Foundational Toolkit take-home exam

What are the critical negative cell cycle regulators?

p16, p21, p27, p53

Why does cell division occur?

development, tissue repair, tissue renewal

What is the pathway for cell renewal?

stem cell division, amplifying divisions, terminal specialization, shedding (death)

What is the pathway for tissue repair?

hemostasis, inflammatory phase, proliferative phase, remodeling phase

What are the stages of the cell cycle?

G1, S, G2, mitosis, cytokinesis

When do cell checkpoints occur?

G1/S checks if DNA synthesis can occur, G2/M checks if DNA synthesis has been completed properly, spindle checkpoint checks if all chromosomes are attached and sister chromatids separated correctly

What is the restriction point?

in late G1 phase, cell commits to mitosis and will only stop due to DNA damage or spindle defects

How do cell checkpoints function?

cyclin dependent kinases (CDKs) are active when bound to cyclin and phosphorylates target substrates

How are cyclin dependent kinases regulataed?

CDK activating kinases (CAKs) and CDK inhibiting kinases (CIKs), p27 also inhibits CDKs

How are cyclins regulated?

on a transcriptional level, their concentrations increase when needed during relevant cell phase then their transcription stops

What are the phases of mitosis?

prophase, metaphase, anaphase, telophase, cytokinesis (kind of)

What occurs during prophase?

chromosomes condense and spindle fibers form

What occurs during metaphase?

chromosomes line up on midline plate

What occurs during anaphase?

sister chromatids are separated

What occurs during telophase?

nucleus divides

What occurs during cytokinesis?

cytoplasm divides

What are the hallmarks of cancer that involve cell cycle dysregulation?

sustaining proliferative signals, evading growth suppressors

What is necrosis?

accidental death of living cells and tissue accompanied by inflammation

What causes necrosis?

trauma from temperatures, electric shock, radiation, atmospheric pressure changes, or mechanical trauma, oxygen deprivation from CO poisoning or cardiopulmonary disease, toxins, venom

What happens to the cytoplasm in necrosis?

cell and mitochondria swell, holes appear, cell bursts open

What is pyknosis?

nuclear shrinkage, occurs during necrosis

What is karyohexis?

nuclear fragmentation

What is karyolysis?

nuclear fading, occurs in necrosis because DNA is not cleaved evenly, creating fragments of all sizes

What is apoptosis?

programmed, controlled cell death

Why does apoptosis occur?

sculpting of fingers, deleting structures, regulate cell number, remove defective cells

What happens to the cell during apoptosis?

cell shrinks, chromatin compacts, blebbing, equal DNA fragments, creation of apoptotic bodies that are engulfed by phagocytic cell

What are intrinsic factors that lead to apoptosis?

originate within cell, when cell is damaged beyond repair, infected, stressed, starved from defective DNA repair, toxic drugs, irradiation

What are extrinsic factors that lead to apoptosis?

originate outside of cell, signal transmitted via death receptors from toxins, cytokines, hormones, growth factors

What are caspases?

cysteine/aspartate proteases activated by being cleaved twice

Describe the extrinsic pathway for apoptosis

death receptors FasL, TNF-R respond to their ligands, recruit DED to create FADD complex, which activates caspase 8

Describe the intrinsic pathway for apoptosis

when extrinsic pathway isn’t strong enough, signal is routed through mitochondria which releases cytochrome c under control of Bcl2, forms apoptosome, activates caspase 9

What is pyroptosis?

combination of necrosis and apoptosis, creates inflammatory response, requires caspases, nucleus condenses, cell swells, membrane ruptures, occurs after pathogen infection

What are the major properties of RTK receptors?

membrane receptor, protein ligand, adapter proteins, monomeric G proteins, serine/threonine kinases, c-kit, transcription factors, cell growth

Describe the pathway of an RTK receptor

ligand binds, RTK phosphorylates, activates GBR2 via SH2 domain, exposes SH3 domains, bumps GDP off of Ras, Ras binds GTP, activates Raf, activates other adapter proteins to stimulate cell growth

How is the RTK signal turned off?

Raf kinase inhibitor protein (RKIP) and GTPase activating protein (GAP)

What are the major properties of GPCRs?

membrane receptor, protein/molecule/energy ligand, trimeric G proteins, cyclic nucleotides, sensory transduction

Describe the pathway of a GPCR

ligand binds, GDP leaves, GTP binds, a subunit breaks off, interacts with effector protein/enzyme

What is adenyl cyclase?

class of GPCR, converts ATP to cAMP, activates protein kinase A (PKA), phosphorylates enzymes and transcription factors

What is phospholipase C?

class of GPCR, cleaves PIP into DAG and IP3, IP3 initiates cascade to transcription factors

How is the GPCR signal turned off?

a subunit hydrolyzes GTP to GDP and reunites with b and y subunits, phosphodiesterases convert cAMP to AMP

Describe the pathway that controls vision

light changes retinal to trans-isomer, GPCR actives, a subunit activates PDE to convert cGMP to GMP, low cGMP causes ion channels to close, cell hyperpolarizes, indicating light was detected

How is the pathway that controls vision turned off?

low calcium stimulates guanylyl cyclase to make more cGMP, ion channels open

What are the classes of steroids?

glucocorticoids, mineralocorticoids, androgens, estrogens, progestogens

Describe the pathway of a steroid receptor

steroid diffuses across plasma membrane to receptor in cytoplasm, complex translocates to nucleus, binds to chromatin directly to influence gene transcription

How are steroids synthesized?

cholesterol synthesized from acetyl CoA within cell or taken up as low density lipoprotein (LDL), transported to mitochondria, then modified into steroid hormones

What is Cushing’s disease?

excessive cortisol from pituitary/adrenal gland tumors or long term administration of steroids causing hair loss, dark skin, urination, drinking, poor wound healing, pot belly

What is Addison’s disease?

hereditary adrenal gland hormone deficiency causing general illness

How are steroids regulated?

concentration determines strength, HMG-CoA reductase regulates cholesterol synthesis from acetyl CoA, steroidogenic acute regulatory protein (sTAR) regulates transport of cholesterol into mitochondria

What are common inheritence patterns?

autosomal recessive/dominant/codominant, sex-linked, mitochondrial, sex-limited, variable penetrance

What is the acrosome reaction?

sperm makes contact with egg, acrosome reacts with zona pellucida and perivitelline space, plasma membranes of sperm and egg fuse, sperm nucleus enters egg, granules from egg are released to prevent any more sperm from fusing

What are the regions of an embryo before gastrulation?

amnion, epiblast, hypoblast

What are the germ layers that form at gastrulation?

ectoderm, mesoderm, endoderm

What does the ectoderm form?

nervous system, epidermis, glands, some cranial bones, pituitary and adrenal medulla,, mouth, anus

What does the mesoderm form?

connective tissue, bone, blood, cartilage, muscles, endothelium of vessels, kidneys

What does the endoderm form?

lining of gut and airways, endocrine, thyroid glands

What are primordial germ cells?

in the nascent amnion in primates

What is neurulation?

after gastrulation, ectoderm forms neural plate which folds into neural tube, neural crest migrates to form the PNS while the neural tube stays and forms CNS

What is a chordoma?

spinal tumor in sacral spine or base of skull, where neural tube folds last, most common in ferrets, commonly due to folate deficiency

What is anencephaly?

failure to close anterior neural tube causing absence of brain skull, and scalp

What is spina bifida?

failure to close posterior neural tube causing spinal cord to remain exposed

What does totipotent mean?

cell can differentiate into any cell, including extraembryonic cells like the placenta

What does pluripotent mean?

cell can differentiate into any germ layer (ecto, meso, endoderm)

What does multipotent mean?

cell can differentiate into a limited number of cells, hemopoietic cells

What does unipotent mean?

cell can only multiply and differentiate into one type of cell, sperm and epidermal cells

What are the defining properties of stem cells?

unlimited self renewal and differentiation into different cell types

How is pluripotency of cells proven?

take cells, inject them into mouse, analyze the resulting teratocarcinoma to see if it has multiple cell types (skin, fat, teeth, etc)

What is an autologous transplant?

use patient’s own stem cells

What is an allogenic transplant?

use donated stem cells from relative or stranger

What is a xenogeneic transplant?

use stem cells from a different species

What is the function of green fluorescent protein (GFP)?

reporter gene added to see if a gene transfer was successful

How is a new segment of DNA added to the genome?

induce a double stranded break using CRISPR Cas 9, zinc finger nucleases, or TALENs that gets fixed by the cell by homologous repair

What is transgene cloning?

inject modified ESCs into embryo to produce chimeras that have both modified and non-modified cells, then breed for homozygotes

What is pronuclear injection cloning?

inject modified DNA into fertilized oocyte, to produce pups that could have transgene or not, analyze DNA to see which ones have transgenic DNA

What is SCNT cloning?

modify a somatic cell, identify which actually have modification, inject nucleus of somatic cell into empty egg, grow embryo, transfer to surrogate to produce clone that definitely has transgene

What is cytosol?

suspends all organelles

What is the plasma membrane?

liquid, non-aqueous lipid bilayer with embedded proteins

What are intracellular membranes?

encase organelles and divide cells into different compartments

What is the role of the endoplasmic reticulum (ER)?

exchanges material within a cell

What is the role of the Golgi complex?

exchanges material with the extracellular space

What is the nuclear envelope?

double layered membrane with nuclear pores

What are nuclear pores?

holes in the nuclear envelope for mRNA and proteins to travel in and out of the nucleus

What is inside the nuclear envelope?

chromatin (DNA), nucleoli (RNA), nuclear lamina (intermediate filaments)

What is outside the nuclear envelope?

basket of intermediate filaments that hold the nucleus in place in the cytosol and anchors of other intracellular structures

What is the function of mitochondria?

has inner and outer membranes to generate ATP

What are the components of the cytoskeleton?

microtubules, actin filaments, intermediate filaments

What is the function of microtubules?

mediate intracellular transport over long ditances, coordinate global cellular events like polarization and division

What is the function of actin filaments?

cortical network of thin filaments that mediate all motile and contractile behavior

What is the function of intermediate filaments?

rigorous network of fibers that follow microtubules, assist cell shape, and provide support for anchoring intracellular structures

What are the molecular components of of a cell?

inorganic molecules, small organic molecules, and macromolecules

What are the inorganic molecules of a cell?

water (70%) and ions (1%)

What are the small organic molecules of a cell?

sugars, fatty acids, amino acids, nucleotides (less than 3%)

What are the macromolecules of a cell?

proteins, nucleic acids (26%)

What are the types of nucleic acids?

DNA and RNA

What are the functions of proteins?

enzymatic catalysis and regulation, transport, storage, motility, structure and support, immune protection, signaling

What are prion diseases?

protein misfolding that propagates and spreads throughout body, transmissible in blood and meat (mad cow disease, scrapies, chronic wasting disease, cruzfelt-jacob’s disease)

What is primary protein structure?

sequence of amino acids bound by peptide bonds with 20 different R groups

What is secondary protein structure?

alpha helices and beta sheets

How are alpha helices structured?

spiral shaped stabilized by intra-chain H bonds with R groups projecting outwards (keratin)

How are beta sheets structured?

antiparallel chains forming sheets with many alanine and glycine groups (silk)

What is tertiary protein structure?

one complete protein chain from N terminus to C terminus, can contain alpha helices and beta sheets (one subunit of hemoglobin)