KOVARI LECTURE OBJECTIVES/NOTES

Question 1

What biochemical events are triggered by growth factor binding to specific receptors?

Answer 1

GF binds to CELL SURFACE receptors (transmembrane proteins with a CYTOPLASMIC PROTEIN KINASE DOMAIN) causes: 1. immediate increase in intracellular Ca2+ (indicates initiation of transmembrane signaling) 2. Reorganization of actin stress fibers: necessary for anchorage dependence of cell attachment that is required for cell cycle progression 3. Activation, nuclear translocation, or both, of transcription factors: TF bind to regulatory regions of DNA of genese that are responsive to GF to induce cell cycle machinary 4. DNA synth + Cell division **GF activates distinct combination of signal transducers and TF to dictate precise gene induction and causes characteristic responses (classes)

Question 2

How do growth factors regulate the cell cycle?

Answer 2

Growth factor signals generated at the plasma membrane can transduce gene induction, cell cycle progression, and proliferation, differentiation, or apoptosis; GF triggers TF activation that regulate induction of components of the cell cycle machinery that monitor and direct cell cycle progression, cell growth arrest, and cell differentiation. Induction of DNA damage that would result in the accumulation of mutations leads to cell cycle arrest and DNA repair; alternatively, if the DNA damage is too great, cell death occurs by apoptosis

Question 3

Summary of aging:

Answer 3

aging = result of chronic chemical modification of all classes of biomolecules According to Free radical theory of aging, ROS = causes changes in DNA sequence (mutations) and therefore changes the protein structure; Longevity = achieved by developing efficient systems to limit and or repair chemical damage; CR = delays aging and extends mean and max lifespan of specific by inhibiting the production of ROS and decreasing damage to biomolecules and delaying many characteristics of aging, including cancer

Question 4

Describe the microscopic structure of the liver

Answer 4

= lots of lobules; each with a polyhedral shape blood sinusoids = from terminal branches of the portal vein; interconnect and interweave through the sheets of hepatocytes before joining the central lobular vein Sinusoids are lined by two types of cells: 1. vascular endothelial cells (loosely connected one w/another); leave numerous gaps, forming a net-like lining to the sinusoids; no basement membrane b.n the endothelial cells and hepatocytes thus allowing for exchange of metabolites b/n plasma and hepatocyte 2. Kupffer cells = mononuclear phagocytes = generally found in the gaps b/n adjacent endothelial cells (immune functino in protecting liver agains infection)

Question 4

Describe the relationship between aging and disease

Answer 4

aging = time dependent deterioration in function of an organism that changes the cell structure and function; result = increased susceptibility to disease AGING IS NOT A DISEASE! Diseases affect a fraction of a population, and aging affects everyone Aging is associated with decreased functionality in biochemical and physiological systems (decreased BMR, protein turnover, glucose tolerance, telomere shortening, decreased lung, cardiovascular, musculoskeletal, nerve conduction, etc.) Humans survive till age 50 without maintenance, with 76 = mean lifespan. lifespan is affected by our genetics and our environmental exposure and death is usually attributable to failure of a critical system death rate = max at mean lifespan; max lifespan = 120 year.

Question 5

Describe the regulation of the cell cycle

Answer 5

Growth factors stimulation induces proteins that are involved in regulating the cell cycle including: cyclins and CDKs (cyclin-dependent kinases) Cyclins = proteins that are specifically degraded at every mitosis CDK = kinase that must bind to a cyclin in order to be active The activity of cyclins is modulated by changes in expression at transcription and translation level; activity of CDK = modulated by phosphorylation state (expressed in relatively constant amts) SO: GF –> + cyclin –> + CDK + CDKI CDK-I = CDK inhibitor (binds to CDK and blocks catalytic activity) cyclins = have a specific CDK they are associated with and together they act at different stages of the cell cycle

Question 5

Differentiate between biological and chemical theories of aging

Answer 5

Biological = aging is a genetically controlled event that is determined by the programmed expression or repression of genetic information. sees aging as birth, growth, maturation, reproduction, death stages; differences in lifespan among a species are closely correlated with the efficiency of DNA repair mechanisms (more efficient DNA repair = longer lifespan); Chemical = aging is a somatic process that results from cumulative damage to biomolecules; 1. error catastrophe theory proposes that aging is the result of cumulative errors in the machinery for replication, repair, transcription, and translation of genetic information; errors lead to accumulation of dysfunctional macromolecules that cause an increasing amount of immunological detectable, but denatured or modified, functionally inactive, enzymes accumulating in cells as a function of age 2.other chemical theories of aging = result of chronic, cumulative chemical (non-enzymatic ) modification damages all biomolecules; damage is most apparent in long-lived tissue proteins (lens crystallin and extracellular collagen); brown color commonly results from formation of a wide range of conjugated compounds (also crosslinking occurs!) sort of like malliard reactions in which bread crusts; chemical integrity to the genome also occurs AGE DEPENDENT MODIFICATIONS: 1. protein modifications (ie: crosslinking, oxidation, deamination etc.) 2. DNA modifications and mutation (ie: depurination, oxidation, point mutations) 3. inactive enzymes 4 lipofuscin

Question 6

What is the role of apoptosis in cellular development?

Answer 6

= programmed cell death necessary to maintain integrity and homeostasis of multicellular organisms; inapropriate apoptosis can lead to degenerative conditions (neurodegenerative disorders) and disruption can lead to cancer or autoimmune disease; 2 key families of enzymes regulate apoptosis: 1. caspases (cysteine protease) 2. BcL-2 (Bcell lymphoma protein2): regulates caspase activity

Question 7

what are some of the characteristics of infectious agents found only in prions?

Answer 7

dont require DNA/RNA like others! -extremely resistant to inactivation (by UV light, xrays and chemical agets) -no humoral immune or inflammatory response -no virus like particles -can be inherited

Question 8

Summary of cancer:

Answer 8

in cancer: proto-oncogenes and tumor suppressor genes = function in signal transduction to mimic the effects of persistent mitogenic stimulation in order to continue the passage of the cell through G1 and present cell cycle exit. 2 suppressor proteins = p53 and Rb = key roles in determining cell cycle progression and apoptosis and the genes for coding the proteins are most frequently disrupted in cancer cells.

Question 8

What is the relationship between hierarchy of protein structure and protein folding diseases?

Answer 8

primary structure (aa sequence) predisposes protein towards its native conformation; folding = spontaneous, but mechanisms depend on: nature of perimary solved (H20 vs lipid) concentration of salts, pH, temperature, and molecular chaperones Native conformation (tertiary structure) = determines biological function (catalysis, protection, regulation, signal transduction, storage, structural , transport) in conformation disorders, the biological function is affected a loss or change of structure may lead to loss of function

Question 9

Rb gene vs Retinoblastoma

Answer 9

Rb gene = tumor suppressor gene (regulates cell cycle) Rb disease = rare; deletion of a specific band on chromosome 13; a single somatic mutation to knock out the remaining copy of Rb gene was sufficient to initiate a cancer Rb disease = rare, but mutations in Rb are not and occur in more common cancers such as lung, breast, and bladder carcinomas

Question 9

What is the role of chaperones in folding and misfolding?

Answer 9

= proteins that prevent faulty folding and unproductive interactions between other proteins; -some are induced by conditions that cause unfolding of newly synthesized proteins -bind predominantly to hyrdophobic regions of unfolded /aggregated proteins they act as a quality control/editing mechanism for detecting misfolded/defective proteins most are associated with ATPase activity they can be found in cytosol, mitochondria, or lumen of ER (like prions.. proteins that are unconventional infections again )

Question 10

Describe the life cyle of a retrovirus (like HIV)

Answer 10

Adsorption of virus to a specific receptor (ie: CD4+ on T-cell to CD4+ receptor on HIV) causes viral penetration which allows reverse transcriptase activity to start (ssRNA to dsDNA); the dsDNA is incorporated into the host genome for translation of host and viral genome to proteins and capsid to allow for budding of a new viral molecules; therefore to stop HIV proliferation, need to block both viral and host proteins for replication

Question 11

what are the mechanisms of proteolysis? (protein catabolism in the liver)

Answer 11

increased plasma ammonia or decreased urea = biomarkers of impairment of protein catabolism

Question 12

Describe the etiology and pathology characteristic of several disease of accelerated aging

Answer 12

Progerias = diseases of accelerated aging caused by defects in DNA repair (biological aging) Werners Blooms syndrome = autosomal recessive; due to mutation of DNA helicase genes that have a role in replication and repair of damaged DNA Werners = premautre aging starting in teenage and the development of diseases early on, leading to death by 40 due to heart disease Alzheimers disease = appearance of neurfibrillary tangles and senile plaques in the cortical brain (AGE/ALE increased in tangles/plaques); oxidative stress = strongly implicated in development or progression of AD and chelators are being evaluated clinically for treatment of AD

Question 13

what is a prion? Describe Creutfeldt-Jakob disease)

Answer 13

prion = protein in misfolded form that causes infection and induce healthy, properly folded proteins to be converted into a disease associated with misfolded prion forms Prp = protease resistant protein Scrapie PrP = infectious form of PrP Normal PrP + Sc PrP = amyloid (insoluble protein) Bovine Spongiform encephalopathy (BSE) = mad cow disease (from cattle that were fed diseased sheep/cattle); BSE transmitted from cattle to humans (CJD) incubation time varies from 4-40 years old ***CJD = due to prion, so it CAN be inherited, but it is STILL INFECTIOUS

Question 14

Describe how HIV binds/fuses/replicates in a host cell

Answer 14

HIV: has two strands of ssRNA and reverse transcriptase inside the virus; GP41 on lipid membrane and GP 120 (receptor for CD4+ ) on top of gp41 (for co-receptor) T-CELL: has CD4+ receptor on cell surface, and co-receptor (CCR5 and CXCR4) how: HIV and gp120 bind to CD4+ on T cell, and the co-receptor then binds to HIV (gp41) and allows fusion an penetration of viral RNA into the T-cell host; then RNA to unintegrated linear DNA via reverse transcriptase and then the DNA gets integrated into the host DNA for proteins and virus budding

Question 15

What are the major mechanisms in cell signaling?

Answer 15

Polypeptide (ie: insulin) binds to extracellular receptor, induces a signal cascade resulting in induction of transcription factors that act on DNA to increase gene expression; Cell-Cell interaction and/or Nitric Oxide (intracellular) also trigger the signal cascade Steroid hormones (pass through membrane) and act on an INTRACELLULAR receptor (transcription factor) that causes an increase in gene expression response = phagocytosis, apoptosis, proliferation, exocytosis, secretion

Question 15

What is the role of mutations in cancer

Answer 15

a single mutation is not sufficient to convert a health cell to a cancer cell; several rare mutation need to occur together (usually~3-7 independent mutations are necessary) Mutations in DNA occur spontaneously at a rate of 10^-6 mutation per gene per cell division; so every human genes is likely to undergo mutation on about 10^10 occasions; incidence of mutations increases exponentially with age spontaneous and induced mutations cause tumors: naturally occuring = point mutations, deletions, translocations Carcinogenic compounds, UV, Xrays, and viruses = increase the rate of mutations

Question 15

Describe the biochemical and genomic structure of HIV (a retrovirus)

Answer 15

3 main sites on genome: 1. GAG (has p24; proteins) 2. POL (contains protease and reverse transcriptase; all enzymes) 3. ENV (envelope; contains GP120 that binds to CD4+ and other proteins) Human retrovirus has 2 copies of single stranded RNA with GP120 and GP 41 on surface on the lipid membrane; and reverse transcriptase is inside ** there are many variations of HIV-1 which makes it complex and difficult for drug development

Question 15

Describe the relationship between viral load and the disease progression

Answer 15

initially the immune system can control the disease and during clinical latency the viral load remains pretty stable (but CD4+ decreases) then by the onset of AIDS, viral load increases a lot and the CD4+ decreases a lot; the lower the viral load = less severe the disease

Question 16

How do tyrosine kinases participate in signal transduction?

Answer 16

After dimerization of the receptor, the intracellular domain becomes transphosphorylated and the tyrosine kinase activity is stimulated; tyrosine phosphorylation of receptor creates ‘docking sites’ that allow protein-protein interactions, leading to recruitment and activation of SIGNALING ENZYMES or ADAPTER MOLECULE; PTK = enzymes that transfer gamma-phosphate group of ATP to tyrosine residues on target substrate proteins = rapid and reversible covalent modification that changes enzymatic activity of target proteins; Signal transducers recruited to Tyr-Pi via protein-protein interaction domains (SH2 domains) contained within the signal transducer; SH2 = Src homology region 2 = specifically recognize a phosphotyrosine and the 3 aa immpediately C-terminal to the phosphotyrosine

Question 17

What is the role of receptor dimerization?

Answer 17

Growth factor binding usually induces receptor dimerization and activation of the tyrosine kinase intrinsic to receptor; ligand binding to the extracellular domain triggers dimerization; this causes a conformational change in the cytoplasmic domain and transphosphorylation that activates the tyrosine kinase catalytic activity

Question 18

What is AIDS?

Answer 18

Acquired Immunodeficiency Syndrome that causes gradual destruction of cell mediated (T-cell) immunity therefor increases susceptibility for infection/cancer); caused by HIV; transmitted by blood contact or bodily fluid (infected mother to fetus transfusions can occur)

Question 18

What are the three pathophysiological effects of HIV infection?

Answer 18

1. Immunodeficiency = opportunistic bacterial and viral infections and unusual cancer 2. Autoimmunity = production of autoimmune antibodies, arthritis, 3. Neurologic dysfunction = AIDS demtia complex, HIV encephalopathy, neuropathies

Question 19

Describe the relationship of the liver and protein metabolism; plasma proteins? what are the changes in hepatic protein synthesis that take place during the acute phase reaction?

Answer 19

decrease in albumin or an increase in prothrombin time indicate impairment of protein synthesis! majority of plasma proteins are synth in the liver; albumin = most abundant protein in the blood (made only in the liver!) ceruplasmin = copper containing ferroxidase ferritin = stores iron transferin = transports iron alpha-fetoprotein = if high, associated with liver cancer measure hepatocyte synthesis function via measuring the production of coagulation factors II, VII, IX, X because all undergo post-translational gamma carboxylation of glutamyl residues (so they can bind Ca2+) in the liver; acute phase protein response = all systemic changes that occur in response to infection or inflammation magnitude of APP response shows the progress in a disease and its response to treatment; ie: [CRP] (C-reactive protein) is used as a marker for infection/inflammation (concentration may increase by a magnitude of 1 or 2 orders!)

Question 19

Describe Heme catabolism

Answer 19

Heme --\> bilirubin via heme oxygenase to biliverdin (IM) to bilidrubin via biliverdin reductase \*bascially: Heme rind uses O2 and reduction equivalent to open up the ring = bilirubin; excess bilirubin = jaundice Normally: RBC --\> spleen for destruction (spleen stores scenescent RBC and unconjugated bilirubin) --\> unconjugated bilirubin is complexed with albumin in the blood--\> bilirubin is taken up into liver for conjugation with glucouronic acid --\> MAJOR PATHWAY: conjugated bilirubin --\> urobilin --\> feces (coloring = due to bilirubin) MINOR PATHWAY: conjugated bilirubin to urobilin to urine (through KIDNEY)

Question 19

what is the role of cytochrome p450 in the metabolism of drugs?

Answer 19

3 genes of cytochrome P450 = for drug metabolism: CYP1 CYP2 and CYP3; each gene has multiple allels; the P450 enzyme encoded by CYP3A4 gene appears to be involved in te metabolism of most drugs; How it works: 1. drug joins P450 Fe3+ 2. NADPH gets oxidized to NADP+ and P450-Fe3+-drug gets reduced to P450-Fe2+-drug; occurs via NADPH cytochrome P450 Reductase 3. Oxygen joins (now P450-Fe2+-drug-O2) 4. Reduction of Fe2+ to Fe3+ via H+ joining O2 to make H2O that leaves 5. No have P450-Fe3+-drug-OH 6. drug-OH leaves P40-Fe3+; now it can bind to another drug molecule and drug-OH can be excreted. OVERALL REACTION (MEDIATED BY P450) RH + O2 +2H + 2e- --\> ROH + H2O (where R = drug)

Question 20

Describe the trends in HIV as an epidemic

Answer 20

started as a gay man's disease, but now increased infection due to heterosexual contact and injection drug use; there is a decrease in overall prevalence it is more prevalent in men than women generally, except in africa (slightly more women/equal) globally = 40 million individual; africa = 26.2 million estimated incidence of AIDs and AIDS related deaths are decreasing; LARGE decrease in perinatally acquired AIDS because of treatments decreasing its transmission; also even in an untreated woman only 25% of children will inherit disease due to placenta blood barrier

Question 20

What are some of the reverse transcriptase inhibitors (anti-retroviral treatments)

Answer 20

1. Nucleoside analogues: dont have OH at 3' end therefore block the chain of DNA from continuing; but the drug gets excised from growing chain therefore the virus continues 2. Non-nucleoside analogues: dont bind to active site, but cause conformational change in rev. transcriptase so that DNA can't bind 3. Protease inhibitors: competitive inhibitors that block proteolytic cleavage of protein precursors necessary for infectious viral particles 4. Fusion inhibitors: part of GP 41 (block the fusion of GP41/co-receptor on T-cell) \*\* mutations in protease gene are associated with drug resistance and so the drugs are not effective and can be toxic to the patient so you need to consider the timing of the drugs

Question 22

What are some key characteristics of growth factors?

Answer 22

Cells need positive signals to grow and divide: polypeptide hormones (insulin), growth factors (PDGF), or cytokines (IL-1, interleukins); BASICALLY: growth factors bind to specific cell-surface receptors and initiate an intracellular signally cascade to counter negative controls in resting cells that prevent growth and block cell cycle progression Proliferation = need several factors not just one GF; but a small number of GF can be used variably some stimulate growth and prolif others just growth.. ie: neuron = always in G0, just growth never prolif) proliferating cells stop growing when they are deprived of growth factors -- go through the cell cycle till G1 and enter G0 resting state

Question 22

HIV subtypes

Answer 22

due to viral envelope B = most prevalent in USA C = most prevalent in world (especially Africa, except sub-Sahara where A is more prevalent) different grades leads to increased variety of HIV also different grades can combine and lead to even more increased variability of HIV and thus more difficulty in treatment because treatments are grade specific

Question 23

How does PDGF receptor activate Ras?

Answer 23

RAS is anchored in the plasma membrane and recruited to the activated PDGF via interaction with Grb2-SOS complex (which binds to Pi-Tyr)

Question 24

Differentiate between Hepatitis A, B, C virus in liver disease

Answer 24

Hepatitis = inflammation of liver infection causes = due to viral infections (Hep A, B, C; C= 4 million people in USA) Toxicologic causes = alcohol and acetaminophen Infection Hepatitis (viral) Hep A: transmission = contaminated food/water (fecal-oral) prognosis = self-limited illness (usually benign; acute) Characteristic = no carriers (alone) Hep B: transmission = all bodily fluids EXCEPT stool (parenteral) prognosis = acute illness may progress to chronic state characteristics = transmitted from mother to child Hep C: transmission = blood, IV drug use, post-transfucion, occupatonal exposure; prognosis = Chronic, Cirrhosis Characteristics = Carrier, Concurrent alcohol use accelerates the progression of disease Hep D transmission = encapsulated with Hep B (Depends on B) characteristics = in US, mainly in IV drug use Hep E transmission = contaminated water (fecal-oral) characteristic = high rate of mortality among pregnant women

Question 25

PAP SMEAR (papanicolaou test) of the uterine cervix

Answer 25

epithelium of uterine cervix = similar to that of skin (basal cells = prolif, apical cells = keratinized and dead) Cervical cancer = strongly associated with human papiloma virus types 16 and 18 and arise from mutations in the basal epithelial cells which are no longer confined to the basal layer as they invade the apical regions (dysplasia) view pap smear sample on microscope: normal keratinized cells = large with condensed nuclei; mutant cells = large nuclei and little cytoplasm so that dysplasia can be identified

Question 26

What are some factors involved in the uncontrolled proliferation of cancer cells?

Answer 26

over-expression of growth factors, G-protein mutations, Kinases that act on TF to promote cell growt/prolif, Growth regulation genes (Jun, Fos, Myc = transcription factors, BcL2 = cell survival) and tumor suppressor genes (1. P53 = cell cycle and apoptosis regulator, = stops cell cycle progression to allow for DNA repair, most frequently mutated geen in human cancer 2. Rb gene = cell cycle regulator by stimulating E2F TF for progression into S phase when it is phosphorylated)

Question 28

Describe the pathway of Heme synthesis

Answer 28

starts in mitochondria: by succinyl CoA (from TCA) + glycine --\> ALA via ALA synthase ALA is transported to the cytosol; ALA to PBG (porphobilinogen) via PBG synthase then PBG to uroporphyinogen III to coproporpysinogen III which is transported back into the mitochondria (with the loss of CO2) and then you get protoporphyrin IX which BINDS Fe2+ to make HEME \*\* lead inhibits PBG synthase (and therefore inhibits Heme synthesis) \*\*[HEME] inhibits (feedback) ALA synthase

Question 29

Explain the precepts of the free radical theory of aging (characteristic oxidation products that accumulate in long-lived proteins with age)

Answer 29

aging = result of cumulative oxidative damage to biomecules: DNA, RNA, proteins, lipids, and glycoconjugates; longer lived organisms have a lower ate of production of reactive oxygen species (ROS),.better antioxidant defenses, and more efficient repair or turnover mainly a chemical theory, but doesn't ignore the importance of genetics and biology in limiting the production of ROS and increasing antioxidant/repair mechanisms EX: accumulation of amino acid oxidation products in human skin collagen increases with age: methioine is oxidized to methionine sufoxide (MetSO) by HOCl or H2O2; ortho-tyrosine is a product of hydroxyl radical addition to phenylalanine levels of each strongly correlate with one another (even though overall more MetSO that hydroxyl radical) = multiple ROS contribute to oxidative damage to proteins EX: AGEs and ALEs due to reaction of proteins with products of oxidation of carbs and lipids; CML (carboxymethyl-lysine) may be formed from either carboydrates or lipids; pentosidine formed from carbohydrates only, malondialdehyde formed frm lipids adducts to lysine AGE/ALE bind to lysine, histidine, and cysteine residues on proteins AGE/ALE = biomarkers of aging and oxidative stress

Question 30

Describe the proliferative/ antiproliferative genes involved in cell proliferation

Answer 30

proliferative = proto- ONCOGENES or oncogenes if they are mutated; proto-oncogenes are mainly signal transducers that act to promote normal cell growth and division Anti-proliferative genes = tumor suppressor genes that normally act to suppress cell growth; a mutation causes loss of expression and thus leads to uncontrolled proliferation; TUMOR SUPPRESSOR (ANTI-P ) = RECESSIVE MUTATION (requires loss/inactivation of both alleles for expression) PROTO-ONCOGENE (PROLIF) = DOMINANT MUTATION (only one mutated allele is necessary for expression)

Question 31

what are the key biochemical tests for liver function?

Answer 31

liver function tests = measure serum/plasma levels of: bilirubin, albumin, and transaminases (aspartate aminotransferase, AST, alanine aminotransferase, ALT), alkaline phosphatase (ALP), which is sometimes conjugated with gamma-glutamyl transferase

Question 32

What are the molecular and cellular characteristics of cancer?

Answer 32

cancer = cell that undergoes mutations that disrupt the regulation of cell division and will divide without regard to the overall needs of the organism (when detected cancers contain 1bilion cells but started from 1) depend on cell type and tissue type (epithelial = carcinoma, CT/muscle = sarcoma) Benign = intact tumor Malignant = metastasis

Question 32

Describe the principals behind the diagnostic tests available for HIV testing

Answer 32

1. ELISA: Enzyme-linked Immunosorbent Assay: checks for presence of HIV antibodies to indicated infection 2. Western blot: virus is digested and separated into components by molecular wts and then proteins are transferred to a filter paper in which an enzyme conjugated with antihuman antibody is added and the substrate added and color is noted; to be HIV positive, need to see all three domains (GAG, POL, and ENV) 3. Patient monitoring: CD4+ count (if

Question 33

Describe the effects of caloric restriction on the rate of aging rodents

Answer 33

(note: antioxidant supplements may improve health but do not increase max lifespan, at least not proven yet) Caloric Restriction = (decrease in total caloric intake regardless of dietary composition) allowed rats to live up to 180 years! and also showed an overall improvement of health of animal; CR limits chemical damage to DNA and promotes turnover of tissue proteins: rates had fewer muscle fibers lacking cytochrome oxidase and decreased levels of deletions in muscle mtDNA and lower rates of chemical damage to proteins and DNA CR also acts as the best cancer-prevention regimen since obesity is a high risk factor for cancer EXPERIMENT: normal food intake mice vs. 60% CR mice: found that 51% of normal mice had tumors but only 13% of CR mice had tumors; thus a reduction in rate of occurrence of age related lesions is seen with dietary restricted lab mice.

Question 34

Describe the function of the gall-bladder and its anatomy/histology

Answer 34

stores/concentrates bile -stimulated via vagal nerve following eating; causes sphincter of Boyden to relax, promoting the release of bile into the common bile duct -cystic duct joins the common hepatic duct to form the common bile duct which joins the pancreatic duct at the ampulla of vater and is under control of the sphincter of oddi -GB = absorptive epithelium that uses Na/K ATPase to create electrolyte gradients that hydrate and concentrate the bile; bile = bile salts phospholipids, cholesterol, leccithin, water, bilirubin, ions

Question 36

What are the cell-cycle elements that correspond to specific cancers?

Answer 36

Breast, testicular, leukemias = due to cyclins, cause hyperpolarization of Rb (E2F activates genes for progression through S phase) Retinoblastomas, osteosarcomas = mutational inactivation of Rb genes; loss of Rb control of the cell cycle Cervical carcinomas = sequestration of Rb by human papilloma virus E7 protein; Loss of Rb control of the cell cycle Melanomas = mutant CDK4 resistance to CDKI; loss of inhibition of cyclin D-CDK4/6 complex (so hyperpol of Rb) Various tumors = deletion of CDK-I; loss of inhibition of cyclin D-CDK4/6 BASICALLY: cyclin problem = Rb hyperpol Inactive/lost Rb = Rb no longer controls cell cycle CDKI/ cyclinD-CDK4/6 = no inhibition of CDK so Rb hyper pol all result in increased E2F-1 transcription factor activity that results in progression through S phase

Question 37

What are some of the various approaches for HIV vaccines?

Answer 37

1. viral surface proteins (ie: gp120) 2. live virus vector (to carry genes encoding HIV proteins) 3. live bacterial vector (to carry genes encoding HIV proteins) 4. Whole live/killed HIV 5. pseudovirons = non-replicating HIV like particles 6. Replicons = non-HIV viruses that do not replicate completely and carry genes encoding HIV proteins 7. HIV peptides = protein fragments 8. Naked DNA = contains HIV genes

Question 38

what is personalized warafin therapy?

Answer 38

warfarin = anticoagulant by genotyping CYP2C9 the population can be divided into average, slow, and fast converters of the drug warfarin; The initial dose of warfarin is adjusted based on the DNA genotyping; Personalized medicine makes the used of drugs more effective and safer

Question 39

What are the 3 phases of the HIV viral infection

Answer 39

1. Primary infection = flu-like symptoms (fever, fatigure, GI problems, headache); increase in viral replication (occurs 204 weeks after HIV exposure) and lasts ~few days-2weeks 2. Latent Phase = chronic asymptomatic phase lack of symptoms but you have a gradual decrease in CD4+ counts (T-cells have CD4+ n the surface and AIDS/HIV have the receptor); lasts ~ 10 years 3. Overt AIDS: when CD4+ \< 200 cells/microL or when patient presents AIDS defining illness ; death usually occurs in 2-3 years if left untreated; caues = HIV-1 or HIV-2 (milder) THUS: TAKES 12-13 years from infection to death (without treatment)

Question 41

what is the role of alcohol in liver disease?

Answer 41

alcohol = oxidized in liver mainly via alcohol dehydrogensase (which increases NADH/NAD+ ratio) excess alcohol can cause steatosis (fatty liver; due to deposition of fat), or fibrosis (cirrhosis) which leads to liver failure or: Alcoholic hepatitis = caused by high level of alcohol consumption and causes a reversible inflammatory liver damage which causes fibrosis \*\*alcohol = most common cause of liver disease in the western world

Question 42

Discuss the role of the mitogenic growth factors

Answer 42

exert effects between the onset of G1 and a restriction point late in G1 (restriction pt = cell is committed and unaffected by extracellular signals) Retinoblastoma Protein (Rb) = tumor suppressing gene (anti-prolif) that prevent excessive cell growth by inhibiting cell cycle progression until a cell is ready to divide; controls expression of genes that commit cells that are at the restriction point late in G1 phase to enter S phase; in early G1 Rb is hypophosphorylated = Rb represses advance of cell cycle by binding and preventing DNA-binding activity at E2F transcription factors in late G1, GF induces cyclinD-CDK4/6 and then the cyclin E-CDK-2 hyperphosphorylates Rb; now E2F is no longer inhibited and can activate the genes necessary for S phase to start

Question 43

Describe the biochemical principles in virus classification

Answer 43

1. DNA vs RNA then: 2. shape (isohedral, helical, complex) 3. enveloped vs. naked 4. genome type (ss vs. ds; linear vs. circular vs. segmented) Families of viruses: -picorna = common cold -flavi = hep C -retro = HIV-1 HIV-2 corona = SARS orthomyxo = flu; segmented DNA can jump between species Hepadna = Hep B Herpes = herpes simplex 1 + 2 Pox = chicken pox Baltimore classification of viruses = according to genome and method of replication; HIV = type VI (retrovirus) in which: coding ssRNA (+) to noncoding ssDNA (-) via reverse transcriptase; then ss(-)DNA to ds(-) (+) DNA as the virus DNA is incorporated into host genome and into cell replication; then dsDNA to ss(+)mRNA for translation into proteins

Question 45

Describe the use of human genomic and pathogen genomic information in drug design and develoment

Answer 45

pathogens can cause DNA damage 20% of human cancers are caused by infectious agents (because there is a shared nucleic acids)

Question 46

What are the non-covalent interactions participating in protein folding and misfolding?

Answer 46

electrostatic interactions, hydrogen bonds, van de waals, hyrdophobic interactions

Question 47

What evidence supports the mitochondrial theories of aging? How does this theory interface with the free radical theory of aging?

Answer 47

= both biological and chemical theory aging = result of chemical damage to mitochondrial DNA (mtDNA) because mtDNA codes for 13 vital proteins and mtDNA IS NOT PROTECTED BY HISTONE AND HAS A LIMITED CAPACITY FOR REPAIR (so MtDNA = sensitive to mutations and is a major site of ROS production) aging of muscle = damage to mtDNA old age = general decrease in skeletal muscle mass (sarcopenia) and strength (contributes to glucose intolerance and frailty) ; occurs due to random deletions in mtDNA which leads to fiber atrophy and breakage and the muscle fiber is only as strong as its weakest link, so small regions of fiber loss affect the overall muscle capacity; muscle loss can be delayed/reversed by resistance exercise

Question 49

Describe the stages of the cell cycle

Answer 49

takes minutes to years; normally a cell cycle is 24 hours; Interphase = G1, S, G2 = cell growth + DNA synth G1 = between mitosis and S S = synthesis G2 = between synthesis and mitosis M = mitosis; cell division = last stage G1 and G2 = take time for cell growth and for checkpoints during which the progress of cell cycle can be controlled and incorporation of DNA damage prevented before cell division; Cell cycle time varies mostly because of G1; becuase cells that are not committed to DNA replication can enter a specialized G0 resting state until they receive the appropriate signals to go further through the cell cycle; thus cell cycle time depends on G1/G0 time (S to M takes 12-24 hours and G1 = variable) In conditions that favor cell growth, the total ribonucleic acid (RNA) and protein content of the cell increases continuously, EXCEPT in M phase when the chromosomes are too condensed to allow transcription

Question 50

What are tumor suppressor genes?

Answer 50

Anti-proliferative genes = tumor suppressor genes that normally act to suppress cell growth; a mutation causes loss of expression and thus leads to uncontrolled proliferation; recessive mutation (two alleles (both) necessary for expression of mutation)

Question 52

Describe the characteristics of MAPK cascades

Answer 52

PDGF binds to receptor; receptor dimerizes and transphosphorylates, activating PTK; Grb2-Sos complex binds to Tyr-Pi and this causes activation of Ras-GDP to Ras GTP (this is reverse, RasGTP--\> RasGDP via GAP); Ras-GTP stimulates Raf (intermediary kinase); Raf stimulates MEK; MEK stimulates MAPK and MAPK travels into the nucleus to stimulate transcription factors for increased gene expression via phosphorylation of Ser and Thr MAPK = signal cascade that links early receptor transduced signals with growth and differentiation-related transcriptional events in the nucleus; MAPK = a generic name of superfamily that includes: 1. Extracellular regulated Kinases (ERK) 2. Stress-activated Protein Kinases (SAPK) 3. p38-reactivating kinase (p38RK) all of which phosphorylate TF SAPK and p38RK selectively induce apoptosis ERK1 and ERK 2 = in some conditions act to promote cell survival and proliferation

Question 53

Describe the cytokine receptor

Answer 53

Heterodimer that can also lead to cell proliferation induces cellular signal transduction and recruitment of JAK, STAT, and other intracellular signaling pathways Fos, Jun, Myc, NF-KB, NF-AT = transcription factors

Question 54

What is the role of the liver in carbohydrate metabolism?

Answer 54

maintains blood glucose levels liver stores glycogen and synthesizes glucose from non-carb precursors (gluconeogen) normally the liver stores 80g of glycgen; in fasting (post-absorptive state) the liver releases ~ 9g of glucose per hour, so by the end of the night, all of the glycogen stores are used up but you still need a supply of glucose so gluconeogenesis starts up; 50% of glucose from glycogenolysis/gluconeo goes to brain, 50% to skel muscle; \*As glycogen supplies decrease, gluconeogenosis contribution increases progressively

Question 55

How do transcription factors turn on and off genes?

Answer 55

TF regulate gene expression by specific regulatory elements: binding of TF to a steroid response element = increases the rate of transcription of message (different elements have a greater/lesser effect on transcription, and some are tissue specific) MyoD = muscle specific factor GRE = glucocorticoid response element = where steroid receptor binds on gene the proteins on the gene interact physically with one another because of their size and the folding of DNA \*\* TF = a protein that binds to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA. Transcription factors perform this function alone or with other proteins in a complex, by promoting (as an activator), or blocking (as a repressor) the recruitment of RNA polymerase (the enzyme that performs the transcription of genetic information from DNA to RNA) to specific gene

Question 56

What is cancer metastasis?

Answer 56

spread of a cancer from one organ or part to another non-adjacent organ or part tumor must be able to escape their adhesion to neighboring cells, invade surrounding tissue, enter the blood/lymph, and invade and colonize a new tissue loss of expression of adhesion E-Cadherin lets cell leave In order to bind o and traverse the basal lamina, cells must express specific integrins to bind laminin and type IV collagenase to digest the lamina.

Question 58

What are the two paths to drug discovery? How does personalized medicine relate to modern drug discovery?

Answer 58

Path 1 = old/classic path: compound --\> physiological effect --\> ? molecular target Path 2 = modern/new path: molecular target --\> compound --\> physiological effect (now drug development is done in the following steps: 1. medicinal need identified 2. relevant mechanism 3. mechanism based screens 4. lead compound 5. drug candidate 6. clinical testing The tools of personalized medicine are refining diseases into molecular categories, and future therapeutics may be dictated by a patient's molecular profile relative to these categories. The adoption of a personalized medicine approach to drug development may improve the success rate by minimizing variability during each phase of the drug development process.

Question 58

What are oncogenes?

Answer 58

proliferative genes; signal transducers that act to promote normal cell growth and division dominant mutation (one allele necessary for expression of mutation)

Question 59

How were oncogenes identified?

Answer 59

first as viral genes that would infect normal cells and transform them into tumors; Rous sarcoma virus (causes CT tumors in chickens) has the Src gene that was responsible for transformation of fibroblast to tumor; realized that the viral oncogene was a mutated homolog of a normal cellular gene; Gene now called c-Src proto-oncogene and has a PTK sgnal transducor that is involve in the normal control of cell growth; it is likely that the Src was accidentally incorporated by the virus from a previous host genome and was somehow mutated in the process because the gene is not essential to the survival of the retrovirus

Question 61

How does the PDGF receptor function?

Answer 61

ligand binding to the extracellular domain triggers dimerization; this causes a conformational change in the cytoplasmic domain and transphosphorylation that activates the tyrosine kinase catalytic activity; tyrosine phosphorylation of receptor creates 'docking sites' that allow protein-protein interactions, leading to recruitment and activation of SIGNALING ENZYMES or ADAPTER MOLECULE adapter molecules = signal transducers = modulate signaling enzymes BASICALLY: transphosphorylation allows for various signal transduction activation such as: Phospholipase C-gamma, GTPase activating protein (GAP), protein tyrosine kinase (PTK) such as Src, Fyn, Abl, phosphotyrosine phosphatase (PTPase and adapter molecules such as (Shc or Grb2)

Question 62

What are the key elements of the human genome project?

Answer 62

It is an international effort to discover all of the physical and functional make up of all of the human genes. Human genome = 3.2 billion base pairs and about 25,000 genes It involves sequencing and analyzing;

Question 64

Explain the Gompertz plot and how it describes the rate of aging in different species

Answer 64

mathematical modeling of aging; m = age specific death at age (t), A = intercept, death rate at birth, and alpha = slope constant (effect of time on death rate); B = correction for infant mortality or accidents m(t) = Ae^(alpha\*t) + B the graphs show that: slope of mice \> dogs\> humans meaning that mice have a faster death rate; humans live the longest \> dogs \> mice; Temperature effects death rate also (in fruitflies): increasing temperature = shorter lifespan and faster deathrate

Question 66

What is the role of caspases in apoptosis?

Answer 66

Cleave target proteins, resulting in disassembly of apoptotic cell by: 1. halting cell cycle progression 2. disabling homeostatic and repair mechanisms 3. initiating the detachment of the cell from its surrounding tissue structure 4. dismantling structural components (such as cytoskel) 5. Flagging dying cell for phagocytosis over-expression of caspases = sufficient to cause cellular apoptosis caspases = expressed as inactive pro-caspases and activation usually occurs by an initial caspase activating downstream caspases and resulting cascade PROTEOLYSIS AND ACTIVATION OF EFFECTOR CASPASE IS FACILITATED BY BINDING TO CYT C (RELEASED FROM MITO DURING APOPTOSIS)

Question 67

what is Kuru?

Answer 67

human to human transmission of Spongiform encephalopathy due to exposure to diseased brain tissue (canabalism or break in skin after handling diseased tissue)

Question 69

what is the role of the liver in lipid metabolism?

Answer 69

increased plasma cholesterol or TAGs = biomarker of impaired lipid metabolism B-ox of FA's used as energy for gluconeogenesis; FA's /TAGs synthesized in the liver are transported to blood and then to peripheral tissue via VLDL

Question 70

Describe cancer treatment options:

Answer 70

1. Error catastrophe: tumor cells produce errors at a higher frequency that normal cells so this method increases the number of mutations to ill cancer cells by "pushing them over the edge" 2. Radiation treatment: with X-rays or neutron radiation; goal = after radiation treatment the healthy tissue will recover and cancer cells will die; drug resistance in cancer chemotherapy = major concern due to high DNA mutation rate in tumors; so combination chemotherapy (using several drug simultaneous) is the most effect treatment to reduce emergence of drug resistance

Question 71

Describe the two phases of drug metabolism

Answer 71

in general, drug metabolism increases the hydrophilicity of drugs and thus increases the ability to be excreted; Phase I: polarity of drug is increased by oxidation of hydroxylation; catalyzed by cytochrome P450 oxidases Phase II: cytoplasmic enzymes conjugate the functional groups that are introduced in phase I (usually glucouridiniation or sulfation)

Question 72

Distinguish between oncogenes and tumor suppressor genes and describe their role in tumor progression

Answer 72

oncogenes = dominant mutation (one allele necessary for expression of mutation) Tumor suppressor genes = recessive mutation (two alleles (both) necessary for expression of mutation)

Question 73

What are some abnormal plasma concentrations of specific liver proteins that are involved in disease?

Answer 73

Ceruloplasmin = major COPPER containing protein of the liver and plasma; functions as iron-oxidaizing (Ferroxidases) enzyme: oxidation of Fe2+ to Fe3+ is necessary for metabolism of stored iron; nutritional iron deficiency = anemia WILSONS DISEASE= genetic deficiency of ceruloplasmin; causes damage to both liver and CNS

Question 74

what are the general functions of the liver?

Answer 74

1. METABOLISM! (maintains body's blood chemistry) regulation of carb and lipid metabolism amino acid metabolism synthesis and breakdown of plasma proteins \*\*first site of metabolism of ingested substances that absorbed from small I 2. storage: of vitamins and metals (iron, copper) and glycogen 3. Aids digestion: hepatocytes continuously secrete bile acids; most of the bile that is produced in the liver is recycled through the ileum via Na+ dependent bile salt co-transporter then travels up the portal vein to the liver as enterohepatic circulation (ALSO metabolize and detoxify xenobiotics )

Question 75

What is personalized and evidence based medicine?

Answer 75

using the human genome sequencing and analysis to screen and prevent conditions based on personalized characteristics; it is a personalized diagnostic and treatment based on genome sequencing

Question 76

Describe the antiretroviral treatment of HIV

Answer 76

Primary treatment = use 3 different types of antretroiviral agents to inhibit HIV viral replication: Usually: 2 nucleoside analog drugs (stop the DNA chain frm growing) + one protease inhibitor (GAP protein can't bind and virus is blocked ) OR 2 nucleoside analog drugs + 1 non-nucleoside analog drug use 3 because HIV is highly drug resistant! Other treatment options: (DONT CURE/STOP DISEASE, but just mediate the responses due to HIV) -immunomodulatory agents to boost immune system -human granulocyte colony stimulatory GF (stimulate neutrophil production) -anti-infective agents (to combat opportunistic infections) -anti-neoplastic agents (to combat associated cancer) -Supportive therapy (nutritional, fluid/electrolyte replacement, pain relief, psychological support)

Question 77

what is fatal familial insomnia?

Answer 77

prion disease of brain; causes PrP conformation to change and protein aggregates into thalamus and the thalamus controls sleep regulation, so the disease progresses into complete sleeplessness and death; disease presents as panic attack, paranoia, hallucinations, inability to sleep

Question 78

How is the cell cycle progression monitored?

Answer 78

at checkpoints/restriction points (in late phase of G1) via cyclins and CDK: stimulation of growth factors leads to cyclin-dependent activation of CDKs and their inhibitors; cyclin/CDK partners cause phosphorylation of Rb (late in G1 near restriction point) which induces E2F transcription factors to make more proteins that promote S phase DNA replication so that the cell can progress

Question 80

what are the characteristics of prehepatic, intrahepatic, and posthepatic jaundice?

Answer 80

Hyperbilirubinemia (\>3mg/dL) 1. prehepatic = increased total plasma bilirubin due to excess [UNCONJUGATED fraction] (increased production of bilirubin) 2. intrahepatic = increased total plasma bilirubin due to: increase CONJUGATED FRACTION, impaired hepatic uptake, or impaired secretion of bilirubin; increases serum enzyme activitys (AST ALT) due to hepatocyte damage ; increased conjugated bilirubin in urine 3. posthepatic = increased total plasma bilirubin due to increase in CONJUGATED FRACTION; due to an obstruction in the bile duct that does not allow passage of bile to the guy and thus stools are usually pale in color (increase in ALP, conjugated bilirubin in urine, prothromibin time due to increased gamma-glutamyl tranferases)

Question 81

Describe the key elements of cellular homeostasis

Answer 81

In unicellular organisms: proliferation is limited by available nutrients In multicellular organisms: there are controls on proliferation in terms of the number of individual cell types and with respect to their spacial organization; in adults MOST CELLS ARE NOT DIVIDING! also, derugulation of growth can lead to cancers and tumors; but under certain conditions (tissue repair and senescence) regulated growth and proliferation is promoted Cellular homeostasis = controls cell survival, proliferation, and cell death (by apoptosis) Proliferative and anti-proliferative genes control normal cell proliferation and mutations in these genes can cause cancer

Question 83

What is kernicterus?

Answer 83

=neonatal jaundice transient jaundice = common in neonates especially in premature infants due to immaturity of enzymes involved in bilirubin conjugation; UNCONJUGATED bilirubin = toxic to immature brain and causes kernicterus in adults/older children, jaundice is harmless, but the blood brain barrier is immature in the newborns and the bilirubin penetrates the brainn and stains the nerve bodies causes irreversible damage; effects range depending on exposure if plasma bilirubin concentration are judged too high then phototherapy w/blue-white light (which isomerizes bilirubin to more soluble pigments that can be excreted with bile) or exchange blood transfusion to remove the excess bilirubin are necessary to avoid kernicterus

Question 84

what are the mechanisms of drug hepatotoxicty

Answer 84

Drugs that exert their toxic effects on the liver may do so through the hepatic production of a toxic metabolite; acetaminophen (paracetamol) is hepatotoxic in excess; Acetaminophen is metabolized into toxic and non-toxic products: NON-TOXIC: conjugation with 1. glucoronic acid or 2. sulfate to yield esters that are excreted by the kidneys in overdose, the capacity of these conjugation pathways is overwhelmed and TOXIC product is produced: oxidized by P450 to NAPQI (N-Acetyl- benzoquinoneimine) which cause free radical mediated peroxidation of membrane lipids therefore causing HEPATOCEULLAR DAMAGE (via lipidoxidation) Antidote of acetaminphen poisoning = N-Acetyl-Cysteine (or conjugation with GSH) to make a non-toxic product

Question 85

Describe how the rate of mutation of DNA is a determinant of rate of aging

Answer 85

differences in lifespan among a species are closely correlated with the efficiency of DNA repair mechanisms (more efficient DNA repair = longer lifespan);

Question 86

What is bilirubin? what clinical condition is it associated with?

Answer 86

product of heme catabolism; body produces 250-300mg of heme daily Cholelithiasis = gall stones = due to excess cholesterol within the gallbladder (or from precipitated calcium or bilirubin)

Question 87

Define the role of BcL-2 protein

Answer 87

anti-apoptotic protein that prevents cytochrome C from leaving the mitochondria (therefore INHIBITS caspases) it is stimulated by survival factors to cause an increase in cell proliferation initially discovered in follicular B cell lymphoma (was found to contribute to neoplastic growth by inhibiting normal B cell apoptosis) it is located in the outer mito-membrane

Question 88

How is apoptosis regulated?

Answer 88

Cell death receptors, such as TNF (tumor necrosis Factor) and Fas mediate cell death by recruiting procaspases such as caspase 8 to their 'death domain' transducing molecules, and induct proteolytic caspase activation cascade. PROTEOLYSIS AND ACTIVATION OF EFFECTOR CASPASE IS FACILITATED BY BINDING TO CYT C (RELEASED FROM MITO DURING APOPTOSIS) vs. BcL-2 regulated cascade which is modulated by survival factors coupled to phsphoinositide 3 kinase (PI3K) which leads to the RESCUE of cells from apoptosis and PROMOTION of cell survival survival factors --\> PI3K --\> PIP3 --\> PDK1 --\> Akt --\> BcL-2/BcL-XL with Bad (and Bad gets Pi by Akt) --\> Bad Pi leaves and BcL2/BcL-xL ANTAGONIZES cell death by PREVENTING release of CYT C and caspase activity therefore PROMOTING CELL SURVIVAL

Question 89

Explain Kovari's research

Answer 89

MDR HIV-1 protease = an expansion in active site = inhibitor can now get in; drug resistance = namely due to mutations frequency in protease activity

Question 90

what are the similarities between bacteria, fungi, protozoa, viruses, and prions (as infectious agents)?

Answer 90

-can be transmitted to a healthy individual (by inoculation with diseased tissue) -can multiply in infected host -have characteristic and reproducible pathologic changes and clinical disfunction in diseased host -strains differ in virulence (species specificity can be recovered from different hosts)

Question 91

what is the liver's role in endogenous (from within an organism) glucose production?

Answer 91

liver stores glycogen and synthesizes glucose from non-carb precursors (gluconeogen); carbon substrates for gluconeogenesis = 1. lactate from glycolysis in peripheral tissues (cori-cycle) 2. hepatic deamination of amino acids from skeletal muscle (alanine cle) \*\*energy for gluconeogenesis = from B-ox of FA's

Question 92

How is DNA damage monitored during the cell cycle?

Answer 92

tumor suppressing protein, p53 = DNA damage sensing protein and regulator of G1/S phase cell cycle progression p53 = stops cell cycle progression to allow for DNA repair by inducing p21CDK-Inhibitor that prevents the CDK-dependent phosphorylation and activation of Rb If minimal DNA damage = p53 is mediated and arrests growth to allow DNA repair if serious, irreparable DNA damage = p53 triggers apoptosis only one copy of p53= predisposed to lots of different cancers by: allowing uncontrolled cell cycle progression and permitting replication of damaged DNA to further amplify carcinogenic mutation; it is the most common genetic lesion in cancer