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Bio 201 last part of lectures
last thrid
167
Biology
04/03/2010

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Term
why would it be necessary to go retrograde
Definition
RER proteins that contain the amino acid sequence KDEL (lys, asp,glu,leu) should stay in RER
Some RER enzymes accidentally “escape” to Golgi in COPII vesicles
These enzymes can be retrieved by KDEL receptors in COPI vesicles and returned to RER
Term
what is the role of lysosomes
Definition
Acidic organelles for degredation and recycling
Term
how do you make the lysosome acidic
Definition
This ATPase is an ATP-dependent H+ pump
The energy of ATP hydrolysis is used to pump H+ into the lysosome
Term
describe Lysosomal enzyme targeting by Mannose-6-P
Definition
1.An enzyme destined for the lysosome is phosphorylated on a mannose sugar in the cis golgi. Where was is made?
2.Mannose-6-P receptors in trans golgi bind this protein and packages it into vesicles
3.Clathrin binds to the outside of these vesicles, targeting them to become lysosomes
4.The lysosomal enzyme is released from the receptor as the lysosome matures
5.Clathrin is released and the receptors are recycled to the golgi
6.Some mannose-6-P receptors that ended up on the plasma membrane are retrieved and recycled. How did they get there?
Term
what are the roles for lysosomes in phagocytosis
Definition
Particles are brought in by endocytosis
The vesicle formed inside the cell is called a phagosome
Lysosomes fuse with phagosomes and transfer their hydrolytic enzymes inside, creating a phagolysosome
The particle gets digested and nutrients pass into the cytoplasm
The leftover, non-digestible material (garbage) is dumped out from residual bodies by exocytosis. This is where some mannose-6-P receptors can make it to the plasma membrane
Term
what are the roles of lysosomes in autophagy
Definition
1. an autphagic vesicle is formed by wrapping ER membranes around a dead mitochondria
2. lysosomes fuse with this to make a autophagolysosome
3. the lysosomes fuse with this to make a autophagolysosome
4. the leftovers remain in the residual body until they can be dumped out of the cell body by exocytosis
Term
what is autophagy
Definition
a way o get rid of dead organelles such as mitochondria and chloroplasts
Term
how does receptor mediated endocytosis work
Definition
1.Ligands bind to receptors on the outside of the cell. A classic example is LDL (low density lipoproteins) binding to LDL receptors
2.Clathrin binds to the transmembrane receptors and endocytotic vesicles form
3.The clathrin coat is shed, the endosome is acidified, the ligand is dissociated from the receptor and the rest is sorted into different endosomes and other compartments
4.If the ligand is needed by the cell, it is transported to the cytoplasm
5.The receptor is recycled to the plasma membrane
6.If new receptors are needed, they are made in RER and trafficked through the endomembrane system
Term
name 3 events where lysosomal fusion with other membranes occur
Definition
autophagy- mitochondria+ER+lysosome=autophagolysosome
Phagocytosis- phagosome+lysosome=phagolysosome
3.receptor mediated endocytosis-
endocytonic vesiclebecomes and endosome, then lysosome combines to generate a late endosome
Term
name some places where receptors can be found
Definition
1. Plasma membrane
A. Facing outside: LDL receptors
B. Facing inside: t-SNARES
2. Cytoplasm (soluble receptors): importin, SRP
3. Nuclear membrane: Nuclear pore filaments
4. RER
A. Facing cytoplasm: SRP receptor
B. Facing lumen: Cargo receptors
5. Golgi
A. Facing cytoplasm: Transmembrane receptors for COPs
B. Facing lumen: Mannose-6-P receptors
6. Transition vesicles: Transmembrane receptors and v-SNARES
Term
when discussing cellular reproduction what 2 topics are we considering
Definition
nuclear division(mitosis) and cellular division(cytokinesis)
Term
what was the procedure of the meselson stahl experiments
Definition
1Grow bacteria on “heavy” nitrogen (15N) to metabolically label all DNA
2Then switch to regular “light” nitrogen (14N). All newly replicated DNA will be “light” but the old, parental DNA will be “heavy”
This way you can tell which DNA is new and which is old.
3. Use density gradient centrifugation to separate heavy and light DNA. They actually used cesium density gradients instead of sucrose.
Term
what were the 3 possibilites of the meselson stahl experiments
Definition
1Dispersive: Hybrid in the first generation. Hybrid means ½ light and ½ heavy.

2. Conservative: Always both heavy and light present

3. Semi-conservative: Hybrid in the first generation but both hybrid and light in the second generation
Term
what were the results of the meselson stahl experiment
Definition
1.In the beginning, all of the DNA is heavy (15N)
2.After the first generation, all of the DNA is hybrid because each double stranded piece has one heavy (old, parental) and one new light strand
3.In the second generation, there are hybrid and light bands and there is so little of the original DNA left that it can’t be seen
Term
in what way do bacteria replicate
Definition
semi conservative
Term
what are some issues that experimenters must overcome when looking at DNA replication in eukaryotes
Definition
Can’t use gradient density centrifugation to separate chromatids or DNA from eukaryotes so
Use metabolically labeled DNA and look at mitotic chromosomes
Term
what method is used to see DNA replication in eukaryotes
Definition
1.Must use mitotic cells to see compacted chromatids
2.Use BrdU (bromodeoxyuridine) to substitute for thymidine in DNA A:T goes to A:BrdU
3.Thymidine stains dark. BrdU doesn’t.
4.All T is dark, all BrdU is light, hybrid is dark
Term
what are some cell cycle highpoints
Definition
Chromatin is dispersed in interphase for transcription and replication

DNA replication only happens in S phase. Histones and centrioles are replicated in S-phase too in preparation for mitosis

Chromatin condenses into chromatids and forms mitotic chromosomes in mitosis. Since it is condensed, transcription and replication stop. Little or no translation either.
Term
what are some cell cycle exceptions
Definition
No G1 or G2. Most or all of interphase is S-phase. Cells divide a lot but don’t grow much. Much mitotic activity. Examples: Embryonic cells, spermatogonia, etc.

2. Stuck in G1 or Go. No division at all. Terminally differentiated cells such as some neurons, some muscle cells, RBCs, etc.

3. Inducible. Can progress from G1 to S if triggered to do so. For example, lymphocytes can be stimulated to proliferate by exposure to antigens. Liver cells regenerate after injury. Lizard tails can grow back after being cut off. Cancer cells start growing.
Term
what happens to the centrioles during s phase
Definition
they replicate and form the mitotic spindles
the mitotic spindles contains 2 centrosomes,
each centrosome has 2 centrioles
Term
what is happening to the chromatin in mitosis
Definition
Fibers of DNA and associated protein that constitute chromosomes
Term
what are chromosomes
Definition
Threadlike strands that are composed of the nuclear DNA of eukaryotic cells and are the carriers of genetic information
Term
what do chromatids do during mitosis
Definition
Paired, rod-shaped members of mitotic chromosomes that together represent the duplicated chromosomes formed during replication in the previous interphase
Term
what are mitotic chromosomes
Definition
Paired chromosomes compacted into paired chromatids
Term
[image]
Definition
Term
Definition
1. At time 1, the first cells in S-phase pick up radioactivity because they are incorporating 3H thymidine into their DNA as it replicates. It takes them a long time before they are seen in mitosis (all of S and G2).
2. At time 2, cells starting in the middle of S don’t take as long to reached mitosis
3. At time 3, the last cells to leave S phase leave. It doesn’t take them as long to get to mitosis as those at time 2 because they spend less time in S
The time spent between time 1 and time 3 estimates the length of S-phase
Term
Do soluble factors control the cell cycle?
Definition
Fusion with a cell in S-phase stimulated the G1 cell to go into S-phase.
Term
how would you test for soluble factors within the cell that control the cell cycle
Definition
1.Take out a little of the cytoplasm of an S-phase cell
2.Microinject it into a G1 phase cell. Microinject water into a control G1 phase cell
3.Grow both cells in 3H thymidine, do autoradiography, see if they are radioactive. If the microinjected G1 cell is radioactive, it means it entered S phase
Term
Can G2 cells be stimulated to replicate DNA again?
Definition
after fusing cells together there was no change seen in the cell
Term
Can G2 cells be affected by M-phase (mitosis) factor?
Definition
: The DNA in the G2 cell started to condense (compact), like they were starting mitosis. Also, G1 can be converted to M and S to M by “M-factor”
Both S-phase and mitosis are controlled by soluble factors
Both S-phase and mitosis are controlled by soluble factors
Term
how do you verify visually if a cell is switching from g1 to a cell in mitosis when fused together
Definition
G1 chromosomes are compacted due to exposure to the cytoplasm of a mitotic cell
Term
what do we visually see when we Fuse an S-phase cell with a cell in mitosis
Definition
Since replicating DNA is rather fragile, the M-phase cell factor that tells the DNA to compact causes the S-phase DNA to “pulverize” instead of compacting
Term
what do we visually see when we Fuse a G2 phase cell with a mitotic cell
Definition
A soluble factor from the mitotic cell causes the G2 chromosomes to condense
Term
What are these soluble factors?
Definition
1.A soluble factor that causes progression from G1 to S

2. Another (different) soluble factor that causes progression from G2 to mitosis
Term
what is MPF
Definition
Maturation-promoting factor. This stimulates entry into mitosis, as seen by compaction of DNA. MPF is a protein kinase.
Kinases are enzymes that phosphorylate specific proteins
Term
what is cyclin
Definition
Part of the MPF complex which regulates its activity
Term
how many different kinds of cyclin are there, and what is their relationship to one another
Definition
G1 cyclin stimulates progression from G1 to S-phase
Mitotic cyclin stimulates progression from G2 to mitosis
as g1 increases in concentration to start s phase its concentration goes down, but at g1 also marks the increasing concentration from g2
Term
will the location of cyclin within the cell affect weather a cell moves to the next phase
Definition
cyclin b is seen to accumulate in the cytoplasm in the g2 phase, and as mitosis begins the cyclin enters the nucleus
Term
how does cell cycle arrest occur
Definition
1.“Sensors” detect DNA damage or cellular abnormalities
2.The cell cycle is arrested, stalling progression to the next step
3. During this delay, DNA damage is repaired or the cell defect is corrected

Term
what factor stops the cell from continuing
Definition
CdK inhibitor proteins can act as “molecular brakes” to stop the cell cycle from progressing to the next step
Term
what does the cell look for at the G1 checkpoint
Definition
the cell checks to make sure the environment is favorable
Term
what does the cell look for at the G2 checkpoint
Definition
the cells checks to make sure the DNA is replicated and to make sure that all DNA damage is repaired
Term
what does the cell look for at the mitosis checkpoint
Definition
the cell double checks to make sure that all chromosomes are porperly attached to the mitotic spindle if so the chromosomes get pulled apart
Term
what are the Effects of a mutation in a checkpoint protein
Definition
The brown mouse is a p27 knockout mouse. It has no p27.
Therefore, there is no cell cycle arrest protein to pause progression into S phase.
More S-phase cells, more cell division, more cells, bigger mouse
Term
what is p27
Definition
a CdK inhibitor. It must be removed before the the cell can move into S phase.
Term
what terms are associated with DNA content and ploidy
Definition
Haploid: Single set of genetic information. Single genome
Diploid: Two full sets of genetic information. Two copies of the genome
Polyploid: Many sets of genetic information. Many genomic copies (up to 800 in cotton)
Ploidy (n): Number of sets of genetic information. Number of copies of the genome.
x: Mass of DNA or amount of DNA
c: Number of base pairs (size of DNA)
Human cells are mostly 2n2x2c in G1
x and c number will always be the same
Term
Changes in human DNA content during G1
Definition
22 autosomes and 1 sex chromosome (XX female or XY male)
That’s 23 kinds of disperse chromatin in G1.
But there are two sets of each because we are diploid (2n) so:
46 pieces of disperse chromatin in G1. They are all linear, double-stranded DNA.
Term
Changes in human DNA content during s phase
Definition
Each piece doubles so: 92 pieces of disperse chromatin in S-phase. The nucleus is still diploid (2n). Same thing in G2.
Term
Changes in human DNA content during mitosis
Definition
The 92 pieces of disperse G2 chromatin condense in mitosis to form 92 chromatids.
The 92 chromatids are paired to form 46 mitotic chromosomes. Still diploid (2n)
Term
what is going on in a G1 nucleus
Definition
All of the DNA is disperse. Transcription and translation can happen
2n2x2c It is diploid
46 strands of disperse chromatin in G1
Term
what is going on in the nucleus of an s phase nucleus
Definition
There are 92 pieces of disperse chromatin in S-phase
they are paired to their sister chromatid cohesion holds the pairs together
Still diploid but now
2n4x4c
Term
what is going on in the nucleus of a mitosis nucleus
Definition
Still 92 pieces of double-stranded DNA (chromatin) but now they are compacted as 92 chromatids.
The paired 92 chromatids make 46 mitotic chromosomes
Still 92 pieces of double-stranded DNA (chromatin) but now they are compacted as 92 chromatids.
The paired 92 chromatids make 46 mitotic chromosomes
Paired homologous sister chromatids form 46 mitotic chromosomes
Term
what is going on in the nucleus of a cell during cytokinesis
Definition
Two daughter cells, both diploid (2n2x2c)
Each daughter cell has the same 46 pieces of disperse chromatin in G1
Term
what is the goal of mitosis
Definition
Make two copies of cells with the same ploidy and DNA content. This is:
Equational Division (no change in n)
Term
what is cohesin
Definition
helps to keep the two pieces of chromatin together after S-phase, through G2 and into the beginning of prophase
Phosphorylation of cohesin in early prophase causes a loss of cohesin between homologous chromatids except near the centromere
its like the clip in you hair
Term
what is condensin
Definition
helps to compact and supercoil DNA in prophase
Term
What phases of the cell cycle would have the most condensin associated with chromatin?
Definition
Prophase, prometaphase, metaphase, anaphase
Term
Which phases of the cell cycle would have the most cohesin associations with chromatin?
Definition
Very early prophase
Term
what provides a scaffold to hold the DNA in the mitotic chromosomes
Definition
condensin cohesin and other proteins helps to hold the DNA in the mitotic chromosomes
Term
how do mitotic spindles form
Definition
1. Pericentriolar material surrounding centrioles serves as the nucleation site (MTOC) for cytoplasmic microtubules
2. The initial spindle pole forms outside of the nucleus
3. Breakdown of the nuclear envelope, ER and golgi
Term
How can you tell you’re in prophase?
Definition
1.Mitotic chromosomes are seen but they aren’t clustered near the middle
2.MTs from the mitotic spindle (aster) have not made contact with any chromosomes
Term
In which phase of the cell cycle would you see centrioles inside the nucleus?
Definition
prometaphase
Term
what happens in prometaphase
Definition
1. A protein complex on the centromere is called the kinetochore.
2. The plus ends of chromosomal MTs start to “capture” mitotic chromosomes at their kinetochores
3. Mitotic chromosomes begin to move (oscillate) and end up near the spindle equator at the end of prometaphase
4. Sister chromatids end up in amphitelic orientation. Each faces opposite poles.
Term
what is the kinetochore
Definition
a protein complex that is attached to the centromere
Term
Is the kinetochore always at the center of human mitotic chromosomes?
Definition
not always
Term
Astral MTs
Definition
Eminate from centrosome into cytoplasm to anchor and position the aster (mitotic spindle)
Term
Chromosomal MTs:
Definition
connect from pericentriolar material of centrosome to kinetochores
Term
polar microtubules
Definition
Extend from centrosome to equator but interact with other polar MTs instead of chromosomes
Term
what are Three main forces for movements in prometaphase
Definition
1. Dynein and kinesin-like motors on the kinetochore corona fibers to grab the MT and position it

2. Polymerization and depolymerization of tubulin to lengthen and shorten MTs


3.“Cargo and rail” action of motor proteins on MTs to position chromosomes and poles
Term
Can there be any movements of mitotic chromosomes in prometaphase if there was no ATP?
Definition
Polymerization and depolymerization of tublin, no energy required,
Cargo and rail action of motor proteins on microtubule to position chromosomes

Therefore no atp movement in prometaphase is possible
Term
What if there was no GTP?
Definition
gtp is required for movements in prometaphase
Term
what does the relationship between kinetochore and coronal fibers and its benefit to move chromosomes
Definition
It helps to move and position the mitotic chromosomes
Term
Can chromosomal MTs shorten at both the plus and minus ends?
Definition
The coronal fibers attach to the dam ring, sits around the microtubule so that the chromosome is pulled as the microtubule is depolemerized, then the use of depolemerase breaks down the plus end near the dam ring. Depolymerization also occurs at the spindle poles due to depolymerase
Term
what is the role of motor proteins in mitosis
Definition
position the mitotic chromosomes and the poles
Term
name 3 ways to properly position the dna of a cell
Definition
1.Polar spindle fiber MT sliding by kinesin causes the poles to move apart
2.Dynein-based movement moves mitotic chromosomes toward the minus ends of chromosomal spindle fibers
3.Kinesin-based movement moves mitotic chromosomes toward the plus ends of chromosomal spindle fibers
Term
what occurs during metaphase
Definition
Mitotic chromosomes align in amphitelic orientation at the metaphase plate.
Amphitelic means that each one of the two sister chromatids face opposite poles
This is in the middle (equator) of the mitotic spindle.
Colchicine and colcemid (inhibitors of MT polymerization) produces metaphase chromosomes because it stops them from being pulled apart in anaphase
Term
How can you tell you’re in metaphase?
Definition
chromosomes are alligened along metaphase plate, attached by chromosomal microtubules to both plates
Term
are microtubules dynamic during mitosis
Definition
The rate of tubulin addition is similar to the rate of loss so the MTs “treadmill” in metaphase
Term
How do you know you’re in anaphase?
Definition
Sister chromatids have come apart but they aren’t very close to the poles yet
Term
what does the spindle checkpoint do
Definition
assures that all mitotic chromosomes reach the spindle equator before anaphase begins
if this check point fails may cause genetic instability
Term
what is happening in anaphase a
Definition
the loss of chromosomal microtubules inorder to move the chromatids, no atp required
Term
what is happening in anaphase b
Definition
polar microtubules are beign added and kinesin is moving these polar microtubules inorder to push the poles apart
Term
How do SCF and APC work?
Definition
They both act by turning off existing signals

They are both multisubunit enzyme complexes.

They cause ubiquitination of many substrates.

A substrate is what an enzyme acts upon.

Ubiquitination attaches ubiquitin to a substrate.

SCF and APC ubiquitinate different substrates.

Ubiquitination labels substrates for destruction.

A substrate with ubiquitin on it is targeted for degredation.

SCF and APC don’t destroy proteins themselves, they target the proteins for destruction by other processes
Term
what is scf
Definition
(S-phase control factor) helps start S-phase but goes away in anaphase
Term
what is APC
Definition
Anaphase promoting factor) has two types, one peaks during anaphase and the other starts at anaphase and ends at S-phase
Term
what does APC do
Definition
1.It targets the destruction of some proteins that hold chromatids together (securin), allowing progression from metaphase to anaphase
2.Since mitotic cyclins keep cells in mitosis, destroying them enables progression into G1
Term
whats the point of all these regulation proteins
Definition
The cell cycle can be regulated not only by the appearance of controlling factors, but also by their regulated disappearance
Term
Two ways to decrease protein amounts
Definition
decrease synthesis or increase degradation
SCF and APC can specifically target proteins for degradation by ubiquitination
Term
what are some ways to regulate proteins involved in the cell cycle
Definition
1.Change their amounts
A. Change rate of transcription or translation
B. Change rate of degredation
2. Change their locations
A. Move them, target them, anchor them
3. Change their activites
A. Covalent modifications (like phosphorylation)
Term
How do you know you’re in telophase?
Definition
Chromatin becomes disperse and clustered near the poles. No mitotic chromosomes seen
Term
what happens in cytokinesis
Definition
1.Contractile ring forms to pinch off cell at the center. This is microfilaments and myosin II

2.Two daughter cells produced, each in G1

3.Each cell has 46 strands of disperse chromatin.

4.Each is 2n2x2c. They are diploid
Term
what is the goal of meiosis
Definition
reduction devision
2n4x4c--1n2x2c---1n1x1c
Term
what is the goal of sexual reproduction
Definition
return to the diploid state
Term
what is mitosis
Definition
is nuclear division (equational division). There is an S-phase in between the next mitosis
Term
what is meiosis
Definition
is 2 nuclear divisions with no S-phase in between (reduction division)
Signals received in pre-meiotic cells trigger them (in G1) to start pre-meiotic S-phase. In other words, the decision about whether to go into mitosis or meiosis is made in G1.
Pre-meiotic G2 cells have 2n4x4c but pre-meiotic G2 cells are a little different than pre-mitotic G2 cells
Term
what is primary meiocvtes
Definition
are cells that have just come out of pre-meiotic G2 and have entered prophase I of meiosis
Meiotic prophase nuclei differ from mitotic prophase nuclei due to formation of synaptonemal complexes and bivalents (tetrads) in meiotic prophase I
Term
what is a mitotic chromosome
Definition
it is paired sister chromatids
both chromatids are generally identicla
same thing in meiosis but it will be known also as meitotic chromosomes
Term
what are bivalent(tetrad) in meiosis
Definition
homologous chromosomes(homologous meitotic chromosomes)
paired meitotic chromosomes
both meiotic chromosomes carry similar information but they are not genetically identical
Term
Bivalents (tetrads) in meiosis
Definition
It is bivalent because it is two meiotic chromosomes
It is a tetrad because it has four chromatids
It is syntelic because both sister chromatids face the same pole
Term
what happens in Leptotene (first part of meiotic prophase I)
Definition
Compacted meiotic chromosomes become visible
Each is a pair of identical chromatids (from S phase duplication)
There are 46 compacted meiotic chromosomes
Term
How can you tell that this is meiotic prophase I and not meiotic prophase II?
Definition
twice as much dna in prophase 1, 1/2 as much in prophase 2
no bivalents in leptotene
Term
what is the goal of meiosis
Definition
haploidization
Term
what happens in zygotene of meiotic prophase 1
Definition
A process called synapsis starts to pair homologous chromosomes
Homologous chromosomes are held together by synaptonemal complexes
Paired homologous chromosomes are called bivalents or tetrads
Term
what is the role of synaptonemal complexes in prophase 1 of meiosis 1
Definition
Homologous chromosomes are held together by synaptonemal complexes
Term
what happens in Pachytene of meiotic prophase I
Definition
Synapsis ends, synaptonemal complexes are fully formed
Some genetic recombination is starting to be seen
Term
what happens in diplotene
Definition
Synaptonemal complexes break down
Homologous chromosomes held together by chiasmata (plural of chiasma)
A chiasma is a crossover point between non-sister chromatids. It is a covalent attachment.

Term
what is chiasmata
Definition
covalent linkages between two non-sister chromatids. This helps to keep bivalents together after cohesion linkages are broken
Chiasmata are also sites of genetic recombination by crossovers
Term
what happens in Diakinesis of meiotic prophase I
Definition
Meiotic spindle forms. This is similar to the mitotic spindle
Some further compaction of the chromosomes can occur
Chiasmata continue to hold homologous chromosomes together, even into metaphase
The nuclear envelope begins to break down and spindle MTs begin to contact the chromosomes
Term
How can you tell this is prophase I of Meiosis I and not prophase II of meiosis II?
Definition
bivalents are seen after leptotene
Term
how does recombination occur
Definition
Crossing-over and recombination occurs between non-sister chromatids in pachytene
Term
Are synaptonemal complexes seen throughout prophase I of Meiosis I?
Definition
No. Only in zygotene and pachytene
Term
what are some differences in the alignment of the dna in mitosis and meiosis
Definition
In mitosis, copies of each chromatid align at the metaphase plate
In meiosis, copies of each meiotic chromosome align at the metaphase plate
Term
when you pull apart cells in mitosis in anaphase what is the result
Definition
Paired sister chromatids
Both chromatids are genetically identical
Same thing in meiosis but we’ll call it a meiotic chromosome for clarity
Term
when you pull apart cells in meiosis(bivalent(tetrad) in anaphase what is the result
Definition
Homologous Chromosomes (homologous meiotic chromosomes)
Paired meiotic chromosomes
Both meiotic chromosomes carry similar information but they are not genetically identical

Term
give your best description of the dna of cells in meiosis
Definition
It is bivalent because it is two meiotic chromosomes
It is a tetrad because it has four chromatids
It is syntelic because both sister chromatids face the same pole
Term
what is the goal of meiosis
Definition
haploidization
by use of meiosis 1 and 2
Term
review concept, can you list the changes in n,x,c of the dna as you change form in meiosis
Definition
First meiotic division (Meiosis I):
Homologous chromosomes pair as bivalents or tetrads (2n4x4c)
Intact meiotic chromosomes (as paired chromatids) separate
No S-phase in between
Second meiotic division (Meiosis II):
Homologous chromatids separate
Each nucleus gets one set of chromatids
Four haploid gametes, all 1n1x1c
Term
How could you tell that this isnt prophase of mitosis
Definition
- if you can see paired miotic chromosomes in prophase you are in meiosis
Term
what is going on in the leptotene phase (first part of meiotic prophase I)
Definition
Compacted meiotic chromosomes become visible
Each is a pair of identical chromatids (from S phase duplication)
There are 46 compacted meiotic chromosomes
Term
How can you tell that this is meiotic prophase I and not meiotic prophase II?
Definition
twice as much dna in prophase 1, 1/2 as much in prophase 2
Term
what are 2 source of genetic variability in normal meiosis
Definition
1. crossing over and recombination
2. independent assortment
Term
what is crossing over and recombination
Definition
This happens in pacytene of prophase I
It changes DNA sequences of chromatids
Term
what happens in independent assortment
Definition
mix and match the dna as they separate from the maternal paternal cells, no crossing over , happens in pacytene of prophase 1

Term
what is aneuploidy and how does it occur
Definition
Abnormal number of chromosomes
this is not supposed to happen
Aneuploidy can result from either primary or secondary nondisjunction
Term
give some examples of aneuploidy
Definition
All of these are caused by nondisjunctions during meiosis
Autosomal polyploidy. This is usually fatal except in the case of trisomy 21 (three chromosome #21)

2. Autosomal monosomy. Only one of the autosomes instead of two. This is usually fatal

Sex chromosome polyploidy.

XXY is male with Kleinfelter’s syndrome

XYY is male and was previously thought to have criminal tendencies because of being “too male”

4. Sex chromosome monosomy.
XO is female with Turner syndrome
Term
compare and contrast mitosis and meiosis in both their goals and methods of achieving their goals
Definition
Mitosis produces daughter cells with the same genotype as the mother cell

No genetic segregation or independent assortment in mitosis

Meiosis produces cells with different mixtures of maternal and paternal genes because of:
Independent assortment
Genetic recombination

Independent assortment and recombination happen in meiosis, not mitosis

Goal of Mitosis:
Faithful division of DNA so the daughter cells are genetically identical to the mother cell. Keep it real, keep it diploid.

Goal of Meiosis:
Mix it up. Produce haploid gametes with different genetic contributions from maternal and paternal sources for further genetic mixing by sexual reproduction.
Term
describe the pathway to make a sperm cell
Definition
1.start with a primary spermatocytes (2n4x4c)

2.use meiosis1
3. now you have a Secondary spermatocyte (1n2x2c)
4. use meiosis 2
5. you should now have Spermatids (1n1x1c)
6. differentiation is used
7.- sperm cells(1n1x1c) are produced
Term
describe the pathway to get to the egg cell
Definition
1. diferentiation occurs
2. primary oocyte is formed(2n4x4c)
3. meiosis 1
4. secondary oocyte (1n2x2c) is formed
5. use meiosis 2
6. you now have a polar body and egg cells each at (1n1x1c)
Term
what is special about fungi
Definition
In fungi, the adults are haploid
Meiosis occurs right after fertilization
Term
describe Plants, Sporic or intermediate
Definition
In plants, the gametophytes can generate gametes by mitosis instead of using them for fertilization
Term
Do all DNA mutations cause protein changes?
What could a change from Q to K do?
Definition
a single change may or may not be harmfull due to the silent mutation of the third base pair, and the ability to code for one protein for many base pair combinations
how ever if there is a change in the protein depending on the position and charge of that protein the protein could become mishapen. this can be good or bad depending on how the body copes with these changes
Term
where do somatic cells come from
Definition
Somatic cells come from one parental cell type. Germ-line cells come from the fusion of gametes
Term
what is a mutation
Definition
Spontaneous change in DNA sequence leading to a change in amino acid sequence of this gene product
Only mutations in germ-line cells are passed on to the progeny

Term
What’s the point of point mutations?
Are all mutations bad?
Definition
Point mutations can be either bad, good or do nothing
Term
can you produce an example of a mutation process
Definition
1.Since the mutant can’t make histidine, it can only grow if histidine is added, This is a His- mutant.
2.The rate of spontaneous mutations is about 1 in 109 nucleotides copied
3.If you screen enough of these bacteria, eventually you can get a revertant that restores normal function
Term
DNA damage and replication mistakes happen. What to do about it?
Definition
1. Proofreading by DNA polymerase I
2. Nucleotide excision repair
3. Base excision repair
4. Double-strand break repair
Term
What happens if you can’t repair the mistake?
Definition
Either cell death, suicide (apoptosis) or the DNA mutations can be passed on during replication.
A. Germ cell: Genetically inherited mutation (not always bad)
B. Somatic cell: Cancer
Term
how do you Edit and correct dna damage using DNA polymerase I
Definition
DNA polymerase I replicates eukaryotic DNA
This enzyme has a proofreading capability, where mismatched bases are excised and corrected
However, some mistakes can get through
The error rate during DNA replication is the spontaneous mutation rate

Term
how do you repair A pyrimidine dimer that has formed within a DNA duplex following UV irradiation
Definition
Nucleotide excision repair (NER) removes bulky lesions, such as thymine dimers and chemically altered nucleotides.
1. DNA damage is recognized by a protein complex
2. The helicase activity unwinds the DNA
3. It cuts it
4. It removes the damaged sequence
5. The gap is filled by a DNA polymerase
6. The DNA is rejoined by a ligase

Term
how does base excision repair work
Definition
DNA glycosylase recognizes the alteration and cleaves the base from the sugar.
An endonuclease cuts the DNA open
A polymerase fills the gap by inserting a nucleotide complementary to the undamaged strand.
The strand is sealed by DNA ligase.
At least 4 enzymes are necessary for this. That’s 4 chances at problems due to inability to fix DNA problems
Term
Repairing DSBs by nonhomologous end joining (NHEJ)
Definition
Ionizing radiation (X-rays, gamma rays) along with some chemicals cause double-strand breaks (DSBs).

DSBs can be repaired by a pathway in mammalian cells in which proteins bind to the broken ends and catalyze reaction to rejoin the broken ends.

Cells that lack one of the Double-strand breakage repair proteins required for NHEJ are very sensitive to ionizing radiation.

Defects in this repair pathway have been linked to increased cancer susceptibility.
Term
Why have apoptosis?
How prevalent is it?

Definition
Cell necrosis is ugly and messy. It generates all sorts of garbage Apoptosis is a neat and orderly way to kill cells

alot of cells die each day in our bodies due to apoptosis
Term
the use of mutants
Definition
An example of the use of mutations in experiments to identify key enzymes in a biochemical pathway
Beadle-Tatum experiments with Neurospora (bread mold)
essentially use spores of bread mold and irradiate with x rays or uv light and grow the spores on a variety of supplemented medium to figure out what is important on a specific metabolic or chemical pathway
Term
name 2 other kinds of genetic mutations
Definition
Change in DNA sequence in another region that regulates the level of expression of this gene

Change in the number of copies of a gene, possibly producing more of the gene product or a template for further mutations and a new gene

Term
what happens when misalignment occurs during genetic recombination
Definition
Unequal crossing-over can produce mutated chromosomes in prophase I
Some gametes could get an abnormally long or short chromosome
Term
what is exon suffling
Definition
Exons are the coding regions, introns are the sequences in between
exons can be swapped from another gene
Term
what happens during horizontal gene transfer
Definition
DNA from one organism can be transferred to another and become part of the genome
this is what we saw in the griffith experiment, the dna of the killers mixed with the non killers resulting in the uptake of the killer genes giving the non killers the ability to kill
another example would be HIV, it changes because they use horizontal gene transfer to pass on resistance
Term
describe horizontal gene trasfer by the retrovirus
Will this genetic defect be passed on to the progeny if the viral DNA is dormant?
Definition
1. The HIV virus binds to an HIV-sensitive cell
2. HIV RNA is reverse-transcribed into DNA
3. The HIV DNA is integrated into the genome
4. It can either stay dormant or be expressed
5. When it is expressed, it makes more viruses, kills the cell and releases
many more viruses

yes
Term
Can HIV infect germ-line cells?
Definition
no
Term
describe Apoptosis and removal of the dead cell by a macrophage
Definition
Apoptosis generates caspases which are specific proteases.

Examples of the target proteins for these caspases are protein kinases, nuclear lamins, cytoskeletal proteins and DNase

Caspases can be activated to cause apoptosis by either an extrinsic pathway (stimulated by receptors) or an intrinsic pathway
Term
where do we see programed death
Definition
during development apopotosis is used to clear up webbing between fingers
in neurons, some neurons are meant to die if it is found that the connection they make is not essential. the target cell releases a survival factor that prevents the neuron from dieing resulting in neurons that fire together wire together. wireing here means the neurons stays alive becaause it is beign used and absorbing the survival factors that the target cell is producing
Term
list some of the effects of DNA damage
Definition
1. DNA gets damaged by radiation, mutagens, etc.
2. BRCA enzymes help repair the damage.
If they are mutated or missing, damage persists
3. A checkpoint should catch this damage and activate p53

4. p53 is a transcription factor that triggers either:
p21 expression and cell cycle arrest or
apoptosis
Term
what is the role of p53
Definition
(a) Cell division does not normally require p53
(b) If DNA is damaged (like by a mutagen), p53 levels rise
p53 acts to either arrest the cell in G1 or go into apoptosis
(c) If no p53 and no cell arrest, the cells proceed to either a tumor or death
Term
what is another way to cause apopotosis
Definition
cell damage can activate bax, bax cause cytochrom c to be released from mitochondria, executioner caspases get activated and apopotosis occurs
Term
is there a way to stop apopotosis
Definition
a survival factor binds to membrane receptor of the plasma membrane
bc12 gene transcription is activated, and bc 12 protein block apoptosis
but if the gene is mutated it may not have the ability to block apoptosis
Term
what is cancer
Definition
Cancer is usually due to somatic genetic mutations that are not heritable.
(You may inherit a genetic predisposition for it though.)
Term
what are oncogenes
Definition
They ignore inhibitory signals (like checkpoints). For example about 50% of human cancers have altered p53
Term
what are tumor suppressor genes
Definition
They don’t need stimulatory signals for cell division
Term
Is p53 just made and degraded constantly if no DNA damage?
Definition
yes
Term
what exactly does p51 do
Definition
once it seses there is dna damage, p53 gets activated causing it to bind with dna to transcribe gene 21
gene21 makes p21 a cdk inhibitor which causes cell cycle arrest by inactivating the soluble factor that sends the cell into the next phase
Term
what are some ways to trigger cancer
Definition
1. Mutate BRCA enzymes. DNA damage not repaired properly
2. Mutate p53. Less expression of p21 and loss of checkpoint control
3. Mutation in p21. Inability to respond to p53 and loss of checkpoint control
4. Increased MDM2 causing ubiquitination of p53, loss of p53, loss of checkpoint control

BRCA, p53 and p21 are tumor suppressor genes

MDM2 can accelerate cell division
Term
what is One way for a mitogen to trigger cancer
Definition
G1-Cdk and G1/S-Cdk are kinases that trigger progression into S-phase
Activation of these kinases causes phosphorylation of a protein that keeps a transcription regulator inactivated
Genes get transcribed that produce proteins to stimulate cell division
Term
why is cancer hard to cure
Definition
some times many mutations are required to cause a cell to go cancerous and there are many ways to make the cell cancerous leading to a variety of causes and symptoms making it difficult to cure
Term
what are telomeres
and what are the roles of telomeres
Definition
bits of dan that is tacked on to the ends of dna
When the telomeres are gone, there are problems with DNA replication and
shortening of DNA strands. Cells deal with this by:
Ceasing to divide (replicative senescence)
Checkpoint arrest and DNA repair
Expressing telomerase to extend telomere length
Apoptosis, cancer or cell death
telomerase can create more telomers
elongation of telomers can be an indication of cancer
Term
compare mutagens and mitogens
Definition
mitogens trigger mitosis and cell division
mutagens change DNA producing mutations
Term
what are possible signals for differentiation
Definition
genetic factor or epigenetic factors
Term
what is pluripotant stem cell
Definition
A pluripotent stem cell can give rise to any kind of cell that can be made from that organism’s genomic DNA