cell bio final key terms

cytoskeleton

• highly dynamic system of polymers responsible for:

  • cell movement

  • chr segregation

  • cytokinesis

  • structural support

  • vesicle transport

  • cell shape + more

• 3 main fams of protein filaments:

  • actin filaments

  • microtubules

  • intermediate filaments

cdc42

• monomeric GTPase

• triggers actin polymerization and bundling to form filopodia or micro-spikes

actin filaments

• fam of protein filaments part of cytoskeleton

• ASYMMETRICAL, has polarity (+ and - end)

• composed of actin subunits (assemble head-to-tail to create polar filaments)

  • assembled by formin

  • ARP complexes promote new filaments to form off og one

• accessory proteins can crosslink + bundle the filaments → large-scale rigid structures

  • contractile bundles, gel-like networks, dendritic networks, tight parallel bundles

• nucleation= rate limiting step in this formation

• binds ATP, two forms

  • T-form= ATP bound

  • D-form= ADP bound

• dynamic nature due to treadmilling

actin

• flexible subunits that make up actin filaments

• assemble head-to-tail to create polar filaments

• slow growing minus end, fast growing plus end

• assembled by formin

formin

• assembles actin filaments

• act as actin nucleators-→ initiate the formation of new filaments + facilitate elongation of existing ones

ARP

• generates mesh-like network that treadmills

• nucleates and elongates filaments, pushing membrane forward

• on actin filaments?

  • helps form branches off og filaments → mesh

    • helps nucleate new actin filaments @angles to each other

nucelation

• rate limiting step in formation of actin filament

• for new actin filament to form, subunits much assemble into an initial aggregate (nucleus)

• cells can catalyze filaments nucleation @ specific sites

treadmilling

• filaments add subunits at plus end while simultaneously losing filaments from minus end

• occurs in actin filaments and microtubules

cofilin

• binds to ADP-containing actin filaments and disassembles these older filaments

profilin

• aids in the assembly of (actin) microfilaments at the leading edge

CapZ

• caps (actin) filaments at a steady pace

• helps stabilize/regulate these actin filaments

cell migration

• depends on the actin-rich cortex beneath the plasma membrane + induce 3 steps:

  • protrusion

  • attachment

  • locomotion

Rho

• monomeric GTPase, triggers actin polymerization + bundling into stress fibers

Rac

• monomeric GTPase, tiggers actin polymerization @ cell periphery, leading to sheet-like lamellipodial extensions (helps w/ cell movement and migration)

microtubules

• family of cytoskeleton protein filament

• composed of 13 protofilaments

• ASYMMETRICAL, has polarity (+ and - end)

• structurally more complex than actin

• highly dynamic, w/ diverse roles in cell

• GTP bound to α subunit= trapped

• GTP bound to β subunit can be converted to GDP

• α + β bond vertically (α + α, β + β bond horizontally)

• MTs are hollow tubes made up of 13 protofilaments

• Mts grow + shrink primarily @ plus end

• number of proteins help assemble/disassemble

  • y-TURC

  • MAPs

  • katanin

• MT undergo dynamic instability

• emanate from the MTOC (centrosome)

• 3 types:

  • kinetochore MT

  • interpolar MT

  • astral MT

dynamic instability

• astral MT undergo this, they grow or shrink rapidly

  • catastrophe= growing → shrinking

  • rescue= shrinking → growing

• T-form grows, D-form shrinks

catastrophe

• dynamic instability category

• transition from growth to shrinkage

rescue

• dynamic instability category

• transition from shrinkage to growth

katanin

• protein interacting w/ MT, helps w/ disassembly

• severs MT @ centrosome

MAPs

• protein interacting w/ MT

• stabilizes microtubules by binding along sides as it grows

y-TURC

• protein interacting w/ MT, helps w/ assembly

• nucleates assembly and remains associated w/ the minus end

• found at centrosomes

tubulin

• subunits that compose microtubules

• y-tubulin found at MTOC + helps w/ nucleation + establishment of MT polarity

centrosome

• microtubule organizing center

• MT emanate from these

kinesin

• motor protein that walks along MT towards plus end (except kinesin 14)

• requires ATP

• kinesin 5, kinesin 4 + 10, kinesin 14,

dynein

• motor protein that walks along astral MT towards minus end

• connected to astral mt and cell membrane, helps pulls apart centrosomes + elongate mitotic spindle during anaphase B

• requires ATP

intermediate filaments

• family of cytoskeleton protein filament

• prominent in cells subjected to mechanical stress

• depend on lateral bundling and twisting of coiled-coils

• DON’T HAVE POLARITY= SYMMETRICAL

  • motor proteins don’t rlly associate w/ it

four phases of eukaryotic cell cycle

• G1

• S

• G2

• M

G1 phase

• first phase cell cycle

• lots of cell growth

S phase

• second phase cel cycle

• DNA and centrosome replication occur

G2 phase

• third phase cell cycle

• thought that cell growth occurs, prep for division

M phase

• last phase cell cycle

• cell division occurs → two daughter cells produced

• stages within:

  • prophase

  • prometaphase

  • metaphase

  • anaphase

  • telophase

  • cytokinesis

interphase

• G1, S, G2

prophase

• part of mitosis

• replicated DNa molecules begin to condense into rod-like sister chromatids

• centrosomes move to opp poles of the cell

prometaphase

• part of mitosis

• nuclear envelope breaks down

• spindle Mt attach to sister chromatids via kinetochore

metaphase

• part of mitosis

• sister chromatids aligned @ spindle equator

  • kinesin 5 helps w/ this

anaphase

• part of mitosis

• sister chromatids are separated and segregated to opposing cell poles

• spindle assembly checkpoint= important checkpoint prior to this to ensure all sister chr attached correctly to MT, checks tension

telophase

• part of mitosis

• mitotic spindle begins to disassemble

• nuclear envelope reforms

cytokinesis

• part of mitosis

• cell is cleaved into two daughter cells

  • contractile ring!

G0 phase

• “quiescent state” where cell is not dividing nor preparing to do so

• can be temporary or permanent

• if conditions not suitable cell can go into this

  • if they are, cells can exit and advance to point of commitment called restriction point

G1/S phase transition

• important regulatory transition of cell cycle

• commitment to either enter cell cycle and proceed to S-phase

  • is environment favorable?

G2/M phase transition

• important regulatory transition of cell cycle

• commitment to enter mitosis

  • is all DNA replicated?

  • is environment favorable?

metaphase-to-anaphase transition

• important regulatory transition of cell cycle

• commitment to sister chromatid separation and completion of mitosis

  • are all chr attached correctly to spindle?

cyclins

• regulates CDK activity which is what controls cell cycle progression

• undergo cycle of synthesis and degradation after each cycle

  • [CDK] constant, [cyclins] changes

• 4 classes

  1. G1/S-cyclins

  2. S-cyclins

  3. M-cyclins

  4. G1-cyclins (not in all cells)

what is cell cycle control led by?

• CDK !!!!!!!!!!!!!! (cyclin-dependent kinases)

  • which are activated at dif times by dif cyclins and phosphorylated by CAK (cdk-activating kinases)

cdks

• cyclin dependant kinases

• control cell cycle progression

• remain constant through cell cycle but dif cdks activated at dif times based off which cyclins are present

• to be active needs to bind specific cyclin and be phosphorylated by CAK (cdk-activating kinase)

• activity can be suppressed by:

  • inhibitory phosphorylation (ex: Wee1)

  • binding cdk inhibitory proteins (CKI)

CAK

• cdk activating kinases

• fully activates cyclin-cdk complex via phosphorylation

CKI

• cdk inhibitory kinases

• inactives cyclin-cdk complex in one of two ways:

  • adds another phosphate group (ex: wee1)

  • physically binds to cyclin-cdk complex

APC/C

• anaphase promoting complex or cyclosome

• ubiquitin ligase

  • tags securin for degradation → separase free to cleave cohesin bt sister chromatids

• triggers metaphase-anaphase transition

• activated by M-CDK and cdc20

extracellular signals 3 major classes:

1. mitogens

2. growth factors

3. survival factors

mitogens

• extracellular signal class

• stimulate cell division primarily by triggering a wave of G1-Cdk + G1/S-Cdk activity

  • cell division

growth factors

• extracellular signal class

• stimulate cell growth by promoting the synthesis of proteins and by inhibiting their degradation

  • cell growth

survival factors

• extracellular signal class

• promote cell survival by suppressing apoptosis

  • cell growth + division!

dna damage response

• cell division blocked by this

• happens to prevent cell from dividing when dna damaged

• p53 (tumor suppressor) phosphorylated to be active

  • goes on to to promoted transcription of inhibitory proteins (p21) to prevent cdk-cyclin active complexes

    • cell cycle can’t progress

chromosome

• single DNA molecule

chromatin

• DNA w/ associate proteins (histones)

• for interphase nucleus it appears as like a thread, 30nm thick

chromatid

• identical copy of a DNA molecule

histone

• most basic level of chromosome structure, help package DNA

• make up nucleosomes → allows DNA to wrap around itself

• octameric, H2A, H2B, H3, H4 (2 of each make it up)

• subject to post-translational modifications

  • can make DNA more or less tightly packed

nucleosome

• histone and associated DNA

• allows DNA to wrap around itself and pack tightly (important when dividing)

• “beads on a string”

heterochromatin

• tightly condensed, less accessible for transcription

• gene poor

• histone methylation

euchromatin

• gene rich, active transcription, loosely packaged

• histone acetylation

• “eu can access it easier”

cohesin

• scaffold protein

• composed of SMC1 + SMC3

• local associations → holds sister chromatids together

• destroyed by separase during anaphase A

• coiled-coil protein w/ ATPases at either end → hinge region

condensin

• scaffold protein

• composed of SMC2 + SMC4

• longer range DNA interactions → loops, plays role in stabilizing these

• coiled-coil protein w/ ATPases at either end → hinge region

topologically associated domains (TADS)

• longe-range interactions of DNA

• condensins help w/ this

• mutations in this can result in syndactyly

centriole

• pair of these makes up the centrosome

• replicate by a semiconservative process

• each mother centriole makes a daughter centriole at a right angle (perpendicular)

• mother centriole radiates astral MT

aster

• during prophase the MTOC nucleates a radial array of MT

• these two move to opp sides of nucleus to initiate formation of two poles of the mitotic spindle

mitotic spindle assembles w/ help from:

• MT associated proteins (MAPS)- generate MT instability

• motor proteins- govern spindle assembly

• kinetochores- attach sister chromatids to the spindle

• once assembled, MT flux helps keep the system dynamic

centromere

• constricted region of chr where sister chromatids are joined (by cohesion)

• point of attachment for the kinetochore

kinetochore

• complex protein structure attached to sister chromatids at the centromere

• attaches sister chromatids to kinetochore MT

• outer kinetochore to kinetochore MT, inner kinetochore to sister chromatid

• NDC80- on outer kinetochore

• aurora B kinase- on inner kinetochore, phosphorylates NDC80 if improper tension (meaning sister chromatids improperly attached, makes attachment unstable so cell can try again to get proper biorientation)

kinetochore mt

• - end at centrosome and + end attaches to sister chromatids via kinetochore to the spindle pole

• undergoes treadmilling

interpolar mt

• hold the two halves of the spindle together, overlap

• majority not anchored at the centrosome

• undergoes treadmilling

• associated w/ kinesins 4 + 10, 5, 14

astral mt

• radiate out and help orient and stabilize the spindle using the cell membrane

• undergo dynamic instability

kinesin 4 + 10

• plus end directed motor protein

• associated w/ interpolar MT

• metaphase:

  • bind chr arms and walk towards plus end of interpolar MT, pushing the sister chromatid toward metaphase plate

  • facilitate alignment of chr at spindle equator

kinesin-5

• plus end directed motor protein

• associated w/ interpolar MT

• metaphase

  • bundles interpolar MT in a parallel array and drives spindle pole separation by sliding MT that are oriented in opp directions

• increases distance bt centrosomes

kinesin-14

• minus end directed motor protein

• metaphase

  • interacts w/ interpolar MT and decreases distance bt centrosomes

• helps create tension and overall structure of the mitotic spindle

Klp10A

• kinesin known to depolymerize MT

• anchors to spindle pole matrix and binds minus ends of MT

• helps w/ MT flux?

dynein

• minus end directed motor protein

• attached to astral MT and cell membrane

• regulates length of astral MT?

biorientation

• the stable conformation of sister chromatids aligned properly at the metaphase plate

• kinetochore from opp poles each attached to just 1 sister chromatids

• generates tension across the MT binding sites which triggers increase in MT binding affinity

  • if improper tension, aurora B kinase phosphorylates NDC80 which weakens the affinity so MT can disconnect and try again

    • b/c phosphorylated Ndc80 has decreased affinity for MT plus ends

mt flux

• the movement of spindle MT towards the spindle poles + the disassembly of the MT minus ends

• helps keep the system dynamic

• MT - ends associated w/ y-TURC in centrosome + katanin severs the MT and KLP10A further helps w/ depolymerization @ - end

  • causes shrinkage of MT, like during anaphase A

• can contribute to treadmilling?

how does cell identify location of chromosomes?

• use of “ran-gradient”

• RanGEF (Rcc1) bound to chromatin even when nuclear envelope breaks down

• Ran-GTP in high concentration near chr

• importins bind to and inhibit TPX2 (protein promoting MT growth)

  • Ran-GTP binds to importin near chr, freeing TPX2 which promotes growth/stabilization of MT near chr

spindle assembly checkpoint

• metaphase→ anaphase transition, ensures all kinetochores are properly attached

• mad2 can inhibit APC/C if improper/unattached kinetochore present

  • does this by binding cdc20 which APC/C needs to be active

anaphase A

• sister chromatids separate to opposite spindle poles

  • kinetochore poleward pull at plus end

  • MT flux at minus end

  • polar ejection forces

• APC/C activated by cdc20 by M-cdk

• APC/C tags securin for destruction (ubiquitylates) which frees separase

• free separase can go cut cohesin, separating the sister chromatids

anaphase B

• separation of the spindle poles

• motor-protein-dependent separation of interpolar and astral MT

• plus end directed, double headed motors like kinesin 5 crosslink MT and help push the interpolar MT apart

• minus-end directed dynein pulls the centrosome apart by pulling on the two sets of astral MT

  • one end attached to cell membrane, the other to an astral MT

• the push and pull of motor proteins drives the spindle poles apart

contractile ring

• composed of actin + myosin (motor protein)

• RhoA GTPase plays key role

• centralspindlin binds + ends of interpolar MT, high concentration @ equator

  • Rho-GEF recruited to these ends

  • Rho-GEF activates RhoA-GTP

    • which then activates ROCK

      • ROCK stimulates myosin + actin formation of contractile ring

apoptosis

• programmed/controlled cell death

  • destroyed from within and then eaten by other cells

    • send dif signals to other cells to do this

      • ex: phosphatidylserine on outside of cell (its not supposed to be, if it is= bad)

• intrinsic and extrinsic pathway

  • intrinsic: mitochondria, cyt c, APAF1, apoptosome

  • extrinsic: Fas signal protein, cell surface death receptors, death inducing signaling complex (DISC)

• driven by a proteolytic cascade

  • uses caspases (initiator and executioner)

• most cells require continuous signaling from other cells to avoid apoptosis

• IAPs= inhibitors of apoptosis, help regulate

necrosis

• trauma response cell death

• they swell and burst, spilling their contents over neighboring cells and eliciting an immune response

caspase

• proteolytic enzymes, drive apoptosis

• initially synthesized as inactive precursors, but once initiator gets apoptotic signal, cleaves itself, now active can cause executioner to cleave itself, now also active can degrade shit

• two main types:

  • initiator

  • executioner

• irreversible + amplifying

proteolytic cascade

• ex: apoptosis

• caspases are activated by this

• amplifying and irreversible

cytochrome c

• apoptotic stimulus leads to this being released from mitochondria during the intrinsic apoptotic pathway

• binds APAF1 in cytostome and forms apoptosome

  • this then activates initiator caspases which activate executioner caspases which kill the cell (by cutting everything up)

filament assembly rate limiting step?

• nucleation= initial formation of a stable small aggregate of subunits

cell junctions

• specialized structures that link cells to each other or to the extracellular matrix

• enables communication and coordination bt cells

cell junctions we need to know (name + function + associated proteins/cytoskeletal element):

• adherens junctions= cadherins, actin, links cytoskeletal elements that are important for coordinating movements/contractions

• desmosome= cadherins, intermediate filaments, links elements of cytoskeleton important for providing strength to cell

• hemidesmosome= integrin, intermediate filaments, anchors cell to ECM/basal lamina

• tight junction= claudin and occludin, helps a sheet of cells form a semi-permeable barrier

• gap junction= connexin and innexin, allows cells to pass macromolecules bt each other

• actin-linked cell matrix junction= integrins, actin, anchors cell to ECM/basal lamina

tight junction

• type of cell junction

• claudin and occludin

• actin?

• helps a sheet of cells form a semi-permeable barrier

• “fences”

adherens junctions

• type of cell junction

• cadherins

• actin

• links cytoskeletal elements that are important for coordinating movements/contractions

desmosome

• type of cell junction

• cadherins

• intermediate filaments

• links elements of cytoskeleton important for providing strength to cell

• present in tissues subjected to high lvls of stress (heart muscle, skin)

gap junction

• type of cell junction

• connexin and innexin

• allows cells to pass macromolecules bt each other

cadherins

• transmembrane glycoproteins that mediate CA2+ dependent cell-cell adhesion

• protrude from opp cell membranes binding each other

• bind w/ relatively low affinity, strong attachment results from the formation of many weak bons in parallel

• associated w/ desmosomes (w/ IFs) and adherens junctions (w/ actin)

• mediate highly selective recognition

adhesion belt

• epithelial cells often form this

• coordinated contraction of this network folds epithelial cells into tubes, vesicles, and other structures

• type of adherens junction?

extracellular matrix

• network of proteins and other macromolecules which surrounds and supports cells in tissues and organs

• 3 major classes of macromolecules:

  • glycosaminoglycans (GAGs)

  • collagen and other fibrous proteins

  • glycoproteins (N-linked)

glycosaminoglycans

• major class macromolecule in ECM

• w/ proteoglycans usually form gel-like “ground substance” for cells

  • helps resist compressive forces

  • permits rapid diffusion of nutrients, metabolites and hormones

• hyaluronic acid= simplest GAG

collagen

• major class macromolecule in ECM

• strengthens and helps organize the matrix while other fibrous proteins like elastin give resilience

• major proteins of the ECM

• major component of skin + bone

• organized in collagen fibrils