Cell Bio and Genetics Exam 2 Flashcards
DNA polymerase 1(3 activities)
1) 5’ to 3’ polymerase (catalyzes chain growth)
2) 3’ to 5’ exonuclease (proofreading activity)
3) 5’ to 3’ exonuclease
DNA polymerase 3
repairs damaged DNA by searching for mismatched base pairs erroneously inserted during DNA replication which it removes processively with it’s 3’ to 5’ exonuclease activity. Polymerization to fill in gaps with correct nucleotides proceeds via 5’ to 3’ polymerase activity.
Where does replication begin?
origin of replication
What causes the replication fork to form?
replication proceeds bidirectionally from origin of replication
What causes DNA to bend and destabilize(melt) at 13-mers?
DNAa binding at ORI occurs at each four 9-mers. As a consequence of bending, the 13-mers become accessible DNA binding sites to which proteins DNAb and DNAc bind. Together, a prepriming complex is formed.
What do DNA helicases do?(DNAb and DNAc)
unwind the DNA double helix, moving along one strand of DNA in 3’ to 5’ direction.
helicases 2 or 3 move along other DNA strand 5’ to 3’
What do single stranded binding proteins do?
bind at replication fork to maintain single strands of DNA
DNA primase
interacts with the pre-priming complex so the synthesis of DNA strands may begin. Moves 5’ to 3’ direction and lays down RNA primer.
How does RNA primer promote DNA synthesis?
3’OH group associated with the primer promotes DNA synthesis by DNA polymerase 3
How does replication differ between the leading and lagging strand?
continuous replication occurs from RNA primer to leading strand
discontinuous happens from the RNA primer on the lagging strands (Okazaki strands)
How is replication in the lagging strand between Okazaki strands repaired?
DNA pol 1 fills in gaps on the lagging strand; it’s 5’ to 3’ exonuclease acmivityremoves RNA primer.
DNA ligase seals the Okazaki fragments together by catalyzing the formation of phosphodiester bonds between 5’ phosphate of one nucleotide and 3’OH groups of an adjacent polynucleotide.
What does Topoisomerase do and what are the common forms?
affect DNA supercoiling by interacting with helices physically
topoisomerase 1 causes a single-stranded break in DNA
topoisomerase 2 causes a double-stranded break in DNA
DNA replication occurs in?
S phase of interphase.
what do condensins do?
in eukaryotic cells DNA molecules are compacted and condensed into mitotic chromosomes. each one comprised of two sister chromatids.
centrosome
a microtubule organizing center that contains two centrioles and pericentriolar material from which microtubules “grow”
mitosis
the process by which a cell separates its chromosomes into two new cells in one division. The new cells produced by this division have the exact same number chromosomes as the parent cell 46 chromosomes
Interphase
the phase that comes before mitosis, the chromosomes make exact copies of themselves producing long thin strands of DNA that connects the centromere
prophase
the replicated chromosomes become visible (now condensed) as short rods of various shapes providing the first signs of mitosis.
prometaphase
the nuclear membrane disappears and the mitotic spinele begins to form
metaphase
the replicated chromosomes move to the center of the cell. Each replicated chromosome is attached to the spindle fiber via its sister chromatids
anaphase
each replicated chromosome separates at the centromere and thus becomes two separate chromosomes during this phase. The cytoplasm now starts to divide and the cell membrane begins to pinch off to form two new cells
telophase
the new nuclear membrane forms around the chromosomes
cytokinesis
the cell membrane pinches off and forms two new daughter cells
Cohesins
proteins that regulate separation of sister chromatids during cell division during both mitosis and meiosis. Specifically, cohesions are proteins that keep sister chromatids connected to each other during metaphase. During metaphase to anaphase transition an anaphase inhibitor is cleaved, which in turn facilitates the removal of chohesin from the chromosomes; this allows for the separation of sister chromatids to opposite poles of the cell
Mitosis is considered what kid of reproduction…
asexual because they are identical to the parent cell
sexual reprodcution
offspring are blended between both parents
Gametogenisis
the differentiation of resulting cells into egg and sperm
meiosis
yields 4 haploid cells from 2 diploid cells. The first division is called reduction-divison a diploid cell is changed into two haploid cells. The second division changed two haploid cells into four haploid cells each with different chromosomes that are mosaics of the parent cells.
What is the purpose of meiosis?
To produce genetic variation in the population allows for evolution and adaptation of organisms to different environments
Chromosomal crossover
the exchange of genetic material between homologous chromosomes that result in recombinant chromosomes. It is one of the final phase of genetic recombination which occurs during prophase 1 of meiosis. Usually occurs when matching regions on matching chromosomes break then reconnect to the other chromosome.
What is cytoskeleton
an extensive network of hardened filaments and tubules connecting various regions, organelle/structures in the cell to one another. cytoskeleton is dynamic
Functions of cytoskeleton
structural support
organization of cellular components
intracellular trafficking
cell motility
types of cytoskeleton
microtubules- made of tubular monomers
microfilaments- actin filaments
intermediate filaments
Microtubules
comprised of round tubule structures which are composed of molecules of tubulin. An array of tublin monomers are called protofilament. There are 13 protofilaments within a single MT. protofilaments are made up of alpha and beta tubulin subunits
What feature does beta tubulin have that alpha tubulin lacks?
They both bind GTP but only beta tubulin has a GTPase activity, which causes GTP to hydrolyze into GDP
What are the building blocks of microtubules?
Alpha and beta tublin dimmers
growth of microtubules
beta tubulin is always exposed at the + end and alpha tubulin is always exposed at the - end. alpha is bound to GTP but beta is bound to GDP because beta subjects GTP to hydrolysis. organized in such a way that there is a GTP cap and GDP microtubule. As the microtubule grows GTP-GTP dimers get added on to the GTP cap. The GDP microtubule is GTP-GDP.
catastrophe
when dis-assembly catches up with GDP microtubual that is not growing
dynamic instability
microtubules are always growing and undergoing dis-assembly at the same time. Dis-assembly causes the MT to shrink . As dis-assembly proceeds the ends of MT begin to fray and fall apart.
How do you start making a MT?
A nucleation event occurs at a microtubule organizing center(MTOC)= a specialized cell structure such as centrioles or basal bodies
What does a centrosome consist of?
two barrel-shaped centrioles made of alpha and beta tubulin
Each centriole is comprised of…. If you look closer at one of these you will see a…. within each… there are…
9 units…each is made of a triplet of MT…MT…13 protofilaments
A centromere is always comprised of….
centrioles organized perpendicular to one another
Centrioles are surrounded by…. that is comprised of…
peri-centriolar material (PCM)… lots of proteins
MTs originate from
the PCM making it a MTOC
What proteins are present in PCM
gamma tubulin and other proteins. Gamma tubulin is present at the ends of MT
Gamma tubulin ring complex is used to…
nucleate and begin to build MT
What tubulin binds to gamma tubulin
alpha tubulin
The negative end of the MT is…. and the positive end is…
the MTOC… actively growing
MTs main role is… and it is carried out by…
transporting things around the cell… MT motors
Kinesins
comprised of 2 heavy chains and 2 light chains. Kinesins are + end directed motors in MT. The heads have catalytic cores bind to Mts and the tails interact with the cargo. the light chains confer cargo specificity
Dyneins
- end of a MT, 2 heads with catalytic cores bind to MTs, 2 heavy chains, intermediate chains, and light chains. they do not bind directly to their cargo, dynactin complex forms a bridge between dyne and its cargo.
Micro filaments
made up of actin
actin monomers
g-actin globular actin
what causes f-actin to be made
f-actin=thin filaments=microfilaments
a nucleation event occurs, then an elongation event
How are MF put together
G-actin binds to ATP. As a result, G-actin nucleates, then elongates to form filaments with a (-) and a (+) end.
How are MFs regulated?
If the concentration of G-actin ATP is high MFs will grow
If the concentration of G-actin ATP is low MFs will shrink
Treadmilling
Molecules of the MF are moving even though the MF stays the same size
What is the motor for MF
myosin, motion is achieved via regulation of G actin
How does a cell move?
The leading edge with its lamellipodia has spikes leading off of it in places, these spikes are called filopodia. Stress fibers are actin filaments that conncect two focal adhesions, stress fibers are involved in pulling the cell up after the leading edge.
how does chemotaxis(cell movement) occur?
Intiated by a receptor-ligand interaction. First single activates WASP. Then WASP activated ARP2/3. Then Arp2/3 begins the nucleation of the actin fillament. If the MF gets capped the MF no longer grows in that direction. Chemotaxis is like tent-raising
What is Arp 2/3?
Arp 2/3 is an actin binding protein that is involved in a nucleation event. can make new actin filaments. to make new filaments one must add actin onto the MF in a particular direction.
myosin’s role in cell movement
responsible for pulling up the cell after the leading edge, there is a myosin actin interaction for this movement
I band in sacromers
a region where actin thin filaments are present
H zone in sacromers
where myosin is present
Contraction in sacromers
causes shortening. the A band doesn’t change in size. rather the overlap between actin and myosin filaments change. The I band shrinks because the overlap of actin and myosin increases. The H zone also shrinks
Troponin
Tropnion is a complex of three proteins (C,I and T) that is involved in regulation of muscle contraction. tropnion c is a calcium binding protein.
Tropomyosin
regulator of contraction, when a muscle is relaxed tropomyosin binds to actin filaments and blocks regions on the actin filament where myosin heads would otherwise interact
What happens to troponin in the presence of calcium and what does that do?
Troponin undergoes a conformational change. Since troponin is bound to tropomyosin, the conformational change that occurs upon calcium binding rolls tropomyosin out of the way. This causes regions on the actin filaments become exposed which myosin heads can now bind
A band
thick myosin filaments
When a G protein is bound to GTP
a conformational change is made that puts the G protein into an active state
When a G protein is bound to GDP
a conformational change is made that puts the G protein into an inactive state
GEF
Guanine exchange factor
The G protein cycle
G-GDP(inactive) a cell signal causes GEF to remove GDP to allow G to bind with GTP making G-GTP(active) that can now couple with an inactive target protein, this coupling causes a conformational change in the target protein so it becomes active and does its job in the cell. Another protein called GAP binds to GTP so it’s enzymatic activity can convert GTP to GDP+P. Once GAP binds the target protein unbinds and becomes inactive
GAP
GTPase activating protein)
chlorophyll optimal wavelengths
680-700nm
light reactions
take place in thylakoid membranes of the cholorplast and produce ATP
dark reactions
the reduction of CO2 by the Calvin cycle and takes place in the stroma of the chloroplasts
oxygenic photosynthesis
involves two light reactions instead of 1, the e- donor is water and oxygen is a byproduct.
the Calvin cycle
a reductive pathway reduces CO2 into hydrocarbon compounds and is very energy demanding, requires 18ATP and 12 NADPH to make 1 molecule of glucose.
RuBisCo
Ribulose Bisphosphate Carboxylase is a key enzyme in Calvin cycle. It fixes atmospheric CO2 into ribulose bisphosphate. 6CO2 into 1 glucose.
Uncouplers
e- transport still occurs but not couples to ATP production, instead of coupling free energy release with ATP production, energy is released as heat and is unavailable to do work. Ex, diet pills and brown fat(used by animals during hibernation)
Inhibitors of oxidative phosphorylation
prevent electron flow ex, azide, cyanide, etc
If GAP does not bind to GTP what is the result?
target protein never gets turned off and can potentially cause cancer.
Mendles law of inheritance
- law of segregation
- law of independent assortment
kineticore
protein that associates with centromere and binds microtubules
topoisomerase
works ahead of fork to prevent super coiling
ligase
seals Okazaki fragments
ploidy
number of sets of chromosomes in a cell
n
number of unique chromosomes
Melson Stall theories of reproduction
Conservative rep, semiconservative rep, dispersive rep
Watson and Crick pairings
A-T G-C in DNA and A-U G-C in RNA
Chase and Hersey Experiment
studying how viruses effected cells determining if proteins or DNA is responsible for replication by radioactively taking S in proteins and P in DNA
Prokaryotic binary fission
- DNA rep
- chromosome segregation
- cytokinesis
contact inhibition
cells grow in a monolayer once cells touch other cells they stop growing. cancer cells don’t have contact inhibition
cyclins
exist between every phase of interphase as a check point for regulation
What phase of DNA reproduction can you start referring to cells as chromosomes?
prophase
incomplete dominance
cases where phenotypes of heterozygote is intermediate between two
codominance
expression in a compound heterozygote of both phenotypes shown by the two alleles
dominant lethal
two copies of dominant alleles is lethal to organism
synaptogenisis
happens in prophase 1, shuffling of genetic info
independent assortment
causes variation in population during meiosis, metaphase lining up is arbitrary
fertilization
causes variation in population because what sperm fertilizes the egg is completely arbitrary
phenotype
the way an organism looks
genotype
the way an organic is constructed
gene expression
the physical way genes express themselves
epistasis
when a gene at on locus modifies the phenotype of a gene at the second locus, resulting in an altered dihybrid ration(gene to gene interactions
environmental impact on phenotype
nothing to do with genotype (ex soil pH effects what color flowers will grow)
aneuploidy
something other than the expected amt of chromosomes
(n+1)- viable depending on where extra chromosomes ends up
(n-1)- causes miscarriage
trisomy 21- down syndrome
nondisjunction
improper segregation of chromatin
profilin
leading edge encourages polymerization (barbed end)
cofilin
leading edge encourages depolymerization (pointed end)
WASP
regulator of actin nucleation
Critical concentration eqs
- Cc-=Cc+ steady state, tread milling
- Cc->Cc+ depolymerization “shrinking”
- Cc-<Cc+ polymerization “growing”
