Molecular Cell Biology - Final exam study cards Flashcards

Terms Definitions
energy factories
Riboflavin-containing protein responsive to blue light and found in both animals and plants; involved in animal circadian rhythms
Lysosome ~4.5Endosome ~5.0-6.0(late) and ~6.5-6.8(early) Golgi ~6.5-6.7Intermembrane space of mito ~7.0Cytosol (+ Nucleus and ER) ~7.4Mito Matrix ~8.0
Precursor of PG
arachidonic acid
what are ORGANELL'S
specialized structures
Protein only; responsible for Creutzfeld-Jakob / mad-cow disease; a mutant protein with abnormal folding which triggers normal proteins to change as well; mutant protein is insoluble aggregate which causes holes in brain tissue.
multicellular cells cannot reproduce. if they do, they can cause ______.
Defence Molecules
Have high antigen specificity.
Proteins injected into mice can induce antibody production specific for the protein.
Genus Homo
humans, characteristics, increased autoimmune system, increased language skills, intellectual ability, larger brain, opposable thumb for fine motor skills. How we are distinguished?
Small membrane-bound organelle that uses molecular oxygen to oxidize organic molecules
Small vesicle originating from fragmented ER produced from cell homogenates
[Cancer][Cell Culture] What is required for immortality?
G-protein which regulates te formation of COPI vesicles.
differentiated to contain many various pigments
structure of the F1/Fo-ATP synthase:the ____ domain is the Fo region, is involved in translocation of protons down their ECG, the _____ (prok) or _____(euk) globular domain in the F1 region, contains catalytic sites responsible for ATP synthase
transmembranecytomito matrix
Southern Blot
Depends on hybridization (denaturation and renaturation).
If too many bands on a gel, certain bands of interest can be highlighted.
Probe binds desired sequence.
(Run gel, transfer DNA to blot, incubate with a probe, expose to film)
ATP production in photosynthesis is dependent on...
basal body
Short cylindrical array of microtubules and associated proteins found at the base of a eukaryotic cilium or flagellum which serves as a nucleation site for the axoneme's growth. Similar in structure to a centriole
Protein with ATPase activity that disassembles vSNARE and tSNARE complexes in vesicle fusion
Mass of cytoplasm containing multiple nuclei enclosed by a single membrane; typically the result of cell fusion or incomplete division cycles of just the nuclei but not the cytoplasm
SNARE proteins
Family of transmembrane proteins present in organelle membranes and vesicles involved in guiding vesicles to correct destinations; they exist in pairs, a v-SNARE of a vesicle binds specifically to a complementary t-SNARE at the target membrane
Small, lipid soluble mobile electron carrier molecule found in the respiratory and photosynthetic transport chains
two groups of cells
1) Prokaryotes2) Eukaryotes
[Cell Cycle] cyclin syntehsis is NECESSARY and SUFFICIENT for continued cell cycle
Most abundant protein in human body; family of fibrous glycoproteins; acts like steel frame for structure; made by fibroblasts; made of α-helical trimer.
A v-SNARE (originating on the vesicle) which binds with a t-SNARE (originating on the target) in an α-helix for endocytosis.
where is a place gene expression occurs?
at the molecular lever, what kingdom the components of archea most similar to?
electrochemical gradients occur where?
across the cell membrane
Gel Electrophoresis
Seperates DNA by size.
Agar slows down DNA. DNA is negatively charged so it moves towards positive charge.
Smaller bands migrate faster.
Differences in restriction fragment lengths provide useful information.
TRUE or FALSE  Although rare, there are some metabolic energy conversions that are 100% efficient.
Receptor Properties
3 physical properties: have binding sites that have properties such as limited capacity and high affinity 10^9 kd ka (most are in the 10^4 – 10^6)/ also a lock and key ‘specificity’. The bind capacity is limited. Saturable
Complex of DNA primase and DNA helicase formed on the lagging strand of a replication fork, thereby improving replication efficiency
adherens junction
Cell junction that attaches actin filaments to the plasma membrane, e.g. adhesion belts linking adjacent epithelial cells and focal contacts on the bottom of cultured fibroblasts
inhibitory neurotransmitter
Type of neurotransmitter that opens transmitter-gated Cl- or K+ channels in the postsynaptic membrane of a nerve or muscle cell, inhibiting the generation of an action potential
antenna complex
Photosystem protein complexes bound to chlorophyll and other pigments and capture light energy and channel it to the photochemical reaction center.
antigen-presenting cell
Cell that displays foreign antigens complexed with MHC molecules on its surface
(nicotinic) acetylcholine receptor
Transmitter-gated ion channel that opens in response to binding of acetylcholine, converting a chemical signal to an electrical one.
Protein that binds tightly to specific sugars; frequently isolated from plant seeds and used to purify glycoproteins or detect them on cell coats
inositol phospholipids (phosphoinositides)
Family of lipids containing phosphorylated inositol derivatives. Although minor components of the PM, they are important in signal transduction in eucaryotes
channel protein
Membrane transport protein that forms an aqueous pore through which specific solutes (e.g. ions) can pass
[Cancer] cancer causing viruses have cellular counterparts... proto-oncogenes that are active in tumors... name some
src, Fos...
Site-directed Mutagenesis
Change single amino acids in a polypeptide and look at the effect on its function.
occurs when K+ channels OPEN, and K+ moves OUT of the cell. this makes membrane potential more NEGATIVE
aqua purine
special PROTEIN found in the MEMBRANE as a CHANNEL for H2O to flow through
occurs when Na+ or Ca2+ channels OPEN, and the ions flow INTO the cell. this makes the membrane potential more positive!
facultative anaerobic
usually a bacterium, that makes ATP by aerobic respiration if oxygen is present but is also capable of switching to fermentation. In contrast, obligate anaerobes die in presence of oxygen.examples: Staphylococcus (Gram positive), Escherichia coli (Gram negative), Corynebacterium (Gram positive), and Listeria (Gram positive). Organisms in the kingdom Fungi can also be facultative anaerobic, such as yeasts.
Determining Composition of a Protein
Sequencing- direct chemical degradation reactions.
Mass Spectrometry- proteins are broken down, ionized, and read by an analyzer.
Most membrane lipids are produced in the
smooth ER
cDNA is produced by making a DNA copy of...
Which polymers are likely to contain phosphorus atoms?
nucleic acids
Cause of Cancer
DNA damage (through radiation) or uncontrolled cell proliferation
Growth Factors
Stimulate growth of the cell; act during G1 phase of cell cycle; difference between GF and mitogen is that GF does not stiumate cell division while mitogen does both (some GF are mitogenic and some are not)
complement system
System of serum proteins activated by antibody-antigen complexes or by microorganisms; eliminates pathogens by directly lysing them or promoting their phagocytosis
effector cell
Cell that carries out the final response/function of a process. e.g. activated lymphocytes in the immune system
combinatorial control
Describes the control of a cellular process step (e.g. initiation of transcription) by a combination of proteins rather than an individual one
Coreceptor found on T cells that bind to the outside of class II MHCs
phosphatidylinositol 3-kinase (PI3K)
Kinase activated by cell surface receptors; involved in intracellular signaling pathways; phosphorylates phospholipids at the inositol ring
coated pit
Region of the plasma membrane coated with protein that continually form and bud off by endocytosis to form intracellular vesicles
nuclear organizer
Region of a chromosome containing a cluster of rRNA genes that gives rise to a nucleolus
CG island
Region of DNA with greater than average density of CG sequences; usually remain unmethylated
[Apoptosis] What does opening of PTP's cause?
mitochondrial swelling
[Cell Cycle] What is G0
perpetually staying in G1
[Cell Cycle][Progression in Interphase] Describe the assembly and regulation of prereplication complexes during G1 phase
Initiation factors MCM(DNA helicase), Cdc6(DNA helicase loading factor), and Cdt1 increase in concentration and bind to an ORC, forming the prereplication complex. cdc6 prevents MCM from moving
Hans Driesch
Isolated the four cells of sea urchin embryos and observed that each became four whole larvae.
voltage dependent Ca2+ channel cells sense the change and open allowing for a small flux in Ca2+ to enter the cytosol
in excitation-contraction coupling when depolarization occurs from an incoming action potential
are transporters and pumps a part of carrier or channel proteins?
carrier proteins
If a DNA strand changes from ATTCG to ATTCCG, the mutation I called a _____ mutation.
frame shift
Oat Cell carcinoma
A lung cancer, unique because it’s got ACTH like peptides which acts on the adrenal gland; over stimulation give you hyperactive adrenal secretions like Cushing’s disease; treatment would require removal of tumor from lungs.
transition state
Transient structure in the course of a chemical reaction and has the highest free energy; formation of this state is a rate-limiting step
genetic map
Map of a chromosome in which relative distance between genes is determined by the amount of recombination that occurs between them
heterogenous nuclear ribonuclear protein (hnRNP)
Proteins that assemble on newly synthesized RNA, compacting it and signals that the pre-mRNA is not fully processed and ready for export
[Apoptosis] What causes ER stress which then induces apoptosis?
Ca++ imbalance, misfolded protein
[Cancer][tumor suppressors] What are the 6 classes of tumor suppressors?
1. intracellular proteins that regulate/inhibit progression through a point in the cell cycle (p16 and Rb) 2. receptors/signal proteins that inhibit cell proliferation (TGFbeta pathway) 3. negative regulators of pathways that promote proliferation (APC). 4. checkpoint control of proteins that stop the cell cycle if DNA is damaged or chromosomes are abnormal. 5. apoptosis promoting proteins. 6. enzymes that repair DNA
[ECM][Proteoglycans+GAG] Describe Heparan sulfate
heavily sulfated, N = 200, functions in anticlotting by activating antithrombin 3, secreted by mast cells, is O-glycosylated
Looked at a drop of pond water and saw organisms termed "animalcules"; also discovered bacteria by scraping his teeth.
do primary or secondary active transports (pumps) use ATP directly?
primary does. secondary DOES NOT!!
where does glycolysis occur?
occurs in both aerobic and anaerobic in the cytoplasm outside the mitochondria
location in cell structure...
barr bodies next to nuclear envelope- (nuc skeleton tells barr body to go there)rRNA genesgolgi bodies adjacent to the RERcentrioles templating perpendicularly on existing centrioles dorsal ventral gradients of proteins INSIDE the cytoplasm
where are ENaC's located?
in the apical membrane of epithelial cells in the distal tube and collecting ducts of each kidney neuron.
which drug blocks Na+ reabsorption by ENaC in the luminal membrane of the kidney dorsal tubule and collecting duct?
the diuretie drug amiloride
Ca++ binding muscle protein
What binds Ca for muscle movement? calmodulin
redox pair
Pair of molecules in which one acts as an electron donor and the other as an acceptor
inhibitory G protein (Gi)
G protein that can regulate ion channels and inhibit adenylyl cyclase
[Apoptosis] Examples of apoptosis in human disease?
uncontrolled cell growth triggers apoptosis...if not... cancer; neurons undergo apoptosis after stroke; neurodegenerative diseases such as retinitis pigmentosa (rhodopsin mutation that leads to photoreceptor apoptosis)
[Cell Cycle][Progression of Interphase] Give an example of a tumor suppressor gene.
Rb, because it inhibits E2F, thus inhibiting Sphase gene expression and cell divison.
[Cell Cycle][Experiment] Describe the experiment of the use of budding yeast to isolate cdc28
Mutate cells with a temperature sensitive mutation in a CDC gene (cell division cycle). These mutants are then transformed with a genomic library from wild type cells and plated at a nonpermissive temperature. Each transformed cell takes up a single plasmid containing one genomic DNA fragment. Most of these genes do not encode for the defective protein, and so the cells that take up these genes won't form a colony. the rare cell that takes up a plasmid containing the WT version of the mutant gene is complemented, which allows the cell to replicate and form a colony at the nonpermissive temperature. Since many of the proteins that regulate the cell cycle are highly conserved, yeast can be used to isolate human genes encoding cell cycle proteins.
[Apoptosis] [Experiment] What happens as a result of knowckouts of neurotrophins?
lack of specific types of neurons
[CAM] where are transitional epithelial cells found?
bladder, function in its contraction and expansion
[Cancer] Adenoma vs adenocarcinoma
adenoma is benign, inside a capsule... adenocarcinoma is malignant, can spread
what 2 things can GLUTS do?
1. carry glucose, galactose, water, painkillers2. mediate transport of soplutes in or out of cells, depending on solute concentration3.
what happens within depolarization?
Na+ channels open, it flows in the cell and down the gradient, and within milliseconds the channel closes. Na+ influx then ceases.
what are the largest cytoskeletal fibers? and what are they made of?
microtubulesmade of tubulin2 dif types of tubulin: alpha and beta
peripheral/secondary lymphoid organ
Lymphoid organs in which T and B cells interact with foreign antigens, e.g. spleen, lymph nodes
[Cell Cycle][Prograssion in Interphase] What model organism was used to identify S-phase promoting factors (SPF) during interphase? Name differences in budding yeast vs fission yeast vs mammalian
Yeast. Cdc28 is the ONLY cdk in buddying yeast, Cdc2 in fission yeast... cdk1 in mammalian for mitotic prograssion.... but the mammalian Sphase cdk is cdk2
[Apoptosis] Examples of immune system apoptosis?
removal of lymphocytes after the immune system has been challenged. Killing virus-infected cells.
[ECM][Proteoglycans+GAG] What are the two main types of proteoglycans?
TM proteins (syndecans) and secreted PG's
[CAM] What are the types of anchoring junctions?
Adherens Junctions, Desmosomes, hemidesmosomes
[Cancer] What are the six major characteristics of cancer cells?
1. activation of proto-oncogenes, leading to self-sufficiency in growth signals 2. insensitivity to anti-growth signals, because of reduced checkpoint control and reduced tumor supressor genes. 3. evasion of apoptosis by inhibiting apoptosis and increased cell survival. 4. limitless replication because of increased telomerase activity. 5. invasion of tissue and metastasis because of cell adhesion breakdown. 6. sustained angiogenesis
[CAM] Experiment 7: What was used to determine where the tight junction was? (stained black, but could not penetrate tight junction)
lanthanum hydroxyde, between cells
where does the protein go from the ER?
ER-->golgi etc. via budding/fussion vesicles
when was the signal hypothesis proposed? and what does it explain?
proposed in the 1970's. it explains how proteins got targeted to the RER.
Consider the two statements below: A In inducible (catabolic) operons like lac, the repressor is usually activated by the substance to be broken down. B. In inducible (catabolic) pathways, the promoter is always active.
Which is true; which is fals
both A and B are false
[Apoptosis] How does the MAPK pathway work?
mitogens activate MAPK pathway --- MAPK promotes transcription of c-fos and myc --- more cell division (cancer). myc increases txn of cyclin D, SCF ubiquitin ligase, both of which increase G1/S cdk, which phosphorylate the Rb protein. Myc also increases synthesis of E2F, causing entry into S phase.
what is the lipid bilayer impermeable to?
ions, small charged molecules, and all large molecules
how are SERCA and PMCA the same?
1. both P-type pumps2. ATP dependent3. use ATP to autophosphoylate a conserved aspartic acid residue
what 6 things are aquaporins involved in?
1. concentration of urine by the kidneys2. digestion3. regulation of body temp4. secretion and absorption of spinal fluid5. secretion of tears/saliva, sweat, bile, 6. reproduction
[Cell Cycle] Describe how MPF is deactivated and during what stage does this occur?
Late Anaphase. There is Inactive APC/C and phosphorylated Cdh1. Cdc14 dephosphorylates Cdh1, so that Cdh1 can complex with APC/C ----APC/C-Cdh1 = Active APC/C. Active APC/C causes polyubiquination of Mcyclin so that it goes to proteasome to be degraded. G1 cyclin CDK then phosphorylates Cdh1, so that it decomplexes from APC/C, deactivating it.
[CAM] Describe the mechanism for signaling integrin activation?
unbound state is a heterodimer and is bent over, which brings the two subunits close together. ligand binds and causes the heterodimer to become erect, allowing the two subunits to separate. This conformational change causes the interactions with adapter proteins to change, leading to downstream effects
[Cancer][oncogenes] What are the two basic results from activation of oncogenes?
more activity per protein molecule, more proteins
what is an ENaC, and what does it do?
epithelial Na+ channel1. regulated by hormones which are not rapidly inactivated2. partially voltage dependent3. 1st found in epithelial cells4. are found in many other cells but still called ENaC's5. mediate bulk flow of Na+ ions, influence water transport across cell layers6. function depends on the Na+ gradient established by the Na+/K+ -ATPase
to illustate a signal transduction pathway, you would need a...
to begin w a ligand binging to a cell-surface receptor
[Cell Cycle][Experiment] What are the advantages of using xenopus oocytes?
oocytes are large, and so are easy to manipulate. can easily tell which phase they're at (spindle is visible to the naked eye); can track MPF activity, can track cyclin B concentration, fertilized egg cycles rapidly and synchronously between S phase and mitosis (15 minutes)
[Apoptosis] What does a lack of a survival signal lead to?
interaction of Bad with Bcl2, leading to Bcl2 inactivation, and thus apoptosis because Bax is allowed to remain open and thus causes swelling
how do yeast and other fungi grow and divide?
budding. (vesicle coming off ER or golgi)
[Cell Cycle] What is the CDK and the important cyclins in S. Cerevisiae?
Cdc28, Cln3 (midG1) and Clb1 and Clb2(late mitosis)
Why are the proteins and lipids called glycoproteins and glycolipids?
bc of the sugar on the proteins makes a coat around the cell
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