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Contrast the major structural features of prokaryotic and eukaryotic cells.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you contrast prokaryotic cells and eukaryotic cells in a minimum of four ways (for example: the presence of a nucleus, size, presence of membrane-bound organelles, presence of internal membrane system, single-celled vs. multicellular
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Summarize the major functions of various organelles and other subcellular structures.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you summarize at least one major function of these organelles (ribosomes, nucleus, cell membrane, mitochondria, Golgi apparatus, lysozomes)
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Differentiate biologically important functional groups in organic structures.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you classify the following groups when present (double bond, aromatic ring, alcohol, thiol, disulfide, amine, aldehyde, ketone, carboxylic acid, ester, amide, phosphoric ester, phosphoric anhydride)
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Classify common organic reactions by general category.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you classify a given reaction according to the following types: oxidation, reduction, condensation, hydrolysis, addition, elimination, isomerization
you identify the species oxidized and the species reduced in a given redox reaction
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Identify polar and nonpolar areas of organic molecules
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you identify regions that are significantly polar and those that are nonpolar
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Identify chiral centers in molecules
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you identify all chiral centers
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Illustrate hydrogen bonding between given molecules or functional groups.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you diagram hydrogen bonds, indicating the specific atoms involved.
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Relate the pH of a solution to the hydrogen ion and hydroxide ion concentration in that solution.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
a list of formulas will be provided.
Criteria
you calculate the pH, hydrogen ion concentration and hydroxide ion concentration of a solution when given any one of these three values
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Relate the pH of a solution to the conjugate base/acid ratio of a given weak acid.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
pKa values and a list of formulas will be provided.
Criteria
you identify the conjugate base and weak acid forms of a given species or functional group
you use the Henderson-Hasselbalch equation or its rearranged form to relate the pH of a solution to the ratio of conjugate base/acid present
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Illustrate the structure and ionization of a given amino acid or peptide.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
instructor's help sheet containing amino acid abbreviations, side groups and pKa's will be provided. The student is expected to know the common portions of amino acid and backbone portions of peptide structure from memory.
the chosen pH will not be exactly at a pKa for any group in the molecule. The student is expected to calculate the net charge to the nearest integer based on the one predominant form for the molecule rather than deal with fractional charges.
Criteria
you determine the predominant form and net charge of an amino acid or peptide at a specified pH
you label the peptide bonds, backbone, N-terminus and C-terminus of a peptide structure
you differentiate between D- and L- forms of a given amino acid
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Explain the four levels of protein structure and the types of interactions responsible for each level.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you contrast the four levels of protein structure (primary, secondary, tertiary, quaternary)
you recognize standard ways of representing various levels of protein structure
you illustrate each level of representing various levels of protein structure with your own drawing
you describe the role of hydrogen bonding in stabilizing secondary structure
you describe the role of hydrogen bonding, hydrophobic interactions, salt bridges and disulfide bonds in stabilizing tertiary structure
you predict the most important stabilizing interaction between a given pair of amino acid side-group structures
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Explain why certain agents denature proteins.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe the disruption in protein structure that occurs in denaturation.
you explain how heat, extreme pH, reducing agents, and nonpolar solvents denature proteins
you use the kinetic energy effects concepts appropriately
you use the changes in electric charge concepts appropriately
you use the changes in breaking of disulfide bonds concepts appropriately
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Contrast the characteristics of myoglobin and hemoglobin
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you contrast major structural features (number of polypeptide chains, hemes and iron(II) ions) of both molecules
you describe location and physiological role (oxygen storage vs. transport) of both molecules
you diagram the oxygen binding curves of both molecules and describes the basis for cooperative binding in hemoglobin
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Explain the general characteristics and metabolic role of enzymes.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you summarize the role of enzymes in increasing reaction rates
you examine the effects of enzyme catalysts on various reaction characteristics (reaction rate, activation energy, free energy change, equilibrium shifts)
you summarize the vocabulary terms associated with enzymes (cofactor, coenzyme, active site, substrate, enzyme-substrate complex, competitive inhibitor, allosteric activators and inhibitors, zymogen and prosthetic group)
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Discuss factors that can alter the rate of an enzyme-catalyzed reaction.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you draw graphs illustrating how the reaction rate of an enzyme-catalyzed reaction varies with various factors (enzyme concentration, substrate concentration, temperature, pH)
you explain why each of the previous rate curves has the shape it does
you illustrate the effects of allosteric activators and inhibitors on the rate curves of allosteric enzymes
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Illustrate the general regulation of enzyme activity by feedback inhibition and by covalent modification.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you apply principles of feedback inhibition to predict likely locations of metabolic control in a given pathway
you explain the role of protein kinases and protein phosphatases in the regulation of some enzymes
you summarize one example of zymogen activation
you rationalize why a particular enzyme would exist as a zymogen
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Describe the components or major structural features of common types of lipids.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you summarize the major components of triacylglycerols (triglycerides)
you summarize the major components of phospholipids
you recognize general structural characteristics of fatty acids (from instructor's list)
you recognize the general ring structure characteristic of steroids
you match the structural formula of a lipid with one of the following categories: fatty acid, triacylglycerol, phospholipid, steroid, prostaglandin
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Associate one significant biochemical role with each of the major classes of lipids studied.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you summarize a significant biological role for triacylglycerols
you summarize a significant biological role for phospholipids
you summarize a significant biological role for steroids
you summarize a significant biological role for eicosanoids
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Produce a labeled diagram representing the structure of a membrane.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you draw and label a diagram of a membrane that illustrates the following features: lipid bilayer, polar heads, nonpolar tails, cholesterol, at least one peripheral protein and at least one membrane-spanning integral protein
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Contrast the various forms of membrane transport.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you contrast simple diffusion, facilitated diffusion, and active transport with respect to energy requirement, protein involvement, and movement with respect to concentration gradient
you describe each process both in words and using drawings
you differentiate between primary active transport and secondary active transport
you explain the concept of a gated channel and contrast ligand-gated channels with voltage-gated channels
you explain/illustrate the processes of endocytosis and exocytosis
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Compare the structures and functions of common types of nucleotides and nucleic acids.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you compare and contrast the major structural features of each of the following: nucleosides vs. nucleotides, purines vs. pyrimidines, DNA vs. RNA
you determine the complementary sequence and strand orientation in either a DNA duplex or a DNA-RNA hybrid
you describe the general information transfer role of each of the following: DNA, mRNA, rRNA and tRNA.
you produce a labeled diagram of a generalized tRNA molecule, indicating stem regions, loop regions, anticodon and amino acid attachment point
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Contrast general features of prokaryotic and eukaryotic DNA.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you contrast both forms with respect to each of the following: linear vs. circular structure, complexation with histone proteins, relative genome size, supercoiling, presence of telomeres
you explain the concept of supercoiling
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Discuss the known directions of genetic information transfer.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you diagram the known directions of genetic information transfer, using the correct term for each process
you define the terms DNA replication, transcription, translation and reverse transcription
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Explain the major events involved in DNA replication.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you use vocabulary terms related to replication, such as origin, semiconservative, leading vs. lagging strands, continuous vs. discontinuous synthesis, primer, proofreading, replication fork and exonuclease
you describe in words and diagrams the major events in the various stages of DNA replication
you explain how various issues in DNA replication are overcome
you contrast general aspects of prokaryotic DNA replication with eukaryotic DNA replication
you describe the function of telomeres and telomerase in eukaryotic chromosome replication
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Discuss the excision-repair mechanism of DNA repair.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe the major events in the excision and repair of damaged DNA
you describe the relationships among ultraviolet radiation, thymine dimers and conditions such as xeroderma pigmentosum and skin cancer
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Explain the major events in mRNA synthesis.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe the major events and molecules involved in the initiation, elongation and termination stages of transcription
you contrast general aspects of gene structure and mRNA synthesis in prokaryotes vs. eukaryotes
you describe general types of posttranscriptional modification of mRNA in eukaryotes
you explain why knowing the DNA sequence of a eukaryotic gene does not allow you to predict the base sequence of the mature mRNA produced by that gene
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Discuss general aspects of the regulation of transcription via regulatory proteins and signal molecules.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you explain how the binding of RNA polymerase to a promoter can affect the level of gene product produced
you contrast positive and negative regulation of transcription
you explain how a signal molecule such as a steroid hormone can interact with a transcription factor to turn on or turn off a eukaryotic gene
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Determine the mRNA and primary peptide structure specified by a given DNA sequence.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
a genetic code table will be provided.
instructions for determining reading frame will be provided.
no post-transcriptional or post-translational modification is assumed for this competency.
Criteria
you provide the correct base sequence of mRNA
you provide the correct amino acid sequence for the peptide
you use initiation and termination codons to determine where translation will start and stop, unless otherwise instructed
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Illustrate how DNA mutations can produce each of the following effects: no effect on protein sequence, a different protein sequence but little change in protein function and a drastic effect on protein function.
Assessment Strategies
a genetic code table and amino acid side-group structure sheet will be provided.
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you use a specific example to explain how a DNA mutation could result in no change in a protein's primary structure
you use a specific example to explain how a DNA mutation could alter a protein's primary structure, but have little effect on the protein's function
you use a specific example to explain how a DNA mutation could have a dramatic effect on a protein's function
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Explain the major events that occur during protein synthesis.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe the major events occurring during each of the three phases of protein synthesis in prokaryotes
you contrast prokaryotic and eukaryotic protein synthesis with respect to the identity of the N-terminal amino acid, the method for determining reading frame, and the coupling of transcription with translation
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Discuss the general types of posttranslational modification that can occur in proteins.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe at least four possible types of polypeptide processing from instructor's list
you explain why knowing the sequence of a eukaryotic gene does not allow one to predict the final amino acid sequence of the protein produced by that gene
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Explain the movement of DNA fragments during gel electrophoresis and the use of complementary probes to make selected fragments visible.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you explain why DNA migrates towards the positive electrode in electrophoresis
you explain the relationship between size and rate of DNA migration
you explain why a complementary DNA probe will make only selected DNA visible in electrophoresis
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Explain the general steps in creating a recombinant DNA molecule using restriction enzymes.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe the base specificity of restriction endonucleases and how "sticky ends" are created in DNA
you describe the process of joining and sealing DNA fragments from different organisms
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Determine the DNA sequence of an oligonucleotide from a diagram of a Sanger-method gel.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you give the correct DNA sequence
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Discuss the utility and some limitations of the PCR reaction.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you summarize the PCR process
you explain why a special DNA polymerase is used in this reaction
you explain how the choice of primers will affect the DNA produced in this reaction
you discuss why it is essential to avoid even trace DNA contamination when performing PCR
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Contrast general aspects of catabolic pathways vs. anabolic pathways.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you contrast the general function, energy requirement, redox behavior and divergence/convergence of each type of pathway
you explain the role of ATP in the coupling of exergonic and endergonic reactions
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Apply the concept of standard free energy change to explain the behavior of metabolic reactions.
Assessment Strategies
formulas relating standard free energy and equilibrium constant will be included in the provided formulas list.
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you interpret the magnitude and sign of a free energy change to determine the direction of spontaneity, the amount of energy involved and the proximity to equilibrium
you explain the fallacy of using standard free energy changes to determine spontaneity in the cell
you calculate the standard free energy change or the equilibrium constant using provided equations relating the two
you calculate the standard free energy of coupled reactions from individual reaction data
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Classify carbohydrates according to their structural features.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you match common carbohydrate names to any of the following applicable categories: monosaccharide, disaccharide, polysaccharide, aldose, ketose, pentose or hexose
you classify a given monosaccharide chain structure according to the type of carbonyl group, number of carbons and the steric arrangement of the penultimate carbon
you compare amylose, amylopectin, glycogen and cellulose with respect to monosaccharide building block, degree of branching and type of glycoside linkages present
you identify anomeric carbons in carbohydrate structures
you classify given carbohydrate ring structures as either alpha or beta
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Illustrate three different biochemical roles of carbohydrates with specific examples.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you give three examples, each significantly different from the others
you use complete sentences in the explanation
examples chosen mention specific carbohydrates, when reasonable
examples chosen come from instructor's notes or the textbook unless supported by information provided by the student
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Provide an overview of glycolysis and the Krebs cycle.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you diagram the glycolysis pathway and the Krebs cycle, showing all of the following: the sequence of metabolites by name, the involvement of other important compounds and major enzymes from the instructor's list.
you sequence a randomized list of metabolite names from glycolysis or the Krebs cycle.
you explain how NAD+ is regenerated in anaerobic glycolysis and in aerobic glucose catabolism
you describe the effect of ADP, ATP, NAD+, NADH, and the availability of intermediates levels on the rate of glycolysis and the Krebs cycle
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Explain the conversion of pyruvate to acetyl-CoA.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you write the net reaction catalyzed by the pyruvate dehydrogenase complex, using names of metabolites
you match names of the five coenzymes involved in the pyruvate dehydrogenase reaction with their roles in the reaction
you describe major regulation of the pyruvate dehydrogenase complex
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Provide an overview of respiratory electron transport and oxidative phosphorylation.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you produce a labeled diagram of a mitochondrion
your overview includes the concepts of electron transfer through 3 respiratory complexes, the use of redox energy to create a proton gradient across the inner membrane and the use of this gradient to produce ATP
you explain the need for mitochondrial shuttles
you provide an adequate explanation for why the malate-aspartate shuttle produces more ATP than the glycerol phosphate shuttle
you explain the role of molecular oxygen in the electron transport chain
you describe the intracellular location of each stage of glucose catabolism
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Calculate theoretical ATP yield from any point along the glucose catabolism pathway.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you determine the amount of ATP that should be produced when a given metabolite is processed through the remainder of the glucose catabolism pathway
you explain the reasoning behind the ATP yield calculation
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Illustrate the linkages between the following portions of glucose catabolism: glycolysis, the conversion of pyruvate to acetyl-CoA, the Krebs cycle, the electron transport chain and the conversion of oxygen to water.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
your diagram shows how the various portions connect
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Provide an overview of the beta-oxidation of fatty acids.
Assessment Strategies
only fatty acids with an even number of carbons will be used in the example.
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you calculate theoretical ATP yield from the activation and oxidation of a given fatty acid
you explain the metabolic logic behind storing caloric reserves as fat
you indicate the intracellular location of the beta-oxidation pathway
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Explain ketone body formation and the metabolic role of ketone bodies.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you give an example of at least one specific ketone body
you describe the conditions leading to ketone body production using the following concepts correctly: relative level of fat vs. carbohydrate catabolism, accumulation of acetyl-CoA and level of Krebs cycle activity
you describe the effect of ketone bodies on blood pH and glucose utilization
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Provide an overview of the general aspects of amino acid catabolism.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you write the general equation for a transamination reaction using names of metabolites
you describe the role of the urea cycle in amino acid catabolism
you explain the role of glycolysis and the Krebs cycle in the catabolism of amino acids.
you explain the basis of dietary restrictions for people with phenylketonuria
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Contrast the metabolic roles of liver glycogen vs. muscle glycogen.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you use the following concepts: fuel for internal use and a means for increasing blood glucose
you illustrate the connections between glycogen metabolism and glycolysis
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Contrast the processes of glycolysis and gluconeogenesis with respect to metabolic role, pathway differences, energy requirements and regulation.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you indicate which pathway is used to provide energy and which requires energy to produce glucose
you indicate the three reactions in which gluconeogenesis is not a simple reversal of glycolysis
you explain the reciprocal regulation of these pathways by ATP, NADH and epinephrine or glucagon (via fructose 2,6-bisphosphate)
you predict the effect of changes in any of the following on glucose metabolism: ATP/ADP ratio, NADH/NAD+ ratio, presence or absence of epinephrine or glucagon
you explain why mammals can produce glucose from pyruvate or most amino acids, but not from fatty acids
you explain the importance of providing glucose as a fuel source for the brain and red blood cells
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Discuss the reciprocal regulation of pyruvate dehydrogenase and pyruvate carboxylase by acetyl-CoA.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe how the level of acetyl-CoA present will determine whether pyruvate is converted to acetyl-CoA or to oxaloacetate
you explain the significance of the pyruvate carboxylase reaction in replacing Krebs cycle intermediates
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Explain how excess nutrients can be converted into fats and cholesterol.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you identify the central metabolite that is the precursor of fatty acids and cholesterol
you explain how even nutrients that are neither fat nor cholesterol can be used to synthesize fat or cholesterol
you define the term essential fatty acid
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Discuss the general metabolic precursors of amino acids.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you list precursors from instructor's list
you explain how ketoacids can be converted to amino acids by transaminations
you define the term essential amino acid
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Provide an overview of lipoproteins in cholesterol metabolism.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you contrast the density, lipid/protein ratio and general role of high-density lipoproteins and low-density lipoproteins
you describe the process of cholesterol uptake, including the role of LDL receptors
you explain how a deficiency of LDL receptors can affect cholesterol levels and atherosclerosis
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Contrast the three general types of hormones with respect to structure and general mode of action.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you give two examples of each of the following types: amino acid derivatives, steroids and polypeptides
you explain the basis for hormones affecting only their target tissues
you contrast the general location (intracellular vs. cell surface) of hormone receptors for nonpolar hormones with those for polypeptide and polar hormones
you explain which types of hormones generally interact with transcription factors to alter gene activity
you explain which types of hormones usually act via a second messenger
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Illustrate the operation of a signal transduction process involving the following components: hormone, receptor, G protein, adenylate cyclase, protein kinases and a protein regulated by phosphorylation.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe and illustrate the operation of the listed components
you explain how the hormone's signal is amplified by this cascade
you explain how the various components of the cascade become inactivated
you predict how a specified defect in this cascade will affect the action of the hormone
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Explain why a lack of insulin can cause ketone body production in the liver.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you use metabolic principles previously discussed to explain ketone body production when insulin is not present
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Construct overview diagrams of catabolism and anabolism.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
each diagram illustrates the connections between metabolites on the instructor's list and has appropriate pathways labeled
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Discuss general roles of various types of dietary components.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe the general roles of each of the following components: carbohydrates, fats, proteins, vitamins, minerals, fiber
you give two specific examples of macronutrients and two specific examples of micronutrients
you explain why some proteins are more nutritionally beneficial than others
you explain the problems with obtaining all calories from carbohydrates, proteins or fats
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Explain the general role of vitamins in metabolism.
Assessment Strategies
in the solution to a problem on a quiz, homework assignment or exam.
Criteria
you describe the general metabolic roles served by vitamins
you classify a given vitamin as water-soluble or fat-soluble
you explain the danger of taking vitamin megadoses, especially for fat-soluble vitamins