Term
| How do bacteria regulate gene expression? |
|
Definition
| Turn ON/OFF genes in response to a particular stimulus |
|
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Term
|
Definition
| An operon is a cluster of different genes that are transcribed together as a single mRNA. |
|
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Term
| What are operons regulated by? |
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Definition
| Repressors and activators |
|
|
Term
| What does the absence of tryptophan do? |
|
Definition
| Turns on trp operon, transcription starts |
|
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Term
| How can transcription be blocked? |
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Definition
| The inactive repressor doesn't bind to the operator |
|
|
Term
| What is the operator?What is it's location? |
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Definition
| A site in the DNA molecule where regulatory proteins bind. Located at the promoter |
|
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Term
| What allows the trp operon to bind tightly to the tryptophan repressor protein? |
|
Definition
| Conformational change of the protein |
|
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Term
| What does the lac operon do? |
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Definition
| Synthesizes the proteins needed for transport and break down of lactose into monosaccharides. |
|
|
Term
| What does transcription of a lac operon require? |
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Definition
|
|
Term
| What stimulates binding of the activator protein to DNA? |
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Definition
| When glucose is low, the concentration of cAMP increases,which binds to inactive CAP protein, which binds to DNA |
|
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Term
| What are the consequences of a repressor binding to an operator? |
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Definition
| Gene is turned OFF, no transcription, translation, or proteins |
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Term
| What happens to the inducer at high and low concentrations? |
|
Definition
Low= operon is off
High= binds to repressor so it can't bind to operator |
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|
Term
| What does the repressor operon do? |
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Definition
| Transcription occurs, tryp avail= gene OFF, low/no trp= operon ON cuz it can't bind to repressor |
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|
Term
| When is the lac operon turned ON? |
|
Definition
| Lactose is present, glucose is not |
|
|
Term
| When is the trp operon turned ON? |
|
Definition
| When tryptophan is absent |
|
|
Term
| What do RNA polymerases (in eukaryotes) require for transcription to occur? |
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Definition
|
|
Term
| Where are regulatory proteins located in eukaryotes for transcription to occur? |
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Definition
|
|
Term
| What help chromatin packing and are present in eukaryotes and not prokaryotes? |
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Definition
|
|
Term
| What are the 3 functions of transcription factors? |
|
Definition
| Position enzyme @ promoter, separate DNA, start transcription |
|
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Term
| Differences between cells due to differential gene expression are mediated by what? |
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Definition
| Changes in chromatin condensation, RNA processing, entry/exit into/out of nucleus, other transcription factors, regulation of translation and proteins |
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Term
|
Definition
| Assist in the assembly of RNA polymerase complex |
|
|
Term
| What do activators bind to and where are they located? |
|
Definition
| Enhancers, located a distance away from gene |
|
|
Term
| How does transcription begin? |
|
Definition
| Activator binding to enhancer |
|
|
Term
| What does the mediator complex interact with? |
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Definition
|
|
Term
| What's an example of cell type specific gene regulation? |
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Definition
| TTR gene in mammals, expressed only in hepatocytes and is controlled by 5 different transcription factors |
|
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Term
| Whether or not a particular gene is expressed at a particular time is dependent on what? |
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Definition
| Concentration of transcription factors in the nucleus |
|
|
Term
| Why are hormones small and lipid soluble? |
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Definition
| So they can diffuse through cytoplasm and plasma membrane and bind directly to the transcription factor they are regulating |
|
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Term
| What is an example of a single protein regulating translation of one mRNA and degradation of another? |
|
Definition
| Iron response element-binding protein (IRE-BP) |
|
|
Term
| When iron level is low what does IRE-BP do? |
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Definition
| Binds to iron response element, operates to increase level of cellular iron |
|
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Term
| When iron level is high what does IRE-BP do? |
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Definition
| System prevents accumulation of free ions. IREBP undergoes a conformation change and cant bind either mRNA |
|
|
Term
| What control specific mRNA translation? |
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Definition
| Sequence specific RNA binding proteins |
|
|
Term
| What does temporary regulation do? |
|
Definition
| Takes protein out of host for a period of time |
|
|
Term
| Describe mRNA degradation |
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Definition
| Protein dicer cuts up double stranded mRNA, perfect binding |
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Term
| What's a practical example of transitional repression? |
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Definition
|
|
Term
|
Definition
| Binds to iron when it's high or imports iron into the cell. OVERALL= prevents excess iron from damaging cells |
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Term
| What did Mendelson and Stahl discover in 1958? |
|
Definition
| The DNA replication was semi=conservative |
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|
Term
| Where does replication occur in Prokaryotes? |
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Definition
|
|
Term
| Where does replication occur in Eukaryotes? |
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Definition
|
|
Term
| What happens as the replication fork proceeds? |
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Definition
| Proteins move away from the origin |
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|
Term
| Why does replication occur in an area rich in A-T bonds? |
|
Definition
|
|
Term
| A group of _________ work at the replication fork. |
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Definition
|
|
Term
| What does DNA helicase do? |
|
Definition
| opens up the double helix by hydrolyzing energy from ATP to break up bonds |
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|
Term
|
Definition
|
|
Term
| What does topoisomerase do? |
|
Definition
| Releases tension of super coils |
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Term
|
Definition
| Pieces together Okazaki fragments |
|
|
Term
| What does DNA templating require? |
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Definition
| Recognition of each nucleotide in the DNA template strand by a free (unpolymerized) complementary nucleotide. |
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Term
| Bloom’s syndrome & Werner’s syndrome result from incorrect DNA replication. What are some symptoms of these diseases? |
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Definition
| Chromosome breaking, early aging, pre-disposed to cancer |
|
|
Term
| What do single stranded binding proteins (SSBs) do? |
|
Definition
| Bind to the separated DNA strands and prevent reannealing of ssDNA |
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Term
| How does the antibiotic Cipro kill anthrax? |
|
Definition
| Inhibit the synthesis of topoisomerase, so cell replication in bacteria is prevented |
|
|
Term
| What does the Sliding β-clamp do? |
|
Definition
| Keeps the polymerase firmly on DNA when it is moving but releases it as soon as the polymerase runs in to dsDNA |
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|
Term
| What are the short fragments synthesized during DNA replication called? |
|
Definition
| Okazaki fragments, which are apart of the lagging strand, which is synthesized discontinuously away from the replication fork |
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|
Term
| The error rate of replication has a high fidelity because of it's proofreading, which is carried out by what? |
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Definition
|
|
Term
| Why is the mutation rate for DNA replication so low? |
|
Definition
| DNA polymerase has a higher affinity for correct bases |
|
|
Term
| What does exonuclease function in? |
|
Definition
| Removing mismatched bp's in lagging strand |
|
|
Term
| What is true about replication in Eukaryotes? |
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Definition
|
|
Term
| Autonomously replicated sequences (ARS)- bound are by what protein? |
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Definition
| ORC= Origin Recognition Complex |
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|
Term
| What happens before S-phase activation? |
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Definition
| Factor binds replication complex |
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|
Term
| What is the role of a metabolite that controls a repressible operon? |
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Definition
| Bind to the repressor protein and activate it |
|
|
Term
| When is the lac operon likely to be transcribed? |
|
Definition
| When the cyclic AMP and lactose levels are both high within the cell |
|
|
Term
| When does transcription of structural genes in an inducible operon being? |
|
Definition
| When the pathway's substrate is present. |
|
|
Term
| What sequence specific factors can regulate gene expression in a eukaryote? |
|
Definition
| Activators and repressors |
|
|
Term
| Where does protein degradation occur? |
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Definition
|
|
Term
| What does the addition of multiple ubiquitin of a protein result in? |
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Definition
|
|
Term
| What binds with the repressor to alter its conformation? |
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Definition
|
|
Term
| What is a repressor protein produced by? |
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Definition
|
|
Term
| What is a DNA element that stimulates transcription of eukaryotic promoters? |
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Definition
|
|
Term
| Why do we need cell cycle regulation? |
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Definition
| Insures proper order of cell division and replication. Makes sure each daughter cell has correct chromosome # |
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Term
|
Definition
| Cell growth & organelles duplicate |
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Term
|
Definition
| Cell grows and prepares for mitosis |
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|
Term
| What happens during S phase? |
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Definition
| DNA replication and chromosome duplication |
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|
Term
| What is passage between cell cycle stages regulated by? |
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Definition
|
|
Term
| What's an example of cells that lack the ability to divide? |
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Definition
|
|
Term
| What cells don’t normally divide but can when given the correct cues? |
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Definition
|
|
Term
| What cells have a high ability to divide? |
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Definition
| Spermatogonia, epithelial, and hematopoietic stem cells |
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|
Term
| Johnson & Rao discovered what in the 1970’s?Which is what? |
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Definition
| What controls the cell cycle- diffusable factors |
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Term
| What nucleus initiates DNA synthesis? |
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Definition
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Term
| What evidence was shown in Johnson and Rao's exprmnt that led to the theory that diffusable factors are responsible for cell cycle regulation? |
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Definition
| Interphase cells fused with G1, S or G2, fused with cells in mitosis, then their nuclear enveloped retracted and chromosomes condensed. |
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Term
| What was found out about G2 and S phase? |
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Definition
| The G2 nucleus stays in G2. The G1 nucleus enters S-phase on it’s own schedule. |
|
|
Term
| What is required for the progression of G2 to M phase? |
|
Definition
| MPF (Maturation promoting factor) |
|
|
Term
| What's required for a female to produce progesterone? |
|
Definition
|
|
Term
| What heterodimeric protein is MPF activity caused by? |
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Definition
|
|
Term
| What happens when cyclin is low? High? |
|
Definition
Low= inactive cuz kinase lacks cyclin subunit
High= Kinase activated, cell enters M phase |
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|
Term
|
Definition
| Phosphorylates protein to activate M phase |
|
|
Term
| What does MPF activity have a direct correlation with? |
|
Definition
| Mitosis and high cyclin levels |
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|
Term
| What are responsible for regulating entry into S-phase? |
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Definition
|
|
Term
| What mechanisms regulate cyclin-cdks? |
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Definition
| 1)Presence and levels of cyclins 2)Phosphorylation of cdk 3)Intrxn w/ inhibitory proteins 4)Subcellular localization |
|
|
Term
| What ubiquitin ligase inhibits S phase? |
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Definition
| SCF, which poly ubiquintinates inhibitors of Sphase cyclin CDKs – marking them degradation |
|
|
Term
| What was found concerning cell size in EM fission of yeast? |
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Definition
| Long cells are about to enter mitosis and short cells just went through cytokinesis |
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|
Term
| How many sites of phosphorylation does cdc2 have? |
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Definition
|
|
Term
| What do cdk's require for activation? |
|
Definition
|
|
Term
| What phosphorylates cdc2? |
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Definition
|
|
Term
| What starts the final phosphorylation of cdc to activate mitosis? |
|
Definition
|
|
Term
| What are cyclin cdk's held together by? |
|
Definition
| Sic1 (a cdk inhibitory protein) |
|
|
Term
| What does SCF do (in late G1)? |
|
Definition
| Adds ubiquitin to Sic1- targets it to proteosome for degradation |
|
|
Term
| What are proteins targets of destruction? |
|
Definition
| After they've been phosphorylated |
|
|
Term
| What inhibits cdk activity and what activates it? |
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Definition
|
|
Term
| When cyclin-cdks are active where do they accumulate? |
|
Definition
| in the nuclues, only during M phase |
|
|
Term
| Pathway of ATM, for damage by radiation |
|
Definition
| cdk2--> p53--> p21--> --> inactivation of cdk,cell cycles arrest |
|
|
Term
| Pathway of ATR kinases For UV damage |
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Definition
| chk1--> cdc25--> inactive cdk--> cell cycle arrest |
|
|
Term
| What's the site of microtubule attachment? |
|
Definition
|
|
Term
| What is condensation mediated by? |
|
Definition
| Condensin, which is activated by M-phase cdk |
|
|
Term
| What holds sister chromatids together? |
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Definition
|
|
Term
| Describe the bipolar mitotic spindle |
|
Definition
| 2 centrosomes appear @ opp. poles of the cell |
|
|
Term
| What lines chromosomes up at the metaphase plate? |
|
Definition
| Rapid shortening and lengthening of microtubules |
|
|
Term
| Cleavage of cohesion is regulated by what? |
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Definition
|
|
Term
| Cleaving of cohesion that triggers anaphase |
|
Definition
| Anaphase promoting complex |
|
|
Term
| What is anaphase A change triggered by? |
|
Definition
| The separtion of sister chromatids |
|
|
Term
|
Definition
|
|
Term
| The presence of ______ stops cell progression into anaphase. |
|
Definition
|
|
Term
| What forms the contractile ring for cytokinesis? |
|
Definition
|
|
Term
| What inhibits anaphase promoting complex (APC)? |
|
Definition
|
|
Term
| What does a mutated wee1 gene cause? |
|
Definition
| Early cell divison, cell goes from G1-->S, skipping G2 |
|
|
Term
| In paracrine signaling, the signaling molecule |
|
Definition
| Acts on cells in close proximity to the secreting cell |
|
|
Term
| When are GTP-binding proteins ON? |
|
Definition
|
|
Term
| What are ligands considered in cell signaling? |
|
Definition
|
|
Term
| Nerve stimulation alone results in activation of glycogen phosphorylase kinase as a result of: |
|
Definition
|
|
Term
| What enzyme is activated directly by cAMP? |
|
Definition
|
|
Term
| Bacteria regulate the expression of their genes according to what? |
|
Definition
| food sources available in the environment |
|
|
Term
| What's the function of enhancers and silencers? |
|
Definition
| To bind to transcriptional activators/repressors |
|
|
Term
| Phosphorylation of proteins can be repressed by what? |
|
Definition
|
|
Term
|
Definition
| Form an imperfect hybrid with imperfect RNAs |
|
|
Term
| Name 3 types of post transcriptional regulation of protein coding genes |
|
Definition
| 1)seq specific RNA binding proteins control translation, 2)phosphorylation of protein leads to translation, 3)repressed by microRNA/RNAi |
|
|
Term
| What activates CAP by binding to it? |
|
Definition
| Increase in cAMP, which increases the affinity for the promoter to start transcription |
|
|
Term
| Describe dispersive DNA replication |
|
Definition
| Pieces break off and rejoin |
|
|
Term
| Describe replication in eukaryotes |
|
Definition
| 2rplctn forks move in opp directions from a single origin.when rplctn fork meets@opp points on the circle rplctn is terminated and 2duplexes detach |
|
|
Term
| Why do we need a primer for replication to begin? |
|
Definition
| Primer initiates chain synthesis |
|
|
Term
|
Definition
| Leading = has a primer towards replication fork, continuous synthesis,lagging= discntns , forms okazaki frags |
|
|
Term
| Describe exonuclease activity |
|
Definition
| Higher affinity glue correct bp, removes RNA primers in lagging stand our incorrect nucleotides |
|
|
Term
| DNA ligase repairs nicks where? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| Autonomously replicating sequences |
|
|
Term
| What do licensing factors do? |
|
Definition
| Bind after mitosis, forming a prereplication complex, activating factors that initiate replication |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
| Describe nucleotide excision repair |
|
Definition
| Can repair damage in.pyrimadine dimers via coupled/global pathway; damage recognized,XPB n XPD act as helicases, gap gets filled in and ligated |
|
|
Term
| Describe base excision repair |
|
Definition
| Fixes deamination, cuts base from backbone, bad stuff removed by an endonuclease, gap filed by DNA pol sealed by ligase |
|
|
Term
| Mismatch repair corrects what? |
|
Definition
|
|
Term
| Sic1 accumulates and binds to what? |
|
Definition
|
|
Term
| Why are only certain cell types affected by retroviruses? |
|
Definition
| Certain cells have the surface receptors that interact w the viral envelope proteins |
|
|
Term
| DNA pol has a 3'-->5' exonuclease activity, what does that mean? |
|
Definition
| Bp doesn't occur when incorrect bp is incorporated.it clips off unpaired residues @primer terminus, continuing until Enough nucleotides have been removed to regenerate a 3OH terminus |
|
|
Term
|
Definition
| Checks cell size, nutrients, growth factors, DNA damage |
|
|
Term
|
Definition
| Checks for chromosome attachment to spindle |
|
|
Term
|
Definition
| Checks for cell size, completion of DNA replication, DNA damage |
|
|
Term
| What does MPF do in the Johnson and Rao experiment? |
|
Definition
| MPF is the cause of premature chromosome condensation |
|
|
Term
| What are cyclin/cdks regulated by? |
|
Definition
| Presence n levels of cyclins, phosphorylation of cdk, interaction w inhibitory proteins n subcellular organization |
|
|
Term
| What are common tools used by signaling transduction pathway? |
|
Definition
| GTP-binding proteins, protein kinases n phosphates,2nd messengers |
|
|
Term
| When are GTP binding proteins on?off? |
|
Definition
| Bound to GTP, bound to GDP |
|
|
Term
| What are the 2diff classes of GTP binding proteins? |
|
Definition
| Trimeric(lg, bind directly).monomeric(linked indirectly cuz adaptor proteins n GEFs) |
|
|
Term
| What are some advantages to having 2nd messengers? |
|
Definition
| Diffuse faster, activation of a single surface receptor can lead to increase of thousands of cAMP or Ca |
|
|
Term
| 2exs of downstream signals |
|
Definition
| 1)adenyl cyclase increasing levels of secondary messengers cAMP, 2)phospholipase C increasing levels of secondary messengers IP3 and DAG |
|
|
Term
|
Definition
|
|
Term
|
Definition
| Allows lactose to enter the cell |
|
|
Term
|
Definition
| Acetylates lactose or related molecules |
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