Term
interactions between cells and their environments
- __ interactions
- __ interactions |
|
Definition
- cell to cell
- cell to extracellular matrix |
|
|
Term
| __: organized network of extracellular materials outside plasma membrane, provides support and determines shape and activity of cell |
|
Definition
|
|
Term
Extracellular matrix components
- collagen
-- fibrous __
-- high __
-- produced primarily by __ in ct, smooth muscle, and epithelial cells
-- triple helix of __
- 2 main types
1. __ (form __): found in tendons, bone, teeth, skin, cornea
2. __ (form __): non __ ends allow assembly into lattice instead of fiber
-- found in __ lining tissues |
|
Definition
-- glycoprotein
-- tensile strength
-- fibroblasts
-- alpha chains (gly-pro-x repeat)
1. fibrillar types (rigid fibers)
2. nonfibrillar types (fibrous lattice); alpha chain globular
-- basement membranes |
|
|
Term
Proteoglycans
- core protein with covalently attached __
- __ = repeating disaccheride with __ and __ groups that bind cations and h2o, form __
- resists __, __ cells
- protects __ from __ and regulates their diffusion |
|
Definition
- glycosaminoglycans
- GAG; SO4-; COO-; hydrated gel packing material
- crushing forces; cushions
- signaling molecules; proteases |
|
|
Term
| connecting proteins connect __ to __; and __ to __ |
|
Definition
|
|
Term
| __: composed of 2 polypeptides (linear series of domains); each polypeptide contains __ and __ |
|
Definition
| fibronectin; binding sites for ecm; cell surface proteins |
|
|
Term
__: guide cell migrations during development (cells adhere to ecm through __ during migration)
- injection of __ prevents neural crest cell migration
- injection of __ (competes w/cell binding domain) prevents neural crest cell migration
- __: similar experiments show its requirement for pgc migration |
|
Definition
fibronectin; (fibronectin)
- anti-fibronectin antibodies
- RGD peptide
- laminin |
|
|
Term
laminin
- __ different polypeptide chains linked by __ and organized into cross-shaped molecules
- also plays role in __, __, and __
- domains for interaction with other __
- major component of __ lining tissues |
|
Definition
- 3; disulfide bonds
- cell migration, growth, differentiation
- proteins (proteoglycans)
- basement membrane |
|
|
Term
| a __ seperates the dermal and epidermal layers of skin |
|
Definition
|
|
Term
| __: attachment of epidermal cells to basement membrane through __ |
|
Definition
|
|
Term
interactions of cells with extracellular matrix through __
- family is ___ proteins
- __ domain interacts with extracellular matrix
- __ domain interacts with cytoskeletal-linking and cell signaling proteins
- __ allows interaction with __ filaments and stimulates proper conformation of __ |
|
Definition
integrins
- integral membrane
- extracellular
- cytoplasmic
- talin; actin; integrin |
|
|
Term
inside out signaling
- __ binds to __ cytoplasmic tails, seperates __ and __, and induces __ that allows __ to bind __ |
|
Definition
| - talin; integrin; alpha; beta chains; conformational change; integrin; extracellular matrix molecules |
|
|
Term
| platelet __ binds ecm connecting proteins __ during platelet aggregation |
|
Definition
| integrin; fibrinogen (dont confuse fibrinogen with fibronectin) |
|
|
Term
platelet __ binds __ of ecm protein (__) during platelet aggregation
- __: competitive inhibitor to __ interaction
- clot buster drugs
-- __ (anti-rgd binding site antibody)
-- __ (rgd peptide) |
|
Definition
integrin; rgd; (fibrinogen)
- RGD peptide; integrin/fibrinogen
-- reopro
-- aggrastat |
|
|
Term
__ also inhibits platelet aggregation
- is a __ and __ inhibitor
- inhibits synthesis of __ and __
- low does preferentially affects __ while high dose affects __ |
|
Definition
aspirin
- cox 1 & 2
- TXA; PCL
- COX 1; both |
|
|
Term
- __ stimulates inside out signaling in platelets
- __ prevents inside out signaling that allows __ to be in conformation needed to bind __ |
|
Definition
- tromboxane 2
- low dose aspirin; integrin; fibrinogen |
|
|
Term
__ causes GI bleeding, selective __ developed to avoid
- __: cox 1 and 2 inhibitor
- solution is selective __ |
|
Definition
aspirin; COX-2 inhibitors
- aspirin
- cox-2 inhibitors |
|
|
Term
hemidesmosome
- __ attachment between cell and ecm in human body
- __ on inner surface of plasma membrane connected to __
- linked to ecm through __
- hemidesmosomal diseases:
-- __: beta integrin mutations
-- __: autoimmune disease (antibodies produced against plaque proteins)
-- __: genetic disease for hemidesmosomal proteins (bubble between dermal and epidermal layers) |
|
Definition
- tightest
- plaque; intermediate filaments (keratin)
- integrins
-- psoriosis
-- bullous pemphigoid
-- epidermolysis bullosa |
|
|
Term
Focal adhesion
- __ equivalent of __
- point of attachment to surface of __ culture dish
- __ structure
- clusters of __ in plasma that connect extracellular material with __ cytoskeleton |
|
Definition
- in vitro; hemidesmosome
- in vitro
- dynamic
- integrins; actin |
|
|
Term
| __ and __ generate muscle like force that deforms __ |
|
Definition
| actin; myosin; collagen substratum |
|
|
Term
| cell interactions with ecm mediated through __ |
|
Definition
|
|
Term
interactions of cells with other cells
- cells in early embryo dissociated, then allowed to reassociate __. __ associated with __ through specific cell adhesion molecules to form distinct tissue layers |
|
Definition
| - in vito; like cells; like cells |
|
|
Term
cadherin forms __ between cells
- tight adhesion between __
- by __ linkages through __ molecules
- cytoplasmic domain linked to __ cytoplasm by __
- transmit signals from __ to __ |
|
Definition
adherens junctions
- like cells
- calcium dependent; cadherin
- actin; beta catenin
- exterior; cytoplasm |
|
|
Term
cell adhesion: molecules in embryonic development
- __: migration of cells to form tissues
- __ play key role in determining adhesive properties of __ cells
- __: loose, non-adhesive migrating cells (__)
- __: tightly adhering, organized cell layer (__) |
|
Definition
- gastrulation
- cadherins; epithelial
- mesenchymal cells (cadherin non-functional)
- epithelial cells (cadherin functional) |
|
|
Term
| __ inappropriately undergo the epithelial to mesenchymal transition |
|
Definition
|
|
Term
__: spread of cancerous cells, enhanced through loss of normal adhesion properties or gain of abnormal ability to penetrate normal barriers
- cadherin levels down: loss of __ and metastasis __
- cahderin levels up: retain __ and metastasis __
- laminin binding up: __ up and metastasis __
- __ degrade and remodel ecm in normal cells but up regulated in metastatic tumors |
|
Definition
metastasis
- cell adhesion; up
- cell adhesion; down
- basement membrane penetration; up
- matrix metalloproteinases (MMP) |
|
|
Term
In fibroblast/carcinoma cell
co-culture model, mesenchymal
(metastatic) carcinoma cells
always follow behind __ |
|
Definition
| MMP secreting fibroblasts |
|
|
Term
| cell to cell interactions function in __ |
|
Definition
|
|
Term
Selectins
- family of integral membrane __
- extracellular domain binds __ on surface of other cells
- allow circulating __ to bind blood vessel walls at sites of inflammation |
|
Definition
- glycoproteins
- oligosaccharides (lectins)
- leukocytes |
|
|
Term
immunoglobulin super family
- characterized by extracellular __, first observed in immune system proteins and cell receptors
- also found in __
- __ needed for neural outgrowth in embryonic development
- L1 dysfunction may also play role in __
- __ mutations in __ genes are associated with autism |
|
Definition
- ig domain
- non immune cell adhesion receptors
- L1
- fetal alcohol syndrome
- copy number varian (CNV); NCAM |
|
|
Term
cell adhesion molecules in inflammatory response
- __ on neutrophils required for loose binding to __ on vessel wall
- binding activates __ on neutrophil
- __ mediate tight binding of neutrophils to __ on vessel wall
- tight binding activates __ cell shape change needed to squeeze between endothelial cells of vessel wall
- these molecules are targets of drugs for __ disease |
|
Definition
- lectins; selectins
- integrins
- integrins; igsf protein
- neutrophil
- inflammatory |
|
|
Term
| __ are specialized cadherins: very tight junction in cells subjected to great mechanical stress |
|
Definition
|
|
Term
desmosomes resemble hemidesmosomes
- __ attachement between cell and ecm
- __ on inner surface of plasma membrane connected to intermediate filaments (keratin)
- linked to ecm through __ |
|
Definition
- tightest in vivo
- plaque
- integrins |
|
|
Term
Hemidesmosome
- attachment of __ to basement membrane through __ |
|
Definition
| - epidermal cells; integrins |
|
|
Term
Desmosome
- similar structure, both have __
- numerous in tissues subjected to __
- contain specialized __ instead of __
- dense __ connect to intermediate filaments through __ |
|
Definition
- cytoplasmic plaque
- mechanical stress (skin, gum, uterine wall)
- cadherins; integrin (desmogleins; desmocollins)
- cytoplasmic plaques; cytoplasmic plaque proteins (desmoplakin) |
|
|
Term
Gap Junctions
- mediating __
- __ of adjacent cells connected by __ allowing flow of __
- connexon composed of __ arranged around central empty core
- permits communication between cells of __ |
|
Definition
- intercellular communication
- cytoplasms; connexon pipeline; small molecules
- 6 connexin subunits
- tissues requiring coordinated activity |
|
|
Term
| __: plant equivalent of gap junction |
|
Definition
|
|
Term
specialized cell-cell adhesions: __
- __ and __
- form __ to separate extracellular spaces on opposite sides of cell |
|
Definition
tight junction
- occludin; claudin
- gasket |
|
|
Term
Tight junctions
- seal the __
- intermittent points of contact between __ of adjacent cells
- row of integral membrane proteins __ and __ surround cells and form seal
- seals extracellular space on __ side of cell from that on __ side
- surround endothelial cells lining capillaries to brain to form __ for some but not all molecules |
|
Definition
- extracellular space
- membranes
- occludin; claudin
- apical (top); basal (bottom)
- blood brain barrier |
|
|
Term
__: plant equivalent of ecm
- __ bacterial, fungal, and plant cells
- __ fibers (collagen like function) embedded in __ and __ (proteoglycan like function)
- __ produced on cell surface
- some __ attack bacterial cell wall synthesis enzymes |
|
Definition
cell walls
- enclose
- cellulose; hemicellulose; pectin gel
- cellulose
- antibiotics (penicillin) |
|
|
Term
The cytoskeleton and cell motility
Key to cytoskeletal functions
1.
2.
3.
4. |
|
Definition
1. structure and support
2. intracellular transport
3. contractility and motility
4. spatial organization |
|
|
Term
fluorescence microscopy in the study of cytoskeleton
- __ in fixed cells (immunostaining)
- __ with red gfp in living cells |
|
Definition
- indirect labeling
- direct labeling |
|
|
Term
microtubules
- hollow tubular structures
- tube wall composed of ___
- dynamic + end: __ and __
- stable - end: __ and __ |
|
Definition
-
- 13 parallel protofilaments (linear arrays of alpha/beta tubulin dimers)
- fast growing and shrinking
- slow growing and shrinking |
|
|
Term
microtubules
- basic subunit: __ has __
- + end regulatable: __ stabilizes, __ destabilizes
- - end non-regulatable: locked in __ bound state
- dynamic end ends with __ subunit
- __ is a g protein regulated by gtp binding and hydrolysis |
|
Definition
- alpha/beta tubulin dimer; polarity (asymmetry)
- gtp; gdp
- gtp
- beta
- Tubulin |
|
|
Term
microtubule dynamic instability
- alpha dimer is always bound to __
- __ dimer incorporated into + end
- tube closure forces __
- __ dimer polymer unstable - disassembly
- battle between __ incorporation and __
- __: alpha/beta gtp incorporation faster, stable polymer
- __: gtp hydrolysis faster, unstable polymer
- increased __ ratio favors growth |
|
Definition
- gtp
- alpha/ beta gtp
- gtp hydrolysis
- alpha/ beta gdp
- alpha/beta gtp; gtp hydrolysis
- growth
- shrinkage
- gtp/gdp |
|
|
Term
conditions and drugs affecting mt stability
- growth or shrinkage dependent on __ content and structure of __
- mt destabilizers include:
- mt stablizers include: |
|
Definition
- gtp; microtubule (mt) cap
- cold temp, calcium, colchicine (gout), vinblastine, vincristine, nocodazole
- taxol (cancer therapeutic) |
|
|
Term
__ alter microtubule properties in cells
- contain __ that binds side of microtubule and __ extending from surface-crosslinks MTs
- many regulated by __ (hyperphosphorylation of __ map found in neurofibrillary tangles of so neurodegenerative disorders such as __)
- __ prevents depolymerization similar to taxol while __ has similar mt stabilizing function |
|
Definition
microtubule associated proteins (maps)
- globular head; filamentous tail
- phosphorylation; (tau; alzheimers)
- map2; tau |
|
|
Term
| __ establishes polarity of microtubule networks in cell |
|
Definition
| microtubule organizing center (mtoc) |
|
|
Term
microtubule organizing centers (mtoc)
- __ of mt polymerization in vivo
- establishes mt __ in cell
- - end always __
- + end always __ |
|
Definition
- nucleator
- polarity
- embedded in mtoc
- emanating from the mtoc |
|
|
Term
mtoc in animals: __
- centrioles: 2 perpendicular barrel shaped structures made up of __ and arranged into __
- pericentriollar material (PCM): __ surrounding material, __ is embedded in it
- __: 3rd class of tubulin |
|
Definition
centrosome
- microtubules (9 fibrils of 3 MTs); barrel (side)/pinwheel (end)
- amorphous; y tubulin
- y tubulin |
|
|
Term
centrosome and y tubulin ring comples
- increases __ rate
- provides template for __ in mt fiber
- establishes __ of mt networks in cell
- caps __ (stabilizes further)
- y tubulin interacts with __ only; establishing polarity |
|
Definition
- nucleation
- 13 protofilaments
- polarity
- minus end
- alpha tubulin |
|
|
Term
role of mt based moters in transporting cellular cargo
- __ of neuron
- __ in mitosis |
|
Definition
- synaptic vesicles
- chromosomes |
|
|
Term
cytoskeletal motors
- chemical energy from __ drives conformational changes in motor protein
- all motor proteins have __ and __
-- both activities in __ domain |
|
Definition
- atp hydrolysis
- atp hydrolysis activity (ATPase); cytoskeleton-binding activity
-- head |
|
|
Term
motor families have directional and cytoskeleton binding specificities
- give the 3 motor families, their cytoskeletal track, and their directionality |
|
Definition
1. Kinesin - microtubules - + end directed
2. dynein - microtubules - - end directed
3. myosin - actin microfilaments - + end directed |
|
|
Term
| myosin motors walk along __ in muscle contraction |
|
Definition
|
|
Term
Kinesin Family
- move cargo along microtubule towards __
- 2 __ chains and 2 __ chains
- __ consists of head, stalk, and tail
- the heavy head involved in __ and __
- the heavy tail and light chain involved in __
- atp hydrolysis powers __
- the motors actually walk on their __ |
|
Definition
- + end
- heavy; light
- heavy
- ATPase motor and mt binding
- cargo carrying
- conformational change (1 alpha/beta tubulin dimer per step)
- heads |
|
|
Term
dynein
- consists of __ and __
- move cargo along microtubules towards __
- function in __ and movement away from __ in endomembrane system |
|
Definition
- 2 heavy; multiple light chains
- - end
- chromosome seperation; p. membrane |
|
|
Term
vesicle connecting activities
- __ connects vesicle cargo to dynein
- __ connects vesicle cargo to kinesin |
|
Definition
|
|
Term
| polarity of mt network can be determined by using __ to locate __ |
|
Definition
| y tubulin immunostaining; MT - end |
|
|
Term
how can + end of in vitro assembled mt be identified?
- add __ to mt fibers |
|
Definition
| - Fl labeled a/b tubulin dimers |
|
|
Term
inner structure of cilium (axoneme)
- __ MTs surround __
-- inner and outer __
- no __ or __
- __ structure resembles __ |
|
Definition
- 9 a/b doublet; 2 central MTs
-- dynein arms
- radial spoke; central MT
- Basal body; centriole |
|
|
Term
__ motors in rotary movement of cilium or flagellum
- __ attached to a tubule
- __ walk along b tubule of neighboring MT doublet
- __ regulate frequency of beat |
|
Definition
dynein
- tails of dynein arms
- outer dynein arms (head)
- inner dynein arms |
|
|
Term
- dynein motors walk along MTs, and induce __ that causes __
- dynein attached to __ walks along __
- a and b tubules slide __ to one another
- __ causes flagellar bending |
|
Definition
- MT sliding; flagellar bending
- A tubule; B tubule (- end)
- relative
- T sliding |
|
|
Term
microfilaments (actin polymers)
- actin filament regulated by __
- 2 strands of an actin polymer wound into __
- actin polymer and monomer have __
- actin-__ assembles into __
- actin-__ disassembles from __
- actin catalyzes __
- __ bound conformation favors __
- __ bound conformation favors __ |
|
Definition
- atp binding
- double helix
- polarity
- atp; + end
- adp; - end
- atp hydrolysis
- adp; disassembly
- atp; assembly |
|
|
Term
actin polymerization
- high [actin-atp]: __
- low [actin-atp]: __
- intmd [actin-atp]: __
- assembly inhibited by __, and disassembly inhibited by __ |
|
Definition
- net assembly into + end
- net disassembly from - end
- steady state equilibrium
- cytochalasin; phalloidin |
|
|
Term
myosin: motor for microfilaments
- most __ end directed
- head domain binds __ and __
- conventional type (type II)
-- assemble into __
-- function in __ and __
- unconventional type (all others)
-- not __
-- function in __ |
|
Definition
- +
- actin; hydrolyzes atp
-
-- filaments
-- muscle; cytokinesis
-
-- filamentous (aka non-filamentous)
-- organelle transport (locomotion, phagocytosis) |
|
|
Term
-__: used in transport of cargo inside cells
-__: used in cell motility and changes in cell shape/size |
|
Definition
- microtubules (tubulin)
- microfilaments (actin) |
|
|
Term
convetional myosis in muscle contraction
- multi nucleated muscle cells (fibers) made up of __ containing repeating array of __ contractile units
- overlapping thin (light stain) __ filamints and thick (dark stain) __ filaments.
- during muscle contraction, __ slides __ toward center of __ |
|
Definition
- myofibrils; sarcomere
- actin; myosin II
- myosin; actin filaments; sarcomere |
|
|
Term
-__: contains actin only
-__: contains actin and myosin
-__: contains myosin only (center)
-__: border on each side |
|
Definition
- I band
- A band
- H zone
- Z line |
|
|
Term
- when relaxed, __ and __ lengthen
- when contracted, __ and __ shorten
- __ length does not change |
|
Definition
- I band; H zone
- I band; H zone
- A band |
|
|
Term
Actinomyosin contractile cycle: atp role
- atp hydrolysis energizes __ to __
- __ induces conformational change in __, causes __
- release of __ allows __ to bind
- __ allows release of __ from __ and new cycle |
|
Definition
- myosin; bind actin
- release of Pi; myosin; sliding actin filament (power stroke)
- adp; atp
- atp binding; release; myosin head; actin |
|
|
Term
coupling muscle excitation (neural stimulation) to muscle contraction
- stimulation of neuromuscular junction
- ap propagated through __
- stimulates opening of __ channels of __ and __ release into __ |
|
Definition
-
- transverse tubules
- calcium channels; sarcoplasmic reticulum; calcium release; myofibril cytosol |
|
|
Term
- influx of calcium though __
- activates calcium dependent __ receptor in __ membrane
- neuromuscular junction
-- calcium released from __ into __
-- calcium activates __ thru calcium binding protein __ |
|
Definition
- voltage gated calcium channel
- ryanodine; ser
-- ser; cytosol of myofibril
-- muscle contraction; toponin c |
|
|
Term
In smooth muscle, calcium release is __ activated
- __ activates cleavage of pip2 of plasma membrane into __ and __
- __ activates protein kinase c
- __ activates ryanodine receptor in release of calcium from smooth er. |
|
Definition
GPCR
- gpcr; dag; ip3
- dag
- ip3 |
|
|
Term
calcium regulation of muscle contraction through __ and __
- stimulation of neuromuscular junction causes opening of calcium channels of __ and release into myofibril cytosol
- myosin binding site on actin obscured by __ in absence of calcium.
- calcium binding to __ triggers conformational change in __ and then __
- conformational change in tropomyosin reveals __ on __ |
|
Definition
troponin (calcium binding); tropomyosin
- sarcoplasmic reticulum
- tropomyosin
- troponin; troponin; tropomyosin
- myosin binding site; actin |
|
|
Term
| Reminder: __ functions in cell shape change and motility |
|
Definition
|
|
Term
| __ allows cells to bind ecm lining culture dish |
|
Definition
|
|
Term
| actin and myosin generate muscle like force that deforms __ |
|
Definition
|
|
Term
nonconventional mysosin and actin in focal adhesion and cell locomotion
- attachement to substratum through __
- __ motor activity |
|
Definition
- integrins
- nonconvetional myosin |
|
|
Term
| __ also provides motility mechanism |
|
Definition
|
|
Term
- actin treadmilling alone provides __
- when - disassembly and + assembly, the __ length stays the same, but crawls to the __ |
|
Definition
- motility force
- actin filament; right |
|
|
Term
| __ reorganization in cell shape changes during embryonic development |
|
Definition
|
|
Term
__ motors localize developmental determinants
- cytoskeleton required for localization of __ and __
-- disrupted by __, __ disrupts anchorage after localization
- __ needed for localization, and __ needed for anchorage
- proteins encoded by __ intiate cascade of transcription regulators specifying abdominal segment specific characteristics |
|
Definition
cytoskeletal
- anterior mRNA; posterior mRNA
-- colchicine; cytochalasin
- MTs; actin
- mRNAs |
|
|
Term
__ include keratin, vimentin, desmin, lamin, neurofilaments,
- intermediate in size to microfilaments and microtubules
- central rod shaped, __ domain flanked by __ proteins
- assembly lacks __
- dynamic assembly and disassembly, subunits assembled into __ of filament rather than __
- no __ required
- assembly regulated by __
- __ mutations associated with epidermolysis bullosa simplex (skin bubbling disorder)
- __ mutations associated with protein aggregations neurodegenerative disease (als, parkinsons) |
|
Definition
intermediate filament
-
- alpha helical; globular
- polarity
- interior; ends
- nucleotide binding
- phosphorylation
- Keratin K15
- neurofilament h |
|
|
Term
| __ seperate during meiosis |
|
Definition
|
|
Term
mendel's law of independent assortment
- different chromosome homologue pairs, and each chromosome homologue pair, segregates __ of other chromosome homologue pairs
- __ of alleles for two different traits during gamete formation |
|
Definition
- indepently
- independent assortment |
|
|
Term
exception to mendels low of ia
- alleles for two different traits on __ usually co-segregate to gametes
- but not always, __ can produce recombinant progeny at low frequency |
|
Definition
- same chromosome
- chromosome recombination |
|
|
Term
| morgan showed linkage breakdown results from __ between homologues, showing chromosomes carry genetic info |
|
Definition
|
|
Term
- __ = hereditary info
- bacterial dna contains __ for virulance, infectious disease causing trait
- viral dna contains __ for viral virulence |
|
Definition
- dna
- bacterial hereditary info
- viral hereditary info |
|
|
Term
- the 2 pyrimidines are __ and __
- the 2 purines are __ and __
- adenine and thymine have __ hydrogen bonds between them
- guanine and cytosine have __ h bonds between them
- __ = __ and __ = __ but __ + __ does not = __ + __
- __ linkage between 3 oh and 5 po4 |
|
Definition
- thymine; cytosine
- adenine; guanine
- 2
- 3
- a;t; g;c; a;t;g;c
- phosphodiester |
|
|
Term
- purines have a __
- pyrimidines have a __
- at have __
- gc have __
- width of at is __ to width of gc |
|
Definition
- double ring
- single ring
- 2 h bonds
- three h bonds
- equal |
|
|
Term
- storage of genetic info: gene is linear array of __ that encodes a linear array of __ in a __
- self duplication and inheritance: each single strand serves as a __ of new strands
- expression of genetic info: single strand serves as specific __ of mRNA intermediary |
|
Definition
- nucleotides; amino acids; protein
- template for replication
- template for transcription |
|
|
Term
- __: labeled dna probe hybridized to dna
- __: labeled dna probe hybridized to rna |
|
Definition
- southern blotting
- northern blotting |
|
|
Term
| __ contain 3 populations of dna with different annealing times |
|
Definition
|
|
Term
highly repetitive dna
- variable number of __ in individual humans allows forensic dna finger printing |
|
Definition
|
|
Term
moderately repetitive dna
- jumping genes aka __
- constitute the middle repetitive dna class
- 3% human genome - __ relics
- te's encode __ that bind sequences at __ and catalyze integration of te into host genome |
|
Definition
- transposable elements (TE)
-
- TE
- transposases; te ends |
|
|
Term
middle repetitve dna includes __
- __ have rna intermediate, __ required |
|
Definition
transposable elements
- retrotransposons; reverse transcriptase |
|
|
Term
genome sequences
- allow sequence comparisons and guesses about functions of human genes from similarities to genes in model systems
- generated __ maps in humans that can be used to map human disease genes |
|
Definition
-
- snp (small nucleotide polymorphism) |
|
|
Term
-__ provide molecular markers for mapping disease associated genes in human populations
- expression of genetic info specific single strand serves as template for __ of mrna intermediatry that is __ into a linear array of amino acids |
|
Definition
- snp's
- transcription; translated |
|
|
Term
|
Definition
| dna (genotype) > rna (phenotype in some cases) > protein (phenotype) |
|
|
Term
-__ and __ take place in the nucleus
- __ takes place in cytoplasm |
|
Definition
- replication; transcription
- translation |
|
|
Term
relationshipe between genes and proteins
- one gene = __
- order of genes is same as order of __ in __ |
|
Definition
- one enzyme
- enzymes; biochemical pathway |
|
|
Term
transcription
- dna template provides info for synthesis of complementary ___
- reaction catalyzed by __
- __(previous) binds __
- RNA polymerase moves __ along template dna strand and assembles rna strand that grows from ___ |
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Definition
- mRNA strand
- RNA polymerase
- rna polymerase; promoter sequence
- 3>5; 5>3 |
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Term
transcription in prokaryotes
- catalyzed by __
- __: consensus sequence at -35 and __ at -10, recognized by __
- __ promotes unwinding of dsDNA
- transcription begins __ of binding site
- __ released after synthesis of 10 nucl. rna-recycled
- __ causes RNA polymerase release at termination site |
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Definition
- rna polymerase
- promoter; pribnow box; sigma factor
- sigma factor
- 10-35 bp downstream
- sigma factor
- rho factor |
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Term
transcription in eukaryotes
- RNA polymerase specialization
-- I: __
-- II: __
-- III: ___
-- __ and __ in plants only |
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Definition
-
-- rRNA
-- mRNA
-- tRNA; 5sRNA
-- 4; 5 |
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Term
Initiation
- __ binds tata box of promoter(24-32 bp upstream of transcription start site)
- __: saddle shaped protein that binds tata box and causes promoter to __
- tbp is a subunit of __, recruits other __
- __ allow RNA polymerase to bind |
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Definition
- tbp (tata binding protein)
- tbp; unwind
- tfid (transcription factor II D); transcription factors
- preinitiation complex |
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Term
elongatioin
- __ is a helicase and a kinase that phosphorylates carboxy terminal domain (CTD) of __, activates it to leave initiation site and begin __
- __ and __ left behind at promoter during elongation phase
- rate of initiation regulated by specific __ that bind sequences upstream of initiation site |
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Definition
- TFIIH; RNA pol II; elongation
- TFIID; TFIIB
- transcription factors |
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Term
mRNA processing in eukaryotes
1) additon of __ to __
2) addition of __ to __
3) removal of __ |
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Definition
1. 7mG cap; 5' end (rna stability, transport to cytoplasm, and translocation)
2. poly a tail; 3' end (rna stability)
3. intervening sequences (pre mrna splicing) |
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Term
pre-mRNA splicing
- __: coding sequence present in mature mRNA
-__: non-coding sequence absent from mature mRNA
- __ removed and __ joined together |
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Definition
- exon
- intron
- introns; exons |
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Term
| chromosome in situ hybridization used to show __ present in genomic dna and __, but absent from __ |
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Definition
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Term
- smaller __ derived from larger __ through splicing
- __: large RNAs in __ that contain __ (synthesized first)
- __: small RNAs in __ that lack __ (produced from __) |
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Definition
- mRNA; hnRNA
- hnRNAs; nucleus; introns
- mRNAs; cytoplasm; introns; (hnRNAs) |
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Term
how are the introns (intervening sequences) removed, by the __
- mRNA processing carried out during __ in __ |
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Definition
spliceosome
- transcription; nucleus |
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Term
spliceosome, the details
- __ complex of snRNA and proteins
- catalytic activity in __
- snRNAs bind through __ |
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Definition
- snRNP
- snRNA
- complementary base pairing |
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Term
splicing reaction
- __ binds __ splice site through
- __ binds __ and forms __
- __ (u4/u6/u5) enters
- __ lost, allowing __ to bind __ and __ splice site
- __ of __ attacks __ splice site and forms __ |
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Definition
- u1; 5'
- u2; intron; a-bulge
- tri-snRNP
- u4; u6; u2; 5'
- 2'oh; a bulge; 5'; lariat |
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Term
self splicing reaction catalyzed by __ of lower eukaryotes
- a bulge at stem loop VI carries out similar attack on __ splice site
- form __ resembling __ of higher eukaryotes
- first hint that catalytic activity in __ |
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Definition
- group II introns
- 5'
- 2 degree; mRNA/spliceosome intmd
- snRNA |
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Term
pre-mRNA splicing
- __ RNA self splicing
- __ forms a structure that is similar to pre-mRNA associated with snRNPs |
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Definition
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Term
potential therapeutic use of RNA
- goal to knock down mRNAs encoding gain of function mutant proteins: design RNA molecules that will hybridize to __ and form an __ in them that will stimulate them to catalyze their own cleavage
- __: degradation of complementary mRNA |
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Definition
- cellular RNAs; A bulge
- dsRNA interference |
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Term
dsRNA interference machinery: targets specific __ for degradation
- dsRNA recognized as __
- cleaved by __ to make __
- __(above) targets complementary __ for degradation by __ |
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Definition
mRNAs
- non-cellular
- dicer; siRNA
- siRNA; mRNA; RISC |
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Term
__ pathway shares components of siRNA pathway: cellular targets
- siRNAs encoded by __ and __
- siRNA binds complementary __ and targets for __
- microRNAs encoded by __
- miRNA binds complementary __ and blocks __ |
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Definition
miRNA
- viruses; transposable elements
- mRNA; degradation
- cellular genome
- mRNA; translation |
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Term
-__: translates language of nucleotides into language of amino acids
-__: synthesizes the protein specified by the nucleotide code |
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Definition
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Term
- language of nucleotides =
- __:- basic unit of DNA code that specifies an amino acid deduced to be at least 3 nucleotides in length, need to encode at least 10 a acids + 1 stop.
- for 2 letter codon, __ possibilities, for 3 letter codon, __ possibilities |
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Definition
- language of amino acids
- codon
- 16; 64 |
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Term
deciphering the code (translation)
- synthesized artificial __ of (semi) known composition
- used bacterial extract to synthesize polypeptide from __ and determined sequence of polypeptide
- code is:
-- __: same in all organisms
-- __: most amino acids specified by more than one codon
--__: each codon specifies only one amino acid |
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Definition
- mRNA
- mRNA
-- universal
-- degenerate
-- nonambiguous |
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Term
- codons on __, anticodons on __
- stope codons are: |
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Definition
- mRNA; tRNA
- uaa; uga; uag |
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Term
__: adapter, brings correct amino acid to ribosome
- top is __ linkage site
- bottom is __ codon binding site
- complementary sequences induce __
- has a cloverleaf 2 degree (l shpaed 3 degree) structure |
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Definition
tRNA
- amino acid
- mRNA
- folding |
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Term
- single tRNA can recognize __
- multiple tRNAs can carry a given __
- laxity is in the pairing requirement at position __
- but a given codon cannot specify __ (code is nonambiguous) |
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Definition
- multiple codons
- amino acid
- 3
- cannot specify multiple amino acids |
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Term
nonambiguity due to __ specificity
- __ links specific amino acid to 3' end of corresponding tRNA
-must have __ activity that detects and removes wrong amino acid
- energy from hydrolysis, __ required
- tRNA with covalently linked amino acid is __ for translation
- each aminoacyl-tRNA synthetase is specific for a given __, and able to recognize all __ specifying it |
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Definition
aminoacyl-tRNA synthetase
- covalently
- proofreading
- 2 atp
- charged
- amino acid; tRNAs |
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Term
| __ recruits amino acid specified by each codon of __ to ribosome |
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Definition
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Term
ribosome assembly occurs in __:
- contains clusters of amplified __ genes
- single large rRNA __ cut into individual __ (requires __)
- 4 __ and 82 __ then assembled into large and small subunits
- each rRNA has complex __ structure
- associate with __ to form ribosome |
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Definition
nucleolus
- rRNA
- precursor transcript; rRNA; (snoRNA)
- rRNAs; ribosomal proteins
- 3d
- r proteins |
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Term
Transcription of rRNA (and ribosome processing genes)
- __: larger rRNAs
- __: snaRNAs (many in introns)
- __: 5s rRNA
- single large rRNA transcription unit made by __
- __ cuts into individual rRNAs
- __: modify nucleotides to alter rRNA conformation and guide exosome activity |
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Definition
- rna polymerase I
- rna polymerase II
- rna polymerase III
- RNA pol I
- exosome
- snoRNAs |
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Term
Translation
1. small ribosomal unit binds __(__); __ and __ required
2. fmet-__ anticodon binds mrna aug codon (__ monitors anticodon/codon pairing)
3. gtp hydrolysis by __ allows progression ( which is __ subunit binding) |
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Definition
1. mRNA (aug at p site); if1; if3
2. tRNA; (IF2 G protein)
3. IF2; (large ribosomal) |
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Term
initiation
- prokaryotes: small subunit binds __ first than __
- eukaryotes: small subunit binds __ first, then __ |
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Definition
- mRNA; charged tRNA
- charged tRNA; mRNA |
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Term
elongation; EF = elongation factor
1. __ binds __; __ monitors pairing
2. __ hydrolyzed if correct
3. __ formed between __ and __, polypeptide linked to tRNA at __
4. gtp hydrolysis by ef g protein induces __ to next codon of mrna; peptidyl tRNA moved to __; __ left open
5. 3rd charged tRNA binds to a site; efg protein monitors pairing... |
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Definition
1. 2nd charged tRNA; a site; EF g protein
2. gtp
3. peptide bond; aa1 (p site); aa2 (a site); a site
4. ribosome shift; p site; a site
5. a site |
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Term
- peptidyl transferase acitivy; links __ to __
-- catalyzed by __
- __ remains after removal of all ribosomal proteins from purified ribosome
- retains characteristics of intact __ (sensitivity to chloramphenicol antibiotic)
- many antibiotics bind __ to interfere with bacterial ribosome |
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Definition
- a site amino acid; p site peptide chain
-- rRNA
- ribosome acitivity
- ribosome
- bacterial rRNA |
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Term
termination
1. ribosome reaches one of 3 codons without complimentary __ anticodon (stop codons: ___)
2. release factors that resemble __ bind __; __ added to peptidyl tRNA instead of __
3. growing __ freed from peptidyl tRNA
4. __ released from ribosome
5. __ subunits dissociate |
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Definition
1. tRNA (uaa; uag; uga)
2. tRNA; A site; h2o; aa
3. polypeptide
4. tRNA
5. ribosomal |
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Term
| - some RNAs function without translation, these include __ |
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Definition
| - snRNA, snoRNA, siRNA, miRNA, piRNA |
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Term
- southern blotting: __ probed with labeled __; detects changes in __
-northern blotting: __ probed with labeled __; detects changes in __
-western blotting: __ probed with labeled __; detects changes in __ |
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Definition
- dna; dna; dna
- rna; dna; mRNA
- protein; antibody; protein |
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Term
how can south blot detect dna changes
- each gene has a characteristic set of __ generated from __, determined by presence or absence of restriction enzyme digestion sites in dna sequence |
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Definition
| dna fragments; restriction enzyme digestion |
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Term
| - a __ is a point mutation, while a __ is a point mutation that leads to a stop codon |
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Definition
| - missense mutation; nonsense mutation |
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Term
microarray technology
- genome wide __ blot
- __ copy of all __ in cell used as probe
- hybridized to short piece of __ from each gene in the genome
- allows __ of expression level of every gene in the genome under two different conditions
- 88% of __ associated with human disease lie in regulatory regions |
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Definition
- northern
- dna; mRNAs
- dna
- comparisons
- SNPs |
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Term
- __: transport into cell
-__: transport out of cell
- secreted proteins and membrane associated proteins translated by __ of __ |
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Definition
- endocytosis
- exocytosis
- ribosomes; endomembrane system |
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Term
- the __ is the first step in the endomembrane system; membranous network surrounding nucleus
- __: __ attached, site of synthesis of secreted and integral plasma membrane proteins
- __: no ribosomes, other specialized functions |
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Definition
- endoplasmic reticulum
- rough er; ribosomes
- smooth er |
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Term
rough endoplasmic reticulum
- system of membranes that seperate __ from __ of __
-- ribosomes located on __ side of membrane |
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Definition
- cytoplasmic space; luminal space; er
- cytoplasmic |
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Term
proteins synthesized on rer ribosomes:
- __, __, and __ proteins
- __ proteins
- soluble proteins that reside within endomembrane __ |
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Definition
- secretory, lysosomal,and vacuolar
- integral
- luminal spaces |
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Term
proteins synthesized on free ribosomes:
- __ proteins
- __ proteins
- __, __, and __ proteins |
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Definition
- cystolic
- nuclear
- peroxisomal, chloroplast, and mitochondrial |
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Term
smooth er (no ribosomes)
- __ specific specialized functions
- endocrine cells: __ production in gonad and adrenal gland (synthesized by cholesterol)
- liver: __ system of oxygen transferring enzymes, release glucose from __, synthesis of __)
- skeletal muscles: sequestration of __ through calcium binding proteins in ser and contraction of postsynaptic muscle cell |
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Definition
- tissue
- steriod hormone
- detoxification; glycogen stores; lipoportein vesicles (ldl and hdl cholesterol vesicles)
- calcium ions |
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Term
targeting proteins to endomembrane system
- on __ during translation |
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Definition
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Term
targeting of scretory protein to rer
- __ of nascent polypeptide binds __
-__ targets complex to __ on er membrane
- signal peptide binds site on __ of er membrane
- __ by srp and srpr causes __
- polypeptide exposed to er lumen where it binds to __
- chaperone promotes proper __ |
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Definition
- signal peptide; SRP (G protein)
- GTP activated SRP; GTP activated SRP receptor
- translocon
- gtp hydrolysis; translocon to open
- chaperone
- folding |
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Term
embedding integral membrane protein in rer membrane
- polypeptides contain hydrophobic __ that blocks further movement through __ into er lumen
- translocon opens along side allowing __ to __ in er lipid bilayer |
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Definition
- transmembrane segment; translocon
- polypeptide; embed |
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Term
proper orientation of integral membrane proteins
- n terminus of embedded membrane protein in ___
- polypeptide moves from __ to __ in vesicle (n terminus inside)
- polypeptide moves from __ to __ in vesicle (n terminus inside)
- vesicle fusion with plasma membrane places __ on __ |
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Definition
- er lumenal space
- er; golgi complex
- golgi complex; plasma membrane
- n terminus; extracellular face (glycosylation out) |
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Term
proteins become __ as they move through the endomembrane space
-__: er
-__: golgi |
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Definition
glycosylated
- n linked
- o linked |
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Term
proteins synthesized in rer become __
- required for proper targeting, folding, and ultimate function
- reactions catalyzed by __ in er membrane
- oligosaccharide chain constructed on carrier lipid __ before transferring to protein
- terminal 2 glucose residues removal after monitored by __ for correct folding |
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Definition
n link glycosylated
-
- glycosyltransferases
- dolichol-po4
- gt enzyme |
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Term
quality control: recognition of misfolded proteins
- single __ targets to __ for monitoring
- removal of final __ by glucosidase allows release from __
- __ monitors protein folding, adds single __ if improper
- targets back to __, ultimately __
- excess unfolded protein induces unfolded protein response, increased chaperone synthesis, decreased translation, and ultimately apoptosis |
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Definition
- glu; calnexin chaperone
- glu; chaperone
- gt enzyme; glu
- chaperone; proteasome |
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Term
golgi complex
- organization similar to __
- membrane separating __ and __ |
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Definition
- er
- cisternal; cytosolic spaces |
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Term
glycosylation groups are added through __ in golgi
- layer specific modifications: chain sequence determined by order of __ through golgi layers
- species diversity in golgi modifications: reflects species diversity of __
-presence or absence of specific __ groups on proteins used as assay for progression of proteins through endomembrane system |
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Definition
o linkages
- passage
- gt enzymes
- glycosylation |
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Term
proteins promoting vesicle formation are __
- COPII: __ er to golgi __ regulated
- COPI: __ movement, __ regulated
- __: move between golgi, lysosomes, and endosomes |
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Definition
g protein regulated
- anterograde; sar1 (g protein)
- retrograde; arf1 (g protein)
- clathrin |
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Term
lysosome
- __ foreign, __ self
- contains >50 __ for every type macromolecule
- __ for enzymes with low optimal ph |
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Definition
- phagocytosis; autophagy
- hydrolytic enzymes
- low internal ph |
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Term
lysosome dysfunction diseases:
- I-cell disease: defect in __ of enzymes to lysosome
-__: deficiency for hydrolytic enzyme for brain membrane protein
-silicon, asbestosis: __, release H+ |
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Definition
- MPR targeting
- tay-sachs disease
- puncture lysosome |
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Term
clathrin-coated pits/vesicles
- target lysosomal enzymes from ___ to __
- __ modifications on lysosomal enzymes bind __ that targets them in clathrin coated vesicles to lysosome |
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Definition
- trans golgi; lysosome
- m6p; mpr |
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Term
clathrin coated pits and lysosome in receptor mediated uptake of external materials endocytosis
- external molecules bind __
- coated pit vesicle forms around receptor bound molecule
- pass through __, then to __
- degraded by hydrolytic enzymes in __
- receptors __ back to plasma membrane |
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Definition
- receptor
-
- endosomes; lysosome
-lysosome
- recycled |
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Term
clathrin coated vesicle formation
-clathrin triskelion
-- __ heavy chains and __ light chains
-- __ bind cytoplasmic tails of plasma membrane receptors
- regulated by dynamin(g protein)
-- form ring around stalk of __
-- __ induces conformational change that causes fission of clathrin coated vesicle from membrane |
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Definition
--3;3
--adaptor proteins
-
--clathrin vesicle
-- gtp hydrolysis |
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Term
- clathrin coated vesicles uptake __ carrying cholesterol through blood from liver to cells
- __ carry cholesterol from cells to liver for excretion
- high total cholesterol associated with __ disease, __ ratio most important factor
- __ moves cholesterol from hdls to ldls, mutations in this protect from cv disease |
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Definition
- uptake ldl vesicles
- hdl vesicles
- cardiovascular; ldl/hdl
- cetp enzyme |
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Term
specificity of vesicle targeting
- __ link vesicle to specific target
- regulated by __
- __ twist together to mediate vesicle fusion |
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Definition
- tethering proteins
- rab g protein
- SNAREs |
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Term
snare proteins mediate __ with target membrane
- synaptic vesicle fusion in __
- alpha helices of __ interact with alpha helix of __ intertwine to fuse membranes |
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Definition
vesicle fusion
- neurotransmitter release
- t-snares(syntaxin, snap-25; v-SNARE (synaptobrevin) |
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