Term
- __ differentiates eukaryotes from prokaryotes
-- feature of eukaryotic ____
-- is a __ membrane
-- layers fused at ___
-- outside membrane contiguous with __
-- inner membrane lined with __
-- chromosomes associated with lamina through __ |
|
Definition
- nuclear envelope
-- true nucleus
-- double layered
-- pores
-- ER
-- lamina matrix (intermediate filament)
-- heterochromatin (highly condensed chromatin) |
|
|
Term
- __: differentiates eukaryotes from prokaryotes
- __: ribosome synthesis
- __: dna complexed with protein
- __: materials move in and out of nucleus through this
-__: nuclear cytoskeleton |
|
Definition
- nuclear envelope
- nucleolus
- chromatin
- nuclear pore
- nuclear matrix |
|
|
Term
- __ containing protein binds __ receptor (__) in cytoplasm
- docks __ extending from outer ring
- stimulates conformational change in central channel ___
- __ binds importin beta subunit to recycle importin to __
- importin alpha returned to cytoplasm by __
- __ is a ras like monomeric G protein |
|
Definition
- nuclear localization sequence (NLS); NLS; (importan)
- cytoplasmic filaments
- FG domains
- ran-gtp; cytoplasm
- exporting
- Ran |
|
|
Term
Nucleosome
- __: sites of covalent modifications
-- some modifications make tata box more accessible (__), while others make it less accessible (__) |
|
Definition
- N terminal tails
- (active euchromatin); (inactive euchromatin or heterochromatin) |
|
|
Term
- __ modifications give a histone code to activity state
-- acetylation: __
-- deacetylation: __
-- methylation (K9H3, K27H3, K20H4): __
-- methylation (K36H3, K4H3): __
-- Phosphorylation (S10H3): __ |
|
Definition
- N-terminal covalent modifications
-- active chromatin
-- inactive chromatin
-- inactive heterochromatin
-- active chromatin
-- mitosis |
|
|
Term
2nd level packaging: 30nm fiber
- increases packaging ratio __
- __ array wound into large diameter fiber
- structure
-- __ most accepted model
-- random __
- folding requires __ at dna entry and exit points around nucleosome
- __ affect 30nm fiber folding |
|
Definition
- 40 fold
- nucleosome
-
-- solenoid
-- zig zag
- histone H1
- N-terminal covalent modifications |
|
|
Term
chromatin 3rd level = ___
- bases of loops thought to be attached to __ |
|
Definition
looped domains
- nuclear matrix/scaffold |
|
|
Term
__: dna complexed with protein
- total of 2 meters dna in typical eukaryotic nucleus with diameter of 10 micrometers
- must be complexed with __ to compact into orderly, accessible structure |
|
Definition
|
|
Term
4th level of packaging in __
- __: metaphase like packaging throughout cell cycle (__)
- __: metaphase like packaging during mitosis only (__) |
|
Definition
metaphase chromosome
- heterochromatin (transcriptionally silent)
- euchromatin (transcriptionally competent during interphase) |
|
|
Term
cloning process:
- reverse differentiated state of somatic cell nucleus (return to __ through loss of __)
--__ is the ability of a single cell to divide and produce all the differentiated cells in an organism
- nucleus injected into __
- __ formed (without union of sperm and egg: fertilization)
- source of __ for gene therapy |
|
Definition
-( totipotency; heterochromatin)
- totipotency
- enucleated egg
- diploid zygote
- stem cells |
|
|
Term
| __ refers to a stem cell that has the potential to differentiate into any of the three germ layers: |
|
Definition
|
|
Term
- all genes have a __ organization making them open for __
- tissue specific genes become __ in tissues where they are not transcribed |
|
Definition
- euchromatic; transcription
- heterochromatic |
|
|
Term
two classes of heterochromatin
- __: developmentally regulated, example is x-chromosome inactivation
- __: needed for __, and composed of __ |
|
Definition
- facultative (regulated) heterochromatin
- constructive (unregulated) heterochromatin; chromosome segregation; repetitive dna |
|
|
Term
- 1 of pair of x chromosomes in female mammals is inactivated by __
- random decision as to which x becomes heterochromatic during early embryogenesis
- heterochromatin state is __
- initiation of X chromosome inactivation requires __ which coats X chromosome first expressing gene for it.
- maintenance (mitotic memory) due to methylation of dna and k-27 histone h3 that recruit ___ |
|
Definition
- facultative heterochromatin
-
- mitotically heritable
- Xist non-coding RNA
- facultative heterochromatin protein (POLYCOMB) |
|
|
Term
- __ operon is inducible (induced by substrate of genes) in that __ activates genes required to catabolize __
- __ operon is repressible (repressed by product of genes) in that __ represses genes required to synthesize __ |
|
Definition
- lac; lactose; lactose
- trp; tryptophan; tryptophan |
|
|
Term
- __ dna binding sites for __ regulatory proteins
-- __: regulatory protein, __ structural genes
-- __: dna promoter sequence, __ structural genes |
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Definition
- cis-acting; trans-acting
-- trans acting; away from
-- cis-acting; adjacent to |
|
|
Term
- __ factors bind __ regulatory sequences in eukaryotic transcription also
-- __ increase tata box activity
-- __ reduce tata boxy activity |
|
Definition
- trans-acting; cis-acting
-- enhancer elements
-- silencer elements |
|
|
Term
- enhancers recruit __ to enhance tata box activity by __ or __
- silencers recruit __ to reduce tata box activity |
|
Definition
- co-activators; histone modification complex; chromatin remodeling complex
- co-repressors |
|
|
Term
co-activators are recruited to __ through enhancers
- two classes
1. __: acetylate n terminal tails, weakin binding of dna to histone
2. __: atp dependent activity, __ induces dna sliding along surface of nucleosome
- both increase likelihood that __ and __ are recruited |
|
Definition
promoters
1. histone acetyltransferase (HAT)
2. SWI/SNF chromatin remodeling complex; nucleosome plow
- tbp; rna poly II |
|
|
Term
co-repressors are recruited to promoters through ___
two types:
1. ___
- removes __ groups from histone n terminal tails (strenghten interaction between dna and histones)
-- __ and __
2. ___
- methylate histone n terminal tails, allow binding of heterochromatic silecer proteins |
|
Definition
silencers
1. histone deacetylase complex (HDAC)
- ac
-- inactive euchromatin; heterochromatin
2. histone methyltransferase (HMTase) |
|
|
Term
differential splicing in drosophilia sex determination
- __ splicing repressor protein (regulates its own splicing)
- female splicing mode: __
- male splicing mode: __ |
|
Definition
- sex lethal
- protein made
- no protein made |
|
|
Term
many mRNAs produced in egg protected from translation until post-fertilization
- __ phosphorylation activates translatioin
- __ of sea urchin egg mRNAs contain binding sites for translation inhibitors, prevent assembly of translation until after fertilization
- some UTR sequences contain ___ |
|
Definition
- CPEB (cytoplasmic poly a element binding protein)
- 3' UTR (untranslated regions)
- mRNA localizing information |
|
|
Term
- siRNA targets mRNA for degradation by __
- histone h3 methyltransferase recruited to TEs through ___ |
|
Definition
- RISC
- RISC like complex (RITS) |
|
|
Term
- __: protein degradation machine
-- protein stability (half-life) is protein specific
-- __ of protein targets it for binding to proteasome cap
-- proteolysis occurs __ of proteosome |
|
Definition
- proteasome
--
-- ubiquitination
-- inside barrel |
|
|
Term
- __ and __ experiment
-- newly incorporated nucleotides contain 14N- allowed newly replicated dna to be followed |
|
Definition
|
|
Term
- __: leads to all hybrid strands
- __: leads to one helix of parents and one helix of daughters
- __: leads to each helix having one parental and daughter strand |
|
Definition
- dispersive replication
- conservative
- semi-conservative |
|
|
Term
- leading and lagging strand synthesis are done __
- leading strand synthesis done __
- lagging strand synthesis done __ |
|
Definition
- simultaneously
- continuously
- fragmentally (okazaki fragments) |
|
|
Term
lagging strand
1. primer synthesis by __
- rna primer provides __
2. elongation by __
3. primer removal and gap filling by __
4. strand sealed by __ |
|
Definition
1. primase
- 3' OH
2. dna poly 3
3. dna poly 1
4. dna ligase |
|
|
Term
- sliding beta clamp
-- allows dna polymerase to move continuously from __ to __ without dissociation
-- allows dna polymerase to move from __ to __ during lagging strand synthesis |
|
Definition
-
-- nucleotide; nucleotide
-- primer; primer |
|
|
Term
- __: stabilizes unwound dna to keep it from re-annealing
- __: binds ssdna to prevent it from winding back on itself in eukaryotes |
|
Definition
|
|
Term
| __, is a protein that acts as a processivity factor for DNA polymerase δ in eukaryotic cells. It achieves this processivity by encircling the DNA, thus creating a topological link to the genome. It is an example of a DNA clamp. |
|
Definition
| Proliferating Cell Nuclear Antigen, commonly known as PCNA |
|
|
Term
- __: plasmid (origin of replication)
- __: binds ARS and recruits MCM, marks origin
- __: licensing factors that give license to replicate only once per cell cycle, recruits activating factor.
- __: initiate replication |
|
Definition
- ARS (autonomous replication sequence)
- ORC (origin replication complex)
- MCM (mini chromosome maintenance)
- activating factors |
|
|
Term
- __ activity only high in proliferating cells (stem cells and cancer cells)
- __: naturally occurs in somatic cells with aging
- __: results with telomerase over-expression, immortalizes cell (stem cell, cancer like)
- __ associated with chronic stress
- __ overexpression results in telomere lengthening may be partially responsible for life span extending activity |
|
Definition
- telomerse
- telomere shortening
- telomere lengthening
- telomere shortening
- sir2 (sirt1) |
|
|
Term
proofreading activity during replication
- prokaryotes:
- eukaryotes: |
|
Definition
- dna poly I, II, III
- dna poly delta |
|
|
Term
- nucleotide excision repair: repair after replication
-- __ replaced
-- preferential pathway for actively transcribed genes, __ couples process
- repair proteins identified as:
-- __ mutated in xeroderma pigmentosa patients with dna repair defects
-- purified human __ proteins that repair dna damage induced in rodent cells
-- yeast __ proteins discovered as mutations that affect dna repair |
|
Definition
-- whole dna strand
-- TFIIH
-
-- XP proteins
-- ERCC
-- RAD |
|
|
Term
base excision repair
- __ replaced
- __ remove altered bases generated by reactive chemicals
- cytosine is easily altered to __
- one of the most highly conserved proteins from e. coli to humans is __ |
|
Definition
- base (then nucleotide
- glycosylases
- uracil
- uracil-dna glycosylase |
|
|
Term
double strand break repair
- __: binds free dsDNA ends (also has function at telomeres)
- __: protein kinase recruited to site |
|
Definition
|
|
Term
Eukaryotic cell cycle
- __: majority of time, single chromatid
- __: dna synthesis, leads to pair of sister chromatids
- __: cell growth, with pair of sister chromatids
- __: nuclear and cell division |
|
Definition
- interphase
- s phase (dna synthesis)
- G2
- mitosis (m phase) |
|
|
Term
- MPF = __ + __
-- __ regulates proteins by phosphorylation
-- __: cell cycle phase specific kinase regulators |
|
Definition
- Cdk (cyclin dependent kinase); cyclin
-- Cdk
-- cyclin |
|
|
Term
- Cdk/Cyclin regulates by __ target proteins
- __ levels are constant, __ levels cycle through regulated synthesis and destruction
-- __ levels are regulated by __ activity |
|
Definition
- phosphorylating
- Cdk; cyclin
-- cyclin; proteasome |
|
|
Term
| - __: cyclin dependent kinase phosphorylates dna replication proteins |
|
Definition
|
|
Term
- SCF: promotes __, ubiquinates __
-- SCF > __
- APC promotes __ and __, ubiquinates __
-- APC > ___ |
|
Definition
- s phase, S phase inhibitors
-- entry to s phase
- anaphase; G1; metaphase stabilizers
-- exit from m phase events |
|
|
Term
-scf and apc target proteins for ___
-- two types of apc: __ and __ |
|
Definition
- ubiquination (destruction)
-- Cdc 20; Cdh1 |
|
|
Term
-S phase inhibitors
-- __: normal cells
-- __: dna damage induced
- scf targeted destruction of __ allows entry into __
- apc targeted destruction of __ allows exit from __ |
|
Definition
-
-- p27
-- p21
- p27; S phase
- M-cyclin; m phase |
|
|
Term
| MCM (licensing factors) recruits __ and __ |
|
Definition
|
|
Term
- activating phosphorylation
-- __: Cdk activating kinase
- inactivating phosphorylation
-- Kinase, PO4 on by __ (cells divide prematurely)
-- Phosphatase, PO4 off by __ (cells unable to divide) |
|
Definition
|
|
Term
DNA damage induces cell cycle arrest
- __ phosphorylates Chk1 and Chk2 (also kinases)
- G1 arrest: __ stabilizes __ (transcription factor for p21 gene)
- G2 arrest: __ inactivates __
-- __ trapped in cytoplasm by __
- both inactivate __ = cell cycle arrest
- __ induces cell death if damage not repaired |
|
Definition
- ATM
- Chk2; p53
- Chk1; Cdc25p
-- Cdc25p; Rad24
- Cdk
- p53 |
|
|
Term
|
Definition
| prophase > prometaphase > metaphase > anaphase > telophase |
|
|
Term
prophase
- __ condenses
- __ disassembles
- __ forms
- __ form
- __ and __ fragment
- __ disappears |
|
Definition
- chromatin
- cytoskeleton
- mitotic spindle
- kinetochores
- golgi complex; ER
- nuclear envelope |
|
|
Term
prometaphase
- __ attach to __
- __ move to __ |
|
Definition
- microtubules; chromosome kinetochores
- chromosome; spindle equator |
|
|
Term
metaphase
- chromosomes aligned at __, attached to __ from each pole |
|
Definition
| - spindle equator (metaphase plate); spindle microtubules |
|
|
Term
anaphase
- __ split, and __ separate
- __ move to opposite poles
- __ move apart |
|
Definition
- centromeres; sister chromatids
- chromatids
- spindle poles |
|
|
Term
telophase
- __ at opposite poles
- chromosomes __
- __ reassembles
- __ and __ reform
- __ (cell cleavage) |
|
Definition
- chromosomes
- decondense
- nuclear envelope
- golgi complex; ER
- cytokinesis |
|
|
Term
| __ allow sister chromatid separation |
|
Definition
|
|
Term
prophase: chromatin condensation
- requires __ and __
- cohesin functions during __ and __
- condensin required only to condense chromosomes during __
- __ phosphorylation activates __ |
|
Definition
- cohesin; condensin
- interphase; m phase
- m phase
- condensin; condensation |
|
|
Term
prophase 4: nuclear envelope disassembly
- __ proteins phosphorylated by __
- __ are intermediate filament proteins |
|
Definition
- lamin; m phase Cdk
- lamins |
|
|
Term
metaphase: alignment of chromosomes at metaphase plate
- __ at centromeres holds sister chromatids together
- balanced action of __ and __ center chromosomes
- __ assembly and disassembly also plays role in alignment |
|
Definition
- cohesin
- +; - directed motors
- microtubule |
|
|
Term
anaphase: separation and movement of sister chromatids to opposite poles
- __ cleaved to allow separation, __ induces
- __ moves chromosome towards pole as __ depolymerize at kinetochore
- equal tension on sister chromatids sensed: triggers __ degradation triggered by __ |
|
Definition
- cohesin; apc-cdc 20
- - end directed dynein motor; MTs
- Mad2; apc-cdc20 |
|
|
Term
| cytokinesis involves __ and __ |
|
Definition
|
|
Term
meiosis resembles mitosis but also includes:
- reductive division (__): __ separate
- followed by no intervening __, and...
- non-reductive division (__): __ separate |
|
Definition
- (meiosis I); chromosome homologues
- S phase
- (meiosis II); sister chromatids |
|
|
Term
human meiotic NONDYSJUNCTION
- con occur during __ or __
- prolonged __ arrest in mammals increases __ nondysjuntion rate
-- results in __ |
|
Definition
- meiosis I; meiosis II
- prophase I; meiosis I
- aneuploid gametes (abnormal chromosome #) |
|
|
Term
| The __ is a protein structure that forms between homologous chromosomes (two pairs of sister chromatids) during meiosis and that is thought to mediate chromosome pairing, synapsis, and recombination (crossing-over). |
|
Definition
|
|
Term
-indirect effector activation through __
- direct effector activation: membrane recruitment of __ |
|
Definition
|
|
Term
- direct activation pathways include
-- receptor tyrosine kinase: __ and __
-- tumor necrosis factor receptor is __ response |
|
Definition
-
-- growth factor response; insulin response
-- cell death |
|
|
Term
Direct activation: __ kinase
- __ binding stimulates receptor dimerizatin
- dimerization stimulates __
- __ receptor binds __ that link to downstream target proteins
-- one type of adapter: __ (contain src homology domain)
-- __ named after src kinase, 1st oncogene discovered |
|
Definition
receptor tyrosine kinase (RTK)
- ligand
- trans autophosphorylation
- phosphorylated; adapters
-- SH2 protein
-- SH2 domain |
|
|
Term
- adapter often links activated __ to cytoplasmic __
- __ ends with __ of some target protein that brings about cellular response
- __ required to return to ground state |
|
Definition
- RTK; kinase cascade
- Kinase cascade; phosphorylation
- phosphatase |
|
|
Term
mitogen (mitosis activating
- growth factor response
-- __ kinase cascade
-- amplifies effect of small amount of __
-- stimulates __ of genes that regulate __ (some downregulate pathways)
-- __ is a g protein that activates downstream kinase cascade |
|
Definition
-- MAP
-- growth factor signal
-- transcription; mitosis
-- Ras |
|
|
Term
__ (insulin receptor) in glucose uptake
- insulin ligand produced by __
- insulin binding to insulin receptor activates __ and __ effector through __ adapter |
|
Definition
RTK
- beta cells of pancreas
- Ras; PI 3 Kinase; IRS (insulin receptor substrate) |
|
|
Term
__: glucose transporter
- __ activates glut4 membrane localization
- mutations in glut4 and other components of insulin pathway responsible for __
- __: failure to make insulin
- system overload due to sustained elevated glucose levels can also lead to __ and __, on the rise with high calorie diets, sedentary lifestyles
- __ may be used to treat type II diabetes, induces __, which stimulates insulin pathway |
|
Definition
GLUT4
- PKB
- type II diabetes
- type I diabetes
- insulin resistance; type II diabetes
- resveratrol; starvation response |
|
|
Term
Life span extending activities:
- __ diet
- mutations in insulin signaling pathway (stimulates __)
- over-expressing __ (__ dependent starvation response regulator)
- Sirt1 activator, __ (component in red wine) |
|
Definition
- calorie restricted
- (glucose uptake)
- sirt1 (NAD+)
- Resveratrol |
|
|
Term
- active insulin signaling, ph domains are __
- no insulin signaling, PH domain proteins are __ and __
- __ activates starvation response genes (also insulin pathway) |
|
Definition
- membrane localized
- cytosolic; nuclear
- Sirt1 |
|
|
Term
indirect activation pathways:
- ex is __ w/
-- __ 2nd messenger
-- __ breakdown in liver , __ efflux in lung
-- lipid derived 2nd messenger: __ muscle contraction |
|
Definition
- g protein coupled receptor
-- camp 2nd messenger
-- glycogen; cl-
-- stomach |
|
|
Term
- indirect activation: __
- GPCRs couple to effectors through __
-- active in __ bound state
-- inactive in __ bound state
-- down regulate themselves through __ activity |
|
Definition
- GPCR (g protein coupled receptors)
- G proteins
-- gtp
-- gdp
-- GTPase |
|
|
Term
adenylyl cyclase synthesizes __ from __
- integral membrane protein located close to __ |
|
Definition
|
|
Term
gpcr and adenylyl cyclase pathway activation
- __ binds receptor (GPCR)
- couples to __ (adapter) between receptor and effector
- __ exchanged for __ on alpha subunit
- gtp alpha subunit activates __ to produce __ which activates downstream effectors to bring about cellular response |
|
Definition
- ligands
- G protein complex
- GDP; GTP
- adenylyl cyclase (effector); cAMP second messenger |
|
|
Term
gpcr and activation of glycogen breakdown in liver (__ effector)
- induced in response to stress and starvation (forced to use glucose storage)
- cAMP binds and activates __
- __ transfer PO4 groups to molecules to change their activities |
|
Definition
(adenylyl cyclase)
-
- protein kinase A
- Kinases |
|
|
Term
GPCR and cAMP in glycogen breakdown in liver
- PKA Kinase activity (phosphorylation):
-- inactivates __ (glycogen synthesis enzyme)
-- activates __ (glycogen breakdown enzyme)
-- activates __ (transcription factor) |
|
Definition
-- glycogen synthase
-- glycogen phosphorylase kinase
-- creb |
|
|
Term
gpcr with ligand of adrenaline
- beta adrenergic receptors couple to Galpha, and ___
- alpha adrenergic receptors couple to Galpha, and __ |
|
Definition
- activate adenylyl cyclase
- inhibit adenylyl cyclase |
|
|
Term
atp binding cassette cftr transporter
- __ inhibits Galpha GTPase activity |
|
Definition
|
|
Term
__ and __ assay: growth of cancer cells in culture
- allowed id of oncogenes |
|
Definition
|
|
Term
two classes of genes that transform cells when mutated
- recessive loss of function mutations in __
-- __ must be mutated, loss of function
- dominant gain of function mutations in ___
-- only __ must be mutated |
|
Definition
- growth suppressor gene
-- both copies
- growth promoting gene (oncogene)
-- 1 copy |
|
|
