B. Biochemistry
B. Biochemistry
Core
B.1 Introduction to biochemistry
Nature of science:
Use of data - biochemical systems have a large number of different reactions occurring in the same place at the same time. As technologies have developed, more data has been collected leading to the discovery of patterns of reactions in metabolism.
Understandings:
The diverse functions of biological molecules depend on their structures and shapes.
Metabolic reactions take place in highly controlled aqueous environments.
Reactions of breakdown are called catabolism and reactions of synthesis are called anabolism.
Biopolymers form by condensation reactions and are broken down by hydrolysis reactions.
Photosynthesis is the synthesis of energy-rich molecules from carbon dioxide and water using light energy.
Respiration is a complex set of metabolic processes providing energy for cells.
Applications and skills:
Explanation of the difference between condensation and hydrolysis reactions.
The use of summary equations of photosynthesis and respiration to explain the potential balancing of oxygen and carbon dioxide in the atmosphere.
B.2 Proteins and enzymes
Nature of science:
Collaboration and peer review - several different experiments on several continents led to the conclusion that DNA, and not protein as originally thought, carried the information for inheritance.
Understandings:
Proteins are polymers of 2-amino acids, joined by amide links (also known as peptide bonds).
Amino acids are amphoteric and can exist as zwitterions, cations and anions.
Protein structures are diverse and are described at the primary, secondary, tertiary and quaternary levels.
A protein’s three-dimensional shape determines its role in structural components or in metabolic processes.
Most enzymes are proteins that act as catalysts by binding specifically to a substrate at the active site.
As enzyme activity depends on the conformation, it is sensitive to changes in temperature and pH and the presence of heavy metal ions.
Chromatography separation is based on different physical and chemical principles.
Applications and skills:
Deduction of the structural formulas of reactants and products in condensation reactions of amino acids, and hydrolysis reactions of peptides.
Explanation of the solubilities and melting points of amino acids in terms of zwitterions.
Application of the relationships between charge, pH and isoelectric point for amino acids and proteins.
Description of the four levels of protein structure, including the origin and types of bonds and interactions involved.
Deduction and interpretation of graphs of enzyme activity involving changes in substrate concentration, pH and temperature.
Explanation of the processes of paper chromatography and gel electrophoresis in amino acid and protein separation and identification.
B.3 Lipids
Nature of science:
Significance of science explanations to the public - long-term studies have led to knowledge of the negative effects of diets high in saturated fat, cholesterol, and trans-fat. This has led to new food products.
Understandings:
Fats are more reduced than carbohydrates and so yield more energy when oxidized.
Triglycerides are produced by condensation of glycerol with three fatty acids and contain ester links. Fatty acids can be saturated, monounsaturated or polyunsaturated.
Phospholipids are derivatives of triglycerides.
Hydrolysis of triglycerides and phospholipids can occur using enzymes or in alkaline or acidic conditions.
Steroids have a characteristic fused ring structure, known as a steroidal backbone.
Lipids act as structural components of cell membranes, in energy storage, thermal and electrical insulation, as transporters of lipid soluble vitamins and as hormones.
Applications and skills:
Deduction of the structural formulas of reactants and products in condensation and hydrolysis reactions between glycerol and fatty acids and/or phosphate.
Prediction of the relative melting points of fats and oils from their structures.
Comparison of the processes of hydrolytic and oxidative rancidity in fats with respect to the site of reactivity in the molecules and the conditions that favour the reaction.
Application of the concept of iodine number to determine the unsaturation of a fat.
Comparison of carbohydrates and lipids as energy storage molecules with respect to their solubility and energy density.
Discussion of the impact of lipids on health, including the roles of dietary high-density lipoprotein (HDL) and low-density lipoprotein (LDL) cholesterol, saturated, unsaturated and trans-fat and the use and abuse of steroids.
B.4 Carbohydrates
Nature of science:
Construct models/visualizations - understanding the stereochemistry of carbohydrates is essential to understanding their structural roles in cells. Haworth projections help focus on the nature and position of attached groups by making carbon and hydrogen implicit.
Obtaining evidence for scientific theories - consider the structural role of carbohydrates.
Understandings:
Carbohydrates have the general formula Cx(H₂O)y.
Haworth projections represent the cyclic structures of monosaccharides.
Monosaccharides contain either an aldehyde group (aldose) or a ketone group (ketose) and several -OH groups.
Straight chain forms of sugars cyclize in solution to form ring structures containing an ether linkage.
Glycosidic bonds form between monosaccharides forming disaccharides and polysaccharides.
Carbohydrates are used as energy sources and energy reserves.
Applications and skills:
Deduction of the structural formulas of disaccharides and polysaccharides from given monosaccharides.
Relationship of the properties and functions of monosaccharides and polysaccharides to their chemical structures.
B.5 Vitamins
Nature of science:
Making observations and evaluating claims - the discovery of vitamins (vital amines) is an example of scientists seeking a cause for specific observations. This resulted in the explanation of deficiency diseases (eg scurvy and beriberi).
Understandings:
Vitamins are organic micronutrients which (mostly) cannot be synthesized by the body but must be obtained from suitable food sources.
The solubility (water or fat) of a vitamin can be predicted from its structure.
Most vitamins are sensitive to heat.
Vitamin deficiencies in the diet cause particular diseases and affect millions of people worldwide.
Applications and skills:
Comparison of the structures of vitamins A, C and D.
Discussion of the causes and effects of vitamin deficiencies in different countries and suggestion of solutions.
B.6 Biochemistry and the environment
Nature of science:
Risk assessment, collaboration, ethical considerations - it is the responsibility of scientists to consider the ways in which products of their research and findings negatively impact the environment, and to find ways to counter this. For example, the use of enzymes in biological detergents and to break up oil spills, and green chemistry in general.
Understandings:
Xenobiotics refer to chemicals that are found in an organism that are not normally present there.
Biodegradable/compostable plastics can be consumed or broken down by bacteria or other living organisms.
Host–guest chemistry involves the creation of synthetic host molecules that mimic some of the actions performed by enzymes in cells, by selectively binding to specific guest species, such as toxic materials in the environment.
Enzymes have been developed to help in the breakdown of oil spills and other industrial wastes.
Enzymes in biological detergents can improve energy efficiency by enabling effective cleaning at lower temperatures.
Biomagnification is the increase in concentration of a substance in a food chain.
Green chemistry, also called sustainable chemistry, is an approach to chemical research and engineering that seeks to minimize the production and release to the environment of hazardous substances.
Applications and skills:
Discussion of the increasing problem of xenobiotics such as antibiotics in sewage treatment plants.
Description of the role of starch in biodegradable plastics.
Application of host-guest chemistry to the removal of a specific pollutant in the environment.
Description of an example of biomagnification, including the chemical source of the substance. Examples could include heavy metals or pesticides.
Discussion of the challenges and criteria in assessing the “greenness” of a substance used in biochemical research, including the atom economy.
Additional higher level
B.7 Proteins and enzymes
Nature of science:
Theories can be superseded - “lock and key” hypothesis to “induced fit” model for enzymes.
Collaboration and ethical considerations - scientists collaborate to synthesize new enzymes and to control desired reactions (ie waste control).
Understandings:
Inhibitors play an important role in regulating the activities of enzymes.
Amino acids and proteins can act as buffers in solution.
Protein assays commonly use UV-vis spectroscopy and a calibration curve based on known standards.
Applications and skills:
Determination of the maximum rate of reaction (V max) and the value of the Michaelis constant (K m) for an enzyme by graphical means, and explanation of its significance.
Comparison of competitive and non-competitive inhibition of enzymes with reference to protein structure, the active site and allosteric site.
Explanation of the concept of product inhibition in metabolic pathways.
Calculation of the pH of buffer solutions, such as those used in protein analysis and in reactions involving amino acids in solution.
Determination of the concentration of a protein in solution from a calibration curve using the Beer-Lambert law.
B.8 Nucleic acids
Nature of science:
Scientific method - the discovery of the structure of DNA is a good example of different approaches to solving the same problem. Scientists used models and diffraction experiments to develop the structure of DNA.
Developments in scientific research follow improvements in apparatus - double helix from X-ray diffraction provides explanation for known functions of DNA.
Understandings:
Nucleotides are the condensation products of a pentose sugar, phosphoric acid and a nitrogenous base - adenine (A), guanine (G), cytosine (C), thymine (T) or uracil (U).
Polynucleotides form by condensation reactions.
DNA is a double helix of two polynucleotide strands held together by hydrogen bonds.
RNA is usually a single polynucleotide chain that contains uracil in place of thymine, and a sugar ribose in place of deoxyribose.
The sequence of bases in DNA determines the primary structure of proteins synthesized by the cell using a triplet code, known as the genetic code, which is universal.
Genetically modified organisms have genetic material that has been altered by genetic engineering techniques, involving transferring DNA between species.
Applications and skills:
Explanation of the stability of DNA in terms of the interactions between its hydrophilic and hydrophobic components.
Explanation of the origin of the negative charge on DNA and its association with basic proteins (histones) in chromosomes.
Deduction of the nucleotide sequence in a complementary strand of DNA or a molecule of RNA from a given polynucleotide sequence.
Explanation of how the complementary pairing between bases enables DNA to replicate itself exactly.
Discussion of the benefits and concerns of using genetically modified foods.
B.9 Biological pigments
Nature of science:
Use of data - quantitative measurements of absorbance are a reliable means of communicating data based on colour, which was previously subjective and difficult to replicate.
Understandings:
Biological pigments are coloured compounds produced by metabolism.
The colour of pigments is due to highly conjugated systems with delocalized electrons, which have intense absorption bands in the visible region.
Porphyrin compounds, such as hemoglobin, myoglobin, chlorophyll and many cytochromes are chelates of metals with large nitrogen-containing macrocyclic ligands.
Hemoglobin and myoglobin contain heme groups with the porphyrin group bound to an iron(II) ion.
Cytochromes contain heme groups in which the iron ion interconverts between iron(II) and iron(III) during redox reactions.
Anthocyanins are aromatic, water-soluble pigments widely distributed in plants. Their specific colour depends on metal ions and pH.
Carotenoids are lipid-soluble pigments, and are involved in harvesting light in photosynthesis. They are susceptible to oxidation, catalysed by light.
Applications and skills:
Explanation of the sigmoidal shape of hemoglobin’s oxygen dissociation curve in terms of the cooperative binding of hemoglobin to oxygen.
Discussion of the factors that influence oxygen saturation of hemoglobin, including temperature, pH and carbon dioxide.
Description of the greater affinity of oxygen for foetal hemoglobin.
Explanation of the action of carbon monoxide as a competitive inhibitor of oxygen binding.
Outline of the factors that affect the stabilities of anthocyanins, carotenoids and chlorophyll in relation to their structures.
Explanation of the ability of anthocyanins to act as indicators based on their sensitivity to pH.
Description of the function of photosynthetic pigments in trapping light energy during photosynthesis.
Investigation of pigments through paper and thin layer chromatography.
B.10 Stereochemistry in biomolecules
Nature of science:
Theories used to explain natural phenomena/evaluate claims - biochemistry involves many chiral molecules with biological activity specific to one enantiomer. Chemical reactions in a chiral environment act as a guiding distinction between living and non-living matter.
Understandings:
With one exception, amino acids are chiral, and only the L-configuration is found in proteins.
Naturally occurring unsaturated fat is mostly in the cis form, but food processing can convert it into the trans form.
D and L stereoisomers of sugars refer to the configuration of the chiral carbon atom furthest from the aldehyde or ketone group, and D forms occur most frequently in nature.
Ring forms of sugars have isomers, known as α and β, depending on whether the position of the hydroxyl group at carbon 1 (glucose) or carbon 2 (fructose) lies below the plane of the ring (α) or above the plane of the ring (β).
Vision chemistry involves the light activated interconversion of cis- and trans- isomers of retinal.
Applications and skills:
Description of the hydrogenation and partial hydrogenation of unsaturated fats, including the production of trans-fats, and a discussion of the advantages and disadvantages of these processes.
Explanation of the structure and properties of cellulose, and comparison with starch.
Discussion of the importance of cellulose as a structural material and in the diet.
Outline of the role of vitamin A in vision, including the roles of opsin, rhodopsin and cis- and trans-retinal.
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