exam 2 (review slides) Flashcards
what is cell fractionation? how does it work? how are pellets separated based on size? and what is a supernatant?
cell fractionation: takes cells apart and separates major organelles and other cell structures from one another
- done using a centrifuge, tube that spins really fast - components of cell settle at the bottom, forming a pellet
- higher speed = pellet w smaller components
- lower speed = pellet w larger components
supernatant: rest of the liquid which is at the top (consists of lighter components that didn’t settle at the bottom - i.e. cytoplasm & other small cell parts)
prokaryotic cells are characterized by having:
- no nucleus
- no membrane bound organelles
- DNA in an unbound region called nucleoid
- cytoplasm bound by plasma membrane
eukaryotic cells are characterized by having:
- DNA in a nucleus that is bounded by a double membrane
- membrane bound organelles
- are also much larger than prokaryotic cells
nucleolus
- site of ribosomal RNA (rRNA) synthesis
- assembles and produces ribosomes
- “command center” inside the nucleus
function of the nucleus
- control center
- hold’s cell’s genetic information
- DNA replication, transcription, and translation happen here
translation vs transcription
- transcription: synthesizing RNA from DNA
- translation: synthesizing proteins fro the RNA
function of ribosomes + 2 types
“protein factories” - site of protein synthesis
free ribosomes: most proteins made on free ribosomes function within cytosol (free ribosomes are not attached to the ER)
bound ribosomes: make proteins destined for insertion into membrane, for packaging within organelles, or for export out of cell (bound to the ER)
what is the endoplasmic reticulum + the 2 types
- cell’s “highway”
- membrane of interconnected tubules that carry stuff around the cell
two types:
rough ER: synthesis and packaging of proteins
- bumpy because ribosomes are attached to it
- also distributes transport vesicles
smooth ER: has enzymes that help create and package lipids and also detoxifying substances and stores calcium ions
order of where the proteins go after synthesis
- membranes & proteins produced by the ER move via transport vesicles to the Golgi
- The Golgi pinches off transport vesicles and other vesicles that give rise to lysosomes, other types of specialized vesicles, and vacuoles
- The plasma membrane expands by fusion of vesicles; proteins are secreted from the cell by exocytosis
what are the 3 destinations for proteins produced by the rough ER
- shipped to another organelle (enzymes to catalyze reactions)
- inserted into plasma membrane (membrane transporters or pumps)
- secreted outside of cell (carry messages to other cells - glycoproteins)
what are transport vesicles
helps move materials, especially proteins from one organelle to another
- distributed by the rough er
function of glycoproteins
enable cells to recognize another cell as familiar or foreign, which is called cell-cell recognition
cis and trans Golgi apparatus
cis: means same
- part of the Golgi apparatus nearest to ER (endoplasmic reticulum), functions primarily in receiving and sorting molecules
trans: means opposite
- part of Golgi farthest from ER, functions in final modifications of proteins before they’re shipped out`
what is the function of the Golgi apparatus?
“post office of cell city”
- processes proteins + packages them before sending them where they need to go via transport vesicles
what are vesicles
sacs that little goodies are packaged into
- used to ship stuff within cell or outside cell
what are lysosomes?
sacs of enzymes that break down cellular waste and debris from outside cell to turn into simpler components for inside cell
- “digestive system of cell”
- membraneous-enclosed sac of hydrolytic enzyme that can digest macromolecules
what is autophagy?
lysosomes use enzymes to recycle the cell’s own organelles and macromolecules
what is the function of the mitochondria?
cellular respiration!
- use oxygen to generate ATP
- cells that need more power (such as muscle cells) have more mitochondria in them
what is the inheritance pattern for mitochondria?
maternal b/c mitochondria self replicates so DNA never mixes with the father’s
what is unique about mitochondria compared to other organelles?
acts like its own cell, does its own replication and even has some DNA
3 similarities between mitochondria and chloroplasts
- enveloped by a double membrane
- contain free ribosomes and circular DNA molecules
- grow and reproduce somewhat independently in cells
function of the chloroplasts
also energy!!
- sites of photosynthesis
- found in plants and algae
endosymbiont theory
idea that some organelles inside eukaryotic cells (like mitochondria and chloroplasts) were once independent, free-living bacteria
- bacteria engulfed by larger cells, instead of being digested, formed mutually beneficial relationship with the host cell
- over course of evolution, host cell and its endosymbiont merged into a single organism
2 main parts of a chloroplast
thylakoids: membranous sacs that capture light to turn into ATP solar panels of the cell
- stack to form granum
stroma: internal fluid that contains enzymes to use chemical energy to produce sugar kitchen of the cell, uses products to assemble
do plant cells have mitochondria?
yes, they have both mitochondria and chloroplast (chloroplasts are used for photosynthesis only)
how are mitochondria and chloroplasts similar?
- both have double-membrane
- have their own DNA and manufacture ribosomes
- grow and divide independently of cell division
- energy producing organelles
photosynthesis (chloroplasts) vs. cellular respiration (mitochondria)
- photosynthesis builds glucose by capturing energy from the sun and stores the glucose for later use
- cellular respiration breaks down glucose to ATP and for use within the cell
cilia and flagella
microtubule containing extensions that project from some cells
cilia: present in lung + throat cells to push up mucus
flagella: present in sperm cells
protozoans move around using cilia and flagella
tight junctions, gap junctions, and desmosomes (anchoring junctions)
tight junctions: “cellular zippers,” connect neighboring tissues tightly to make sure there are no leaks
- ex. present in digestive tract
gap junctions: “communication tunnels,” allow quick communication through openings that allow molecules and ions to pass directly
- ex. present in heart cells
desmosomes: fasten cells together into strong sheets, important in tissues subjected to mechanical stress, like skin and heart muscles
factors that affect membrane fluidity (3 factors + give reasons for why)
- membranes with more unsaturated fatty acids are more fluid (because of the kinks, they cannot pack together as closely)
- as temperature cools, becomes less fluid and more solid
- cholesterol molecules embedded in membrane - reduce fluidity but prevent total tight packing (helps because when you reduce temperature, membrane won’t solidify as quickly)
membranes must be fluid to work properly
membranes are held together by ___________________ bonds
weak hydrophobic
phospholipids form main fabric of membrane, but ________ determine most of membrane’s functions
proteins
- protein composition of membranes varies among cells within an organism, and among intracellular membranes within a cell
_____________ & ____________, _____________ molecules can enter the membrane easily
small & nonpolar, hydrophobic
how does the polarity of a molecule affect its crossing of the cell membrane?
- nonpolar molecules are hydrophobic and have easy time passing through
- polar molecules are hydrophilic and have difficulty passing (get stuck) or pass really slowly (including water)
proteins that are built into the membrane can help certain things pass
passive transport vs. active transport
passive transport: diffusion of substance across membrane with no energy required, goes down concentration gradient (high to low)
active transport: requires energy to move substances, movement against concentration gradient (low to high)
- if 2 substances in a solute, moves down its OWN concentration gradient, not the overall concentration gradient
2 things that the selective permeability of a membrane is dependent on
- natural permeability of a lipid bilayer (i.e. polar and nonpolar)
- specific transport proteins built into the membrane
osmosis
diffusion but basically only for water
- high to low water concentration
- low to high solute concentration
sodium-potassium pump + ratio of Na and K
- example of active transport
- exchanges sodium for potassium against the electrochemical gradient
- pumps sodium ions out and potassium ions in
- ATP is hydrolyzed to ADP
- carrier protein changes conformational shape
- 3 Na+ into cell, 2 K+ out
electrogenic pump
an active transport protein that generates voltage across a membrane while pumping ions
- in animals, it is Na+/K+ pump
membrane potential
- all cells have voltages (electric potential energy, separation of opposite charges)
- inside cell is more negative compared to the outside of the cell
- pumps regulate this by pumping ions using energy
affects the movement of ions
facilitated diffusion
speeds transport of solute by providing efficient passageway to go through
still passive bc doesn’t go against the concentration gradient
- ex. channel proteins
what is osmoregulation
control of solute concentration and water balance
- important for organisms that live in very hypo or hypertonic environments
bulk transport + 2 types + 3 types of endocytosis
- large molecules, like polysaccharides and proteins, need to cross inside vesicles CAUSE THEY FAT
exocytosis: vesicles transport materials outside of the cell
- ex. nerve cells releasing neurotransmitters
endocytosis: vesicles transport into the cell
- two types: phagocytosis and pinocytosis
phagocytosis: devouring action, engulfs invader and then destroys
pinocytosis: drinking action, cell membrane folds and creates little pocket to bring things in (for fluids and other small substances)
receptor-mediated endocytosis: vesicle formation is triggered by solute binding to receptors, allows cell to acquire bulk quantities of specific substances
kinetic energy, potential energy, thermal energy, and chemical energy
kinetic energy: energy associated with motion
- ex. water gushing through a dam turns turbines
potential energy: energy stored ready for action, has to do with position or structure
- ex. book on shelf can fall and do work or stretched rubber band
- molecules possess energy due to the arrangement of electrons in bonds between their atoms
thermal energy: associated with heat, the more heat something has = more thermal energy
chemical energy: energy stored in bonds b/w molecules
- ex. potential energy stored in food
how to tell if a reaction occurs spontaneously or not?
- by the free energy change
spontaneous: reaction will proceed without an input of energy
*negative ∆G = reaction will be spontaneous
positive ∆G = reaction is NOT spontaneous*
entropy
∆S
- measure of disorder in a system (represents dispersion of energy)
- disordered state = high entropy state
enthalpy
∆H
- measure of the total heat content of a system
- positive = heat is absorbed
- negative = heat is released
Gibbs free energy + equation
describes the amount of work that can be done in a system given the thermodynamic environment
∆G = ∆H - T∆S
*temperature in Kelvin
when G is positive = endergonic reaction
when G is negative = exergonic reaction
exergonic vs endergonic reactions **
- exergonic: energy out, more energy released than absorbed, products store less free energy than reactants (∆G is negative = so reaction is spontaneous)
- endergonic: energy in, more energy absorbed than released, products store more free energy than reactants (∆G is positive = nonspontaneous reactions)
ATP coupling
cells manage their energy resources by energy coupling
- using energy released from an exergonic reaction to drive an endergonic reaction
- most energy coupling in cells is mediated by ATP
energy is released from ATP by…
the phosphate bond being broken by hydrolysis
- energy comes from the chemical change of system to a state of lower free energy in products (not from phosphate bonds)
why does hydrolysis release so much energy?
phosphate group has negative charge that causes a lot of repulsions (hence energy) when it breaks
in cells, energy from the _____________ is used to drive __________ reactions
(ATP coupling)
exergonic hydrolysis of ATP; endergonic
activation energy definition + barrier
initial energy needed to break the bonds of reactants
- provides a barrier that determines rate of spontaneous reactions
active site
region on enzyme, often a pocket or groove, that binds to substrate
induced fit (in regards to enzyme-substrate)
enzyme changes shape slightly to fit the substrate
- kinda like how you change grip on hand to shake someone else’s hand
noncompetitive (allosteric) vs. competitive inhibitors
competitive inhibitors: “molecular rivals” that are competing with the substrate to bind to the active site
- increasing substrate concentration can overcome inhibition
- blocks substrate = reduces enzyme productivity
noncompetitive inhibitors: “molecular blockers” that bind to a different site on the enzyme, changing its shape to make it less effective at catalyzing reaction
- ex. toxins, antibiotics, pesticides
allosteric regulation (activator and inhibitor)
- “remote control” - controls from a distance, molecule binds elsewhere and changes function and shape of protein
allosteric activator: “protein cheerleader,” encourages the protein’s activity
allosteric inhibitor: when binds, slows down or blocks protein activity
are mostly bad bc once binded, change the shape forever and the enzyme just becomes useless - ex. toxins, poisons, etc.
feedback inhibition
“brake system” for controlling a process
- when product accumulates to a specific level, “feeds back” to inhibit or slow down earlier step in the proces
cell cycle consists of _________ & _________
Interphase and Mitotic (M) phase
interphase + the 3 phases
interphase: cell growth & copying of chromosomes in preparation for cell division
G1 phase: (“first gap”) - cell grows
S phase: (DNA synthesis) - chromosome replication
G2 phase: continued growth and preparation for cell division
cell grows during all 3 phases of interphase, but chromosomes are only duplicated during what phase?
S phase
which cell cycle does a cell spend 90% of its time?
interphase
list the steps of mitosis and a fact about each step (in order)
PMAT C
- Prophase: chromatin fibers become more tightly coiled, condensing into discrete chromosomes, mitotic spindle begins to form
- Metaphase: chromosomes line up along the center of the cell, called the metaphase plate
- Anaphase: sister chromatids of each chromosome separate and move toward opposite ends of the pole, each chromatid thus becomes an independent chromosome
- Telophase: cell begins to separate but not entirely yet. The nuclear envelope re-forms around each set of chromosomes
- cytokinesis: division of the cytoplasm, in animal cells cytokines involves formation of a cleavage furrow, which pinches the cell in 2
when a cell is not dividing, and even as it replicates its DNA in prep for cell division, each chromosome is in the form of a ______________
after DNA replication, chromosomes _______
long, thing chromatin fiber
condenses (each chromatin fiber becomes densely coiled and folded – chromosomes shorter and thicker)
each duplicated chromosome in cell division has _________
2 sister chromatids
(joined copies of original chromosome)
mitotic spindle
a structure made of microtubules that controls chromosome movement during mitosis
- helps separate chromosomes during cell division (mitosis)
- begins to form in cytoplasm during prophase
at metaphase, chromosomes are all lined up at ____________
metaphase plate
(an imaginary plane midway between the spindle’s 2 poles)
how is cytokinesis different in plant cells?
plants need to create a cell wall
in plant cells, a cell plate forms during cytokinesis – made from vesicles derived from Golgi apparatus move along microtubules to middle of the cell where they combine – site where new cell wall forms
2 types of regulatory proteins that are involved in cell cycle control
cyclins: “traffic lights” – proteins that regulate progression of cell cycle by turning specific phases on and off
cyclin-dependent kinases (cdks): “drivers of the cell cycle” – enzymes that work with cyclins to activate or deactivate processes in the cell cycle
- when cyclins bind to CDKs, the green light for the cell to proceed to the next phase.
MPF (maturation-promoting factor)
- cyclin and cdk binded together
- approves cell to go past G2 checkpoint into M phase
density- dependent inhibition & anchorage dependence + relation to cancer cells
density-dependent inhibition: phenomena in which animal cells stop dividing when they come into contact with each other
anchorage dependence: cells only divide and grow when they are attached to a surface or substrate
cancer cells exhibit neither type of regulation of their division
loss of control in cancer cells is caused by what factors?
- cancer cells do not heed the normal signals that regulate cell cycle (do not stop dividing when growth factors are depleted)
- cancer cells make their own growth factor and may convey growth factor’s signal w/o presence of a growth factor
local vs long distance signaling between cells
local: animal cells communicate using secreted messenger molecules that travel short distances – paracrine signaling (neighbors chatting over fence)
- ex. growth factors stimulating nearby target cells to grow and divide or synaptic signaling in neurotransmitters
long distance: plants and animals use hormone molecules
GPCRs (G protein-coupled receptors)
- “cellular doorbells”– when rung by signaling molecules, set off a series of events inside the cell to produce a response
- coupled with G proteins (which are like the “butlers”)
G proteins bind to the energy rich GTP which binds to GPCR
Receptor Tyrosine Kinases (RTKs)
“cellular radio station”
- antenna takes the signal outside (membrane receptor) that then
- radio signal (signaling molecule) carries information inside
- station receives signal and broadcasts (transmission)
RTK adds “phosphate tag” to certain proteins which triggers responses within the cell
ligand-gated ion channel receptors
- contains a region that acts as a gate that opens and closes when receptor changes shape
- when signal molecule binds as ligand to receptor, the gate allows specific ions, such as Na+ or Ca2+ through a channel in receptor
intracellular receptors
- found in cytoplasm or nucleus of target cells
- small, hydrophobic chemical messengers can readily cross membrane and activate receptors
- ex. steroid and thyroid hormones in animals, NO (nitric oxide)
what is a ligand
signaling molecule that works like a messenger
- binds to specific receptors on cell surfaces and conveys information to elicit a response from the cell
ligand binding causes a __________ in receptor
shape change
- directly activates receptor, enabling it to interact with other molecules in or on cell
- initial transduction of signal
“first messenger” & “second messenger” in intracellular receptors
- “first messenger” is the extracellular signaling molecule (ligand) that binds to membrane receptor
- second messenger is a small, nonprotein that spreads throughout cell by diffusion (initiated by GPCRs and RTKs)
relays messages in a cell from a receptor to a target where an action within cell takes place
2 examples of second messengers
cyclic AMP (cAMP) & calcium ions (Ca2+)
cyclic AMP pathway (list the steps)
- ligand binds to GPCR = conformational change in receptor complex occurs
- activates a G protein that in return activates adenylyl cyclase - adenylyl cyclase breaks down AMP into cAMP
- cAMP activates protein kinase A, which phosphorylates various other proteins
what is a kinase
“cellular switch” that can turn on or off specific activities inside a cell
- key function is to transfer phosphate group from ATP to another molecule (phosphorylation)
an electron _______ potential energy when it shifts from a ______ electronegative atom towards a _______ electronegative one
loses
less
more
redox reactions that move electrons closer to electronegative O atoms _______ chemical energy that can be put to __________
release; work
NAD+ functions as an __________ agent during cellular respiration
oxidizing
(because it gets reduced)
if there is oxygen present then what happens to the pyruvate from glycolysis? what if there is no oxygen present?
- oxygen: continues along cell respiration
- no oxygen: goes to fermentation
goal of fermentation
regenerate NAD+ so that glycolysis can continue = so cell can continue to produce ATP
which part of cellular respiration starts to produce CO2?
pyruvate oxidation
(only 2 times makes CO2 is pyruvate oxidation and Krebs cycle, aka citric acid cycle)
how does anaerobic respiration use an ETC?
anaerobic respiration uses an ETC but does not use O2 as a final electron acceptor
3 points about the evolutionary significance of glycolysis
- early prokaryotes likely used glycolysis to produce ATP before oxygen accumulated in the atmosphere
- used in both cellular respiration & fermentation – most widespread metabolic pathway on Earth
- occurs in cytosol without requiring any membrane bound organelles of eukaryotic cells
“the versatility of catabolism”
- its role in carbs, proteins, fats
carbs: used in glycolysis
proteins: become intermediates of glycolysis and citric acid cycle
fats: glycerol converted into G3P, fatty acids are broken down by beta oxidation and yield acetyl coA, NADH, and FADH2
autotrophs & heterotrophs definition
autotrophs: “self feeders” that sustain themselves without eating anything derived from other organisms
heterotroph: obtain organic material from other organisms, consumers
the 2 stages of photosynthesis
1. light dependent reactions
- in thylakoid membranes
- release O2 as by-product
- reduce NAD+ to NADH
- generate ATP from ADP by photophosphorylation
2. Calvin Cycle, light independent reactions
- occurs in stroma
- makes sugar from CO2, using ATP and NADH generated during light reactions
what is unique about the cyclic electron flow compared to the linear electron flow?
cyclic electron flow uses photosystem I ONLY
- produced ATP, but not NADPH or oxygen
what are the products of linear electron flow and what are the products of cyclic electron flow during light reactions of photosynthesis?
linear: ATP and NADPH
cyclic: ATP
where are ATP synthase complexes located in plant cells?
thylakoid membrane and inner mitochondrial membrane
