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Option B - Biochemistry

B.1 Introduction to biochemistry

Essential idea: Metabolic reactions involve a complex interplay between many different components in highly controlled environments.

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. (3.1)

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.

Guidance:

Intermediates of aerobic respiration and photosynthesis are not required.

B.2 Proteins and enzymes

Essential idea: Proteins are the most diverse of the biopolymers responsible for metabolism and structural integrity of living organisms

Nature of science:

Collaboration and peer reviewseveral different experiments on several continents led to the conclusion that DNA, and not protein as originally thought, carried the information for inheritance. (4.4)

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 proteins 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.

Guidance:

The names and structural formulas of the amino acids are given in the data booklet in section 33.
Reference should be made to alpha helix and beta pleated sheet, and to fibrous and globular proteins with examples of each.
In paper chromatography the use of Rf values and locating agents should be covered.
In enzyme kinetics Km and Vmax are not required.

B.3 Lipids

Essential idea: Lipids are a broad group of biomolecules that are largely non-polar and therefore insoluble in water.

Nature of science:

Significance of science explanations to the publiclong-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. (5.2)

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 highdensity
lipoprotein (HDL) and low-density lipoprotein (LDL) cholesterol, saturated, unsaturated and trans-fat and the use and abuse of steroids.

Guidance:

The structures of some fatty acids are given in the data booklet in section 34.
Specific named examples of fats and oils do not have to be learned.
The structural differences between cis- and trans-fats are not required.

B.4 Carbohydrates

Essential idea: Carbohydrates are oxygen-rich biomolecules, which play a central role in metabolic reactions of energy transfer..

Nature of science:

Construct models/visualizationsunderstanding 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. (1.10) Obtaining evidence for scientific theoriesconsider the structural role of carbohydrates. (1.8)

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.

Guidance:

The straight chain and a-ring forms of glucose and fructose are given in the data booklet in section 34.
The component monosaccharides of specific disaccharides and the linkage details of polysaccharides are not required.
The distinction between a- and - forms and the structure of cellulose are not required.

B.5 Vitamins

Essential idea: Vitamins are organic micronutrients with diverse functions that must be obtained from the diet.

Nature of science:

Making observations and evaluating claimsthe 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). (1.8)

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.

Guidance:

The structures of vitamins A, C and D are provided in the data booklet section 35.
Specific food sources of vitamins or names of deficiency diseases do not have to be learned.

B.6 Biochemistry and the environment

Essential idea: Our increasing knowledge of biochemistry has led to several environmental problems, while also helping to solve others

Nature of science:

Risk assessment, collaboration, ethical considerationsit 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. (4.8)

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.
Hostguest 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 hostguest 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.

Guidance:

Specific names of green chemicals such as solvents are not expected.
The emphasis in explanations of host-guest chemistry should be on non-covalent bonding within the supra-molecule.

B.7 Proteins and enzymes

Essential idea: Analyses of protein activity and concentration are key areas of biochemical research.

Nature of science:

Theories can be supersededlock and key hypothesis to induced fit model for enzymes. (1.9) Collaboration and ethical considerations, scientists collaborate to synthesize new enzymes and to control desired reactions (ie waste control). (4.5)

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 (Vmax) and the value of the Michaelis constant (Km) 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 BeerLambert law.

Guidance:

The effects of competitive and non-competitive inhibitors on Km and Vmax values should be covered.
The HendersonHasselbalch equation is given in the data booklet in section 1.
For UV-vis spectroscopy, knowledge of particular reagents and wavelengths is not required.

B.8 Nucleic acids

Essential idea: DNA is the genetic material that expresses itself by controlling the synthesis of proteins by the cell.

Nature of science:

Scientific methodthe 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. (1.3) Developments in scientific research follow improvements in apparatusdouble helix from X-ray diffraction provides explanation for known functions of DNA. (3.7)

Understandings

Nucleotides are the condensation products of a pentose sugar, phosphoric acid and a nitrogenous baseadenine (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.

Guidance:

Structures of the nitrogenous bases and ribose and deoxyribose sugars are given in the data booklet in section 34.
Knowledge of the different forms of RNA is not required.
Details of the process of DNA replication are not required.
Limit expression of DNA to the concept of a four-unit base code determining a twenty-unit amino acid sequence. Details of transcription and translation are not required.

B.9 Biological pigments

Essential idea: Use of dataquantitative measurements of absorbance are a reliable means of communicating data based on colour, which was previously subjective and difficult to replicate. (3.1)

Nature of science:

Scientific methodthe 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. (1.3) Developments in scientific research follow improvements in apparatusdouble helix from X-ray diffraction provides explanation for known functions of DNA. (3.7)

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 hemoglobins 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.

Guidance:

The structures of chlorophyll, heme B and specific examples of anthocyanins and carotenoids are given in the data booklet in section 35; details of other pigment names and structures are not required.
Explanation of cooperative binding in hemoglobin should be limited to conformational changes occurring in one polypeptide when it becomes oxygenated.
Knowledge of specific colour changes with changing conditions is not required.

B.10 Stereochemistry in biomolecules

Essential idea: Most biochemical processes are stereospecific and involve only molecules with certain configuration of chiral carbon atoms.

Nature of science:

Theories used to explain natural phenomena/evaluate claimsbiochemistry 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. (2.2)

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 a and , depending on whether the position of the hydroxyl group at carbon 1 (glucose) or carbon 2 (fructose) lies below the plane of the ring (a) or above the plane of the ring ().
Vision chemistry involves the light activated interconversion of cis- and transisomers 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.

Guidance:

Names of the enzymes involved in the visual cycle are not required.
Relative melting points of saturated and cis-/trans-unsaturated fats should be covered.