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Cell Biology
n/a
109
Biology
Undergraduate 3
09/07/2008

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Term
cell size- linear vs. volume
Definition
limiting factor of cell size is surface area
* eukaryotes solved by having membranous internal organelles
Term
cytoskeleton- Eukaryotes vs. Prokaryotes
Definition
although prokaryotes don't have microtubules, actin filaments, and intermediate filaments--> they have homologous cytoskeletal structures
Term
Light Microscopy
Definition
light source passes through condenser through specimen- through objective lens and through occular (two lens system)
Term
resolution
Definition
= 0.61(lambda)/ n sin ø

lambda=wavelength
n=refractive index of medium separating specimen from objective and condenser
ø-half the angular width of cone of rays from specimen (sinø- max of 1)
Term
contrast
Definition
need dyes to see parts of cell- inside has similar refractive index as water
Term
Dyes-

Sudan Black
Silver Nitrate
Hematoxylin
Eosin
Definition
sudan black- lipids and cholesterol(fingerprints)
silver nitrate- internal organelles (golgi)
hematoxylin- + binds - (nucleic acids, DNA)
eosin- - binds +

**often have to be dead to stain
Term
phase microscope
Definition
optical tricks (lighting from the sides) allows you to visualize cells without staining (so they can be alive)
Term
Antibodies for visualization
Definition
primary antibody binds to target molecule- secondary marked antibody binds to 1º antibody

when labelled with a fluorophore- cimmunofluorescence
Term
immunofluorescence-
Definition
beam splitting mirror lights specimen with excitation wavelength- transmits light emitted from flurophore
Term
GFP- jellyfish flurophore
Definition
can be incorporated into host DNA- makes a protein that fluoresces. (can be attached to target protein)
Term
laser trap
Definition
demonstrated flexibility of membrane. can be used to calculate force to move things in a cell
Term
Electron Microscopy
Definition
gives resolution ~0.1 nm.

(TEM)- sectioned
(SEM)- surface

must be dead- fixed and stained
Term
Building blocks of the Cell
Definition
sugars-> make polysaccharides
fatty acids-> make fats, lipids, membranes
amino acids-> make proteins
nucleotides-> make nucleic acids, RNA, DNA
Term
saccharide condensation
Definition
monosaccharides condense (lose H2O) creates disacchardes- hydrolysis consumes water to reproduce monosaccharides
Term
lactose
Definition
condensation reaction between glucose and galactose- lactose intolerence happens when monosaccharides can't be reproduced
Term
amino acid
Definition
amino group- alpha carbon - carboxyl group
-R Group

NH2-C-COOH -->ionized form +NH3-C-COO-
Term
protein and protein folding
Definition
proteins- polymers of amino acids joined by peptide bonds O=C-N-H

folding of the protein is dependent on charges of R group (can be acidic, basic, non-polar, uncharged polar)
Term
ATP
Definition
cAMP phosphorylated by ATP and acetyl Co-A. energy from sunlight or food add an inorganic phosphate --> ATP
Term
DNA
Definition
uses deoxyribose instead of ribose (no OH group on 2' C)
Nitrogenous Bases-
Adenine, Guanine, Thymine, Cytosine
Term
central dogma DNA
Definition
DNA replication- transcription to RNA- translation to protein
Term
Amphipathic
Definition
have both hydrophilic and hydrophobic ends
Term
fatty acid
Definition
hydrophilic carboxylic acid head, hydrophobic hydrocarbon tail
Term
lipids
Definition
one tail- cone shaped- congregate as spherical micelle
Term
fats and oils
Definition
3 hydrocarbon tails connected by glycerol

H
I
H2C-C-CH2
I I I
Carboxylic Ends of fatty acids
Term
fats vs. oils (saturated vs. unsaturated)
Definition
saturated with Hydrogens, pack tightly
unsaturated- packing broken up with C=C bonds
Term
trans fat
Definition
breaking and reforming of C=C bonds can be carcinogenic
Term
soap
Definition
made of fatty acids- carboxylic acids mix with water, hydrocarbon tails with oils
Term
phospholipids
Definition
2 fatty acid tails, glycerol, phosphate group

makes bilayer in water- energetically favorable to form sphere
Term
lipid bilayers
Definition
self-healing to keep hydrophobic tails from being exposed to aqueous environment

*in oil and water phospholipids form monolayer
Term
fluid mosaic model
Definition
saying that there is diffusion of phospholipids in membrane- there would be a disposition to homogeneity
Term
lipid bilayer fluidity
Definition
based on length of tails, number C=C bonds, which polar head groups, and amount of cholesterol in membrane

move by
-laterally diffusing
-rotating
-flexing (back and forth)
Term
molecular segregation- phospholipids
Definition
-structural interactions(kinkedness)
-hydrophobic length mismatches
-polar head group interactions
-interactions with membrane proteins

*form microdomains
Term
Synthesizing Phosphatidic Acid
Definition
Acyl-CoA synthetase adds to fatty acid-> acyl Co-A fatty acid

Glycerol kinase adds to Glycerol -> gylcerol-3-phosphate

2 Acyl-CoA Fatty Acids embed in cytosolic leaf of ER--> Acyl transferase joins two and adds glycerol-3-phosphate making phosphatidic acid in cytosolic leaf of ER
Term
synthesizing phospholipids
Definition
phosphatase dephosphorylates phosphatidic acid-> diacylglycerol

CDP carrier molecule brings polar head group
(choline, ethanolamine, serine, inositol)

*all are synthesized using head group specific phosphotransferases (ex// choline phosphotransferase)
Term
control points in phospholipid variation
Definition
1) what fatty acids are made? (chain length)
2) which acyl-transferases become active? (which fatty acids are inserted in ER membrane)
3) which head group transferase is activated? (which group is added?)

Gives approx 1000 different lipids in a eukaryotic cell
Term
common fatty acids
Definition
palmitic acid (16 C)
-palmitoleic

stearic acid (18 C)
-oleic, linoleic

* all are in synthesized in 2C increments (12-20)
Term
choline
Definition
charged,
precursor for phosphatidlycholine(most common), and sphingomyelin
Term
ethanolamine
Definition
terminal amine, charged
Term
serine
Definition
terminal amine, uncharged polar
Term
inositol
Definition
uncharged polar, rare
Term
phospholipids in membranes
Definition
different amounts of each are in different cell types

many can undergo alterations to become another type
(ex// phosphatidyl-ethanolamine can be methylated to become phosphatidlycholine

phosphatidyl-serine can be decarboxylated to form phosphatidyl-ethanolamine)
Term
membrane growth
Definition
phospholipids only grow on ER cytosolic leaf- Must be flipped to ER lumenal leaf.
Term
phospholipid flip
Definition
ER scramblase- nonspecificallly flips phospholipids to lumenal leaf

flippase then specifically flips PS and PE back to cytosolic leaf
Term
membrane leaf composition
Definition
PI, PS, and PE are present on the cytosolic face. PC and glycoproteins are on the lumenal or extra-cellular leaf

* most negatively charged phospholipids are on cytosolic leaf
Term
phospholipid transport
Definition
phospholipids are moved between organelles by vesicle budding, fission, and fusion. Those that do not contact vesicles(mitochondria and chloroplasts) are often directly contacted to ER.

*drugs can block vesicles, don't block organelle growth- therefore they probably contact ER directly
Term
cytosol vs. cytoplasm
Definition
cytosol- cell contents separate from organelles
cytoplasm- cytosol and organelles
Term
regulating membrane fluidity
Definition
1) higher and more C=C make harder to freeze
2) shorter tails- less interaction between phospholipids- more fluidity
3) cholesterol- makes membranes less deformable, but less able to freeze
Term
cholesterol
Definition
ER site of sterol synthesis, hydrophobic tail, small polar head group.

contributes to hydrophobic environment inside bilayer- decreases h20 intake
Term
evidence for fluid mosaic model
Definition
fusion of mouse and human cell- proteins mix
Term
Lipid Rafts
Definition
longer saturated hydrophobic regions(sphingomyelin), and GPI-linked proteins (important for signaling)
Term
Caveolae
Definition
allow transport of lipid rafts to other places in cells-transcytosis
or to other organelles-endocytosis
(ex// gut side to blood side of gut cell)
Term
phospoholipase
Definition
cleaves phospholipids at specific places-- can form molecules important in cellular signaling
Term
phospholipase A2
Definition
cleaves PI or PC to create arachidonic acid-> which can be modified later to make prostaglandins
Term
arachidonic acid
Definition
storehouse in membranes- can come from phosphoatidylinositol or phosphatidly choline.

*has four unconjugated double bonds
Term
prostaglandins
Definition
-inflammation response (especially arthritis and psoriasis)
-pain and fever
-blood pressure regulator
-blood clotting inducer
-labor inducer

*acts like a paracrine hormone
often binds g-protein-coupled receptors
effects mediated by intracellular cAMP response
local mediators
Term
prostanoic acid
Definition
carbons 8-12 of arachidonic acid been cyclized
Term
cycloxygenases (prostaglandin synthase)
Definition
cyclizes and oxygenates arachidonic acid to prostanoic acid
Term
prostaglandin synthesis
Definition
2 production peaks= more than one synthase
Term
NSAIDS
Definition
non-steroidal anti-inflammatory

*act by blocking COX fxn
Term
aspirin
Definition
modifies cox1 and cox2 by acetylating serine in active site (also blocks unwanted clotting-heart)
Term
tylenol
Definition
weakly binds cox3- no significant anti-inflammatory response
Term
ibuprophen
Definition
competitive inhibitor for COX binding site
Term
cox1 vs. cox2
Definition
cox 1 has good roles
-platelet and microphage fxn
-mucus formation (ulcers- too much ibuprophen)
-hematopoiesis (generation of blood cells)

cox2- mostly inflammatory response
-may contribue to cancer cell growth
Term
caveolin
Definition
inserts itself into membranes- associations between caveolin proteins-> caveolae
Term
proteins
Definition
1º- string of amino acids with R groups
2º-alpha helices and beta sheets stabilized by H-bonds

R groups can effect hydrophobicity or philicity (sides or sheets, outside or inside of helix)
Term
integral membrane proteins
Definition
often pass through membrane with alpha helix- hydrophobic R groups

ex// glycine -H
phenylalanine- CH2-ring
leucine- CH2-CH-(CH3)2
Isoleucine- CH-CH2-CH3
I
CH3

serine, tyrosine


Can also be Beta Barrels, or single leaf associated
Term
hydropathy plot
Definition
try 'pushing' 10AA regions of protein through membrane to see how much energy it takes- more energy=hydrophobic region
Term
asymmetries of protein reactions relative to bilayer
Definition
often the cytosol is a reducing environment- Sulfide is reduced to -SH

outside the cell sulfide usually formed disulfide bonds(helps folding)
Term
membrane associated proteins
Definition
can also be lipid-linked and peripheral, or associate via van der waals, ionic or H-bonding with membrane bound proteins

some can be modified or released for signalling and recruiting
Term
myristyl and farnesyl anchors
Definition
regulated and reversible recruitment of proteins at membrane surface
Term
detergents
Definition
ionic- strip protein and make it charged
gentle- allow reformation of membrane with purified protein (ex// Na+/K+ pump)
Term
FRAP
Definition
bleach one area once-

quantify immobile phase by the % of proteins not moving from bleached area

limitations- where is rescue coming from?
measures only mobile phase- how fast lipids move
Term
FLIP
Definition
continually bleach one spot- measure another area

allows determination of non-mobile phase
demonstrates continuity of membrane
Term
single phospholipid tracking
Definition
can label one or small number molecules with gold bead
Term
proteins restricting lateral mobility
Definition
self-congregating proteins, cytoskeletal elements, extracellular matrix (including glycocalyx)

ex// sperm cells (acrosomal membrane, PM, tail)
Term
glycolipid and glycocalyx
Definition
serine replaces glyerol- no phosphate = glycolipid

glycocalyx- cell coat comprised of oligosaccharide side chains from glycolipids and membrane proteins
*also protects against mechanical stresses
Term
other formations of arachidonic acid
Definition
elongase can add 2C to other cleaved phospholipids

B oxidation can also remove 2C at a time

*for both- desaturase is needed to form the 4 unconjugated double bonds
Term
membrane permeability
Definition
hydrophobic molecules, small neutral non-polar molecules can diffuse through PM

some water can

organic molecules, ions, proteins need help
Term
ion concentrations
Definition
K+ high inside cell
Na+ high outside cell
Cl- high outside cell

mg++ slightly higher outside
ca++ higher outside

H+ higher (more acidic) inside cell
Term
membrane potential (and experiment)
Definition
K+ channels through synthesized membrane
K+ moves down concentration gradient, like charge repulses like, K+ moves back across (to equilibrium). relative higher Cl- on other side line up along membrane, K+ on opposite side = membrane potential
Term
electrochemical gradient
Definition
concentration plus membrane potential gradient

resting K+ chanels and K+/Na+ ATPase channels mostly responsible for human cell resting potential
Term
membrane transport
Definition
channels-pores
carriers-alternate solute bound conformations
Term
Carrier Proteins
Definition
-requires conformational change
-no direct communication
-very selective
-slow
Term
Channel Proteins
Definition
-weak interactions
-fast
-direct communication
-conformational change(closed or open)
Term
carrier proteins- enzyme rate
Definition
V-max is where rxn rate levels off with increase in substrate concentration

Km- @ 1/2 vmax, concentration-> lower km means tighter binding to substrate
*same vMax has to be same Km
Term
channel proteins-energy
Definition
facilitated diffusion, moves according to concentration gradient-> passive transport
Term
carrier proteins-energy
Definition
carrier-mediated(facilitated diffusion)-passive

pumps require energy- active transport
*against concentration gradient
Term
red blood cell- osmosis
Definition
high concentration of inorganic counter ions- too much osmolarity causes lysis of cell

pumps regulate ion concentration-osmolarity
Term
Na+/K+ pump functions
Definition
regulates osmolarity

major player in keeping Na+ gradient
Term
coupled carriers
Definition
often Na+ is coupled to another molecule- Na+ gradient drives the carrier

in yeast and prokaryotes this is replaced by an H+ pump
Term
Na+/K+ pump
Definition
driven by ATP- autophosphorylation cuases conformational change pumping 3 Na+ out of cell and 2 K+ into cell {electrogenic}
*this maintains the Na+/K+ disequilibrium
Term
other stuff about Na+/K+ pump
Definition
ouabain- inhibits ATPase activity-> cells burst
digoxin-heart meds. low amnts reduce Na+ removal, indirectly causes Ca++ influx (Na+/Ca++ antiporter)- Ca++ helps muscle contractility
Term
ATPase pumps
Definition
reversible- can make ATP if electrochemical gradients reversed
Term
K+ resting channels
Definition
tetramer- 2.5 transmembrane domain with P loop(necessary)- some have 6.5 TMD but conserved 2.5 area

K+ moves out of cell according to gradient
main source of membrane potential (Cl- inside)
Term
K+ resting channel mechanism
Definition
has vestibule- 'waiting area' that in effect shortens the membrane

carbonyl groups from amino acids of protein act like hydration residue to move K+ through channel
*Thr, X, Gly, Tyr, Gly (inside to out)


when internal membrane is + charged, K+ channel closes
Term
Na+ cotransporters
Definition
Na+/Glucose symporter
Na+/K+/Cl- symporter
Na+/Ca++ antiporter
Na+/Mg++ antiporter
Term
Na+/Glucose symporter
Definition
Na+ binds, making site for glucose to bind. glucose binds, conformational change switches open side of protein. Na+ release drives glucose release

2 Na+(down), 1 glucose(up gradient)
Term
gut cell- glucose transporters
Definition
Na+/glucose symport from intestinal side. passive trancytosis of glucose to basal lateral domain- where Na+/K+ pump active to maintain disequilibrium driving Na+/glucose pump

*tight junctions important for gradient and asymmetry of pumps
Term
other glucose transporters
Definition
important in moving glucose to astrocytes(across blood/brain barrier)- where it can be made into something functional for brain

*defects can cause seizures, diabetes, developmental defects
Term
P-type transporter
Definition
hydrolyze ATP to drive conformational change
Term
V-type transporter
Definition
generate ATP as byproduct (often turbine/rotor-like carriers, lollipop-like)
Term
ABC-type transporter
Definition
drugs and immunity-2 AtpBindingCassetes, 6 transmembrane domains(dimerize, or one protein 12 TMD)

substrate binding forms ATP site
Functionally very diverse(ions, AA's, etc.)
Eukaryotes-mostly export
Term
V-type example (eukaryotes)
Definition
inner mitochondrial membrane- e- transport chain drives H+ pump- H+ gradient drives ATP synthase

gradient turned into mechanical energy (10-14H+ per turn, 4H+=1 ATP)
Term
H+ ATPases
Definition
also important for endosomes and organelles with lower acidity than cytosol

-acidify urine
-osteoclast bone breakdown
-maintain pH(macrophage)
Term
flagellum
Definition
move by rotor-like motion. could be V-type pump that moves it. also reversible
Term
ABC-multidrug resistence
Definition
cancer cells mutate to get around medications
(decrease intake, comparmentalization, repair DNA, change membrane protein, increased or altered drug targets)--> ABC efflux pumps

MDR1 pumps out entire class of hydrophobic drugs
Term
TAP immunological response
Definition
ABC transporter on ER membrane
recruits ATP- pulls peptides into ER (from broken up virus). MHC binds, presents to outside of cell for T-cell response
Term
Cystic Fibrosis
Definition
CFTR moves Cl- into cell- regulates ENac Na+ intake
when CFTR is inhibited, Na+ not taken up- thick extracellular fluid=CF
Term
Cholera
Definition
cholera toxin attaches to digestive system- hyperactivates cAMP-> activates Protein Kinase A(PKA) turns on CFTR
*instead of thick fluid, watery diahrrea
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