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119 Cards in this Set

  • Front
  • Back
What is a homodimer? A heterodimer?
A dimer comprised of two identical subunits. / A dimer comprised of two non-identical subunits.
Metastatic cells have the three following traits that allow them to initiate the formation of secondary tumors:
1. Metastatic cells must be less adhesive than other cells to break free of the tumor mass.

2. The must be able to penetrate numerous barriers, such as the extracellular matrices of surrounding connective tissue and the basement membranes that line the blood vessels that carry them to distant sites.

3. They must be able to invade normal tissues if they are to form secondary colonies.
What are desmosomes and where are they found?
"They're disk-shaped adhesive junctions approximately 1um in diameter. They're found in many tissues that are subjected to mechanical stress
What is signal transduction?
When a signal sent from outside a cell is converted into changes that occur inside the cell.
What is a second messenger?
Small substrates that typically activate (or inactivate) specific proteins.
G proteins are called that because?
Because they bind guanine nucleotides.
What does adenylyl cyclase do?
It forms cyclic AMP from ATP.
What does CREB stand for?
cAMP response element-binding protein. It's a transcription factor. That's kind of key.
What is keratin?
It's an intermediate filament.
Of Microtubules, microfilaments and intermediate filaments, which of these is non polar? Which two are polar?
Intermediate filaments are non-polar. Microtubules and microfilaments are polar.
What are intermediate filaments made of?
Two antiparallel dimers formed into a tetramer.
Which filaments have motor proteins for intracellular transport?
Only microtubules and microfilaments. Intermediate filaments don't because they're non-polar.
What shape arrays are spectrin filaments organized into?
Hexagonal or pentagonal arrays.
Which type of filaments are helpful in the construction of villi?
Actin filaments.
What are keratinocytes?
Skin cells.
Basal cells are undifferentiated/differentiated?
Relatively undifferentiated.
When cells specialize, which keratins up-regulate, and which down-regulate?
Keratin 5 and 14 down-regulate, and 1 and 10 down regulate.
EB-Simplex blistering is associated with a defective gene in keratin __ or keratin __ which is associated with the basal/cornified layer?
5/14. Basal.
What is a erythrocyte?
Why, it's a red blood cell!
Our instructor keeps talking about moieties. What is a moiety, and why would she use such an annoying word?
It's a functional group, or part of a molecule, or protein.

And I don't know. I just don't know.
What are the three subsets of selectins, and where are they found?
L-selectin: leukocytes
E-selectin: endothelial cells
P-selectin: platelet cells (and endothelial cells)
What is a selectin?
It's an integral membrane glycoprotein. It binds sugars that project from cell surfaces.


One example involves interacting with leukocytes and vessel walls at sites of inflammation and clotting.
What is IgSF?
It's the immunoglobulin superfamily.
What is IgSF involved with?
It's a group of Ig proteins (domains) that are involved in the recognition, binding or adhesion processes of cells.

They can mediate calcium independent cell-cell adhesion.
What are ICAMs?
Intercellular adhesion molecules. Many IgSF proteins are ICAMs. Integrins act as receptors for ICAMs.
What are VCAMs?
Vascular cell-adhesion molecules.
What are integrins?
They're proteins that are cell surface receptors that interact with the ECM and mediate various intracellular signals. They define cellular shape, mobility, and regulate the cell cycle. They also play a role in the attachment of cells to other cells.
What are the four main steps in neutrophil invasion?
1. Rolling of neutrophil, encounters increased selectin on endothelial, binds carbohydrate of neutrophil.

2. Interleukin 8 or protein activating factor binds to G-protein coupled receptor.

3. G-protein coupled receptor leads to integrin activation.

4. Integrin binds ICAM (VCAM) then extravasation.
Cadherins mediate calcium independent/dependent cell adhesion and IgSF mediate calcium independent/dependent cell adhesion.
Cadherin mediates calcium dependent cell adhesion, and IgSF mediates calcium independent cell adhesion.
Cadherins prefer to bind what?
To similar cadherins on neighbouring cells.
What two main things do catenins do?
They tether cadherins to the cytoskeleton, and transmit signals to the cytoplasm.
What are the three main types of cadherin, and where are they found?
E-cadherin - epithelial cells
P-cadherin - placenta
N-cadherin - neural cells
Where are cadherins found?
They're widely distributed over the surface of the cells, but also form specialized intercellular junctions: synapses, adherens junctions, and desmosomes.
How is E-cadherin involved with cancer?
The loss of E-cadherin is associated with cancer, as cells without E-cadherin are not associated with a neighbour, and are more likely to escape a tumour and move somewhere else, and start replication. The presence of E-cadherin suppresses the potential of metastasis.
What are three features of MMPs (not specific to a single MMP)
1. Promote cancer cell growth.
2. Development of blood vessels.
3. Degrade proteins and proteoglycans.
Do selectins bind to sugars, oligosaccharides, or carbohydrates?
Yes, they sure do! (all of them, which are all essentially the same thing)
Which junction type is involved with the blood-brain barrier?
Tight junctions.
What are tight junctions mainly made up of?
Occludin and claudin.
What are the three vital functions of tight junctions?
1. They hold cells together.
2. They block the movement of integral membrane proteins between the apical and basolateral surfaces of the cell, allowing specialized functions of each surface.
3. They prevent the passage of molecules and ions through the space between cells.
Adherens junctions are made up of calcium dependent/independent linkages formed between what molecule?
Calcium dependent. Cadherins.
Adherens junctions are linked to the cytoskeleton in what way?
They have cadherins that are linked to actin filaments of the cytoskeleton.
Caherin clusters of adherens junctions have two main features:
1. They connect the external environment to the actin cytoskeleton
2. They provide a pathway for signals to be transmitted from the cell exterior to the cytoplasm.
Where are desmosomes primarily found?
They're found in tissues that are subject to mechanical stress, ie. cardiac muscle, and epithelial layers of skin.
Which junctions are disk shaped?
Desmosomes!
Which protein group are desmogleins and desmocollins part of?
They're part of the cadherin family.
What are gap junctions specialized for?
They're specialized for intercellular communication.
What are gap junctions composed of?
They're composed entirely of an integral protein called connexin.
What are connexons made of? What do two connexons form?
Connexons are made of six connexins. Two connexons form a gap junction.
How big of a molecule can pass through a gap junction?
One that's less than about 1000 daltons (1 kDa).
What is one thing that causes gap junctions to close?
Abnormally high levels of Ca2+.
Are gap junctions selective or non-selective?
Relatively non-selective.
What are two differences of hemidesmosomes from desmosomes?
Hemidesmosomes attach the cell to the extracellular matrix instead of to another cell, and they use integrin cell adhesion receptors instead of cadherin.
With focal adhesion, what do cells adhere to?
Substratum.
What is RGD?
It's a peptide in substrate protein, which about half of integrins can bind to.
What is inside-out signalling?
It's the activation of an outside surface protein from inside the cell. (i.e. integrin)
What is glycocalyx, where does it come from, and what does it do?
It's a cell coat. It's excreted by the cell into the ECM, and it mediates cell-cell and cell-substratum interactions.
Where is collagen found, and why is it so special?
It's found only in the ECM, and it's the most abundant protein in humans.
What kind of bonds connect both fibronectins and laminins? (to themselves)
Disulfide bonds.
What is a kinase, and what does it do. What does the opposite?
A kinase is an enzyme that transfers phosphate groups from high-energy donor molecules (i.e. ATP) to target molecules (substrates). This process is called phosphorylation.

Phosphatase removes phosphate groups from targets.
What is Ras?
It's a signal transduction protein, that is similar to heterotrimeric G proteins, and is linked with cancer.
What are GEFs, GAPs, and GDIs, and what effect do they have on Ras?
GEF - guanine nucleotide-exchange factor. Stimulate dissociation of the bound GDP, promote GTP binding. Turn Ras cycle on. (ex. Sos)

GAP - GTPase activating proteins. Turn Ras cycle off.

GDI - guanine nucleotide-dissociation inhibitors. Inhibit the release of bound GDP, maintaining the inactive GDP. Keep Ras cycle off.
Why are secondary messengers useful?
A first messenger only binds to a single receptor, while second messengers often stimulate a variety of cellular activities.
What's the deal with cAMP?
It's a secondary messenger, produced by an integral membrane protein adenylyl cyclase, which is an effector. It's produced due to binding of a first messenger (hormone or ligand) to a receptor on the outside of the cell.

It also activates PKA (protein kinase A).
What are the five (!) main second messengers we're forced to learn about?
cAMP
Ca2+
phosphoinositides
inositoltriphosphates (IP3)
diacyclglycerol DAG
What are the four general steps in the production of second messengers?
1. Hormone first messenger (e.g. epinephrine)
2. G protein activation
3. Effector activation
4. Second messenger production
What three main things does protein kinase A (PKA) do when activated? What activates it?
(epinephrine pathway)

cAMP activates PKA.
1. It turns off glycogen production from glucose.
2. It turns on breakdown of glycogen.
3. It turns on transcription factors for cAMP dependent genes (CREB)
What is chemotaxis, and what does it depend on?
It's cellular movement in respect to chemical attractants. It depends on the production of phosphoinositide messengers to inform the cell of the target location.
What is a calcium wave triggered by?
It's triggered by formation of IP3 (a second messenger) by the PLC (phospholipase C)
What makes Ca2+ different from cAMP as a second messenger?
Unlike cAMP, Ca2+ can activate a number of effectors via calcium-binding proteins (e.g. calmodulin).
What is EGF? What is it involved with?
It's epidermal growth factor, and it binds to RTK.
What is PDGF? What is it involved with?
It's platelet derived growth factor. It binds to RTK.
What are the two mechanisms for receptor dimerization?
1. Ligand mediated dimerization.
2. Receptor mediated dimerization.
What are the two main functions of autophosphorylation?
1. Regulate kinase activity.
2. Function as binding sites for signaling molecules (docking sites)
How do extracellular signals effect RTK (receptor protein-tyrosine kinase) and cytoplasmic protein-tyrosine kinase?
RTK is directly activated by extracellular signals. Cytoplasmic protein-tyrosine kinase is regulated indirectly by extracellular signals.
What's the deal with ligand mediated dimerization?
RTKs contain two receptor binding sites, making it possible for a single growth factor to bind to both at the same time.
What is receptor mediated dimerization?
Some growth factors contain only a single receptor binding site, so the ligand binds to the site inducing a conformational change in the extracellular domain of a receptor.
What are transcription factors?
Proteins that bind to specific parts of DNA using DNA binding domains, they are part of the system that controls transcription.
What are the three main domains of transcriptions factors?
1. DNA binding domain
2. Trans-activating domain
3. Ligand binding domain
What are the two types of transcription factors?
1. Transcriptional activators
2. Transcriptional repressors
What are the four common motifs of DNA binding domains in transcription factors?
1. zinc finger
2. helix-turn-helix;helix-loop-helix (HLH)
3. high mobility group proteins (HMG-box)
4. leucine zipper
What are the five main methods to regulate transcription, and are they repressors or activators?
1. transcription factors (both)
2. DNA methylation (repression)
3. histone acetylation (activation)
4. histone deacetylation (repression)
5. histone methylation (repression?)
How many of each type of histone does the nucleosome core have?
Two of each of H2A, H2B, H3, H4.
H2A and H2B form a heterodimer, as do H3 and H4.
What are the two types of chromatin, along with the relevant subtypes?
1. euchromatin
2. heterochromatin
- facultative heterochromatin
- constitutive heterochromatin
Does heterochromatin remain compact during interphase?
Yes.
What are the traits of constitutive heterochromatin and facultative heterochromatin?
1. constitutive heterochromatin is compressed all the time. It's mostly the DNA near the centromere.

2. facultative heterochromatin is compressed at specific developmental times or in differentiated cells (e.g. X chromosome)
What does the activity of a region of chromatin depend on?
The state of modifications of histone tail amino acids.
What type of repeated or non-repeated DNA are histones found?
They're found in the moderately repeated DNA fraction.
What are the three types of highly repeated DNA sequences, and what makes that type unique?
1. Satellite DNA - found in centromeres.
2. Minisatellite DNA - unstable, changes from generation to generation. Used in DNA fingerprinting.
3. Microsatellite DNA - scattered evenly through the genome, used to study evolution.
What does DNA denaturation and renaturation tell us? Why is that?
Death to the other side of this card!

It allows us to determine the complexity of the genome. The higher the GC content, the higher the melting temperature.

The longer it takes the DNA to renature, the more complex the DNA is.
Do you know what telomeres are?
Yes, I do.

They're repetitive caps on the end of DNA strands, 500-5000 repeats. They're required for complete replication of the chromosome and protects the chromosome from nucleases.
What are the two types of cloning we talked about in class?
Reproductive cloning and therapeutic cloning.
What are adult stem cells?
They're undifferentiated cells found among differentiated cells in a tissue or organ.
What makes adult stem cells special?
They're not immortal, and they have a property known as plasticity.

And plasticity is... the ability of a partially differentiated adult stem cell to change its genetic program and differentiate into cells of another type.
What are totipotent and pluripotent cells?
Totipotent - the capacity to form all cells the developing organism will need.

Pluripotent - the capacity to form all cell the developing organism will need except for extraembryotic tissue.
Why is an egg needed in reproductive cloning?
The egg can reprogram the DNA in a differentiated cell that is encrypted by heterochromatin, so that it can be ready to produce an embryo.
What makes embryonic stem cells special?
They're totally undifferentiated cells capable of self renewal and commitment.
What are six important sources of DNA damage? What's the bonus one?
1. UV exposure (from the sun)
2. chemical carcinogens
3. replication induced damage
4. X-rays
5. gamma rays
6. radon gas

7. mold on some nuts
What activates ATR?
Single strand DNA breaks.
What activates ATM?
Double strand DNA breaks.
What are the three steps in DNA damage response reactions?
1. Repair of DNA damage
2. Activation of a DNA damage checkpoint and arrest of the cell cycle.
3. Apoptosis
What is ATM's transducer?
What is ATR's transducer?
ATM - Chk2, but ATM can also act as a transducer.
ATR - Chk1.
What is necrosis, and why is it bad/good?
When cells die accidentally from injury, and release their intercellular contents into the tissue or bloodstream. This releases antigens not seen before by the immune system, and activates an immunogenic response, that leads to inflammation.
Bleb? Weird.
They're buds formed during apoptosis.
What are the seven steps in apoptosis?
1. Overall shrinkage in the volume of the cell and nucleus.
2. Loss of adhesion to neighbouring cells.
3. Bleb formation at the cell surface.
4. Chromatin fragmentation.
5. Nuclear fragmentation.
6. Cellular fragmentation.
7. Phagocytosis of the cell and apoptotic bodies.
What is TNF?
Tumour Necrosis Factor, which is often excreted by immune cells in response to adverse conditions. TNF causes apoptosis when protein synthesis in the cell is blocked, meaning preexisting cellular factors can suppress apoptotic stimuli.
What are caspases and what do they do?
Caspases are proteolytic enzymes activated early in apoptosis. They cleave a group of proteins.
Which five types of proteins do caspases cleave?
1. More than 12 protein kinases
2. Lamins
3. Proteins needed for cell structure IFs (intermediate filaments), actin
4. Caspase activated DNAse
5. DNA repair enzymes
What four things intrinsically trigger apoptosis?
1. Irreparable genetic damage.
2. Extremely high cytososolic Ca2+.
3. Severe oxidative stress.
4. Starvation of growth factors.
What are the three main types of tumours?
1. Sarcomas (relatively rare) - solid tumours of the connective tissues such as bone, cartilage, and fibrous tissue.
2. Leukemias and lymphomas (8%) - arise from blood forming cells and cells of the immune system respectively.
3. Carcinomas (90%) - originate from epithelial cells.
Three steps of metastasis?
1. Cells break away from the parent mass (promoted by cell surface changes)
2. Enter lymphatic or vascular circulation.
3. Spread to distant sites in the body where secondary tumours are established.
Six properties of cancer cells:
1. Chromosomal rearrangements and duplication.
2. Failure to undergo programmed cell death (apoptosis)
3. Anchorage independence
4. Contact inhibition (involves some motility)
5. Growth factor independence
6. Immortal
What are five examples of tumour suppressor functions?
1. Transcription factors.
2. Cell-cycle regulators
3. Regulators of signaling pathways.
4. Phosphoinositide phosphatase
5. A protein that regulates DNA polymerase II elongation?
What is Knudson's two hit hypothesis?
Both copies of the RB gene must be inactivated before the cancer arises.
What protein does the RB gene encode for and why is it useful?
It encodes for pRb, a cell cycle regulator, which can act as a brake by binding to transcription factors in G1, which prevents entry into S.
What does p21 do?
p21 stops cdks from phosphorylating pRb and relieving repression of S phase genes.
What are the two main functions of BRCA1 and BRCA2?
1. They're transcription factors.
2. DNA repair.
What is the difference between the effectiveness of tumour-suppressors and oncogenes?
Only need one oncogene to induce a tumour, but need two copies of a tumour suppressor to have an effect.
What are the three possible activation paths for proto-oncogenes?
1. Mutation such that the gene product has an added function
2. A mutation in the regulatory sequence can alter the expression of the gene (increased)
3. A chromosome rearrangement, can alter expression of function in resulting proteins.
What are the six types of proteins encoded by proto-oncogenes?
1. Growth factors (EGF)
2. Growth factor receptors (Erb2/Her2)
3. Proteins kinases or proteins that activate protein kinases (Src)
4. Cell cycle control proteins (c-myc)
5. Proteins regulating apoptosis (Bcl-2)
6. Transcription factors (c-myc)