Gauvrit Section Flashcards
What kind of samples can electron microscopy visualize?
dead fixed cells
What are the four components of cell theory?
- all organisms are composed of one or more cells
- cells are the structural unit of life
- cells only arise from division of a pre existing cell
- cells contain genetic information to pass on to the next generation
Who are the first cells cultured froma tumor of a cancer patient called?
HeLa cells (Henrietta lacks)
What is the ancient cell that all life is derived from?
LUCA
What are three characteristics that distinguish prokaryotic and eukaryotic cells?
eukaryotic cells have a membrane bound nucleus
- eukaryotic cells divide by meiosis or mitosis where prokaryotic cells divide by binary fission
- eukaryotic cells use cilia and flagella where prokaryotes only have flagella
What are viruses that infect bacteria called?
bacteriophages
What are viruses that are pathogens and interfere with host cells called?
Viroids
What are the two types of viral infection?
Lytic infection - makes more virus particles then pops the host cell open to release them
Integration - virus integrates its DNA (provirus) into host cell chromosome
What are the four classes of macromolecules?
proteins
lipids
nucleic acids
polysaccharides
What macromolecule is long lived?
DNA
What is the difference between glycogen and starch?
glycogen is in animals, starch is in plants
What do lipids dissolve in?
organic solvents, not water
What is the difference between saturated and unsaturated fatty acids?
Saturated has no double bonds
What are the building blocks of proteins?
Amino Acids
What is the primary structure of a protein?
linear amino acid sequence
What is the driving force for protein folding?
hydrophobic interactions
What disease results froma single amino acid change in hemoglobin?
sickle cell anemia
What is the secondary structure of proteins?
conformations of portions of polypeptide chain
- alpha helices and beta sheets
What is the tertiary structure of a protein?
entire 3d conformation
What are prions?
misfolded proteins that can transmit their misfolded shape
can proteins be similar at the tertiary level but not primary level?
yes
What determines if proteins have quaternary structure?
if they have subunits
Can all proteins self assemble into tertiary structure?
No, some need helper proteins or molecular chaperones
What disease is from protein misfilding?
Alzheimers
What is the main differing function between DNA and RNA?
RNA transfers genetic information, DNa stores it
What base is swapped in DNA and RNA?
T (DNA) for U (RNA)
Which nucleotides bind to eachother?
A binds to T, C binds to G
Does denaturation affect amino acid sequence?
no
What does it mean when we say membranes are amphipathic?
contain both hydrophobic and philic regions
What are the three membrane lipids?
Phosphoglycerides, sphingolipids and cholesterol
What are phosphoglycerides?
Lipids with a phosphate group are phospholipids
phospholipids with a glycerol backbone are phosphoglycerides
hydophobic
What determines a persons blood type?
glycolipid carbohydrates of red blood cell plasma membrane
What are integral membrane proteins?
proteins that span the membrane
- function as receptors, channels or transporters
- are amphipathic
What are peripheral membrane proteins?
only associate on the edge of a membrane via weak electrostatic bonds
- can be added or removed as needed
What are lipid anchored proteins?
covalently bonded to lipid group within a membrane
- can be on internal or external side of mem
- external called GPI proteins
What is homology modelling?
used to learn abput strucutres and function of a protien family
What are lipid rafts?
outer specialized region of PM where cholesterol and sphingolipids pack tightly to form favorable environment for surface cell receptors
What enzyme can flip a phospholipid from one side of the membrane to the other?
flippases
How will membrane proteins diffuse after cell fusion?
concentrations will be uniform throughout cell
Is phospholipid diffusion restricted within a bilayer?
yes
What are the names and functions of the three membrane domains?
Apical - absorbs stuff from lumen
Lateral- cell contact and adhesion
Basal - substratum contact and generation of ion gradients
cells swell in a _ solution and shrink in a _ solution
hypotonic, hypertonic
What are the names and functions of 3 gated channels?
Voltage gated channels - state depends on difference in ionic charge on either side of the membrane
- Ligand gated channels - conformation state depends on ligand binding
- Mechano gated channels - conformation depends on mechanical forces applied to membrane
NaK ATPase is an example of what?
Active transport, uses ATP to pump 2 K in and 3 Na out
What are the three kinds of pumps in active transport?
P type pump - uses phosphorylation
V type pump - transport H - vacuolar, lysosomes
ABC transporters
What is secondary active transport?
coupling an energetically unfavorable reaction with an active transport reaction
What occurs to generate an action potential?
When cells are stimulated, Na channels open causing depolarization, triggering the action potential
What type of behaviours do action potentials exhibit?
All or none
Do APs lose intensity travelling down the nueron?
no
What sites on a neuron are where action potentials can be generated?
Nodes of ranvier
Where do neurons communicate with eachother?
the synapse, across the synaptic cleft
- chemicals, neurotransmitters, released from the presynaptic cleft diffuse to receptors on the post synaptic cell
- depolarization of pre synaptic cell causes ca channels to open, stimulates fusion of vesciles within membrane
- neurotransmitter binding to ion channel receptors can either stimulate or inhibit action potentials
What do acetylcholine, glutamate and GABA do?
- Acetylcholine inhibits heart but stimulates muscle contractility
- Glutamate is primary excitatory neurotransmitter
- GABA is primary inhibitory neurotransmitter
Facilitated diffusion is (2)
much slower transport than diffusion across a channel
- similar to an enzyme catalyzed reaction
can mitochondria fuse and split with one another?
yes
Four points about mitochondria function:
- are often associated with fatty acid oil droplets from which they derive raw materials to be oxidized to make ATP
- are the sites of synthesis of amino acids and heme groups
-play a role in uptake and release of calcium ions - regulate events involved in cell death
What is contained in the mitochondrial matrix?
ribosomes
mitochondrial DNA
strong oxidizing agents have a _ affinity for electrons?
high
strong reducing agents have a _ affinity for electrons?
weak
What two components compose the electron gradient?
ph and electric potential
What is the glycocalyx and what are its four functions?
formed by carbohydrate projections on the outer surface of the plasma membrane
- mediator of cell cell and cell substratum interactions
- mechanical protection
- barrier to molecular movement towards plasma membrane
- regulatory factor binding site
What is one of the best defined extracellular matrixes and what does it do?
basement membrane - surrounds muscles nersves and fat cells
underlies the epidermis on skin
What shape of proteins are in the ECM?
fibrous, globular is inside cells
What is collegen, list some shit abt it
Collagens are a large family of fibrous glycoproteins in ECM
- triple helix of three a helical chains
- most abundant protein in the human body
- produced by fibroblasts
- 28 types
-
What disease can result from collegen deficency?
Scurvy - technically due to vitamin C but vitamin C lets collagen retain structure
What is special about type IV collagen?
contains non helical segments and globular domains at each end
- allows for flexibility and lattice like character
What are proteoglycans?
component of ECM
- protein polysaccharide complex
- have repeating A B A B structure
- common in basement membranes and cartilidge
-act as filler
What is fibronectin?
Component of ECM
- linear array of FN domains
- found in blood clotting factors and membrane receptors
- binds to numerous ECM components
- Binds to cell surface receptors to attach cell to ECM
- important for cell adhesion
What is laminin?
Component of ECM
- 3 polypeptide chains
- role in potential for growth, migration and differentiation
- role in neuronal outgrowth
- strengthen basement membrane
Explain the dynamic properties of the ECM in space and time
Spatially - ECM fibrils can stretch to several times their normal length
Temporally - ECM components are under continual degradation and reconstruction to allow ECM remodelling
What degrades ECM components?
Matrix metalloproteinases (MMP)
What is integrin?
family of membrane proteins unique to animals
- composed of two membrane spanning polypeptide chains , a and b chain
- activated integrins become clustered and strengthen cell - ECM interactions
What are the two conformations of integrin?
Bent - corresponds to inactive state
upright - active with a bound ligand
What are the two major functions of integrin?
- adhesions of cells to ECM or other cells
- transmission of signals between external environment and cell interior
— intracellularly, integrins bind ligands such as Talin causing inside out signalling
— extracellularly - integrins bind differenct ECM components such as collagen, laminin and fibronectin causing outside in signalling
What does outside in signalling by integrin do?
can cause a conformational chainge in talin (intracellular)
- actin filament polymerization
- cytoplasmic protein kinases activation to phosphorylate other proteins - life saving signals
- signals influence cell differentiation, motility, growth and survival
What are focal adhesions?
scattered, discrete sites of cell anchorage
- play a key role in locomotion
- dynamic structure
- create mechanical forces or respond to forces form the environment
- actin filaments are the source of these forces
What are hemidesmosomes?
Cell-ECM attachment seen at basal surface of epithelial cells
- contain dense cytoplasmic plaque with keratin filaments
- keratin filaments are linked to ECM through integrins
How do separated organ cells redistribute themselves?
each cell will readhere to the same type of cell
Cell cell adhesion is mediated by (4)
- selectins
- members of the IgSF
- members of the integrin family
- cadherins
What are selectins?
family of membrane glycoproteins that bind to specific oligosaccharides
- have small cytoplasmic segment, single membrane spanning domain and a large extracellular portion
- on platelets, leukocytes
What are selectins involved in?
cell cell adhesion
- transmembrane signal transduction
- signalling for cell growth, differentiation, migration or survival
What is the IgSF?
Ca dependent or not?
immunoglobulin superfamily
- 765 distinct domains in genome
- involved in immune functions
- developmental roles in neuronal growth and circuitry
- Ca independent
What are cadherins?
membrane glycoprotein family
- typically join cells of a similar type to one another
- Ca dependent
- possibly the single most important factor in molding cells into cohesive tissue in embryos and holding them together in the adult
What two junctions are cadherins found in?
adherins junctions and desmosomes (both Ca dependent)
- adherins junction - actin filaments
- desmosomes - intermediate filaments
What are tight junctions?
occur between neighboring epithelial cells
- prevent solute distribution where different solute concentrations are in adjacent compartments
- points of cell cell contact where integral proteins if two adjacent membranes meet within the extracellular space
- major proteins are claudins
What are gap junctions?
- sites between animal cells that are specialized for intercellular communication
- plasma membranes of a gap junction contain channels that connect the cytoplasm of one cell with the cytoplasm of the adjoining cell
- plasma membranes come close but DO NOT make direct contact at a gap junction
- composed of several integral membrane proteins connexin, and organized into multi subunit complexes called connexons that span the membrane
What is the role of cell cell adhesion in inflammation?
white blood cells can get to the cells they need to be in to fight infection
- recruitment focused on selectins, integrins and IgSF proteins
What is the role of cell cell adhesions in metastasis?
cancer can escape the normal growth control mechanisms
- have special cell properties that allow it to escape
What 5 structures make up the endomembrane system?
ER, golgi complex, endosomes, lysosomes, and vacuoles
Generally, what is the endomembrane system doing?
materials are packaged in small membrane bound vesicles
- bud off from a donor membrane compartment
- move via motor proteins on cytoskeleton
- fuse with the membrane of the acceptor compartment
-
What are the three pathways in the endomembrane system?
Biosynthetic pathway
Secretory Pathway
Endocytic Pathway
What are the two secretion modes in the endomembrane system?
Constitutive secretion - materials are transported in secretory vesicles and discharged in a continual manner
Regulated secretion- materials are stored in vesicles and discharged in response to a stimulus
– occurs in endocrine cells and nerve cells, used in biosynthetic or secretory pathway
What is the biosynthetic pathway?
Pathway in endomembrane system
- proteins are synthesized in the ER, modified at the Golgi complex and transported to various destinations
What is the secretory pathway?
Proteins synthesized in the ER are discharged from the cell
What is the endocytic pathway?
Pathway in the endomembrane system
- materials move from the outer surface of the cell to compartments, such as endosomes and lysosomes
What does autoradiography do?
visualizes biochemical processes by radioactively labelling molecules
What does GFP tagging do?
allows microscope viewing of protein movement in living cells
- cells are infected with VSV which has a viral-GFP gene infusion
What are microsomes?
vesicles derived from the endomembrane system during homogenization
What are liposomes?
used for studying proteins
- vesicles whos surface consist of an artificial bilayer that is created from purified phospholipids
What is the endoplasmic reticulum?
network of membranes that penetrates the cytoplasm and has a lumen separated from the cytosol by the ER membrane
- highly dynamic structure 2 compartments
- RER/ SER
Three distictions between the RER and SER
RER has ribosomes bound to its cytosolic surface, SER lacks ribosomes
- RER has flattened sacs (cisternae) SER membranes are highly curved and tubular
- RER is continuous with outer membrane of nuclear envelope, SER is continuous with RER
What are the functions of the SER? 3
- Steroid hormone synthesis in endocrine cells of the gonad and adrenal cortex
- detoxification of organic compounds in the liver via oxygenases including cytochromes
- calcium ion sequestration and regulated release
What is the function of the RER
Has ribosomes to make proteins
- starting point of biosynthetic pathway for secretory proteins
- one third of proteins are synthesized here and released into the ER lumen via co translational translocation
What determines protein synthesis on the RER?
site of protein synthesis is determined by sequence of amino acids in N terminal portion of polypeptide
- secretory proteins contain a signal sequence at N terminus that direct emergind polypeptide and ribosome to ER membrane
- polypeptide moves to cisternal space of ER cotranslationally
- proteins contain built in address codes for protein trafficking pathways (signal hypothesis)
What determines the synthesis of secretory, lysosomal or vacuolar proteins?
co translational translocation deposits protein in ER lumen
- polypeptide signal sequence targets polypeptide to ER membrane
- signal sequence is recognized by signal recognition particle (SRP)
- SRP binds polypeptide and ribosome - stopping synthesis
- complex is recruited to ER membrane
- ribosome is handed off to translocon, a protein channel in ER membrane, upon recognizing signal sequence, polypeptide is inserted into translocon channel
What regulates the synthesis and trafficking of secretory proteins?
binding or hydrolysis of GTP
- SRP and receptor are G proteins that interact with eachother in GTP bound states, GTP hydrolysis triggers release of signal sequence by SRP
How are signal peptides removed and how are carbohydrates added in ER?
signal peptide is removed by signal peptidase and carbs are added by oligosaccharyltransferase
- both enzymes are integral membrane proteins associated with the translocon
How are integral membrane proteins synthesized on ER bound ribosomes
cotranslationally, hydrophobic transmembrane segments are shunted from the translocon into lipid bilayer
- inner lining of translocon orients polypeptide so more positive end faces the cytosol
- in multispanning proteins, transmembrane segments typically have opposite orientations, so arrangement is determined by direction in which the first segment is inserted
- tail anchored proteins lack a signal sequence but are synthesized in cytoplasm and targeted to ER thru GET pathway
3 things common to all membranes
- membranes exist from pre existing membranes
- membranes are enzymatically modified as they move from ER into other cellular compartments
- membranes are asymmetric with a cytosolic face and luminal / extracelluar face established in ER
what do nearly all proteins produced in the RER become?
glycoproteins
Where does modification of the oligosaccharide after its transfer to the polypeptide occur?
In the RER
What happens to misfolded proteins?
Glucose tagged, mannose deficient and ultimately degraded by proteosomes
What does the accumulation of misfolded proteins trigger?
Unfolded protein response UPR
- sensors in ER are kept inactive by BiP
- when misfolded proteins accumulated BiP cannot inhibit sensors
- activated sensors send signals to trigger proteins involved in destruction
What is the first step in vesicular transport?
ER to golgi complex
What is the golgi complex?
stack of flattened cisternae
- cis face faces Er
- trans face on opposite side
What are the functions of the two parts of the golgi complex?
cis golgi network - sorts proteins for ER or next golgi station
trans golgi network - functions in sorting proteins to plasma membrane or various intracellular destinations
Where does the assembly of carbs found in glycolipids and glycoproteins take place?
golgi complex
What determines the sequence of incorporation of sugars into oligosaccharides?
glycosyltransferases
What are the two functions of protein coats?
- cause membrane to curve and form a vesicle
- select the components to be carried by vesicle
What are the three types of vesicle transport?
COPII-coated vesicles - move materials from Er forward to ERGIC intermediate compartment and golgi complex
COPI-coated vesicles - move materials from ERGIC and golgi backwards to ER, or from trans golgi to cis golgi
Clathrin coated vesicles - move materials from TGN to endosomes lysosomes and plant vacuoles
What is ERGIC?
endoplasmic reticulum golgi intermediate compartment
Explain the properties and use of COPII coated vesicles
- bud off specialized domains of ER called ER exit sites (ERES) - this begins the biosynthetic pathway
- ER export signals found in cytosolic tails of proteins
-COPII coats select and concentrate enzymes - all vesicles have two distinct layers- an outer scaffold and an inner layer of adaptor like proteins
Explain the properties of COPI coated vesicles
COPI coat is made of cotamers made of seven proteins
- clearly used in backwards transport
- organelle proteins are maintained by
– retention of resident molecules excluded from transport vesicles
– retrieval of escaped molecules back to normal compartment
- resident proteins of ER contains AA sequence at C terminus as a retrieval signal
What does sorting and transport of lysosomal enzymes use?
clathrin coated vesicles
- lysosomal proteins are tagged in cis golgi with phosphorylated mannose residues
- tagged lysosomal enzymes are recognized and captured by mannose 6 phosphate receptors
What are the four steps that occur between vesicle budding and fusion?
- movement of besicle towards specific target compartment mediated by microtubules and associated motor proteins
- tethering vesicles to target compartment - mediated by tether proteins
- docking vesicles to target compartment, membranes come in close contact via interations between integral proteins
- fusions between vesicle and target membranes
What are Rabs?
family of small g proteins that cycle between active GTP bound and inactive GDP bound states
- GTP bound rabs associated with membranes by lipid anchor
- over 60 diff rabs genes
- used for vesicle sorting
What are SNAREs?
family of integral proteins that bring the vesicle and target compartment in close contact
VSNARES found in transport vesicles
TSNARES in target compartments
What is exocytosis?
discharge of secretory vesicle after fusion with PM
- triggered by Ca
- forms a fusion pore
- luminal part of vesicle becomes outer surface, cytosolic part becomes inner surface
why are extracellular vesicles useful maybe for drug delivery?
can move thru body unnoticed and pass thru blood brain barrier but have short half life before phagocytosis
What are lysosomes? What is autophagy?
- white blood cells digest shit by fusing phagosomes and lysosomes
- play role in autophagy - organelle turnover
- a phagopore envelopes an organelle to produce a double membrane vesicle called an autophagosome
- this fuses with a lysosome generating an autolysosome, degrading all contents
What are the two ways to get shit into the cell?
Endocytosis - cell internalizes cell surface receptors
Phagocytosis - uptake of particulate matter
What are the two categories of endocytosis?
bulk phase - non specific
receptor mediated - specific
What do coated pits do in receptor mediated endocytosis?
substances that enter cell become bound to coated pits on PM, pit regions invaginate and then pinch free of cytoplasm via clathrin
- contain adaptors between clatherin lattice and surface like AP2
- adaptors engage tails of specific receptors to do different things
What is the structure of clathrin
used in coated pits
- 3 heavy chains and 3 light chains called a triskelion
- triskelions overlap
What is dynamin?
G protein required for fission of vesicle from membrane that it forms on
- assembles into a helical collar around invaginated coated pitq
What are vesicle bound materials called after internalization?
endosomes
What are LDLs?
Low density lipoproteins
- complex of protein and cholesterol
- receptors transported to membrane and bound to coated bit
- taken up by RME and taken to lysosomes releasing cholesterol for use by cells
How does phagocytosis work?
folds produce a vacuole called phagosome that pinches off inwardly of PM and fuses w lysosome (phagolysosome)
What are peroxisomes? And they import proteins —— Ttranslationally
small membrane bound organelles that contain enzymes
- proteins are imported postranslationally ( same in other organelles but not RER which is cotranslationally)
- two subcompartments
- possess targeting signal for matrix or membrane
Various metabolic functions
What is the TOM complex? What is the TIM complex?
outer mitochondrial membrane protein import complex
- TIM compex is for proteins destined for inner mito membrane
Integrins
Selectins
Cadherins
Igsf
All do what kind of interaction, what does integrin also do, what kind of things are they
Cell cell
Cell ecm
Membrane proteins
4 ecm components
Collagen
Fibronectin
Proteoglycans
Laminin
