BPM 1 Spring 2019
FTM Module - Lecture and DLA
Objectives
Term 1 Professionalism Objectives
1. Students will learn and practice communication skills for giving and receiving feedback.
2. Using role played interactions, students will identify and analyze value-laden conflicts.
3. Students will discuss benefits and challenges related to team and group work during Basic Sciences.
4. Students will reflect on the use of donor bodies in medical education and medical history.
5. Students will explore the balance between wellness, studying, and good grades.
Week 1
DLA Cellular Organization
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Lecture 1 Cellular Organization I
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Lecture 2 Cellular Organization II
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DLA Cell Cycle
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January 21st - January 25th
Describe the ultrastructure of the cell membrane.
List the three major classes of membrane lipids.
Describe the structure and function of phospholipids in the plasma membrane.
Describe the structure and function of cholesterol in the plasma membrane.
Describe the structure and function of glycolipids in the plasma membrane.
List the two major classes of membrane proteins.
Describe the categories of integral membrane proteins.
Describe the freeze fracture technique to visualize integral membrane proteins.
Describe the structure and function of the glycocalyx.
Explain the fluid mosaic model of membrane structure.
List the two major types of vesicular transport.
Describe the precise targeting of vesicles within the cell.
List and describe the three different mechanisms of endocytosis.
Describe the role of endosomes in vesicular transport.
List and describe the four pathways for processing internalized ligand-receptor complexes.
List and describe the two general pathways of exocytosis.
List the domains of cellular life.
Identify, list and describe the structure & function of the nucleus, ribosomes, endoplasmic reticulum (RER & SER), Golgi
apparatus, lysosome, peroxisome and mitochondria.
Identify & describe the structure and function of the nucleolus, nuclear envelope and nuclear pore complex.
Describe the organization & structure of chromatin.
Distinguish euchromatin and heterochromatin in a nucleus.
Predict cellular activity based on the chromatin structure.
Describe the bi-directional vesicle transport between the endoplasmic reticulum and Golgi apparatus.
Describe protein trafficking for lysosomes, secretion, plasma membrane, nucleus, mitochondria, cytosol and peroxisomes.
List and describe the three cellular pathways to lysosomal degradation.
Discuss the basic concepts of peroxisomal disorders and Zellweger syndrome.
Discuss the basic concepts of lysosomal storage diseases and Tay-Sachs disease.
Describe the process of autophagy.
Describe the structure and function of the proteasome.
List the three major types of protein filaments that form the cytoskeleton.
Identify & describe the structure, function and assembly of microtubules, intermediate filaments and microfilaments.
Discuss the compounds that affect microtubules.
Discuss the compounds that affect microfilaments.
Describe the structure and function of the centrosome.
Identify & describe the structure and function of primary cilia, motile cilia and flagella.
List and describe the molecular motor proteins associated with microfilaments and microtubules.
Describe role of the cytoskeleton in intracellular transport and cellular motility.
Describe cell motility across a substrate.
Describe the three types of membrane protrusion structures.
Describe the role of actin polymerization in membrane protrusion and motility.
Describe the types of intracellular inclusions.
List and describe the sequence of events occurring in interphase.
List and describe the sequence of events occurring in mitosis.
Identify & describe the phases of mitosis.
Describe the structure and function of the centromere, kinetochore, centrosome and mitotic spindle.
List and describe the sequence of events occurring in meiosis.
List and describe the 5 stages of prophase I in meiosis I.
List and describe the two events in meiosis that increase genetic diversity.
DLA Cell Cycle Regulation
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Lecture 3 Homeostasis
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DLA Membrane and Gas Transport
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Describe the role of cyclins and cyclin-dependent kinases in cell cycle regulation.
Describe the role of pRB, p53 and CDC25 in cell cycle regulation.
List and describe the checkpoints in cell cycle regulation.
Describe the role of the anaphase-promoting complex in mitosis and cell cycle regulation.
Define proto-oncogene, oncogene and tumor suppressor gene.
Describe the correlation between cell cycle control and cancer.
Describe the role of the retinoblastoma (Rb) and p53 tumor suppressor genes in the cell cycle and cancer.
Explain the role of telomerase in cell senescence and tumor growth.
Explain how abnormal cell division can result in clinical syndromes.
Understand the general concepts of homeostasis and the principles of positive and negative feedback in physiological
systems.
List the typical values and normal ranges for plasma Na+, K+, H+ (pH), HCO3-, Cl-, Ca+2, and glucose, and the typical
intracellular pH and concentrations of Na+, K+, Cl-, Ca+2, and HCO3.
Define the term “steady state” and differentiate it from “equilibrium.”
Contrast the following units used to describe concentration: mM, mEq/l, mg/dl, mg%.
Differentiate between the terms osmolarity and osmolality. List the typical value and normal range for plasma osmolality.
Describe the composition of a cell membrane. Diagram its cross section, and explain how the distribution of phospholipids
and proteins influences the membrane permeability of ions, hydrophilic and hydrophobic compounds.
Differentiate the following terms based on the source of energy driving the process and the molecular pathway for: simple
diffusion, facilitated diffusion, secondary active transport, and primary active transport.
Describe the linear relationship between forces and flows (Ohm’s Law, Fick’s Law of diffusion, and the law of hydrodynamic
flow).
Write Fick’s Law of diffusion, and explain how changes in the concentration gradient, surface area, time, and distance will
influence the diffusional movement of a compound.
Based on the principle of ionic attraction, explain how a potential difference across a membrane will influence the
distribution of a cation and an anion.
Describe how transport rates of certain molecules and ions are accelerated by specific membrane transport proteins
(“transporter” and
“channel” molecules).
Describe how energy from ATP hydrolysis is used to transport ions such as Na+, K+, Ca+2, and H+ against their
electrochemical differences (e.g., via the
Na+ pump, sarcoplasmic reticulum Ca+2 pump, and gastric H+ pump).
Explain how energy from the Na+ and K+ electrochemical gradients across the plasma membrane can be used to drive the net
“uphill”
(against a gradient) movement of other solutes (e.g., Na+/glucose co-transport; Na+/Ca+2 exchange or counter-transport).
Describe the mechanisms of endocytosis and exocytosis.
Contrast the gating of ion selective channels by extracellular ligands, intracellular ligands, stretch, and voltage.
Describe the functional significance of polarized distribution of various transport proteins to the apical or the basolateral cell
membrane.
Explain Dalton’s Law and how percentages of a gas within a gas mixture are used to measure total pressure contribution.
Explain Henry’s Law and the factors that determine the amount of gas that will dissolve into liquid.
Using a cell membrane as an example, define reflection coefficient and partition coefficient, and explain how the relative
permeability of a cell to water and solutes will generate an osmotic pressure. Contrast the osmotic pressure generated across
a cell membrane by a solution of particles that freely cross the membrane with that of a solution with the same osmolality,
but particles that cannot cross the cell membrane.
Draw an epithelium, labeling the tight junctions, the apical membrane, and the basolateral membrane. Trace the movement
of a compound that
travels across an epithelium by a transcellular pathway and a compound that travels via a paracellular pathway.
Explain the role of the “tight” junctions in leaky and tight epithelia.
DLA Structure and Function of Lipids
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DLA Membrane Structure and Transport
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Lecture 4 Tonicity and Osmolarity
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Lecture 5 Resting Membrane Potential
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Review the grouping of lipids (Fatty acids, triacylglycerols, phospholipids, sphingolipids, steroids)
Discuss the structure and the biomedical importance of cholesterol
Describe fatty acid structure and discuss the melting points related to chain length and desaturation and relate its
significance to fluidity of the cell membrane
Discuss the biological importance of dietary essential fatty acids and describe in detail the structures of linoleic acid (ω-6)
and a-linolenic acid (ω-3)
Discuss the grouping of fatty acids into the ω-6 and ω-3 families and describe in general the synthesis of arachidonic acid and
of docosahexaenoic acid (DHA)
Describe the structures and functions of triacylglycerols.
Distinguish between phospholipids (Sphingophospholipid and glycerophospholipids) and glycolipids with examples for each
Classify complex lipids: Phospholipids which can be further classified based on the alcohol as Sphingophospholipid (Eg:
Sphingomyelin), Glycerophospholipids (Eg: Phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine,
phosphatidylinositol, cardiolipin), Glycolipids (or Sphingoglycolipids or Glycosphingolipids) – Contain a carbohydrate group:
Examples: Cerebrosides, Globosides, Gangliosides and sulfatides
Indicate the composition and functions of: Glycerophospholipids: Phosphatidylcholine, phosphatidylethanolamine,
plasmalogens, phosphatidylserine, phosphatidylinositol, cardiolipin, Sphingophospholipid: Sphingomyelin, Glycolipids (or
Sphingoglycolipids or Glycosphingolipids): Cerebrosides, globosides and gangliosides
Discuss role of lung surfactant (Dipalmitoyl phosphatidylcholine/ DPPC) in respiratory distress syndrome
Describe the fluid mosaic model for membrane structure.
Discuss in general complex lipid (phospholipids and glycolipids) composition of the plasma membrane.
Discuss the function of cholesterol in the plasma membrane.
Discuss the factors involved in regulating membrane fluidity.
Differentiate between active and passive transport systems based on energy requirement and movement along the
concentration gradient.
Discuss facilitated diffusion using the families of the glucose transporters GLUT 1-5 as examples and indicate their main
locations and characteristics.
Describe the clinical features of hereditary GLUT-1 deficiency.
Distinguish between primary active transport (Na+/K+ -ATPase) and secondary active transport (SGLT).
Explain the role of ABC transporters. Describe the CFTR channel.
Predict the effects of CFTR mutations in the lung epithelial cells and in the pancreas. Identify lab tests used for diagnosis of
cystic fibrosis.
Differentiate between the terms osmolarity and tonicity.
Describe the role of water channels (aquaporins) in facilitating the movement of water across biological membranes.
Understand how regulation of the concentrations of K+, Cl-, and other Na+ solutes influence cell volume.
Understand that movement of water is driven by solute movement.
Understand that the difference in free energy of a solute or solvent between two components can have chemical, electrical
and/or hydrostatic pressure components. At equilibrium, for a given component, the free energy difference between the two
compartments is zero.
Based on the principle of ionic attraction, explain how a potential difference across a membrane will influence the
distribution of a cation and an anion.
Write the Nernst equation and indicate how this equation accounts for both the chemical and electrical driving forces that act
on an ion. Explain the effects of altering the intracellular or extracellular Na+, K+, Cl-, or Ca2+ concentration on the equilibrium
potential for that ion.
Based on the Nernst equilibrium potential, predict the direction that an ion will take (follow) when the membrane potential
a) is at its equilibrium potential, b) is higher than the equilibrium potential, or c) is less than the equilibrium potential. List
values in a typical non-excitable cell for the membrane potential, for E Na , E K , E Cl , and E Ca .
Define the concepts of electrochemical equilibrium and equilibrium potential and give internal and external ion
concentrations. Be able to calculate an equilibrium potential for that ion using the Nernst equation. Contrast the difference in
E K (the Nernst potential for K+) caused by a 5 mEq/l increase in extracellular K+ with the change in E Na (the Nernst potential
for Na+) caused by a 5 mEq/l increase in extracellular Na+.
Describe the normal distribution of Na+, K+, and Cl- across the cell membrane, and using either the Goldman-Hodgkin-Katz
chord conductance equation explain how the relative permeabilities of these ions create a resting membrane potential. Given
an increase or decrease in the permeability of K+, Na+, or Cl-, predict how the membrane potential would change. (Not
required to calculate on exams)
Lecture 6 Action Potentials
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DLA Early Embryology
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Lecture 7 Apoptosis and Necrosis
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DLA Epithelium
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Define the following properties of ion channels: gating, activation, and inactivation.
Contrast the gating of ion selective channels by extracellular ligands, intracellular ligands, stretch, and voltage.
Know the properties of voltage-gated Na+, K+, and Ca2+ channels, and understand that voltage influences their gating,
activation, and inactivation.
Understand how the activity of voltage-gated Na+, K+, and Ca2+ channels generates an action potential and the roles of those
channels in each phase (depolarization, overshoot, repolarization, hyperpolarization) of the action potential.
Describe ionic basis of an action potential.
Draw a typical action potential and explain why afterhyperpolarization coincides with the greatest fractional K conductance
but not the greatest absolute K conductance.
Using the Nernst equation and knowledge of sodium channel voltage dependent gating mechanisms (activation and
inactivation gates), contrast the mechanisms leading to weakness and paralysis due to hypo- and hyper-kalemia.
Draw a graph that shows how the voltage sensitivity of the voltage gated sodium channel changes with extracellular calcium
concentration.
Contrast the role that chronic depolarization (e.g. with hyperkalemia) plays in the activation of the K and Na conductances
versus rapid depolarization (graded potential towards threshold).
Briefly describe the process from fertilization to the formation of the blastocyst, paying attention to the location and
timeframe of each event
Describe the location and process of implantation of the blastocyst.
Describe the sequence of events that leads to development of the amniotic cavity, bilaminar embryo, primitive umbilical
vesicle (yolk sac), extraembryonic mesoderm
Describe the formation of the three germ layers - gastrulation.
Describe the development of the notochord and its role in induction of the neural plate.
Describe the fate of the intraembryonic mesoderm, including the development of the somites and intraembryonic coelom.
Describe the folding of the embryo, paying particular attention to the sequence and timing at which folding occurs.
Describe the embryology and clinical presentation of sacrococcygeal teratoma
Define the terms neoplasm, benign, malignant & metastasis.
Describe the classification of cancer cells including carcinoma, sarcoma and leukemia.
Discuss the hallmarks of cancer.
Describe tumor growth and progression.
Define the terms “primary tumor” and “metastases” (secondary tumors).
List the main modes for spread of malignant neoplasms.
Describe karyotyping and cytogenetic studies and explain their clinical significance.
Describe fluorescent in situ hybridization (FISH)
Compare and contrast the morphological and biochemical features of necrosis vs. apoptosis.
Describe the intrinsic apoptosis pathway.
Describe the extrinsic apoptosis pathway.
Describe the role of caspases in apoptosis.
List examples of physiological processes involving apoptosis.
Discuss methods to assess necrosis and apoptosis.
List and describe the four basic tissue types.
Define epithelium.
Describe the structural and functional characteristics that distinguish epithelial tissues from the three other basic tissues.
Describe the classification of epithelial tissue.
Identify & describe the structure, function and localization of each type of epithelia.
Identify & describe the structure, function and localization of cilia.
Identify & describe the structure and function of the basal body.
Describe the terminal web.
Identify & describe the structure, function and localization of microvilli.
Identify & describe the structure, function and localization of stereocilia.
Discuss the basic concepts of immotile cilia syndromes and Kartagener’s syndrome.
Describe the histogenesis of the four basic tissue types.
Lecture 8 Epithelium and Glands
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SOM.1ai.BPM1.1.FTM.3.HCB.BT.0320
DLA Structure and Function of Nucleic
Acids
DLA DNA Packaging
Lecture 9 DNA Replication
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.1
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.2
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.3
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.4
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.5
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.6
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.7
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.8
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.9
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.10
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.11
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.12
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.9.13
SOM.1ai.BPM1.1.FTM.4.BCHM.MB.9.14
Identify & describe the structure, function and localization of zonula occludens.
Identify & describe the structure, function and localization of zonula adherens.
Identify & describe the structure, function and localization of gap junctions.
Identify & describe the structure, function and localization of desmosomes,
Describe the terminal bar.
Identify & describe the structure and function of lateral digitations.
Identify & describe the structure, function and localization of focal adhesions.
Identify & describe the structure, function and localization of hemidesmosomes.
Identify & describe the structure and function of basal infoldings.
Describe the structure of the basement membrane.
Describe the structure and function of the basal lamina.
Compare and contrast basement membrane vs. basal lamina vs external lamina.
Compare and contrast exocrine vs. endocrine glands.
List and describe the three modes of secretion in exocrine glands.
Describe the classification of multicellular exocrine glands.
Identify & describe serous glands.
Identify & describe mucous glands.
Identify & describe mixed glands.
Describe the histology of a compound salivary gland.
Identify parotid, submandibular and sublingual salivary glands.
Distinguish between purines, pyrimidines; ribonucleosides, deoxyribonucleosides; ribonucleotides and deoxyribonucleotides.
Describe the phosphodiester bond
List and describe the important features of the Watson-Crick DNA double helix (complementary, antiparallel, and forces
stabilizing the helix).
Discuss some of the physicochemical properties of DNA
Describe the basic structures and roles of the major classes of RNA (mRNA, tRNA, rRNA, snRNA, miRNA)
Predict the sequence of the complementary strand if the sequence of one of the DNA strands is provided.
Analyze the nucleotide composition of double stranded DNA using the Chargaff’s rule
Define the term supercoiling
Differentiate between a supercoiled and a relaxed molecule.
State the reasons why supercoiling of DNA molecules is important.
Compare and contrast DNA packaging in prokaryotes and eukaryotes.
Describe the action of DNA gyrase.
List the antibiotic drugs that interfere with DNA gyrase.
Describe the structure of chromatin and histone proteins.
Explain how dsDNA and histones associate to form the nucleosome.
Describe the different structural conformations of DNA packaging in eukaryotes (10 nm
Fiber , 30 nm fiber and metaphase chromosomes).
Describe how histone modification can influence transcriptional activity
Describe semi-conservation replication of DNA
Compare and contrast the similarities and differences between DNA Pol I and DNA Pol III of E. coli
Describe how DNA is synthesized from its 5’ to 3’ end
Explain the significance of the origin of replication
Explain the problems associated with unwinding of the DNA double helix
Describe the role of helicase enzymes in unwinding DNA prior to its replication
Describe the role of single-strand binding protein & topoisomerases in DNA replication
Outline the order of events from RNA priming to completed DNA during replication in E.coli.
Distinguish between synthesis of leading and lagging strands of DNA. Identify the significance of DNA ligase in lagging strand
synthesis
Analyze the significance of the various proteins and enzymes required for replication. Predict the effects of mutations of
these proteins and enzymes on DNA replication
Evaluate the proofreading activity of DNA polymerase
Differentiate between DNA replication in eukaryotes and prokaryotes
Describe the role of telomeres and telomerase in eukaryotic DNA replication
Outline the mechanisms of action of drugs that interfere with DNA replication
Week 2
DLA RNA Polymerase and Transcription
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.10.1
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SOM.1ai.BPM1.1.FTM.3.BCHM.MB.11.3
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SOM.1ai.BPM1.1.FTM.3.BCHM.MB.11.9
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.10.7
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.8.6
Lecture 10 Post Transcriptional
Modification
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.11.8 Differentiate between the structures of prokaryotic and eukaryotic mRNAs
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.11.9 Describe the post-transcriptional modifications of eukaryote mRNA and the significance of these modifications (5’ capping,
polyadenylation, and splicing)
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.11.10 Predict the effects of splice site mutations on the mature mRNA and ultimately the translated protein
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.11.11 Describe how RNA editing affects our understanding of the transmission of genetic information from the genome to protein
SOM.1ai.BPM1.1.FTM.3.BCHM.MB.11.12 Describe human disease conditions that may be associated with mRNA modification and errors in this process
Lecture 11 Mitosis, Meiosis and non-
disjunction
SOM.1a.BPM1.1.FTM.3.GNET.MB1001
SOM.1a.BPM1.1.FTM.3.GNET.MB1002
SOM.1a.BPM1.1.FTM.3.GNET.MB1003
SOM.1a.BPM1.1.FTM.3.GNET.MB1004
SOM.1a.BPM1.1.FTM.3.GNET.MB1005
SOM.1a.BPM1.1.FTM.3.GNET.MB1006
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SOM.1a.BPM1.1.FTM.3.GNET.MB1008
SOM.1a.BPM1.1.FTM.3.GNET.MB1009
SOM.1a.BPM1.1.FTM.3.GNET.MB1010
SOM.1a.BPM1.1.FTM.3.GNET.MB1011
SOM.1a.BPM1.1.FTM.3.GNET.MB1012
Lecture 12 Genetic Variation, Genes and
Chromosomes
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SOM.1ai.BPM1.1.FTM.1.GNET.GN.0102
SOM.1ai.BPM1.1.FTM.1.GNET.GN.0103
SOM.1ai.BPM1.1.FTM.1.GNET.GN.0103
DLA Mendelian Patterns
January 28th - February 1st
Describe the structural features of a gene and their functions
Describe the types and functions of the four different cellular RNAs (mRNA, tRNA, rRNA, snRNA)
Describe the major steps of RNA synthesis in prokaryotes and eukaryotes
Explain the function and structure of DNA sequences that are involved in the initiation (promoters) and termination of
transcription
Predict the sequence of the transcribed RNA if the template DNA strand or the coding strand of the RNA is provided
List the RNAs that are transcribed by the different types of RNA polymerases in eukaryotes
Describe the major steps of RNA synthesis in prokaryotes and eukaryotes.
Explain the function and structure of DNA sequences that are involved in the initiation (promoters) and termination of
transcription.
Describe the post-transcriptional modifications of eukaryote mRNA and the significance of these modifications (5’ capping,
polyadenylation, and splicing).
Explain how antibiotics and other compounds target and inhibit specific components of the transcription process.
Describe the effect of the antibiotic drugs that interfere with DNA gyrase such as ciprofloxacin
Recognize differences in rates of cell division in different tissues
Summarize and distinguish the sequence of events that occur during the phases of the cell cycle: Analyze stages of the cell
cycle - (G1, Go, S, G2, M)
Indicate the role of p53 in the cell cycle: Role in genome surveillance and Role in initiation of apoptosis
Describe the chromosomal structure changes in different phases of the cell cycle
Explain the significance of mitosis, summarize the events, and analyze structures of mitosis including: Prophase: Events in the
nucleus, formation of spindle in cytoplasm, Metaphase: Association of chromosomes with spindle fibres, Anaphase:
Separation of sister chromatids, Telophase: Cytokinesis, re-formation of nuclei
Recognize the significance of meiosis and summarize its main achievements
Describe the sequence of events that comprise meiosis. Analyze the effect of a nondisjunction of the sex chromosomes in
both male and female gametogenesis. Predict the outcome of nondisjunction if it occurs in either meiosis 1 or in meiosis 2.
Interpret the significance of recombination in prophase I. Identify the role of meiosis in gametogenesis. Analyze events and
structures that occur in meiosis
Compare and contrast the overall features of mitosis with meiosis
Explain how meiosis introduces diversity into the genotype
Outline the differences between meiosis in males and females
Compare and contrast the outcome of nondisjunction that might occur during meiosis or in mitosis
Analyze the structure of DNA and discuss how human variation and heredity is controlled by this information storage system
Compare and contrast different types of repetitive DNA
Discuss the structure of chromosomes in the human (male and female), and general terminology used to describe karyotypes
Analyze dosage compensation by X-chromosome inactivation
Describe basic definitions of human genetics
Describe symbols used in human pedigree construction
From a description or a pedigree, identify autosomal dominant inheritance • •
Calculate recurrence risk of autosomal dominant disorders within families
From a description or a pedigree, recognize autosomal recessive inheritance
Calculate recurrence risk, and carrier risk of autosomal recessive disorders
Discuss the 2/3 rule for AR carrier risk
Describe pseudoatosomal dominance
-Give an example
Describe co-dominance
-Give an example
Describe incomplete dominance
-Give an example
Lecture 13 Mendelian Inheritance: AD
and AR
SOM.1a.BPM1.1.FTM.3.GNET.GN 0201 Compare and contrast Mendelian and non-Mendelian genetics
SOM.1a.BPM1.1.FTM.3.GNET.GN 0202 Interpret a family pedigree incorporating standard genetic symbols. Interpret a pedigree and identify features, disorders,
genotype, carrier status, recurrence risk, and genetic principles
SOM.1a.BPM1.1.FTM.3.GNET.GN 0203 Summarize and distinguish the characteristics of the following patterns of inheritance using pedigrees: autosomal dominant,
autosomal recessive, X-linked dominant and X-linked recessive
SOM.1a.BPM1.1.FTM.3.GNET.GN 0204 Demonstrate how disease liability is transmitted for autosomal dominant diseases, autosomal recessive diseases and X-
linked diseases
SOM.1a.BPM1.1.FTM.3.GNET.GN 0205 Distinguish and explain: locus, gene, allele, genotype, phenotype and zygosity
SOM.1a.BPM1.1.FTM.3.GNET.GN 0206 Propose how the basic risk calculations are performed for the different categories of genetic transmission
SOM.1a.BPM1.1.FTM.3.GNET.GN 0207 Identify obligate carriers in a pedigree: AR, X-linked, or AD with reduced penetrance
SOM.1a.BPM1.1.FTM.3.GNET.GN 0208 Determine the risk that immediate family members might be carriers of disease alleles (AR or X-linked) given that other
members in the family are either known carriers or known affected. Calculate the risk that a sibling of a known affected for an
AR disease will himself be a carrier of the disease allele (2/3)
SOM.1a.BPM1.1.FTM.3.GNET.GN 0209 Distinguish the modes of inheritance of the disorders listed below, be able to identify the main clinical features, and
interpret the genetic principles illustrated by the following common genetic diseases: Autosomal Dominant (Huntington
disease, myotonic dystrophy, familial hypercholesterolemia, osteogenesis imperfecta, Marfan syndrome, Achondroplasia, NF,
acute intermittent porphyria), Autosomal Recessive (CF, PKU, Tay Sachs disease, Sickle cell anemia, thalassemia,
hemochromatosis, homocystineuria, SCID due to ADA deficiency, alkaptonuria), X linked (Hemophilia A and B, G6PD
deficiency, Duchenne and Becker muscular dystrophy, red/green color blindness. Lesch Nyhan syndrome, X-SCID)

SOM.1a.BPM1.1.FTM.3.GNET.GN 0210 Identify pseudodominant inheritance and indicate factors that result in this inheritance pattern. Be able to identify this
concept from clinical scenarios and pedigrees
SOM.1a.BPM1.1.FTM.3.GNET.GN 0211 Define the terms: haploinsufficiency, dominant negative effect, gain of function mutations, loss of function mutations

DLA X - Linked Patterns

Describe some examples of X - linked disorders
Explain how a woman who is a carrier of an X - linked disorder might manifest symptoms of the condition (manifesting
heterozygote)
- Skewed X - inactivation, non - random X – inactivation
Discuss X - linked dominant condition
Compare and contrast variable expressivity and incomplete penetrance
-Give examples of each
Describe pleiotropy
Compare and contrast locus heterogeneity and allelic heterogeneity
-Give examples
Describe locus heterogeneity in terms of complementation groups
Explain how allelic heterogeneity allows the formation of a compound heterozygote in autosomal recessive disorders
Compare and contrast locus heterogeneity and allelic heterogeneity
-Give examples
Describe locus heterogeneity in terms of complementation groups
Explain how allelic heterogeneity allows the formation of a compound heterozygote in autosomal recessive disorders

Lecture 14 X – Linked Inheritance

SOM.1a.BPM1.1.FTM.3.GNET.GN 0401 Summarize and distinguish the characteristics of the following patterns of inheritance using pedigrees: autosomal dominant,
autosomal recessive, X-linked dominant and X-linked recessive
SOM.1a.BPM1.1.FTM.3.GNET.GN 0402 Demonstrate how disease liability is transmitted for autosomal dominant diseases, autosomal recessive diseases and X-
linked diseases
SOM.1a.BPM1.1.FTM.3.GNET.GN 0403 Distinguish the different characteristics of recessive and dominant X-linked traits using pedigrees
SOM.1a.BPM1.1.FTM.3.GNET.GN 0404 Identify obligate carriers in a pedigree: AR, X-linked, or AD with reduced penetrance
SOM.1a.BPM1.1.FTM.3.GNET.GN 0405 Distinguish the modes of inheritance of the disorders listed below, be able to identify the main clinical features, and
interpret the genetic principles illustrated by the following common genetic diseases: X linked (Hemophilia A and B, G6PD
deficiency, Duchenne and Becker muscular dystrophy, red/green color blindness. Lesch Nyhan syndrome, X-SCID)

SOM.1a.BPM1.1.FTM.3.GNET.GN 0406 Differentiate between locus and allelic heterogeneity

SOM.1a.BPM1.1.FTM.3.GNET.GN 0407 Explain what is meant by the term ‘compound heterozygote’
SOM.1a.BPM1.1.FTM.3.GNET.GN 0408 Discriminate and discuss the concept of penetrance and variable expression
SOM.1a.BPM1.1.FTM.3.GNET.GN 0409 Comprehend how the classic pattern of inheritance may be disrupted by incomplete penetrance, variable expressivity and
variable age-of-onset. Be able to identify these concepts from clinical scenarios and pedigrees
SOM.1a.BPM1.1.FTM.3.GNET.GN 0410 Calculate the recurrence risk based on penetrance for autosomal dominant and autosomal recessive disorders
SOM.1a.BPM1.1.FTM.3.GNET.GN 0411 Define pleiotropy with examples. Be able to identify concepts if given a clinical scenario
SOM.1a.BPM1.1.FTM.3.GNET.GN 0412 Recognize occurrence of new mutations as a cause of new genetic diseases in families. Be able to identify this concept from
clinical scenarios and pedigrees
SOM.1a.BPM1.1.FTM.3.GNET.GN 0413 Explain the phenomenon of germinal (germ-line) mosaicism
SOM.1a.BPM1.1.FTM.3.GNET.GN 0414 Identify genetic disorders that have a delayed age of onset, and be able to identify this concept from clinical scenarios and
pedigrees
SOM.1a.BPM1.1.FTM.3.GNET.GN 0415 Explain the phenomenon of a manifesting heterozygote in X-linked recessive disorders, and be able to identify this concept
from clinical scenarios and pedigrees
DLA & Lecture 15 Translation and Post
Translational Modification
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1101
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1102
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1103
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SOM.1a.BPM1.1.FTM.3.BCHM.MB.1109
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1201
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1202
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1203
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1204
DLA Properties of Amino Acids
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0401
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0402
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0403
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SOM.1a.BPM1.1.FTM.3.BCHM.BT.0408
Lecture 16 Structure and Function of
Proteins
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0501
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SOM.1a.BPM1.1.FTM.3.BCHM.BT.0505
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0506
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0507
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0508
SOM.1a.BPM1.1.FTM.3.BCHM.BT.0509
Lecture 17 Unexpected Events in
Inheritance
SOM.1a.BPM1.1.FTM.3.GNET.GN 0601
SOM.1a.BPM1.1.FTM.3.GNET.GN 0602
SOM.1a.BPM1.1.FTM.3.GNET.GN 0603
SOM.1a.BPM1.1.FTM.3.GNET.GN 0604
SOM.1a.BPM1.1.FTM.3.GNET.GN 0605
SOM.1a.BPM1.1.FTM.3.GNET.GN 0606
SOM.1a.BPM1.1.FTM.3.GNET.GN 0607
SOM.1a.BPM1.1.FTM.3.GNET.GN 0608
SOM.1a.BPM1.1.FTM.3.GNET.GN 0609
SOM.1a.BPM1.1.FTM.3.GNET.GN 0610
Explain why the genetic code is collinear with DNA, triplet in nature, redundant (degenerate), and non-overlapping.
Define the terms: reading frame and frame-shift mutation.
Translate and interpret the standard genetic code table and be able to identify the initiation codon as well as the 3
terminator codons.
Explain the universal nature of the genetic code (with minor differences in mitochondria) and predict the sequence of a
peptide if the coding strand of the DNA is provided.
Discuss how protein synthesis proceeds from the N-terminal to their C-terminal ends and explain how this creates a naming
convention for peptides.
List and describe the major function of the major types of RNA in cells, including mRNA, tRNA, rRNA, snRNA, snoRNA, miRNA.
Describe the subunit composition and the basic structure of prokaryotic 70S and eukaryotic 80S ribosomes, including the
basis for their names and be able to identify the A site, the P site, and the E site on the ribosome.
Describe the structure, function, and charging of tRNAs.
Describe the codon/anticodon interaction and discuss the wobble hypothesis.
Describe the sequence of events that occurs during translation in prokaryotes (initiation, elongation and termination) and list
the major differences between prokaryotic and eukaryotic translation.
Explain how diphtheria toxin interferes with eukaryotic translation and explain the mode of action of common antibiotics
that interfere with translation: Initiation inhibitors (streptomycin), Elongation inhibitors (Tetracycline, chloramphenicol,
erythromycin, puromycin, cycloheximide).
List and review the major types of post-translational modifications: Zymogen activation (trypsinogen à trypsin as example),
Serine/threonine phosphorylation (regulation of enzymes in metabolism), Tyrosine phosphorylation (Insulin receptor as an
example), O-linked glycosylation, N-linked glycosylation and Lipid anchoring (e.g. farnesyl groups to RAS).
Describe proteolytic processing using insulin as an example.
Describe the general structure and stereochemistry of amino acids.
Classify amino acids based on their R groups (with examples for each group).
Name the amino acids with a charged side chain, the amino acids containing a hydroxyl group and the amino acids containing
sulphur.
Discuss the acid/base properties of amino acids with the aid of a graph (e.g. histidine).
Discuss the role of histidine residues in buffering in haemoglobin.
Describe the concept of the formation of biological active amines
Discuss the biomedical importance of derivatives of amino acids (GABA, histamine, serotonin and catecholamines).
Describe the main features of the peptide bond.
Outline the general functions of proteins.
Discuss in general the synthesis of proteins and the concept of formation of peptide hormones from precursor proteins.
Differentiate between the hierarchical levels of protein structure.
Discuss the significance of bond forces involved in maintenance of protein structure (covalent bonds and hydrogen bonds,
ionic bonds, hydrophobic forces and Van der Waals forces).
Describe the structure of insulin.
Define secondary structures including α-helix and β-pleated sheet.
Discuss the change of the protein secondary structure in Prion disease.
Describe the role of chaperone proteins in protein folding.
Discuss protein denaturation in vivo and in the laboratory.
Describe the genetic abnormalities that may result in a non-Mendelian pattern of inheritance
Disorders due to mutations in mitochondrial genes: Leber hereditary optic neuropathy (LHON), MELAS, MERRF
Identify the phenomenon of heteroplasmy in mitochondrial disorders and indicate its genetic basis
Predict the effect of imprinting in the transmission of genetic disease
Identify imprinting defects (Prader Willi syndrome, Angelman syndrome)
Explain the phenomenon of uniparental disomy and microdeletion in Prader-Willi and Angelman syndrome
Analyze how triplet repeat expansion mutations result in anticipation which and how this may be thought about as a non-
Mendelian aspect to the inheritance of the disorder (Huntington disease, myotonic dystrophy, Fragile X syndrome)
Recognize the phenomenon of anticipation and its genetic basis. Identify this concept from clinical scenarios and pedigrees
Explain the phenomenon of digenic inheritance using retinitis pigmentosa as an example
Determine a strategy for identifying Non-Mendelian disorders, investigating them and providing appropriate genetic
counselling for the families
Week 3 February 4th - February 8th
DLA Molecular Diagnosis and Lecture 18
The Use of Molecular Genetics in
Medicine
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1301 Identify the differences between the structure of DNA versus RNA and Protein and which structures are affected in the
diseased state
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1302 Explain the concept of hybridization between two complementary single stranded DNA molecules and which class of
mutation is being investigated
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1303 Explain the general principles and utilization of the various molecular biology techniques
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1304 Summarize how a DNA fragment is cloned into a vector molecule and how different vectors are used for different purposes
such as DNA replication, expression and sequencing
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1401 Compare data from RFLP, ASO, DNA sequencing and allele specific PCR: from normal homozygotes, carriers (heterozygotes)
and affected homozygotes
SOM.1a.BPM1.1.FTM.3.BCHM.MB.1402 Predict the application of molecular biology techniques for detection of a single base mutation versus small insertion or
deletion of DNA sequence, and changes in the expression of genes in the form of mRNA or protein.

Lectures 19 Signal Transduction

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.01 Describe the different types of cell signalling: endocrine, autocrine, paracrine, neuronal & contact-dependent.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.02. Describe the different types of extracellular signal molecules.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.03 Discuss the events involved in signal transduction

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.04. Indicate the four different classes of receptors (steroid receptors, ion-channel receptor, receptor enzyme, G-protein-coupled
receptors) with specific examples for each class.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.05. Indicate the role of G-protein subunits (Gs, Gi, Gq).

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.06. Describe the different target (effector) enzymes of G proteins.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.07. Describe the two major second messenger systems (adenylate cyclase and phosphoinositide systems) associated with G-
proteins and signal termination.

Lectures 20 G-protein Coupled

Receptors (GPCR)
SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.05. Indicate the role of G-protein subunits (Gs, Gi, Gq).

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.06. Describe the different target (effector) enzymes of G proteins.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.07. Describe the two major second messenger systems (adenylate cyclase and phosphoinositide systems) associated with G-
proteins and signal termination.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.06.08. Explain how cholera toxin modifies Gs and how pertussis toxin modifies Gi. Predict the effects of these modifications in the
respective cells.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.07.09. Discuss the roles of cAMP, IP3 and DAG as mediators of signal transduction in different cell types.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.07.10. Indicate the action of phosphodiesterase.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.07.11. Describe the activation of adenylate cyclase and phospholipase C by the respective G proteins.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.07.12. Describe formation of cGMP and its biological role. Indicate the function of guanylate cyclase.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.07.13. Identify the mechanism of action of nitric oxide and their role in smooth muscle relaxation and vasodilatation. Indicate the
formation of nitric oxide from nitroglycerin.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.07.14. Compare and contrast the activation of protein kinases A and C.

SOM.1ai.BPM1.1.FTM.3.BCHM.Cp.07.15. Identify the signalling mechanisms associated with α and β adrenergic receptors, glucagon receptors and insulin receptors.

SOM.1ai.BPM1.1.FTM.3.BCHM.CP.07.16. Predict the changes when an inhibitor of a specific signalling pathway is used.
DLA Genomics
Lecture 21 Use of Genomics in Diagnosis
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Lecture 22 Genetics and Genomics Cases
- Objectives from previous lectures
DLA Properties of Enzymes
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Lecture 23 Enzymes
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Explain how triplet repeat expansion disorders are diagnosed
Discuss why each triplet repeat expansion disorder needs its own unique test for diagnosis
Explain how a G-band karyotype is prepared
Describe FISH and how it can be used in diagnostic applications
Compare and contrast
-Metaphase FISH
-Interphase FISH
-Chromosome painting (SKY FISH)
Consider the relative pros and cons of these techniques, and their limits of resolution
Describe the strategy behind the microarray
-CGH Microarray
-SNP Microarray
-cDNA Microarray
Analyze how PCR can be used to obtain a diagnosis of a genetic disorder
Analyze genomic approaches that are used in the diagnosis of human disorders
Describe the different types of mutations that may be observed in the human genome and explain how they are categorized.
Outline the properties of enzymes and the chemistry of the active site.
Discuss the significance of coenzymes and apoenzymes.
Describe the role of enzymes related to the activation energy and delta G of a reaction with the aid of a graph.
Describe the factors that influence enzyme reaction rates (substrate, pH and temperature).
Discuss enzyme regulation via the concentrations of substrates or products.
Describe enzyme regulation via the modulation of enzyme concentrations.
Discuss conformation of enzymes and changes of conformation in relation to enzyme regulation. (reversible covalent
modification, proteolytic cleavage and allosteric regulation).
Describe the concept of proteolytic activation of digestive enzymes (eg: zymogens such as trypsinogen).
Discuss the kinetics of allosteric enzymes and explain the sigmoidal graph.
Describe allosteric enzymes and their regulation related to changes of K 0.5 or Vmax. Discuss in general the regulation of
metabolic pathways related to feedback inhibition and feed-forward activation.
Outline the properties of enzymes and the chemistry of the active site.
Discuss the significance of coenzymes and apoenzymes.
Describe the role of enzymes related to the activation energy and delta G of a reaction with the aid of a graph.
Describe the factors that influence enzyme reaction rates (substrate, pH and temperature).
Describe Michaelis-Menten kinetics
Define Km and Vmax and discuss their significance with the help of a graph.
Discuss the inhibition caused by statin drugs (enzyme inhibited, biochemical effect).
Compare and contrast the mode of action and kinetics of reversible competitive and noncompetitive inhibitors.
Discuss the graph of Michelis-Menten and compare it to Lineweaver-Burk.
Indicate in the Lineweaver-Burk plot the intercepts with the y-axis and x-axis
Graphically differentiate competitive and noncompetitive inhibition
using the Michaelis-Menten graph and the Lineweaver-Burk plot.
Distinguish between reversible and irreversible inhibitors.
Discuss the inhibition caused by DFP and aspirin (enzymes
inhibited, biochemical effects of inhibition).
Discuss suicide inhibition of enzymes using allopurinol as example.
Discuss enzyme regulation via the concentrations of substrates or products.
Describe enzyme regulation via the modulation of enzyme concentrations.
Discuss conformation of enzymes and changes of conformation in relation to enzyme regulation. (reversible covalent
modification, proteolytic cleavage and allosteric regulation).
Describe the concept of proteolytic activation of digestive enzymes (eg: zymogens such as trypsinogen).
Discuss the kinetics of allosteric enzymes and explain the sigmoidal graph.
Describe allosteric enzymes and their regulation related to changes of K 0.5 or Vmax. Discuss in general the regulation of
metabolic pathways related to feedback inhibition and feed-forward activation.
Lecture 24 Clinical Enzymology
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Lecture 25 Cell Adaptation
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Discuss how inherited enzyme deficiencies and
nutritional deficiencies may result in disease.
Discuss the effects of necrosis and inflammation on serum enzyme levels.
Describe the structure and function of isozymes in general.
Differentiate the isozymes of creatine kinase and lactate dehydrogenase based on tissue location
and subunit composition.
Discuss the utility of serum injury markers following myocardial infarction: Use of CK-MB/total CK ratio for MI evaluation.
Discuss the utility of serum injury markers following MI: Use of serum cardiac troponins I and T as markers.
Discuss the utility of serum injury markers following MI: Time frame of serum injury markers (myoglobin, cardiac troponins,
CK-MB) with the help of a graph.
Describe the application of sALT, sAST, sALP and sGGT as markers of hepatocellular disease, biliary disease and alcohol liver
disease.
Discuss the significance of serum amylase and serum lipase related to pancreatic disease.
Indicate specific serum injury markers for bone disease (sALP), prostate cancer (PSA) and liver cancer (alpha-fetoprotein).
Outline the cellular responses to stress or injury.
Compare physiological vs. pathological responses.
Discuss common causes of cell injury.
Discuss the cellular systems affected by injury.
Compare reversible vs. irreversible injuries.
Describe the early cellular responses to injury.
Explain how organs increase in functional cell mass.
Define the term “hypertrophy” and list examples.
Define the term “hyperplasia” and list examples.
Define the term “atrophy” and list examples.
Define the term “involution” and list an example.
Define the term “metaplasia” and list examples.
Define the terms “failure of differentiation” and “cellular atypia”.
Define the terms “dysplasia” and “neoplasia” and list examples.
Compare and contrast benign vs. malignant neoplasms.
Define the terms “carcinoma in situ” and “invasion”.