CMB Exam 3 Reading Guide

What are the different modes of cell-cell signaling? How is each type of signaling carried out by the cell?

1. Direct cell-cell signaling: Integrins and cadherins functions as signaling molecules that promote proliferation and survival in response to cell-cell and cell-matrix contacts.

Signaling by secreted molecules

2. Endocrine signaling - the signaling molecule (hormones) are secreted by special endocrine cells and carried through the circulatory system (ex. estrogen)

3. Paracrine signal - A molecule is released by one cell acts on neighboring cells (ex. neurotransmitters)

4. Autocrine signaling - A molecule acts on the cell that produces them (ex. T lymphocytes)

What characteristics of steroid hormones enable them to carry out their mode of signaling?

Steroid hormones diffuse through the plasma membrane and bind to transcription factors inside their target cells

What are the major steps in glucocorticoid signaling?

1. Glucocorticoid diffuses through plasma membrane

2. Ligand binds to glucocorticoid receptors, displacing Hsp90 allowing nuclear importation as receptor dimers (2)

3. The activated receptors bind to recognition sites on DNA and associate with HAT to stimulate transcription of their target genes.

How are genes under the control of the Thyroid Hormone Receptor regulated? Specifically, what role does HDAC and HAT have in switching these genes on and off?

1. In the absence of thyroid hormone, the corepressor HDAC associates with the thyroid hormone receptors resulting in repression of target gene expression (transcription)

2. In the presence of the hormone, it binds to the receptor causing a conformational change that displaces HDAC and allows HAT to bind, inducing transcription

Whats the role of nitric oxide (NO) in stimulating synthesis of cyclin GMP? What is the mechanism of signaling used by these small gas molecules?

Nitric oxide is a paracrine signaling molecule in the nervous system. It alters the activity of the intracellular target enzyme guanyl cyclase, stimulating synthesis of cGMP inside the cell.

How does nitroglycerin work in the treatment of heart disease (with a focus on cell signaling by NO)?

It dilates blood vessels NO diffuses to neighboring smooth muscle cells where it activates guanyl cyclase, resulting in the synthesis of cyclic GMP which induces muscle cell relaxation and blood vessel dilation. With that, increases blood flow to the heart

What are the main groups of peptides signaling molecule (peptide hormones, neuropeptides, growth factors)?

Peptide hormones: Insulin, , follicle-stimulating hormone, prolactin, growth hormones (nerve growth factor [NGF], epidermal growth factor [EGF], platelet-derived growth factor [PGF], membrane-anchored growth factors)

Neuropeptides: enkephalins and endorphins (natural analgesic that decrease pain response in the CNS)

What is the basic structural unit of a peptide signaling molecule?

Amino acids. They range in size from only a few to more than 100 amino acids…

Do peptide signaling molecules act at the surface of the cell or do they cross the plasma membrane?

Peptide hormones, neuropeptides, and growth factors are unable to cross the plasma membrane of their target cells, so they act by binding to cell surface receptors.

What are the structural characteristics of GPCRs

7 transmembrane α helices, an extracellular ligand-binding domain, and an intracellular domain with guanine-nucleotide exchange factor (GEF) activity

GPCRs typically have carbohydrate groups attached to the extracellular potion of the protein. What might be the role of those carbohydrates

It acts as a quality control tag, ensuring that only properly folded GPCRs are transported to the plasma membrane

They can influence how ligands interact with the receptor and maintain the correct shape of the binding site

What are the main steps leading up to the hormonal activation of adenyl cyclase by the hormone epinephrine?

1. Epinephrine binds to the GPCR outside of the cell

2. This activates the phosphorylation of the α subunit G protein

3. Activated α g protein subunit dissociates from βγ and attaches to adenyl cyclase, catalyzing the conversion of ATP to cAMP

What role do “GTPase activating proteins” (GAP) have in regulating G-protein signaling?

GAP proteins stimulate termination of the activity of the α subunit, causing it to reassociate with the βγ complex

What are the main steps leading to the regulation of glycogen breakdown?

What amino acid residue is phophorylated?

Names of enzymes and how they are regulated

1. Epinephrine binds to GPCR → Activation of the α subunit → activation of adenyl cyclase which converts ATP to cAMP

2. cAMP molecules bind to protein kinase A causing the dissociation of the catalytic subunits (C).

3. Protein kinase A activates phosphorylase kinase which activates glycogen phosphorylase, which catalyzes the breakdown of glycogen to glucose-1-phosphate

How does cholera toxin negatively impact the normal signaling pathway for adenyl cyclase activation

What is the mechanism of action for cholera toxin?

Cholera prevents the GTP hydrolysis of the α subunit, causing it to be “locked on”.

This causes massive increase in cAMP (ATP → cAMP by adenyl cyclase), causing excessive ion and water secretion and therefore severe diarrhea

How is Protein Kinase A regulated? (activated/inactivated)

PKA is regulated with the binding of cAMP, which activates is and dissociates the C subunits, which are then enzymatically active.

PKA activates target proteins by converting ATP → ADP and tagging target protein with that extra phosphorous

It is inactivated by protein phosphatase 1, which removes the phosphate group from the target

What are the main steps that lead to expression of cAMP-inducible genes?

1. Hormone binds to GPCR, activating the α subunit which binds to adenyl cyclase

2. Now activated adenyl cyclase converts ATP → cAMP

3. cAMP binds to Protein Kinase A, releasing the C subunit which is now enzymatically active

4. The C subunit translocates to the nucleus and phosphorylates CREB (CRE-binding protein), leading to the recruitment of coactivators and expression of cAMP-inducible genes

Compare the differences between receptor tyrosine kinases and nonreceptor tyrosine kinases

Nonreceptor tyrosine kinases - associate with the cytosolic domains of receptors that lack intrinsic enzymatic activity

Receptor tyrosine kinases -

What are the main steps that lead to activation of receptor tyrosine kinases

What is the role of Ras in ERK MAP kinase signaling, and how is it reglulated?

Under what circumstances would Ras be directly responsible for causing abnormal cell growth?

PI 3-kinase/Alt pathway forms the initial steps in many signaling pathways. What are the steps that lead to AKT activation?

What are FOXO induced genes, regulation of mTOR, GSK and Bad all regulated by?

Akt activation

What are the main steps leading to activation of transcription for the TGF-β/Smad pathway?

What role does ubiquitination and proteasomes play in the activation of the NF-kB pathway?

What is the mode of cell signaling in the Notch signaling pathway?

What are DNA damage checkpoints?

What are their functions during cell cycle progression?

What are the evens that lead to the activation of the maturation promoting factor (MPF)?

What are the events that lead to termination of MPF activity?

Note: You should be familiar with sites of phosphorylation (Thr 161, Tyr 15,
Thr 14) and the types of enzymes involved in MPF regulation (Kinases,
phosphatases, ubiquitinases)

How does Cdk4,6/CycD activity drive G1 progression?

What are the main targets of CDK4,6/Cyclin D and what are their roles in the regulation of transcription?

Compare the 2 different responses to DNA damage. What are the checkpoint kinases and what role do they play in cell cycle arrest in response to DNA damage

What is MDM2s role in the regulation of p53, both in the absence of DNA damage and when there are high levels of DNA damage

How is p53 modified by MDM2?

What role does the spindle assembly checkpoint have in the metaphase to anaphase transition?

What would you expect to see if cells had misaligned chromosomes?

What roles do APC/C ubiquitin ligase, Securin, and Separase play in the metaphase to anaphase transition

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What role do cohesins and condensins have in chromatin condensation?

Which kinases regulate chromatin condensation

What structural changes occur between g2, prophase, and metaphase?

What type of remodeling occurs at the nuclear envelope during mitosis and what are the enzymes and structural proteins involved?

Compare the differences between embryonic and tpyical eukaryotic cell cycles. What could account for the different cell cycle times?

How is the progression of animal cells regulated through the cell cycle?

What occurs at each phase during the cell cycle?

How is regulation of the cell cycle for budding yeast controlled? At what point in the cycle is regulation primarily controlled and how?

Compare the difference between plant and animal cytokinesis

How is the centromeric region maintained during chromatin condensation?

How are cohesins replaced by condensins?

What is the difference betwee endothelial and epithelial cells

What is the role of Vascular Endothelial Growth Factors (VEGF) in cell proliferation?

What are stem cells and how do they proliferate to become fully differentiated cells?

What are the steps leading up to replacing damaged cells that have shed from the surface epithelium? What type of cells are involved in this process?

What is a hematopoetic stem cell transplantation and how is it applied to the treatment of cancer?

What are induced pluripotent stem cells? How are they made? Why was it necessary to make iPSCs?

What is transdifferentiation? What is the medical significance of it?

What are the medical applications of stem cell therapy

Not: many mentioned w/in the text

What role do phagocytes play in the removal of apoptotic cells?

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What interactions take place between apoptotic cells and phagocytes?

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hat are the alternative pathways of programmed cell death?

What are the mechanisms that lead to cell death for these alternative pathways?

What role do caspases have during the process of apoptosis?

What are the roles of effector proteins in the mitochondrial pathway of apoptosis?

Focus on Bax and Bak

What steps lead to cytochrome C release in the mitochondrial pathway of apoptosis?

What role does p53 have in DNA damage-induced apoptosis. What are the main molecules involved in this apoptotic pathway

What role does Caspase-8 have in the mitochondrial pathway of apoptosis? What type of enzyme is Caspase-8?