Cell Biology Exam 4

what is cilia

-found in protozoa

- in respiratory system in the body it traps dust

ciliary escalator

decreased cilia activity as you age, makes you more prone to respiratory diseases

order of cytoskeleton components from thinnest to thickest

1. actin thinnest

2. intermediate filaments

3. microtubules thickest

what are actin filaments

- microfilaments made of long globular actin protein MONOMERS

- highly concentrated in cortex layer

what are intermediate filaments

- made of fibrous intermediate filament proteins

- form the nuclear lamina

- form ropes that have high tensile strength

what are microtubules

- hollow cylinders

- made of tubulin protein DIMERS

what are desmosomes

points of contact on the membrane that the cytoskeleton binds to which creates a network and then holds cells together to form tissue

general intermediate filament unit

2 alpha helices form a coiled coil

2 coiled coils form a dimer

two staggered antiparallel dimers form a tetramer

8 tetramers form an octamer = basic intermediate filament unit

what are the cytoplasmic intermediate filaments

1. keratin filaments - in epithelial cells, most diverse

2. vimentin and vimentin-related filaments - in connective tissue, muscle, glial cells

3. neurofilaments - in nerve cell axons

what are the nuclear intermediate filaments

nuclear lamins made of lamin protein present in all animal cells

what is laminin

different from the nuclear lamins proteins

laminin is a protein present in extracellular parts

what is epidermolysis

when the keratin filament gene is mutated -> intermediate filaments are affected -> skin blisters easily

what is plectin

protein that links the web of intermediate filaments to make them stable and stronger

what do plectin mutations cause

causes:

1. issues with muscle cells -> muscular dystrophy

2. issues with nerve cells -> neurodegeneration

3. epidermolysis

what is the nuclear lamins

- nuclear meshwork of intermediate filaments

- protects nuclear envelope from breaking down

- if nuclear lamins is phosphorylated then it becomes unstable and can be broken down

what is progeria

when there is a defect/mutation in the nuclear lamins

- causes impaired cell division and increased cell death

- person will age quicker since everything is sped up and DNA errors are not easily fixed

what are the distinct ends of the microtubule

positive end and negative end

- microtubules have dynamic instability so they're constantly growing and shrinking

- it primarily grows on the positive end

what does microtubule growth/shrinkage depend on

1. a supply of tubulin dimers in the cytoplasm

2. energy from GTP in the beta subunit

3. how quick GTPase activity at the beta subunit is

how does a microtubule form, and what is the structure of it

tubulin heterodimer has a POS beta and NEG alpha end

- subunits stack pos neg pos neg

- heterodimers are added to the plus BETA end

- 13 protofilaments/heterodimer stacks form a microtubule

alpha, beta, and gamma tubulin

alpha-beta tubulin heterodimer forms the microtubule

gamma tubulin forms a ring on the centrosome surface that allows the microtubule to grow out of the centrosome

- microtubules extend out of the centrosome with positive end facing out

what are capping proteins

located underneath membrane, bind to growing end of microtubule to stabilize it so it doesn't shrink

what allows microtubule to GROW

when Beta unit of dimer has GTP it has affinity for accepting more dimers

what causes microtubule to shrink

1. GTPase activity at Beta subunit hydrolyzes GTP into GDP

2. when Beta subunit has GDP bound it has lower affinity with other dimers

3. growth is not favored so microtubule shrinks

what is taxol

binds to POS beta end and stabilizes microtubule which stops them at a certain length

*stops dynamic instability

what is colchicine/colcemid

binds to tubulin dimers and stops them from being added to the microtubule

*stops dynamic instability

what is vinblastine/vincristine

binds to tubulin dimers and stops them from being added to microtubule

*stops dynamic instability

what is dynein

motor protein that walks and moves cargo towards the NEGATIVE end of microtubule

what is kinesin

motor protein that walks and moves cargo towards the POSITIVE end of microtubule

how do motor proteins work

- made up of a tail and two globular heads

- the tail grabs an organelle

- it has ATPase activity -> hydrolyzes ATP so the globular heads can walk along the microtubule to move the cargo it's attached to

what is the function/purpose of motor proteins

organizes the cell interior by positioning organelles in the cytoplasm

what is the configuration of microtubules in cilia and flagella

9+2 configuration

9 microtubule doublets in a circle with a pair of microtubule singlets in the middle

- nexin links the doublets

- dynein holds the doublets in a circle position

what is kartanger's syndrome

when the ciliary dynein is mutated it negatively affects cilia and flagella function

- can cause male infertility if sperm can't swim

- can cause respiratory infections in males and females

actin structure

has a positive and negative end

MONOMERS added to positive end for growth

what are cell components that are made up of actin

- microvilli

- contractile bundles

- pseudopodia

- contractile ring

what is myosin and what does it interact with

a protein involved in muscle contraction

actin-dependent movement depends on interaction with myosin and actin

how does actin form/polymerize

through treadmilling

1. ATP binds to actin monomer

2. monomer binds to positive end of growing actin

3. phosphate leaves the monomer

4. actin associated with ADP falls off at the negative end of the actin

what is phalloidin

binds and stabilizes actin filament to stop monomers from being added

what is cytochalasin

binds to actin filament and caps it at the positive end to prevent actin monomers from being added

what is latrunculin

binds to the free actin monomers to stop them from being added to growing actin polymer

what are thymosin and profiling and what do they do

naturally occurring proteins in the cytoplasm that bind to actin monomers and prevent polymerization

*regulates actin filament growth

what are formin and actin related proteins, and what do they do

naturally occurring proteins in the cytoplasm that promote actin polymerization

*regulates actin filament growth

what are filament-severing proteins

naturally occurring proteins in the cytoplasm that cuts the actin filament to make it shorter

*regulates actin filament growth

what are myosin motor proteins

naturally occurring proteins in the cytoplasm that interact with actin to drive contraction

what is the actin cortex

under the plasma membrane there is a cortex/meshwork of actin filaments

how do cells crawl

1. actin polymerizes at the plus end and a lamellipodium/pseudopod protrudes out

2. the pseudopod grabs the surface at focal contacts which have integrin protein

3. myosin and actin interact to contract at the back of the cell

4. cell moves forward

lamellipodia vs filopodia

both are actin projections

lamellipodia - branched projections for cell movement

filopodia - finger like projections that act as sensors

how do signals affect actin

a signal from a neurotransmitter can tell actin and myosin to contract

myosin molecule vs filament structure?

******??????

how does contraction occur

- myosin heads face left and right and tails are antiparallel

myosin pulls on actin filaments so they overlap

*NO change in actin or myosin filament length

structure of muscle cells

muscle cell is a hollow tube

the tube is stuffed with many long myofibril stacks

myofibril made up of actin and myosin filaments/myofilaments

sarcomere is the unit where contraction takes place between two z discs

what is a sarcomere

the section between 2 Z discs made up of the overlapping actin and myosin filaments

during contraction the Z disc moves like an accordion and the sarcomere length shortens

what molecule triggers muscle contraction

sudden rise in cytosolic Ca2+

specialized ER in myofibrils called the sarcoplasmic reticulum releases Ca2+

what is the mechanism that triggers muscle contraction to start

1. Ca2+ binds to C subunit of troponin complex

2. shape change pulls tropomyosin away from actin; tropomyosin doesn't let myosin interact with actin when it's bound to actin

3. allows myosin to bind to actin

4. contraction starts

what is different about early embryonic cells vs normal cells

early embryonic cells divide very quickly which doesn't allow enough time for them to grow before dividing -> daughter cells get tinier

normal cells grow before division to make cloned daughter cells

what is anaphase promoting complex

involved in controlling cycle during anaphase

where are each of the cell cycle check points

End of G1

End of G2

During Anaphase of M Phase

what is cdk and when is it activated

cdk triggers steps within the cell cycle

it is activated by cyclin at each of the three checkpoints

different cdks and cyclins for different stages of cell cycle

cyclic activation

cdks are cyclically activated so their concentration goes up and down in cycles based on which stage of the cell cycle is occuring

what are the types of cdks that exist and what stage are they for

G1 cdk - G1 phase

G1/S cdk - S phase

S cdk - S phase

G2 cdk - G2 phase

M cdk - M phase

what are the three ways cyclin concentrations are regulated

transcription: expressing the genes that produce cyclin

proteolysis: breaks down cyclin

APC: specifically breaks down M-cyclin by adding ubiquitin to it which sends it to proteosome

How does APC regulate cell cycle

APC causes Ubiquitylation on M-cyclin

this adds a protein tag which sends M-cyclin to the proteosome to be broken down -> M-cdk activity is stopped so cell can focus on anaphase and not rush into mitosis

What are the ways to regulate kinase activity which thus regulate cell cycle stages

1. regulating expression and destruction of cyclin

- use APC

- transcription

- through proteolysis

2. phosphorylating to block cyclin from binding and dephosphorylating cdk to activate it

3. inhibitory proteins clamp cdk and cyclin so they can't interact with things

what is cdc 25

an activating phosphatase that removes inhibitory phosphate from M-cdk to activate it

what is Wee1

kinase that adds the inhibitory phosphate to M-cdk to inactivate it

what happens when cdk is phosphorylated

phosphorylated cdk changes its conformation and then is blocked from binding with cyclin -> inactivated

what is p27

inhibitory protein that grabs onto an active cyclin-cdk complex and inactivates it

how does the cell fix a small problem that needs a quick pause

inactivate the cyclin-cdk complex for a quick pause

-> can do it through inhibitory protein p27

how does the cell fix a bigger problem that needs more time

cell will sit at G0 phase until problem is fixed

or the cell is never fixed and dies

what are terminally differentiated cells

highly differentiated cells will stop replication

ex. cornea cells

what is a mitogen

anything that promotes production of cyclins to start cell cycle

why do people with retinoblastoma have uncontrolled cell div

mutated Rb protein is always inactive, so transcription of cyclins and cell cycle proteins is never blocked

what does Rb do when its active vs inactive

active Rb protein - attaches to a transcription regulator and inactivates it -> blocks cell cycle

G1 cdk and G1/S cdk when active phosphorylate Rb which pulls it away from transcription regulator

inactive Rb protein - it's pulled away from transcription regulator which activates it and allows transcription of cell cycle proteins

what is the mechanism/events that occur after DNA damage

1. DNA damaged by X-rays or something

2. causes protein kinases to be activated and phosphorylate p53

3. p53 activated and binds to p21 regulatory gene

4. p21 gene is transcribed

5. p21 inhibitory protein clamps G1/S cdk and S cdk and inactivates

6. cell division is halted at the G1 PHASE

what happens if p21 gene is mutated

if p21 gene is not transcribed, then p21 inhibitory protein can't be active

cell cycle will continue but with damaged DNA, which can cause cancer

what is cdc 6

prevents progression from G1 to S phase

binds to ORC (origin recognition complex) and attracts helicase to the strands

eventually cdc6 dissociates and is replaced by helicase

how does the cell progress from G1 to S phase

1. cdc 6 dissociates from ORC after being phosphorylated by S cdk and helicase binds

2. S-cdk adds phosphate to helicase to activate it

3. helicase separates the strands and DNA replication starts

4. **cdc 6 gets degraded so that replication only happens once during S phase

what does the cell do if replication is incomplete

if there's errors in DNA replication the cell will stop at G2

- make sure M-cdk is not activated by making sure cdc 25 is inactivated

cdc 25 phosphatase activates M-cdk by dephosphorylating it

what does cohesin do

cohesin forms rings along the length of the chromosome to keep sister chromatids together

what happens if cell lacks cohesins

chromosomes can't stick together so an unequal amount of chromosomes are sent to either cell

what are condensins

form rings around chromosomes to help condense them

what is the contractile ring

made out of actin and myosin and pinches cell into two daughter cells

interpolar microtubules direct the formation of the ring

what happens during interphase

1. cell size increases

2. DNA replicated

3. centrosome duplicated during S phase because of G1/S cyclin-cdk

what happens during prophase

1. condensins make chromosomes visible

2. mitotic spindle starts to form bc of dynamic instability

3. centrosomes start moving to opposite poles

what happens during prometaphase

1. M-cdk phosphorylates lamin proteins so nuclear envelope breaks down

2. kinetochore microtubules attach to kinetochores of each sis chromatid

what happens during metaphase

1. chromosomes align at equator of spindle due to dynamic instability

what happens during anaphase

anaphase a:

- kinetochore microtubules shrink

anaphase b:

- centrosomes move apart

1. cohesins broken down

2. sister chromatids pulled apart

what happens during telophase

1. sis chromatids now considered chromosomes

2. chromosomes arrive at each spindle pole

3. nuclear envelope reassembles when nuclear lamins proteins are dephosphorylated

4. contractile ring assembly begins

what happens during cytokinesis

1. contractile ring pinches

2. cell splits non specifically into 2 daughter cells

what are aster microtubules

extend from centrosome to connect spindle pole to plasma membrane

what are interpolar microtubule

microtubules that bind each other from opposite ends of the cell

kinetochore microtubules

attach to kinetochores of each sister chromatid

why are cohesins broken down

so that sister chromatids can separate during anaphase

how are cohesins broken down

1. active APC adds ubiquitin to securin

2. securin unbinds from separase

3. securin is proteolysed, while separase is released and thus activated

4. active separase cleaves cohesins during/allowing anaphase

what is anaphase a

kinetochore microtubules shorten which causes forces to move the chromosomes toward their spindle pole

what is anaphse b

interpolar microtubules generate sliding force which pushes the centrosomes at either pole apart

what happens if a microtubule isn't attached to a chromatid

in prometaphase if not all chromatids are attached to microtubule, then separation is stopped

1. unattached chromosome sends stop signal

2. signal blocks activation of APC

3. securin not degraded

4. separase not released

5. cohesins not degraded

6. sis chromatids stay glued together

what does spindle assembly checkpoint do

stops cycle from proceeding to anaphase if all chromosomes didn't attach to microtubule during prometaphase

what is the mechanism of nuclear envelope reforming

during telophase nuclear envelope reforms when proteins are dephosphorylated

nuclear envelope vesicles and pore proteins fuse when dephosphorylated

how do mitochondria and chloroplasts assort into daughters

they divide during cell growth and are separated unevenly but there's so many that it's enough for each daughter

how is ER assorted into daughter cells

ER fragments when nuclear envelope fragments, and is then rearranged and taken into daughter cells by microtubules