Midterm 2 Flashcards
plasma membrane
the outer boundary of the cell separating the cellular content from the outside world
What holds the lipid bilayer together?
The van der whal interactions between the acyl tails of phospholipids
Functions of the plasma membrane
1)Compartmentalization
2)Scaffolding for biological activities
3)Selective permeable barrier
4)Allowing transport of solute
5)Responds to stimuli
6)Cell to cell communication
7)Energy transduction
Lipid Bilayer
the structural backbone and barrier to prevent random movements of materials into and out of the cell
What type of interaction holds lipids and proteins together in the bilayer
noncovalent bonds
Three lipid types found in mammalian membranes
1)Phosphoglycerides
2)Sphingolipids
3)Cholesterol
Phosphoglycerides
Contain 2 fatty acids, a glycerol, and phosphate group usually linked to a small polar group
Sphingolipids
Lipids derivatived from ceramide that can add groups to their terminal alcohol
Glycosphingolipid
Sphingolipid with an additional carbohydrate found exclusively on the exoplasmic face of the plasma membrane
cholesterol
A polar ampipathic molecule that stabilizes and adds fluidity to membranes composed of a polar head group, steroid ring and hydrocarbon tail
Why is lipid asymmetry between the different leaflets of the bi layer important?
1) Negatively charged cytosolic face can help proteins bind via its charge
2)Signalling can be done via movement of material from the inner layer to the outer layer
3)Glycolipids only are found on the extra cellular side acting as a ligand receptor
glycosylation
Post transcriptional modification which adds carbohydrates to protiens
Three sub classes of membrane proteins
1)Integral membrane proteins- fully integrated into the bilayer
2)Peripheral Membrane proteins- anchored to the outside of the bilayer
3)Lipid anchored proteins- Covaletly linked to the membrane by a membrane protein
Functions of Integral Membrane proteins
1)Transporters: moving ions and solutes across the membrane
2)Anchors: binding intra- or extra- cellular components to the membrane
3)Receptors: binding ligands to initiate signal transduction pathways
4)Electron Transporters: transfer electrons during photosynthesis and respiration
Structure of Integral Membrane proteins
Composed of Alpha Helices and Beta Barrels
Why would the cytosolic side of a integral membrane protein be positively charged?
To anchor to the negatively charged cytosolic side of the membrane
Hydropathy plot
measures the hydrophobicity of amino acids where hydrophobic = +ve, hydrophilic = -ve
Peripheral Membrane proteins
Protiens which do not interact with the core of the lipid bilayer and are anchored via non covalent bonding between the head groups, they are easily removed via changes in Ph or ionization strength
Three types of Lipid anchored membrane proteins
1)Fatty acid- anchored membrane proteins
2)Isoprenylated membrane proteins
3)GPI-anchored membrane proteins
Fatty acid-anchored membrane proteins
Synthesized within the cytosol Attached to a saturated fatty acid, usually myristic acid(14C) or palmitic acid(16C), that is embedded in the membrane
Isoprenylated membrane proteins
Attached to multiple isoprenyl groups(5C), usually farnesyl(15C) or geranygeranyl(20C) groups,then embedded in the membrane, Synthesized in the Cytosol
GPI-anchored membrane proteins
synthesized in the ER, post-translationally attached to the C-terminus and can be released from the membrane via cleavage by phospholipase C
Fluid Mosaic Model
Membranes consists of a mosaic of proteins/lipids in a fluidic state
Why is membrane fluidity important
Vesicle formation, fusion, secretion
Cell division
Muscle contraction
Cell migration
Signalling mechanisms
What is membrane fluidity
Ability for the bilayer components to rotate about their axis and for lateral movement of particles through the bilayer
What happens when the membrane is too rigid
Membrane components can’t organize properly, as proteins can’t move and interact with binding partners.
What happens when the membrane is too viscous
Lose mechanical support (the ability to orientate properly), with excessive fluidity resulting in an increase in membrane permeability
transition temperature
Temperature at which the lipid bilayer undergoes a phase transition from solid to liquid
Factors that lead to high fluidity of the membrane
Unsaturated acyl tails,shorter tails,
Cholesterol function in the lipid bilayer
1)Sterols decrease the permeability of membranes to ions and small polar molecules
2)Cholesterol acts as a fluidity buffer (broadens the temperature range of transition)
Cholesterol effect on unsaturated fatty acids
cholesterol decrease fluidity by wedging itself in between the packing of the lipids
Cholesterol affect on saturated fatty acids
Increases fluidity by disrupting the tightly packed acyl tails
Homeoviscous Adaptation
The ability of a cell to regulate membrane fluidity in response to temperature changes by altering lipid composition and maintain membrane fluidity
Lipid rafts
Localized regions of membrane lipids in association with specific proteins These structures are believed to serves as floating platforms that concentrate proteins into “compartments” on the membrane
Flip-Flop
Movement of a lipid through the hydrophobic sheet reorienting itself 180 degrees, typically very slow but will be aided by flippase
FRAP
Flouresent recovery after bleaching, membranes that have been dyed with flouresecnt materiel once bleached of colour after a period of time will patch the bleach hole.
Different levels of membrane mobility
A.Random Movement
B.Immobile (intracellular tethering)
C.Directed Movement
D.Reduced Mobility (crowding)
E.Fenced or Corralled
F.Extracellular Entanglement
Passive transport
Movement of molecules down the concentration gradient without costing energy or specifically requiring a protien
Active transport
Goes against a concentration gradient and requires ATP and a protein pump to move the solutes
Three factors that affect permeability
1) Molecule size, smaller= faster
2)Partition coefficient, the greater lipid solubility= faster
3)Charge,Charged molecules will not pass the membrane
Two components of electrochemical gradient
Concentration gradient: Non charged Molecules move down a concentration gradient
Electric Potential gradient:Charged molecules want to move to their opposite charge
Simple diffusion
Unassisted Movement of gases, non polar molecules and small polar molecules down a concentration gradient at a speed proportional to concentration gradient and permeability
Example of passive diffusion
Movement of O2 diffusing into RBC in the lungs and diffusing out once at the tissues
Osmosis
Movement of water to areas of high solute to low solute, Hypertonic:Movement into cell, Hypo tonic: water moves out the cell, Isotonic, NO movement
Facilitated transport
Requires a protein to help get the molecule across the membrane using integral proteins, Made of two types Carriers and Channels
Carriers
Transporters that move molecules via an alternation of two conformations
Channels
Water filled pores which ions or small molecules can diffuse through
Three types of channels
1)Ion Channels: Highly specific conducting ions
2) Porins: Allows movement of hydrophillic solutes based on size
3)Aquaporins: Allows water to flow through but blocks any ions of solutes
Ion Channels
Channels which allow for bidirectional movement of ions based on chemical gradients, they are highly specific due to their cores acting as a size filter
Porins
Low specificity water filled beta barrels that have a nonpolar side embedded in the membrane and a polar side facing the water
Three types of Ion Channels
1)Voltage gated: Open and close in response to changes in charge
2)Ligand gated:Open and close via the binding of a specific ligand
3)Mechanosensitive gated: Respond to mechanical changes in the membrane
Carrier Proteins
Allow movement of solute though an alternation of conformation
Steps in solute transport of a carrier protein
1)Solute binding side is open at one end
2)Solute binding cause a conformational change
3) The protein changes conformation so that the solute binding side now opens to the opposite side of the membrane
4)Solute is released
Similarity of carrier activity to enzyme activity
1)High specificity
2)Regulated activity
3)Exhibit saturation kinetics
Types of carrier proteins
1)Uniporters:Transport a single solute
2)Symporters: Transports two solutes in teh same direction
3)Antiporters: Transport solutes to opposite sides across the membrane
GLUT1
Uniporter carrier protein that can carry glucose in and out of the cell depending on the concentration gradient of Na+ with an exchange rate of 2 Na+ per glucose
Chlorine Bicarbonate exchanger
Antiporter that allows movement of chlorine and HCO3- in and out of the RBC, Chlorine will move out in the lungs and in at the tissues
Active transport
Movement of solute against its concentration gradient
Importance of active transport
1)Helps to uptake essential nutrients
2)Removal of waste product
3)Creation of graidents that maintain the non equilibrium of the cells
Ions that are essential to life and their locations of highest concentration
Intracellular:K+
Extracellular:Na+,Cl-,Ca2+
Direct Active transport
Solute accumulation if couples directly to an exergonic reaction such as ATP
Indirect Active transport
Solute accumulation is done via Endergonic reaction coupling with an exergonic reaction
ATPase
Proteins that harness the energy of ATP hydrolysis to move ions or small molecules against the concentration gradients
4 types of ATPase and their respective location
1)P-ATPase, P1=All organizims P2-P5=Eukaryotes
2)V-ATPase Eukaryotes only
3)F-ATPase Bacteria Mitochondira and chloroplasts
4)ABC-ATPase All organisims
P-ATPase
Reversibly phosphorlayted ATP pumps that are found in the plasma membrane which are used to help maintain the concentration of sodium and potassium
V-ATPase
Pump H+ into organelles like vacuoles,vesicles,lysosomes,golgi in order to create and acidic environment and are composed of an integral and peripheral segment out of the membrane
F-ATPase
Bi directions transport of H+, when done up a gradient ATP is used and when used down the gradient generates ATP
ABC-ATPase
Contain two nucelotide domains for ATP an two transmembrane domains that act as both importers and exporters and help to uptake nutrients and are involved in drug resistance
MDR Protein transporters
Sub class of ABC transporters that can remove hydrophobic drugs out of cells, including antibiotic and cancer drugs
Indirect active transporters
Utilizes potential energy stored in ionic gradients to move other solutes such as the movement of Na+ and Glucose through the gut cells
Energy
capacity to cause specific physical or chemical changes
Bioenergetics
A subset of thermodynamics that analysis the biological world of energy usage
Catablolic reactions
Reactions which gain energy through the transfer of electrons from carbon
Chain of reactions in catabolysis
1)Methane
2)Methanol
3)Formaldehyde
4)Formic acid
5)Co2
Two laws of thermodynamics that bioenergetics mus follow
1)In every physical or chemical change the total energy of the universe remains constant although the form of energy may change
2)In every physical or chemichal reaction the universe trends towards higher entropy
Gibbs free energy
Exergonic
Delta G is less than zero and is energetically favourable occurring spontaneously
Endergonic
Delta G is greater than zero and is energetically unfavourable and cannot occur spontaneously
Gibbs free energy in non standard conditions
Where Q is the ratio of reactants and products
7 Features of catalysts
1)Required in small amounts
2)Function at physiological Ph and Temperature
3)Reusable
4)Highly specific to substrate
5)Produce a specific product
6)Regulated to meet the needs of the cell
7)Change the rate of reaction not the thermodynamics
Dynamic steady state
The ever changing state of reactants,products, and intermediates kept at levels far from equilibrium
Metastable State
The state in which the number of molecules possessing enough energy to overcome the activation energy for a reaction is incredibly low
How to enzymes reduce activation energy
1)Maintain substrate orientation
2)Change substrate reactivity with charge distribution
3)Exert phsyiological stress and destabilize the reactant
Co-Enzymes
Organic catalyst that do not act as substrate and only loosely bind to reactants
Metals
Inorganic materials that increase the catalysis rate via electron contribution, binding tightly to the catalyst
ApoEnzyme
Enzyme not bound to its cofactor
HoloEnzyme
Enzyme bound to its cofactor
What is the rest of an enzymes structure for
1)Supports the structures that create the active site
2)Regulation of the enzyme
3)Interactions with other proteins
4)Substrate channels
Affect of Ph and Temperature on reactivity
At Low Temp higher temp increases reaction rate but past optimal the reaction rate decreases with temp, outside of optimal ph function quickly decreases
Regulation mechanisms
1)Amount of enzyme present via degradation and synthesis
2)Enzymes turning on or off
3)Localization of substrates and reactants
Competitive inhibition
Inhibitor and substrate compete for the same active site, Km is increased
Noncompetative inhibition
Inhibitors and substrate bind different sites, when the inhibitors binds conformatational changes occur at the active site changing Vmax and Km
Allosteric regulation
Regulation of an enzyme via the bind of an effector molecule at a site other than the active site
Phosphorylation/Dephosphorylation
Addition of phosphate to serine,theronine,tyroside leading to changes in ligand binding which can activate or deactivate the molecule
Kinases
phosphorylates an enzyme
Phosphatases
dephosphorylates an enzyme
Km
Micheals constant, concentration of substrate at half of Vmax, Km is higher when more substrate is required to bind and Km is lower when less substrate is needed to bind
Vmax
Max speed of reaction collisions, caps out the reaction rate
3 elements of microscopy
1) Illumination, a light source
2)Specimen to observe
3)System of lenses to focus illumination onto sample and form the image
4 components of a microscope
1)Light source
2)Condenser lens-placed in front of the light source to focus light onto specimen
3)Objective lens-Forms the primary image of the specimen,closest to object of interest
4)Ocular lens- magnifies image produced by the objective lens
Magnification
Size of image relative to the size of the sample
Factors that affect magnification
1)Refraction index of the lens and medium the sample is in
2)Focal length of the lens, the smaller the better
Resolution
Increases the clarity of the image, it is defined as the minimum distance two objects can be together and still be legible
Factors that affect resolution
1)Wavelength of illumination
2)Refraction index
3)Angular aperture
6 types of microscopy
1)Bright field
2)Phase contrast
3)Fluorescence
4)Stained bright light
5)Differential interference
6)Confocal
Bright field microscopy
Visualizes white light passing through a sample which allows for living samples to be used, the only problem being most living cells lack pigments
Stained Bright field
Uses dyes that bind to specific bio molecules, only works on non living specimens and requires performing fixation to prevent degredation
Section vs whole mount
Whole mount the entire object is in tact and put on a slide, section requires fixing and slicing the sample into segments
Phase contrast microscopy
Takes advantage of differences in the refractive index and thickness of specimens to image cells without stains, this allows viewing of dynamic evenets
DIC (Differential interference contrast)
Uses a show casting effect to make one end of the cell darker and the other lighter due to differences in optical path creating a higher contrast image
Fluorescence microscopy
Shows the location of specific molecules in the cell as fluorescent substances can absorb UV radiation to emit visible light
Confocal microscopy
Uses a laser beam to illuminate a single plane of a fluorescent labelled sample
Components necessary to complete a confocal microscopy
1)Excitation filter-Transmits light of a specific wave length
2)Dichoric Mirror:Reflects light below a certain wave length and transmits light above a certain wave length
3)Emission Filter:Prevents light that does not match emission wave length from emitting microscope
Three ways to perform fluorescent tagging
1)Immunofluoresence- Uses fluorescent antibodies
2)Fluorescent stains- uses dyes that associate with a specific cellular structure
3)Florescent protein technology-protein is fused to desired protein to visualize in the cell
Immunofluoresence
Using antibodies to locate a specific molecule can be direct:the florescent dye is on the primary antibody or indirect:The florescent dye is on a secondary antibody
Pros and Cons of Immunofluresence
Pros: High specificity, strong signal, protein in native state
Cons:Not done on living cells, might not have the right antibody
GFP
Green fluorescent protein, commonly used to visualize a pattern of gene protein expression in living cells and organisms allowing visualization of protein fusion
Pros and Cons of GFP
Pro: Works in living cells and organizims
Cons:Can interact negatively with your desired protein, difficult to introduce GFP tagged protein into organism
Confocal Fluorescence microscopy
Produces focused images via optical sectioning, in excludes out of focus light and uses a computer to reconstruct a specimens 3d shape
Pros of using fixed cells
1)Can view thick sections of tissue
2)Easy to manage samples
3)No disruptive proteins
Pros of using living cells
1)Observe movement
2)Provides context to observations
FRET
When fluorescent molecules are close together they can be used to excite the other releasing light
Electron microscope
Uses a beam of electrons and electro magnets rather than light and glass lenses
Two types of electron microscopy
1)Scanning electron microscope-scans the surface of a specimen with electrons being deflected off its outer surface
2)Transition electron microscope-electrons are transmitted through the specimen
Immuno ET
Antibodies are linked to electron rich substances that form dense spots under the microscope allowing use to see the form of a specimen
Gyro ET
Taking multiple images at different angles and using computer soft ware to create a 3d reconstruction
Eukaryotes
Organisms that have a nucleus internal compartmentalization of functions,complex cytoskeleton,transport material in and out of the cell
Nuclear Envelope
Composed of an inner membrane which defines the nucleus and an outer membrane which connect to the endoplasmic reticulum
Nuclear Pore
Fuse the two membranes of the nuclear membrane together and act as a conduit for transport between cytoplasm and nucleoplasm
Function of the nucleus
Contains DNA, controls replication,transcription, and RNA processing
Nucleoulus
Subdomain of the nucleus where ribosomal RNA is transcribed and ribosomes are assembled
Endoplasmic reticulum
Consists of tubular membranes and flattened cisternae and an internal lumen, continuous with the outer nuclear membrane
Rough ER
Synthesis path way for proteins, most membrane lipids are produced here, covered in ribosomes
Smooth ER
Synthesis of lipids and steroid hormones occurs here, storage of important ions can also be done here such as the sarcoplasmic reticulum which stores and releases calcium during muscle contractions
Golgi Apparatus
Consists of flat stacked vesicles known as cisternae, the cis side uptakes molecules from the RER and the trans side sends out modified proteins to the plasma membrane
Lysosomes
Digestive organelles that have single membrane and store hydrolosases that are pH activated. They have a low internal Ph using H+ pumps and a special carbohydrate coating on the inner membrane to prevent self digestion
Degradation pathway of a lysosome
1)Endocytosis-cells absorb external material via engulfing through the membrane
2)Phagocytosis- ingestion of larger molecules
3)Autophagy- material from a damaged cell is absorbed and recycled
Components of the endomembrane system
Golgi,ER,Vesicles,Lysosomes
Exocytosis
Protein leave the cell and are added to the plasma membrane
Endocytosis
Cellular uptake of particles and macromolecules
Peroxisome
Small single membrane organelles found in the liver and kidney used in detoxification and breakdown of fatty acids via the generation and degradation of hydrogen peroxide
2 Membranes of the miochondira
Outer membrane-Contains porins which allow the free movement of small molecules across the membrane
Inner membrane-acts as a permeability barrier, folds into cristae that assist in cellular respiration
3 regions of the mitochondria
1)Matrix-Within inner membrane, contains most of the enzymes associated with Mitochondria function and houses DNA and ribosomes
2)Intermmebrane space- area between inner and outer membrane
3)Intracristal space- localized region where protons can accumulate during electron transport
Chloroplasts
Site of photosynthesis, contains an inner membrane and outer membrane which contains the thylakoids where photosynthesis occurs
Vacuoles
In plants used to store amino acids,ions,proteins, polysachharides and keep toxic materials
Cytoskeleton
3d arrangement of interconnected microfillaments,microtubules and intermediate filaments which provide strength and structure and assist in cell division
Extracellular matrix
Comprised of protiens,glycolipids,glycoaminoglycansens and supports cells to form tissues,substrate for motility, growth promoting, and rigidity of plants
