exam 4 Flashcards
What is the four phases of the eukaryotic cell cycle
Gap phase 1, S phase, Gap phase 2, M phase
what is the purpose of G1 and G2 phases
they separate S and M phases
can delay progress through G1 and go to G0 if conditions are not favorable
what is the purpose of S phase
DNA synthesis and chromosome duplication (10-12 hours in a mammalian cell)
the centrosome also gets replicated
what is the purpose of M phase
Mitosis (nuclear division) and cytokinesis (cytoplasmic division)
What does the cell cycle control depend on
cyclically activated cyclin-dependent protein kinases (CDKs)
when does each CDK usually get activated during the cell cycle
(G1/s cyclin, S-cyclin, and M-cyclin)
G1/S cyclin– triggers midway through G1 and helps the transition from G1 to S
S-cyclin– triggers start of S phase and triggers DNA replication
M-cyclin– triggers entry into M phase at G2/M transition (end of G2 phase)
How can CDK activity be suppressed
Inhibitory phosphorylation and CDK inhibitor proteins– calls over p27 cyclin CDK complex to inactive or uses Wee1 kinase, or makes a t-loop
What does positive feedback generate
the switch-like behavior of cell-cycle transitions, as seen with CDC 25 which can be partially activated or reversed by a phosphatase
What promotes the metaphase to anaphase transition
APC/C aka the anaphase-promoting complex/cyclosome which gets phosphorylated
does so by adding a polyubiquitin onto the m-cyclin
when does s-CDK activation occur
In late G1, the DNA helicases get activated by S-CDK which then starts the replication
What is cohesion and what does it do
it holds the sister chromatids together and it has four subunits
SMC 1 and 3, and SCC 1 and 3
what do SMCs and SCCs do
SMC: the structural maintance of chromosomes
SCC: subunits that connect the ATPase head domains
mitosis has how many phases
six: prophase, prometaphase, metaphase, anaphase, telophase, and cytokinesis
what occurs in prophase
two centrosomes move apart, sister chromatids are linked by cohesion, and chromosomes are condensed
what occurs in prometaphase
the nuclear envelope disappears, sister chromatids are attached to the mitotic spindle via their kinetochores and undergo active movement.
what occurs in metaphase
sister chromatids are aligned at the equator, and centrosomes at the pole
what occurs in anaphase
the sister chromatids are pulled by the spindle to the opposite poles,
kinetochore microtubules get shorter and spindle poles move apart.
what occurs in telophase
the nuclear envelope reassembles and chromosomes are packaged into separate nuclei,
the spindle disassembles and the contractile ring starts to contract for the division of the cytoplasm.
what occurs in cytokinesis
the cytoplasms is divided into two by a contractile ring of actin and myosin
this pinches the cell into two daughter nuclei.
What does condensin do?
it helps configure duplicated chromosomes for separation
it makes a DNA Hinge that extends ATP-dependent motor activity and the DNA loop using the ATPase domains
What is the mitotic spindles made of
microtubules, either astral, kinetochore, or interpolar
What do astral microtubules do
they contact the cell cortex (dynein), and it positions the spindles and pulls the spindle pole apart.
what do Kinetochore microtubules do
they pull the chromatids by shortening of the spindles at the plus end, and they connect they spindle poles with kinetochores of sister chromatids
what do interpolar microtubules (non- kinetocore) do?
they interdigitate (interlock) and push the two spindle poles apart, they also interact with kinesin 5, 14, 4/10, and dynein.
which direction do dyneins/ kinesins move on interpolar microtubules
dynein to minus end and pull poles apart
kinesins move to the plus end
-4 and 10 move to the plus end and bring sister chromatid to the equator
-5 and 14 push the simdle poles apart during movement
are there many copies of kinetochores in the centromere
no, there is typically one kinetochore in a centromere to ensure proper chromosome segregation, (monocentric)
how does this connection (the microtubule being attached to the kinetochore by interactions with the Ndc80 complex on plus end of a microtubule) allow the kinetochore microtubules to become shorter and shorter?
the plus end alternates between growth (polymerization) and shrinkage (depolymerization). This process is crucial for chromosome movement during mitosis.
what triggers the sister-chromatid separation and the completion of mitosis
APC/C– it gets activated by Cdc20 and triggers the destruction of securin via ubiquitination (which normally holds separase in an inactive state)
what allows for a new trial for attachment to a kinetochore in mitosis
unattached kintechore blocks the activation of Cdc20/apc/c to allow a new trial for attachment
How do actin and myosin II in the contractile ring guide the process of cytokinesis
actin “spirals” the pinching of the two molecules separating the two
why arent actin filaments totally remobilized during cytokinesis
- they need to be present in one spot to generate tension
- it would cost alot of energy to completely mobilize them
- it ensure proper directionality of the segregation of daughter cells
what causes the local activation of RhoA which triggers the assembly and contraction of the contractile ring
GEF in the cortex of the division site active RhoA via a GTP.
can either lead to formin making actin filaments, or rho-associated kinases
who acts upstream of RhoA
guanine exchange factors (GEF) and GTPase activating proteins
how many divisions occur in meiosis to a diploid nucleus
two cell division after one round of DNA replication
why are chromatids still linked by cohesins at the centromere but not by the arms at the end of meiosis I
it ensure the proper segregation of homologous chromosomes while maintaining sister chromatid cohesion
why do two kinetochores from each chromatid get fused to one and attached to the spindle at the end of meiosis I .
it ensures proper segregation as it supports the monopolar attachments in meiosis I and the transition to bipolar attachment in meiosis II
what do mitogens do in regards to cell division and cell growth
they stimulate G1/S-CDK and S-Cdk activities (trigger ras which triggers MAP kinase) which in the long run causes G1-cdk to phosphorylate Rb leading to DNA synthesis
how are immediate early genes and delayed response genes defined
they are defined based on their timing and activation of activation in response to extracellular stimuli
Immediate: first responders to stimuli
delayed response genes: downstream and do more specific responses
is P53 a tumor-promoting protein or tumor-suppressing protein
tumor suppressor protein, it gets phosphorylated when DNA damage occurs which activates it, it then deactivates G1/S-cdk and s-cdk complexes to stop gene expression.
what are the two distinct forms of cell death
- programmed cell death or apoptosis: cells shrink and condense and it causes the cytoskeleton
- cell necrosis: cells swell and burst spilling their neighbors to elicit an inflammatory response or causing additional infections (bad)
why do we do apoptosis
to eliminate unwanted cells
– get rid of infected cells
– get rid of DNA damage
– help sculpt hands and feed during embryonic development
what does apoptosis depend on
an extrinsic or intrinsic intracellular signal (cascade) that is mediated by caspases (makes a dimer and gets trans cleaved)
what does initiator caspases do
cleave executioner cases, activating them
what do executioner caspases cleave
- nuclear lamins
- a protein that keeps DNA degrading endonuclease out of active state (therefore activating it)
- cytoskeletal components
- cell-cell adhesion proteins
What does DNA fragmentation lead to in apoptosis
- Endonuclease CAD is activated executioner caspase
- activated CAD then cuts the chromosomal DNA in the linker regions between nucleosomes, leading to a ladder pattern
why do we see a ladder pattern when we run a gel after CAD cuts chromosomal DNA in the linker regions
it cuts randomly at these sites so there is several different lengths
what are the key components of cell-surface death receptor pathways (EXTRINSIC pathway of apoptosis via INITIATOR CASPASE)
a fas ligand activates a fas death receptor
a FADD death adaptor protein gets activated and actives caspase-8 and makes copies of it and then dimerizes
what does the dimerization of caspase-8 lead too
apoptosis of the cell via the triggering of executioner caspases 3 and 7
what are the key components of the INTRINSIC pathways of cell death
the activation of Apasf 1 by the interaction of cytochrome C, which then causes several apaf1 to come together and recruit Caspase-9
what does the recruitment of Caspase-9 do
it leads to the dimerization of caspase-9 which then cleaves and activates executioner caspases leading to apoptosis
caspase-8 vs caspase-9
caspase-8: extrinsic, activated by death receptor signals,
caspase-9 intrinsic, activated by mitochondrial cytochrome C
What are the Bcl2 proteins and what are BH 1-4 domains
Bcl2 proteins are the critical controllers of the intrinsic pathway
the domains get bound by the proteins
which BH protein is anti-apoptotic family protein
all of them
which BH protein is a pro-apoptotic Bcl2 family effector
BH 1-3
which BH protein is pro-apoptotic BH3- only proteins
BH3 – the only domain that is shared by all Bcl2 domains
what do pro-apoptotic Bcl2 family effectors induce
MOMP, anti-apoptotic Bcl2 family proteins block it.
given that XIAP can inhibit caspase-9 which doesn’t let Caspases 3 and 7 operate, how does intrinsic cell death still occur
MOMP can directly activate cytochrome c and also releases two anti-IAP (anti- inhibitor or apoptosis) proteins (Omi and Smac) which inhibit XAIP
this leads the activation of caspase-9, 3, and 7 leading to apoptosis
Why is apoptosis necessary in neurons
we make too many of them, so it is important to get rid of them, but some nerve cells receive insufficient amounts of survival factors and undergo apoptosis
how do survival factors regulate extracellular apoptosis
usually inhibits it, either by stimulating the production of more anti-apoptotic Bcl2 proteins,
or inhibiting BH3 (pro-apoptotic protein: BAD) via the creation of active ATK kinase which phosphorylates Bad
what do malignant tumors typically give rise too
metastasis (before malignant were benign)
Benign tumor vs malignant tumor
benign: remains inside the basal lamina (boundary)
malignant (carcinoma): develops from a benign tumor and destroys the integrity of the tissue (leaves barrier)
how can we tell that it take more than one mutation for cancer to occur
it would have to occur equally at all ages for it to be one mutation, but cancer is more prominent later in life.
how is cancer a microevolutionary process
takes a progressive random accumulation of a single lineage of cells and spontaneous mutations occur at 10^-6
additionally, the cancer cell must be naturally selected within the tissue and if traveling in a foreign environment
what helps cancer cells outcompete non-cancer cells
they (may) harbor stem cells that allow them to divide indefinitely (transit amplifying cells)
when it divides and differentiates a new stem cell regenerates
What does the foci formation in cancer cells demonstrate
cancer cells have altered control growth and homeostasis (not controlled by contact dependence)
which cells do cancer cells have similar metabolisms to
a growing embryo cell or a proliferative tissue (they consume a lot more energy) known as the Warburg effect
most of the energy consumption is for lactate production
do cancer cells influence the environment they are in
Yes! They influence the microenvironments of surrounding areas by outcompeting neighboring cells via communication and competition
Qualities of oncogenes
mutated forms of proto-oncogenes, dominate (only need one copy), a gain of function (overactive)
qualities of tumor suppressor genes
loss of function functions, recessive (need both alleles) (underactive)
how can genes become overactice
- deleted of a point mutation in a coding sequence
- regulatory mutation
- gene amplification
- chromosome rearagnement
what can a cancer development do to a EGF (extracellular epidermal growth factor)
cause it to be active even in the absence of the of the growth factor
what is the genetic aspect to hereditary retinoblastoma (tumors in eye)
when you inherit one defective Rb gene, so your cancer likelihood is higher, but it is a loss of function, recessive mutation. so you still have to loose the other active gene..
what is the function of Rb gene in cell cycle
it is a tumor suppressor that prevents the cell from going from the G1phase to the S phase (stops uncontrolled cell division)
what are the three major cellular pathways that contribute to tumorigensis
Rb, Ras, p53
what does a Rb mutation do
it is downstream of Ras and is involved in cell cycle reentry.
what does a ras mutation do
upstream and is a signaling cascade that derives cell growth, usually getting mutated via a gain of function mutation
rare in benign tumors, but common in relatively large tumors
what does a p53 mutation do
it regulates tolerance and stress to DNA damage, farthest downstream and usually is the last line of cancer defense
rare in bengin tumors but common in carcinomas
what does a APC mutation do
usually detected in an early benign tumor and farthest upstream
What are important factors to take into place when populations move in regards to cancer
diet, air quality, lifestyle, environment, government regulation, etc
what is a PARP inhibitor
it kills cancer cells that have defects in Brca1 or Brca2 genes because a tumor cell loses a DNA repair pathway
which DNA repair pathway does parp inhibitor inhibit and which does it leave alone
it inhibits repair pathway 1 which uses PolyADP ribose polymerase (PARP) to repair single stranded breaks
repair pathway 2 is left alone which is recombination-depended process that uses Brca1 and Brca2 (which doesn’t work in cancer cells already)
can small molecules and translocations affect oncogenic proteins
yes, it is able to inhibit specific oncogenic proteins, usually done so my a translocation
like the Alb (chromosome 9) gene and the Bcr gene (chromosome 22)
is the substituation of the Bcr fragment (chromosome 22) onto Abl fragment (chromosome 9) a proto-oncogene or tumor suppressor gene why?
it makes it hyper-reactive, or gain a function, therefore a proto-oncogene
what are the effects of blocking a kinase with GLEEVEC that is infected with CML (bone marrow cancer and effects white blood cells)
it stops the single on a oncogenic kinase for cell proliferation which prevents leukemia
however, it can attack all kinase activity and you still need some activity, and it can attack other types of kinases.
what are other ways to cure CML
genetic changes like making. a gene knockout in the promoter and putting in a new, less active one (but still active)
what is a innate immune response
a rapid response and often the first line of defense, but not super effective
how is the innate immune response triggered
recognition of the pathogen-associated molecular patterns (PAMP) by the pattern recognition receptors (PRR)
what is the adaptive immune response
a slower response that involves two classes of white blood cells known as lymphocytes
what do B lymphocytes do
secrete antibodies
what do T lymphocytes do
kill infect cells and product secreted or cell-surface signal proteins
What does TLR3 do
it is a PRR (pattern recognition receptor) and it recognizes double-stranded viral RNA in the endosomal lumen as a homodimer – its cytosolic domains are brought together to make several responses
In general, what do pattern recognition receptors trigger
mostly induces the secretion of a variety of cytokines and other signaling molecules to stimulate an inflammatory response.
list one PRR and give its location, ligand, origin of ligand, and type/ class
an example could be:
receptor: TLR5
Location: plasma membrane
ligand: flagellin
origin of ligand: bacteria
class: Toll-like receptor (TLR)
Why would a virus block class I MHC (major histocompatibility complex) transcription, assembly, or transport
to prevent detection by cytotoxic T cells from inducing apoptosis from them as they recognize a peptide fragment bound to class I MHC.
what do natural killer cells monitor to see if a cell is sick
the levels of class I MHC proteins as sick cells make much less of it, they also recognize other surface proteins in virus-infected or cancer cells
What do dendrites make the link between
innate and adaptive immune responses by creating MHC proteins which will present the microbial fragments into the T-cells in the lymph nodes
When B cells are in the bone marrow what are they
immature, they must interact with cells to learn which antibodies to produce
– but they finish developing in the bone marrow and are mature in the lymph node
where do T cells go to mature and what does this allow them to do
the thymus, which allows them to secrete a variety of cytokines that act locally to kill the infected cells or initiate other responses
when exposed to a antigen for the first time what happens
naive cells make effector cells, and memory cells. However, the response takes a long time on the first exposure and does not have many effector cells
what is a effector cell
activated cells that defend the body during an immune response
B cells, cytosolic T cells, helper t cells, and regulatory T cells are all in this category
what is a memory cell
a cell that remembers a specific antigen by having membrane-bound antibodies and will persist for the life time of an animal
when epxosed to a antigen for a second + time what happens
a fast response happens as the memory cells have already been made allowing for a fast response (making effector cells) for that antigen
how does the covid -19 vaccine work
The mRNA of COVID-19 is modified in vitro with nucleosides that prevent it from binding to PRRs that trigger a response.
basically it puts the virus mRNA into the body with replication deficiency
why do B cells make immunoglobulins (Igs)
they can act as both cell-surface antigen receptors and secreted antibodies
what are Igs made of
each Ig is bivalent (light and heavy chain) with two identical antigen binding sites with the tail determining the ability to activate the complement system or be recognized by a receptor protein
where do the first Igs that get synthesized by newly formed B cells go
they are inserted into the plasma membrane as receptors for antigen
what is the first class of Ig that gets made
IgM
what is the IG that is the major antibody class (most abudant) in the blood and coats microorganisms
IgG
why do Ig light and heavy chains need variable regions
it allows them to recombine and are critical for antigen binding
why do we have constant (nonvariable) regions of Immunoglobins (Ig)
in the heavy it activates the complement system or is recognized by receptor proteins on phagocytic cells
how do variable Ig genes get assembled
During B cell development, a DNA rearrangement will usually occur through the V and J regions for light chains and V, D, J, regions for heavy
do light or heavy chains have more diversity
Heavy chains have far more diversity (5520 recombination possibilities) compared to light chains (295)
how many total antigen binding sites can be made via ig gene recombination
1.5x10^6
what is AID and why do we need it
AID is activation-induced deaminase, and it helps Ig rearrangements by cutting and rejoining DNA in switch sequences
this allows B cells the ability to switch the class of Ig they make
What are cytotoxic T-cells
they kill infected cells
what are helper T cells
help B cells secrete antibodies and undergo the Ig class switch, activate macrophages to destroy intracellular pathogens, and induce naive t-cell to become effector t cells
what are regulatory T cells
they suppress the activity of other immune cells
What do T cell receptors do that is similar to something we have learned
Similar recombination strategies of VDJ to generate diversified antigen binding sites,
but only have one active binding site at a time
Which cells activate Naive T cells
activated dendritic cells,
via co-stimulatory proteins, CD4 and CD8 co-repressors, and cell-cell adhesion molecules
What recognizes when a foreign peptide binds to a MHC protein
T cells (either cytotoxic or helper or regulatory) via their TCR (t cell receptor)
What do the CD4 and CD8 corepressors on the t cells N TERMINUS bind too
invariant parts of MHC proteins
Do cytotoxic T cells express CD8 or CD4 and does it bind to class I or class II MHC proteins
CD8, and class I MHC proteins (via its N-term)
Do helper or regulatory T cells express CD8 or CD4 and does it bind to class I or class II MHC proteins
CD4, and class II MHC proteins (via its N-term)
describe the structure of Class I MHC proteins
A long extracellular N terminus chain that allows peptides to bind in the groove, and a single leg in the intercellular compartment
describe the structure of Class II MHC proteins
Almost symmetric extracellular N terminus chains, and has two legs in the intercellular compartment
What molecules to cytotoxic T cells secrete to trigger a cell to kill themselves
perforin and granzyme
what does perforins do
they polymerize to make a pore to allow granzyme to enter the cell
what is granzyme and what does granzyme do
it is an initiator caspase that is a protease that will cleave an executioner caspase to initiate apoptosis
What is a fas ligand
it is a ligand on the surface of cytotoxic T cells that gets recognized by a fas receptor
what happens when a faz ligand gets recognized by a fas receptor
it induces apoptosis in the target cell. However, it is a slow (minor) pathway
