Eukaryotic Cells: organelles, plasma membrane, mitosis, and senescence Flashcards
genes can be genetically mapped by a specific location on that chromosome, a ______
locus
in other words, the locus is the specific location of that gene
in addition to providing support and structure, the nuclear matrix also helps regulate gene expression. How does it do so?
the DNA chromosomes are attached to the matrix at specific sites, and these appear to be involved in regulating gene expression
the nucleolus functions as the _____ factory
ribosome
hence, the nucleolus is the site of rRNA transcription
Name functions of RNA Pol I, II, & III
RNA Pol I: transcribes rRNA
RNA Pol II: transcribes mRNA
RNA Pol III: transcribes tRNA
Since ribsome assembly is initiated in the nucleus, where are the protein components of the ribosome made?
the protein components of the ribosome areNOT produced in the nucleolus or the nucles, but rather the cytoplasm (because all transcription occurs in the cytoplasm). These proteins must be shuttled into the nucles from the cytoplasm
Why is it that ribosomes are only partially assembled in the nucles before they’re shuttled to the cytoplasm to finish their assembly?
because if ribosomes were to be completely assembled in the nucleus, there is an increased risk of them translating hnRNA before it gets spliced into mRNA.
True or False: The ER lumen is isolated from the cytoplasm
True
Nuclear pores can freely diffuse molecules
60
where is the e- transport chain performed in mitochondria
the inner membrane
is the inner membrane or outer membrane of the mitochondria impermeable to the free diffusion of polar substances?
the inner membrane: it must be impermeable to H+ in order to carry out the e- transport chain
the space between the inner and outermembrane of the mitochondria is called the ________
intermembrane space
How is mitochondrial DNA different from the cellular genome?
mitochondrial DNA more resembles prokaryotic DNA because it is circular DNA with it’s own genetic code. It also has its own unique RNA Pol, DNA replication machinery, ribosomes, and amino-acyl tRNA synthetases compared to the rest of the cell
what is the endosymbiotic theory of mitochondrial evolution?
the theory that mitochondria originated as independent unicellular organisms living within larger cells
mitochondria are only inherited from the _____
mother
the rough ER translates proteins that are targeted from the ____ pathway
secretory
function of smooth ER?
has enzymes that are involved in steroid hormone biosynthesis (gonads) and that degrade toxins (liver)
What are the 4 destinations of proteins that are transcribed in the cytoplasm?
these proteins are headed toward peroxisomes, mitochondria, the nucleus, or will remain in the cytoplasm
What are the main destinations of proteins synthesized in the RER?
proteins secreted into the extracellular environement, incorporated into the plasma membrane, ER, Golgi, or lysosomes,
the secreted and lysosomal proteins (made in the RER) have a ___ sequence located at their N terminus, which binds to the _____ particle, forming a complex which can then bind to the ribosome for translation
signal sequence, signal recognition particle
when the signal sequence binds to the signal recognition particle, followed by binding to the ribosome, this complex then docks onto a ____ receptor on the cytoplasmic surface of the RER
SRP (signal recognition particle) receptor
When and where is the signal peptide (of secreted/lysosomal proteins) removed?
the signal peptide is removed in the RER lumen once translation of that peptide is complete
integral membrane proteins have _____ domains, that are essentially signal sequences that are found on the interior of the protein. Are these domains hydrophilic or phobic, and are the located at the N terminus?
transmembrane domains
these domains are hydrophobic (being that they are found on the interior of the protein). because they are found on the interior of the protein, they are not located at the N terminus
For a protein destined to integrate into the plasma membrane, the portion of that integral membrane protein that faces the extracellular environment is located in the ______ (ER lumen or cytoplasm) during translation in the RER
ER lumen
The gogli and the ____ are responsible for post-translational protein modification
RER
For secretory proteins that need to go the Golgi, ER, or lysosome contain ____ signals that help the protein go to those location instead of being excreted.
targeting signals
proteins made in the cytoplasm but need to go to an organelle (hence, proteins that are not part of the secretory pathway) contain sequences called ____ signals to help direct them
localization
Which proteins have a signal sequence?
Which proteins have transmembrane domains?
Which proteins have localization signals?
signal sequences: Proteins made in the RER/secretory pathway: excreted, plasma membrane, RER, Goli, lysosomes.
Only plasma membrane proteins have a transmembrane domain
localization signals: proteins made in the cytoplasm (with the exception of cytoplasmic proteins): perioxisomes, nucleus, mitochondria
Which proteins have targeting signals?
proteins designated to the RER, Golgi, and lysosomes
note that these are all secretory pathway proteins, but of the secretory pathway proteins, excreted and plasma membrane proteins do not have these targeting signals
glycolysis enzymes are translated in the _____ (cytoplasm or the RER)
cytoplasm because they are cytoplasmic proteins (note glycolysis occurs in the cytoplasm)
where are histone proteines and proteins that make up DNA and RNA Polymerase synthesized?
in the cytoplasmic ribosomes
Kreb cycle enzymes are proteins synthesized in the ______
cytoplasm
note that kreb cycle enzymes are destined to go to the mitochondria, and mitochondrial proteins are synthesized in the cytoplasmic ribosomes
Where is catalase synthesized?
in the cytoplasmic ribosomes
note that catalase is a peroxisome enzyme
The golgi has mostly a unidirectional pathway. What is the directionality of this pathway?
RER → cis Golgi → medial Golgi → trans Golgi
In addition to modifying proteins, the Golig also synthesizes certain ____ to be secreted
macromolecules i.e polysaccharides
distinguish between the constitutive secretory pathway and the regulated secretory pathway
constitutive secretory pathway refers to proteins that are sent in vesiscles from the Golgi immediately to the cell surface (they are not held and released at certain times)
the regulated secretory pathway refers to the proteins that are stored in the secretory vesicles and released only at certain times, usually in response to a change or signal from the environment
Distinguish between the function of lysosomes and peroxisomes
lysosomes: degrade biological macromolecules (both intra and extracellular) via acid hydrolases. they perform autophagy, phagocytosis, and crinophagy (digestion of unneeded/excess secretory products)
peroxisomes: essential for lipid breakdown and contains catalse, which converts H2O2 into H2O and O2. In the liver they assist in detoxification of drugs and chemicals
What does the lysosome do with the molecular building blocks once it breaks the macromolecules down via hydrolysis?
they will release the molecular building blocks into the cytoplasm for reuse
why is it important that acid hydrolases in the lysosome only work at a low pH?
this is a protective mechanism so that if a lysosome bursts, their hydrolases won’t continue to degrade cellular components, as the cellular environment has a pH of slightly over 7, whereas the lysosome has a pH of 5
Free FA form ____ whereas phospholipids form ____
FA = micelles
phospholipids = bilayers
why do phospholipids form bilayers?
because its the lowest energy state for these molecules, as the hydrophobic components are conglomerated together away from the hydrophilic components
What types of molecules can freely diffuse accross the plasma membrane?
small, nonpolar molecules i.e. CO2, O2, and steroid hormones
Name whether the following will increase or decrease membrane fluidity:
1) saturated FA
2) unsaturated FA
3) cholesterol
1) decrease fluidity d/t increased van der Waals interactions
2) increase fluidity d/t decreased van der Waals
3) increased fluidity at cold temperatures (i.e. acts like antifreeze) and decreased fluidity at high temperatures
What molecules do channel proteins allow to pass through the plasma membrane?
they selectively allow ions or molecules to cross the membrane
integral plasma lipids and proteins are free to diffuse ____ (tranversely or laterally)
laterally
*they can only move in a 2D direction; they are not allowed to flip flop
all glycosylations are found on the ____ of the plasma membrane
exterior
some _____ are anchored to the cytoplasm and cannot move in any direction
proteins
Equation for Molarity (M)
mol of sollute / #L of solution
⇒ M = mol/L
Equation for molality (m)
molality = #mol solute / #kg of solvent
m = mol/kg
which values can fluctuate with changes in temperature: molarity or molality. Why?
molarity can vary with changes in temperature because the volume of a solution can increase or decrease as temperature increases or decreases (assuming that pressure of the solution remains constant)
molality does not change with temp because it doesn’t involve volume. it involves mass
Equation for mole fraction (XS)
XS = #mol of substance S / total # mol in solution
it expresses the fraction of moles of a given substance relative to the total amount of moles of solution. is used when >1 solute is present
distinguish between strong, weak electrolytes, and nonelectrolytes
strong electrolytes are ions that dissociate completely in solvent
weak electrolytes are ions that do not dissociate completely in solvent; some remain ion paired to some extent
nonelectrolytes are covalent compounds that don’t dissociate into ions
what is the van’t Hoff factor?
aka the ionizability factor: tells us how many ions one unit of substance will produce in a soltion
i.e. glucose (C6H12O6) = 1
NaCl = 2
HNO3 = 2
CaCl2 = 3
What are colligative properties?
refers to vapor pressure, BP, MP/FP, and osmotic pressure
colligative properties depend on the ____ in the solution, not the ___ of the particle
depends on the number of solute particles, not the identity/type of particle
hence, colligative properties does not depend on the size, type, or charge of the solute particles
will adding an ionic solute to a solvent increase or decrease the vapor pressure. Why?
it will decrease the vapor pressure because adding solute increases the intermolecular forces within the solution
The boiling poing (BP) is the temperature at which the vapor pressure of the solution is equal to the ____ pressure over the solution
atmospheric
if you add ionic solute to a solution, will it increase or decrease the BP?
it will increase the boiling point because there will be more molecular interactions and therefore more forces that need to be overcome to transition from liquid to gas state
Equation for ∆Tb
∆Tb = kbim
kb = solvent’s BP elevation constant
i = van’t Hoff factor
m = molality concentration of solution
kb ≈ 0.5C˚/m
If you add ionic solute to a solvent, will in increase or decrease the FP/MP.
it will decrease the FP/MP
Equation for ∆Tf
Distinguish between diffusion and osmosis
diffusion refers to passage of solutes along their concentration gradient (high to low)
omosis refers to passage of solvent (H2O), not solutes, across a semipermeable membrane (flows from areas of low solute concentration to high solute concentration)
what is osmotic pressure?
the pressure it would take to stop osmosis from occuring
equation for osmosis (Π)
Π = MiRT
M = molarity
i - van’t Hoff factor
R = universal gas constant = 0.0821 L·atm/K·mol
T = temp in Kelvins
distinguish between simple and facilitated diffusion
simiple diffusion occurs without the help from an integral membrane protein
facilitated diffusion is a diffusion of a solute down its concentration gradient through an intergral membrane protein
listed which type of signal/response the following channel proteins respond to:
voltage-gated ion channels
ligand-gated ion channels
voltage gated opens in response to a change in the electrical potential across the membrane
ligand-gated open in response to the bindingn of a specific molecules i.e. neurotransmitter
can ion channels move ions against their concentration gradient?
no
how to carrier proteins differ in their transport of molecules compared to ion channels?
carrier proteins don’t form a tunnel/channel; rather, they bind to the molecules being transported at one side of the membrane, which induces a conformational change of the carrier protein, causing the molecule to be transferred from one side of the membrane to the other
distinguish between uniport, symport, and antiport carrier proteins
uniport: carry one molecule across the membrane
symport: carry >1 molecule across the membrane in the same direction
antiport: carry 2 molecules in opposite directions
distinguish between a channel and a pore in a membrane
a channel is selective or which type of molecule it allows to pass
a pore is not selective, and will allow any molecule under a certain size from passing through the membrane
what are porins?
they are the polypeptides that form pores
does simple diffusion exhibit saturation kinetics?
no. it is only limited by surface area and the size of the driving force (gradient)
does facilitated diffusion exhibit saturation kinetics?
yes. the increase in driving force will increase the flux (rate of diffusion), but only to a certain extent. Once all transport proteins become saturated, no further increase in flux is possible.
Active transport is movement of solutes ____ their concentration gradient, which requires _____
against, energy
Distinguish between primary and secondary active transport
primary: transport is coupled to ATP hydrolysis
secondary: transport is not directly r/t ATP hydrolysis; ATP is first used to create a gradient, then the potential energy in that gradient is used to drive the transport of some other molecules across the membrane i.e. the glucose/Na+ pump is connected to the Na+/K+ ATPase
Na+/K+ ATPase:
1) How many Na+ ions does it pump and in which direction?
2) How many K+ ions does it pump and in which direction?
3) what is the purpose of the K+ leak channels?
1) 3 Na+ out of the cell
2) 2 K+ into the cell
3) allows movement of K+ down it’s concentration gradient (K+ flows out of the cell), which then creates an electrical potential accross the plasma membrane with a net negative charge on the interior of the cell (this is the resting membrane potential)
What are the 3 main functions of Na+/K+ ATPase?
maintain osmotic balance between interior and exterior of cell
establish the resting membrane potential
provide Na+ concentration gradient used to drive secondary active transport
where are the Na, K, and Cl concentrations highest, inside or outside the cell?
Na+ and Cl- are highest on outside of cell
K+ is highest on the inside of the cell
Distinguish between phagocytosis, pinocytosis, and receptor-mediated endocytosis
phagocytosis: nonspecific uptake of large particulate matter into a phagocytic vesicle, which later merges with a lysosome. No invagination occurs with this process
Pinocytosis: nonspecific uptake of small molecules & extracellular fluid via invagination
Receptor-mediated endocytosis: very specific uptake of molecules. inside the cell are pits coated with clathrin, which are attached to receptors that bind to a specific molecule outside the cell. i.e. a lipoprotein that is carrying cholesterol binds to the exracellular receptor, the complex internalizes, and then taken into a vesicle that is termed an endosome, which gets taken to a lysosome for digestion.
what is a ligand?
a molecule that serves as the key for a given receptor, which once bound will trigger a response within a cell via a process called signal transduction
what is a catalytic receptor?
a receptor with an enzymatic active site, that once bound to it’s ligand, this enzymatic active site (which is present on the cytoplasmic side of the membrane) will carry out a catalytic role of an enzyme inside the cell i.e. protein kinase, which attaches phosphate groups to proteins, which then regulates that protein’s activity
G-protein linked receptor:
1) ____ binds to G-protein receptor on extracellular surface
2) G-proteins (on cytoplasmic side of receptor), dissociate from ____ and bind to _____
3) the activated G protein then diffuses across the plasma membrane to activate ____
1) ligand
2) GDP, GTP
3) adenylyl cyclase
In the G-protein receptor cascade, once adenylyl cyclase is activated, it makes ___ from ____.
cAMP from ATP
Once cAMP is made in the G-protein cascade, cAMP activates ____ in the cytoplasm, which ____ certain enyzmes, with the end result being mobilization of energy
cAMP-dependent kinases, phosphorylates
distinguish between Gs and Gi G receptor proteins
Gs refers to G protein activation that stimulates adenylyl cyclase (and increases production of cAMP)
Gi refers to G protein activation that inhibits adenylyl cyclase (and therefore decreases the production of cAMP)
Some G protein linked receptors are not always associated with cAMP. Some activate ______, which ulitmately increases cytoplasmic Ca++ levels
phospholipase C
Distinguish between microtubules, microfilaments, and intermediate filaments
microtubules: made of alpha tubulin and ß tubulin, which together form an alpha-ß tubulin dimer, which forms tubes. the tubes can be extended only from one end, with the other end attached to the MTOC (microtubule organizing center). *note the MTOC contains the centrioles (a ring of 9 microtubule triplets) essential to mototic divisions. microtubules also form cilia and flagella
microfilaments: made of globular protein called actin, which forms 2 chains wrapped around each other to form the filament. responsible for gross movement of the cell.
intermediate filaments are comprised of a variety of polypeptides (heterogenous); they provide strong cell structure and help to resist mechanical stress
eukaryotic flagella are made of microtubules, which differs from prok. flagella in that euk flagella have a ____ arrangement
9+2 arrangement of microtubles
Distinguish between tight-junctions, desmosomes, and gap junctions
tight-junctions: aka occluding junctions. they are bands between cells that block the flow of molecules across the entire cell layer and also block flow of molecules w/in the plane of the plasma membrane i.e. membrane proteins on apical surface of intestinal lining cannot transport laterally to basolateral surface of of the cell.
desmosomes: do not form a seal like tight-junctions, rather they are concise points that the plasma membranes between cells are anchored via a plaque called keratin. these points do not freely diffuse laterally across a plasma membrane; they are anchored in place by intermediate filaments of the cytoskeleton
gap junctions: form pore-like connections between adjacent cells, allowing passage of ions, AA, and carbs, but not polypeptides and organelles i.e. allow for membrane depolarization of an action potential in smooth and cardiac muscle
In what phase of a cell cycle does DNA replication occur
S phase, which is in the interphase portion of a cell cycle
when does the cleavage furrow form during mitosis?
during anaphase
distinguish between sister chromatids and nonhomologous chromosomes
sister chromatids are identical copies of a chromosome, attached to each other by 1 centromere
nonhomologous chromosomes are equivalent but not identical and do not come anywhere near eachother during mitosis
what is a karyotype?
a display of an orgnamism’s genome
Distinguish between a protooncogene, and oncogene, and tumor suppressor genes
protooncogenes: normal versions of genes that allow for regular growth patters, but can be converted into oncogenes under the right circumstances (i.e. mutation or exposure to mutagen)
oncogene: mutated genes that induce cancer
tumor suppressor genes: code for proteins that prevent conversion of cells into CA cells. they detect damage to genome and halt cell growth and division until the damage can be repaired; or can trigger apoptosis if damage is too severe to fix i.e. p53 is a protein scaled up when genetic damage or oncogene is detected, & if repair is not possible, it induces apoptosis
which enzymes are responsible for carrying out apoptosis?
caspases
explain how initiator caspases and effector caspases work in apoptosis
initiator caspases will cluster together when they detect cellular death signals. Their clustering activates each other, which then activates effector caspases.
effector caspases cleave a variety of cellular proteins to trigger apoptosis
what is oxidative stress?
occurs when levels of reactive O2 species increase to the point where it outstrips the cell’s ability to detoxify them, ultimately generating free radicals and casuing damage to DNA, proteins, & lipid bilayers
phagocytes may produce nitric oxide or superoxide to kill pathogens. hence, the immune system uses _____ stress to kill pathogens
oxidative
what is regenerative capacity?
refers to an organisms ability to restore damage tissues and depends on stem cells w/in an organism i.e. newts can regrow their tails if chopped off, or multipotent stem cells w/in bone marrow regenerate blood and immune system
what is senescence?
refers to biological aging, which can occur through shortening of telomeres throughout time, or can be caused by environmental exposures and behavioral factors
distinguish between retrograde and anterograde
retrograde means moving in the backwards direction
anterograde means moving in the forwards direction
