Exam 1

Question 1

What is the importance of non-coding DNA?

Answer 1

Promoter/enhancer regions-TFs
Organize chromatin
Noncoding regulatory RNAs
Mobile genetic elements-things found all around genome
Telomeres/centromeres

Question 2

What are the two most common DNA variations?

Answer 2

SNPs

CNVs

Question 3

How are single nucleotide polymorphisms used?

Answer 3

Can be useful markers if inherited with a genetic disease via physical proximity
Used for multigenetic complex diseases(DM II, HTN)
Are regulatory and neutral at times
Not helpful fro prevention

Question 4

How are copy number variations used?

Answer 4

Large stretches of DNA
Can underlie large portion of phenotypic diversity
Influence on susceptibility not well known

Question 5

What role do histones play, including the modifying factors?

Answer 5

Histones can be regulated via methylation, acetylation, and phosphorylation, by writers
When associated with DNA a single core is nucleosome

Consist of H1 on linker and the core of H2a,b, H3, H4 with positive charge to attract negative DNA

Question 6

How does histone methylation, acetylation, and phosphorylation affect DNA?

Answer 6

M-increase/decrease transcription based on AA(Lys, Arg)
A-increase transcription via HAT, decrease via HDAC(Lys)
P-increase/decrease transcription based on position of serine

Question 7

What does DNA methylation do?

Answer 7

Decreases transcription(silencing genes) via methyltransferases, demethylating enzymes and methylated-DNA-binding proteins

As opposed to histones which can increase/decrease transcription

Question 8

What are chromatin organizing factors?

Answer 8

Believed to bring TFs, gene promoters/enhancers into closer proximity(spatial relationships)

Question 9

Why is miRNa important?

Answer 9

Silences mRNA postranscriptionally, all eukaryotes

Pri to pre in nucleus, pre to miRNA via DICER, binds RISC and either directly binds and cleaves RNA or is imperfect and stops translation physically

Question 10

How are siRNAs used?

Answer 10

Made specifically for certain RNAs and can fit in Dicer and RISC to silence that protein translation(pathogenic)

Question 11

What does lncRNA do and what is an example?

Answer 11

Promote histone modification inc/dec, facilitate/ inhibit TF binding, and assembly of protein complex for increased gene activity

XIST and X chromosome inactivation, XIST forms a cloak on X chromsome but itself is not silenced

Question 12

Name the major parts of the cell and their functions

Answer 12

Nucleus-holds DNA and helps regulate transcription
Mito-powerhouse of the cell(ATP), apoptosis
RER- Protein production(membrane and secreted)
SER, Golgi-protein modification, sorting, catabolism
Lysosomes-catabolism
Proteosomes-peptide breakdown
Peroxisomes- break down FA

Question 13

What does phosphatidylinositol do?

Answer 13

Is a linkage for membrane proteins on inner membrane

PLC can turn it into IP3 and DAG(stays on surface)

Question 14

What is phosphatidylserine an indicator of?

Answer 14

Normally on IM but if flipped(flipase) can signal cell death(apoptosis)

Helps BLOOD CLOT

Question 15

What do glycolipids and sphingomyelin do?

Answer 15

On EM of cell

Cell to cell/matrix interactions

Question 16

No including the specific phospholipids, what can be found on the cell membrane?

Answer 16

TM proteins-alpha helices(positive holds to PL negative charge)
Lipid rafts-accumulation of lipids/proteins
GPIs, Prenyl groups or FAs- to anchor proteins(farnesyl, palmitic acid)
Peripheral proteins attached to TM proteins
Glycocalyx-barrier molecule

Question 17

What is important about the lipids, proteins and their interactions on cell membranes?

Answer 17

They help in communication, interaction with ECM, polarity of cell, and anchoring to BM

Question 18

What can cross the cell membrane passively and how?

Answer 18

Small, non polar molecules-O2, CO2
Hydrophobic molecules- steroids
Polar <75Da-H2O, EtOH, urea

water in large quantities via AQP

NO ions, glucose

Typically driven by electrical/chemical gradient

Question 19

What are carriers and channel proteins used for?

Answer 19

Allow nutrient and waste transfer of cell if smaller than 1000Da
Ions, sugar, nucleotides

Channels create hydrophobic pores while carriers change conformation to allow transport

Question 20

How does active transport work and what is an example?

Answer 20

ATP is used to move solutes against concentration gradient

MDR protein, pumps polar compounds(chemo) out of cells to render cancer resistant to Tx
Multidrug resistant

Question 21

Describe caveolae mediated endocytosis

Answer 21

Non-coated membrane assocaited with GPI, cAMP binding proteins, SRC kinases and folate receptor

Potocytosis-cell sipping

Typically used to internalize receptors and integrins

Question 22

Describe pinocytosis and receptor mediated endocytosis and what is an example

Answer 22

Cell drinking

Plasma membrane engulfs EC cargo in clathrin coated pit, then clathrin vesicle and returns that membrane to keep wall size normal, endo/exocytosis must be tightly regulated.
To degrade receptor, the clathrin coat is destroyed and the endosome binds to a lysosome, to recycle it goes back the membrane before the lysosome fusion

LDL and transferrin, the acidic environment of the lysosome causes release of cholesterol and iron(reabsorbed in cytoplasm), the receptors are resistant and can be recycled,

defect in LDL receptor transport causes familial hypercholesterolemia

Question 23

Why, in general, is cytoskeleton important to the cell and what are the major classes or proteins?

Answer 23

Movement, structure, polarity, organization

Actin microfilaments
Intermediate filaments
Microtubules

Question 24

Describe the function and importance of actin filaments.

Answer 24

Two types- G(globular) and F (filamentous) polymerized G-actin make up F-actin
Add at + end, subtract at - end(movement via addition and subtraction)

In muscles myosin binds actin and moves across, non-muscle cells bind actin binding proteins and help movement of cell in space

Question 25

Describe intermediate filaments. (Especially the specifics for cell types)

Answer 25

Ropelike, are polymers usually and do not change size like actin, impart strength, and bear stress Lamin A, B, C-nuclear lamina-can cause MD/progeria(premature aging) Vimentin-mesenchymal cells(fibroblasts,endothelium) Desmin- muscles cells, myosin, actin interaction Neurofilaments-axons, strength and rigidity Glial fibrillary acidic protein- glial cells around neurons Cytokeratins-cell markers due to wide variety(acidic-I, basic/neutral-II) Skin and hair strcuture

Question 26

Describe microtubules and how they are used

Answer 26

Made of alpha and beta-tubulin, size changing hollow tubes Polar -,+ ends, with - being in MTOC/centrosome, + end grows or shrinks Kinesins move anterograde, dyenins move retrograde, via ATP motor proteins, important in mitosis, separating chromatids Also provides motility to cilia(bronchial epithelium) and flagella(sperm)

Question 27

Why are occluding(tight) junctions important in cell-to-cell interaction and what constitutes them?

Answer 27

Restricts paracellular movement or solutes Contain occludin, claudin, zonulin, and catenin Divides apical/basolateral cell(polarity) Dynamic and can dissociate during proliferation and movement

Question 28

What is the importance of anchoring junctions(desmosomes)?

Answer 28

Attach cells to other cells or ECM Between cells-spot desmosome or macula adherens -cadherins or desmoglein, desmocollin(link to intermediate filaments and can dissipate stress over many cells) Cell to ECM-hemidesmosome - integrins-link cytoskeleton to ECM - FAC generate IC signals due to shear stress Broad bands are called belt desmosomes -E-cadherins associated with actin influencing shape and motility

Question 29

Why do cells need communicating(gap) junctions?

Answer 29

Allow passage of chemicals between cells nand create syncytium (i.e., cardiac myocytes), permeability reduced by decrease in pH or increase Ca2+ Made of connexons which are made of hexamers of connexin Permit ions, sugars, nucleotides, AA, vitamins

Question 30

What role does the endoplasmic reticulum play in the cell?

Answer 30

Synthesis of transmembrane proteins and lipids for PM, or molecules to be exported Can have ribosomes(RER) or not(SER) To be transcribed on RER mRNA must have signal sequence otherwise it is done by free ribosomes RER proteins will be modified at the E(sugar groups, disulfide bonds) If the protein does not fold correctly it will be destroyed or build up in the ER leading to UPR and stress leading to apoptosis *CFTR is the most common degraded mutant protein, cystic fibrosis, deletion of F508*

Question 31

How is the golgi apparatus important for cells?

Answer 31

It modifies proteins and lipids like the ER and received from the ER from cis to trans(away from ER), certain sugar moieties are removed from the ER modification, M6P can be used to direct to lysosomes Cis-golgi can send proteins back to ER, trans to the membrane or vesicles *golgi is larger in secretory cells(goblet, plasma cells)*

Question 32

What does the SER do and in what cell is it most prominent?

Answer 32

It acts as a transition zone from RER to cis-golgi SER can by hyperplastic in steroid producing cells(adrenal) and breakdown of lipid soluble molecules(liver) *phenobarbital catabolism by CP450 in the liver causes hyperplasia of SER* In cells the SER sequesters Ca2+ for apoptosis and in muscles to contract and relax

Question 33

What is important about lysosomes?

Answer 33

Contain acid and enzymes to breakdown various molecules Enzymes are directed to lysosomes by M6P Connected to pinocytosis and endocytosis, forming early endosome with acid(not much breakdown), late endosome with significant breakdown and finally lysosome, all while gaining acidity Play a role in autophagy and phagocytosis

Question 34

Describe autophagy

Answer 34

Proteins and organelles no longer needed by the cell are engulfed in a double membrane of ER forming autophagosome, fuses with lysosome *used to preserve cell viability in nutrient depletion*

Question 35

Describe phagocytosis

Answer 35

Cells engulf proteins and debris from outside the cell in a phagosome which fuses with a lysosome for degradation

Question 36

Why are proteasomes important in cells?

Answer 36

They degrade cytosolic proteins, mainly denatured or misfolded(similar to ER), proteins destined for degradation are marked with multiple ubiquitin groups, unfolded and sent into the cylindrical protease, broken into peptides

Question 37

What general roles does the mitochondria play in the cell?

Answer 37

Energy production Cell death Intermediate metabolism

Question 38

Describe mitochondrial energy generation

Answer 38

Metabolites are oxidized causing protons to be pumped from matrix to intermembrane space. The gradient allows H+ to go back down its gradient to the matrix and produce ATP forming CO2 as well, this also forms ROS which are important to the cell but too many can be problematic *thermogenin can use the gradient to produce heat for non-shivering thermogenesis*

Question 39

Describe intermediate metabolism by mitochondria

Answer 39

Glucose and glutamine are taken up more and Ox Phos is attenuated. This allows TCA cycle intermediates to by shuttled off to make lipids and building blocks due to increased carbon moieties. *in benign and malignant cells this is known as Warburg effect*

Question 40

Describe mitochondrial mediated cell death

Answer 40

Necrosis occurs if the mitochondria is injured and ATP is no longer generated Apoptosis is mediated by the mitochondria via intrinsic or extrinsic signals, releasing Cyt C ultimately activated caspases *defects in apoptosis can lead to malignancy*

Question 41

What are the general cell signal modalities?

Answer 41

Damage to neighbor cells-danger signals Contact with neighborcells- GJ(Ca2+ or cAMP) Contact with ECM-integrins Secreted molecules- GF, cytokines, hormones

Question 42

What are the 4 modalities of extracellular communication based on distance?

Answer 42

Paracrine-in the vicinty Autocrine-same cell Synaptic- NTs via neurons Endocrine-mediator in bloodstream can travel through body

Question 43

Describe the two major cell receptor types and how they work

Answer 43

Intracellular-TFs, lipid soluble ligands - Vit D, steroids-nuclear hormone receptors- * NO causes guanylyl cyclase to create cGMP* Cell surface receptors-transmembrane proteins bind ligand -cause channel to open, activate G protein, activate RTK, change conformation activating latent TF

Question 44

Describe RTKs

Answer 44

Receptors for GFs(insulin, EGF, PDGF) | Intrinsic kinase activity phosphorylates dimer

Question 45

Describe non-receptor RTKs

Answer 45

These are like RTKs but do not phosphorylate the dimer of receptor, a cytosolic protein is phosphorylated *important in rous sarcoma virus, SRC family, SH2 binds phosphorylated groups on other proteins, SH3 mediates protein protein interactions

Question 46

Describe GPCRs

Answer 46

Serpentine 7 TM receptor ligand binds activating GTP binding protein which GDP bound, exchanges GDP for GTP, adenyyl cyclase is activated generating cAMP, or PLC generatig DAG and IP3, then Ca2+

Question 47

Describe Notch pathways

Answer 47

Cleavage of the receptor allows cytoplasmic piece to form transcription complex

Question 48

Describe Wnt signaling

Answer 48

Wnt binds, activates Frizzled, regulating IC B-catenin, which is constituently degraded, however Wnt-Frizzled recruits Disheveled which inhibits the degradation of B-catenin which translocates to nucleus forming TF complex

Question 49

What must a TF possess to be effective?

Answer 49

Protein:protein interaction domain Recruits histone modification proteins, RNA polymerase, chromatin remodeling complexes

Question 50

What would occur if a GOF mutation happened in GFs?

Answer 50

They are proto-oncogenes so you would get unchecked cell proliferation and tumor formation

Question 51

What are some characteristics of EGF and TGF-alpha?

Answer 51

EGF family Produced by macrophages and epithelial cells Mitogenic for hepatocytes, fibroblasts and epithelial cells Receptors-EGFR1 or ERB-B1 or EGFRm mutations occur in breast, brain, lung, head, and neck CA ERB-B2 or HER2is overexpressed in breast CAs

Question 52

What are characteristics of HGF or scatter factor?

Answer 52

Mitogenic for hepatocytes and epithelial cells Morphogen in embryo development, cell migration and hepatocyte survival Produced by fibroblasts and mesenchymal cells as pro-HGF activated at active site by serine proteases MET is receptor, intrinsic RTK, over-expressed in tumors-renal and thyroid carcinomas, inhibitor as therapy possibility

Question 53

Describe characteristics of PDGF

Answer 53

AA,AB,BB are constituently active CC,DD must be activated Stored in platelet granules, released on activation, also produced by macrophages, endothelium, smooth muscle cells Receptors are PDGF alpha/beta, both RTKs Induce fibroblast, smooth muscle and endothelial cell proliferation Chemotactic for these cells as well

Question 54

Describe characteristics of VEGF

Answer 54

A,B,C,D and F(placental) VEGF-A is VEGF, major angiogenic factor B and F are in embryo vessel development C and D are used in lymphatic as well as angiogenic development Also used for maintenance in brain, kidney and retina *Induces vasodilation and permeability, due to hypoxia mostly* HIF-1 mediates hypoxia driven VEGF along with PDGF and TGF-alpha Receptors are RTKs, VEGFR 1,2,3 2 is higly expressed on endothelium, used for angiogenesis Abs for receptors treat renal and colon CAs since the require angiogenesis, as well as “wet” age-related macular degeneration(AMD) And DM macular edema VEGFR-1...=....s-FLT-1 (soluble versions) indicated in preeclampsia by sopping up free VEGF required for normal endothelium maintenance

Question 55

Describe characteristics of FGF

Answer 55

FGF family, acidic(aFGF, FGF-1) and basic(bFGF, FGF-2) FGF-7 known as KGF FGF associates with heparan sulfate e in ECM, which is a reservoir for inactive factors for wound healing FGFR1-4 are RTKs, used in wound healing, hematopoiesis, and development FGF-2/bFGF can aid in angiogenesis

Question 56

Describe characteristics of TGF-beta

Answer 56

Not TGF-alpha, three forms TGF-B1,2,3 Family includes BMPs, activins, inhibins, mullerian inhibiting substance TGF-B1 has widespread distribution and is known as TGF-B Secreted as precursor needing activation Type I and II receptors (serine/threonine kinase), phosphorylate Smads, join Smad 4 in heterodimers to allow nuclear translocation “Pleitropic with a vengeance” because of the different effects it causes Produces collagen, fribronectin, and proteoglycans Inhibits collagen degradation by inhibiting MMP and increasing TIMPs Forms scars and drives fibrosis Anti-inflammatory serving to limit and terminate inflammatory response Inhibts lymphocyte proliferation and leukocyte activity

Question 57

What are key functions of the ECM?

Answer 57

Mechanical support-anchoring and movement, cell polarity Control of cell proliferation-binding GFs and signaling, latent GFs Scaffolding for tissue renewal-require BM, deficit in liver cirrhosis Establish tissue microenvironments-acts as boundary between CT and cells, functional in kidneys *possible therapy involving regrowing tissue/organs*

Question 58

Briefly describe the two forms of ECM

Answer 58

Interstitial matrix-space between cells in CT, supportive vascular and smooth muscle structures Made by mesenchymal cells(fibroblasts) forming amorphous gel (Fibronectin, elastin, proteoglycans, hyaluronate) Basement membrane-ogranized matrix arround cells(epithelial, enothelial, smooth muscle, forms mesh, Type IV collagen and laminin

Question 59

What are the three groups of ECM proteins?

Answer 59

Fibrous structural-collagen, elastins for strength and recoil Water hydrated gels-proteoglycans, hyaluronan Adhesive glycoproteins-connect ECM elements to one another and to cells

Question 60

Describe collagens

Answer 60

Types I, II, III, IV, form fibrils in blood vessels, tendon, bone, cartilage and skin *scars* Cross-linked triple helices via lysl oxidase depend on vit C Deficiency in Vit C leads to bleeding easy Collagen defects leads to Ehlers-Danlos and osteogenesis impercta Basement membranes contain non fibrillar type IV collagen, regulare fibril diamtere via FACITs(type IX), or anchor to BM via type VII

Question 61

Why is elastin important?

Answer 61

Recovers shape after deformation I.e. cardiac valves, and large blood vessels, as well as uterus, skin and ligaments Core of elastin and covering of fibrillin *defect in fibrillin leads to skeletal abnormalities and weakened aortic walls(Marfan syndrome)*

Question 62

How do proteoglycans and hyaluronan work together?

Answer 62

``` Form highly compressible gel used in joint cartilage, and lubrication for bone surfaces Form glycosaminoglycans(keratan sulfate and chondroitin sulfate) linked to long hyaluronic polymer(hyaluronan) like bristles The highly negative charge pulls in cations and thus water to make the gel like matrix *used to bind chemokines and GF to increase concentration in ECM* ```

Question 63

Describe fibronectin

Answer 63

Made by fibroblasts, monocytes and endothelium Binds to ECM components and integrins Provides scaffolding in wound healing for ECM deposition, angiogenesis and reepithelialization

Question 64

Describe laminin

Answer 64

Most abudant glycoprotein in BM, cross shaped Connects type IV collagen and heparan sulfate Modulates cell proliferation, motility and differentiation

Question 65

Describe integrins

Answer 65

Part of cell adhesion molecules Alpha/beta subunits Attach to ECM components such as laminin and fibronectin, linking IC to outside world Mediate firm adhesion in leukocytes and transmigration to inflammation Critical role in platelet aggregation Attach via RGD(Arg-Gly-Asp) motif Can trigger signaling cascade for cell proliferation, motility, shape and differentiation