9-30-2013 exam

How do you best learn? What does this teach you about how patients might best learn?

...

How is the rate of germline mosaicism determined for a disease? Name several other diseases with a high rate of germline mosaicism.

...

Thompson and Thompson Genetics in Medicine, p.253 #2

...

Understand specifics regarding patient privacy and information sharing (i.e. HIPAA guidelines and communication between providers)

...

Give the recurrence risks for the common autosomal trisomies (21, 18, 13).

1%

Even though the gene therapy protocols have been described more than 10 years ago why is it that patients have not reaped the benefits yet? Provide three reasons with a brief explanation of each.

1. gene studies are fairly expensive - can't afford to give them to everyone. also, since it's a new frontier, insurance companies have to decide what to cover. 2. it's an unexplored frontier - there are still a lot of things we don't know which makes it a slow process. (what does this gene mean? we haven't seen it yet!) also a lot of docs don't know about it or have consistent data to tell their patients to do this. 3. not everywhere has the resources - equipment & trained staff - to do this.

Alzheimer's Disease

A cognitive disorder characterized by: 1. Memory impairment 2. One or more of the following Aphasia Apraxia Agnosia Disturbances in executive function Prevalence 2000: 4 million patients 2010: 5.8 million patients 2050: (projected): 14.3 million patients Common or uncommon?

To evaluate the possible clinical applicability of a genetic test through review of a published study(s) on juvenile Huntington disease.

A genetic test could give families an idea of what is causing the illness, thus helping them to choose the best treatment option. It could also potentially quicken the process that comes with false diagnosis.

What is genetic anticipation?

Anticipation is the appearance of a genetic trait at an earlier age or with greater severity in successive generations.

Define genetic anticipation and explain how it can occur

Anticipation refers to the appearance of a genetic trait at an earlier age or with greater severity in successive generations. Expansion of the repeat region causes the disease. With each successive generation, the repeat region is longer, causing an increase in the severity of the disease.

Understand the patient's perspective through closed loop communications.

Ask-Tell-Ask

Genetic Labs ordered

Chromosome Analysis with 5 cell prelim Microarray testing Chromosome analysis: 11/22/12 46,XY[5] preliminary report 11/29/12 46,XY final report

Trisomy 13

Craniofacial: *Scalp defects.

Explain the role and limitations of dietary therapy for metabolic disorders

Dietary therapy is very effective for PKU. There are few side effects, although it can be inconvenient for patients to maintain their diets. In tyrosinemia, diet is effective at lowering levels of tyrosine in the body, but it is not sufficient to prevent cirrhosis of the liver, so it must be supplemented by medication. The reason diets have limitations is because not everything comes from diet, and we need to make sure we get the necessary nutrients for survival.

List 4 characteristics of Down syndrome, Turner syndrome and Klinefelter's syndrome

Down syndrome: typical facial features, round face, upward slanting palpebral fissures, epicanthic folds, small open mouth with large tongue; congenital heart disease; gastrointestinal malformations (esp. duodenal atresia); mental retardation Turner syndrome: sexually immature features, infertility, short stature, webbing of the neck; underdeveloped ovaries or only streak ovaries; mildly reduced intelligence/spatial perception; psychological distress due to lack of secondary features Klinefelter's syndrome: small testes, infertility, poorly developed secondary sex characteristics; tall and thin; partial gynecomastia (breast development); affected social development & intelligence

Explain how enzyme inhibitors may be used to treat genetic disorders

Enzyme inhibitors may be used to prevent buildup of enzyme products or to increase substrate levels. - check Thompson for more details

Define epigenetics and give an example.

Epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence. Epigenetic effects are mediated by methylation of cytosine residues, acetylation and methylation of histones, and interference RNAs. Examples given in class include imprinting effects, such as Prader-Willi and Angelman syndromes, hereditary glomus tumors, Beckwith-Wiedemann syndrome, and effects of nutrition, smoking, pesticides, parental behavior (licking and grooming in rats).

Describe the typical mechanism whereby expansion of polyglutamine tracts cause disease

Expansion of polyglutamine tracts occurs within an exon. This repeat segment is responsible for interacting with other proteins, so that function is lost. Additionally, the mutant protein formed instead is toxic to neurons.

Orphan Drug Act

FDA Act passed in 1983 because of the observation that medications for rare diseases were not being developed. Background (from the Act) 1. Many diseases affect small numbers of people in the US 2. Adequate drugs have not been developed for these diseases 3. Because so few individuals are affected by any one rare disease or condition, a pharmaceutical company which develops an orphan drug may reasonably expect the drug to generate small sales in comparisons to the cost of developing the drug. 4. There is reason to believe that some promising orphan drugs will bot be developed unless there are incentives to develop these drugs [beyond usual market forces] - Orphan Drug Act, 1983, 21 CFR Part 316

Map nutrition resources in your assigned community.

Food desert! Humboldt Park doesn't have enough chain grocery stores.

What are key dietary problems in the US today?

Not enough fruits & veggies or calcium, too much saturated fat, cholesterol, and calories.

Compare and contrast Prader-Willi and Angelman syndromes with respect to their differing clinical features and genetic causes.

Prader-Willi syndrome is characterized by hypotonia, poor feeding, and failure to thrive in infancy, with development of a voracious appetite during childhood and consequent obesity. Other features are characteristic facial features, small hands and feet, hypogonadism and developmental delay. It is caused by failure to express genes on the paternally inherited chromosome 15q11-13, because of deletion, maternal uniparental disomy, imprinting defects. Angelman syndrome is characterized by poor growth, severe intellectual disability, ataxia and seizures. It is caused by failure to express genes on the maternally inherited chromosome 15q11-13, paternal uniparental disomy, imprinting defects, and mutations in UBE3A.

There are many methods to quantify RNA expression. Name one.

RT-MLPA

Describe the limitations of targeted mutation analysis for genetic diagnosis

Results describe the patient's genotype but not the phenotype. Tests can be time-consuming and expensive. Family members must be tested to know which mutations run in the family.

Thompson and Thompson Genetics in Medicine, p.253 #1

Risks: Psychological stress. Benefits: Early treatment, better outcomes.

Describe the effect of the parent's sex on the expression of imprinted genes

Some syndromes are only present when a gene is inherited from the father, and others only when it's inherited from the mother.

With no other family history, what is Stacy's risk to be a carrier of DMD? If Stacy is a carrier, what does this mean for her current pregnancy? (9/27 worksheet A3)

Stacy's risk: 1/3. Each twin has a 1/12 chance of being affected and 1/12 chance of being a carrier

The Diagnostic Odyssey

The Example of Fabry Disease

What types of intracellular processes would you expect to be altered in mitochondrial disorders?

The Respiratory Chain, energy production

You are told that a young boy with Down syndrome has a 14;21 Robertsonian translocation, as does his normal father. How many chromosomes does the boy have? How many does his father have ? How many does his 38 year old mother have? What's the risk for his parents having another child with Down syndrome?

The boy has 46 chromosomes, father has 45, mother has 46. There is a 5% risk of recurrence.

What should a doctor know and do about diet in patient care?

The doctor should know the dietary guidelines and should counsel patients on how to improve their eating habits.

You are told that a young girl with Down syndrome has an isochromosome 21 (fusion of two # 21 long arms at the centromere), as does her normal father. How many chromosomes does she have ? How many does her father have? How many does her mother have? What's the risk for her parents having another child with Down syndrome?

The girl has 46 chromosomes, father has 45, mother has 46. There is a 100% risk of recurrence.

Who are the vulnerable subgroups least likely to meet their nutrient needs?

The poor! African Americans, Hispanics. Elderly & young.

Describe the use of metabolite scavengers in treating metabolic diseases

The scavengers bind the substance whose concentration is too high, sequestering it.

Cycle Sequencing

The sequencing method developed by Fred Sanger forms the basis of automated "cycle" sequencing reactions today. Fluorescent dyes are added to the reactions, and a laser within an automated DNA sequencing machine is used to analyze the DNA fragments produced.

Why do we need dietary guidelines and who establishes them?

They give everyone a way to know what they should be eating, established by the USDA.

Define heteroplasmy and explain its relationship to the threshold effect, and the phenotypic variability in mitochondrial disorders, even within a single family

Variation within a cell. This creates a mosaic-like effect with a varying proportion of mutated/non-mutated mtDNA in each cell, with higher levels of mutation being harder to tolerate. Organs with lower levels of oxidative phosphorylation have a higher threshold for mutation than those with high levels of oxidative phosphorylation. Children of a mother with mutant mtDNA can inherit really varied proportions of mutant vs. normal mtDNA, resulting in different phenotypes.

Thompson 257.2

X inactivation. Fragile X. ???

How do I determine if the clinical utility of a genetic test has been shown, either directly or indirectly through a chain of evidence? Why is clinical validity necessary but not sufficient to show clinical utility? That is, what type of data would I expect to find if genetic testing has "clinical utility" in the diagnosis of patients with juvenile Huntington disease?

You determine whether the test gives you enough information to contribute to a decision-making process. Clinical validity is necessary because if the test is not predictive of an outcome, it cannot be used to make a decision. However, some tests will not help in a decision making process; they may help clarify a prognosis, but that doesn't change what we do for the patients. This kind of test is valid but lacks utility. In a disease like JHD, if there are multiple treatments that work best for diff types of JHD, then a genetic test that can differentiate btw these types would have clinical utility.

Given what you know about the role of the mitochondrial genes in oxidative phosphorylation . . . . a. What symptoms do you think a patient with a mitchondrial gene mutation would experience ? b. Can you think of a metabolite which you might measure in a patient suspected of a mitochondrial disorder ? (Hint : What happens when aerobic metabolism is impossible?)

a. Effects on the brain and nervous system (seizures, deafness, encephalopathy, optic atrophy, dementia, migraine, stroke-like episodes), effects on muscle (myopathy, weakness, exercise intolerance, cardiomyopathy) b. Lactic acid.

To understand the evidence-based medicine (EBM) approaches to assessing genetic tests with emphasis on the concepts of analytic validity, clinical validity, and clinical utility.

analytic validity = is the test robust, specific, selective, and reliable? clinical validity = can the test reliably predict outcome? clinical utility = does giving the test change the outcome?

What concepts are used in an evidence-based approach to genetic testing? That is, explain analytic validity, clinical validity, and clinical utility.

analytic validity = is the test robust, specific, selective, and reliable? clinical validity = can the test reliably predict outcome? clinical utility = does giving the test change the outcome?

Compare and contrast the uniparental heterodisomy and isodisomy

both involve only have genes for one allele from one parent. uniparental heterodisomy means you inherited one parent's two different alleles. isodisomy means you inherit two copies of the same allele from one parent

TELL Information

briefly! be systematic Support success Personalize Stay simple Avoid alarm More resources

To describe the uses of genetic testing.

clinically, for diagnosis, prognosis, and therapy selection

Recognize the influence of economics, culture, access and social policy on diet and nutrition.

economics: some people cannot afford good food culture: people eat foods that are culturally significant to them - it's what they know how to make and it's what their loved ones eat access: some don't have health food stores nearby social policy: food stamps and other programs like school lunch programs help those with poor access get enough to eat.

To describe some of the unique challenges associated with genetic testing such as penetrance, patient confidentiality, genetic counseling, and informed consent.

penetrance = some people have the genes but don't show the phenotype patient confidentiality = genetic info is confidential b/c part of medical record genetic counseling = who else does this impact? family members? informed consent = do we test children?

Thompson and Thompson Genetics in Medicine, p.253 #3

phenotypic? yes?

Explain the inheritance of Fragile X syndrome, including the role of repeat length in determining phenotype

the CGG repeat length (~200 repeats) causes the upstream CpG island to be ovemethylated, meaning that the FMR1 gene is transcribed less frequently-->lower levels of gene product

List the types of tissues that are most significantly affected in mitochondrial disorders

the ones with high energy requirements: nervous system, heart, skeletal muscle

You examine a child who recently moved to Chicago. He is unusually tall for his age and id developmentally delayed. His mother, who is a poor history taker, says that doctors told her to give him a supplement of vitamin B6 (pyridoxine), but she doesn't remember why, or what his diagnosis is. What is the purpose for this medication?

to prevents misfolding of a mutant enzyme

Know key principles of giving information: information sharing and counseling.

• Explain rationale for diagnostic procedures (e.g., exam, tests) • Teach pt about his/her own body & situation (e.g., provide feedback from exam/tests, explain anatomy/diagnosis) • Encourage pt to ask questions • Adapt to pt's level of understanding (e.g., avoid/explain jargon)

Develop a lens through which to view medical knowledge and clinical skills learning that includes quality and safety concepts

"Freedom from accidental Injury" "Ensuring patient safety involves the establishment of operational systems and processes that minimize the likelihood of errors and maximizes the likelihood of intercepting them so won't occur."

What types of conditions are dominantly inherited?

"Structural" proteins, proteins whose levels are very tightly regulated, cell receptor proteins

Discuss the role of infectious agents H. pylori, HPV, EBV, Hepatitis B Virus, Hepatitis C Virus, HIV, HTLV-1 in the development of human cancer.

(1) Helicobacter pylori - a bacterial carcinogen: First incriminated as a cause of peptic ulcers, H. pylori now is the first bacteria classified as a carcinogen. Helicobacter pylori - infection leads to chronic gastritis and gastric cancer. (2) Viral Carcinogens: Viruses play a role in the etiology of certain human cancers. • Human papilloma virus (HPV) (DNA virus). Benign lesions - squamous epithelial lesions: warts, laryngeal papilloma, condylomata accuminata (genital warts of vulva, vagina, anus, penis). Mechanism of HPV induced cancer: The oncogenic action of HPV is due to overexpression of E6 and E7 viral proteins (HPV-16 and HPV-18). • Epstein-Barr (EB) virus: (A human herpes virus - large double stranded DNA genome). Involvement in human tumors: African Burkitt's lymphoma; B-cell lymphoma of immunosuppressed patients; some cases of Hodgkin disease; Nasopharyngeal carcionomas. a) Burkitt's lymphoma of African children (B cell lymphoma). • Hepatitis B virus (DNA virus). Partially single-stranded, partially double-stranded DNA virus. Association with hepatocellular carcinomas of liver. HBV may act in concert with aflatoxin B1, a toxin produced by the fungus aspergillus flavus. HBV X protein binds to p53 tumor suppressor protein. • Hepatitis C virus (RNA virus): Single stranded RNA virus. Responsible for 50% of acute viral hepatitis. Development of chronic liver disease, cirrhosis of liver and liver cancer. • Human immunodeficiency virus (HIV). Several different types of cancer are observed at an increased frequency in acquired immune deficiency syndrome (AIDS) patients and in other immunosuppressed individuals. Most of these are virus-associated cancers. Kaposi's sarcoma (KS) is the most common neoplasm that occurs in patients with AIDS (AIDS-KS). KS is believed to be caused by Kaposi's-sarcoma-associated herpesvirus/human herpesvirus 8 (KSHV/HHV-8). AIDS-lymphoma is another significant cause of morbidity and mortality in human immunodeficiency virus (HIV)-infected individuals. Over 50% of AIDS lymphomas are associated with Epstein-Barr virus (EBV) and/or KSHV infection. EBV activates B-cell precursors, leading to a transformed phenotype. Human papillomavirus (HPV)-related cancers are another type of AIDS-related malignancy. There are likely to be two mechanisms by which papillomaviruses induce neoplasia — by altering the tumour microenvironment, and by directly disrupting cell differentiation, to induce cell proliferation. • Human T- Cell Leukemia Virus type I (HTLV-1): A human T-lymphotropic virus that is associated with form of T-cell leukemia/lymphoma. Endemic in parts of Japan/Caribbean. HTLV-I has tropism for CD4+ T cells and promotes cell proliferation which can lead to leukemia/lymphoma if mutation occurs.

Understand the role of physical carcinogens UV light, ionizing radiation and asbestos in human carcinogenesis.

(1) Ultraviolet light UV-C light includes wavelengths between 200 and 280 nm. UV-B can cause the formation of pyrimidine dimers in DNA; these when unrepaired lead to mutations; UV-B can also cause mutations in tumor suppressor p53 gene in skin. Cancers caused by UV exposure: squamous cell carcinoma, basal cell carcinoma and melanoma can result from DNA damage induced by solar ultraviolet (mostly UV-B 280 to 320 nm range; and to a lesser extent UV-A 320-400 nm range) radiation. (2) Ionizing radiation Several cancer types have increased incidence in persons exposed to ionizing radiation. (3) Asbestos and other fibers Asbestos exposure may cause malignant mesothelioma of the pleura and peritoneum and lung cancer. Asbestos - Family of related fibrous silicates. Mechanism - Chronic inflammation (ROS) may be the predominant mechanism. Exposure to asbestos: mining and manufacturing of asbestos, installation of asbestos insulation, contaminated air in buildings.

Summarize limitations of gene sequencing that may lead to a false negative result.

*Complex *Still requires target enrichment *Requires software and bioinformatics to analyze

Early Gene Therapy Studies

*First gene therapy clinical trial *T lymphocyte-directed gene therapy for ADA-SCID *ADA-SCID: adenosine deaminase (ADA) deficiency resulting in severe combined immunodeficiency - Build up of adenosine in T-cells results in cell death - Highly compromised immune function ("Boy in the Bubble") *In 1990, two chidren were treated with a retrovirus encoding ADA, using an ex vivo approach *Result: number of blood T cells normalizd as did many cellular and humoral immune responses - Complication to data interpretation: conventional protein was continued during the course of gene therapy - Not completely clear that gene therapy was beneficial

Complete Androgen Insensitivity Syndrome "Testicular Feminization"

*Normal testosterone production, with failure of virilization at puberty *Aromatization of androgens to estrogens results in female secondary sexual characteristics *Lack of response to androgen results in absence of pubic, axillary and facial hair *No neurologic disease

Be able to choose the most appropriate molecular test method for a given mutation.

*Sanger may still be the best test if the phenotype is associated with few genes (e.g. cystic fibrosis) *Panels may be the best test when multiple mutations in multiple genes have phenotypic overlap (e.g. cardiomyopathy) *WES may be best if mutations in hundreds or thousands of genes can lead to a similar phenotype or for 'gene discovery'

Explain the advantages and disadvantages of Sanger sequencing v. gene panel sequencing v. whole exome/ whole genome sequencing

*Sanger may still be the best test if the phenotype is associated with few genes (e.g. cystic fibrosis) *Panels may be the best test when multiple mutations in multiple genes have phenotypic overlap (e.g. cardiomyopathy) *WES may be best if mutations in hundreds or thousands of genes can lead to a similar phenotype or for 'gene discovery'

Explain the advantages and disadvantages of signal amplification versus target amplification methods.

*Target amplification methods have the advantage of greater analytical sensitivity (lower limit of detection) *However, target amplification carries a risk of contamination of negative samples with amplified product leading to false positive results

Where do Mitochondria Come From?

*The ovum! Virtually all of the cytoplasm in the fertilized egg comes from the ovum. *The sperm does not contribute any mitochondria during fertilization *Therefore, all of the mitochondria, and all of the mtDNA, come from the mother

What testing should be offered to the family? Who should be tested first? What is the testing strategy for DMD? What prenatal testing options are available to Stacy? (9/27 worksheet)

*Whole exon sequencing *Test Tommy to see which mutation he has. *See if Tommy's mom wants testing. *Prenatal testing

Recognize the structures of the nucleus.

*the nuclear enveope *nuclear pore complexes *nuclear lamina *heterochromatin & euchromatin *nucleoli *assorted nuclear bodies

How do non-health issues like employment, education, and place of residence affect health?

- Ex: Health Inequities within countries: o In Bolivia, babies born to women without education have infant mortality >100/1000 live births o Babies born to women with at least high school education is 40/1000 live births

Which of the above gametes could result in live viable offspring?

-trisomy 13 (for about a year) -trisomy 21 -normal -carrier

What are the possible gametes produced from a carrier of a Robertsonian translocation of chromosome 13 and chromosome 21 [der(13;21)(q10;q10)]?

-unbalanced trisomy 13 -monosomy 13 -unbalanced trisomy 21 -monosomy 21 -normal -balanced Robertsonian translocation carrier

1 8/27 Epithelium Quiz

...

10 8/27 Epithelium Quiz

...

11 8/27 Epithelium Quiz

...

12 8/27 Epithelium Quiz

...

13 8/27 Epithelium Quiz

...

14 8/27 Epithelium Quiz

...

15 8/27 Epithelium Quiz

...

16 8/27 Epithelium Quiz

...

17 8/27 Epithelium Quiz

...

18 8/27 Epithelium Quiz

...

19 8/27 Epithelium Quiz

...

2 8/27 Epithelium Quiz

...

20 8/27 Epithelium Quiz

...

21 8/27 Epithelium Quiz

...

22 8/27 Epithelium Quiz

...

3 8/27 Epithelium Quiz

...

4 8/27 Epithelium Quiz

...

5 8/27 Epithelium Quiz

...

6 8/27 Epithelium Quiz

...

7 8/27 Epithelium Quiz

...

8 8/27 Epithelium Quiz

...

8/28 Connective Tissue Quiz 1

...

8/28 Connective Tissue Quiz 10

...

8/28 Connective Tissue Quiz 11

...

8/28 Connective Tissue Quiz 12

...

8/28 Connective Tissue Quiz 13

...

8/28 Connective Tissue Quiz 2

...

8/28 Connective Tissue Quiz 3

...

8/28 Connective Tissue Quiz 4

...

8/28 Connective Tissue Quiz 5

...

8/28 Connective Tissue Quiz 6

...

8/28 Connective Tissue Quiz 7

...

8/28 Connective Tissue Quiz 8

...

8/28 Connective Tissue Quiz 9

...

8/29 Problem Set A

...

8/29 Problem Set B

...

8/29 Problem Set C

...

8/29 Problem Set D

...

8/29 Problem Set E

...

8/29 Problem Set F

...

8/29 Problem Set G

...

9 8/27 Epithelium Quiz

...

9/16 PPT #59

...

9/16 PPT #61

...

9/16 PPT #63

...

9/16 PPT #65

...

9/16 PPT #67

...

9/16 PPT #69

...

9/16 PPT #71

...

9/16 PPT #73

...

9/16 PPT #76

...

9/16 PPT #78

...

9/16 PPT #80

...

9/16 PPT #83

...

Calculate recurrence risks based on pedigree analysis

...

Conrast the phenotype of Becker muscular dystrophy with DMD. What is the postulated basis for the milder phenotype of Becker muscular dystrophy?

...

Describe ethical considerations that might affect disclosure of genetic test results

...

Describe risks, benefits, and limitations of genetic testing

...

Describe the potential psychological effects of conveying a genetic diagnosis

...

Explain the inheritance of breast/ovarian cancer, and its variable penetrance

...

Genetics in Medicine p. 174 #1

...

Genetics in Medicine p. 174 #3

...

MDM Student Guide 9/12 1

...

MDM Student Guide 9/12 2

...

MDM Student Guide 9/12 3

...

MDM Student Guide 9/12 a

...

MDM Student Guide 9/12 b

...

MDM Student Guide 9/12 c

...

MDM Student Guide 9/12 d

...

MDM Student Guide 9/12 e

...

MDM Student Guide 9/12 f

...

MDM Student Guide 9/12 g

...

MDM Student Guide 9/12 h

...

MDM Student Guide 9/12 i

...

What are the underlying causes of medical errors?

...

Understand the nomenclature/classification of neoplasms and the differences between benign and malignant tumors.

1) Prefix - Refers to line of differentiation Ex: Adeno - Glandular, Lipo - Fatty, Osteo - Bone, Chondro - Cartilage 2) Suffix - Tells you if it's benign or malignant -oma - generally benign -sarcoma - malignant mesenchymal tumor -carcinoma - malignant epithelial tumor Lymphoma - malignant lymphoid tumor Melanoma - malignant melanocytic tumor ***Important exception: Adenomas of the GI tract are not benign, but rather dysplastic lesions that can evolve into invasive malignant neoplasms (carcinomas) Differentiation: Well differentiated: Closely resembles tissue of origin (B) Poorly differentiated: Loses morphologic similarity to tissue of origin (M) Rate of Growth: Usually progressive and slow; may come to a standstill or regress; mitotic figures rare and normal (B) May be slow to rapid; mitotic figures may be numerous and abnormal (M) Local invasion: Usually cohesive, expansile, well-demarcated masses that do not invade or infiltrate surrounding normal tissues (B) Often locally invasive, infiltrating surrounding tissue; (M) Metastasis (spread of tumor to a distant site) Absent (B) Often occur, metastatic potential is the defining characteristic of malignant neoplasms (M)

Identify medically relevant inhibitors of oxidative phosphorylation.

1. Cyanide, carbon monoxide (CO), hydrogen sulfide (H2S), and sodium azide bind to the iron in the heme of the cytochrome aa3 component of cytochrome oxidase preventing electron transfer to O2. Acute cyanide or CO poisoning can occur from smoke inhalation or exposure to cyanide or thiocyanate containing chemicals such as pesticides. Some foods such as almonds, pits of stone fruits, sorghum, cassava, soybeans, spinach, lima beans, sweet potatoes, maize, millet, sugar cane and bamboo shoots contain cyanoglycosides (such as amygdalin). HCN is released from cyanoglycosides by β-glucosidases in intestinal bacterial or in the plant. Hospitals and laboratories us sodium azide as a bacteriostatic agent in bulk and stock solutions. 2. Antimycin A and dimercaprol bind to cytochrome c reductase in Complex III, thereby inhibiting the oxidation of CoQ in the electron transport chain of oxidative phosphorylation. Antimycin A is the active ingredient in a commonly used fish poison used commercially. 3. Barbituates such as Amytal (Amobarbitol) and the fish poison and insecticide Rotenone inhibit the transfer of electrons from iron-sulfur centers in Complex I to CoQ. 4. Atractyloside inhibits the ADP-ATP transporter in the inner membrane. 5. Oligomycin inhibits the F0F1ATPase by blocking the proton channel in the F0 subunit.

Describe how the human genome is organized into repetitive and non-repetitive sequences.

1. Genes are arranged linearly along each chromosome. A gene encompasses the DNA sequence that encodes a protein or RNA along with the sequences flanking the coding sequence that contain information necessary for transcription and processing of the gene. Each gene occupies a position on the chromosome referred to as a genetic locus. Every locus on a chromosome homolog is matched by a version of the same gene on the other homolog. Each version of the gene is called an allele. 2. Large amounts of repetitive DNA, each present in many copies are found in the human genome. Repetitive DNA is distributed in two groups in chromosomes. a) Satellite DNAs are clustered in discrete areas, such as centromeres. b) Interspersed repeats are distributed throughout the genome. (1) SINEs: short interspersed nuclear elements (2) LINEs: long interspersed nuclear elements (3) transposable elements

Describe the events in the processing of membrane and secreted proteins in the ER.

1. N-linked glycosylation. Many secreted and membrane proteins are covalently modified by the attachment of complex oligosaccharide structures to asparagine residues. These modifications are important for the function of the protein and protein stability. 2. Folding of proteins in the ER lumen is assisted by chaperones, isomerases and calcium binding proteins which monitor folding and trimming of the oligosaccharides. 3. Protein oligomerization utilizes chaperones to help balance the unequal synthesis of multiple components of oligomeric protein complexes ensuring that only correctly assembled complexes exit the ER.

Describe how signal sequences are used to target proteins and RNA to different cellular compartments.

1. Nuclear transport 2. Mitochondrial protein import 3. Peroxisomal protein transport 4. ER: import into ER, retention and recycling 5. Membrane protein sorting

Identify and describe the mechanisms of antibiotics that inhibit translation.

1. Streptomycin binds to the 30S subunit of prokaryotic ribosomes distorting their structure and interfering with initiation 2. Tetracycline binds to the 30S subunit of prokaryotic ribosomes and inhibits binding of aminoacyl-tRNAs to the A site. 3. Erythromycin and clarithromycin (macrolide antibiotics) bind to the P site of the 50S subunit of prokaryotic ribosomes and inhibit translocation. 4. Chloramphenicol interferes with the 50S ribosomal subunit of prokaryotes. High levels are toxic in humans because it also inhibits human mitochondrial protein synthesis. 5. Puromycin is an aminoacyl-tRNA analog and becomes incorporated into the polypeptide chain inhibiting elongation. 6. Diptheria toxin inactivates EF-2 preventing translocation. 7. Ricin removes an adenine from eukaryotic 28S rRNA and inhibits ribosome function.

List 3 mechanisms that underlie imprinting

1. methylation/de-methylation of cytosines & histones 2. acetylation/de-acetylation of histones 3. interference RNAs

If Joe's carrier screening had included full gene sequencing and was negative, what risk number should have been given to the family to have a child affected with CF? 9/27

1/2401

Refer to pedigree #1 in 9/27/2013 folder. What is the chance he is affected?

1/4 (0.25)

Based on their carrier screening results, what risk number should have been given to the family to have a child affected with CF? 9/27

1/800

What is a GWAS?

260,000 - 474,000 SNPs capture all common SNPs in Phase I data set in Caucasians Multimarker haplotypes requires fewer markers. Independent Number of statistical tests 150 tests in CEU and CHB+JPT 350 tests in YRI

What morphologic properties define a malignant tumor?

3 Factors determine tumor growth rate What proportion of cells are dividing How fast they divide Ratio of cell division to cell death Morphologically, growth rate is manifest by mitotic activity

List the 9 essential and 11 non-essential amino acids.

9 essential: VH MILK FTW valine histidine methionine isoleucine leucine lysine phenylalanine threonine tryptophan 11 non-essential: whatever is left! alanine cysteine aspartate glutamate glycine asparagine proline glutamine arginine serine tyrosine

Describe how motor proteins are involved in spindle dynamics.

A combination of motor proteins and changes in microtubule length result in the orderly movement of sister chromatids to the spindle poles. a) In Anaphase A, the kinetochore fibers shorten, moving the chromatids toward the poles. b) In Anaphase B, the spindle elongates and the poles separate due to motor driven interactions between interpolar microtubules and intrinsic mobility of the poles themselves. c) The interpolar microtubules reorganize into a central spindle between the chromatids.

State the purpose and the components of the Community Health Assessment.

A community health assessment is the "systematic examination of the health status of a population, usually defined by geography," in order to identify key health problems, assets, and strategies for health improvement.

Define 'critical value' and explain the importance of timely communication of critical values to healthcare providers.

A critical result is one that, if not acted upon immediately/soon, will yield a morbid or even mortal consequence to the patient

What information is conveyed by the karyotype 47,XY,+13

A male with trisomy 13.

Define linkage disequilibrium

A measure of the association of alleles on a chromosome. Two loci are in linkage disequilibrium when their alleles are not randomly associated.

What is linkage disequilibrium?

A measure of the association of alleles on a chromosome. Two loci are in linkage disequilibrium when their alleles are not randomly associated.

Describe ligand-receptor signaling

A signal (e.g. ligand) is captured by a cognate receptor, which conveys the signal intracellularly by a transducer (e.g. G protein or receptor-encoded kinase) and results in the production of second messengers. Signal amplification occurs, along with diversification in signaling pathways. Pathways comprise circuits, which form networks. Altogether, these function to produce a biological response: DNA synthesis or repair, metabolism, cell division, proliferation, differentiation, cytoskeletal rearrangement, chemotaxis, secretion, stimulus propagation, and survival/apoptosis.

What is a haplotype tagging SNP (htSNP) and what is its relevance to GWAS?

A subset of SNPs which account for the majority of the genetic variation in a given genomic fragment. being organized in the GWAS project.

Identify the precursor molecules for biosynthetic reactions from glycolysis.

A. 5-carbon sugars for nucleotides through the pentose phosphate pathway. B. amino acids C. fatty acids (from acetyl CoA) and glycerol-P for triglyceride synthesis D. gluconeogenesis E. bisphosphoglycerate shunt (in red blood cells)

Identify the membrane transport mechanisms that move charged molecules in and out of mitochondria.

A. Adenine nucleotide translocase (ANT) exchanges ATP and ADP in a 1:1 exchange. Similar transporters exist for other metabolic anions. B. Symports transport phosphate and pyruvate along with a proton. C. The calcium uniporter transports calcium into the mitochondria driven by the electrochemical potential across the inner membrane. D. Other transporters: dicarboxylate transporter (phosphate-malate exchange); tricarboxylate transporter (citrate-malate exchange); aspartate-glutamate transporter; malate-α-ketoglutarate transporter. E. NADH produced in the cytosol cannot penetrate the inner membrane. Two shuttle mechanisms exist to transfer electrons (reducing equivalents) from the cytoplasm to the mitochondrial matrix. F. Mitochondrial Permeability Transition Pore (MPTP). Under certain pathological conditions such as traumatic brain injury and stroke, a mitochondrial permeability transition occurs and mitochondria become more permeable to small molecules. Induction of the permeability transition pore can lead to mitochondrial swelling and cell death through apoptosis or necrosis. The MPTP is believed to form by association of the VDAC and the ANT. Increased matrix calcium, excess phosphate or increased reactive oxygen species (ROS) activate opening of the pore. Cytosolic ATP prevents opening of the pore. Under ischemic conditions when not enough O2 is available, the proton gradient cannot be maintained and the F0F1ATPase hydrolyzes ATP to pump protons from the matrix and restore the gradient. The ADP produced is hydrolyzed to adenine and the nucleotide pool shrinks such that there is not enough ATP present to inhibit pore opening. This leads to a cascade of events resulting in mitochondrial damage and cell death.

Describe the types of post-transcriptional processing.

A. Alternative splicing is influenced by specific factors that bind to the hnRNA and regulate splice site selection. B. Alternative splicing is important in a number of diseases including cancer. C. In some transcripts, alternative polyadenylation sites are used. D. In some cell types, specific RNAs are edited to change their sequence, such as by deamination of cytidine to uridine.

Identify the precursor molecules for biosynthetic reactions from the TCA cycle.

A. Amino acids from OAA and -ketoglutarate (also neurotransmitters). B. Heme synthesis from succinyl CoA. C. Glucose from malate. D. Fatty acids and cholesterol from citrate. E. Anaplerotic reactions.

Identify the mechanisms used to repair DNA damage.

A. Base excision repair (BER) removes non-helix distorting lesions. B. Nucleotide excision repair removes helix distorting changes such as bulky adducts caused by oxidized benzo[a]pyrene (from cigarette smoke) and cyclobutane pyrimidine dimers (UV damage). C. Mismatch repair fixes errors caused by misincorporation of bases during DNA replication. D. Repair of double strand breaks.

Identify and describe the three mechanisms for reversible enzyme inhibition.

A. Competitive inhibitors bind at the substrate recognition site and prevent substrate from binding. Increasing the substrate concentration can overcome competitive inhibitors. Competitive inhibitors increase the apparent Km of the enzyme but have no effect on Vmax. B. Noncompetitive inhibitors do not compete with a substrate for binding, but may compete with a second substrate or otherwise interfere with the active site. Noncompetitive inhibitors lower the concentration of active enzyme thereby lowering Vmax, but do not change Km for the substrate. C. Uncompetitive inhibitors will bind only to enzymes already containing substrate. Uncompetitive inhibitors decrease Vmax for the enzyme and the apparent Km of the substrate.

Describe the general structures and functions of ground substance molecules. How do glycosaminoglycans (GAGs), proteoglycans, and glycoproteins differ from each other?

A. GAGs. These are repeating, unbranched disaccharides with negative charges. The longest GAG (thousands of sugar molecules) is hyaluronan (formerly called hyaluronic acid). It gives the gel-like quality to connective tissue ground substance, cartilage matrix, synovial fluid, and the vitreous humor in the eye. Other common examples are chondroitin sulfate and keratin sulfate (both in cartilage) and heparin. B. Proteoglycans have GAGs attached to a linear core protein like the bristles radiating from a test tube brush, and the number of GAGs on the core protein varies greatly. They (aggrecan molecules) can be linked to hyaluronan to help stiffen cartilage matrix, or they can be smaller, transmembrane molecules (syndecan) that function in cell-matrix interactions. The smallest (decorin) helps regulate collagen fibril synthesis. C. Multiadhesive glycoproteins are small proteins with a variety of configurations that have binding sites for most components of connective tissues (cells, fibers, GAGs, etc.) and basal cell membranes of epithelia. They help stabilize the connective tissues.

Identify the factors that regulate transcription.

A. Gene specific transcription factors have a DNA binding domain and a domain that binds to coactivators, corepressors, or TATA-binding protein-associated factors (TAFs). B. Steroid hormone/thyroid hormone receptors are specific transcription factors that can activate or inhibit genes. C. Transcription factors are regulated by their synthesis, by binding to an inhibitory or stimulatory ligand, by regulated nuclear entry and exit, and by post-translational modification (in particular, phosphorylation). D. Transcriptional cascades can regulate multiple genes, very important during differentiation of cells.

Describe the different mechanisms for translation regulation.

A. Inhibition of initiation can be achieved by several means. B. miRNAs can regulate protein expression by binding to complementary sequences on the mRNA and blocking translation or inducing degradation of the mRNA. C. Internal Ribosome Entry Sites (IRES) have been identified in several viruses and in ~100 human mRNAs. D. Frame-shifting occurs in some mRNAs where the ribosome shifts one or two nucleotides to translate two different proteins from the same mRNA.

Describe the key events in translation: initiation, elongation and termination.

A. Initiation in eukaryotes involves the formation of a large complex of proteins and RNAs. 1. The initiator tRNA, methionyl-tRNAiMet binds eukaryotic initiation factor 2 (eIF2), which is a small GTP-binding protein. 2. The tRNA-eIF2 complex then binds to the small (40S) ribosomal subunit at the P (peptidyl) site. Prior to initiation, the ribosomal subunits exist as two separate particles. 3. The 5' cap structure of the mRNA binds to the initiation factor, cap binding protein (CBP), which contains ~20 subunits including eIF4E. The binding of CBP to the cap recruits several other initiation factors 4. The mRNA-CBP complex associates with the methionyl-tRNAiMet-40S ribosome complex. 5. An RNA helicase in an eIF subunit unwinds secondary structure in the 5'-end of the mRNA using ATP hydrolysis as an energy source and the ribosome complex scans the mRNA until it reaches the AUG start codon. Usually, the first AUG encountered is the start codon. However, the AUG is efficiently recognized as a start codon only when it is embedded in a suitable initiation codon recognition sequence or Kozak sequence. 6. The GTP bound to eIF2 is hydrolyzed and the initiation factors are released. 7. The large (60S) ribosomal subunit binds with the methionyl-tRNAiMet bound to the ribosome at the P site. B. In prokaryotes the initiation process is slightly different than eukaryotic initiation. 1. The initiator methionyl-tRNA is formylated, producing formyl-methionyl-tRNAfMet. 2. Only 3 initiation factors are required (IF-1, IF-2, IF-3). 3. The ribosomes are smaller (30S and 50S). 4. Bacterial mRNA is not capped. 5. Prokaryotes do not require ATP for initiation. 6. Identification of the AUG start codon occurs when the Shine-Dalgarno sequence in the mRNA binds to a complementary sequence on the 16S rRNA of the 30S subunit. C. Elongation. After the initiation complex is formed, the addition of amino acids to the growing polypeptide chain involves the cyclic binding of aminoacyl-tRNAs to the ribosome, formation of the peptide bond and translocation of the ribosome to the next codon. The process of elongation is similar in eukaryotes and prokaryotes. 1. After intitiation, a methionyl-tRNAiMet is bound to the P site on the ribosome. An aminoacyl-tRNA specified by the codon in the A (aminoacyl) site of the ribosome binds. 2. In eukaryotes, the aminoacyl-tRNA is bound to an elongation factor EF1α containing bound GTP (EF1α is a heterotrimeric G-protein). In prokaryotes this protein is EF-Tu. Upon binding to the A site, GTP is hydrolyzed to GDP and the EF1α is released. 3. Elongation occurs when the amino acid on the tRNA in the A site forms a peptide bond with the initiator methionine or peptide bound to the tRNA in the P site. The peptidyltransferase that catalyzes the bond formation is the rRNA of the large ribosomal subunit (a ribozyme). The growing peptide chain is now attached to the tRNA in the A site and the tRNA in the P site is uncharged. 4. Translocation of the ribosome to the next codon requires another G-protein, elongation factor EF2 (EF-G in prokaryotes). This elongation factor binds to the ribosome inducing a conformational change that moves the mRNA and bound tRNAs with respect to the ribosome. The spent tRNA that was in the P site is released and the peptidyl-tRNA now occupies the P site and the A site is unoccupied. The process repeats. D. Termination of translation occurs when a stop codon enters the A site. Because no tRNAs bind to stop codons, release factors bind to the ribosome and cause hydrolysis of the peptide chain from the final tRNA. The polypeptide chain is released from the ribosome and the ribosomal subunits dissociate, releasing the mRNA.

Identify the mechanisms by which oxidative phosphorylation is regulated in cells.

A. Naturally occurring uncoupling proteins (UCP) in the inner mitochondrial membrane create a "proton leak" allowing protons to re-enter the matrix without the generation of ATP. The energy is released as heat. UCPs are present in brown adipose tissue in mammals, but humans only have brown fat until shortly after birth. Other UCPs have been identified in humans but there significance is unknown. There is also a "proton leak" probably due to other proteins in the inner membrane. Some estimates suggest that 20% of our resting metabolic rate is due to energy expended to restore the proton gradient lost to the leak. B. Synthetic uncouplers such as the proton ionophore 2,4-dintrophenol or high doses of salicylates (such as aspirin) can also uncouple OXPHOS. Because they uncouple electron transport from ATP synthesis, the energy is released as heat. Overdoses result in hyperthermia, sometimes fatally. C. Inhibitors of specific complexes.

Describe how the urea cycle converts amines into urea.

A. Nitrogen enters the urea cycle as NH4+ ( from bacterial action in the gut or the glutamate dehydrogenase reaction) and aspartate. 1. NH4+ forms carbamoyl phosphate. 2. carbamoyl phosphate reacts with ornithine to form citrulline 3. aspartate reacts with citrulline, eventually donating its nitrogen for urea 4. arginine is formed in two successive steps 5. cleavage of arginine by arginase releases urea and regenerates ornithine B. The urea cycle is regulated by three mechanisms. 1. substrate availability in a feed-forward mechanism. 2. allosteric activation of carbamoyl phosphate synthetase I (CPSI) by N-acetylglutamate (NAG) 3. induction/repression of urea cycle enzyme synthesis during high protein diet or during starvation

Identify other nitrogen containing compounds synthesized from amino acids.

A. Porphyrins B. Catecholamines C. Histamine D. Serotonin E. Creatine F. Melanin

Describe the processing of different types of RNA transcripts.

A. Processing of rRNA. rRNA of both eukaryotes and prokaryotes is synthesized as a long pre-rRNAprecursor containing the 28S, 18S and 5.8S rRNAs (23S, 16S and 5S in prokaryotes). Eukaryotic 5SrRNA is synthesized separately by RNAP III. The pre-rRNAs are cleaved by endoribonucleases, the ends of the individual rRNAs are trimmed by exoribonucleases and some of the bases are modified. As this processing occurs, ribosomal proteins previously synthesized bind to the rRNA and ribosome assembly occurs. The rRNA modifications and assembly are assisted by snoRNAs. B. Processing of tRNA. tRNAs are synthesized as longer molecules that are trimmed at their ends for form the mature tRNA. Uracil residues at the 3' end are removed and replaced by the sequence CCA. Some tRNAs also have a small intron in the anticodon loop that is removed. All tRNAs have extensive base modification, primarily dihydrouracil, pseudouracil and other methylated bases. C. Processing of mRNA. The collection of all RNAP II transcripts in the nucleus is referred to as heterogenous nuclear RNA (assembled with proteins into hnRNPs) and includes transcripts that will become mRNA and other transcripts that will be long non-coding RNAs. Processing of mRNA is co-transcriptional, that is, it occurs as soon as the partial transcript is accessible to the processing enzymes. 1. 5' capping is the first processing event for pre-mRNA. A 7-methylguanosine "cap" is added backward to the 5' end of the pre-mRNA. Additional methylation of the cap will take place in the cytoplasm. 2. Intervening sequences, or introns, do not code for protein sequence and are removed by splicing during transcription. The intron-exon junctions are recognized by snRNPs and other sequence specific RNA-binding proteins to form a spliceosome. The spliceosome contains the catalytic activity required for cutting and religating the mRNA. 3. Poly(A) addition. After termination of transcription, the 3' end of the pre-mRNA is cleaved and a 40-200 nucleotide long polyadenosine tail is added by poly(A) polymerase. The poly(A) "tail" immediately interacts with a specific poly(A)-binding protein that helps to stabilize the tail against degradation by nucleases. The poly(A) tail complex is also involved in stimulating translation initiation. D. Processing of snRNA. Several classes of snRNAs exist, some of which also contain a 7-methylguanosine cap. E. Processing of miRNA. Primary miRNAs are capped at the 5' end and polyadenylated. A "Microprocessor Complex" associates with the individual miRNAs in the primary miRNA and cuts them from the long precursor. These are now called pre-miRNAs. miRNAs encoded in introns bypass this step. Some miRNAs are then modified by RNA editing which deaminates adenosines to inosines. The pre-miRNA is transported to the cytoplasm where it is cleaved by an RNase called Dicer to give a RNA duplex of 22 nucleotides. One strand of the duplex is then incorporated into a RNA-induced silencing complex (RISC).

Identify common post-translational modifications to proteins.

A. Proteolytic trimming to remove parts of the protein occurs in some cases. B. Modification of amino acid side chains. There are numerous covalent post-translational modifications of amino acid side chains in proteins. Some are important for the protein's structure while others regulate the protein's function or signal its degradation. Many of these modifications are reversible.

Describe how checkpoints function to regulate progression through the cell cycle.

A. The G1 checkpoint blocks the activation of G1/S-Cdk and S-Cdk complexes. B. In G1, DNA damage is signaled by a kinase called ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PK) which phosphorylates p53 and stabilizes it. C. p53 is a transcription factor that cause increase in the transcription of the CKI protein p21Cip1, thereby inhibiting the S-phase Cdk2-cyclin E activity. D. Un-repairable DNA damage triggers cell death (apoptosis) or senescence through p53.

Describe how translation of membrane proteins is coupled to their transport into the ER.

A. The Signal Hypothesis. B. Cotranslational translocation of proteins into the ER requires both cytoplasmic and membrane associated factors in addition to the remainder of the protein translation machinery. C. Protein folding, modification and oligomerization in the ER lumen.

Identify the types and topology of membrane proteins.

A. Transmembrane 2. Classified by topology a) Type I: single pass protein anchored to the lipid membrane with a stop-transfer anchor sequence and have their N-terminus targeted to the ER lumen b) Type II: single pass protein anchored with a signal-anchor sequence and the carboxyl terminus in the ER lumen c) Type III: single pass protein with a signal-anchor sequence and the amino terminus in the ER lumen d) Type IV: multi-pass protein, amino terminus on either side B. Monotopic/peripheral C. Peptides that interact with transmembrane protein complexes or oligomerize to form channels.

Enumerate the currently known categories/mechanisms of epigenetic gene regulation

A. Trithorax-group (trxG) and Polycomb-group (PcG) proteins B. DNA methylation C. Histone code D. Nuclear compartmentalization E. RNAi

Describe the role of the Anaphase Promoting Complex in the transition from metaphase to anaphase.

APC is not activated until all chromosomes have a bipolar orientation and all kinetochores are associated with microtubules. Inhibitory proteins associated with kinetochores prevent its activation. 1. The triggering event in anaphase is the sudden loss of Cdk1 activity. This begins with the gradual destruction of cyclin A from prometaphase through metaphase and finishes with the activation of the APC. The APC is a ubiquitin-ligase complex that targets cyclins and the cohesion complex. 2. Separation of sister chromatids does not require the spindle microtubules. The cohesion complex must be degraded by a protease called separase. Separase is inhibited by a protein called securing. Securin is ubiquitinated by the APC targeting it for proteasome degradation, thus activating the separase.

Evaluate social determinants of health and other underlying factors related to disparities for people of low socio-economic status, immigrants, minorities, and their children.

According to Healthy People 2020, social determinants of health are conditions in the environments in which people are born, live, learn, work, play, worship, and age that affect a wide range of health, functioning, and quality of life outcomes and risks. Conditions (e.g. social, economic and physical) in these various environments and settings (e.g. school, church, workplace and neighborhood) have been referred to as place. In addition to the more material attributes of place, the patterns of social engagement and sense of security and well-being are also affected by where people live. Resources that enhance quality of life have a significant influence on population health outcomes. Examples of these resources include safe and affordable housing, access to education, public safety, availability of healthy foods, local emergency/health services, and environments free of life-threatening toxins.

Evaluate and describe design principles of common objects.

Affordances Perceived & actual properties that give an idea how the device might be used Mappings Connection between what is intended and the means to accomplish it Conceptual model Mental picture of 'how things work' Constraints Physical / cultural limits to 'what can be done' Forcing Function: like the paper bins that can only fit paper through the hole.

What is the function of the globular domain at the C-terminus of procollagen?

Align the α chains for triple helix formation.

Identify the amino acid pool, its sources and fates.

All of the free amino acids in the body belong to the amino acid pool supplied by three sources: 1) Degradation of body proteins. Proteins of the body have widely different half-lives from minutes to the lifetime of the organism in the case of cartilage collagen. 2) Dietary protein. 3) synthesis of non-essential amino acids. The amino acid pool has three possible fates: 1) Synthesis of body proteins. 2) Precursors for essential nitrogen-containing small molecules. 3) Conversion to glucose, glycogen, fatty acids or CO2.

Describe the difference between genotype and allele frequency

Allele frequencies A=p and a=q=(1-p) Genotype frequencies are: AA Aa aa p2 2pq q2

How are stereocilia different from microvilli?

Although these are called stereocilia they are more closely related to microvilli. They are very thin, long extensions of the apical surface and contain actin filaments at their core. They likely increase the absorptive surface of epithelial cells where they are found. Actin-filled microvilli extend from the apical surface of epithelial cells in tissues like the gut. When epithelial cells have a plethora of these thin finger-like extensions, they are sometimes referred to as a brush border based on their appearance at the LM level. Brush borders are important for absorption by increasing the apical membrane surface area. The actin filaments in each microvillus arise from the terminal web of actin that runs parallel along the length of the apical surface.

How would one test to determine if a given compound is mutagenic?

Ames Test

Develop a plan for how to study histology; and determine the role of the Rhodin electron micrographs in your study of histology.

Answer learning objectives before each class and review flash cards afterwards. Confirm answers with Dr. Cochard. Micrographs will be used in class.

What do plasma cells secrete?

Antibodies

What are the characteristics of a complex genetic trait?

Any phenotypic trait that exhibits evidence for familial aggregation and genetic involvement but is not inherited in an easily determined manner (dominant, recessive, x-linked etc)

How does necrosis differ from apoptosis?

Apoptosis: Death of single cells Cytoplasmic blebbing Cell shrinkage Chromatin condensation Lysosomes and other cytoplasmic organelles intact Fragmentation of nucleus and cytoplasm Phagocytosis of apoptotic bodies by adjacent cells and macrophages No inflammatory response Requires protein synthesis Energy dependent De novo transcription Nonrandom oligonucleosomal length DNA fragmentation ladder Necrosis Death of many contiguous cells Plasma membrane disruption Cell swelling Nuclear swelling and lysis Lysosomal breakdown/enzyme release Cell lysis and disintegration Phagocytosis by macrophages Inflammatory response inevitable Cessation of protein synthesis Energy not required Cessation of transcription Random DNA degradation

Recognize the differences between necrosis and apoptosis at the visual and mechanistic levels.

Apoptosis: Death of single cells Cytoplasmic blebbing Cell shrinkage Chromatin condensation Lysosomes and other cytoplasmic organelles intact Fragmentation of nucleus and cytoplasm Phagocytosis of apoptotic bodies by adjacent cells and macrophages No inflammatory response Requires protein synthesis Energy dependent De novo transcription Nonrandom oligonucleosomal length DNA fragmentation ladder Necrosis Death of many contiguous cells Plasma membrane disruption Cell swelling Nuclear swelling and lysis Lysosomal breakdown/enzyme release Cell lysis and disintegration Phagocytosis by macrophages Inflammatory response inevitable Cessation of protein synthesis Energy not required Cessation of transcription Random DNA degradation

How would you design an experimental protocol to test whether a given compound (chemical) is a tumor promoter for mouse skin?

Apply the chemical to the mouse's skin in the same spot multiple times. If papillomas develop, withdraw chemical treatment from half of the mice. If it is a tumor promoter, then the papillomas should heal when the chemical is removed. The mice who have continued chemical treatment should develop invasive squamous cell carcinomas.

What is healthcare quality and patient safety?

Are patients getting good care? How can we tell?

What does this result mean for Stacy directly? (9/27 worksheet)

As a carrier, she might experience muscle weakness, dilated cardiomyopathy, and cramps. She should inform her PCP of this.

Describe S phase and the role of cell cycle factors in regulating DNA replication.

At each cell cycle, the cell must accurately replicate its DNA and ensure that replication only occurs once prior to mitosis. A. To ensure that each origin of replication only initiates replication once each cell cycle, a regulatory system of "licensing" is in place. B. S-phase entry or firing of replication origins in triggered by Cdk-cyclin pairs, first by Cdk2-cyclin E and then Cdk2-cyclin A. C. Organization of DNA replication in the nucleus. D. The synthesis of histones is tightly coupled to DNA replication to ensure packaging of the newly replicated DNA. E. Centrosomes also duplicate during S phase in preparation for the next mitosis.

What evidence is there for desmosomes function in adhesion?

Autoantibodies in certain skin diseases (pemphigus) target desmosomal components and induce desmosome disruption.

Describe the characteristics of autosomal dominant, autosomal recessive and X-linked dominant and recessive inheritance

Autosomal dominant inheritance: Trait is expressed when only one allele is for trait, i.e. heterozygous. "Vertical" transmission. Males and females are equally affected. When parent is affected, risk of recurrence in siblings is 50%. If neither parent is affected, appearance of trait may result from new mutation Autosomal recessive inheritance: Trait expressed only when both alleles are for the trait, i.e. when homozygous. "Horizontal" transmission. Males and females are affected equally. Risk of recurrence in a sibling is 25%. The family history is usually "negative." X-Linked Dominant Traits Trait is expressed in males and females (dominant). Transmitted from mothers to sons and daughters, and from fathers only to daughters. No father to son transmission If mother has the trait, 50% of daughters will be have it, and 100% of sons will be affected. If the father has the trait, all of the daughters will have it, and none of the sons will have the trait X-Linked Recessive Traits Trait is usually expressed only in males (recessive). Both parents are normal. If mother is a carrier, 50% of daughters will be carriers, and 50% of sons will be affected. If the father is the carrier, all of the daughters will be carriers, and none of the sons will have the trait.

Know the normal ranges of temperature (oral, rectal, and axillary: Celsius and Fahrenheit), pulse rate, respiratory rate, blood pressure and BMI

Average oral temperature is 37C (98.6F). Rectal temperatures are higher than oral by 1.0 degree F. Axillary temperatures are 1 degree lower than oral. • Normal pulse is 60-100 beats per minute. The normal adult takes about 10-20 breaths per minute. Normal Systolic: <120 Normal Diastolic: <80 • Healthy weight = BMI 18.5-24.9

From what cell type do plasma cells differentiate?

B lymphocytes

Identify the important protein machinery in transcription.

B. Prokaryotic gene transcription. 1. Promoters have characteristic sequences at -35 bp upstream of the start site where the holoenzyme complex forms with the core enzyme and sigma factor. 2. A second site at -10 is called a Pribnow box or TATA box. This sequence is where the helix unwinding begins for a transcription bubble to form. 3. Local unwinding of the DNA allows the polymerase to start polymerizing the RNA. Unwinding requires a topoisomerase to relieve supercoiling. 4. Several short RNA molecules are made by the polymerase until an RNA longer than 10 nucleotides is made. This causes the release of sigma factor and the polymerase can then extend the transcript. During elongation, a short DNA-RNA hybrid is formed near the moving polymerase. 5. A termination sequence at the end of the gene encodes an RNA sequence that forms a hairpin structure. This weakens the DNA-RNA duplex and the polymerase is released from the template. In another mechanism, a helicase called rho factor binds to specific sequences and destabilizes the DNA-RNA duplex. 6. Some antibiotics inhibit prokaryotic transcription by either binding to the polymerase subunits and inhibiting their activity (rifampicin). Other antibiotics intercalate into the DNA and prevent movement of the polymerase (dactinomycin). C. Eukaryotic gene transcription. 1. The greatest mass of RNA in the cell is rRNA transcribed by RNAP I. rRNA genes are linked in tandem with the region between genes containing the terminator of one gene and the promoter for the next gene. Promoters for rRNA genes are immediately 5' to the start of transcription and extend into the beginning of the gene. 2. RNAP III transcribes tRNA genes recognizing DNA sequences near the start site, but the actual promoter lies downstream of the start site, split into two segments. 3. Transcription from RNAP II genes is more complex. The promoters of some RNAP II genes have sequence ~25 bp upstream of the start site called the TATA or Hogness Box, which is nearly identical to the Pribnow box. In genes that are constitutively expressed, there is usually not a TATA box, and it is replaced by a GC-rich sequence. An additional sequence is found in many genes ~70-80 bps upstream of the start site called a CAAT box. These sequences are recognition binding sites for transcription factors (TFs), which in turn interact with each other and RNAP II. 4. Transcription factors are grouped into two categories: general TFs and specific TFs. General TFs bind to the core promoter and are the minimal requirement for recruiting the polymerase and initiating transcription. Specific TFs bind within and outside the core promoter and modulate the frequency of initiation, mediate which genes are active at any period of time, and mediate the response of genes to external stimuli such as hormones. Specific TFs also bind other proteins called coactivators that can modulate transcription (including proteins that modify histones). 5. Some key members of the general TF complex include TFIID that binds the TATA box, TFIIF that recruits the polymerase and TFIIH that is a helicase and also a protein kinase that phosphorylates the polymerase allowing it to clear the promoter. 6. RNAP II genes also sometimes have additional DNA sequences called enhancers that increase the rate of initiation. Although located on the same chromosome as the gene, enhancers can be upstream or downstream of the start site, can be close to or thousands of bps away from the start , and can be in any orientation relative to the direction of transcription. Enhancers bind specific TFs that bend or loop the DNA to interact with other transcription factors at the promoter. 7. Elongation proceeds past the stop codon and through the 3' untranslated region. After passing a sequence called the polyadenylation signal, the polymerase encounters a non-specific termination signal and the transcript is released from the polymerase complex. An enzyme complex that binds to the polyadenylation signal cleaves the mRNA 10-20 nucleotides downstream forming the 3' end. Poly(A) polymerase binds to the end and adds an ~200 nucleotide poly(A) tail in an non-templated reaction. 8. microRNAs are transcribed by RNApP II or RNAP III, typically as long precursors called a primary miRNA containing several miRNAs. Some other miRNAs are found within introns or 3' UTRs.

Calculate the body mass index (BMI).

BMI = weight in kilograms divided by the height in meters squared (kg/m2)

Appreciate the magnitude of the quality and safety problems in healthcare

Based on conservative estimates preventable adverse events are the 3rd to 5th leading cause of death, more prevalent than deaths from all accidental injuries and breast cancer.

Begin to think about how will you word questions and structure your interview so you and your patient feel comfortable discussing things like spirituality, relationships, and values.

Be open-ended and do not show a strong reaction when they say things so that it's clear you're not judging.

If you offered genetic testing to the family, who would you test first? 9/27

Betty

How is signaling specificity achieved? What is meant by biological noise? Is noise good or bad for homeostasis?

Biological noise is the concept that there are a ton of signals. It keeps anything from changing too fast and thus is good for homeostasis. Specificity is achieved by ligand-receptor shape and localization of signals and receptors.

Debate various governmental and industry proposals intended to influence personal health. Working in small groups, students will define a 'pro' and 'con' for each proposal during a gallery walk activity.

Bonuses for not smoking, etc.

What are some important aspects of taking family history with regards to cancer genetics? 9/27

Breast cancer: both breasts is more severe, in males is more hereditary, diagnostic age, patients don't know exactly what cancer they had or genetic cause pre-testing. Has anyone had historectomies? Did they take birth control? Find out what type of cancer they had.

Describe how fatty acids are activated and oxidized to acetyl CoA.

C. Saturated long chain fatty acids (C16-C20) are primarily degraded by β-oxidation in the mitochondria. They must be activated by ATP-dependent attachment of coenzyme A at the outer mitochondrial membrane, peroxisomal membrane or endoplasmic reticulum. The multiple locations of the fatty acyl CoA synthetase reflect the different pathways that long chain fatty acids must enter. D. Activated long-chain fatty acids cannot cross the inner mitochondrial membrane. Carnitine acyl transferases reversibly transfer an activated fatty acyl from CoA to carnitine. The carnitine is transferred at the outer mitochondrial membrane by carnitine palmitoyl transferase I (CPTI). The fatty acylcarnitine is transferred across the inner membrane by a translocase, and the carnitine is exchanged for CoA by CPTII. The released carnitine returns to the cytosol using the same translocase. E. β-oxidation of long chain fatty acids. Fatty acids are shortened 2 carbons at a time by a series of 4 reactions: an oxidation that produces FADH2, a hydration step, an oxidation that produces NADH, and a thiolytic cleavage that releases one molecule of acetyl CoA. For even numbered carbon chains, the four steps are repeated until the final four carbon fatty acid is cleaved to 2 acetyl CoAs.

What are the broad major categories of malignancy?

Carcinoma - Epithelial derivation Sarcoma - Mesenchymal derivation Lymphoma - Lymphocytic derivation Melanoma - Melanocytic derivation

Describe the traffic of membranes from the trans-Golgi network to the plasma membrane and endocytic pathway.

Cargo that arrives in the TGN can be distributed to specific cellular compartments via distinct transport carriers. Sorting of components can be either through protein motifs that enable the formation of unique vesicle coat complexes or through interactions with unique lipid environments in the membrane of the TGN. A. Trafficking of hydrolytic enzymes to the lysosomes occurs largely through mannose-6-phosphate receptors (M6P receptors). B. Clathrin coated vesicles are delivered to the early or late endosomes, which become lysosomes. C. Bulk proteins to be secreted at the plasma membrane are not actively sorted, but become concentrated in the TGN as ER and other Golgi proteins are recycled via sorting signals. D. In specialized endocrine, exocrine or neuronal cells selected proteins are packaged in storage granules for discharge at the plasma membrane in response to hormonal or neuronal stimulation. E. Exosomes are small vesicles released from the plasma membrane and have roles in coagulation, intercellular signaling, and waste management.

Describe the regulation of G1 phase by growth factors.

Cells enter G1 phase after completing mitosis following a proliferation cycle. The bias toward continued proliferation left over from the previous cell cycle is erased by inactivating the Cdks by proteolysis of the cyclins and synthesis of inhibitory proteins. The cell cannot re-initiate the cell cycle unless it receives the proper growth promoting signals from the extracellular matrix, nutrients, or growth factors. Unless all the criteria for growth are met, the cell arrests in G1 at a point called the restriction point. A. The restriction point is the first checkpoint that a cell must pass to progress through the cell cycle. B. Passage through the restriction point occurs when Cdk4/6-cyclin D phosphorylates pRb and releases it from the complex, allowing activation of the growth promoting genes. C. The extracellular matrix and growth factors signal phosphorylation of pRb by stimulating either receptor tyrosine kinases or integrins to initiate signal transduction cascades stimulating transcription of the cyclin D gene. D. After passing the restriction point, Cdk4/6-cyclin D also binds up excess p21 and p27, which are inhibitory for the G1/S-phase Cdk2-cyclin A and E complexes, allowing them to continue phosphorylating pRb.

Describe the organization and properties of cellular membranes.

Cellular membranes are composed of a lipid bilayer with associated proteins and glycoproteins.

Describe the role of chaperones in protein folding.

Chaperones are proteins that bind to unfolded proteins and help to overcome kinetic barriers to folding. Chaperones utilize ATP hydrolysis as an energy source to assist in folding. Cis-trans isomerases and disulfide isomerases also assist in protein folding.

Cystic fibrosis is an inherited disorder. Cholera is an infectious disease. How are the two related?

Cholera toxin requires normal host CFTR proteins to function properly; it was hypothesized that carriers of mutant CFTR genes benefited from resistance to cholera and other causes of diarrhea.

Describe the structure of a chromosome and the landmarks used for chromosome identification

Chromosome structure: packaged DNA (histones, solenoids, and chromatin loops) centromere (p-arm & q-arm) telomere Chromosome identification: length centromere (metacentric, submetacentric, acrocentric) banding pattern nomenclature

Explain the limitations and appropriate applications for these technologies.

Chromosomes + Detects balanced as will as unbalanced rearrangements Mechanism of abnormality is apparent (unbalanced translocation vs deletion) - Requires dividing cells Subjective method Limited Resolution FISH + Interphase FISH does not require dividing cells Higher resolution (for a particular locus) than chromosome studies Relatively quick as compared to chromosome analysis - May require dividing cells (metaphase) Dysmorphologist needed to suspect specific syndrome Only detects abnormalities of the locus probed Not ideal for detection of duplications Microarray + Does not require dividing cells (amenable to stored frozen tissue/autopsy specimens/non-viable tissue Higher resolution than chromosome studies More objective assay - Cannot detect balanced rearrangements Cannot distinguish mechanism (free trisomy vs translocation) Detect "CNVs" Copy number variants of uncertain significance

Identify centromeres and telomeres in chromosome structure.

Chromosomes also have a region enriched in repetitive DNA (called α-satellite DNA in human chromosomes) called the centromere. Specific repetitive DNA binding proteins associate with centromeres and function in chromosome segregation during mitosis. Centromeres are most easily visualized during mitosis. The chromatin of centromeres is entirely composed of constitutive heterochromatin and very little transcription occurs in this region. Specific proteins associate with centromeres (CENP-A-F) and are responsible for kinetochore formation during mitosis. At the ends of each chromosome are specialized DNA sequences called telomeres. The telomeres stabilize the end of the linear chromosome and help prevent recombination with the ends of other chromosomes. A specific complex of proteins called the shelterin complex associates with the telomere and maintains its structure. Telomeres may also help position chromosomes within the nucleus.

Set the stage by providing a confidential environment, determining the patient's agenda, and establishing a personal connection

Close the door before you confirm their name.

How does coagulative necrosis differ from liquefactive necrosis?

Coagulative necrosis is really dry, liquefactive looks wet.

Identify the coding and sense strands of DNA.

Coding strand is the DNA strand read 5' to 3' that is the same as the sequence of the RNA to be made (with T instead of U). In genetics, a sense strand, or coding strand, is the segment of double-stranded DNA running from 5' to 3' that is complementary to the antisense strand of DNA, which runs from 3' to 5'. The sense strand is the strand of DNA that has the same sequence as the mRNA, which takes the antisense strand as its template during transcription, and eventually undergoes (typically, not always) translation into a protein.

Reticular fibers are composed of

Collagen

Describe the differences between male and female meiosis.

Commences: Puberty (M) vs. Early embryonic life (F) Duration: 60-65 Days (M) vs. 10-50 years (F) No. mitoses in gamete formation: 30-500 (M) vs. 20-30 (F) Gamete produced per meiosis: 4 spermatids (M) vs. 1 ovum and 2-3 polar bodies (F) Gamete production: 100-200 million per ejaculate (M) vs. 1 ovum per menstrual cycle (F)

List the differences between male and female meiosis

Commences: Puberty (M) vs. Early embryonic life (F) Duration: 60-65 Days (M) vs. 10-50 years (F) No. mitoses in gamete formation: 30-500 (M) vs. 20-30 (F) Gamete produced per meiosis: 4 spermatids (M) vs. 1 ovum and 2-3 polar bodies (F) Gamete production: 100-200 million per ejaculate (M) vs. 1 ovum per menstrual cycle (F)

Define 'turnaround time' and compare and contrast testing priorities (i.e., 'stat', 'timed' and 'routine') and provide a clinical scenario where each would be appropriate.

Commonly defined as in lab (received) to result time i. Routine: Collected at set time or whenever convenient, analyzed in batch or as received, prioritized after stat and timed. Used for standing orders (e.g., collect every day at 4:00). ii. Timed: Collected at specific time and analyzed in batch or as received, prioritized with/after stats. Collect at specific time that is correlated with a drug dosing pattern (e.g., trough or peak) or timed protocol (e.g., OGTT). iii. Stat: Collected immediately and analyzed/reported without delay - first priority. Urgent/emergency settings (e.g., ED, ICU, etc)

Describe the connective tissue fiber types, and their locations. Relate their composition to their mechanical properties. What fiber type is defective in Marfan syndrome, and what is the defective component? What is the molecular/genetic basis of osteogenesis imperfecta?

Connective tissue fibers are classified as collagen, elastic, and reticular fibers. Type I Collagen forms fibers of high tensile strength in all of the proper connective tissues. The collagen molecule is a triple helix of polypeptide α chains, and at least fifty genetically distinct α chains have been described. Elastic connective tissue is in the form of a thin fiber meshwork (along with collagen) in loose connective tissue, denser fibers in the ligamentum flava of the vertebral column and vocal cords (among some other locations), and fenestrated elastic plates (lamellae) interspersed with smooth muscle layers in elastic arteries (e.g., aorta). Elasticity is achieved by the random coiling of the elastin molecule within fibers and the random attachments between molecules. Reticular fibers are named for their arrangement as a reticulum, a branched, interconnecting meshwork in the loose connective tissue stroma (supporting tissue) of lymphatic tissues (except the thymus gland) and hemopoietic tissues. (And yes, elastic fibers form a reticulum, too.) Marfan's syndrome relates to a defect in the autosomal dominant fibrillin gene, resulting in dysfunctional elastic tissue throughout the body. Fibrillin is part of an elastic fibril, both in its interior and on the surface. Osteogenesis imperfecta is frequently caused by defect in the gene that produces type 1 collagen, an important building block of bone.

What are the connective tissue cell types, and which are resident and which are transient? What are their functions?

Connective tissue fibers can be produced by fibroblasts, smooth muscle cells, and some other cell types. Resident cells: 1. Fibroblasts are the connective tissue workhorse cells that produce all of the fiber and matrix component molecules. 2. Macrophages (histiocytes) are phagocytic cells derived from monocyte blood cells. 3. Mast cells are the c.t. equivalent of basophils in the blood, although they develop via different pathways. 4. Adult stem cells. B. Transient cells in connective tissue are blood cells that leave blood vessels to migrate into connective tissue in response to injury and infection, or to mount an immune response. 1. Monocytes migrate into c.t. and differentiate into macrophages as indicated above. 2. Lymphocytes are involved in the immune response. 3. Granulocytes. Monocytes and lymphocytes lack prominent granules like the three white blood cell types below.

Describe the impact of sociocultural factors on individuals' health beliefs, behaviors, health care experiences, and health outcomes

Culture is not static or rigid and does not define individuals Individuals have multiple cultural identities. Culture refers to more than race or ethnicity

Describe the mechanism for replication of eukaryotic DNA.

DNA is replicated by separation of the 2 strands with each serving as a template for replication of a new complementary strand. Each of the 2 daughter molecules contains one strand from the parent helix and one new strand.

Enumerate the morphological features of an apoptotic cell.

Death of single cells Cytoplasmic blebbing Cell shrinkage Chromatin condensation Lysosomes and other cytoplasmic organelles intact Fragmentation of nucleus and cytoplasm Phagocytosis of apoptotic bodies by adjacent cells and macrophages No inflammatory response

Relate the consequences of defective DNA repair to disease.

Defects in DNA repair processes result in cancer and other diseases. Defects in the components of the damage recognition machinery called XP proteins result in the disease xeroderma pigmentosum.

Describe the characteristics of storage disorders that distinguishes them from other inborn errors of metabolism

Deficient enzyme activity may result in accumulation of substrate (e.g., mucopolysaccharidoses, Tay-Sachs, I-cell, glycogen storage diseases, urea cycle defects), deficiency of product (e.g., glycogen storage disease, biotinidase deficiency), and/or toxic effects of abnormal metabolites (e.g., galactosemia).

Describe the characteristic features and genetic cause of neurofibromatosis, type 1.

Diagnostic Features of NF1 6 or more café-au-lait spots, = 0.5 cm axillary or inguinal freckling 2 or more neurofibromas OR 1 plexiform NF optic pathway tumor 2 or more iris Lisch nodules a distinctive osseous lesion (sphenoid dysplasia or dysplasia of a long bone, e.g., the tibia) a first degree relative with NF-1

Identify the sources of dietary monosaccharides.

Dietary glucose. Fructose makes up about 10% of calories in the Western diet from sucrose, fruits and high fructose corn syrup. Fructose is metabolized via glycolysis. Galactose is also part of the diet from lactose. Taken up into cells by glucose transporters. The pathway of galactose is also known as the Leloir Pathway. Galactose must be converted to glucose to enter glycolysis.

Understand the intrinsic properties of malignant tumors that distinguish them from benign neoplasms.

Differentiation: Well differentiated: Closely resembles tissue of origin (B) Poorly differentiated: Loses morphologic similarity to tissue of origin (M) Rate of Growth: Usually progressive and slow; may come to a standstill or regress; mitotic figures rare and normal (B) May be slow to rapid; mitotic figures may be numerous and abnormal (M) Local invasion: Usually cohesive, expansile, well-demarcated masses that do not invade or infiltrate surrounding normal tissues (B) Often locally invasive, infiltrating surrounding tissue; (M) Metastasis (spread of tumor to a distant site) Absent (B) Often occur, metastatic potential is the defining characteristic of malignant neoplasms (M)

What is the basis for dividing chemical carcinogens into direct and indirect acting groups?

Direct acting groups are highly carcinogenic and increase risk of developing secondary cancers 10-15 years post-use. Indirect-acting groups are much less toxic.

Practice the verbal and nonverbal communication tasks that are required of a physician.

Don't interrupt.

What is involved in the medical management of women with BRCA mutations? 9/27

Early and more frequent mammograms and ultrasound screenings. Can also offer preventive mastectomy and/or oopherectomy (at 35).

A mutation in the fibrilin gene (e.g., in Marfan's syndrome) results in what defective structures?

Elastic fibers

Recognize cellular organelles and identify their major roles.

Endoplasmic reticulum (ER): protein synthesis and glycosylation, calcium storage, drug metabolism, lipid synthesis. Golgi apparatus: modification, sorting, and packaging of proteins and lipids for either secretion or delivery to another organelle. Endosomes: sorting of endocytosed material Lysosomes: degradation of cellular components and extracellular particles Peroxisomes: oxidative reactions, especially of toxic molecules Mitochondria: ATP production by oxidative phosphorylation, steroid synthesis Also look up pictures of them.

To understand the basic organization of epithelial compartments within the context of different organ types.

Epithelial tissues are composed of a single or stratified layer of densely packed cells that line body surfaces and cavities providing an interface between various biological compartments

Discuss multi-stage carcinogenesis in human cancers, with clinical examples.

Evolution of colon cancer through the adenoma/carcinoma sequence. In the molecular model for adenoma-carcinoma sequence of colorectal carcinoma development, the mucosal cells develop mutations of cancer suppressor gene such as APC; second hit inactivation of APC or beta-catenin; activation of protooncogene K-ras; homozygous loss of p53 tumor suppressor gene and additional mutations. Although APC mutation is an early event and loss of p53 occurs late in the process of tumorigenesis, the timing for the other changes may be variable. Note also that individual tumors may not have all of the changes listed. Cells that gain oncogene signaling without loss of p53 eventually enter oncogene-induced senescence. Other examples of multistep carcinogenesis include: development of cervical cancer of the uterine cervix; development of esophageal cancer in areas of Barrett's esophagus and pancreatic intraepithelial neoplasia and pancreatic carcinoma. Environmental versus Hereditary Cancers: Both intrinsic factors and a variety of extrinsic (environmental) factors cause cancer. About 90-95% of cancers are estimated to be environmentally induced, with the remainder of cancers due to inherited predisposition. Genetic or hereditary conditions account for about 5-10% of all cancers. Thus, a majority of cancers is caused by extrinsic or life-style related factors; these include: physical agents; microbial (mainly viral) agents; chemicals; hormones; diet; chronic infections/inflammation (viral, bacterial and parasitic infections); and others. Comprehension of the general principles by which these different etiologies lead to the development of cancer is essential for understanding the disease and in instituting public health measures aimed at cancer prevention. It will be emphasized that carcinogenesis is a multi-stage process: initiation, promotion, and progression and that each of these steps is controlled/regulated by a series of genetic events. Chemical carcinogenesis studies in animals provide the concepts of multistage carcinogenic process.

Describe appropriate uses for FISH methodology

FISH + Interphase FISH does not require dividing cells Higher resolution (for a particular locus) than chromosome studies Relatively quick as compared to chromosome analysis - May require dividing cells (metaphase) Dysmorphologist needed to suspect specific syndrome Only detects abnormalities of the locus probed Not ideal for detection of duplications

Describe the organization of fatty acid synthase and how it produces fatty acids.

Fatty acid synthase is a dimeric enzyme containing 7 different active sites: coordinated catalysis speeds the reactions. When energy levels are high and glucose is adequate, the concentration of mitochondrial citrate becomes elevated. The higher concentration of citrate allows it to leaves the mitochondrion for the cytosol. This citrate shuttle moves acetate groups as acetyl CoA to the cytosol for fatty acid synthesis.

Identify alternative routes for fatty acid oxidation and where they occur.

Fatty acids that are not easily oxidized by β-oxidation are oxidized in alternative pathways in peroxisomes and microsomes. These pathways convert unusual fatty acids to compounds that can be oxidized as fuels or that can be excreted in bile or urine. These pathways also act on xenobiotic (organic compounds foreign to an organism) carboxylic acids that resemble fatty acids.

Describe how collagen molecules are packaged into fibrils, the functional units of most connective tissues, and fibrils into fibers. How do collagens differ from each other and how is their nomenclature designated?

Fibrils exhibit a banding pattern because the triple helix molecules are staggered end to end in an orderly manner (called a "quarter stagger" pattern), with charged groups aligned on the surface. And because of the banding pattern, don't confuse collagen fibrils with striated muscle fibers! While many collagens are fibrillar, some have interruptions in the triple helix for flexibility in connecting fibrils to molecules in the matrix. The three alpha chains in a collagen molecule may be similar (homotrimeric) or genetically distinct (heterotrimeric), and the designation indicates the collagen type and nature of the alpha chains. Type I collagen is [α1(I)]2α2(I), which refers to the type I collagen molecule (I) with two genetically distinct alpha chains, two copies of α1 and one copy of α2. The homotrimeric type II collagen in cartilage is [α1(II)]3.

What is the significance of Helicobacter pylori in gastric cancer?

First incriminated as a cause of peptic ulcers, H. pylori now is the first bacteria classified as a carcinogen. H. pylori infection implicated in the genesis of both gastric adenocarcinomas and gastric lymphomas. The gastric lymphomas are of B-cell origin, and because the tumors have some of the features of normal Peyer's patches, they are often called "lymphomas of mucosa-associated lymphoid tissue" or MALTomas. Helicobacter pylori - infection leads to chronic gastritis and gastric cancer. The major underlying theme in all these chronic infections (including viral hepatitis B and C virus infections) is increased epithelial cell proliferation in a background of chronic inflammation. Chronic inflammation/infection --- and generation of reactive oxygen species (ROS) and oxidative damage.

Describe how the ends of linear chromosomes are replicated.

Following the removal of the RNA primer in the extreme 5'-end of the lagging strand, a gap remains at the end of the chromosome. With no way to fill in this gap in normal somatic cells, the telomeres shorten with each round of DNA replication. If telomeres shorten sufficiently beyond a critical length, the cell activates a pathway to permanently stop dividing called replicative senescence. In germ cells, stem cells and cancer cells an enzyme complex called telomerase remains active. The telomerase complex contains a protein with reverse transcriptase activity (RNA-dependent DNA polymerase) and a small RNA that acts as a template. The RNA template base pairs with the ssDNA segment of the telomeric DNA and the reverse transcriptase uses it as a template for 5' to 3' DNA polymerization, extending the already longer 3'-end of the chromosome. Telomerase then moves to the new end and repeats the process. Once the new strand is sufficiently long, primase uses it as a template to synthesize an RNA primer that is extended by DNA polymerase as in normal replication.

Without vitamin C, what process is diminished or prevented?

Formation of hydrogen bonds between collagen α chains in the triple helix.

Describe how fructose and galactose are oxidized in glycolysis.

Fructose: 1. Transported into cells by the glucose transporter GLUT5. 2. Phosphorylated to fructose 1-phosphate by fructokinase or fructose 6-phosphate by hexokinase (only under very high fructose concentration). 3. Fructose 1-phosphate hydrolyzed by aldolase B to DHAP and glyceraldehyde-3-P, both intermediates in glycolysis. Galactose: 1. Phosphorylated by galactokinase (GALK) to galactose-1-P. 2. Galactose 1-phosphate converted to UDP-galactose in an exchange reaction with UDP-glucose catalyzed by galactose 1-phosphate uridyltransferase (GALT). 3. UDP-galactose epimerized to UDP-glucose by UDP-hexose epimerase (GALE). The "new" UDP-glucose can then either enter glycolysis or be used for glycogen synthesis or participate in the GALT reaction. UDP-galactose can also participate in biosynthetic reactions to form lactose, glycolipids, glycoproteins or glycosaminoglycans.

What distinguishes a gap junction from a tight junction?

Gap junctions are not formally part of the intercellular junctional complex as they do not participate in adhesion or barrier functions of epithelial cells.

Define gene product replacement, and distinguish it from enzyme product replacement

Gene product replacement = enzyme replacement. Enzyme product replacement = replacement of product of an enzyme-catalyzed reaction.

Provide an overview of a promising and highly experimental approach to treat diseases known as gene therapy.

Gene therapy can be defined as a set of approaches used for the treatment of human disease based on the transfer of genetic material (DNA or RNA) into an individual.

If Tommy and Stacy's mother had testing as was negative for the familial mutation, how would you interpret this result? 9/27

Germline mosaicism mutation.

Define the key recommendations of the 2010 U.S. Dietary Guidelines for Americans.

Get enough nutrients while limiting empty calories, saturated & trans fats, sodium and cholesterol. Eat only the minimum number of calories per day and stay active!

Describe the pathway for the oxidation of glucose to pyruvate to generate ATP.

Glycolysis is the most widely used metabolic pathway to generate ATP from glucose. The pathway is present in the cytoplasm of all cells in the body and is used in some form by all animal cells. In this pathway, 1 mole of glucose (6 carbons) is oxidized to 2 moles of pyruvate (3 carbons) directly generating ATP by substrate level phosphorylation. Glycolysis can be divided into two phases: a preparative phase and an ATP-generating phase.

Identify the key enzymes in each oxidative pathway and describe how their activities are regulated by the energy state of the cell.

Glycolysis: 1. Hexokinases product inhibited by glucose 6-P except liver isozyme. 2. PFK-1 is rate limiting enzyme. a) Allosterically regulated by MgATP, citrate, AMP and fructose 2,6-bisphosphate b) Tissue specific isoforms affected differently by allosteric effectors. 3. Fructose 2,6-bisphosphate produced by PFK-2. Regulated by insulin/glucagon. 4. Aldolase exists in three isoforms A (most tissues), B (liver), and C (brain). 5. Pyruvate kinase isozymes in liver regulated by allosteric effectors and post-translational modification. Not regulated in other tissues. TCA: 1. isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase c) physiologically irreversible. d) Large negative free energy change e) Products are rapidly removed. f) Reverse reactions slowly catalyzed 2. succinate dehydrogenase 3. malate dehydrogenase g) thermodynamically and kinetically reversible. h) Positive free energy change. i) Allow for high relative concentrations of substrate to be maintained for regulation and synthetic reactions. 4. Citrate synthase regulated by OAA levels. j) OAA concentration normally kept very low. k) Product inhibited by citrate. l) When ATP levels are low, isocitrate dehydrogenase becomes more active, creating more OAA and removing citrate inhibition. Isocitrate -(isocitrate dehydrogenase) a-ketoglutarate (a-ketoglutarate dehydrogenase)succinyl-CoA (succinate dehydrogenase)fumaratemalate (malate dehydrogenase)OAA (citrate synthase)citrateisocitrate

Identify the differences in glycolysis and gluconeogenesis and the key control points.

Glycolysis: glucokinase (glucose to glucose-6-P) phosphofructokinase-1 (Fructose-6-P to Fructose-1,6-P) pyruvate kinase (phophoenolpyruvate to pyruvate) pyruvate dehydrogenase (pyruvate to acetyl CoA) Gluconeogenesis: pyruvate carboxylase (pyruvate to OAA) PEP carboxykinase (OAA to phosphoenolpyruvate) fructose bisphosphatase (Fructose-1,6-P to Fructose-6-P) glucose-6-phosphatase (Glucose-6-P to glucose)

What is responsible for the viscosity of connective tissue matrix?

Glycosaminoglycans

Focus on the behavior change needed to achieve the goal rather than simply the goal itself. Ex: weight loss

Goal: Lose Weight Strategy: 1. Decrease Dietary total calories 2. Decrease Total fats 3. Increase Physical activity Target: Decrease Portion sizes Slow down eating Decrease fried foods Decrease added butter, dressings Use stairs Take an afternoon walk Need to 'drill down' to actual behavior

What psychological reactions are expected after the diagnosis of DMD in a child? (9/27 worksheet)

Guilt, fear, stress

Evaluate a slide specimen in a systematic way; and describe what the most common stains are designed to demonstrate

HEMATOXYLIN AND EOSIN STAIN (H&E) nuclear stain = hemoxylin; eosin = cytoplasmic MALLORY'S CONNECTIVE TISSUE STAIN collagen & reticular fibers stain blue; elastic fibers = yellow or pink; nuclei = red MASSON'S TRICHROME METHOD Nuclei stain blue; cytoplasm = red; collagen green. PERIODIC ACID-SCHIFF METHOD (PAS) structures rich in glycan polymers or oligomers; e.g., glycogen, basement membrane and mucus, glycoproteins (thyroglobulin) and glycolipids PHOSPHOTUNGSTIC ACID HEMATOXYLIN (PTAH) astroglial fibers WRIGHT'S STAIN blood VERHOEFF STAIN connective tissue

Compare the types of proteins involved in dominant disorders with those involved in recessive disorders

Haploinsufficiency - Familial hypercholesterolemia This dominantly inherited disorder results from mutations in the LDL receptor gene. Dominant negative - Insulin Chicago This rare disorder illustrates how the product of the abnormal allele can interfere with the action of the normal gene product by competing with it (i.e., a dominant negative effect). Achondroplasia and the Wolf-Hirschhorn (4p-) syndromes These two syndromes illustrate the very different effects of dominant mutations (either gain of function or dominant negative) and haploinsufficiency. Gain of function - Familial male precocious puberty This fascinating sex-limited (not X-linked!) disorder affects only males. Osteogenesis imperfecta (OI; brittle bone disease) This is a group of disorders characterized by extreme bone fragility and multiple fractures (in the more severe cases, fractures are present at birth).

Compare and contrast haploinsufficiency, dominant negative and gain of function effects

Haploinsufficiency: The level of gene product required for normal function might be so critical that the amount produce by a single functioning allele would be inadequate (50% is not enough). Dominant negative effects: The abnormal protein (the product of the mutant allele) interferes or competes with the normal function of the normal protein (the product of the normal allele). Gain of function: The abnormal protein has new properties which produce disease.

Discuss the principles of the major behavior change theories: Health Belief Model, Social Cognitive/Ecological Model, Theory of Planned Behavior, Self Determination, Stages of Change, and Behavior Therapy.

Health Belief Model: What about the patient who doesn't seem to understand the need to change a health behavior? Social Cognitive/Ecological Model: It's important to know the supportive resources and barriers patients have to changing their behaviors. Theory of Planned Behavior: Considering the patient's perceived control over behavioral change is also important. Self Determination: One of the most frustrating and distressing situations in clinical care is when a patient seems to lack motivation for change. Stages of Change: Counseling patients begins with assessing whether the patient is ready to make changes in their behavior. Behavior Therapy: There are 3 key traditional cognitive behavior therapy techniques for treating patients with obesity: self-monitoring, stimulus control and cognitive restructuring.

Why is it important for physicians to understand the principles of quality and safety and to be actively involved in and leading improvement activities?

Healthcare is complex. By this we mean that there are many steps to any task in healthcare, involving many people. Teamwork and communication are the root cause of 80% of sentinel events - things you would never want to happen; making specific communication skills and effective medical teamwork essential to the delivery of safe, high quality medical care.

Identify the specific variable(s) likely to account for the test interference in a given clinical scenario.

Hemolysis, lipemia, hyperbilirubinemia, cross-reactivity, etc.

Describe the distribution of quantitative traits in the population

Heritable

Define the gene dosage effect

Heterozygotes ("carriers"), who have one normal and one abnormal allele, typically have about 50% of normal enzyme activity.

Define histology and indicate its importance in understanding physiology, pathology, and functional anatomy

Histology is the microscopic study of cells, tissues, and organs. Easier to understand anatomy and physiology (integration). Histology illuminates function. Knowledge of histology is a prerequisite for the study of pathology and physiology.

Demonstrate taking a dietary history and performing dietary counseling (role playing).

History: Ask open ended questions, planned/unplanned, how often they eat fruits & veggies, targeted disease-specific questions. Counseling: assess understanding of link btw health/disease and diet. Assess readiness. Make specific suggestions.

Describe homeostasis and allostasis, and their central place in understanding health and disease.

Homeostasis: The property of a system that regulates its internal environment and tends to maintain a stable, relatively constant condition of properties such as temperature or pH. Allostasis: The process of achieving homeostasis through physiological or behavioral change. Homeostasis maintains stability; allostasis gets the system to a stable state. Health = organism is at homeostasis. Disease = organism is not at homeostasis; alleostasis mechanisms may be working or broken.

Be familiar with general principles of electronic health records

How does the electronic health record work as a repository for these data? How does use of the computer affect communication? Can you create a pedigree for this patient?

Compare and contrast allelic heterogeneity and locus heterogeneity

However, delineation of the specific enzyme defects provided evidence of even greater genetic heterogeneity, in that patients with very similar phenotypes were found to be lacking different enzymes (locus heterogeneity). Perhaps more surprising was the discovery that rather dissimilar phenotypes (i.e., the very severe Hurler syndrome and the very mild Scheie syndrome) were caused by allelic mutations (allelic heterogeneity, all caused by á-iduronidase deficiency).

Demonstrate understanding of Human Factors and the predictable ways that humans err.

Human Factors is defined as a discipline of study that deals with the human-system/machine interface. Human Factors involve the psychological, social, physical, biological, and safety characteristics of a user and the system in which the user is interacting; specifically, how object or process design can facilitate or prevent error.

When co-cultivated, fibroblasts from a Hurler syndrome patient (type IH) and a Scheie syndrome patient (type IS) will not mutually correct the intracellular accumulation of mucopolysaccharides, as happens when fibroblasts from a Hurler syndrome patient and a Hunter syndrome patient (type II) are co-cultivated. Explain.

Hurler and Scheie syndromes result from allelic mutations; in both disorders "-iduronidase is deficient. In Hunter syndrome a different gene is involved (the one encoding iduronate sulfatase) so that the Hunter cells can provide "-iduronidase to the Hurler cells, and the Hurler cells can provide iduronate sulfatase to the Hunter cells.

In which of the following does "accumulation of substrate" contribute to the pathophysiology? In which does "lack of product" contribute? Hurler syndrome Galactosemia Biotinidase deficiency Tay-Sachs disease Glycogen storage disease Urea cycle disorders

Hurler syndrome - accumulation of substrate Galactosemia - accumulation of substrate Biotinidase deficiency - product deficiency Tay-Sachs disease - accumulation of substrate Glycogen Storage disease - accumulation of substrate, product deficiency Urea cycle disorders - accumulation of substrate

Understand the basis for increase in size of the specified organ in the condition specified: uterus in pregnancy, breast in pregnancy and lactation, gynecomastia in an alcoholic, weight lifter's muscles (drug-free), omentum and subcutaneous fat in an obese child.

Hyperplasia!

Discuss the clinical relevance of hyperplasia, metaplasia, and dysplasia (as they are known as preneoplastic conditions) to neoplasia. What can be learned from the condition known as Barrett's esophagus?

Hyperplasia, metaplasia, and dysplasia can all be insults to a cell, acting as one of multiple steps in the development of cancer. Other examples of multistep carcinogenesis include: development of cervical cancer of the uterine cervix; development of esophageal cancer in areas of Barrett's esophagus and pancreatic intraepithelial neoplasia and pancreatic carcinoma.

Distinguish the differing forms of cellular adaptation.

Hyperplasia: Hyperplasia is an absolute increase in the number of cells in a tissue or organ; size of cells may also be increased. Hypertrophy: Hypertrophy simply means increase in either cell or organ size. Atrophy: It is a reversible adaptive response on the part of the cell to reduce the size (volume/mass) of functional cytoplasm. Hypoplasia: Hypoplasia is a reduction in cell number -- tissue and organ size markedly reduced; it can be physiological or pathological. Metaplasia: Embryonic development ensures the emergence of about 200 types of differentiated cells; the cell lineages are well orchestrated and fidelity maintained by the precursor stem cells (see above). Dysplasia: Dysplasia (Greek dys, 'bad' or 'difficult'; plasis, 'forming, molding') means bad development; aggressive, much less differentiated, highly proliferative, pleomorphic, and less architecturally organized; dysplasia occurs in tracheobronchial epithelium, uterine cervix, oral cavity, etc.; what causes hyperplasia and metaplasia can also contribute to the dysplastic process; dysplasia is more susceptible to neoplastic change. Neoplasia.

Would you approach testing for Betty's brother and niece? 9/27

I would approach Betty's brother and discuss with him whether to offer testing to her niece or wait until she is 18 (and then let the niece choose with no pressure).

Identify the different levels at which gene expression can be regulated.

I. Regulation of gene availability for transcription. II. Regulation of transcription. III. Post-transcriptional processing of RNA. IV. Regulation by non-coding RNAs. V. Regulation by nucleocytoplasmic transport. VI. Regulation of translation. VII. The stability of the mRNA plays a role because more protein can be produced from a long half-life mRNA.

Describe the structure of DNA and RNA.

II. The structure of DNA. In a DNA double helix, the two strands have anti-parallel orientations coiled around a central axis of symmetry. The spatial relationship between the two strands creates a wide (major) groove and a narrow (minor) groove. DNA binding proteins and some DNA intercalating drugs have preferences for binding to the major or minor groove. The DNA double helix forms due to the hydrogen bonding between complementary purine and pyrimidine bases on opposite strands. Adenine-Thymine pairs form 2 hydrogen bonds while Guanine-Cytosine pairs form 3 bonds. Since one polynucleotide chain of the double helix is always the complement of the other strand, if the sequence of one strand is known, then the sequence of the other strand is also known. The specific base pairing in DNA results in Chargaff's Rule: In any sample of double-stranded DNA (dsDNA), the amount of adenine equals the amounts of thymine, the amount of guanine equals the amount of cytosine, and the total number of purines equals the total number of pyrimidines. The helix can have 3 forms A- and B-DNA which form right handed helices, or Z- DNA which forms a left handed helix. B-DNA is the most common. The form of DNA is determined by the base composition and can transition between the different forms depending on what other factors are associated with the helix. III. The structure of RNA. The nucleotides that make up RNA are the same as DNA with the exception that Uridine replaces Thymidine and all of the ribose sugars are hydroxylated at the #2 position. While we typically think of RNA as single stranded, it also forms double stranded RNA structures by anti-parallel base pairing within a strand, or between two separate strands of RNA. RNA can also form RNA-DNA hybrids by inter-strand base pairing.

Describe the process of cytokinesis.

III. Cytokinesis is the process that divides the mitotic cell into two daughter cells. A. The contractile ring is composed of an actin-myosin complex that can contract. B. A cleavage furrow forms where the plasma membrane is constricted and the cell pinches in two.

Compare the roles of the different cytoskeletal systems in cellular functions.

IV. Intermediate filaments have high tensile strength and can withstand stretching of the cell. They have a ropelike structure with a 10nm diameter made up of filamentous proteins aligned laterally. There are four classes of cytoplasmic intermediate filament proteins and one class of nuclear intermediate filament proteins. Their filaments span the cells and link cells together through intercellular junctions V. Microtubules play a crucial role in organizing cells and are the major component of the mitotic spindle. VI. Actin filaments are necessary for movement of the cell and the movement of specialized membrane structures at the cell surface such as phagocytic vesicles and the contractile ring in cytokinesis. Actin filaments are also a major component of muscle, and this function will be covered in a later lecture.

Describe how the G2-M checkpoint senses DNA damage and prevents the transition into mitosis.

If DNA is damaged after replication, the cell can use the non-damaged homologous DNA in the sister chromatid to repair the damage by homologous recombination during G2. Once the sister chromatids have separated, this is not possible and the damaged DNA will be passed on to a daughter cell. 1. The cell possesses "sensors" that resemble the proteins involved in DNA replication. 2. If the sensors detect damage, they activate one of several protein kinases of the inositol 1,4,5-triphosphate kinase (IP-3) family. 3. The effector Chk1 phosphorylates Cdc25 on a specific residue inactivating the phosphatase. 4. When the DNA damage is repaired, other kinases reverse the arrest caused by Chk1 and p21 and allow mitosis to initiate.

Cerezyme

Imiglucerase, treats type 1 Gaucher disease.

Describe how DNA is packaged into chromatin.

In eukaryotes, the nuclear DNA is distributed among several linear DNA molecules packaged in highly organized structures containing protein and RNA called chromosomes. In general, the DNA-protein complex is referred to as chromatin. The DNA in the organelles (mitochondria and chloroplasts) of eukaryotes is circular and packaged similarly to bacterial DNA.

What is protein suicide? Dominant negative effect? Haploinsufficiency? Gain of function mutation?

In multimeric proteins, the abnormal protein might interfere with assembly or stability of the multimer, and result in shortened half-life ("protein suicide"). Dominant negative effects The abnormal protein (the product of the mutant allele) interferes or competes with the normal function of the normal protein (the product of the normal allele Haploinsufficiency The level of gene product required for normal function might be so critical that the amount produce by a single functioning allele would be inadequate (50% is not enough). Gain of Function effects The abnormal protein has new properties which produce disease.

What is the molecular basis of anticipation in myotonic dystrophy?

In myotonic dystrophy, anticipation occurs as the result of increasing expansion of the CTG repeat (in the 3'-untranslated region of the gene) in successive generations.

Identify the major types of DNA damage.

In spite of a robust proofreading activity in the DNA polymerases involved in DNA replication, errors including the insertion of the wrong base or insertion of extra nucleotides can occur. In addition, environmental insults such as radiation or oxidization can create abnormal bases or breaks in the DNA. Bases are also spontaneously lost or altered at a rate of tens of thousands per day in a eukaryotic cell. Healthy cells possess several DNA repair processes to correct these errors and prevent mutation.

Gel Electrophoresis

In the early days of DNA manipulation, DNA fragments were laboriously separated by gravity. In the 1970s, the powerful tool of DNA gel electrophoresis was developed. This process uses electricity to separate DNA fragments by size as they migrate through a gel matrix.

Explain genetic events or mutations which are believed to occur during human colon carcinogenesis.

In the molecular model for adenoma-carcinoma sequence of colorectal carcinoma development, the mucosal cells develop mutations of cancer suppressor gene such as APC; second hit inactivation of APC or beta-catenin; activation of protooncogene K-ras; homozygous loss of p53 tumor suppressor gene and additional mutations. Although APC mutation is an early event and loss of p53 occurs late in the process of tumorigenesis, the timing for the other changes may be variable. Note also that individual tumors may not have all of the changes listed. Cells that gain oncogene signaling without loss of p53 eventually enter oncogene-induced senescence.

Define incidence, prevalence, rate.

Incidence - number of new diagnoses of a disease or condition that develop over time in a population (rate) Prevalence - proportion of a given disease or condition in a population at a snap shot in time (cross-section) Incidence Rate: number of events per person-years of follow-up time: good for long and variable follow-up time

What do you think the family expects to gain from the conversation with the genetic counselor? (9/27 worksheet)

Information, comfort, guidance

How does radiation induce cancer?

Interaction of ionizing radiation with intracellular water may lead to the formation of hydroxyl radicals (OH.). The hydroxyl radical may react with macromolecules DNA, RNA, and protein. Leads to the formation of 8-hydroxydeoxyguanosine in DNA.

Explain the importance of intermediates in metabolic cycles, and their role in the pathogenesis and treatment of disorders of these cycles

Intermediates in metabolic cycles are very important. They provide more places for the cycle to shut down, but they also provide more places where we can intervene and keep the cycle going. For example, if there is a defect in the urea cycle enzyme, the cycle stops. However, by adding the product of that reaction directly, we can skip that part of the cycle and allow it to finish releasing Nitrogen in the form of urine.

Describe how fibroblasts assemble collagen molecules and fibrils. What steps are intracellular and what steps are extracellular? What is the role of vitamin C?

Intracellular: mRNA formed from collagen gene --Single α chain polypeptides formed with globular heads at each end --Hydroxylation of proline & lycine (vitamin C required) --Sugar groups added --Triple helix formed from the C-terminal end to the N-terminal --Hydrogen and disulfide bonds form between α chains to stabilize the triple helix --Procollagen molecule transported to the golgi apparatus --Procollagen molecules associate into bundles --Bundles of procollagen packaged into vesicles that release them to extracellular "coves" bounded by fibroblast cell membrane Extracellular: --Globular ends cleaved to complete the collagen molecule --Molecules align and self-assemble head to tail in quarter stagger arrangement to form fibrils --Molecules cross linked with covalent bonds at lysine-hydroxylysine aldehyde groups --Other collagen types added to the fibril

Define isozyme and isoform

Isozymes are distinguishable proteins with the same or similar substrate specificities. Isoforms are proteins with similar functional and/or structural properties. They may be derived from genes at different loci, or from alternative splicing or post-translational modification.

Appreciate the relevance of epigenetics in clinical settings

It gives us an understanding of how parents' experiences can be passed through later generations.

A 5 day old infant is brought to the emergency department because over the last 2 days he has become less interested in feeding and last night did not awaken during the night to feed. This morning his mother noticed that he was still very sleepy, les responsive, and wouldn't take the bottle. When you examine him, he is unresponsive ,except to pain. His initial albaratory studies come back and he is not acidotic, but his plasma ammonia level si very high. You initiate treatment with sodiu mbenzoate. Why?

It is an ammonia scavenger that forms hippurate.

Describe the limitations of gene product replacement

It is limited by our ability to get the gene product to the appropriate organ, the appropriate cell type, and the appropriate intracellular organelle.

Describe the different mechanisms which can cause Down Syndrome

It results in trisomy 21 (nondisjunction) in about 95% of cases, and from Robertsonian translocation (usually involving chromosome number 13 or 14) in the remaining 5%.

How about abdominal pain?

It will help you narrow down items in the differential diagnosis.

Why is DMD considered a genetic lethal condition? What features define a condition as being genetically lethal?

It's hereditary and death usually occurs at an unnaturally early age (~18). This is characteristic of genetically lethal conditions.

Describe the synthesis of ketone bodies.

Ketone bodies are synthesized when fatty acid levels are elevated during fasting, starvation or as the result of a high fat low carbohydrate diet. 2 acetyl coA from fatty acid synthesis-->acetoacetyl coA-->3-hydroxy-3-methylglutaryl-CoA-->acetoacetate-->B-hydroxybutyrate

List which amino acids are glucogenic and which are ketogenic.

Ketones: WILK Glucogenic: all others

Describe the curricular content and organization of the Lifestyle Medicine Thread

LM includes the factors that influence lifestyle practices: self-care, diet, physical activity, sexual activity, behavior, body weight control, treatment plan adherence, coping, spirituality, mind body techniques, substance abuse, socialization, socioeconomic status, society, culture, access to care, and global health.

Apply the systems approach to understanding healthcare quality and safety issues through discussions of error cases

Like the MRI flying objects case.

Describe the Cdk and cyclin-dependent events in the G2-M transition.

Like the other phases of the cell cycle, the transition from G2 to M is regulated by a Cdk-cyclin pair, specifically Cdk1-cyclin B1. The regulation of this transition by Cdk1-cyclin B1 is elaborate, involving network of stimulatory and inhibitory activities. This ensures a rapid and irreversible transition into mitosis and provides a number of ways to delay entry into mitosis if damage to chromosomes is detected. 1. After Cdk1 binds cyclin B1, it is rapidly phosphorylated and activated by a protein kinase called CAK (Cdk-activating kinase) and another inhibitory kinase, Wee1. 2. The Cdk1-cyclin complex and Cdc25 continuously shuttle rapidly in and out of the nucleus until the G2-M transition. 3. The S-phase Cdk-cyclin, Cdk2-cyclin A is also believed to play a role in the G2-M transition including in chromosome condensation by phosphorylating subunits of the condensing complex and in changing the dynamics of microtubule assembly.

Understand basic concepts of linkage studies and of association studies

Linkage Analysis Co-segregation in families of genes at two or more loci on the same chromosome Parametric analysis (LOD Scores) - assume explicit mode of inheritance, Mendelian Traits Nonparametric analysis (Affected Sib Pairs) - no assumption about mode of inheritance, complex traits Allelic Association Studies Studies based upon the comparison of the frequency of a specific allele or haplotype in affected and unaffected individuals in a population A specific polymorphism or haplotype is associated with a trait/disease if the polymorphism or haplotype is present in a significantly higher frequency among affected compared to control individuals

What are the most common forms of cancer in the US.

Lung cancer is currently the most common cause of cancer death in women, with the death rate more than two times what it was 25 years ago. In comparison, breast cancer death rates were virtually unchanged between 1930 and 1990, but have since decreased by about 24%. The death rates for stomach and uterine cancers have decreased steadily since 1930; colorectal cancer death rates have been decreasing for over 50 years.

Genetics in Medicine p. 174 #2

Male-to-male transmission can disprove X-linkage; other criteria of multifactorial inheritance can be examined, as in the text.

What functional properties define a malignant tumor

Malignant May be well or poorly differentiated Usually fast rate of growth Often invades adjacent tissues Can metastasize

Describe how newborn screening is performed and the types of disorders that are identified.

Mandated by state law in all 50 states. Progress toward a uniform panel of tests/disorders. Tests are performed on a dried blood spot on a filter paper at least 24 hours after birth. Wilson and Jungner Principles and Practice of Screening for Disease (1968) 1. The condition sought should be an important health problem. 2. There should be an accepted treatment for patients with recognized disease. 3. Facilities for diagnosis and treatment should be available. 4. There should be a recognizable latent or early symptomatic state. 5. There should be a suitable test or examination. 6. The test or examination should be acceptable to the population. 7. The natural history of the condition, including development from latent to declared disease, should be adequately understood. 8. There should be an agreed policy on whom to treat as patients. 9. The cost of case finding (including diagnosis and treatment of patients diagnosed) should be economically balanced in relation to possible expenditure on medical care as a whole. 10. Case-finding should be a continuing process and not a "once and for all" project.

Define mean, range, normal distribution, variance, and standard deviation.

Mean - also the average value, measure of central tendency; sum of values/number of values Range - minimum to maximum value In probability theory, the normal (or Gaussian) distribution is a very commonly occurring continuous probability distribution—a function that tells the probability of a number in some context falling between any two real numbers. In probability theory and statistics, the variance is a measure of how far a set of numbers is spread out. Standard Deviation - amount of variation or dispersion from the mean

How are meiosis and mitosis different?

Meiosis II is like mitosis (with a haploid set). Meosis I involves recombination.

Describe the events occurring during meiosis and be able to compare/contrast this to mitosis

Meiosis is a specialized form of cell division that occurs only during gametogenesis comprised of MI and MII shuffles the genetic material through recombination divides genetic material in half Meiosis I reduction division(46->23, 2n->1n, diploid->haploid) occurs only in meiosis Meiosis II identical to mitosis in somatic cells except only 23 chromosomes are present

Define segregation, assortment, penetrance, expressivity and mosaicism

Mendel's first law: Independent segregation: Equal probability that an allele will be transmitted to an offspring Mendel's second law: Independent assortment: Transmission of an allele at one locus is independent of transmission of alleles at other loci Penetrance: the proportion of people with a particular allele (genotype) who manifest the trait (phenotype) Expressivity: Severity. Many traits are not just present or absent, but are present to varying degrees In genetics, a mosaic or mosaicism denotes the presence of two or more populations of cells with different genotypes in one individual who has developed from a single fertilized egg.

Describe appropriate uses for microarray methodology

Microarray + Does not require dividing cells (amenable to stored frozen tissue/autopsy specimens/non-viable tissue Higher resolution than chromosome studies More objective assay - Cannot detect balanced rearrangements Cannot distinguish mechanism (free trisomy vs translocation) Detect "CNVs" Copy number variants of uncertain significance

Define microdeletion and contiguous gene syndrome, and describe how they may be identified

Microdeletion: A syndrome caused by a chromosomal deletion spanning several genes that is too small to be detected under the microscope using conventional cytogenetic methods. Depending on the size of the deletion, other techniques, such as FISH or other methods of DNA analysis can sometimes be employed to identify the deletion Contiguous gene syndrome: A contiguous gene syndrome is a syndrome caused by abnormalities of 2 or more genes that are located next to each other on a chromosome.

Describe the clinical characteristics of Fragile X syndrome

Moderate to severe mental retardation (IQ<50), more common in males, normal looking children. adults have prominent ears, long face, prominent jaw, large head circumference, large testes (macroorchidism) in male pts.

From what cell does a macrophage originate?

Monocyte

How does the HPV tumor virus cause cell transformation?

More than 70 subtypes. Causes benign lesions of squamous epithelium: Warts (benign papillomas of epithelium), laryngeal papillomas, condylomata acuminata. Squamous intraepithelial lesions (SIL). Occasionally condylomata acuminata and laryngeal papillomas under malignant transformation to SCC, but this is rare.

What does the term "monocyte" refer to?

Morphology of the nucleus

What is the difference between a balanced and unbalanced chromosome rearrangement?

Most balanced translocation have a normal phenotype, unless the breakpoint disrupts a gene or deletion occurs at the breakpoint If a balanced de novo translocation in prenatal setting is detected there is an ~5% risk of developmental delay of other abnormality Carriers of balanced translocation are at increased risk for multiple miscarriages as well as abnormal liveborn offspring The outcome for offspring inheriting an unbalanced chromosome from a balanced translocation carrier parent depends on the chromosomes involved and the size of the piece of DNA duplicated or deleted.

Based on the examples presented and what you have learned previously, would you expect most inherited disorders to be recessive, dominant, or X-linked?

Most inherited disorders are autosomal recessive because of: 1) the gene dosage effect (for most genes it's only when both copies of the gene are non-functional that the disease occurs); and 2) there are many more autosomal genes than X-linked genes

Why are most inherited metabolic disorders autosomal recessive?

Most inherited disorders are autosomal recessive because of: 1) the gene dosage effect (for most genes it's only when both copies of the gene are non-functional that the disease occurs); and 2) there are many more autosomal genes than X-linked genes

Describe the G0 phase and its role in the cell cycle.

Most of the cells in our bodies are differentiated and do not divide. This ensures that the structural organization and integrity of tissues is maintained. Cell division does occur in tissues to replace damaged or dead cells, but only enough to restore tissue integrity. Cells that exit the cell cycle, but remain competent to re-enter the cycle and divide are said to be in the G0 phase. This phase may last hours or the lifetime of the organism, in the case of some neurons. The entry into G0 may be triggered by insufficient growth factors to drive progression through G1 including contact with other cells and/or growth regulating proteins. A. One prominent member of the growth regulating protein family is transforming growth factor β (TGF-β). B. In muscle, the transcription factor myoD, the master regulator of muscle development, activates the transcription of p21Cip1, inhibiting several Cdk-cyclins. C. Cells that become crowded and make contacts with their neighbors enter G0 in a process called contact inhibition. D. G0 cells may re-enter the cell cycle in response to injury of surrounding cells or tissue turnover.

What are the possible consequences of multiple alleles at a given locus?

Multiple alleles as a locus may result in 1) no phenotypic effect, 2) genetic variation in phenotype, 3) disease susceptibility, or 4) disease, with various phenotypes.

What are the most common features of NF1 that will likely lead to its diagnosis?

Multiple cafe-au-lait spots Axillary and/or inguinal freckling Neurofibromas Optic pathway tumors Specific bone dysplasias ("pseudarthroses," sphenoid dysplasia) Iris Lisch nodules A first-degree relative with neurofibromatosis

Predict what a gain-of-functon in Jak2 might result in? Loss-of-function in Jak2?

Mutations in JAK2 have been implicated in polycythemia vera, essential thrombocythemia, and myelofibrosis as well as other myeloproliferative disorders by making hematoipoietic cells more sensitive to Epo. Loss-of-function in Jak3: Down Syndrome or acute megakaryoblastic leukemia

How do you think Nancy and her sisters are feeling after receiving this news? 9/27

Nancy is probably scared and maybe feeling cheated, confused & uncertain. She also might be glad that she knows this info because now she is more likely to catch any problems. She doesn't have kids and is 34 - how long to wait before having her ovaries removed? Her sisters probably feel relieved for themselves and scared for their sister, guilty for not having it.

Know the definitions and nomenclature in histopathology of neoplasia: neoplasia, neoplasm, metaplasia, dysplasia, anaplasia.

Neoplasia means "new growth". Neoplasms = tumors, and they can be benign (locally limited, non-invasive with favorable prognosis), or malignant (i.e., cancer) (invasive - invading into adjacent tissue and metastatic - spreading to distant sites with poor outcome). Metaplasia is the transformation of one differentiated cell type to another. Dysplasia means disordered growth. Anaplasia: Tumor cells lose their resemblance to tissue of origin (Squamous tumors will stop making keratin, cartilage tumors will stop making chondroid, glandular tumors will stop forming glands)

Describe the roles of the Golgi complex in protein processing.

Newly synthesized secretory proteins are transferred to the Golgi complex for maturation prior to packaging into secretory granules. A. Structure of the Golgi complex. B. Flow of materials through the Golgi. C. Modifications of oligosaccharides in the Golgi. D. Proteolytic processing of protein precursors.

Where can epithelial cells found NOT to be in direct contact with the basement membrane?

Non basal cells in a stratified epithelium.

Relate Human Factors to the quality and safety challenges in healthcare.

Not only do all human beings err, but they err frequently and in predictable, patterned ways Most errors do not lead to harm Errors occur in a complex system of multiple layers of defenses, which not only prevent harm but usually prevent detection When patient harm occurs, it is both unusual and a strong signal that there are likely major systems problems that allowed the error to surface unchecked or result in an adverse outcome

Define non-communicable diseases and the impact on global health

Not spread through contact - these diseases burden global health.

To be familiar with the general morphological characteristics which distinguish various epithelia.

Number of Cell Layers Cell Shape Keratinization

Recognize and interpret basic cytogenetic nomenclature

Number of chromosomes present Sex chromosome composition Descriptive characters of abnormalities (lowest number first) + gain of a whole chromosome - loss of a whole chromosome add additional material of unknown origin del deletion der derivative chromosome dic dicentric chromosome dup duplication inv inversion iso isochromosome mat maternal origin pat paternal origin mos mosaic r ring t translocation rob Robertsonian translocation

List types of chromosome abnormalities detected by cytogenetic analysis and the clinical and genetic consequence of each.

Numerical (euploidy, aneuploidy) Structural (deletions, duplications, translocations, inversions, rings, isochromosomes) EUPLOID = exact multiple of haploid set - not viable ANEUPLOIDY = loss or gain of single whole chromosome (Trisomy 21, Turner syndrome)

When would it be appropriate, if at all, for siblings Mary and Bobby to undergo testing for the familial deletion? 9/27

Offer to Bobby so that he can get quicker treatments that require genetic testing. Offer to Mary when she wants kids of her own.

Diabetes is one of the most common diseases. How could insulin-resistant diabetes arise?

Once leptin signalling has been disrupted, the individual becomes prone to further overeating, weight gain, and insulin resistance. Since insulin is the primary hormonal signal for energy storage into fat cells, which tend to retain their sensitivity in the face of hepatic and skeletal muscle resistance, IR stimulates the formation of new fatty tissue and accelerates weight gain. Mice without JNK1-signaling do not develop insulin resistance under dietary conditions that normally produce it. The speculation is that some substance is produced in that portion of the small intestine that signals body cells to become insulin resistant. If the producing tissue is removed, the signal ceases and body cells revert to normal insulin sensitivity. No such substance has been found as yet, so its existence remains speculative.

Describe how your histology lab groups will function

One person reads the excerpt, one person navigates computer, a third navigates the textbook.

What factors (i.e. gender, racial, language, religious, socio-political, etc.) may affect your ability to communicate effectively with patients and/or affect your clinical decision-making?

Our culture is also shaped by our age, sex, gender identity, class, education, religion, politics, and abilities.

Describe how electrons from reduced coenzymes are used by mitochondria to produce ATP.

Overview: The coenzymes NADH and FADH2 carry electrons from the oxidation of fuel molecules. The coenzymes in turn donate their electrons to a specialized set of electron carriers in the inner membrane called the electron transport chain. As the electrons are transferred through the electron transport chain, the free energy lost is used to pump protons from the matrix to the intermembrane space. The energy from the resulting electrochemical potential gradient across the inner membrane is used to produce ATP from ADP and inorganic phosphate, a process called oxidative phosphorylation (OXPHOS). Some of the stored energy in the gradient is used to drive transport processes across the inner membrane or to generate heat.

Describe the PSDA cycle (Plan, Do, Study, Act)

PDSA cycles form part of the improvement guide, which provides a framework for developing, testing and implementing changes leading to improvement. The model is based in scientific method and moderates the impulse to take immediate action with the wisdom of careful study. The framework includes three key questions and a process for testing change ideas.

Explain the differences in clinical impact for carriers of a paracentromeric vs pericentromeric inversion.

Paracentric inversions: recombinant gametes result in unstable chromosomes (acentric and dicentric) multiple miscarriages (recombinant gametes) normal healthy offspring (non recombinant gametes) Pericentric inversions: recombinant gametes result in stable chromosomes with unbalanced DNA content multiple miscarriages (non viable recombinant gametes) abnormal liveborn offspring (viable recombinant gametes) normal healthy offspring (non recombinant gametes)

What are the differences between personal responsibility and environmental influences on diet and health?

Personal responsibility has more to do with good or bad eating choices. Environmental influences have to do with lack of eating choices.

Distinguish polymorphism and mutation

Polymorphism refers to the occurrence of two (or more) allelic traits in a population such that the frequency of the rarer is at least 1% (i.e., the occurrence of the rarer trait can not be explained by recurrent mutation alone).

Can you think of two ways in which triploidy (69 chromosomes) could arise?

Polyspermy Failure of division during one of the meiotic divisions

Define population health, public health, global health, epidemiology, and the social determinants of health.

Population Health-the physical, mental, and social well-being of defined groups of individuals and the differences or disparities in health between and among population groups. Public Health-activities that society undertakes to ensure the conditions in which people can be healthy. These include organized community efforts to prevent, identify and counter threats to the health of the public. Global Health- the area of study, research and practice that places a priority on improving health and achieving equity in health for all people worldwide Epidemiology helps identify risk factors and causes of health problems Social determinants of health are conditions in which people are born, grow, live, work and age, including the health system. These conditions are shaped by the distribution of money, power and resources at global, national, and local levels, which are themselves influenced by policy choices.

Describe factors contributing to Hardy Weinberg Equilibrium

Population is infinitely large Random mating no population stratification Assortative mating Consanguinity or inbreeding No selective advantage for any one genotype No mutation, migration, and random drift

What characteristics are required for a population to be in Hardy Weinberg equilibrium?

Population is infinitely large Random mating no population stratification Assortative mating Consanguinity or inbreeding No selective advantage for any one genotype No mutation, migration, and random drift

Describe the characteristics of a population and/or mutation that can result in unusually high gene frequency.

Potential mechanisms explaining unusually high gene frequencies: Heterozygote advantage (Sickle cell, thalassemias) Founder effect: When a few individuals migrate and found a new, isolated population, which is (by chance) different from the population that the settlers came from. Genetic drift: A change in the frequency of a gene resulting from its transmission (by chance) at higher or lower frequency than predicted. This has greatest impact in small populations.

What are principles on which to base improvement and the re-design of healthcare organizations and systems?

Preoccupation with failure: Encourage reporting of errors; elaborate experiences of a near miss for what can be learned; wary of the potential liabilities of success including complacency, the temptation to reduce margins of safety, and the drift into automatic processing Reluctance to simplify interpretations: Take deliberate steps to create more complete and nuanced pictures; position themselves to see as much as possible; encourage those who have diverse experience, skepticism toward existing wisdom, encouraged differences of opinion Sensitivity to operations: Ongoing concern with the unexpected; frequent assessment of the overall safety health of the organization; focus is less strategic and more operational; aware of close tie between sensitivity to operations and sensitivity to relationships; identification of latent failures Commitment to resilience: Develop capabilities to detect, contain, and bounce back from inevitable errors; not disabled by errors; combination of keeping errors small and improving workarounds that keep the system functioning Deference to expertise: Cultivate diversity, which helps to notice more in complex environments and do more with the complexities that are identified; push decision-making down and around; decisions are made on the front line, and authority migrates to the people with the most expertise, regardless of rank; emphasize expertise over experience

What are the benefits of newborn screening?

Prevention of morbidity by instituting treatment for disorders before they have irreversible effects.

Describe the four levels of proteins structure.

Primary sequence. The order of amino acid residues in a polypeptide. Secondary structure - motifs and domains. Linear segments of polypeptide fold spontaneously to form either α-helices, β-strands or random segments depending on the composition of amino acids in that segment. Tertiary structure. The tertiary structure of a protein is the final folded and stabilized pattern of secondary structure elements in a protein. Quaternary structure. Some proteins exist as oligomers of two or more subunits. Multi-subunit proteins are stabilized by the same amino acid interactions that stabilize the tertiary structure of monomeric proteins. Many metabolic enzymes have complex quaternary structures with multiple regulatory and catalytic subunits. Structural proteins of the cell also act by adopting ordered quaternary structures.

In active fibroblasts, what is the primary constituent in the lumen of distended rough endoplasmic reticulum complexes?

Procollagen molecules

Identify and describe the roles for the three major cofactors involved in amino acid metabolism.

Pyridoxal phosphate (PLP) is the quintessential coenzyme of amino acid metabolism. The coenzyme tetrahydrofolate (FH4) is required in certain amino acid pathways to either accept or donate a one-carbon group. The carbon can be in various states of oxidation. The coenzyme tetrahydrobiopterin (BH4) is required for ring hydroxylations. The reactions involve molecular oxygen, and one atom of oxygen is incorporated into the product. The second is found in water. BH4 is important for the synthesis of tyrosine and neurotransmitters

Describe the difference between qualitative and quantitative traits

Qualitative: The trait is either present or absent, e.g., cleft lip, pyloric stenosis Quantitative: The trait varies in degree, e.g., height, intelligence

Demonstrate an understanding of the theoretical frameworks, principles, and disciplines that are related to improving quality and safety in healthcare

Quality and safety in healthcare can be improved by applying methods and knowledge from other disciplines: Human Factors Engineering, Industrial Engineering; Management Disciplines of Operations, Teamwork, Quality Improvement, and Change Management; Cognitive Psychology and Error Science.

Use the histology lab learning guide effectively

Read it before class.

Recognize that being a culturally competent provider does not mean being an expert in every group's health beliefs, but rather recognizing the patient as the expert regarding the cultural aspects that are relevant to their health care, and recognizing the ways that one's own culture and personal biases may affect clinical decision-making

Read the other side.

Understand the importance of targeting receptor tyrosine kinases in cancer

Receptor tyrosine kinases have been shown not only to be key regulators of normal cellular processes but also to have a critical role in the development and progression of many types of cancer. Receptor tyrosine kinases are part of the larger family of protein tyrosine kinases, encompassing the receptor tyrosine kinase proteins which contain a transmembrane domain, as well as the nonreceptor tyrosine kinases which do not possess transmembrane domains.

Describe the relationship between degree of relatedness and incidence of a multifactorial trait

Recurrence risk in first degree relatives approximates the square root of the population incidence The risk of expressing the trait decreases logarithmically with decreasing degree of relationship to the proband.

Describe how connective tissues are organized into regular and special connective tissues, and how regular connective tissue is categorized as loose, dense regular, and dense irregular c.t. What are some examples of each? What are the types of embryonic connective tissue?

Regular (Proper): Loose, Dense regular, Dense irregular; Special: Cartilage, Bone, Fat, Blood. Dense regular connective tissue is dense with parallel collagen fibers packed around the fibroblasts that secrete them. Tendons and ligaments are composed of dense connective tissue. Dense irregular connective tissue refers to the irregular arrangement of the collagen fibers. "Irregular" can refer to the meshwork orientation of fibers as in the dermis of the skin, capsule of an organ, dense fascia, etc., or the irregular distribution of patches of fibers as in the mammary gland. Loose connective tissue is more cellular with relatively fewer fibers. It often has a high fat content as in the superficial fascia under the skin. It serves as "packing material" throughout the body and has a variety of cell and fiber types. Embryonic connective tissue is mesenchyme, a loose connective tissue derived from mesoderm, and mucous connective tissue filling the umbilical cord.

Identify other mechanisms used by cells for regulating enzyme activity.

Regulation through conformational changes in the enzyme. Many enzymes are regulated by changes in the conformation of the protein that changes the affinity of the enzyme for its substrate. Regulation by protein-protein interactions. Modulator proteins can bind to other proteins causing conformational changes or by blocking access to the active site. Regulation by compartmentation.

Define empiric risk

Relative risk is a concept you will encounter in many different contexts depending on how the "populations" are defined. With respect to multifactorial traits, it is the risk to an individual relative to the risk in the general population.

Observe a faculty member using clinical reasoning to guide the history of present illness and physical exam toward a diagnosis

Remember the professor who had dyspnea.

What are some risks, benefits, and limitations of genetic cancer testing? 9/27

Risks: Psychological stress Benefits: Early screening can often make cancer treatable. Limitations: You can still get cancer without the mutation, so can be misleading.

Understand the three pathways of metastatic spread and the steps involved in metastasis.

Routes of Spread: 1. Lymphatic spread: Transport through lymphatics is the most common pathway for initial dissemination of carcinomas. 2. Hematogenous spread Tumor cells enter the thin-walled vessels (veins) and naked sinuses in highly vascular tumors; detach and embolize to other sites/organs, ie lungs, liver, etc. 3. Seeding of body cavities and surfaces: Peritoneal cavity, pleural cavity; pericardial, and cerebrospinal membranes (typical of some carcinomas, ie ovarian). The sequential steps involved in metastasis: 1. A metastatic subclone of cells in the primary tumor invades the basement membrane: Detachment/attachment to basement membrane and extracellular matrix by receptors; Destruction of basement membranes. 2. Migration through ECM. 3. Penetration/Invasion of the vessel wall, i.e., intravasation (lymphatic or vein) and entry of tumor cells into the lumen. 4. Survival and transport via lymphatics or blood vessels. 5. Arrest in target organs (e.g., lymph node in case of lymphatic spread; liver, lung etc., with hematogenous spread) 6. Extravasation in secondary sites. 7. Survival and growth at metastatic site.

Describe the nature, extent and type of health disparities in the United States.

SDH determines the extent to which a person possesses the physical, social and personal resources to identify and achieve personal aspirations, satisfy needs and cope with the environment.

Demonstrate the principles of independent learning, recognizing the critical role it plays in the ongoing career of a physician.

STUDY.

Draw the possible gametes which result from meiosis from carriers of balanced translocations, Robertsonian translocation and inversions.

See notes.

Tommy and Stacy's mother did not want to have genetic testing. Why do you think this is? 9/27

She is an obligate carrier. She might be in denial until she hears that final confirmation.

Try to apply the biopsychosocial model to the patient we interviewed in class.

She was affected by her PKU medically (had to comply with treatments to avoid mental fog), psychologically (changes idea of who she is), and socially (cannot go get steak with friends). She had an excellent doctor, a job, and a son and boyfriend who gave her a great support network.

Name three types of epithelia that contain squamous cells? What distinguishes these three epithelial tissue types.

Simple Squamous Epithelium: Composed of a single layer of flat, irregularly shaped cells anchored to a BM and forming a continuous surface. Non-keratinizing, stratified squamous epithelium This type of epithelium is found covering certain internal body surfaces that are moist, such as the oral cavity. Keratinizing, stratified squamous keratinizing epithelium Again the basal cells are either cuboidal or columnar and sometimes can be found undergoing cell division in histological sections.

To recognize and name distinct epithelial tissue types at the Light Microscopic (LM) level.

Simple Squamous Epithelium: At the light microscopic (LM) level, the nuclei are prominent whereas the cytoplasm of the cells is attenuated.

Goblet cells are commonly found in what type of epithelium? What is the defining characteristic of a goblet cell at the LM level.

Simple columnar. They are goblet-shaped.

Why is it inappropriate to offer prenatal diagnosis for a female fetus in this situation? (9/27 worksheet)

Since the female could only be a carrier, the testing wouldn't change anything, so it's a waste of money and a confidentiality issue - when she has children, she can get tested.

Your patient, a Marlborough smoker for 30 years, developed hemoptysis. A diagnosis of squamous cell carcinoma of the lung was made. How did he develop a squamous tumor in that location?

Smoking damaged his lung tissue, disturbing differentiation. This led him to develop squamous metaplasia.

Describe and assess health disparities experienced by people due to income and socio-economic status.

Social Determinants of Health (SDH): the economic and social conditions under which people live determine their health.

Describe how mechanism based inhibitors inhibit enzyme activity.

Some inhibitors inactivate enzymes by forming covalent bonds with the enzyme active site or binding essentially irreversibly to the active site.

What are so called non-dividing cells? And what is the biological implication if they undergo cell death?

Some mature, fully differentiated cells/tissues in the adult have no or markedly limited capacity to divide or enter into cell cycle. These include adult neurons, adult cardiac myocytes, and adult skeletal muscle cells. Once these cells die, there is no replacement. The loss is permanent and the lost tissue is replaced by scar tissue (collagen).

How do stem cells contribute to the process of hyperplasia, metaplasia, and dysplasia?

Stem cells are the cells that proliferate in these processes.

Describe the structure of mitochondria and relate the structure to the generation of ATP.

Structure: The mitochondria have a unique structure among organelles as they have an outer and inner membrane. Overview: The coenzymes NADH and FADH2 carry electrons from the oxidation of fuel molecules. The coenzymes in turn donate their electrons to a specialized set of electron carriers in the inner membrane called the electron transport chain. As the electrons are transferred through the electron transport chain, the free energy lost is used to pump protons from the matrix to the intermembrane space. The energy from the resulting electrochemical potential gradient across the inner membrane is used to produce ATP from ADP and inorganic phosphate, a process called oxidative phosphorylation (OXPHOS). Some of the stored energy in the gradient is used to drive transport processes across the inner membrane or to generate heat.

Explain the major ways that performance is measured in healthcare and the pros and cons of different kinds of measurement

Structures: Generally static characteristics of health care provider or care settings Useful if causal relationship between the structural characteristics and important quality outcomes Often easiest and cheapest to measure Processes: Measurements of what takes place during the delivery of care Often most actionable by healthcare providers Examples: Tests or assessments performed Treatments prescribed Procedures done Counseling given Outcomes: Measurements of health status or clinical condition Can include the costs of care or patient reported outcomes such as satisfaction with care What consumers care about most Often tied more to characteristics of the patients than actions of providers

What are the possible consequences of enzyme deficiencies which can produce disease?

Substrate accumulation, product deficiency, and more proximal and distal alterations in metabolite concentrations.

Describe theoretical models of the systems approach to error occurrence in healthcare.

Swiss Cheese Model: Due to alignment of gaps in the current systems and processes, an adverse event occurred

Describe the Behavior Change Plan (BCP) assignment.

The Behavior Change Plan (BCP) provides students with an opportunity to experience and implement behavior change strategies (e.g. Behavior Therapy, PDSA cycle) while improving their personal health. In addition, this activity lays the foundation for assisting patients to adopt new behaviors in the course of clinical practice.

What quality and safety topics and skills will be addressed in the FSM undergraduate medical education?

The Quality and Safety Thread will consist of learning the definitions of quality and safety; the epidemiology of risk in healthcare; the systems approach to error occurrence and human factors; risk assessment and error reporting; effective medical teamwork and communication. Students will learn about other high risk, high reliability industries such as aviation, nuclear power, etc. and what makes these industries safe and highly reliable. Principles and practices from other high reliability organizations will be explored for their applicability in healthcare. The skills of situational awareness and evidence-based safety practices will be presented.

Describe the pathway for the complete oxidation of acetyl CoA to CO2 by the TCA cycle.

The TCA cycle converts acetyl CoA from glucose, fatty acids and ketone bodies to CO2 while generating reduced cofactors to produce ATP.

Describe how the enzyme active site enables an enzyme to catalyze a reaction.

The active site binds the substrates and prosthetic groups and contains the amino acid residues involved in the making and breaking of bonds. The active site residues are widely separated in the primary sequence of the protein, but are brought together by protein folding. Active sites are typically clefts or crevices in the protein structure to restrict the entry of molecules to substrates and reactants.

A second mutation is not identified in Joe. What could this mean? 9/27

The baby got the disease from a de novo mutation. He's not the father. Gene line mosaicism.

Compare the structures of prokaryotic and eukaryotic genes.

The basic structure of prokaryotic and eukaryotic genes is similar, a promoter sequence 5' or "upstream" of the coding sequence where the polymerase binds (initiation); the coding region that specifies the RNA sequence to be synthesized (elongation); and a terminator sequence that signals the polymerase to stop transcription (termination). Multiple polymerase complexes transcribe the same gene simultaneously.

Identify the phases of the cell cycle.

The cell cycle can be divided into two distinct phases mitosis and interphase. Interphase is the time when the cell grows and replicates its DNA. This phase can be further divided into three phases G1, S, and G2. Cells have two fates, they can either remain in a state of proliferation (growth and division), or differentiate and no longer divide (or divide very infrequently). The conditions a cell finds during the G1 phase of interphase will determine if it will continue through the cell cycle. Once past a certain point in G1, the cell is committed to completing the cycle.

What is responsible for the elasticity in elastic connective tissue?

The coiling of elastin molecules and their random interconnections.

Understand how stem cell biology influences organ repair.

The concept of the stem cell is functionally defined by its ability to regenerate tissues over a lifetime. Two types of stem cells exist: embryonic - derived from the blastocysts, they can generate an entire organism (i.e. totipotent), and adult - these generate committed progenitor progeny who can function to maintain normal cellular turnover within an organ, or serve to provide regenerative capacity within an organ, and in this sense can generate cells of restricted (pluri-/multi-potent) lineage.

Identify the three cytoskeletal systems in cells and describe their physical properties.

The cytoskeletal system consists of three different polymer systems: the microtubules, the intermediate filaments, and the microfilaments. A. All three forms of cytoskeletal proteins form helical structures. B. Actin microfilaments and microtubules are relatively easy to break. In intermediate filaments, multiple protofilaments align side to side creating a polymer that is flexible and resistant to breakage. C. Actin microfilaments and microtubules are polar structures whereas intermediate filaments are non-polar.

Describe the mechanisms responsible for protein turnover in cells.

The degradation of cellular proteins to maintain protein homeostasis in the cell occurs primarily by two pathways, lysosomal degradation and the ubiquitin proteasome system. Some cellular proteins have half-lives of only minutes whereas other proteins may have half-lives of years. The half-life of a protein is influenced by the nature of the amino terminal residue - the N-end Rule. Proteins rich in sequences containing proline, glutamate, serine and threonine (PEST sequences) have short half-lives.

What are the mechanisms that can account for unexpectedly high gene frequencies in specific populations?

The founder effect and genetic drift, heterozygote advantage, inbreeding

What is the gene dosage effect?

The gene dosage effect refers to the relationship between the number of functioning copies of a gene and the amount of gene product produced.

Describe the genetic code read during translation and the RNA components necessary.

The genetic code is the language by which the genetic information encoded in a gene sequence is transcribed into a messenger RNA (mRNA) which is then "read" to translate a protein with a specific and defined sequence. A. Codons are the 3 nucleotide sequences in mRNA that specify the order of amino acids to be assembled into a polypeptide chain. B. Codons are "read" by transfer RNAs or tRNAs

What is homeostasis? How does the cell/body maintain this state?

The human body and its cells and tissues strive for the unperturbed physiologic steady state, termed homeostasis. However, in the real world these can be stressed and directly injured. To enable continued survival in response to stressors, the body/tissue/cells will enter a new steady state through adaptation. If a cell cannot adapt to a stressor, it will become injured, the damage from which may result cell/tissue/body death. Cellular adaptations, as defined below, frequently result in changes in cell size, number, differentiation state, or combinations thereof. Both systemic and local controls are thought to control cellular adaptation; however, these regulatory mechanisms remain only partially characterized.

Describe how motor proteins move cargo on cytoskeletal networks.

The motor proteins are a large and diverse group of proteins that utilize the energy from ATP hydrolysis to couple large scale structural changes in the motor protein to generate a mechanical force. The movement of organelles and macromolecular complexes that are too large to move efficiently by diffusion is achieved using motor proteins and the cytoskeleton networks. Cell movement and cell division also rely on motor proteins. A. All motors have the same basic structure consisting of a head domain that contains the motor activity and a cargo binding domain. All utilize ATP for movement and are therefore ATPases. B. Kinesins belong to a large superfamily with related structure and functions. All move on microtubules toward the plus end. Since microtubules all have the same orientation in cells, kinesins move away from the MTOC toward the cell periphery (anterograde movement). C. Dyneins belong to a small family of motors with similar structures to kinesins but move toward the minus ends of microtubules (retrograde movement). Dyneins are divided into two groups cytoplasmic dyneins found in all cells, and axonemal dyneins found in cilia and flagella. D. Myosins are also a large superfamily of motor proteins that interact with actin microfilaments or thin filaments (in muscle) to generate force.

Describe the various ways genetic alterations can affect protein structure and function

The occurrence of multiple alleles at a locus may have one of four possible consequences: (1) no phenotypic effect (e.g. "silent" polymorphism), (2) contribute to the normal variation of a specific trait observed within the species, (3) affect disease susceptibility (which is usually multifactorially determined), or (4) directly disturb protein function and cause a monogenic disease.

Describe the levels at which polymorphisms may be manifest

The occurrence of multiple alleles at a locus may have one of four possible consequences: (1) no phenotypic effect (e.g. "silent" polymorphism), (2) contribute to the normal variation of a specific trait observed within the species, (3) affect disease susceptibility (which is usually multifactorially determined), or (4) directly disturb protein function and cause disease (a monogenic disorder).

List the potential consequences of genetic polymorphism

The occurrence of multiple alleles at a locus may have one of four possible consequences: (1) no phenotypic effect (e.g. "silent" polymorphism), (2) contribute to the normal variation of a specific trait observed within the species, (3) affect disease susceptibility (which is usually multifactorially determined), or (4) directly disturb protein function and cause disease (a monogenic disorder).

Describe the role of the pentose phosphate pathway in producing ribose 5-phosphate and NADP.

The pentose phosphate pathway bypasses the first stage of glycolysis to generate NADPH for other reactions and pentose sugars such as ribose 5-phosphate for nucleotide synthesis.

Describe the role of the pyruvate dehydrogenase complex in linking glycolysis to the TCA cycle.

The pyruvate dehydrogenase complex (PDC) links glycolysis to the TCA cycle by oxidizing pyruvate to acetyl CoA. PDH is a mitochondrial large multi-subunit enzyme complex made of 3 functional proteins comprised of a total of ~100 protein subunits located in the mitochondrial matrix. It is a member of the α-ketoacid dehydrogenase family (like α-ketoglutarate dehydrogenase of the TCA cycle). The enzyme complex has a very high catalytic activity due to substrate channeling.

Relate the velocity of an enzymatic reaction to substrate concentration.

The rate of all enzyme-catalyzed reactions is dependent upon substrate concentration. In order to determine useful information from an experimental reaction setup, we make several assumptions.

What are the main differences between a desmosome and a hemidesmosome?

Their protein components are quite distinct.

What information can you still provide to Nancy's sisters regarding their risk for cancer? Who else in the family should be told about their risk to be a carrier?

Their risk is not elevated, but it is still possible for them to get cancer. Their mother and grandmother should be told, as well as #28, #36, and the other son.

What are the features of this pedigree that suggest inherited versus sporadic cancer? 9/27

There are multiple family members with the BrCa mutation.

Define culture and cultural competence

There are multiple, sometimes conflicting definitions of culture, but to help guide today's discussion and future sessions on cultural competence, we will employ the following definition: Culture refers to "integrated patterns of human behavior that include the language, thoughts, communications, actions, customs, beliefs, values, and institutions of racial, ethnic, religious, or social groups."

Describe how G protein couple receptors relay their signal

There are two principal signal transduction pathways involving the G protein-coupled receptors: the cAMP signal pathway and the phosphatidylinositol signal pathway. When a ligand binds to the GPCR it causes a conformational change in the GPCR, which allows it to act as a guanine nucleotide exchange factor (GEF). The GPCR can then activate an associated G-protein by exchanging its bound GDP for a GTP. The G-protein's α subunit, together with the bound GTP, can then dissociate from the β and γ subunits to further affect intracellular signaling proteins or target functional proteins directly depending on the α subunit type

To recognize different junctional complexes and junctions at the EM levels and understand their basic organization and function.

Tight junctions: Tight junctions (TJ) acts as a barrier or 'gate' to the passage of materials from the lumen into the connective tissue between the contacting cells of the epithelium. Adherens Junctions: There is a small gap between the contacting membranes at the adherens junction (AJ). Desmosome: The desmosome also possesses a gap between the contacting membranes that contains an electron dense midline in the extracellular space.

Identify and describe the two pathways for amino acid degradation in cells.

Transamination a) Alanine aminotransferase (ALT) transfers the amino group from alanine to α-ketoglutarate to form glutamate. Glutamate acts as a collector on nitrogen from alanine. b) Aspartate aminotransferase (AST) transfers amino groups from glutamate to oxaloacetate to form aspartate, which is used as a nitrogen source for the urea cycle. c) Aminotransferase reactions require the coenzyme pyridoxal phosphate, a derivative of vitamin B6. d) ALT and AST are released from cells due to injury or disease so their levels in plasma have diagnostic value for liver damage, myocardial infarction and muscle disorders.

Identify the key regulatory proteins of the cell cycle and their activities.

Transitions between cell cycle phases are triggered by a network of protein kinases and phosphatases. A. The cyclin-dependent kinases (Cdks) are a family of 11(in humans) related protein kinases that are crucial for cell cycle progression and other activities. B. The Cdk-cyclins have only partial kinase activity. C. Several small inhibitory proteins of the cyclin-dependent kinase inhibitor (CKI) and inhibitor of Cdk4 (INK4) families bind to and inactivate the Cdk-cyclin complexes. D. Cdk-cyclins are also regulated by movement between the cytoplasm and nucleus. E. Four classes of cyclins affect Cdk activity at defined points in the cell cycle. F. Checkpoints allow the system to arrest at specific points for quality control.

Hereditary Glomus Tumors: How do they illustrate imprinting?

Tumor can skip a couple of generations. This implies unaffected carriers. Imprinting explains why these are unaffected while others are affected.

Discuss mechanisms by which chronic inflammation can cause cell injury, DNA damage and promote the growth and dissemination of neoplastic cells.

Tumor cell development and invasion can be promoted by alteration of the adaptive immune response through stromal-epithelial interactions. Cytokines produced by inflammation including IL-6, TNF(alpha) and CCL2 lead to recruitment of lymphocytes and macrophages. Activated leukocytes and macrophages can produce reactive oxygen species (ROS), reactive nitrogen species (RNS), and cytokines as part of chronic inflammation and can cause DNA damage in nearby epithelial cells. Also, when cells age or are exposed to genotoxic stress, they may also be a source of cytokines and ROS/RNS. Production and accumulation of cytokines, growth factors, free radicals, matrix proteinases and prostaglandins can induce cancerous changes in cells including DNA damage, protein modifications and changes in gene expression profiles.

Discuss the role of inflammation in the development and progression of cancer. Identify products of inflammation that may cause DNA mutation, cancer growth and progression.

Tumor cell development and invasion can be promoted by alteration of the adaptive immune response through stromal-epithelial interactions. Cytokines produced by inflammation including IL-6, TNF(alpha) and CCL2 lead to recruitment of lymphocytes and macrophages. Activated leukocytes and macrophages can produce reactive oxygen species (ROS), reactive nitrogen species (RNS), and cytokines as part of chronic inflammation and can cause DNA damage in nearby epithelial cells. Also, when cells age or are exposed to genotoxic stress, they may also be a source of cytokines and ROS/RNS. Production and accumulation of cytokines, growth factors, free radicals, matrix proteinases and prostaglandins can induce cancerous changes in cells including DNA damage, protein modifications and changes in gene expression profiles.

Early DNA Sequencing

Two sequencing techniques were developed independently in the 1970s. The method developed by Fred Sanger used chemically altered "dideoxy" bases to terminate newly synthesized DNA fragments at specific bases (either A, C, T, or G). These fragments are then size-separated, and the DNA sequence can be read.

Describe the mitochondrial permeability transition pore and its role in cell survival.

Under certain pathological conditions such as traumatic brain injury and stroke, a mitochondrial permeability transition occurs and mitochondria become more permeable to small molecules. Induction of the permeability transition pore can lead to mitochondrial swelling and cell death through apoptosis or necrosis. The MPTP is believed to form by association of the VDAC and the ANT. Increased matrix calcium, excess phosphate or increased reactive oxygen species (ROS) activate opening of the pore. Cytosolic ATP prevents opening of the pore. Under ischemic conditions when not enough O2 is available, the proton gradient cannot be maintained and the F0F1ATPase hydrolyzes ATP to pump protons from the matrix and restore the gradient. The ADP produced is hydrolyzed to adenine and the nucleotide pool shrinks such that there is not enough ATP present to inhibit pore opening. This leads to a cascade of events resulting in mitochondrial damage and cell death.

How can you make information clearer to a patient with low health literacy?

Use diagrams

Explain desirable and undesirable causes and consequences of variation in healthcare.

Widespread Lack of connection between cost and quality Often large variation in areas where the clinical evidence is weak Examining variation can potentially reveal innovative or best practices (high end outliers) Removing unwanted variation takes deliberate, systematic effort (more to come)

Explain the unique characteristics of the sex chromosomes.

X and Y carry different genes, but they have the same material in "pseudoautosomal region" which allows them to line up.

Can Stacy's risk be further modified using Bayes theorem? If so, what is her posterior probability to be a carrier? What is her chance of having an affected son? (9/27 worksheet)

Yes! Posterior probability of being a carrier is 1/4. Chance of having an affected son is 1/4*1/2*1/2 = 1/16

What are some effective patient-centered communication skills that can help you to form a constructive and collaborative therapeutic alliance with the patient?

[1] What do you think has caused your problem? [2] Why do you think it started when it did? [3] What do you think your sickness does to you? How does it work? [4] How severe is your sickness? Will it have a short or long course? [5] What kind of treatment do you think you should receive? [6] What are the most important results you hope to receive from this treatment? [7] What are the chief problems your sickness has caused foryou? [8] What do you fear most about your sickness? Then comes reconciling doctor and patient models

Describe three mechanisms which could account for deficiency of more than one enzyme in a single person.

a) A subunit may be part of several different multimers (e.g., $-subunit in Hex A and Hex B). b) Modification of multiple enzymes required before they function (e.g., holocarboxylase synthetase deficiency, I-cell disease) c) Lack of production of a vitamin or cofactor which is needed by multiple enzymes (e.g., biotin deficiency in biotinidase deficiency)

Describe the formation of the mitotic spindle and its relevant components.

a) Assembly requires at least 7 kinesins and dynein. b) Kinetochore microtubules have plus ends embedded in the kinetochore and minus ends in the spindle pole. c) Interpolar microtubules are long microtubules extending across the length of the spindle, but not necessarily associated with the spindle poles. d) Astral microtubules radiate from the spindle poles and help orient the spindle in relation to the cell cortex. e) The kinetochores of sister chromatids become attached to kinetochore fibers from opposing spindle poles.

What is the magnitude of the quality and safety problem?

a) Based on conservative estimates preventable adverse events are the 3rd to 5th leading cause of death, more prevalent than deaths from all accidental injuries and breast cancer. b) High risk, high reliability industries, such as nuclear power and commercial airlines, have developed methods to increase safety, with less than < 1/100K deaths. However, in healthcare, the risk of death is in an unsafe range of > 1/1,000 which is more akin to the risks of extreme sports such as bungee jumping.

Understand the electrophilic theory of chemical carcinogenesis. Identify 'direct' and 'indirect' carcinogens with clinical importance in human cancer. Discuss Benzo[a]pyrene and aflatoxin B1 as important indirect-acting carcinogens.

a) Direct-acting chemical carcinogens. A small number of carcinogens do not require metabolic conversion (referred to as 'metabolic activation') to become carcinogenic. Most are weak carcinogens but are clinically important because some are cancer chemotherapeutic drugs (e.g., alkylating agents) that have cured, controlled or delayed recurrence of certain types of cancer (leukemias, lymphomas, ovarian cancer) only to evoke later a second form of cancer, usually acute myeloid leukemia. These are called direct-acting carcinogens. Examples: nitrogen mustards, nitrosomethylurea, cyclophosphamide and benzyl chloride. b) Indirect-acting chemical carcinogens. Most chemical carcinogens require metabolic activation to an "ultimate carcinogen" before becoming active. Most of the known carcinogens are metabolized by the cytochrome P450-dependent mixed function mono-oxygenases. Chemicals requiring metabolic activation are known as indirect-acting carcinogens. The ultimate carcinogens are the electrophilic derivatives that actually initiate the neoplastic event. 1) Polycyclic aromatic hydrocarbons such as benzo[a]pyrene - a polycyclic aromatic hydrocarbon that is produced by incomplete combustion of organic materials. Present in chimney soot, grilled meats, auto exhaust, and cigarette smoke. These require metabolic activation and induce tumors in a wide variety of tissues. 3) Aflatoxin B1 - an illustrative example of an indirect-acting chemical carcinogen is aflatoxin B1, a naturally occurring agent produced by some strains of Aspergillus (a mold that grows on improperly stored grains and nuts). We will discuss in lecture the strong correlation between the dietary level of aflatoxin B1 and the incidence of hepatocellular carcinoma in some parts of Africa and the Far East. Aflatoxin B1 produces mutations in the p53 gene, and in regions where high dietary levels of aflatoxin B1 are consumed, in individuals who develop hepatocellular carcinoma, 90% or more of these mutations are a characteristic G:C to T:A transversion in serine codon 249. The significance of "signature mutation" as a carcinogenic 'footprint' will be discussed.

What type of mutation causes Kennedy disease (haploinsufficiency, dominant negative, gain of function, etc)? Huntington disease? Fragile-X syndrome?

a) Kennedy disease results from a gain of function mutation (expansion of the CAG repeat encoding a polyglutamine tract). b) Huntington disease is probably also caused by a gain of function mutation. Haploinsufficiency could not explain the same severity of disease in both heterozygotes and homozygotes. c) Fragile-X syndrome appears to result from haploinsufficiency.

A pair of twins is born; one with a 46,XY karyotype, and the other with a 47,XY, +21 karyotype. They are identical for all of the genetic markers tested. How could this be?

a) Mitotic non-disjunction (leading to mosaicism) followed by the twinning event b) Meiotic non-disjunction, followed by anaphase lag (leading to loss of one of the #21s) and then twinning at the two cell stage.

A girl with normal parents has hemophilia B (an X-linked recessive disorder). What are three possible explanations?

a) She's a genetic male (46,XY) with complete androgen insensitivity b) She has Turner syndrome (45,X) c) "Random" Lyonization (X-inactivation) has resulted in disproportionate inactivation of the normal X. d) She has a "balanced" X;autosome translocation. Typically in X;autosome translocations, the normal X is preferentially inactivated. If the hemophilia mutation is on the translocated X, it will be preferentially "expressed." In all of these cases the mother is presumed to be a carrier of the mutation.

Understand what a GWAS is

a. 260,000 - 474,000 SNPs capture all common SNPs in Phase I data set in Caucasians b. Genotyping arrays available for >1,000,000 SNPs c. 2007 four largeT2 diabetes mellitus GWAs i. Multiple variants appear in multiple studies ii. Not in same order of significance iii. Previously identified candidate genes show weak effects iv. All variants together account for less than 20% population attributable risk

Describe the major findings of the HAPMAP project

a. Characterize common genetic variation across genome in three major world populations b. Define linkage Disequilibrium (LD) pattern across the genome c. HapMap Phase I - Genotype common 1 variant every 5 kb across the genome in 269 DNA samples (MAF ≥ 0.05) d. HapMap Phase II - Genotype an additional 4.6 million SNPs i. Proxy SNPs 1. 20% of SNPs have >20 perfect proxies 2. 60% of SNPs have >5 perfect proxies 3. 20% of SNPs have no prefect proxies 4. Varies by population (YRI has fewer ii. Haplotype tagged SNPs (htSNPs) 1. A subset of SNPs which account for the majority of the genetic variation in a given genomic fragment. 2. Reduce redundancy of genotyping with minimal loss of information 3. Increase laboratory efficiency 4. Decrease number of statistical tests 5. Selection based on LD most efficient 6. Small set of very informative markers capture most information 7. Substantial number of SNPs have no proxies

Elicit the patient's story of her health problem and/or progress, exploring the clinical details and including psychosocial/emotional factors.

a. Practice using open-ended questions. b. Understand what constitutes a "history of present illness" (HPI) c. Practice eliciting the cardinal features of disease (OLDCARTS) d. Understand the concept of clinical reasoning, as it applies to the cardinal features

Explain the role of the following phases associated with laboratory testing: pre-analytical, analytical and post-analytical. Identify examples of commonly encountered errors in each phase.

a. Pre-analytical: quality (in) = quality (out) i. Patient variables that may affect test results ii. Blood-draw tubes - correct order and different tube types iii. Specimen rejection criteria iv. Common errors in specimen collection and processing b. Analytical i. Equipment malfunctions ii. Poor precision or calibration (bias) iii. Test interferences. c. Post-analytical i. Alarms and flags ii. Common errors in post-analysis • improper data entry • results assigned to incorrect patient • long turnaround-time (TAT) iii. Critical values

Practice completing the medical history

a. Understand what comprises a past medical history, family history and social history b. Be familiar with the review of systems

You obtain plama amino acid levels, which reveal a diagnostic abnormality. Based on this you recomend a second medication for the child. The medication will...

acts as a methyl donor for the remethylation of the abnormal amino acid

Identify the three key enzymes involved in nitrogen disposal from amino acid catabolism.

alanine aminotransferase, aspartate aminotransferase, glutamate dehydrogenase

Identify the sources of carbon skeletons for the non-essential amino acids.

alanine: pyruvate cysteine: homocysteine + serine aspartate: oxaloacetate glutamate: a-ketoglutarate glycine: serine asparagine: aspartate proline: cyclize glutamate glutamine: glutamate arginine: urea cycle serine: 3-phosphoglycerate; glycine tyrosine: phenylalanine

Identify the precursors for glucose synthesis.

amino acids from proteins (mainly alanine), lactate from red blood cells and muscle and glycerol released from triacylglycerols

Describe common second messengers

cAMP, Ca2+, diglycerol, 3'phosphorylated inositol lipids.

Identify different types of receptors

cell-surface vs. intracellular nucleus membrane: ion-channel-linked, g-protein-linked, enzyme-linked cytokine/hematopoietic growth factor receptors linked to non-receptor tyrosine kinases multimeric: T Cell or B Cell

Analyze class data from HRA to compute epidemiological statistics

done.

Where and in which conditions would you encounter dysplasia?

dysplasia occurs in tracheobronchial epithelium, uterine cervix, oral cavity, etc.; what causes hyperplasia and metaplasia can also contribute to the dysplastic process

Reticular fibers are a predominant component of

early wound healing.

Polymerase Chain Reaction (PCR)

enables researchers to produce millions of copies of a specific DNA sequence in approximately two hours. This automated process bypasses the need to use bacteria for amplifying DNA.

Define the difference between ex vivo and in vivo gene therapy treatments. Give an example of each.

ex vivo = genes introduced into patients' cells in vitro and then returned; gene transfer requires cell division; integrated into host genome, stable gene persists for life. in vivo = direct delivery; delivery into differentiated nondividing cells as well as dividing cells; episomal, unstable; treatment needs to be repeated

A patient presents with features suggestive of an unspecified genetic syndrome, many features (but not all) are consistent with Williams syndrome. The physician orders three tests: chromosome analysis, FISH for ELN and microarray testing. Are these orders appropriate?

extraneous - do not need to order both FISH and microarray. I would skip FISH.

Prepare for the online Health Risk Assessment (HRA) and workshop

fast!

Speculate on how epigenetics will impact disease diagnosis and treatment

help us understand concepts like imprinting that are relevant to disease mechanisms

Identify the different subtypes of necrosis.

i. Coagulative necrosis: most commonly encountered following severe acute cell injury from ischemia or due to exposure to toxic agents (chemicals/poisons/toxins). ii. Liquefaction necrosis: it is a form of coagulative necrosis the necrotic area is rapidly liquefied due to extensive lysis; most frequently seen in the brain after ischemic injury from arterial occlusion, severe cerebral trauma or bacterial infections of brain; grossly, the necrotic area is soft and the center becomes liquefied as a result of the release and activation of hydrolytic enzymes from lysosomes of infiltrating leukocytes; as necrotic tissue is digested, a cyst filled with cellular debris and fluid may be formed. iii. Caseous necrosis: commonly associated with foci of tuberculous infection in tissues, these are whitish gray, sharply demarcated from surrounding non necrotic tissue, soft, granular and friable reminiscent of dry cheese, hence the name caseous; slowly, the center of such lesions undergoes liquefaction; this form of necrosis has the characteristics of both coagulation and liquefaction. iv. Fat necrosis: almost exclusively found in adipose tissue contiguous to the pancreas and more rarely at distant sites. v. Gangrenous necrosis: this is not, strictly speaking, a different type of necrosis; however, since it is still used clinically to describe variants of coagulation necrosis, it merits mention: it is characteristically localized to the soft tissues of the lower limbs that have been compromised by protracted hypoxia and ischemia; where the extent of vascular occlusion is global, leukocytes cannot migrate to the areas of coagulation necrosis, and it is not digested and removed and becomes desiccated and mummified (dry gangrene); if overlying skin is devitalized, bacteria and/or leukocytes will enter into the area of necrosis, and extensive liquefaction may ensue (wet gangrene). vi. Tumor necrosis: cell death in tumors may be in the form of apoptosis and/or necrosis, Factors responsible: 1) tumor blood supply: hypoxic zones: "tumors outgrow their blood supply"; 2) abnormal production of pro-angiogenic factors in the tumor by tumor cells and infiltrating immune system cells; 3) apoptotic factors produced by dying tumor cells; 4) therapy leads to necrosis.

Describe ways that the clinical laboratory contributes to patient care.

i. detect disease or predisposition to disease ii. confirm or reject a diagnosis iii. establish prognosis iv. guide patient management v. monitor efficacy of therapy

Define paracrine and autocrine.

ii) paracrine action is when a cell produces a peptide (growth factor, chemokine, etc.), releases it into extracellular space, and then that peptide acts on adjacent cells (locally) possessing receptors that recognize that specific peptide (simply, the cell responds to the products generated by the neighboring cells). iii) autocrine action is when a particular cell produces a growth factor releasing the peptide into the extracellular space, and that released peptide acts on the same cell by interacting with specific receptors present on the cell's plasma membrane, i.e., the product that is released acts on the releasing cell (self-stimulatory).

Define genomic imprinting, and describe the changes that occur during development

imprinting: the differential expression of genes which is determined by the sex of the parent from whom the genes were inherited changes: *methylation/de-methylation of cytosines *acetylation/de-acetylation of histones *methylation/de-methylation of histones *interference RNAs

What applications are available for genetic testing? That is, explain the differences between testing used in hereditary breast cancer with testing used to predict recurrence in women with breast cancer.

in hereditary breast cancer, it has clinical utility - do we treat with preventive chemotherapy? what is the cancer risk? predict recurrence is useful and clinically valid, but it does not affect treatment, so it would not have clinical utility.

List the genomic locations and where trinucleotide repeats may occur

in the untranslated region, intronic or exonic

What might the cardinal features of a patient with dyspnea tell you about their disease?

it might give you an idea of the diagnosis.

Identify the different types of RNA and describe their functions.

mRNAs = code for proteins rRNAs = form the core of the ribosome and catalyze protein synthesis miRNAs = regulate gene expression tRNAs = serve as adaptors between mRNA and amino acids during protein synthesis Other small RNAs = used in RNA splicing, telomere maintenance, and many other processes

Describe maternal inheritance and how it differs from X-linked and autosomal dominant inheritance

maternal inheritance: 100% of children will inherit maternal DNA; 0% of children will inherit paternal DNA. X-linked & autosomal dominant are both mendelian; the father's genes matter in these cases.

Understand and discuss the medical, psychological and social factors that contribute to the patient's health status

medical: disease psychological: stress, homelife, work status social factors: community involvement

To recognize apical cell surface specializations at the LM and electron microscopic (EM) levels.

microvilli cilia stereocilia

To date all therapy protocols that have been approved deal with the alteration of somatic cells and do not result in a gene being added to the germ line. Yet in some ways this would be the ultimate cure. What are the possible dangers of using current methods to alter the germ line of individuals with crippling genetic diseases?

might cause unintentional harm; could be like sterilization - ethics issues. ethics issues with messing with babies before they're born - "slippery slope" to choosing eye color, etc.

Describe the fundamental principles of the molecular basis of cancer

o Non-lethal damage is essential for carcinogenesis o Tumors are monoclonal. Clonality can be assessed by the study of polymorphic X-linked markers o Four classes of normal genes are the principal targets of genetic damage: the growth-promoting oncogenes, the growth-inhibiting tumor suppressor genes, genes that regulate programmed cell death (apoptosis) and genes involved in DNA repair. Oncogenes are dominant genes. Tumor suppressor genes are recessive (both copies need to be lost for transformation); exception: haploinsufficiency o DNA repair genes have an indirect effect by influencing the ability of the organism to repair non-lethal damage. A propensity to mutations is called mutator phenotype o Carcinogenesis is a multistep process at both the phenotypic and the genetic levels.

Define key elements of the cell cycle and understand abnormalities of the cell cycle that are present in cancer cells

o Resting (non-dividing) cells are in the G0 phase of the cell cycle o The orderly progression of cells through the various phases of the cell cycle is dependent on cyclins, the cyclin-dependent kinases (CDKs) and their inhibitors o Cyclins are synthesized during specific phases of the cell cycle o CDKs are expressed all the time but in inactive form. They are activated by phosphorylation after binding to the cyclins o Cyclins D, E, A and B appear sequentially during the cell cycle o Cyclins are degraded through the ubiquitin-proteasome pathway o Cyclin D-CDK4 complex phosphorylates the RB protein. This phosphorylation is the molecular ON-OFF switch of the cell cycle. o The activity of the cyclin-CDK complexes is tightly controlled by the CDK inhibitors; the two main classes of CDK inhibitor are the Cip/Kip and the INK4/ARF families. o The two main checkpoints of the cell cycle are at the G1/S and the G2/M transition o At the G1/S checkpoint the cell cycle arrest is mediated through p53 by the cell-cycle inhibitor p21. At the G2/M the cell cycle arrest is mediated both by p53-dependent and independent mechanisms

List the essential alterations for malignant transformation

o Self-sufficiency in growth signals o Insensitivity to growth-inhibitory signals o Evasion of apoptosis o Defects in DNA repair o Limitless replicative potential o Sustained angiogenesis o Ability to invade and metastasize

OLDCARTS is classically applied to a chief concern of pain. Which off the "oldcarts" items can be applied to a patient with shortness of breath (dyspnea)?

onset, duration, characteristics, aggravating/alleviating, treatment, significance

Identify the conditions that lead to the Unfolded Protein Response and ER associated degradation.

oxidative stress, glucose deprivation, aberrant calcium regulation, viral infection. ERAD has been linked to ~60 human diseases, including obesity induced Type II diabetes, neurodegeneration, ischemia/reperfusion injury, cystic fibrosis, HIV.

Describe the curricular content and organization of the Health & Society Curriculum Element Group (CEG) for the Foundation module

personal health, population health, and global health

Define the determinants of health for Healthy People 2020

physical environment health services biology & genetics individual behavior social environment

Identify the major enzymes and protein components involved in DNA replication.

prepriming complex: specific DNA binding proteins that bind to the origin and to the resulting single DNA strands: unwinds the helix to initiate replication. 1. Type I DNA topoisomerases reversibly cut one strand, the intact strand is passed through the break and the topoisomerase relegates the cut strand relieving the supercoiling. 2. Type II DNA topoisomerases make transient breaks in both strands. In bacteria, this enzyme is called DNA gyrase. 1. The strand polymerizing in the direction of the moving replication fork is called the leading strand and is synthesized continuously. 2. The strand polymerizing in the direction away from the replication fork is made in small fragments (Okazaki fragments) near the replication fork. A specific RNA polymerase called primase synthesizes a short ~10 nucleotide long stretch of RNA that is complementary to the parent strand. The addition of primase to the prepriming complex that forms the replication bubble creates the primosome. 1. In prokaryotes, priming is carried out by DnaG. 2. In eukaryotes, priming is carried out by a subunit of DNA Pol α (alpha). DNA is synthesized in the 5' to 3' direction by DNA polymerases. 1. In prokaryotes, chain elongation is catalyzed by DNA Polymerase III on both strands. The ends of the DNA are joined by enzymes called DNA ligases. In eukaryotes, Pol δ displaces the RNA primer as it elongates the preceding Okazaki fragment, creating a RNA and DNA flap. The flap is removed by Flap Endonuclease I (FEN1) and the free ends ligated by DNA ligase. In germ cells, stem cells and cancer cells an enzyme complex called telomerase remains active. Transposons that utilize an RNA intermediate are called retrotransposons

Identify a personal health behavior that you would like to increase or reduce

sleep more!

Compare and contrast substrate accumulation, activation of alternate pathways, and product deficiency

substrate accumulation: substrate cannot be converted by enzyme so it accumulates in cell. activation of alternate pathways: to use up the accumulating substrate, alternate pathways are used to work around malfunctioning enzyme. these often have entirely different products. product deficiency is another result of a malfunctioning enzyme. since the substrate cannot be converted into the usual product, it has a lower concentration than usual.

What is Barrett's esophagus? What is the clinical relevance?

the stratified squamous epithelium of the esophagus is replaced by intestinal columnar epithelium. Barrett's esophagus is of great clinical significance since 1 in 10 individuals with severe chronic heartburn (reflux esophagitis -- reflux of gastric acid into the lower third of the esophagus) develop this condition (glandular metaplasia of the lower third of the esophagus), and in 10 years, 1 in 10 of these with Barrett's esophagus patients develop adenocarcinomas of the esophagus.

Define the contemporary definition of epigenetics

the study of mitotically and/or meiotically heritable changes in gene function that cannot be explained by changes in DNA sequence. A cellular 'memory'.

What are the hallmarks of a neoplastic (cancer) cell and how do signaling abnormalties result in cancer?

uncontrolled growth: Acquisition of self-sufficiency in growth signals, leading to unchecked growth. Loss of sensitivity to anti-growth signals, also leading to unchecked growth. Loss of capacity for apoptosis, in order to allow growth despite genetic errors and external anti-growth signals.

Understand the global burden of communicable and non-communicable diseases

we spend a lot of resources trying to solve problems of disease globally.

Define how a test result is determined to be within normal limits or abnormal.

within 2 sd's from mean on either side.

Describe the concept of cellular aging and the cellular responses to telomerase shortening

• After a fixed number of divisions normal cells enter replicative senescence • Telomeres are specialized structures at the end of chromosomes, that are shortened after each cell division. Telomere shortening acts like a clock that counts cell divisions. • In germ cells telomerase presents telomere shortening. • In cancer cells telomerase is reactivated, maintaining their replicative potential

Review how angiogenesis is essential for tumor growth and establishment of metastases

• Angiogenesis is essential for supplying nutrients to growing tumors • Neovascularization also stimulates tumor growth by secreting growth factors such as PDGF • The tumor blood vessels differ from normal vessels in that they are tortuous and leaky (except in cases of vasculogenic mimicry) • Angiogenic switch is essential for tumor growth and involves increased production of angiogenic factors or loss of angiogenic inhibitors • Much attention is recently focused on the use of angiogenesis inhibitors against human tumors (e.g., endostatin)

Describe a patient's general appearance in specific terms.

• Apparent state of health-(i.e. frail, vigorous, ill, feeble) • Level of consciousness-awake, alert, responsive • Signs of distress • Height and weight • Dress, grooming and personal hygiene • Posture, gait and involuntary motor activity

Locate the radial pulse, and accurately determine the pulse rate.

• Compress the radial artery with your index and middle fingers. • Note whether the pulse is regular or irregular. • Count the pulse for 15 seconds and multiply by 4.

Understand the basic concepts of grading versus staging of tumors.

• Grading of cancer depicts the degree of histologic differentiation. • Staging of cancer is based on the extent of tumor spread - size of the primary tumor, lymph node involvement and distant metastatic spread are taken into consideration in the staging of a given cancer in a particular patient.

Determine blood pressure, identifying the Korotkoff sounds and recording blood pressures; compare readings with other students and with the preceptor.

• Inflate the cuff 20-30 mmHg above the estimated systolic pressure. • Release the pressure slowly at 2-3 mm Hg per second. • Evaluate for Korotkoff sounds, which are low-pitched sounds originating in the vessel that are related to turbulence produced by partially occluding an artery with a blood pressure cuff. • The systolic pressure is the point at which the initial tapping sounds are heard. • Continue to lower the pressure until the sounds muffle and disappear. The disappearance point is the diastolic pressure. • Record the blood pressure as systolic over diastolic.

Discuss the definitions of initiation, promotion and progression and the importance of these processes in understanding cell transformation and tumorigenesis.

• Initiation - an event characterized by irreversible damage to DNA in a critical target gene. • Promotion is the process whereby initiated cells are selected for and expanded up into a benign tumor or a benign preneoplastic condition. • Progression: The process by which cells in a benign neoplasm or benign condition like dysplasia progress to malignant cells (i.e., with invasive potential).

Understand the importance of the mechanisms of tumor invasion and metastasis

• Invasion and metastasis are biologic hallmarks of malignancy • Invasion and metastasis are a major cause of cancer-related morbidity and mortality • The tumor cells need to possess the right combination of gene products to complete all the steps involved in metastasis; metastasis signature • The metastatic cascade can be divided into two phases: o Invasion of the extracellular matrix and vascular dissemination and homing of tumor cells • Invasion of the extracellular matrix (ECM) is an active process that involves the following steps: o Detachment of tumor cells from each other o Attachment to matrix components o Degradation of ECM o Migration of tumor cells • Receptor-mediated attachment of tumor cells to laminin and fibronectin is important for invasion and metastasis • Proteases (such as metalloproteinases) are very important for the metastatic process • Within the circulation the tumor cells have to escape the immune system. They tend to aggregate and form tumor-platelet aggregates • At the distant site the tumor cells have to adhere to the endothelium and go through the basement membrane. Adhesion molecules and proteolytic enzymes are once again important. The CD44 adhesion molecule plays an important role. • The specific sites of metastatic spread are determined in part by the anatomic location as well as the tissue environment ("favorable or unfavorable soil") for the growth of the metastatic foci. A number of cytokines and chemokines play a major role. • Several genes have been proposed as suppressor of metastasis genes, (primary example: NM23) but no single "metastasis gene" has been identified.

Understand the physiologic importance of the different DNA repair mechanisms and list examples of how their disruption may lead to cancer development

• Normal cells constantly repair DNA damage and prevent mutations on critical genes that regulate cell growth, proliferation and apoptosis • DNA repair mechanisms are critical in maintaining the integrity of the human genome • Individuals born with defects of their DNA repair genes are at great increased risk of developing cancer; genomic instability syndromes • Important types of defects of DNA repair systems are as follows: o The mismatch repair o The nucleotide excision repair o The recombination repair • The hereditary nonpolyposis cancer syndrome (HNPCC), a condition of familial cancers of the colon (cecum and proximal rectum) results from defects in DNA mismatch repair genes (the genome "spell checkers") • Cells with mismatch repair defects are thought to have the replication error phenotype. The hallmark of defective mismatch repair is the microsatellite instability. • The xeroderma pigmentosum, a condition prone to the development of skin cancer, results from defects of the nucleotide excision repair (NER) pathway • A group of autosomal recessive disorders such as the ataxia-telangiectasia syndrome (caused by a mutation of the ATM gene), the Bloom syndrome and the Fanconi anemia result from defects in DNA repair by homologous recombination • The BRCA-1 gene (on chromosome 17q21) and BRCA2 gene (on chromosome 13q12-13) are two tumor suppressor genes associated with the development of breast cancer and ovarian cancer. These patients have a 60-85% lifetime risk for the development of breast cancer and a 15-40% lifetime risk for the development of ovarian cancer. Both genes participate in the process of homologous recombination of DNA repair.

Understand the concept of oncogenes, tumor suppressor genes and apoptosis-regulating genes. Be able to list important members of these categories of genes and their associations with human malignancies

• Oncogenes o Oncogenes are genes that promote autonomous cell growth in cancer cells; protooncogenes are their normal cellular counterparts. o Protooncogenes were first discovered through the study of acute transforming retroviruses that contain the viral oncogenes (v-onc) o Concept of insertional mutagenesis: viral DNA is inserted near a protooncogene inducing a change in this cellular gene converting it into a cellular oncogene (c-onc) o Protooncogenes participate in cellular growth, proliferation and apoptosis. Oncogenes more or less are involved in the same function but are independent of the normal cell control mechanisms o Oncogenes can function as growth factors, as growth factor receptors, as signal transducing proteins, as nuclear regulatory proteins and cell-cyle regulators and as suppressors of apoptosis o The RET protooncogene is associated with the dominantly inherited MEN type IIA and IIB, familial medullary thyroid carcinoma and Hirschsprung disease o Overexpression of protooncogenes is another mechanism of abnormal function Examples: EGFR overexpression in lung tumors, glioblastomas and head and neck tumors ERB-B2 (HER2/neu) overexpression in breast cancer Note: Innovative therapies directed against specific alterations in the cancer cells are called "targeted therapies" Examples: 1) HERCEPTIN against breast tumors that overexpress HER-2/neu 2) Targeted blockade of receptor tyrosine kinase activity of c-kit in GI stromal tumors o Mutation of the RAS oncogene is the single most common abnormality of dominant oncogenes in human tumors. These mutations most commonly involve codons 12, 59 or 61. 90% of pancreatic adenocarcinomas have RAS mutations. In general carcinomas have KRAS, bladder tumors have HRAS and hematopoietic neoplasms have NRAS mutations. Efforts continue to develop anti-RAS modalities of targeted therapy o Another highly effective targeted therapy is the use of imatinib mesylate in chronic myeloid leukemia (CML). It targets specifically the fusion protein BCR-ABL tyrosine kinase. o Transcription factors contain specific amino acid sequences or motifs that allow them to bind DNA at specific locations. Mutations affecting these motifs are associated with malignant transformation. o The MYC oncogene is also commonly found in tumors. Examples: Dysregulations of MYC expression in Burkitt lymphoma, Amplification of MYC in breast, colon, lung carcinomas N-MYC amplification in neuroblastomas • Tumor suppressor genes o Failure of growth inhibition is one of the fundamental alterations in carcinogenesis o Proteins that regulate growth inhibition are products of tumor suppressor genes o The concept of the "two-hit" hypothesis proposed by Knudson explains the loss of function of tumor suppressor genes in cancer. In hereditary cases the first genetic change ("first hit") is inherited from an affected parent. The second mutation ("second hit") happens subsequently in one of the cells that already carries the first mutation o Because both copies of a normal tumor suppressor gene need to be lost for cancer to develop, these genes are recessive cancer genes o A classic paradigm of the two hit hypothesis is the development of retinoblastoma. The RB gene is located on chromosome 13q14. Germ line loss or mutation of the RB gene predispose to the development of retinoblastoma and less frequently osteosarcomas o The importance of RB lies in its enforcement of G1 or the gap between mitosis (M) and DNA replication. o Other examples: WT-1 gene in Wilms tumor on chromosome 11, vonHippel Lindau (VHL) gene in clear cell renal carcinoma o Studies of LOH (loss of heterozygosity) are very helpful in localizing tumor suppressor genes o The emerging paradigm is that loss of normal cell cycle control is central to the malignant process and at least 4 regulators of the cell cycle (cyclin D, CDK4, RB and p16INK4a), are dysregulated in most human tumors o The P53 gene is the "guardian of the genome". It is located on chromosome 17p13.1 and is mutated in >50% of human tumors. o Individuals may inherit a mutated p53 allele (as in Li-Fraumeni syndrome) or both alleles may accumulate mutations as in sporadic tumors. o The p53 protein functions as a critical gatekeeper against the formation of cancer. It acts as a "molecular policeman". Its activity is cell-cycle arrest and initiation of apoptosis in response to DNA damage. P53 is also involved in the regulation of apoptosis. o Radiation and chemotherapy act by inducing apoptosis. Tumors that have intact p53 respond very well to these modalities (e.g., leukemias, testicular tumors). Tumors with mutated p53 (e.g., lung, colon) are relatively resistant. o The APC/β-catenin pathway is also very important in carcinogenesis. Individuals with mutated allele of the APC gene (on chromosome 5q21) develop thousands of adenomatous polyps in their colon at a very early age and one or more of these polyps subsequently become malignant. Colonic tumors also develop in individuals with mutations in the β-catenin gene. o Examples of other tumor suppressor genes The INK4a/ARF locus: association with familial melanomas The TGF-β pathway: association with colonic carcinoma in patients with HNPCC The NF-1 gene in neurofibromatosis type 1. The neurofibromin protein is a member of the GTP-ase activating proteins. The NF-2 gene in neurofibromatosis type 2. The merlin protein is involved in establishing stable cell-to-cell junctions. The VHL gene on chromosome 3: association with familial and sporadic renal cell cancers The PTEN on chromosome 10q23: association with endometrial carcinomas and glioblastomas The WT-1 gene on chromosome 11p13 in Wilms tumor (the WT-2 gene is associated with Beckwith-Wideman syndrome) The DCC gene on chromosome 18q21, in colon and renal carcinomas The Cadherin family of genes in breast, esophagus, colon, ovarian cancer • Regulation of apoptosis o Cell survival is the end result of the effects of genes that promote and inhibit apoptosis o BCL-2 is the prototype anti-apoptotic gene. It is overexpressed in B-cell follicular lymphomas. 85% of there lymphomas carry the characteristic translocation t(14;18) (q32;q21), in which the BCL-2 gene from 18q21 is translocated to the immunoglobulin heavy-chain locus on 14q32 o P53 and MYC are also involved in apoptosis; p53 increases the expression of BAX a gene promoting apoptosis

Determine the location of the brachial pulse, and proper placement of the BP cuff bladder and stethoscope.

• Place the blood pressure cuff above antecubital fossa (approximately 2.5 cm above the antecubital fold). • Palpate for the brachial artery. • Place the bell of the stethoscope over the artery (the diaphragm is often used, but the bell helps to distinguish the low pitched Korotkoff sounds)

Observe and record the respiratory rate.

• Respirations are best counted immediately after taking the patient's pulse. Direct your eyes to the chest and evaluate respirations while holding the wrist. The patient is unaware that you are no longer taking the pulse and will not breathe differently because of observation. • Counting the number of respirations in a 30-second period and multiplying the number by 2 yields the breath per minute.

Know how to measure waist circumference accurately.

• Stand to the patient's side (not in front of the patient) • Place a measuring tape in a horizontal plane around the abdomen at the level of the iliac crest • Ensure that the tape is snug but does not compress the skin • Ensure that the tape is parallel to the floor • The measurement is made at the end of a normal expiration

Understand the different mechanisms of dysregulation of cancer associated genes

• The genetic damage in cancer cells may be large enough to detect in a karyotype • Karyotypic abnormalities may involve changes in the chromosome number (aneuploidy) or chromosomal translocations (e.g., ABL gene in CML, C-MYC in Burkitt's lymphoma) and inversions • Another is the production of fusion genes by reciprocal translocation between 2 separate genes (e.g., BCR-ABL in CML, EWS-FL1 in Ewing's tumor) • Gene amplification is another mechanism of oncogene activation that results in overexpression of the gene products. • Two patterns of amplification are seen: double minutes (dms) and homologous staining regions (HSR) • Examples of gene amplification: o N-MYC in neuroblastoma (associated with poor prognosis) o ERB B2 in breast cancer • Tumor suppressor genes may also be inactivated not by structural changes (e.g., mutations) but by hypermethylation (e.g., BRCA1, in breast cancer, VHL in renal cell carcinomas) • Methylation is also involved in genomic imprinting

Understand the concept of multistep carcinogenesis and discuss the well described example of the colorectal adenoma-carcinoma sequence

• The study of oncogenes and tumor suppressor genes provided the molecular framework for the concept of multistep carcinogenesis that was initially proposed by cancer epidemiologists • No single oncogene is sufficient for malignant transformation but cells can be transformed by a combination of oncogenes. • Human cancers harbor multiple genetic alterations involving activation of multiple oncogenes and the loss of two or more of tumor suppressor genes • The best example of a molecular model for multistep carcinogenesis is the adenoma-carcinoma sequence of colorectal cancers. • Oncogenes and tumor suppressor genes are known as "gatekeeper genes" • Genes that do not directly control tumor growth but affect genomic stability are called "caretaker genes" (e.g., DNA repair genes) • Mutations in either category of genes increases the risk for development of malignancy; however the risk is higher with defects of a gatekeeper gene • Cells that are unusually susceptible to additional mutations are thought to have a "mutator phenotype"