Option B Human

Biochemistry
IB CHEMISTRY SL

Michael Sugiyama Jones

WWW.MSJCHEM.COM
B.1 Introduction to biochemistry

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.
• International-mindedness:
• Metabolic reactions in the human body are dependent on the supply of nutrients
through a regular balanced diet. Globally there are significant differences in the
availability of nutritious food, which have major and diverse impacts on human
health.

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Introduction to biochemistry

• Biochemistry is the study of chemical reactions that occur in living organisms.

• These chemical reactions are known as metabolism.
• The chemical reactions involved in metabolism are organised into metabolic
pathways.
• Each chemical reaction is controlled by a specific catalyst called an enzyme, and
occurs in a controlled aqueous environment.

Catabolism and anabolism

• Catabolism is the breaking up of large molecules to form smaller molecules

(energy is released).
• An example of catabolism is cellular respiration. In cellular respiration, glucose is
broken down into smaller molecules (CO2 and H2O) and energy is released.

glucose + oxygen ⟶ carbon dioxide + water (ΔH is negative)

C6H12O6 + 6O2 ⟶ 6CO2 + 6H2O

• The energy released in catabolic reactions is used in anabolic reactions.

• Anabolism is the building up of smaller molecules to form larger molecules (energy is

required).
• An example is the synthesis of proteins from amino acids.

Exercises:

1. Using examples, describe the difference between anabolism and catabolism.

2. Classify catabolic and anabolic reactions as exothermic or endothermic.

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Condensation and hydrolysis reactions

• A condensation reaction is a chemical reaction in which two molecules react to form

a larger molecule with the loss of a small molecule (usually water) forming a covalent
bond.

• Biopolymers are long chain molecules formed in condensation reactions.

• Each molecule (monomer) must have two reactive functional groups.

• A hydrolysis reaction is a chemical reaction in which a water molecule reacts with a

large molecule breaking the covalent bond and forming two smaller molecules.

• Hydrolysis reactions are catalysed by enzymes in the human body.

• They also take place in the presence of an acid or an alkali (such as NaOH).

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Exercises:

1. Outline the differences between condensation and hydrolysis reactions.

2. In a saponification reaction, a triglyceride is broken down to form glycerol and 3

smaller molecules (see below). Explain why this can be classified as a hydrolysis
reaction.

3. Suggest a reason why a monomer must have two reactive functional groups to form
a biopolymer.

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Photosynthesis and respiration

Photosynthesis

• Photosynthesis is the process by which plants synthesize energy rich molecules such
as carbohydrates (anabolism).

• The process occurs in green plants in the presence of a light absorbing pigment
called chlorophyll.

6CO2 + 6H2O ⟶ C6H12O6 + 6O2 ΔH positive

Respiration

• Cellular respiration is a process that occurs in the cells of living organisms.

• Energy rich molecules such as carbohydrates are broken down to produce carbon
dioxide and water, releasing energy in the process (catabolism).

C6H12O6 + 6O2 ⟶ 6CO2 + 6H2O ΔH negative

• The products of cellular respiration are the reactants in photosynthesis (and vice
versa).

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B.2 Proteins and enzymes

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.

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.

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Introduction to proteins
• Proteins are found in such foods as meat, fish, and eggs.
• Proteins are important biological molecules (composed of amino acids) and are used
for many different purposes in the human body.
• Hair and finger nails are made of keratin which is a structural protein.
• Enzymes (biological catalysts) are made of proteins that have specific 3D structures.
• Transport molecules such as haemoglobin are also made of proteins.

Amino acids
• Proteins are composed of amino acids.
• The structure of an amino acid can be seen below.

amino group (NH2) carboxyl group (COOH)

• Amino acids have an amino group (NH2) and a carboxyl group (COOH).
• The R represents a side chain, which is different for every amino acid.

Amino acids bond in condensation reactions

• The bonding of amino acids produces dipeptides, tripeptides, and polypeptides

(proteins).

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Exercise: draw the structure a tripeptide that is produced in the reaction of the 3 amino
acids below.

How many different tripeptides could be produced from 3 amino acids?

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Structure of proteins

• Proteins are long chain molecules (polymers) composed of amino acids (monomers).
• The three structures of proteins are primary, secondary, tertiary and quaternary.

Primary structure
• The primary structure of a protein refers to the sequence of amino acids in the
polypeptide chain, which can be seen in the diagram below).

• The bond responsible for the primary structure is the peptide bond (or amide link).

Secondary structure

• The secondary structure of a protein refers to the folding of the polypeptide chain as
a result of hydrogen bonding.
• The two types of secondary structure are the α-helix and the β-pleated sheet.

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Tertiary structure

• The tertiary structure of proteins refers to the twisting and folding of the secondary
structure to form a specific 3D shape (as a result of interactions between the side
chains).

peptide bond between

COOH and H-N

• Hydrophobic interactions (London dispersion forces) between non-polar side chains.

• Hydrogen bonding between polar side chains.
• Ionic bonding between charged side chains.
• Disulfide bridges (covalent bonds) between the side chains of cysteine which contain
a sulfhydryl group (CH2-SH).
• Peptide bonds between COOH and N-H.

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Quaternary structure
• The quaternary structure of proteins refers to the interactions between polypeptide
chains.
• An example is hemoglobin that has a quaternary structure composed of four
polypeptide chains.

Exercises:

1. State the type of bonding that is responsible for the primary and secondary
structures of proteins.

Primary:

Secondary:

2. Describe and explain the tertiary structure of proteins. Include in your answer
all (5) of the bonds and interactions responsible for the tertiary structure.

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Fibrous and globular proteins
• Fibrous proteins are elongated molecules in which the secondary structure (α-helix
or β pleated sheets) forms the dominant structure. They are insoluble in water, and
form structural components in the body.
• Globular proteins are spherical molecules that are soluble in water. All have tertiary
structures and some have quaternary structures.

fibrous protein globular protein

Properties Fibrous proteins Globular proteins

Shape long and narrow rounded/spherical

Role structural (strength and support) functional (catalysts and

transport)

Solubility in water mostly insoluble mostly soluble

Sequence of repetitive amino acid sequence irregular amino acid

amino acids sequence

Stability less sensitive to changes in heat and more sensitive to

pH changes in heat and pH

Examples collagen, keratin hemoglobin, insulin,

catalase

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Acid-base properties of amino acids
• Amino acids form zwitterions – electrically neutral molecules with a positive and
negative charge.
H+

• Amino acids are amphoteric (amphiprotic); they can act as Bronsted – Lowry acids or
bases by donating a proton (H+) or accepting a proton (H+).

A proton (H+) can be a A proton (H+) can be

donated by the NH3+ accepted by the COO-

• Donating a proton (Brosnted-Lowry acid)

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 • Accepting a proton (Bronsted-Lowry base)

Isoelectric points of amino acids

• The charge on an amino acid depends on the pH.
• The isoelectric point is the pH at which the amino acid has no overall charge.

⇌ ⇌
pH < pH of isoelectric Isoelectric point pH > pH of isoelectric
point no overall charge point
positively charged negatively charged

no overall charge

Exercise:
The pH of the isoelectric point of glycine is 6.0. Draw the structure of glycine at pH 3.0 and
pH 9.0

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Protein analysis
• The two methods of protein analysis are gel electrophoresis and paper
chromatography.
• Before proteins can be analysed, they must be broken down into their component
amino acids in a hydrolysis reaction.
• In the hydrolysis reaction with concentrated hydrochloric acid, the peptide bonds
between the amino acids are broken.

Paper chromatography
• A small sample of the amino acid mixture is
spotted near the bottom of the filter paper
(the origin).
• The filter paper is suspended in a solvent with
the spot above the level of the solvent.
• As the solvent rises up the filter paper by
capillary action, the amino acids in the mixture
will distribute themselves between 2 phases –
the stationary phase (the filter paper) and the
mobile phase (the solvent).
• The different amino acids separate according
to how strongly they adsorb onto the
stationary phase versus how readily they
dissolve in the mobile phase.

• Once the paper is removed, it is sprayed

with ninhydrin (a locating reagent – organic
dye).
• Most amino acids will take a purple colour
and can be distinguished as separate spots
on the paper.
• The position of each amino acid can be
expressed as a Rf value and compared with
known Rf values.
• Finally, the amino acids in the mixture can
be identified.

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Gel electrophoresis
• Electrophoresis is a technique for the analysis and separation of a mixture based on
the movement of charged particles in an electric field.
• Amino acids carry different charges depending on the pH and therefore can be
separated when placed in a buffer solution.

• The amino acid mixture is placed in the

centre of a gel (usually polyacrylamide).
• A potential difference is applied.
• Depending on the pH of the buffer
solution, the amino acids will move at
different rates towards the oppositely
charged electrodes.
• After separation, the amino acids are
sprayed with a locating agent (ninhydrin
– an organic dye).
• The amino acids are identified by
measuring the distance travelled and
comparing with known samples.

Exercise: Outline the processes of protein analysis in chromatography and gel

electrophoresis.

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Enzymes
• Enzymes are protein molecules that function as biological catalysts.

Enzymes increase the rate of a

reaction by providing an
alternative route for a
chemical reaction with lower
activation energy (Ea).

How enzymes catalyse reactions

• The substrate enters the active site, which changes shape to fit the substrate.

• The substrate binds at the active site forming an enzyme-substrate complex.

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 • The catalysed reaction takes place and the products leave the active site. The active
site is available for the next substrate molecule.

• Enzymes are highly specific for the reaction that they catalyse.
• The action of an enzyme depends on its specific 3D structure (conformation).
• Factors that affect an enzyme’s conformation affect its ability to bind with the
substrate; changes in temperature, pH, and presence of heavy metal ions.

Enzyme activity and substrate concentration

• a - at low substrate concentration, the rate of reaction is proportional to the

substrate concentration - there are plenty of active sites available to bind to the
substrate.
• b - as the substrate concentration increases, the rate of reaction decreases and is no
longer proportional to the substrate concentration - some of the active sites are
occupied by substrate.
• c - at high substrate concentration, the rate of reaction is constant and independent
of the substrate concentration - the enzyme is saturated with substrate (point of
saturation).

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Factors that affect enzyme activity
• The activity of an enzyme depends on its tertiary structure (conformation).
• Any factor that disrupts the tertiary structure of an enzyme will affect the ability of
the enzyme to catalyse a specific reaction.
• If the tertiary structure of an enzyme is disrupted, the substrate can no longer bind
to the active site.
• Loss of the tertiary structure is known as denaturation (irreversible).
• The factors that can disrupt an enzyme’s tertiary structure are temperature, pH, and
the presence of heavy metal ions.

Temperature
• The optimum temperature is the temperature corresponding to the maximum rate
of reaction for an enzyme.

• Beyond the optimum temperature, the bonds and interactions that maintain the
enzyme’s tertiary structure are disrupted.
• The substrate is no longer able to bind at the active site (rate of reaction decreases).
• If the tertiary structure of an enzyme is disrupted, the substrate can no longer bind
to the active site.
• Loss of the tertiary structure is known as denaturation (irreversible).
• The factors that can disrupt an enzyme’s tertiary structure are temperature, pH, and
the presence of heavy metal ions.
• Lowering the temperature deactivates the enzyme and is reversible.
• The activity of the enzyme decreases but the tertiary structure is maintained.
• This explains why keeping food in the refrigerator prevents it from spoiling (going
bad).

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pH
• The optimum pH is the pH at which the enzyme is most active (maximum rate of
reaction).

• Above or below the optimum pH, the charges on the acidic (COOH) and basic (NH2)
groups change.
• The enzyme’s tertiary structure is disrupted and the shape or charge of the substrate
can also be affected so that it cannot bind to the active site.

• At point X (low pH), the enzyme is protonated (has a positive charge), therefore the
substrate is unable to bind effectively at the active site.
• At point Y (optimum pH), the substrate is able to bind effectively at the active site.
• At point Z (high pH), the enzyme is deprotonated (has a negative charge), therefore
the substrate is unable to bind effectively at the active site.

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 • Pepsin is more active in the stomach where pH is low. Trypsin is more active in the
intestine where the pH is higher (alkaline).

• Changes in pH can denature an enzyme in the same way as temperature by

disrupting the bonds and interactions that are responsible for the tertiary structure.

Heavy metal ions

• Heavy metal ions (Ag+) can react with the sulfhydryl group on cysteine, replacing the
hydrogen atom with a heavy metal ion.

• The tertiary structure is disrupted and the substrate is no longer able to bind at the
active site.

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B.3 Lipids

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.
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.

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Introduction to lipids

• Lipids are organic molecules with long hydrocarbon chains that are soluble in non-
polar solvents.

Lipids and their functions

lipid function

triglycerides energy storage

thermal insulation

phospholipids components of cell membranes

electrical insulation in nerves

steroids hormones in the human body

• Lipids are also involved in the transportation of fat soluble vitamins (A, D, E and K).

Energy content of fats and carbohydrates

• Carbohydrates and lipids are both used for energy storage in the human body.
• Gram for gram, lipids provide more energy than carbohydrates.
• In lipids, the ratio of H to O is greater than in carbohydrates (they are more
reduced).
• When oxidized, lipids release more energy.

Solubility of carbohydrates and fats

• Glucose is soluble in water - it has polar OH groups that form hydrogen bonds with
water molecules.
• Fats are insoluble in water - they have non-polar hydrocarbon chains.
• Because they are soluble in water, carbohydrates are more rapidly transported in the
body and are used for short term energy supply.
• Because they are insoluble in water, fats are more slowly transported in the body
and are used as long term energy storage.
• Lipids provide more energy than carbohydrates because they are more reduced and
insoluble in water.

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Fatty acids
• Fatty acids are carboxylic acids with a long hydrocarbon chain.

• Fatty acids can be saturated, unsaturated or polyunsaturated, depending on the

number of carbon to carbon double bonds in the molecule.

Saturated fatty acids

• Carbon to carbon single bonds.
• 109.5o bond angle between carbon atoms (tetrahedral arrangement).

• Saturated fatty acids have carbon to carbon single bonds with 109.5 o bond angles
which allow the molecules to pack closely together.
• This leads to stronger London dispersion forces between molecules and a higher
melting point.
• Triglycerides composed of saturated fatty acids have higher melting points and are
solids at room temperature (fats e.g. butter).

Monounsaturated fatty acids

• Carbon to carbon double bond.
• 120o bond angle between carbon atoms in double bond (trigonal planar
arrangement).

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Polyunsaturated fatty acids
• Multiple carbon to carbon double bonds.
• 120o bond angle between carbon atoms in double bonds (trigonal planar
arrangement).

• Unsaturated fatty acids have carbon to carbon double bonds with 120o bond angles
(kink) meaning the molecules cannot pack closely together.
• This leads to weaker London dispersion forces between molecules and a lower
melting point.
• Triglycerides composed of unsaturated fatty acids have lower melting points and are
liquids at room temperature (oils e.g. olive oil).

Triglycerides

• Triglycerides are produced in condensation (esterification) reactions between a

molecule of glycerol and 3 fatty acids.

glycerol (propane-1,2,3-triol fatty acid (stearic acid C18H36O2)

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 • The glycerol and 3 fatty acids react in a condensation (esterification) reaction to
form a triglyceride and 3 molecules of water.

• An ester link (COOC) is formed between the glycerol molecule and the 3 fatty acids.

Melting points of triglycerides

• Saturated fatty acids (fats) have higher melting points than unsaturated fatty acids
(oils).
• The kink resulting from the C=C bond prevents the chains from packing close
together and weaker London dispersion forces between molecules.

Saturated fatty acids - close packing

of molecules, stronger London
dispersion forces between
molecules, higher melting point.

Unsaturated fatty acids - kink in

chain prevents close packing of
molecules.
Weaker dispersion forces between
molecules, lower melting point,

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Phospholipids

• A phospholipid is composed of a glycerol backbone with two fatty acids and a

phosphate group bonded in condensation reactions.

• Phospholipids are found in cell membranes where they form a phospholipid bilayer.

Hydrolysis of lipids

• Fats and oils are hydrolysed in the human body by the enzyme lipase.

lipase

triglyceride + water  glycerol + 3 fatty acids

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 • Acid hydrolysis - triglycerides can be hydrolysed in a hot aqueous solution of strong
acid.

• Alkaline hydrolysis produces the salt of the fatty acid (soaps). This is known as
saponification.

• Phospholipids are also hydrolysed in the human body.

phospholipid + water  glycerol + 2 fatty acids

Summary:
• Triglycerides and phospholipids are broken down in hydrolysis reactions to form
their component molecules.
• The reactions use water and can occur in alkaline or acidic conditions.
• Alkaline hydrolysis produces soaps (saponification).
• The digestion of triglycerides and phospholipids in the human body involves the use
of enzymes.

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Rancidity of fats
• Rancidity of fats and oils causes a disagreeable smell, texture or appearance.
• The two types of rancidity are hydrolytic and oxidative.

Hydrolytic rancidity
• The sites of reactivity are the ester linkages in the triglyceride.

• This reaction occurs more quickly in the presence of heat and moisture.
• It is catalyzed by the enzyme lipase.
• The rancid smell is due to the release of fatty acids.
• Hydrolytic rancidity can be reduced by refrigeration.

Oxidative rancidity

• Oxidative rancidity (auto oxidation) occurs when oxygen is added across a carbon to
carbon double bond.
• The sites of reactivity are the carbon to carbon double bonds.

• The reaction is catalyzed by light, enzymes or metal ions.

• It occurs in oils with a high proportion of carbon to carbon double bonds.
• Hydrolytic rancidity can be controlled with anti-oxidants.

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Steroids
• Steroids are lipids with a structure consisting of 4 fused hydrocarbon rings (steroidal
backbone).
• The male and female sex hormones are examples of steroids.

female sex hormone (estrogen) male sex hormone (testosterone)

Uses of steroids:
• Female steroid hormones are used in the oral contraceptive pill and hormone
replacement therapy (HRT).
• Steroids are also used to build up depleted muscle due to lack of activity and to
assist in recuperation from an illness.
Abuses of steroids:
• Anabolic steroids are sometimes used by athletes to increase muscle and strength
for an unfair advantage in sport.

Cholesterol
• Cholesterol has a steroidal backbone (4 fused hydrocarbon rings).

• Cholesterol is transported around the body by lipoproteins.

• LDL (low density lipoprotein) transports cholesterol to the arteries where it leads to
thickening of the walls of the arteries (atherosclerosis).
• The main sources of LDL cholesterol are saturated fats; lauric acid, myristic acid and
palmitic acid.

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 • HDL (high density lipoprotein) removes cholesterol from the walls of the arteries.
Iodine number
• The addition of iodine (I2) to unsaturated fats can be used to determine the number
of carbon to carbon double bonds in the fat.
• The iodine number is defined as the number of grams of iodine that reacts with 100g
of fat.
• One mole of double bonds reacts with one mole of I2, according to the equation
below.

Exercises:

1. Calculate the mass of iodine that reacts with the following: (M I2 = 254 gmol-1)

(i) One mol of a monounsaturated fatty acid (one mol of carbon to carbon double
bonds).

(ii) One mol of a fatty acid with two mol of carbon to carbon double bonds.

(iii) One mol of a fatty acid with three mol of carbon to carbon double bonds.

2. Linolenic acid (M = 278 gmol-1) has the following formula.

(i) Determine the number of carbon to carbon double bonds in linolenic acid.

(ii) Determine the mass of iodine (I2) that reacts with 278 g (one mol) of linolenic acid.

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(iii) Calculate the iodine number of linoleic acid (the mass of iodine that reacts with
100g of fat)

3. Linoleic acid (M = 281) has the following formula.

Calculate the volume of 1.00 mol dm-3 iodine solution required to react exactly with
1.00 g of linoleic acid.

(i) Determine the number of carbon to carbon double bonds in linoleic acid

(ii) Calculate the mass of iodine that reacts with one mol of linoleic acid (M I2 = 254 gmol-1)

(iii) Calculate the mass of iodine that reacts with 1.00 g of linoleic acid and therefore
the amount in mol, using the equation n=m/M.

(iv) Use the equation V=n/C to calculate the volume of 1.00 moldm-3 iodine solution
that reacts with 1.00 g of linoleic acid.

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B.4 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.
Guidance:
• The straight chain and α-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 α- and β- forms and the structure of cellulose are not
required.

Monosaccharides
• Monosaccharides have a carbonyl group and at least 2 hydroxyl groups.
• The empirical formula of monosaccharides is CH2O
• Glucose and fructose are examples of hexose sugars (6 carbon atoms C6H12O6).

glucose (aldose sugar) fructose (ketose sugar)

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 • In aqueous solutions, straight chain sugars form ring structures with an ether
linkage.

α-glucose β-fructose

Disaccharides

• Disaccharides are formed from monosaccharides in condensation reactions.

• The bond between glucose monomers is a 1,4 glycosidic link.

α-glucose + α-glucose → maltose + water

C12H22O11

• Disaccharides are formed from monosaccharides in condensation reactions.

• A molecule of water is eliminated as an OH group from each sugar molecule
reacts together.
• The bond between sugar molecules in a disaccharide is called a glycosidic link.
• Disaccharides are soluble molecules that can be hydrolyzed into
monosaccharides by acid hydrolysis or enzyme catalyzed reactions.

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Polysaccharides
• Polysaccharides are composed of long chains of monosaccharides bonded
by glycosidic links.

• Starch is a polysaccharide composed of α-glucose with 1,4 glycosidic links between

molecules.
• Polysaccharides are used for energy storage.
• Starch is used as carbohydrate storage in plants.
• Glycogen is used as carbohydrate storage in humans.
• Cellulose is used as structural material in plants and as dietary fiber as part of a
balanced diet.

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B.5 Vitamins
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.

Vitamins
• Vitamins are organic micro-nutrients (substances needed in small amounts in the
human body <0.005% of body mass).
• They are not made in the human body (except vitamin D) so must be obtained from
the diet.
• Vitamins can be classified as fat soluble or water soluble.

Vitamin A

• Fat soluble – non-polar hydrocarbon chain and ring.

• Vitamin A is important for low-light vision.
• A lack of vitamin A causes night blindness.

OPTION B SL WWW.MSJCHEM.COM 37
Vitamin C

• Water soluble – large number of polar OH groups which are able to form hydrogen
bonds with water molecules.
• A lack of vitamin C causes scurvy.
• Due to its solubility in water, it is not retained by the body for long periods.
• The carbon to carbon double bond and OH groups in vitamin C are readily oxidized
(by air and light).
• Keeping food containing vitamin C in the refrigerator slows down this process.
• Water soluble vitamins such as vitamin C are sensitive to heat and are destroyed by
cooking.

Vitamin D

• Fat soluble – non-polar hydrocarbon chains and rings.

• Vitamin D stimulates the uptake of calcium ions, important for healthy bones and
teeth.
• A lack of vitamin D can cause rickets. Vitamin D is made in the body by the action of
sunlight on the skin.

OPTION B SL WWW.MSJCHEM.COM 38
Vitamin deficiencies
• Millions of people worldwide suffer from a lack of vitamins in their diet (malnutrition).
Common vitamin deficiencies and their causes.

Disease Deficiency

Night blindness lack of vitamin A

Pellagra lack of vitamin B3

Scurvy lack of vitamin C (found in citrus fruit)

Rickets lack of vitamin D (produced during exposure to sunlight)

Causes of vitamin deficiencies:

• Lack of distribution of global resources
• Depletion of nutrients in the soil
• Lack of education about balanced diets
• Over-processing foods
Solutions to vitamin deficiencies:
• Fortifying staple foods with micronutrients
• Taking nutritional supplements
• Genetically modifying foods to increase nutrient content
• Educating people about balanced diets

OPTION B SL WWW.MSJCHEM.COM 39
B.6 Biochemistry and the environment
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.
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 supramolecule.

OPTION B SL WWW.MSJCHEM.COM 40
Xenobiotics
• Xenobiotics are chemical substances found within an organism that are not naturally
produced by or expected to be present within that organism.

• Antibiotics are xenobiotics in animals – they are not produced by animals, nor are
they part of a normal diet.
• Certain bacteria can become resistant to antibiotics. Sewage treatment plants can
promote the spread of antibiotic resistance between bacteria.
• Water discharged into lakes and rivers from sewage treatment plants can contain
significant concentrations of the genes that make bacteria antibiotic resistant.
• Dioxins and polychlorinated biphenyls (PCBs) are toxic chemicals that persist in the
environment.
• Once dioxins enter the body, they accumulate due to their chemical stability and also
their ability to be absorbed by fatty tissue.
• Long term exposure to these substances causes a range of adverse effects on the
nervous, immune, and endocrine systems. They may also be carcinogenic (cancer
causing).

OPTION B SL WWW.MSJCHEM.COM 41
Biodegradable plastics
• Biodegradable (compostable) plastics can be consumed or broken down by bacteria
or other living organisms.
• PLA (polylactide) is a biodegradable plastic derived from renewable resources such
as corn starch.

• The breakdown of starch based plastics (bioplastics) produces carbon dioxide and
water.
• Bioplastics can be broken down in hydrolysis reactions due to the the presence of
ester linkages or glycosidic links (requires heat and moisture).
• When some biodegradable plastics decompose in landfills, they produce methane
gas which is a very powerful greenhouse gas (anaerobic conditions).

Host-guest chemistry
• The host selectively binds a guest in order to produce a host-guest complex
(supramolecule) through non-covalent interactions.
• The four types of non-covalent interactions between the host and guest are:
hydrogen bonds, ionic bonds, van der Waal’s forces and hydrophobic interactions.
• Host-guest chemistry can be applied to the removal of xenobiotics in the
environment.
• The binding between a xenobiotic and a host produces a supramolecule.
• Examples of xenobiotics in the environment are radioactive cesium-137, and
aromatic amines which are known to be carcinogenic.

OPTION B SL WWW.MSJCHEM.COM 42
Biomagnification
• Biomagnification is the increase in concentration of a xenobiotic in a food chain.

• DDT is an insecticide that was used to control mosquito populations that spread
diseases such as malaria and typhus.
• DDT is readily soluble in fat and does not break down therefore it accumulates in
fatty tissue.
• In the 1960s birds of prey such as ospreys suffered a decline in numbers which was
due to the toxic effects of DDT.
• The use of DDT as an insecticide was banned in many countries in the 1970s.

Green chemistry - atom economy

• The % atom economy tells us the percentage by mass of the reactants that do not
end up in the desired product (they are wasted).
• The higher the atom economy for a chemical reaction, the less waste is produced
and the more efficient the reaction is.

Example:
Fe is produced by the reduction of Fe2O3 in a blast furnace. Calculate the atom economy of
the reaction.

OPTION B SL WWW.MSJCHEM.COM 43
 Option B Human
Biochemistry
IB CHEMISTRY HL

Michael Sugiyama Jones

WWW.MSJCHEM.COM
B.7 Enzymes and proteins
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 Beer–Lambert law.
Guidance:
• The effects of competitive and non-competitive inhibitors on Km and Vmax values
should be covered.
• The Henderson–Hasselbalch equation is given in the data booklet in section 1.
• For UV-vis spectroscopy, knowledge of particular reagents and wavelengths is not
required.

OPTION B HL WWW.MSJCHEM.COM 2
Enzyme kinetics
• Effect of substrate concentration on rate of reaction

• Maximum rate of reaction Vmax - the point where all the active sites are bound to
substrate (enzyme is saturated).
• Michaelis constant Km - the substrate concentration which is equal to half its
maximum value (½ Vmax).

Value of Vmax
• Vmax reflects how fast the enzyme can catalyse the reaction.
• A low value of Vmax means that the enzyme does not convert much substrate to
product per unit time when the enzyme is saturated with substrate.
• A high value of Vmax means the opposite. The Vmax is a measure of how fast the
enzyme can work when it is completely saturated with the substrate.
Value of Km
• Enzymes have varying tendencies to bind their substrates (affinity).
• A high value of Km means a high concentration of substrate must be present to
saturate the enzyme, therefore the enzyme has a low affinity for the substrate.
• A low value of Km means only a small amount of substrate is needed to saturate the
enzyme, indicating a high affinity for the substrate.

OPTION B HL WWW.MSJCHEM.COM 3
Exercise: Use the graph to determine Vmax and the Michaelis constant Km

OPTION B HL WWW.MSJCHEM.COM 4
Competitive inhibitors
• Competitive inhibitors bind at the active site of the enzyme (they compete with the
substrate for the active site).
• They usually have a chemical structure similar to the substrate.
• Once they bind to the active site, they do not form products, they just block the
active site and make it unavailable to the substrate.

• Increasing the [substrate] reduces the extent of the inhibition as fewer of the
inhibitor molecules are able to bind at the active site.

• Vmax is not changed as there is still a substrate concentration where full enzyme
activity can be achieved.
• Km is increased as it takes a higher substrate concentration to reach Vmax

OPTION B HL WWW.MSJCHEM.COM 5
Non-competitive inhibitors
• Non - competitive inhibitors bind away from the active site (called the allosteric site).
• This results in a change in the proteins' conformation which alters the shape of the
active site, inhibiting its ability to bind to the substrate.

• Increasing the concentration of substrate does not reduce this type of inhibition as
the active site is unavailable.
• The value of Vmax is decreased but the value of Km is unchanged.

OPTION B HL WWW.MSJCHEM.COM 6
Summary:

Competitive inhibitor Non-competitive inhibitor

Binds at active site Binds away from active site (allosteric site)

Is similar in structure to the substrate May have different structure to substrate

Vmax is unchanged Vmax is lowered

Km increased No change in Km

Increasing concentration of substrate Increasing concentration of substrate has no

has an effect effect

Calculating pH of buffer solutions

• Amino acids can act as acid-base buffers by reacting with the hydronium ion (H3O+)
or the hydroxide ion (OH-), minimizing the change in pH when small amounts of acid
or base are added.

• Response to added acid (H3O+):

• Response to added base (OH-)

OPTION B HL WWW.MSJCHEM.COM 7
 • The Henderson-Hasselbalch equation can be found in section 1 of the data booklet.

[HA] = initial concentration of the weak acid

[A-] = the initial concentration of the salt

Assumptions when using the Henderson-Hasselbalch equation:

• The concentration of the weak acid at equilibrium is approximately equal to the
initial concentration of the weak acid.

• The salt fully dissociates, so the concentration of the A- is approximately equal to the
initial concentration of the salt.

Exercise: Calculate the pH of a solution prepared by mixing 50.0 cm3 of 0.200 mol dm-3
CH3COOH(aq) and 50.0 cm3 of 0.100 mol dm-3 NaOH(aq). The pKa of ethanoic acid is 4.75 at
298 K.

OPTION B HL WWW.MSJCHEM.COM 8
Beer-Lambert law
• The Beer – Lambert law expresses the linear relationship between the absorbance
and concentration of a compound at a fixed wavelength.

• A calibration curve can be obtained by using a range of solutions with known

concentrations and measuring the absorbance using a spectrophotometer.

• The absorbance of a compound at a fixed wavelength is directly proportional to its

concentration.
• The calibration curve can be used to determine the concentration of
an unknown CuSO4 solution by measuring its absorbance with the
spectrophotometer.
• From the graph, we can determine the concentration of a copper sulfate
pentahydrate solution with an absorbance of 0.170 at 635 nm (0.016 mol dm -3).

OPTION B HL WWW.MSJCHEM.COM 9
Analysis of protein concentration
• UV-visible spectroscopy is a technique used in protein assays to measure the
concentration of a protein in a sample.
• UV-vis spectroscopy depends on the interaction of molecules with the UV and visible
light portions of the electromagnetic spectrum (180 - 750nm).

• Absorption spectra are produced using a spectrophotometer.

• The protein is made into a coloured compound using a dye so that the intensity of
the colour depends upon the concentration of protein in the sample.
• The wavelength of maximum absorbance is selected.
• The λmax is the wavelength at which absorption is the greatest.

• The amount of light absorbed at this wavelength is given by the equation for the
Beer – Lambert law.

• A calibration curve can be obtained by using a range of solutions with known

concentrations and measuring the absorbance using a spectrophotometer.

OPTION B HL WWW.MSJCHEM.COM 10
 • The calibration curve can then be used to determine the concentration of
an unknown protein solution.

B.8 Nucleic acids

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.

OPTION B HL WWW.MSJCHEM.COM 11
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.

Nucleic acids (polynucleotides)

• DNA stores the information that controls the genetic characteristics of an organism
and RNA enables the information stored in DNA to be expressed.
• DNA and RNA are both examples of polynucleotides which are polymers composed
of nucleotides (monomers).

DNA has a double helix structure

(double stranded polynucleotide).
The sugar phosphate backbone is
on the outside and the
nitrogenous bases are on the RNA is a single
inside. stranded
The two strands are held together polynucleotide
by hydrogen bonds between the
nitrogenous bases.

OPTION B HL WWW.MSJCHEM.COM 12
Nucleotides
• A nucleotide contains a phosphate group, a pentose (5 carbon) sugar and an organic
nitrogenous base.
• The nitrogenous base, pentose sugar and phosphate group bond in condensation
reactions, releasing a molecule of water.

• The nitrogenous base joins at the C1 of the sugar and the phosphate to C5, the 5
prime position (5’).
• Nucleotides bond in condensation reactions involving the phosphate group at the 5’
position of one nucleotide and the OH group at the 3’ position of the next
nucleotide.
• These bonds are called phosphodiester links.

OPTION B HL WWW.MSJCHEM.COM 13
Nitrogenous bases
• There are two types of nitrogenous bases, purines and pyrimidines.
• Pyrimidines are smaller and contain only 1 ring.
• Purines are larger and contain 2 fused rings.

Base pairing
• Only certain base pairings involving one purine and one pyrimidine are possible.
• In DNA, adenine forms 2 hydrogen bonds with thymine and guanine forms 3
hydrogen bonds with cytosine.

Stability of DNA
• The double helix structure places the non-polar bases in the centre surrounded by
the charged phosphate groups.
• Base stacking (London dispersion forces) and hydrogen bonding both contribute to
the stability of the double helix structure.
• The cellular environment is aqueous and therefore polar, so surrounding the non-
polar bases with charged phosphates maximizes the solubility of DNA.

OPTION B HL WWW.MSJCHEM.COM 14
DNA packaging
• DNA is tightly packed in the nucleus of every cell.
• DNA wraps around special proteins called histones, which form loops of DNA called
nucleosomes.
• Histones contain a large proportion of the positively charged basic amino acids lysine
(Lys) and arginine (Arg).
• DNA is negatively charged due to the phosphate groups that link the deoxyribose
sugars in the backbone of the molecule.
• The result of these opposite charges is a strong attraction and high binding affinity
between histones and DNA.

Differences between DNA and RNA

• DNA has deoxyribose as its pentose sugar.
• RNA has ribose as its pentose sugar.
• Deoxyribose lacks an oxygen atom on carbon 2.

• RNA has uracil instead of thymine as its base.

• RNA is a single-strand nucleic acid; DNA is a double-strand nucleic acid.
Protein synthesis
• The information required to make proteins is passed from DNA to mRNA in a process
called transcription.

OPTION B HL WWW.MSJCHEM.COM 15
 • In transcription, a segment of DNA is copied into mRNA by the enzyme RNA
polymerase.
• The newly formed mRNA leaves the nucleus for the ribosome, where translation
takes place.

• In translation, messenger RNA (mRNA) is decoded by a ribosome to produce a

polypeptide chain.
• In translation, a triplet code is used with each sequence of three nucleotides (bases)
representing one amino acid.
• The triplet code allows for up to 64 permutations, known as codons.

• Each codon consists of three nucleotides, corresponding to a single amino acid.

• The 64 permutations represent the 20 naturally occurring amino acids.

The table below shows the DNA codon, the RNA codon and amino acid for which it codes.

OPTION B HL WWW.MSJCHEM.COM 16
GM foods
• Genetically modified foods (GM foods), are foods produced from genetically
modified organisms that have had changes introduced into their DNA through
genetic engineering.
• Genetic engineering allows DNA to be transferred from one species to another.
• An example is corn that has been genetically modified to express a protein taken
from bacteria that acts as a natural insecticide.

Benefits of GM foods:
• Increased crop yields, which could help by feeding more people in developing
countries.
• Improved food quality - a tomato was genetically engineered to stay fresher for
longer, extending its shelf life in the supermarket.
• Increased resistance to disease or pests thereby reducing the use of pesticides.
• Increased resistance to adverse weather such as droughts.
• GM foods can be engineered to have a high content of a specific nutrient that is
lacking in the diet of a local population group.

Concerns over GM foods:

• The ability of a GM food to trigger an allergy in humans. Genes used in GM
technology might be taken from a food that causes allergies in certain people.
• Lack of information regarding the long-term effects of GM foods.
• Other organisms in the ecosystem could be harmed, which would lead to a lower
level of biodiversity.
• Given that some GM foods are modified using bacteria and viruses, there is concern
regarding the emergence of new diseases.

OPTION B HL WWW.MSJCHEM.COM 17
B.9 Biological pigments
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.
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.
• International-mindedness:
• Artificial colours are commonly added during the commercial preparation and
processing of food. The list of approved food colours varies greatly by country,
which raises questions for international trade.

OPTION B HL WWW.MSJCHEM.COM 18
Biological pigments
• Biological pigments are coloured compounds produced by living organisms (by
metabolism).
• Pigment molecules absorb light in the visible region of the spectrum (400 – 700 nm).

Absorption spectrum
for chlorophyll a

• Chlorophyll appears green because it absorbs wavelengths of visible light at 430 and
660 nm and reflects the remaining wavelengths.

Conjugated systems
• Highly conjugated systems (alternating single and double bonds) absorb wavelengths
of light in the visible region of the spectrum (400 – 700 nm).

• A conjugated system has a region of overlapping p orbitals with delocalized π

electrons.
• The delocalized π electrons absorb wavelengths of light in the visible region and are
excited to higher energy levels.
• A colour wheel can be used to determine the colour of a pigment.
• The colour that is reflected (the colour that we see) is the complementary colour of
the colour that is absorbed.

OPTION B HL WWW.MSJCHEM.COM 19
 • A pigment that absorbs wavelengths of green light will appear red (the
complementary colour).

Examples of biological pigments

• β-carotene (absorbs blue light, reflects orange)

• Retinol (absorbs violet light, reflects yellow)

Exercise:
Use the colour wheel to determine the wavelength of light absorbed and reflected by β-
carotene and retinol.

OPTION B HL WWW.MSJCHEM.COM 20
Porphyrin compounds
• Porphyrin compounds are planar ring structures with extensive conjugated systems.
• Porphyrin compounds are chelates of metals with large nitrogen containing
macrocyclic ligands.
• The porphyrin structure is made up of four rings that act as ligands.
• The non-bonding pairs of electrons on the nitrogen atoms form coordinate covalent
bonds with the central metal ion.
Chlorophyll
• Chlorophyll is a biological pigment found in plant cells.
• The metal ion in chlorophyll is the magnesium ion (Mg2+).
• In chlorophyll-a, the R group is a methyl (CH3) group, and in chlorophyll-b, an
aldehyde (CHO) group.

Stability of chlorophyll
• The thermal stability of chlorophyll depends on the pH.
• When heated, the cell membrane of the plant deteriorates, releasing acids which
decrease the pH.
• This magnesium ion in the porphyrin ring is displaced by two hydrogen ions,
resulting in the formation of a brown colour.
• Sodium hydrogen carbonate is added to cooked vegetables to keep their green
colour (chlorophyll is more stable in an alkaline solution).

Heme
• Heme is the prosthetic group of hemoglobin, myoglobin, and the cytochromes.
• The iron(II) ion in heme can form two additional coordinate bonds with a protein
residue (histidine) and molecular oxygen (O2).

OPTION B HL WWW.MSJCHEM.COM 21
Hemoglobin
• Hemoglobin carries molecular oxygen (O2) within the blood.
• It contains four heme groups, each bound within a polypeptide chain (quaternary
protein).
• The porphyrin group is bonded to an iron(II) ion.

Myoglobin
• Myoglobin is a protein composed of a single polypeptide chain and one heme group.
• It is found in muscle cells, where it stores molecular oxygen (O2).
• The porphyrin group is bonded to an iron(II) ion.
• Myoglobin only binds one O2 molecule compared to four in hemoglobin.

OPTION B HL WWW.MSJCHEM.COM 22
Summary:
• Porphyrin compounds are composed of 4 nitrogen containing macrocyclic ligands
which are bonded to a central metal ion by coordinate covalent bonds.
• Because of their highly conjugated systems, they absorb light in the visible region of
the spectrum.
• Chlorophyll is the light absorbing pigment in plants.
• Hemoglobin and myoglobin are protein molecules and are able to bind molecular
oxygen (O2); hemoglobin transports O2 in blood cells and myoglobin stores O2 in
muscle cells.

Colour stability of haem

• The purplish-red colour of meat is caused by myoglobin.
• In myoglobin iron is in the Fe2+ state (+2 oxidation state). When it is oxidized, the
state of the iron changes from Fe2+ to Fe3+ (from +2 to +3 oxidation state).
• In the Fe3+ state (+3 oxidation state), it is called metmyoglobin (MMb) and has an
undesirable brown colour.
• The stability of colour and the rate of brown MMb formation can be minimized if the
meat is stored in oxygen free conditions by using packaging films with low gas
permeabilities.
• Air is removed from the package and a storage gas (100% CO2) is used.

Carotenoids
• The carotenoids are an important group of pigments in plants, where they function
as accessory light-harvesting pigments in photosynthesis.
• Carotenoids have extensive conjugated systems (alternating single and double bonds
with delocalized π electrons).

• Carotenoid pigments exhibit strong light absorption in the blue portion of the visible
spectrum.
• Carotenoids are responsible for the yellow, orange, and red colours of many plants
(carrots, tomatoes, pumpkins).

OPTION B HL WWW.MSJCHEM.COM 23
Accessory pigments
• While the chlorophylls are efficient in absorbing the red and blue portions of the
light spectrum, they do not efficiently absorb other parts of the sunlight spectrum.
• The range of light absorption in leaves is extended by accessory pigments such as the
carotenoids.
• Carotenoids cannot transfer sunlight energy directly to the photosynthetic pathway,
but instead pass their absorbed energy to chlorophyll.

Oxidation of carotenoids
• The presence of multiple carbon to carbon double bonds makes carotenoids
susceptible to oxidation in the presence of oxygen catalysed by light (photo-
oxidation).
• Oxidation results in the loss of colour, loss of vitamin A activity and off-odors.
• The oxidation of carotenoids can be reduced by preventing exposure to air (oxygen)
and light.

Anthocyanins
• Anthocyanins are water soluble pigments that appear red, blue, or purple depending
on the pH.
• They belong to a class of molecules called flavonoids.
• As with all biological pigments, they have highly conjugated systems (alternating
single and double bonds) with delocalised π electrons that absorb light in the visible
region of the spectrum.

• The polar hydroxyl groups allow the molecule to form hydrogen bonds with water
molecules.

OPTION B HL WWW.MSJCHEM.COM 24
 • Anthocyanins can act as pH indicators.

red at low pH violet at pH 7-8 blue at high pH

• Cyanidin has less conjugation at low pH; green light is absorbed and red light
transmitted.
• Cyanidin has more conjugation at high pH; orange light is absorbed and blue light
transmitted.

Stability of anthocyanins
• Anthocyanins are stable and the most highly coloured at low pH and low
temperature.
• Anthocyanins form deeply coloured coordination complexes with Fe3+ and Al3+ ions,
a source of which can be metal cans - this can cause a discoloration in canned fruit.
• Anthocyanins also become less stable when exposed to heat, causing a loss of colour
and browning.

Cytochromes
• Cytochromes are a group of protein molecules that contain the heme prosthetic
group.
• They are responsible for electron transport during the redox reactions that take
place during aerobic respiration and photosynthesis.
• Cytochromes become successively reduced and re-oxidized as they accept and pass
electrons.
• The iron ion in the heme group interconverts between iron(II) and iron(III) during
these redox reactions.

OPTION B HL WWW.MSJCHEM.COM 25
Oxygen saturation of hemoglobin
• Hemoglobin carries oxygen in the blood and myoglobin stores oxygen in the muscles.
• They do this by binding reversibly with oxygen, which forms a weak bond with the
iron(II) ion in heme.
• The binding of oxygen does not change the oxidation state of the iron ion (+2),
therefore hemoglobin and myoglobin are oxygenated rather than oxidized.
• The oxygenated products are known as oxyhemoglobin and oxymyoglobin.

• The binding of oxygen to hemoglobin is a cooperative process.

• The ability to bind oxygen is increased by the initial binding of the first oxygen
molecule.
• The first oxygen molecule binds with low affinity, but increases the binding affinity of
further oxygen molecules.
• This results in a sigmoidial or S-shaped saturation curve.

Effect of partial pressure on % saturation of hemoglobin

• The ability of hemoglobin to bind or release oxygen depends on the partial pressure
of the oxygen (pO2).
• When the pO2 is high (in the lungs), each molecule of hemoglobin can carry its
maximum of four oxygen molecules.

OPTION B HL WWW.MSJCHEM.COM 26
 • As the blood circulates around the body, the blood experiences lower levels of
partial pressure.
• At low pO2 the hemoglobin releases some of the oxygen it is carrying.

Effect of temperature on the oxygen saturation of hemoglobin

• An increase in temperature reduces the affinity of hemoglobin for oxygen (the

dissociation curve has shifted to the right).
• Therefore, hemoglobin more readily releases oxygen at higher temperatures in the
cells during high metabolic activity such as exercise.

Effect of pH and [CO2] on the oxygen saturation of hemoglobin

• A decrease in pH reduces the affinity of hemoglobin for oxygen (the dissociation

curve has shifted to the right).
• Increasing the [CO2] has the same effect as CO2 dissolves to form carbonic acid
(H2CO3).
• During cellular respiration, CO2 is produced which decreases the pH, causing
hemoglobin to release oxygen.

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Greater affinity of fetal hemoglobin for oxygen

• Hemoglobin exists as a different form in fetal blood.

• It has a greater affinity for oxygen than normal hemoglobin so more oxygen binds at
lower partial pressures (the dissociation curve has shifted to the left).
• This allows the fetal blood in the placenta to take up oxygen from the mother’s
blood.

Effect of CO on the binding of oxygen to hemoglobin

• Carbon monoxide (CO) is an odorless, colourless gas that is highly toxic.
• CO is produced during incomplete combustion of hydrocarbons (car exhausts,
tobacco smoke).

• CO has a much higher affinity for hemoglobin than oxygen (it is a stronger ligand).
• It acts as a competitive inhibitor and therefore prevents oxygen from binding to
hemoglobin.
• Carbon monoxide forms an irreversible complex with the iron(II) ion in hemoglobin
(carboxyhemoglobin).

• Competitive inhibitors bind to the active site of an enzyme as they are similar in
structure to the substrate.
• CO acts like a competitive inhibitor; it effectively binds irreversibly to the heme.

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Oxygen-hemoglobin saturation curve

• Carbon monoxide shifts the oxygen-hemoglobin saturation curve to the left and
changes it to a more hyperbolic shape.
• Therefore, less oxygen is available for body tissues.
• Hemoglobin has four oxygen binding sites. The binding of CO at one of these sites
increases the oxygen affinity of the remaining three sites. This causes hemoglobin to
retain oxygen that would otherwise be delivered to body tissues.

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B.10 Stereochemistry in biomolecules
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.
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.

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Stereochemistry of amino acids
• A chiral carbon atom is a carbon atom bonded to four different atoms or groups.
• Amino acids are optically active (with the exception of glycine) and exist as
enantiomers.
mirror

• The CORN rule can be applied to name the two stereoisomers.

• If the CORN (COOH – R – NH3) is clockwise, it is the D-isomer.

• If the CORN (COOH – R – NH3) is counter-clockwise, it is the L-isomer.
• All naturally occurring amino acids are the L-configuration.
• The proteins in our bodies are only composed of the L-enantiomers of amino acids -
19 of the 20 naturally occurring amino acids exist as L-enantiomers.
• The D and L convention refers to the optical activity of the enantiomers
of glyceraldehyde.
• D-glyceraldehyde is dextrorotatory (right) and L-glyceraldehyde is levorotatory (left).
• This refers to the direction of the rotation of plane-polarized light.

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Stereochemistry of lipids
• Unsaturated fats and oils contain carbon to carbon double bonds.
• They exist in two forms which are known as cis-trans isomers.

• oleic acid – cis isomer (melting point 13oC)

• elaidic acid – trans isomer (melting point 45oC)

• Trans-fatty acids have higher melting points than cis-fatty acids because the
molecules in the trans-fatty acids are able to pack more closely together.
• This results in stronger intermolecular forces between molecules and therefore a
higher melting point.
• Naturally occurring unsaturated fat is mostly in the cis form, but the processing of
food can convert it to the trans form.

• In partial hydrogenation, only some of the carbon to carbon double bonds are
broken and those that remain get modified from the cis position to the trans
position (trans fats).
• Trans fats increase the level of LDL cholesterol which can cause heart disease; they
also lower levels of HDL cholesterol.

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 Stereochemistry in carbohydrates
• All simple sugars are chiral molecules as they contain at least one chiral carbon
atom.

• Naturally occurring sugars are D isomers.

• The D and L isomers are determined on the basis of the chiral carbon atom and how
its orientation compares to glyceraldehyde.
• The D isomer has the OH group to the right of the chiral carbon atom.

• In aqueous solutions, glucose forms a ring structure.

• Due to the restricted rotation around the carbon atoms, two isomers are formed,
alpha (α) glucose and beta (β) glucose.

α-glucose β-glucose
The OH group on The OH group on
carbon 1 is below carbon 1 is above
the plane of the the plane of the
ring. ring.

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Exercise: Classify the isomers of fructose as α or β

Starch, glycogen and cellulose

• Starch is used as carbohydrate storage in plants.
• It is a polymer composed of α-glucose with α-1,4 glycosidic links between glucose
molecules.

• Starch is a mixture of two polysaccharides; amylose and amylopectin.

• Amylose has α-1,4 glycosidic links and amylopectin has α-1,4 and α-1,6 glycosidic
links.

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Cellulose
• Cellulose is used as the structural material in plants and as dietary fiber as part of a
balanced diet.
• It is a polymer of β-glucose with β-1,4 glycosidic links.
• The alternating β-glucose molecules are upside down with respect to each other.

• The hydroxyl groups in the cellulose molecules form hydrogen bonds with the
hydroxyl groups of other cellulose molecules lying parallel to each other.

• Cellulose forms cables, known as microfibrils, of parallel chains that give it a rigid
structure.
• Wood, which is composed of cellulose, has a rigid structure and is a useful building
material.

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Glycogen
• Glycogen is used as carbohydrate storage in animals.
• It is a polymer of α-glucose with α-1,4 glycosidic and α-1,6 glycosidic links.

Dietary fibre
• During digestion, polysaccharides such as starch are broken down by enzymes into
glucose before passing into the blood stream.
• The human body lacks the enzyme cellulase to break down the polysaccharide
cellulose.
• Therefore, cellulose passes through the alimentary canal intact.
• Cellulose is known as dietary fibre.
• It stimulates the walls of the digestive tract producing mucus that allows for the
smooth passage of undigested food.
• Dietary fibre helps reduce conditions such as haemorrhoids and irritable bowel
syndrome.

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Stereochemistry in vitamins
• Vitamin A (retinal) is involved in the visual cycle.

cis / trans isomers of retinal

• The visual cycle involves the biological conversion of light into electrical signals in
the retina of the eye.
• The retina of the eye contains two types of light sensitive cells; rods and cones.
• The major photoreceptor in the rods is rhodopsin, a large conjugated protein
molecule.
• Opsins are a group of light-sensitive proteins found in photoreceptor cells of the
retina.
• The aldehyde group of cis-retinal can reversibly bind to a lysine residue of the
protein opsin, producing rhodopsin.

cis-retinal opsin rhodopsin

• Rhodopsin is also known as visual purple – it absorbs wavelengths of green light (500
nm).
• When rhodopsin is exposed to light, cis-retinal is converted to trans-retinal
(isomerization).
• The trans form of retinal does not fit as well into the protein, and the protein
undergoes a change in its conformation.
• As the conformation of the protein changes, it initiates a series of biochemical
reactions which trigger a nerve impulse that is sent to the brain along the optic
nerve.

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