BIO130 2nd Half Flashcards
Week 7
Structures unique to animal cells and what they do for the cell
Membrane stuff
Extracellular matrix
>large network of proteins and other molecules that surround, support, and give structure to cells and tissue in the body.
>specialized material outside the cell (release materials into space)
>special composition in animal cell
-Lysosomes
>membrane enclosed organelles contain an array of enzymes capable of breaking down stuff (degradation).
-Animal cells do not contain: cell wall, vacuole, or chloroplast
Week 7
Components of Eukaryotic cells and what they include (How the cell is broken up, broadly)
Membrane stuff
-Cytoplasm
>contents of cell outside nucleus, includes ribosomes and cytoskeleton
-Cytosol
>aqueous part of cytoplasm, does not include membrane bound organelles
-Lumen
>inside organelles, between nucleus membrane
Week 7
Membrane structure - Bilayers
Membrane stuff
-Bilayer
>fluid mosaic model of membrane due to mobility of lipids
Lipid bilayer
>1 membrane, 2 layers/leaflets, forms with the heads out and the tails inward , packed tightly.
-Phospholipid molecule
>hydrophilic head and 2 hydrophobic tails
Week 7
Lipids (used to form bilayers)
Membrane stuff
-Phospholipids
>must have a glycerol group (Phosphoglyceride), there are many phosphoglycerides
>composed of a group, phosphate, glycerol, and hydrocarbon tail
>kink: unsaturated, cis double bond (Tail)
>this bilayer forms balls that are energetically favorable called liposomes
-Sterols
>sub group of stereroids with a hydroxyl group
-Glycolipid
>lipid with carbohydrate attached covalently
Week 7
Ways in which a membrane may move and effects on fluidity
Membrane stuff
-Membrane can be deformed without damage
>diffuse laterally (back/forward)
>rotate
>flex (wiggle)
>flip flop, 1 leaflet to another (RARE)
-Temperature effects
>lower temp less fluid
-Composition:Saturation effects
>more fluid with cis double bonds (kink means can’t pack as tight, must remain fluid)
-Composition:Tail length effects
>more fluid with shorter tails
-Composition:Lipid effects
>less fluid with cholesterol (stabilizer)
Week 7
How do plant and animal cells reduce fluidity of the membrane
Membrane stuff
-Stiffens membrane and makes it less permeable for polar molecules
-Animal
>cholesterol
>1:1 ratio cholesterol:phospholipids
-Plants
>sterols
Week 7
Explain the flip flop movement of lipids
Membrane stuff
-Flip flop is a rare movement of lipids between leaflets
-Enzyme in the ER membrane preforms the flip
>scramblase catalyzes
>flipase moves
-Why does this happen
>phospholipids synthesized in systolic leaflets of endoplasmic reticulum, they need to be mixed in
Week 7
Explain the difference between scramblase and flipase
Membrane stuff
-Scramblase
>no ATP required
>non specific and bi directional
>mixed properly
-Flipase
>need ATP
>specific and mono directional
>in the golgi (asymmetric)
Week 7
Model Eukaryote
Membrane stuff
Saccharomyces cerevisiae
>has a cell wall
Week 7
What causes the flip flop of lipids catalyzed by flipase
Membrane stuff
-Glycolipids and glycoprotein
>formed by adding sugar group on luminal face of golgi
>something on the membrane facing the noncytosolic side of the cell
>to get it into the cell and to a subunit the membrane needs to stay intact the way it is, therefore it will form a vacuole with the glyco.. inside of it
Week 7
Describe integral membrane proteins
Membrane stuff
-Proteins insert in some way into the membrane
>transmembrane
>monolayer associated
>lipid linked
-Proteins are directly attached to lipid bilayer
>inserted in bilayer
>attached to lipid insterted in bilayer
-Extraction
>detergents
>lipid bilayer destroyed
Week 7
Describe peripheral membrane protiens
Membrane stuff
-Associated with membrane or integral membrane proteins non covalently
>protein attached
-Do not insert into membrane
>bound to other proteins and lipids
-Extraction
>gentle
>lipid bilayer intact
Week 7
Describe transmembrane proteins
-What is it
-Whats special about its structure
-Structure
-Orientation
Membrane stuff
-INTEGRAL
-Amphipathic
>has both hydrophobic and hydrophilic parts
>hydrophobic membrane spanning domains, AA side chain non polar (part that runs through the membrane)
>hydrophilic domains, AA side chain polar (outside the membrane)
-Membrane spanning domains
>single alpha helix (20 hydrophobic AA)
>multiple alpha helix
>betta barrel
-Each transmembrane protein has a specific orientation essential for function
>transporters and channels
>anchors
>receptors
>enzymes
Week 7
List ways that transmembrane proteins can be identified
Membrane stuff
-X ray crystallography
>determines 3D structure
-Hydrophobicity plots
>identify single alpha helicies
>positive value indicates free energy is required for transfer to water, value assigned is the amlount of energy needed
>peaks in hydropathy index indicate positions of hydrophobic segments
Week 7
Describe monolayer associated proteins
Membrane stuff
-Proteins anchored on cytosolic face by amphipathic alpha helicies
>connected into the bilayer but does not rub through to the non cytosolic side
>hydrophobic segment is in the bilayer the rest is in the cytosol
Week 7
Describe lipid linked membrane proteins
Membrane stuff
-GPI anchor
>glycosylphosphatidylinostiol
>synthesized in ER lumen
>ends up on non cytosolic face
-Another lipid anchor
>cytosolic enzymes add anchor
>directs protein to cytosolic face
Week 7
Describe the different ways to extract a membrance protein and the differences in methods
Membrane stuff
-Detergent
>INTEGRAL
>TritonX100
>amphiphilic
>form spheres (micelles)
>disinigrate the lipid bilayer by inserting in between the bilayer breaking it apart (lysed)
>micelles can extract lipids from the bilayer, cause insymmetry, and it will break
>can grab onto proteins
>protein might not be in the right direction
-FRAP
>Floursecence recovery after photobleaching
>lateral diffusion within the leaflet (no flip flop)
>protein fused to GFP outside the cell, photobleach with laser, labelled proteins diffuse, neighboring unbleached proteins migrate in to replace bleached patch
Week 8
Permeability
-What is permeability
-How can we move difficult objects through
-What can get through the lipid bilayer
Membrane stuff
-Permeable
>movement via simple diffusion through lipid bilayers
>always towards a lower concentration (down the gradient)
>more hydrophobic or non polar, faster diffusion rate
-Impermeable
>require membrane proteins for transport
-Lipid bilayer, no assistance
>small non polar molecules
>small uncharged polar molecules
-Lipid bilayer, assistance or not at all
>larger uncharged polar molecules
>ions
Week 8
Describe transmembrane transport proteins
Membrane stuff
-Includes channels and transporters
>create protein lined path across cell membrane to transport polar and charged molecules
>each transport protein is selective
-Channel
>selective based on size and charge
>brief interactions as solute passes through, kept open, no conformational change
-Transporter
>selective based on binding site
>binding of solute, opens and closed, conformational change
Week 8
Describe the 2 different types of transport
Membrane stuff
-Passive
>with the concentration gradient
>does not directly require energy
-Active
>against the concentration gradient
>directly requires energy
Week 8
Explain the electrochemical gradient
Membrane stuff
-Made up of the concentration gradient and membrane potential
>want to move positive to negative space
>concentration gradient alone has no membrane potential
Week 8
Describe channel proteins and different types
Membrane stuff
-Hydrophilic pore across membrane
>selective
>passive transport
-Ion channels
>non gated, always open
>gated, some type of signal to open
>mechanically gated, mechanical stress
>ligand gated extracellular, ligand
>ligand gated intracellular, ligand
>voltage gated, change in voltage across membrane
Week 8
Describe transporter proteins and different types
Membrane stuff
-Binds a specific solute
-Conformational change
-Passive, Uniport
>one solute
>down gradient
>direction of transport reversible
>GLUT uniporter
-Active, Gradient driven pump
>against gradient, needs energy
>symport, 2 solutes want to go same direction, conc opp
>Na+ glucose symporter
>antiport, 2 solutes want to go opp direction, conc same
>Na+H+ exchanger
>free energy from 1st moving down the gradient can be used to move the second against the gradient, something is always moving with its gradient
-Active, ATP driven pump
>moves against gradient with the energy from ATP hydrolysis
>p pump, phosphorylated during pumping cycle to move ions
>sodium potassium pump 3Na 2K
>ABC, 2 atp to move small molecules
>v pump, used to pump H+ to acidify
>f type ATP synthase, opp v pump to create ATP
Week 8
Explain the transcellular transport of glucose by transporters
Membrane stuff
-Relies on
>GLUT Uniporter
>Na glucose symporter
>NaK pump
-Epithelial cells
>line surfaces, cavities, and organ
>many form villus
>have microvillus
>apical side (faces gut lumen), lateral (side), basal domain (extracellular facing)
>tight junctions, stop things from going between cells and keep apical and basal lateral proteins on the right side
>glucose must go through the cell
>sodium and glucose move inwards Na moves with the gradient the energy can then be used to move glucose
>sodium potassium pump keeps sodium low inside cell so that sodium wants to move inside the cell with the gradient
>GLUT uniporter releases glucose to the inside
Week 8
What is membrane potential and how is it created
Membrane stuff
-Difference in electrical charge on 2 sides of the membrane
-K leak channel
>animal
>major role
>outward flow of K
-NaK pump
>animal
>10% membrane potential
>3Na out 2K in
-Equilibrium
>resting membrane potential
>always measure from the perspective of the inside of the cell
-Plasma membrane p type pump
>plants
>H pump
>used by gradient driven pumps to carry out active transport (H driven symport)
>negative inside cell
Week 9
Volumes of intracellular compartments
Protein sorting stuff
-Differ based on the type of cell
-Cytosol is half the cell volume
>protein synthesis and degradation
>metabolic pathways
>cytoskeleton
Week 9
List volumes of membranes within the cell
-Compare liver and pancreas
Protein sorting stuff
-Smooth ER
>phospholipid synthesis, detox
-Rough ER
>membrane bound ribosomes
>synthesis of soluble proteins and transmembrane proteins for the endomembrane
-A lot more membrane in the cell than around the cell
-ER is about 50% of the membrane
-Liver
>hepatocyte
>detox
-Pancreas
>exocrine
>secreting digestive enzymes
Week 9
Organelle
-List some membrane bound organelles
Protein sorting stuff
-Discrete structure or subcompartment of eukaryotic cell that is specialized to carry out particular function, most are membrane enclosed
>nucleus
>ER
>golgi
Week 9
Explain protein sorting
Protein sorting stuff
-Proteins are nuclear encoded
-mRNA arrives in cytoplasm
>translation starts on ribosomes in cytosol
>makes your protein
-Cytosolic protein
>no sorting signal
-Co translational sorting
>typically ER first
>some proteins do have a sorting sequence (N terminus), the protein is then moved to correct location, translation is paused, translocon opens, protein will be fed through channel and translation can continue, signa peptidase cleaves signal sequence (soluable proteins)
>if the signals internal, not at N terminus, it will form an alpha helix, the signal will not be removed (transmembrane)
-Post translational sorting
>fully synthesized in sytosol before sorting
>folded: nucleus and peroxisomes
>unfolded: mitochondria and plastids
-Signal seqence
>stretch of amino acids in a protein that direct protein to the correct compartment
>specifies destination in cell
>recognized by sorting receptors
Week 9
List and describe the different signal sequences
Protein sorting stuff
-Nuclear
>if mutated will stay in cytosol
>transcription activators are required in nucleus for eukaryotic transcription
-Peroxisomes
>contain enzymes for oxidative rxns
>detox, break down fatty acid
>enzymes imported into peroxisomes through transmembrane protein complex
-Mitochonrdia + Chloroplast
>have own genomes and ribosomes butj more proteins for these organelles are nuclear encoded
>translated in cytosol
>unfolded by association with hsp70 chaperone proteins
Week 9
What makes up the endomembrane system
Protein sorting stuff
-ER, Golgi, endosomes, and lysosomes
Week 9
Endomembrane system pathways
Protein sorting stuff
-Secretory pathway
>proteins and lipids made in ER delivered to other compartments
-Endocytic pathway
>contents move into cell
-Retrieval pathway
>retrieval of lipids, selected proteins for reuse
Week 9
How does the endomembrane absorb or expel contents
Protein sorting stuff
-Exocytosis
>vesicle content: delivered to extracellular space
>vesicle membrane: becomes part of the plasma membrane
-Endocytosis
>vesicle luminal content: extracellular space
>plasma membrane: forms vesicle membrane
Week 9
Describe the function of the secretory pathway
Protein sorting stuff
-Constructive exocytosis pathway
>all eukaryotic cells
>continual delivery
>constitutive secretion of soluble proteins
-Regulated exocytosis pathway
>regulated secretion in specialized cells
>extracellular signal, vesicle fusion with plasma
