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B. Sc. Biochemistry & Molecular Biology
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#affinity
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#algorithm
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#amino acid
(12)
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(1)
#angiogenesis
(1)
#apoptosis
(1)
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#autophagy
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(7)
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(13)
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(4)
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(1)
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(21)
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(4)
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(3)
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(6)
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(5)
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(2)
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(5)
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(1)
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(13)
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(26)
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(6)
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(7)
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(10)
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(23)
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(15)
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(3)
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(4)
Account for why a given ligand may be bound tightly by an enzyme or covalently modify an enzyme (transition state analogues).
[
BIOC 4701
]
Analyze optical spectra (absorption, emission, fluorescence anisotropy, LD, CD, IR, Raman) with respect to polypeptide structure and environment and with relation to quantum mechanical basis of a given spectroscopic technique.
[
BIOC 4702
]
Apply fundamental principles of chemistry and physics (e.g. molecular bonding, thermodynamics, kinetics) to explain important concepts in biochemistry.
[
BIOC 1040
]
Apply Henderson-Hasselbalch equation to calculate the properties of a buffer and the net charge of amino acids and proteins.
[
BIOC 2300
]
Assimilate and integrate the knowledge in a developing field of protein science to deliver a presentation or formulate a literate essay.
[
BIOC 4700
]
Calculate association constants, given tables or graphs of raw data from experiments.
[
BIOC 4700
]
Choose and explain a suitable method to analyze the binding interaction of proteins with small molecules or between proteins.
[
BIOC 4700
]
Compare representative mitochondrial genomes (human, plants, algae) in terms of gene content, organization, and expression.
[
BIOC 4403
]
Compare two classifiers based on their performances.
[
BIOC 4010
]
Demonstrate basic skills in a biochemistry laboratory, including the awareness of chemical and biological safety, the practice of experimental technique, and the recording, interpretation and written communication of laboratory observations.
[
BIOC 1040
]
Demonstrate understanding of hydrodynamic characterization by NMR (DOSY and spin relaxation), analytical ultracentrifugation and single molecule methods.
[
BIOC 4702
]
Describe effects of spin-relaxation phenomena upon the experimental observable and the manner in which these are modulated by dynamic processes.
[
BIOC 4702
]
Describe regulatory process and patent application process as they apply to medical biotechnology-based products.
[
BIOC 4501
]
Describe the basic principles of intracellular signal transduction and discuss how these processes may alter gene expression, protein function and cellular fate.
[
multiple courses
]
Describe the biochemical and physiological principles of fluid and electrolyte balance.
[
BIOC 4306
]
Describe the reciprocal pathways of fatty acid synthesis and oxidation.
[
BIOC 3300
]
Describe the role of food technologies in the protection of the food supply.
[
BIOC 4306
]
Develop a knowledge of the subtleties of amino acid function within the whole protein context. (Post-translation modifications of side chains).
[
BIOC 4700
]
Develop an appreciation of particular techniques in protein science that are unavailable to students in the context of Dalhousie undergraduate program.
[
BIOC 4700
]
Discriminate between and calculate the roles of entropy, enthalpy, and molecular interactions in protein stability, folding and ligand binding.
[
BIOC 3700
]
Discuss the necessity of protein turnover within cells and organisms and the degradative and regulatory mechanisms that govern protein turnover.
[
BIOC 4700
]
Distinguish between cis and trans regulation.
[
BIOC 4404
]
Distinguish between gene activation and gene repression.
[
BIOC 4404
]
Distinguish between receptor/non-receptor kinases.
[
BIOC 4305
]
Distinguish between tumour suppressor and oncogene activity.
[
BIOC 4305
]
Distinguish properties and behaviour of infrared vs. Raman active chromophores.
[
BIOC 4702
]
Draw energy level diagrams showing the quantum mechanical basis of electronic absorption and emission spectroscopy with specific reference to the Franck-Condon principle.
[
BIOC 4702
]
Explain how enzymes can increase the rates of biochemical reactions at the molecular level, and how they may be inhibited or regulated by drugs and toxins.
[
multiple courses
]
Explain how given techniques (spectroscopy, radioactivity, HPLC) may be used to measure enzyme activity in direct or indirect assays.
[
BIOC 4701
]
Explain how metabolic pathways are controlled by compartmentalization within and between organelles and tissues.
[
BIOC 3300
]
Explain how protein tagging techniques can be used to determine protein localization or protein interactions in living cells or to affinity-purify proteins from cells.
[
BIOC 4501
]
Explain regulation exerted by different mechanisms of translational control.
[
BIOC 4404
]
Explain what a Python script does using a combination of read, write and file operations.
[
BIOC 4010
]
Explain what is a Hamiltonian/Eulerian path and what it means to the genome assembly problem.
[
BIOC 4010
]
Explain what is an algorithm.
[
BIOC 4010
]
Explain why structural alignment is the “ground truth” for a sequence alignment.
[
BIOC 4010
]
Explain why the quality of a simulation is more dependent on the speed of a calculation rather than its accuracy.
[
BIOC 4010
]
Formulate a literate essay.
[
BIOC 4700
]
Given a pH-dependent kinetic mechanism, derive an initial velocity equation and sketch the plot of kinetic constants as a function of pH.
[
BIOC 4701
]
Given free energy of product and substrate or the reduction potential of half reaction, calculate the free energy changes of a reaction and decide whether the reaction would be spontaneous.
[
BIOC 2300
]
Given the architecture of an enzyme active site, write a mechanism and show how general acid/base, covalent, or electrophilic catalysis may occur.
[
BIOC 3700
]
Given the kinetic mechanism (with or without inhibition), derive an initial velocity equation using either the steady-state assumption or the rapid equilibrium approach.
[
multiple courses
]
Identify and define major components of the human diet: macronutrients, minerals, vitamins.
[
BIOC 4306
]
Identify and distinguish intervening sequences (group I introns, group II introns, twintrons, split intron, inteins), using key structural and mechanistic features.
[
BIOC 4403
]
Identify how post-translational modifications modulate the biophysical and the chemical properties of amino acid side chains to expand the functionality of proteins, particularly enzymes.
[
BIOC 4700
]
Identify key evidences/arguments for hypothesis on the origin/evolution of genes from an RNA world.
[
BIOC 4403
]
Interpret features of bacterial genome organization: non-random positioning and orientation of certain genes in relationship to overlapping rounds of genome replication.
[
BIOC 4403
]
Interpret given diagrams of enzyme regulation/activity.
[
BIOC 2300
]
Interpret plasmid maintenance and evolution in terms of plasmid genes (poison-antidote mechanism).
[
BIOC 4403
]
Keep a clear record of research activity.
[
BIOC 3620
]
Present your experimental results to other members of the lab.
[
BIOC 3620
]
Provide rational biochemical arguments for genetics and the manipulation of our food supply.
[
BIOC 4306
]
Provide rational biochemical arguments for the impact of dietary fructose on metabolism.
[
BIOC 4306
]
Recall principles of redox equivalent transfers within respiratory chains.
[
BIOC 4700
]
Recall the three main classes of macronutrients and their digestion.
[
BIOC 2300
]
Recognize GTPases as on/off switches in vesicular transport and cellular signaling.
[
BIOC 3300
]
Recognize high energy intermediates and their role in reaction energetics: substrate level phosphorylation.
[
BIOC 3300
]
Recognize how changes in lipoprotein metabolism influence atherosclerosis.
[
BIOC 3300
]
Recognize the pathway for cholesterol biosynthesis and its regulation.
[
BIOC 3300
]
Recognize the role of experimental science, case studies and epidemiology in defining optimal nutrition.
[
BIOC 4306
]
Recognize the structures and functions of glycerolipids.
[
BIOC 3300
]
Relate the concept of accuracy with this of specificity, sensitivity and F-score.
[
BIOC 4010
]
Show how entropic contributions lead to huge intramolecular rate enhancements.
[
BIOC 4701
]
Specify methods to investigate gene regulation.
[
BIOC 4404
]
Summarize in writing research done on a recombinant DNA-related topic.
[
BIOC 4501
]
Understand angiogenesis.
[
BIOC 4305
]
Understand the concept of apoptosis.
[
BIOC 4305
]
Use the scientific literature and other available resources to research topics in human biochemistry and, in a small group tutorial setting, to answer guided questions and attain learning objectives.
[
BIOC 1040
]
Use vector diagrams to explain the major NMR experiments employed for protein NMR.
[
BIOC 4702
]
Acquire skills in reading and interpreting the primary scientific literature.
[
BIOC 4404
]
Apply Michaelis-Menten equation to calculate Vmax and Km in absence/presence of effectors.
[
BIOC 2300
]
Collaborate with team members to research and orally debate a medical biotechnology-related issue.
[
BIOC 4501
]
Compare and contrast ensemble measurements to single molecule measurements, with emphasis on experimental approaches allowing observation of single molecules and information uniquely obtainable by single molecule measurements.
[
BIOC 4702
]
Compare and contrast the nutritional requirements in the elderly and the newborn to adult values.
[
BIOC 4306
]
Compare mobile genetic elements (DNA transposons, retrotransposons) as drivers of genome evolution.
[
BIOC 4403
]
Contrast the challenge of finding exons versus finding ORFs.
[
BIOC 4010
]
Create and give an oral presentation based on independent research of a recombinant DNA-related topic.
[
BIOC 4501
]
Define hormone action and recognize the steps of the main hormonal signaling mechanisms.
[
BIOC 2300
]
Deliver an effective oral presentation.
[
BIOC 4700
]
Describe the concept of feedback regulation of cholesterol biosynthesis.
[
BIOC 3300
]
Describe the physical and chemical structure of the human genome, and provide examples of technologies currently used to elucidate and manipulate its content.
[
BIOC 1040
]
Describe the physiology and biochemistry of digestion of macronutrients.
[
BIOC 4306
]
Determine the effects of loss of function or gain of function mutations of regulating enzymes or metabolic enzymes on the rate of a reaction given a schematic of enzyme regulation.
[
BIOC 2300
]
Distinguish the regulators of cell cycle.
[
BIOC 4305
]
Explain cellular pathways for protein transport and modification and their effects on protein function.
[
BIOC 3300
]
Explain the Greedy method of genome assembly and its limitations.
[
BIOC 4010
]
Given the kinetic parameters for an enzyme-catalyzed reaction and the corresponding nonenzymatic reaction, calculate the efficiency, rate enhancement, proficiency, and extent of transition state stabilization.
[
BIOC 4701
]
Given the steady-state velocity expression for a multisubstrate enzyme, predict the product inhibition pattern and binding order in the presence of fixed and variable substrate concentrations.
[
BIOC 4701
]
Identify general features of the common classes of biomolecules: carbohydrates, lipids, nucleotides and amino acids.
[
multiple courses
]
Identify the different types of protein factors regulating bacterial gene expression.
[
BIOC 4404
]
Interpret genetic mobility of introns and inteins, by comparing mechanisms of intron/intein homing and transposition.
[
BIOC 4403
]
Interpret roles of DNA methylation in genome evolution (CpG islands) and gene regulation (epigenetics).
[
BIOC 4403
]
Outline in some molecular detail the processes by which genetic information is replicated and expressed, leading to protein synthesis, targeting and turnover.
[
BIOC 1040
]
Provide rational biochemical arguments for the adoption of vegetarian and vegan diets.
[
BIOC 4306
]
Recall DNA replication, transcription, and RNA processing.
[
BIOC 4403
]
Recall the activity of the main vitamin classes and their association with enzyme as cofactors.
[
BIOC 2300
]
Recognize different types of non-coding RNAs, and recognize/identify their roles in gene expression.
[
BIOC 3400
]
Understand the concept of signal transduction.
[
BIOC 4305
]
Understand the principles of bioenergetics, including the implications of free energy change occurring in a chemical reaction.
[
BIOC 2300
]
Analyze the detailed mechanism for the generation of the proton motive force across bioenergetic membranes.
[
BIOC 4700
]
Classify different regulatory mechanisms of gene transcription.
[
BIOC 4404
]
Compare and contrast the essential features in the digestion and absorption of carbohydrate, lipid and protein.
[
BIOC 4306
]
Derive the steady-state velocity equation for a given kinetic mechanism for a multisubstrate enzyme using the King-Altman method.
[
BIOC 4701
]
Describe and interrelate the hierarchical levels of protein structure (1˚ to 4˚) and provide examples of how this structure relates to the function (or dysfunction) of various classes of proteins.
[
multiple courses
]
Describe how organisms obtain, store, and utilize energy through metabolic interconversion of biomolecules.
[
BIOC 2300
]
Describe the structural features of nucleic acids and be able to distinguish them; describe the basis for information content in a DNA sequence; describe the flow of genetic information and be aware of different discoveries emerging in this area.
[
BIOC 2300
]
Distinguish between normal and abnormal cell signalling.
[
BIOC 4305
]
Distinguish relevant signalling domains.
[
BIOC 4305
]
Distinguish the lipids involved in signal transduction.
[
BIOC 4305
]
Draw the structure of a peptide with defined stereochemistry at a given pH.
[
BIOC 3700
]
Explain how dietary carbohydrates, fats and proteins are converted to energy.
[
BIOC 3300
]
Explain steroid hormone signaling and receptor action.
[
BIOC 3300
]
Explain the steps of protein synthesis identifying the differences between prokaryotes and eukaryotes.
[
BIOC 3400
]
Explain where the OLC/Eulerian_path algorithm may fail to give the correct genomic sequence.
[
BIOC 4010
]
Given hypothesis on the origin of nuclear genome (composite nature) and organelle genomes (endosymbiosis), identify key evidences and arguments.
[
BIOC 4403
]
Given the substrates, products, and cofactors for a particular class of enzyme-catalyzed reaction, write a mechanism for the reaction.
[
BIOC 3700
]
Identify structure of mono, di, polysaccharides (bonds) and lipids. Explain their distribution, storage, and mobilization.
[
BIOC 2300
]
Identify uniform and differential binding from site-directed mutagenesis studies or substrate mutilation studies to discern the role of residues in transition state and ground state binding.
[
BIOC 4701
]
Organize an effective literature search and apply it to a presentation or an essay.
[
BIOC 4700
]
Recall the steps of glucose metabolism, citric acid cycle, fatty acid metabolism, amino acid metabolism; identifying the intermediates, enzymes, and regulatory steps.
[
BIOC 2300
]
Recognize modifications of cholesterol in the synthesis of steroid hormones.
[
BIOC 3300
]
Recognize the main mechanism of action of insulin and/or glucagon and their pathways.
[
BIOC 2300
]
Understand genomic stability versus instability.
[
BIOC 4305
]
Understand loss of function versus gain of function mutations.
[
BIOC 4305
]
Understand the concept of phosphorylation-mediated signal transduction.
[
BIOC 4305
]
Understand the established principles of protein folding.
[
BIOC 4700
]
Understand the phases of cell cycle.
[
BIOC 4305
]
Analyze implications of molecular spectroscopy (absorption, emission, CD, NMR) results on polypeptide structure and environment in direct context of the physical basis of the technique in question.
[
BIOC 3700
]
Analyze the quantity of energy produced from each dietary component (carbohydrates, fatty acid and amino acids).
[
BIOC 3300
]
Associate insulin, glucagon, and epinephrine action with the body’s metabolic state and the activity of metabolic pathways in different tissues.
[
BIOC 3300
]
Define energy balance and describe the biochemical changes that occur in energy excess.
[
BIOC 4306
]
Describe the structural features of monosaccharides and be able to depict them; describe the linkages that join monosaccharides to form larger molecules; identify some of the main polysaccharides that occur in nature.
[
BIOC 2300
]
Design a protein engineering experiment to answer questions about structure/function relationships in new protein.
[
BIOC 4700
]
Distinguish the nucleotides that compose DNA and RNA.
[
BIOC 3400
]
Explain how energy and glucose homeostasis are maintained in the human body, and recognize the roles of peripheral and central signals.
[
BIOC 2300
]
Explain the biophysics of the non-covalent forces and kinetics and mechanisms governing protein folding and stability.
[
BIOC 4700
]
Explain why ab initio protein folding, or the prediction of tertiary structure from a sequence, is considered one of the most challenging problems in computational biology.
[
BIOC 4010
]
Given an enzyme mechanism, design a reversible or irreversible inhibitor.
[
multiple courses
]
Given DNA sequence data design (probes), recognize their use in different techniques such as PCR, microarray, southern blotting.
[
BIOC 3400
]
Identify steps and mechanisms of evolutionary gene transfer from organelle genomes to nuclear genome.
[
BIOC 4403
]
Outline the major metabolic pathways by which biomolecules (carbohydrates, lipids, amino acids) are synthesized, degraded and transported, and identify the key points at which these pathways are regulated.
[
multiple courses
]
Predict the fate of a protein based on features of the primary sequence.
[
BIOC 3400
]
Provide examples and biochemical principles of disease states associated with excess and deficiency of macronutrients.
[
BIOC 4306
]
Provide rational biochemical arguments for trans fatty acid supplements and disease.
[
BIOC 4306
]
Recall the role of photosynthesis in plants and the importance of this process in the biosphere; understand the light and dark reactions of photosynthesis at the molecular level.
[
BIOC 2300
]
Recognize common features in pathways for amino acid synthesis.
[
BIOC 3300
]
Recognize metabolic defects in nucleic acid metabolism.
[
BIOC 3300
]
Understand cell migration.
[
BIOC 4305
]
Apply peptide bond properties and hydrogen-bonding to predict primary and secondary structuring preferences.
[
BIOC 3700
]
Apply/use knowledge on DNA replication to explain the behavior of these molecules in different stages and under specific conditions (UV, analogs, salt concentration).
[
BIOC 3400
]
Assign two-dimensional homonuclear and heteronuclear NMR data for a polypeptide and apply these assignments for structure determination.
[
BIOC 4702
]
Describe how humans obtain, store, and utilize energy through metabolic transformations of biomolecules, and outline the fundamental principles of nutritional balance.
[
BIOC 1040
]
Discriminate and quantify the components of the NMR Hamiltonian in terms of their contribution to the experimental observable in the solution- and solid-state.
[
BIOC 4702
]
Distinguish between cell migration and metastasis.
[
BIOC 4305
]
Distinguish between RNA dependent and DNA dependent Polymerases and identify the process where they are involved.
[
BIOC 3400
]
Explain how lipids form membranes and lipoproteins and influence their function, and list different transport mechanisms across membranes.
[
BIOC 2300
]
Explain how metabolic pathways are controlled to maintain homeostasis of organisms under normal physiological conditions, and give examples of how this may be influenced by nutrition, drugs, and certain pathological states such as diabetes and obesity.
[
BIOC 1040
]
Explain regulation by mRNA structure and stability.
[
BIOC 4404
]
Explain the molecular basis of procedures such as gene cloning, cDNA and genomic DNA library screening, polymerase chain reaction (PCR) amplification of DNA, DNA sequencing, microarray technology, nuclear transfer somatic cell and induced pluripotent stem cell cloning, gene therapy.
[
BIOC 4501
]
Explain the problems related to the parametrization of Force Fields.
[
BIOC 4010
]
Explain the process of chain termination DNA sequencing.
[
BIOC 3400
]
Explain the processing (splicing, editing) of RNA (mRNA, tRNA, rRNA). Predict the effects of mutations in the primary RNA sequence.
[
BIOC 3400
]
Given a DNA sequence and restriction enzyme data, analyze a band pattern in a gel and generate a restriction map.
[
BIOC 3400
]
Given an irreversible inhibitor, design an experiment to determine the efficiency of inactivation and the binding affinity.
[
BIOC 4701
]
Identify the specific nucleotide and recognize the distinguishing features.
[
BIOC 3400
]
Integrate amino acid catabolism with other metabolic pathways.
[
BIOC 3300
]
Interpret data obtained from electrophoresis based methods (eg blotting, restriction enzyme, PFGE, gel mobility assays and CHIP).
[
BIOC 3400
]
Provide rational biochemical arguments for dietary modulation of cardiovascular disease.
[
BIOC 4306
]
Provide rational biochemical arguments for nutritional approaches to weight loss.
[
BIOC 4306
]
Recall basic principles of regulation of anabolic and catabolic pathways in biochemistry.
[
BIOC 3300
]
Recall the steps of insulin and glucagon signaling, and associate possible disruptions of insulin signaling to the development of diabetes.
[
BIOC 3300
]
Recognize how metabolic pathways are controlled to maintain homeostasis of organisms under normal physiological conditions, and how this may be disrupted by certain pathological states.
[
BIOC 2300
]
Recognize nitrogen fixation by plants and bacteria as a starting point for the amino group in proteins.
[
BIOC 3300
]
Analyze data obtained from molecular biology procedures and explain problems associated with expression of human protein products in bacteria or other host cell systems.
[
BIOC 4501
]
Apply the principles underlying structure and folding of simple soluble proteins to the more complex physical environment in which membrane proteins operate.
[
BIOC 4700
]
Based on the properties of the polynucleotides predict the outcome of differential chemical or enzymatic treatment.
[
BIOC 3400
]
Classify pathways for protein catabolism and their roles in cell biology and metabolism.
[
BIOC 3300
]
Compare different types and mechanisms of RNA editing and translational recoding.
[
BIOC 4403
]
Describe cellular mechanisms of transport that enable the cell to maintain membrane asymmetry and the cellular distribution of lipids.
[
BIOC 3300
]
Design a strategy for manipulating DNA molecules in particular scenarios (eg. Radio labeling and sub cloning).
[
BIOC 3400
]
Design oligonucleotides probes and primers for molecular biology applications including manipulation of genes, PCR and other hybridization-based approaches.
[
BIOC 4501
]
Discriminate the classes of lipoproteins by physical and chemical properties and their functions.
[
BIOC 3300
]
Distinguish Force Field and statistical mechanics energies.
[
BIOC 4010
]
Distinguish the differences between prokaryotes and eukaryotes in terms of genome organization, gene structure, and expression and DNA replication.
[
BIOC 3400
]
Given a type of DNA damage explain the repair mechanisms that can occur.
[
BIOC 3400
]
Identify the effects of mRNA localization on the consequences and regulation of gene expression.
[
BIOC 4404
]
Identify/recognize and explain the roles of the major proteins involved in the process of DNA replication/RNA synthesis and its regulation.
[
BIOC 3400
]
Integrate amino acids into purine and pyrimidine metabolism.
[
BIOC 3300
]
Integrate glucose metabolism and insulin action with diabetes and obesity.
[
BIOC 3300
]
List the major macro- and micronutrients essential for human health, and explain their actions at the biochemical level.
[
BIOC 1040
]
Recognize adipose tissue as an endocrine organ and describe the changes in obesity.
[
BIOC 3300
]
Understand autophagy.
[
BIOC 4305
]
Associate the principles of the central control of food intake with the development of obesity.
[
BIOC 3300
]
Compare different techniques of next generation DNA sequencing in terms of advantages/disadvantages and fields of application.
[
BIOC 4403
]
Distinguish the differences in DNA packaging/chromatin organization between prokaryotes and eukaryotes.
[
BIOC 3400
]
Identify the different types of DNA and RNA sequence elements regulating eukaryotic gene expression.
[
BIOC 4404
]
Identify the different types of protein factors regulating eukaryotic gene expression.
[
BIOC 4404
]
Identify the RNA molecules that participate protein synthesis and explain their contributions.
[
BIOC 3400
]
Interpret roles of alternative RNA splicing in expansion of the proteome.
[
BIOC 4403
]
Predict the mRNA and the amino acid sequence given a DNA sequence.
[
BIOC 3400
]
Explain how different types of DNA and RNA sequence elements are involved regulating eukaryotic gene expression.
[
BIOC 4404
]
Explain the contribution of DNA packaging/chromatin to gene expression and regulation.
[
BIOC 3400
]
Provide evidence for the roles of catalytic RNA in different cellular process such as protein synthesis and RNA splicing
[
BIOC 3400
]
Recognize the implications of differential RNA splicing.
[
BIOC 4404
]
Identify techniques to study DNA packaging/chromatin (eg CHIP, DNA sensitivity).
[
BIOC 3400
]
Understand chromatin remodelling.
[
BIOC 4305
]
Describe the challenges and opportunities for gene regulation offered by chromatin structure.
[
BIOC 4404
]
Distinguish among various mechanisms for the modulation of chromatin effects.
[
BIOC 4404
]
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