Cell Mechanics unit Flashcards
What is cell fractionation (4 steps )
Method to take apart a cell to study function
1 homogenization
2 centrifuge
3 decant supernatant
4 repeat centrifuge increase speed, time
What are 2 main processes in cell franctionation
homogenization - disrupt cell membrane without damaging organelle
centrifuge - spin it to separate based on density
Main types of homogenization methods 4
use sound - high frequency
add detergent, good at pulling apart lipid
high pressure - force cells through small hole
shear - shear cells between rotating plunger and thick walls of vessel (like mortar and pestle)
Why is centrifugal step repeated what changes
repeated to separate each thing by density
what changes is the speed (increase) time, (increase`)
supernatant vs pellet
supernatant - lighter stuff, in liquid above pellet
Pellet - denser stuff on bottom
from centrifuge
Fluid mosaic model (meaning, devs)
dev by singer and nicholson (1972)
fluid -means movement in membrane
Mosaic - membrane is made from many diff molec
orientation phospholipids in cell membrane
polar head facing outside,
non polar hydrophobic end inside
makes bilayer with hydrophobic core
Each layer Is leaflet
because cell int and ext are both polar
polytopic vs monotobic
+ 2 subcatagories
Polytopic - faces both sides of membrane
Multipass - crosses membrane twice
Single pass - crosses membrane once
monotopic - does not span whole bilayer
for integral proteins
integral vs peripheral proteins
integral - can be poly/monotopic
if poly, can be multipass or single pass
Peripheral - noncovalently bound to one side of membrane , does not go in, can have same function as integral protein
Function of membrane protein (6)
signal receptor
enzymatic activity
recognition
attachment
transport
cell adhesion
What does receptor protein do
has binding site for ligand
once bonded to ligand
does conformational change
sends message to int of cell
What is ligand
thing that bonds to receptor protein
what does enzymatic activity membrane protein do
has binding site like enzyme
takes in substrate
changes substrate to new product
what does Recognition protein do
can be peripheral
recognizes glycoprotein of other cells
What is glycoprotein
carbohydrate group on surface, used to identify cell
Uses of carbs on surface of cell
Cell recognition and signalling
Glycoprotein - receptors for chem signaling
glycolipid- used in cell recognition
What do attachment proteins do
(2 types )
Extracellular (integral) - attached to ECM (Exterior extracellular matrix), does not move, for structural support, cell signaling, anchoring
Intercellular (inner peripheral or integral )- attached to cytoskeleton, anchored
What does exterior extracellular matrix do
cell structure
anchored to cell
used in cell signalling
has glycoproteins
what does intracellular cytoskeletal protein do
attachment protein
can be peripheral on interior
attached to cytoskeleton
anchored, immoble
3 main components of cytoskeleton, org by size
(microfilament) actin (smallest)
intermediate filament
(microtubules) - tubulin
Types of transport proteins and def
channel - passive, tunnel
- Gated
- ungated
Pump/carrier - like revolving door, conformational change
what are the 3 main forms of cell adhesion
channel forming junction
occluding(tight) junction
anchoring junction
Describe channel forming junctions, gap junction
+ example
makes channel between cells to pass small molecules
found in plants
makes keeps gap between cells
Describe occluding, tight junction
fuses membranes on adjacent cells
tight, no space between
makes impermeable barrier
found in digestive system
only O and CO2 passes
found by putting dye in and seeing where it cant penetrate
Describe Desmosome, ANchoring proteins
bind to desmosomes in adjacent cell
makes strong sheets
attached to cytoskeleton
to resist shear forces, mech strength
bladder tissue
Functions of peripheral protein
Attachment
recognition
What affect membrane fluidity
saturation of fatty acid
hydrophobic restriction
cholesterol, temp
Saturated vs unsaturated fatty acids for fluidity
unsaturated fatty acids keep the membrane more fluid
makes it harder to compact the membrane,
Types of movement within mebrane (5)
Lateral - on same leaflet
rotation - when molecs rotate around axis
swing - tails swing from side to side
flextion - contractile movement of tails
Transverse diffusion - whole phospholipid switches side
WHat is transverse diffusion
related to hydrophobic restriction
phospholipid moves from one leaflet to another
with enzyme flippase
rare because polar head must cross hyrophobic core
Why cholesterol helps fluidity
large, non polar
effect depends on temp
warm temp - makes less fluid by restricting movements of phospholipid
cold temp - gets in the way of compacting the bilayer
what is the importance of cholesterol in cell
Structure
regulates fluidity
WHen to use diff types of membrane transport
Passive - when goes with conct gradient
Active- when goes against concentration gradient
bulk membrane - for large moleculs
What is passive transport
No energy used
go from high concentration to low concentration area
Simple diff vs facilitated diff
Simple - does not need protein, for O2 and CO2
- until equilibrium is achieved
Facilitated diffusion - needs transport protein (carrier, channel)
Channel protein vs carrier protein
Channel - tunnel, some have swing gate
- for ions (small charger molec)
Carrier - revolving door, conformational change
- can moves charged or uncharged (glucose)
What are the proteins needed for osmosis
Osmosis is passive transport
needs aquaporins
Uniport, symport, antiport
definitions/example
Uniport - moves one thing at a time
- channel prot
Symport - moves 2 things at a time same direct
- Na/glucose symporter
Antiport - moves 2 things diff direct at time
- Na/K pump
Describe water movement direction
goes from high concentration of water to low concentration
moves in direction of dilute to solute
moves in opposite direction of solut
Hypotonic meaning, effect on plant, animal, RBC
Outside env lower solute cont than inside
solute moves out
water moves in
animal cell could burst (osmotic lysis)
RBC - hemolysis
Plant cell is good (turgid)
Hypertonic meaning, effect on plant, animal, RBC
More solute conct on outside than inside
solute moves in
water moves out
animals cell shrivels
RBC - crenation
plant cytoplasm shrinks away from cell wall (plasmolysis)
Isotonic meaning, effect on plant, animal, RBC
Same concentration of solute in and out
animal cell is good
RBC is at equilibrium
PLant - flaccid
WHy is osmosis important in CFTR (cystic fibrosis transmembrane conductance regulator )
Good CFTR takes chlorine out
Bad CFTR builds up concentration of chlorine in cell
draws in more water with osmosis
less water on outside causes mucus to form
Active- vs passive transport
Passive - no eng needed
- goes with cont gradient
Active- - needs eng (ATP)
- goes against cont gradient
- needs pump (like carrier prot)
How is builk membrane transport diff from other types
Does not use transport protein
for large molecules
for large amts
involces folding of membrane to make vesicle
Types of bulk memb transport
endocytosis
- pinocytosis
- phagocytosis
- receptor mediated endocytosis
exocytosis
What is phagocytosis
+ examples in ppl and other
“eating” of cell
ingest other cells or large particles
uses vacuoles
amoebas use to eat
used to humans to defend body
ex phagocyte (WBC)Ha
Mechanism of phagocytosis
6 steps
1 cell engulfs molecs with Pseudopodia
2 encloses molecs in Vacuole called phagosome
3 Lysosome fuses with it to become phagolysosome
4 lysosome digests the stuff inside
5 leaves behind residual body
6 vacuole disposes of res body outside
What is pinocytosis
“drinking” of cell
uses vesicles
for dissolves materials(smaller stuff)
anything can be ingested
Phagocytosis vs pinocytosis
Phago - for large molec, makes large vacuoles
Pino - for small molec, makes vesicle
What are the steps in receptor mediated endocytosis
Ligand binds to receptor
membrane becomes vesicle
ligand detaches from receptor
vesicle pinches into 2 parts
- empty receptors
- ligand
Ligand part fuses with lysosome
receptors return to cell surface
What is exocytosis
movement of materials from inside to outside of cell
vesicles come from golgi body
reverse of endocytosis
What are the 3 main functions of exocytosis
restoring cell membrane - keep up with endocytosis
secreting - release waste and toxin from cell
recycling of membrane proteins (receptors )
What are the types of enzymes
hint: cofactor or not
SImple - only has protein component
COmplex - requires a cofactor in addition to protein body, Has 2 forms (apoenzyme, holoenzyme)
Apoenzyme vs holoenzymes meaning
States of complex enzymes
apoenzyme is inactive state due to not having cofactore
holoenzyme is active form of enzyme with cofactor
What are the types of cofactors (2 + 2)
Inorganic - metal ions (Zn, Cu, Fe)
organic - vitamins
in addition, they can be
- prosthetic - permanently bonded to enzyme (Heme )
- coenzyme - reversible bonded to enzyme (NADH)
what is enzyme (def, component)
Usually made from protein
Catalyst, speeds up reaction
is reusable
decreases activation energy
ends in -ase (sucrase)
can create or reverse productW
has active site - substrate area
enzyme only works on specific substrate
What is the induced fit model
As substrate binds the enzyme changes to tighter fit
brings in chem groups to catalyze reaction
binding induces favorable change in enzyme
What is free energy graph for (what does it display)
used for reactions that release energy
shows how much energy is needed to start reaction
energy given in heat eng
amount it rises above beginning is Activation energy
amount it goes below beginning energy is change in free energy ( Delta G)
What is Delta G in free energy graph
Difference in free energy between start and products
Negative in exorgonic reactions
new bonds release more energy than the initial investment to break bonds
not changed by enzymes
What is Activation energy in free eng graph
The amount of eng needed to start the reaction
enzyme lowers the act eng
reactants absorb eng, becoming unstable
until bond breaks
Mechns by which enzyme lower act eng (4)
1 proximity, orientation
2 bond strain -
3. microenvironment - R groups in enzyme make good env for reactants
4 covalent catalysis - bonds with reactants to help orient, change chem of active site
What limits enzyme and reaction rate
substrate concentration
temp
pH level
availability of cofactors
What is an inhibitor
molecule that bonds to enzyme,
stops it from doing job
can be reversible depending on connection
can be competitive or non competitive
Competitive vs non competitive inhibition
Comp - inhibitor binds to active site, directly blocks substrate
non comp - inhibitor binds somewhere other than active site, changes the shape of enzyme to be ineffective
How does competitive inhibition affect saturation curv+ how to overcome
Makes curve less steep but reaches same height in the end
add more substrate
How does non competitive inhibition affect saturation curv+ how to overcome
lowers plateau of curve
add more enzymes
Why does inhibition exist naturally
used to regulate production of stuff, so as not to overdo product
negative feedback
What is negative feedback
When the product is also the inhibitor of one of the enzymes in the chain that produces it
cannot be inhibitor of last enzyme in chain
Characteristics of allosteric enzyme (4)
has second binding site, other than active site
has 2 conformations (active, inactive)
naturally oscillates between 2 conformations
binding of effector can stabilize the shape
What is the allosteric site
Binding site other than active site
can be found in between subunits (where they join)
What is an effector? (def, types)
Something that binds to allosteric enzyme
binds weakly
allosteric activator - stabilizes active form
allosteric inhibitor - stabilizes inactive form (same as non competitive inhibition)
what is allosteric regulation
regulation enzyme activity with effector in allosteric site
causes inhibition or Activation
What is cooperativity (conditions, )
when the binding of one effector in one subunit effects all other subunits
only occurs in enzymes with multiple subunits
can increase or decrease productivity
Negative vs positive cooperativity
pos - activator, in active site, allosteric (substrate binding, activator binding )
neg - inhibitor, only allosteric (some forms of noncomp inhibition)
does positive cooperativity need allosteric site
no
one example of positive cooperativity is the substrate
causes other subunits to become better for other substrates
allosteric inhibition vs negative cooperativity
allosteric inhibition can be negative cooperativity
cooperativity must have many subunits AlloInhib does not
both must have allosteric enzyme, involve allosteric site
What are the 6 classes of enzymes (order matters )
- oxidoreductase
- transferase
- hydrolase
- Lyase
- isomerase
- LIgase
What is Oxidoreductase (def, funct, react, ex)
First enzyme class
F: shuffles electrons
R: Redox reactiosn:
electrons are moved around through transfer of H and O
Dehydrogenase
What is transferase (def, funct, react, ex)
class 2
F : moves chem groups
R : transfers phosphates and methyl to other substrate
ex. polymerase
What is hydrolase (def, funct, react, ex)
class 3
F : breaks molecules with water
R: hydrolysis reactions
ex protease
What is lyase (def, funct, react, ex)
class 4
F : break molecules without water
R: removal or addition of groups
ex. decarboxylase
What is isomerase (def, funct, react, ex)
class 5
F: changing molec shape
R: shuffling atoms around in molec
Ex: mutase
What is LIgase (def, funct, react, ex)
class 6
F : forming bonds between molec
R: Dehydration synthesis, joining 2 molecules
Ex synthetase
Describe Na/K pump
Is active transport
antiport
has 2 conformational states
3 Na + go out
ATP is used
2 K+ goes in
