Molecular Cell Biology I 2 Flashcards

Terms Definitions
Lysosomes contain...
digestive enzymes
FRAP
Fluorescence recovery after photobleaching: studies the movements of membrane proteins.
Pointed end
(-) negative, slower
iron-sulfur center
Electron-transporting groups consisting of 2 or 4 Fe atoms bound to an equal number of S atoms; found in a class of electron-transport proteins
Alzheimers
When brain MAP (microtrubule associated proteins) 'tau' has increased phosphorylation the microtubule array becomes malformed and synaptic transmission is interrupted.
Proteosome
Organelle where proteases digest polyubiquitinized peptides for "quality control" in protein synthesis.
chloroplasts
are differentiated with chlorophyll and have enzymes, etc. for photosynthesis
Myosin Thick Filament
composed of myosin
nucleoside
Molecule composed of a purine/pyrimidine base linked to a sugar
spliceosome
Large assembly of snRNP ribonucleoproteins that performs pre-mRNA splicing
[CAM] Are Cadherins Ca++ dependent?
YES!!!
Cytoplasmic Dynein
Molecular motor associated with microtubules; (-) end direction; has high molecular weight with two heavy chains and many light and medium chains; involved in chromosomal and vesicular movement, Golgi body positioning, and cilia and flagella motion.
Viroids
Nucleic acid particles without a protein coat; 1/10 size of typical viral genome; hijacks host RNA polymerase to reprodue itself; eg) cadang attacked cconut tree monoculture.
how do cells perpetuate?
by dividing themselves
cytoskeleton
is a cellular "scaffolding" or "skeleton" contained within the cytoplasm. The cytoskeleton is present in all cells; it was once thought this structure was unique to eukaryotes, but recent research has identified the prokaryotic cytoskeleton. It is a dynamic structure that maintains cell shape, protects the cell, enables cellular motion (using structures such as flagella, cilia and lamellipodia), and plays important roles in both intracellular transport (the movement of vesicles and organelles, for example) and cellular division
all cells use:
DNA, dsDNAcircular: prokslinear: euks
 
 
DNA Sequencing
 
Modified "Sanger" Method.
Uses ddNTP (missing 3' OH) to arrest polymerization.
Each ddNTP is a different color.
Primer, template, polymerase, normal dNTPs, and small amount of labeled ddNTP.
Run modified gel electrophoresis with detection laser to read colors.
Electron transfer phosphorylation is important to...
Anaerobic respiration
Drug blocks microtubule assembly
Vinblastine, Colchicine, podophyllotoxin, etc. taxol (anti-cancer drug, stabilizes microtubules), colchicines (binds tubulin and blocks polymerization), vinblastine (depolymerization and formation of vinblastine-tubulin paracrystal), nocodazole (depolymerization of microtubules)
action potential
Rapid, transient, self propagating electrical excitation in the PM of a cell; makes long distance nervous system signaling possible.
phospholipase C-γ
Cleaves membrane phospholipids to diacylglycerol (DAG) and inositol triphosphate (IP3);
Activated by receptor tyrosine kinases
neutrophil
White blood cell that enters inflamed/infected tissues and uptakes particulate material by phagocytosis
synaptonemal complex
Structure that holds paired chromosomes together during prophase I; promotes genetic recombination
degenerate
Describes multiple states with the same result: e.g. multiple codons for the same amino acid
cadherin
Family of proteins that mediates Ca2+-dependent cell-cell adhesion in animal tissues
homeodomain
DNA-binding domain that defines a class of gene regulatory proteins important in animal development
fluorescein
Dye that fluoresces green when illuminated with blue or UV light
glycerol
Small three-carbon molecule with one hydroxyl per carbon and is the parent compound of many small molecules including phospholipids
[CAM] Gap junctions are basically hexagonal cylindrical pores that connect adjacent cells
Immunoglobin Superfamily (IgSF)
Cell-adhesion molecules; basis of immunology.
VCAM: vascular cell adhesion
NCAM: neural cell adhesion - CNS
 L1: adhesions between cells, nerve outgrowth, synapse development
what is the simplest form of bacteria?
mycroplasma
alkalinophiles
grow best at a pH ABOVE 7
 
 
Immunoprecipitation (IP)
Specific molecules can be precipitated by antibody binding.
ChIP- chromatin can be used to find a specific gene that a protein is binding.
The carbon-containing end product of the complete aerobic respiration of glucose is...
carbon dioxide
Dynamic Instability
Applies to microtubules; implies that they are shortening and lengthening unlike filaments. GTP binding and monomers are tubulin (protein, at least 2: alpha and beta) Applies to microtubules; implies that they are shortening and lengthening unlike filaments. GTP binding and monomers are tubule (protein, at least 2: alpha and beta)
cellularization
The formation of cells around each nucleus in a multinucleate cytoplasm, transforming it into a multicellular structure
bright-field microscope
Normal light microscope that obtains images by simple transmission of light through the viewed object
synapsis
The initial formation of base pairs between complementary DNA strands in genetic recombination, OR the pairing of maternal/paternal chromosomes as they become attached along their length
polysome
mRNA molecule with a number of actively translating ribosomes attached
minus end
Comparatively slower-growing end of a microtubule or microfilament
[mitochondrial] matrix space
Central subcomparment of a mitochondrion, bounded by the inner mitochondrial membrane; corresponds to the stroma in a chloroplast
metaplasia
Replacement of a differentated type of cell with another differentiated type; usually caused by abnormal stimuli
citric acid cycle
Aerobic metabolic pathway that oxidizes acetyl groups from food into CO2 and H2O; occurs in the mitochondria
inner nuclear membrane
Nuclear envelope membrane that contains binding sites for chromatin and the nuclear lamina
[Apoptosis] What does loss of death ligand receptors (Fas receptors) lead to?
cancer
[CAM] In hemidesmosomes, what kind of interaction is it?
cell-ECM
what are voltage dependent Na+ channels activated by?
membrane depolarizationtranslate electrical signals
 
 
DNA Cloning
Library Production
 
 
An extension of cloning where an entire set of genes can be stored.
Genes that are always turned on are called...
Constitutive
The enzyme(s) used for _____ is/are RNA molecules.
protein synthesis
Smooth muscle contraction
calcium from intra or extracellular source. Major difference is that smooth muscle is not well organized into sarcomeres; the myosin light chain phosphorylates enabling contraction causes a conformational change
Ames Test
test carcinogens for the ability to mutate
co-translational
Describes import of a protein into the ER before the polypeptide is completely synthesized
lepotene
First phase of meiosis I in which paired duplicated homologous chromosomes condense and become visible in light microscopy
mismatch repair
DNA repair process that corrects errors during DNA replication by removing a short stretch of newly synthesized DNA and replacing it with the correct sequence based on the template strand
adhesion belt (zonula adherens)
Beltlike adherens junction that encircles the apical end of an epithelia cell and attaches it to adjacent cells.
high-mannose oligosaccharide
Chain of sugars generated by a trimming of original mannose-rich oligosaccharide that leaves most of the mannose residues with no subsequent addition of sugars
kinesin
Type of motor protein that uses ATP hydrolysis to move along a microtubule; transports intracellular cargo along microtubule tracks
4 Functions of the Cell
1)maintain selective barrier2)inherit and transmit genetic material3)catalyze chemical rxns4)manifest several types of motility
[ECM][Adhesive Interactions] Describe cell-cell adhesion in leukocyte extravasation
In the absence of inflammation/infection, leukocytes and endothelial cells are in resting state. inflammatory signals released that activate P-selectin exocytosis from epithelials. exposed selectins lead to loose binding of leukocytes with carbohydrate ligands on the leukocytes; also, epithelials release platelet activating factor and ICAM1. PAF induce changes in the leukocyte shape and activation of leukocyte integrins such as alphaLbeta2. activated integrins on leukocytes tightly bind with CAMs on the epithelium, so there is firm adhesion and movement into the underlying tissue.
[CAM] Tight Junctions, what kind of interaction?
cell cell
[Apoptosis] What is pyknosis?
irreversible condensation of chromatin in the nucleus, resulting in large visible black circles under the microscope
[Apoptosis][Experiment] Using chick embryo, emputate one of two developing limb buds. What happens to motor neuron generation? What happens to motor neuron survival?
generation, 100%, like normal. survival: 10%, lower than the normal limb's 50%.
Transmission Electron Microscopes
Form images using electrons that are transmitted through the specimen.
L. Bilayer is permeable to ______, but not to _______.
H20. ions.
define the anatomy of the mitochondria
2 lipid bilayersmito matrixintermembrane space; contain DNA
what maintains the OM Na+ and K+ gradients?
Na+/K+ ATPase
 
 
Determening 3-D Structure of a Protein
X-ray Crystallography- Crystallize protein and hit with X-ray. Get diffraction pattern.
NMR (Nuclear Magentic Resonance)- Measure distance between atoms. Advantage: no need to crystallize protein.
Disadvantage: Can only do with small proteins <40kD
The nucleolus is the site of _____ production.
ribosomal RNA
Cytoskeletal Fiber Length
if an actin or microtubule maintains the same length it’s called tread milling. The dissociation = to association
animal pole
In yolky eggs, the yolk-free side that cleaves more rapidly than the other pole.
Ca2+ ATPase (calcium pump)
Transport protein of the sarcoplasmic reticulum that pumps Ca2+ out of the cytoplasm into the sarcoplasm using ATP
induction [developmental bio.]
Change in the developmental fate of one tissue caused by interaction with another tissue
focal adhesion kinase (FAK)
Cytoplasmic tyrosine kinase present at cell-matrix focal adhesions in association with the cytoplasmic tails of integrins
N-linked oligosaccharide
Chain of sugars attached to a protein through the NH2 of an asparagine
coenzyme A (CoA)
Small molecule used in the enzymatic transfer of acyl groups in the cell
[CAM] For Desmosomes, what kind of function do they mediate?
strength, durability, signaling
[Cell Cycle][Progression in Interphase] What regulates G1cyclin?
SCF, a E3 ubiquitin ligase, (Skp1/Cul1/Fbox protein), mediates the breakdown of Sic1, a G1cyclin inhibitor
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Cytoskeletal Elements (3 Types)
1) Tubulin aka Microtubules 2) Actin Superfamily 3) Intermediate Filaments
what signal regulates heart rhythm and muscle contraction?
Ca2+ signaling regulates these
Consider the two statements below: A. One tRNA  may match with more than one mRNA codon.B. One tRNA may combine with more than one amino acid.
 
Which is true, which is false? 
A is true; B is false
allele
One of a set of alternative forms of a gene, of which a diploid cell will have two occupying the same position on homologous chromosomes
ER resident protein
Protein that remains in the ER lumen or its membranes and functions there, as opposed to proteins that are in transit in the ER
Cell theory2 theories
1) all organisms are composed of cells 2) all living cells are similar to one another in structure and function.
[Cell Cycle][Progression of Interphase] What are the three functions of E2F
1. induces DNA replication, thus cell division 2. induces more production of G2-CDk, which is what activated E2F 3. induces production of more E2F
[Cell Cycle][Experiment] What stain was used to detect cyclin, protein B, protein C? and in what organism?
35S methionine, early sea urchin embryos
[ECM][Basal Lamina] Functions of the basal lamina?
separates endothelial cells and connective tissue; filters (in kidneys, intestine, capillaries), provides highways for cell migration, acts as a scaffold for cell regeneration
[Cell Cycle] Describe the activating phosphorylation events on Cdk.
CAK phosphorylates cdc2-T161 to activate it
[ECM][Proteoglycans+GAG] Describe the structure of cartilage.
Hyaluronan forms the core. attached to it are long linking sugars, to which keratan sulfate, then chondroitin sulfate (longer) attach. look at the picture. Resists compression because of Hyaluronan
[CAM] What is the function of Selectins?
responsible for leukocyte-endothelium interaction and heterophilic cell cell interaction in general
[ECM][Basal Lamina] What is the Basal Lamina specialized for?
selective permeability, cell attachment (provides scaffold), migration)
what are 3 types of transporters and where do they get their energy from?
1. unitransporters2. symporters (cotransporter)--> both molec's are moving in same direction across the membrane3. anti-porter: (exchangers) moving in opposite directionsthey get their energy from electochemical gradients to facilitate movement of substrates across the membrane
2 types of chromitin
1. hetero: stains darkly due to heavy complex of protein2. euchromitin: stains lightly due to not much protein
Mini Chromosome Maintenance (MCM) complex
Protein complex that binds to origin recognition complexes in eucaryotic DNA in early G1 and are involved in forming the pre-replicative complex
[Cancer] genes involved in cancer can be classified into two categories
oncogenes: cause cancer when activated/expressed at high levels -- gain of function mutations (proto-oncogenes, genes that when mutated become oncogenes). tumor suppressors: genes that cause cancer when their function is lost, caused by mutation or inactivation, usually recessive mutations
[Cell Cycle] What does the nuclear lamina consist of?
lamin tetramers aka. two dimers.
[ECM][Collagens] Describe how Collagen 4 is assembled
a collagen monomer (the triple helix) has a head and a tail. If a dimer is formed, take two and put them tail to tail. If a tetramer is formed, take 4 and put them head to head -- to form the network for ECM
[ECM][Collagens] How are the different types of collagens distinguished from each other?
length of alpha chain, modifications to alpha chain, presence of segments that interrup the triple helix
[Cell Cycle][Experiment] Describe the cycling of MPF
low during G2... rises during meiosis one but then declines...rises again during meiosis II and remains high during metaphase of meiosis 2 arrest.. then declines upon fertilization... then rises again during first embyonic mitosis, decreases... then rises again for second mitosis...
[Cell Cycle] What is MPF?
mitotic cyclin (Cyclin B) + mitotic cdk (cdk1=cdc2)
what are the 2 MAJOR components of the ECG across the euk PM?
K+ and Na+ gradients
why are Ca2+ channels highly sensitive?
bc of selectivity filters\\they have a permeation factor rate of 10^6/s
Ca2+ concentrations are _________ in the extracellular fluid and in the ____ and ____.
higherERSRthey are 10^4 times lower in the cytoplasm for resting cells
the secretion of H+ into the luminal filtrate (urine) does what?
the apical membrane Na+/H+ exchanger
where do ETS and ATP synthesis occurin proks and where does it occur in euks?
across the membranePROKS: plasma membrane EUKS: inner mitochondrial membrane
why is GTP-binding and hydrolysis required by SRP and SR?
they are required for proper targeting of nascent chains to the ER, and for their transfer to the transLOCATION channel and the recycling of SRP to the cytosol.
[CAM] What is the funciton of gap junctions?
communication between cells, transport of small molecules from cell to cell, dispersion of signals (Ca, cAMP, ions...)
[CAM] For Adherens junctions, what is it formed by?
Cadherins: Cadherin termini bind to p-120 Catenin and petaCatenin, then betaCatenin binds to alphaCatenin, then alphaCatenin binds to F-actin ---> attaches to actin in the cytoskeletons of the two cells
[Cell Cycle] What happens during prometapahse?
the spindle forms, the nuclear envelope degrades, the chromosomes finish condensing, the chromosomes are held together at their centromeres by spindle microtubules
[ECM][Basal Lamina] What tissues does the basal lamina surround and connect?
epithelial cells (such as in the capillaries), muscle, fat, Schwann cells
[Apoptosis][Apoptosis] What was the result of NT-3-/- or TrkC-/- mutations?
lack of neurotrophin 3 and TrkC, loss of balancing/proprioceptive neurons
[Apoptosis] What is the basic pathway of intrinsic death?
Injured mitochondria release cyt c from between their inner and outer membranes... free cyt c binds to adaptor protein Apaf-1.... cyt c-Apaf1 bind and activate procaspase 9, leading to the formation of the apoptosome (cyt c-Apaf1-procaspase 9).. apoptosome assembly is essential for the activation of procaspase 9 and the initiation of the intrinsic apoptotic pathway... now active caspase 9 activates a downstream effector caspase that triggers apoptosis
how many cellular compartments do proks contain?
1. unless you count the compartments b/t the cell membrane and cell walls
what does action potential begin w?
the opening of the voltage gated Na+ channels, rapid flow of Na+ ions into the cell-->membrane depolarization
[Cell Cycle][Experiment] What did the plot of intensity of cyclin band and %cells that had divided during previous 10 min interval vs. min postfertilization show?
Cyclin B peaks early in mitosis, falls abruply just before cell cleavage, then accumulates again during the next interphase to peak during early mitosis...falls abruptly before second cleavage
[Cell Cycle][Machines that drive cell division] Describe how centriole replication occurs.
1 centrosome = 2 centrioles. These two centrioles separate at the end of G1. During S, a new centriole grows next to each old centriole, resulting in a total of 4 centrioles. During G2, the new centrioles continue to grow, and the chromosomes mature. During prophase, the two centrosomes migrate to the two poles to form the mitotic spindle
[CAM] What are the molecules that make up tight junctions?
occludin, ZO proteins (anchor to actin), claudin (TM protein), JAM
where are IMP's formed, and what are they for?
they are formed in the voltage dependent Na+ channels and are important bc they transport Na+ ions down their electrochemical gradient
[CAM] Does the Gap junction connect to the cytoskeleton?
possibly, but would have to be indirectly, via adaptor proteins or other types of junctions
what does the size of the hydration shell depend on?
the size of the ion and charge density
[CAM] Experiment 5: Grew 1. WT mice 2. collagen 2 null mice 3. perlecan null mice
WT grew normally, collagen 2 and perlecan null mice resulted in dwarfism... very underdeveloped. ECM components are crucial for development!
what does a gram (+) cheek cell look like?
It will stain a darker purple because of the Thicker cell wall the cell wall surrounds the plasma membrane
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