Term
| 3 reasons that cells divide |
|
Definition
1. grow
2. repair
3. reproduce |
|
|
Term
| difference between chromatin and chromosomes |
|
Definition
chromatin: the material of dna and histones
chromosome: a structure of dna and associated proteins |
|
|
Term
name the stages in which the following exist:
1. chromatin
2. replicated chromosomes
3. condensed replicated chromosomes |
|
Definition
1. G1 - resting
2. S and G2
3. M - condense in prophase and stay condensed until end of mitosis |
|
|
Term
| explain cell cycle pulse-chase experiment |
|
Definition
| cells labeled at S phase then looked at over time to discover the timing of cell cycle, as well as stages |
|
|
Term
| name the parts of the cell cycle from longest to shortest duration of time |
|
Definition
1. Mitosis (2 hr)
2. G2 (4 hr)
3. S (8 hr)
4. G1 (10 hr) |
|
|
Term
|
Definition
| cells tagged so they glow. more fluorescence = more amount of DNA. sharp peak is G1 because longest phase but lowest amt of sna. wide dip is S because ranging amounts of DNA based on the stage. M and G2 highest amounts of DNA because replicated at these points |
|
|
Term
interphase
include all 3 subdivisions |
|
Definition
- cells grow in size - G1
- organelles replicate (centrosomes) - G1
- chromosomes replicate - S
- checkpoint for replication - G2 |
|
|
Term
|
Definition
-chromos condense
-spindle apparatus forms |
|
|
Term
|
Definition
- nuclear envelope disappears
- kinetochore microtubules attach to chromos |
|
|
Term
| what are sister chromos attached with? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| cohesin breaks down to initiate chromo separation/migration |
|
|
Term
|
Definition
- nuclear envelope reappears
- spindles break down |
|
|
Term
|
Definition
- cytoplasmic division
- actin-myosin work to create cleavage furrow and pinch apart cells |
|
|
Term
|
Definition
|
|
Term
|
Definition
| non dividing growth period, goes into it at G1 checkpoint if something is wrong |
|
|
Term
|
Definition
| always protruding, anchor and position centrosomes |
|
|
Term
|
Definition
| interact with one another to link the two spindle poles, just for orientation |
|
|
Term
|
Definition
| connect to kinetochores on chromosome |
|
|
Term
| how do spindles grow and shrink? |
|
Definition
- at + end because - hidden in centrosome
- by alpha/beta tubulin dimers |
|
|
Term
|
Definition
| mitosis-specific protein on centromeres |
|
|
Term
| how do kinetochores and kinetochore microtubules attach? |
|
Definition
- bipolar attachment (strong, to put force on chromosome)
- attach with corona fibers (and a lime) |
|
|
Term
| how do chromosomes move towards the centrosomes |
|
Definition
- motors walk chromosomes there, depolymerizing the microtubules as they go
- fibers extend beyond point of attachment before depolymerizing |
|
|
Term
| spindle checkpoint: what and when |
|
Definition
- proteins check for tension at kinetochore before proceeding to avoid nondisjunction
- between metaphase and anaphase
- often fails in cancer cells |
|
|
Term
| compare cytokinesis in plants and animals |
|
Definition
plants: components delivered to cell plate
animals: actin/myosin to make cleavage furrow
- forms contractile ring |
|
|
Term
|
Definition
- forms when no cytokinesis
- a bag of cytoplasm with cells (or nuclei?) around the edge |
|
|
Term
| what regulates/initiates mitosis |
|
Definition
| MPF - mitosis promoting factor |
|
|
Term
|
Definition
- cyclin and cdk
- is a heterodimer |
|
|
Term
| 3 general things that regulate cdk |
|
Definition
- cyclin must be attached
- phosphorylation
- cyclin proteolysis |
|
|
Term
| concentrations of cyclin/cdk throughout mitosis? |
|
Definition
- cdk is constant
- cyclin oscillates - once mitosis is initiated, it degrades to turn off mph |
|
|
Term
| similarities of all cyclin/cdk's? |
|
Definition
- protein families
- sequence homology leads to structural homology aka they look alike |
|
|
Term
| procedure for cyclin/cdk complex |
|
Definition
1. increased [C] of cyclin binds to and activates CDK
2. complex has affinity for a target protein
3. CDK phosphorylates target protein |
|
|
Term
| how specifically does cyclin activate CDK? |
|
Definition
| changes conformation of T-loop to open up active site |
|
|
Term
| explain the phosphorylation regulation of CDK |
|
Definition
- inactivated by wee-1, which puts inhibitory phosphate on CDK
- activated by cdc 25, which removes inhibitory phosphate
- total of 2 phosphate spots on cdk - one active one inhibitory |
|
|
Term
| explain cyclin proteolysis regulation |
|
Definition
- occurs by the ubiquitin-proteosome system
1. ATP attaches ubiquitin proteins (like a tag) to target
2. recognized by proteasome
3. protein degradation in cytosol
4. destroyed cyclin deactivates cdk |
|
|
Term
| what is the "restriction point" of mitosis |
|
Definition
| commitment to s-phase at end of G1 |
|
|
Term
| name all 3 checkpoints and what they check for |
|
Definition
- metaphase (spindle) - check tension
- G2 checkpoint: damaged/incompletely replicated DNA
- G1 checkpoint: damaged DNA/bad extracellular environment |
|
|
Term
| what mechanism of DNA rep is useful at G2 checkpoint |
|
Definition
| - nuclear excision repair to check for damaged DNA |
|
|
Term
| connect G1 checkpoint to kinase cascade |
|
Definition
- G1 checks for extracellular environment
- would receive an extracellular signal which could activate an RTK receptor and signal the cell to proliferate - social control |
|
|
Term
| why is the G1 checkpoint so fucking awesome (2 reasons) |
|
Definition
1. commits to division if passing into S
2. under social control (control by other cells) |
|
|
Term
| name two proteins involved in G1 checkpoint and their main functions |
|
Definition
- Rb/mitogen, checks outside environment
- p52, checks for damaged DNA |
|
|
Term
|
Definition
| pro-proliferation growth factor, social control example |
|
|
Term
| explain how mitogen works |
|
Definition
1. binds to membrane receptor
2. intracellular signal pathway --> activates a G1 complex in nucleus
3. CDK phosphorylates Rb protein
4. Rb drops transcription regulator like it's hot
5. trans regulator starts transcription, makes protein that starts S phase
summary: mitogen stops Rb from stopping S phase entry |
|
|
Term
|
Definition
1. dna damage activates kinases that phosphorylates/activates p53
2. p53 binds to gene, activates transcription of a CDK inhibitor protein |
|
|
Term
|
Definition
| p53 can also detect this, which causes mutations |
|
|
Term
| 3 possible results of p53 |
|
Definition
1. stops cell cycle
2. apoptosis
3. if no damage, degraded in proteasomes |
|
|
Term
|
Definition
1. cell volume shrinks
2. loss of adhesion
3. forms membrane-bound blebs
4. engulfed by phags and destroyed by lysosomes |
|
|
Term
| what defines a cancer cell |
|
Definition
1. uncontrollable growth
2. ability to metastasize |
|
|
Term
| what is diff b/w benign and malignant |
|
Definition
| malignant when populates other cells/gets into bloodstream |
|
|
Term
|
Definition
- purifying selection- lesser chance of inheriting damaged alleles
- greater diversity to adapt to bad things |
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|
Term
|
Definition
| complete set of chromos in a cell |
|
|
Term
|
Definition
| 2 nonidentical versions of each chromo |
|
|
Term
|
Definition
-two chromosomes of have type
- have same size/shape but different alleles |
|
|
Term
|
Definition
| different sequence version of same gene |
|
|
Term
|
Definition
| number of each chromosome an organism contains |
|
|
Term
| how many pairs of chromos do you have |
|
Definition
|
|
Term
| how do you get a colored karyotype |
|
Definition
- attach sequence dependent fluorophores
- labeled sequences = probes, make each one a diff color so you can sort |
|
|
Term
| name the ploidy at each stage of meiosis |
|
Definition
- at beginning of meiosis 1, 2 replicated homologues (2n)
- at beginning of meiosis 2, 1 replicated homologue in each of 2 daughter cells (n)
- at end of meiosis 2, 4 separate unreplicated homologues (n) |
|
|
Term
|
Definition
| a cell that will give rise to a gamete |
|
|
Term
|
Definition
|
|
Term
| differences between meiosis 1 and mitosis |
|
Definition
- separating homologues instead of sister chromatids
- 2n to n
- crossing over |
|
|
Term
|
Definition
|
|
Term
| name 2 sources of variation in meiosis 1 |
|
Definition
1. crossing over
2. orientation of chromos relative to spindle poles |
|
|
Term
| when does crossing over occur |
|
Definition
|
|
Term
| what do homologous chromosomes form in prophase 1 |
|
Definition
-tetrads/bivalents
- condensation AND matching up of homologues |
|
|
Term
| difference between mitosis and meiosis II |
|
Definition
- mitosis of a haploid organism
- 4 daughters instead of 2 |
|
|
Term
|
Definition
- the process of exchanging chromo segments
- happens in crossing over |
|
|
Term
|
Definition
| homology - must be in exact position to exchange sequences |
|
|
Term
| what facilitates crossing over |
|
Definition
| synatonemal complex - keeps homos together (like malibu rum!) |
|
|
Term
|
Definition
| genes are inherited independently of each other |
|
|
Term
| crossing over supports independent assortment |
|
Definition
|
|
Term
|
Definition
| when homologues or sisters don't separate before being pulled away |
|
|
Term
| what regulates nondisjunction |
|
Definition
| spindle (mitotic) checkpoint |
|
|
Term
|
Definition
|
|
Term
| why is aneuploidy most common in the smaller chromos |
|
Definition
| the bigger ones would be detected and the organism would die |
|
|
Term
|
Definition
| 2 or more versions of a gene (has alleles) |
|
|
Term
|
Definition
| traits maintain integrity throughout generations (no blending) |
|
|
Term
|
Definition
| most are x-linked so boys are fucked - make sure you can predict sex-linked diseases |
|
|
Term
|
Definition
closer 2 genes are on a chromo, more likely to be crossed over together and/or both appear in an organism
- see linkage map/ probabilities |
|
|
Term
| incomplete dominance and ex. |
|
Definition
- red flower doesn't completely dominate white, hetero is pink
- explains blending hypothesis |
|
|
Term
|
Definition
- no dominance - 2 alleles are equally expressed phenotypically
- ex: blood type I^a and I^b (but not i) |
|
|
Term
|
Definition
| one characteristic controlled by many genes |
|
|
Term
|
Definition
| single allele effects many traits |
|
|
Term
| multiple allelism and ex. |
|
Definition
more than 2 alleles for the same gene (opp of pleiotropy)
- ex: blood type: Ia, Ib, i |
|
|
Term
| name the structure of a nucleotide |
|
Definition
| sugar, phosphate, nitrogenous base |
|
|
Term
| name dna primary structure |
|
Definition
- sugar-phosphate backbone
-has phosphodiester bonds |
|
|
Term
| what bond joins nucleotides |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| difference between dna and rna molecules |
|
Definition
| dna has only one H where RNA has OH on bottom right of sugar |
|
|
Term
| what did hershey and chase discover |
|
Definition
| DNA is the hereditary material |
|
|
Term
| what drives DNA synthesis (energetically) |
|
Definition
| - chemical energy stored in nucleotides: originally have 2-3 phosphates but release 1-2 to attach nucleotide to growing chain |
|
|
Term
|
Definition
| has a 5' phosphate and 3' OH end |
|
|
Term
| in what direction is DNA synthesized |
|
Definition
|
|
Term
| what did watson and crick do |
|
Definition
| discover structure of DNA helix |
|
|
Term
| what does twisting of DNA do (2) |
|
Definition
- maximizes base energy interactions
- condense to take less space |
|
|
Term
| name the 2ndary, tertiary, quaternary structure of RNA |
|
Definition
2: "hairpins" - double helix stem and single stranded loop
3: forms 3d shapes
4. associations between several RNA moles |
|
|
Term
| where do DNA and RNA store info |
|
Definition
|
|
Term
|
Definition
| a pre-exisitng oligonucleotide with a free 3' OH end |
|
|
Term
| what catalyzes replication |
|
Definition
|
|
Term
| name the 2 fidelity mechanisms of DNA replication |
|
Definition
1. fingers of DNA polymerase close down to catalyze sticking of base pair only if correctly paired
2. exonuclease (proofreading enzyme) can detect/ correct mistake |
|
|
Term
| what kind of replication is dna rep |
|
Definition
|
|
Term
| what are the experiment results of conservative and dispersive replication |
|
Definition
|
|
Term
| difference of replication bubbles b/w eukaryotes and bacteria |
|
Definition
|
|
Term
| name all the enzymes/proteins in dna rep (7) |
|
Definition
1. topoisomerase - unwinds
2. helicase - unzips
3. primase - synthesizes RNA primer
4. DNA polymerase - puts nucleotides on, attaches at primer
5. ligase - closes gap b/w old stuff and primer
6. telomerase - extends end of dna
7. nuclease - cuts out mistakes |
|
|
Term
| what is dna polymerase held in place by |
|
Definition
|
|
Term
| difference between polymerase III and I |
|
Definition
III - attaches at primer
I - goes over to fix primer |
|
|
Term
| all the proteins at the fork are collectively called... |
|
Definition
|
|
Term
|
Definition
| okazaki fragments make it so end isn't replicated |
|
|
Term
| telomerase - what and how |
|
Definition
| prevents telomere shortening by extending the end of DNA with a repeating sequence that we don't need |
|
|
Term
| 5 ways DNA sequence changes arise |
|
Definition
1. replication errors
2. spontaneous damage
3. exogenous chemical/radioactive mutagens
4. transposition (jumping genes) - wtf
5. viral transduction |
|
|
Term
| 2 examples of spontaneous dna change and what they do, and how this affects replication |
|
Definition
1. depurination - releases G and A from DNA - spot skipped over during replication
2. deamination - converts C to U - makes an G turn to an A during replication |
|
|
Term
| name 2 chemical/radioactive mutagens |
|
Definition
1. thymine dimer (UV)
2. double strand breaks (gamma) |
|
|
Term
|
Definition
1. nucleotide excision repair
2. base excision repair
3. mismatch repair
4. double strand break repair
basically, a type of repair for every type of damage |
|
|
Term
| how does base excision repair work (what it applies to and what the process is) |
|
Definition
-detects big bulky problems (like thymine dimer)
- excises bad part and repairs with polymerase and ligase |
|
|
Term
| why are codons 3 bases long |
|
Definition
| only way rot account for 20 aa's through combination (64>20) |
|
|
Term
| what is the central dogma theory |
|
Definition
|
|
Term
| degeneracy of genetic code |
|
Definition
| - different codons/sequences can code for same AA |
|
|
Term
| genetic code is universal |
|
Definition
| same genes code for same trait in every animal (generally) |
|
|
Term
| 4 types of point mutations - just name them |
|
Definition
| silent, missense, nonsense, frameshift |
|
|
Term
|
Definition
| doesn't change the AA - neutral in damage |
|
|
Term
|
Definition
| replacement, changes AA - changes in primary structure - can be good or bad |
|
|
Term
|
Definition
| early stop codon - premature termination - BAD |
|
|
Term
|
Definition
| addition/deletion - shifted reading frame - BAD |
|
|
Term
|
Definition
- single nucleotide polymorphism
- places where genome differs by species - different alleles
- 1/1000 nucleotides |
|
|
Term
|
Definition
set of SNP's that are always inherited together b/c rarely cross over
- connect to linkage! |
|
|
Term
| 4 types of cell-cell signaling |
|
Definition
1. contact dependent
2. paracrine - local mediator
3. synaptic - neuron
4. endocrine - hormones |
|
|
Term
| can hormones be lots of different materials |
|
Definition
|
|
Term
| the slow cellular response vs. fast - what happens in each |
|
Definition
slow: altering the protein synthesis, because takes longer to express a gene and make a protein
fast: altered protein function, because the protein already exists |
|
|
Term
|
Definition
|
|
Term
| explain lipid soluble signaling |
|
Definition
- goes right into cell through membrane
- receptor in cytosol itself brings about change in cellular behavior |
|
|
Term
| who's more popular: lipid soluble signals or surface signals? |
|
Definition
| surface signaling more common |
|
|
Term
|
Definition
| multiple phosphorylation sites on a signal integration protein --> very specific |
|
|
Term
|
Definition
one pathway can stimulate/inhibit another - not linear
- cells are dynamic yay! |
|
|
Term
| name the 5 second messengers |
|
Definition
| cGMP, DAG, IP3, cAMP, Ca2+ |
|
|
Term
| transduction step in each signaling mech |
|
Definition
RTK: when RTK changes comf. and is phosphorylated
G PCR: conformational change in G protein which exchanges GDP for GTP |
|
|
Term
| amplification step in each one |
|
Definition
RTK:phosphorylation cascade
G: effector enzyme uses GTP to make 2nd messenger |
|
|
Term
|
Definition
2nd messengers
ion channels |
|
|
Term
|
Definition
| peptide growth factors, paracrine signals, promote growth |
|
|
Term
|
Definition
| enzyme that activates another protein by phosphorylation |
|
|
Term
| prokaryotic quorum sensing |
|
Definition
| prokaryotes release signals which reach a threshold and induce an organized response |
|
|
Term
|
Definition
- secretion of EPS to protect cells (antibiotic resistance)
- facilitates more communication |
|
|
Term
|
Definition
1. phosphodiesterases and phosphatases - negative regulatory mechanisms
2. receptor-down regulation by lysosoming receptor, inactivating receptor or inactivating signal protein |
|
|
Term
|
Definition
| self-regulated by phosphorylation |
|
|
Term
| what makes cells so sensitive |
|
Definition
| small signals can make big responses and then be turned off quickly |
|
|
Term
|
Definition
| Ras is biggest growth protein so a mutation can lead to it being always active and lead to cancer |
|
|
Term
| what properties make 2nd messengers effective |
|
Definition
- small, diffusable
- short-lived so does job quickly then quickly leaves |
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|
