long lived or short lived?
short lived
(unlike endocrine which travels through blood stream)
What are the four cell responses to signals?
Grow + divide,
survive,
die,
differentiate (eg- nerve cell develops from epithelial cell)
the process of programmed cell death that may occur in multicellular organisms
apoptosis
(apoptotic cells)
The signal molecule acetylcholine triggers various responses. What are these responses?
acetylcholine:
1. decreases heart rate (& force of contraction)
2. stimulates release of secretory vesicles (like saliva)
3.stimulates skeletal muscle contraction
Molecular responses to extracellular signal:
Fast response- what response and how fast is fast?
altered protein function, cell structure

sec to mins
Molecular responses to extracellular signal:
Slow response- what response and how slow is slow?
altered gene expression and protein synthesis

minutes to hours
What are INTRAcellular receptors?
receptors that are either in the cytoplasm or nucleus (as opposed to the more common cell-surface receptors)

A SMALL HYDROPHOBIC signal molecule (eg: hormones) is able to penetrate cell membrane to reach it intracellular destination.
What are 4 common hormones that are INTRAcellular signal molecules?
cortisol- a steroid
estradiol- an estrogen/female hormone
testosterone
thyroxine- thyroid hormone
What is the function of NO (nitric oxide)
diffuses across cell membrane
, binds to intracellular receptor & causes relaxation in smooth muscle cells around blood vessels.
What are the 3 classes of SURFACE RECEPTORS?
1) ion-channel-coupled receptors (for neurotransmitter)
2) G-protein-coupled receptors (7 pass)
3) enzyme-coupled receptors (with dimer signal)
signal transduction cascade sequence?
1- binding of signal (or ligand) to receptor
2-signal transduced to adaptor proteins
3- signal multiplied and amplifed through activating intracellular proteins (activated through phosphorylation and GDP)
4- integration or divergence of signals to effector proteins (fast or slow).
a molecule/protein that binds to a protein and thereby alters the activity of that protein (come in fast or slow variety)
effector
two types of activation in intracellular signaling molecules?
phosphorylation (W/atp & GTP binding)
What are the 3 types of effector proteins and which are fast or slow?
Fast:
METABOLIC ENZYME (alters metabolism)
CYTOSKELETAL PROTEIN (alters cell shape or movement)

slow:
TRANSCRIPTION REGULATOR (signal to nucleus, changes gene transcription / translation)
what does kinase do?
phosphorylation (signaling):
adds a phosphate to a protein to "turn it on"
what does phosphatase do?
DEphosphorylation:
removes a phosphate (by hydrolysis) from a protein which "turns it off"
How does GDP/GTP work?
GTP BINDS to a protein activating it

GTP HYDROLYSIS= loses a phosphate and become GPD which INACTIVATES the protein (needs to bind another phosphate to reactivate)
Name that substance:
morphine or opioid peptide
-stimulates g-protein coupled opiate receptors
-- pain relief, inhibits neurotransmitter release
endorphin
What substance binds and activates nicotinic acetylcholine receptor
nicotine
What is unique about the structure of a G- protein liked receptor?
7-pass transmembrane proteins
structure of a g-protein
3 subunits (heterotrimer)
alpha subunit binds GDP & GTP
Break into two signaling units
upon activation alpha & beta-gamma
what are the 2 things that can bind to intracellular receptors?
1. for small hydrophobic signal molecules, e.g. hormones
2. for NO gas which diffuses across cell membrane
What is the sequence after a a signal molecule is bound to a G-protein-linked receptor?
signal goes from receptor and activates the GDP--->GTP on G-Protein
-protein breaks into activated alpha subunit and activated beta-gamma complex
-then they activate different transmembrane proteins and enzymes (such as adenylyl cyclase and phosphorylipase C)
which subunit of a G protein holds the GTP/GDP?
Alpha
senses regulated by g-proteins?
Vision
Smell
Taste
Chemoreception

* they could also act indirectly on enzymes or ion channels
How does Adenylyl cyclase work?
SLOW (takes minutes to hours)
1. activated alpha subunit of G-protein activates Adenylyl cyclase enzyme
2. adenylate cyclase converts ATP into cyclic AMP and 2 phosphates! (cleaves 2 phosphates)
3. cyclic AMP binds to and activates PKA (protein kinase A)
4. active PKA turns on (polyphosphates) the TRANSCRIPTION REGULATOR which activates gene transcription!!!
How does phosphorylipase C work?
1. activated alpha subunit of G-protein activates phosphorylipase C enzyme
2.activated phosphorylipase C breaks down inositol phospholipid into 2 things:
a) DIAGLYCEROL (in membrane)...
b) IP3 (into cytoplasm): opens Ca+ channel on SMOOTH ER membrane and releases Ca+ into cytoplasm

**BOTH the Ca+ and the Diaglycerol can activate PKC!! (a kinase)
what are the important 2nd messengers in Adenylyl cyclase & phosphorylipase C?
phosphorylipase C: Ca +2
Adenylyl cyclase: cAMP
How does an Enzyme-linked Receptor work?
Growth factor receptors
example we used is Receptor tyrosine kinase (RTK)

The ENZYME is KINASE which binds phosphates (energy!)
1- Dimerization of signal molecule
2. Phosphorylation/activation of (tyrosine) receptors (auto- or cross)
3. these activated receptors then activate intracellular signaling proteins (or adaptors)
Ras is a ____ binding protein.
GTP
Sequence for Ras Protein strting with signal molecule!
1) -Enzyme-linked Receptor recieves signal molecule & phosphorylates (with kinase).
2-receptor activates adapter protein
3- adapter protein activates Ras activating protein
4- Ras activating protein activates Ras
5; Ras activates MAP KKK activates MAP KK, activates MAP K, activates target proteins (involved in changes in protein activity or gene expression)
What does the "MAP" in MAP protein stand for and what is its function?
mitogen activated protein

Mitogen induces cell proliferation which is why a mutant Ras can cause cancer.
The sequence is X-Ras-Y. Know what happen if any of these get LOF or GOF!!
LOF- shut down whole system unless some unless down the line has a GOF!
Just the opposite for GOF....continually operating unless some unit down the line has a LOF. (loss of function/gain of function)
If Ras protein cannot hydrolyze GTP what occurs?
can't lose a phosphate (hydrolyze) from its GTP:
GOF -gain of function: this causes cancer (mitogen activation=cell proliferation)