Topic 2: Molecular Biology - 21hs

2.1 Molecules to metabolism

Nature of Science
Falsification of theories—the artificial synthesis of urea helped to falsify vitalism. (1.9)


Interactive metabolic pathways by Merck


• Molecular biology explains living processes in terms of the chemical substances involved.

• Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.

• Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

• Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism.

• Anabolism is the synthesis of complex molecules from simpler molecules including the formation of macromolecules from monomers by condensation reactions.

• Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

Consensation and hydrolisis simulation

Applications and skills

• Application: Urea as an example of a compound that is produced by living organisms but can also be artificially synthesized.
• Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.
• Skill: Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

2.2 Water

Nature of Science
Use theories to explain natural phenomena—the theory that hydrogen bonds form between water molecules explains the properties of water. (2.2)

Theory of Knowledge

Claims about the “memory of water” have been categorized as pseudoscientific. What are the criteria that can be used to distinguish scientific claims from pseudoscientific claims?

Memory of water Elsevier

Water memory in Frozen 2

International Mindedness

There are challenges for the increasing human population in sharing water resources equitably for drinking and irrigation, electricity generation and a range of industrial and domestic processes.

Where is Earth’s Water?

Water by UN


• Water molecules are polar and hydrogen bonds form between them.

• Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water.

• Substances can be hydrophilic or hydrophobic.

Water by CrashCourse

Applications and Skills

• Application: Comparison of the thermal properties of water with those of methane.

• Application: Use of water as a coolant in sweat.

• Application: Modes of transport of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in blood in relation to their solubility in water.

Water simulation by PBS

Properties of water animation by Merlot

2.3 Carbohydrates and Lipids

Nature of Science

Evaluating claims—health claims made about lipids in diets need to be assessed. (5.2)


You are what you eat by CrachCourse

International Mindedness

Variation in the prevalence of different health problems around the world could be discussed including obesity, dietary energy deficiency, kwashiorkor, anorexia nervosa and coronary heart disease.

How do Carbohydrates impact your health? TedEd

Theory of Knowledge

There are conflicting views as to the harms and benefits of fats in diets. How do we decide between competing views?

Battling bad science TedX


• Monosaccharide monomers are linked together by condensation reactions to form disaccharides and polysaccharide polymers.

Carbohydrates animation by WISC

• Fatty acids can be saturated, monounsaturated or polyunsaturated.

• Unsaturated fatty acids can be cis or trans isomers.

• Triglycerides are formed by condensation from three fatty acids and one glycerol.

Lipids animation by Wisc

Applications and Skills

• Application: Structure and function of cellulose and starch in plants and glycogen in humans.

• Application: Scientific evidence for health risks of trans fats and saturated fatty acids.

• Application: Lipids are more suitable for long-term energy storage in humans than carbohydrates.

• Application: Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids.

• Skill: Use of molecular visualization software to compare cellulose, starch and glycogen.

• Skill: Determination of body mass index by calculation or use of a nomogram.

Global database of BMI by WHO


Potatoes have been genetically modified to reduce the level of amylose to produce a more effective adhesive.

A Genetically Modified Potato, Not for Eating, Is Stirring Some Opposition in Europe by NYT

2.4 Proteins

Nature of Science
Looking for patterns, trends and discrepancies—most but not all organisms assemble proteins from the same amino acids. (3.1)


Should we eat bugs? TedED


• Amino acids are linked together by condensation to form polypeptides.

• There are 20 different amino acids in polypeptides synthesized on ribosomes.

• Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

Structure of aminoacids

• The amino acid sequence of polypeptides is coded for by genes.

• A protein may consist of a single polypeptide or more than one polypeptide linked together.

• The amino acid sequence determines the three-dimensional conformation of a protein.

• Living organisms synthesize many different proteins with a wide range of functions.

• Every individual has a unique proteome.

Applications and Skills

• Application: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions.

• Application: Denaturation of proteins by heat or by deviation of pH from the optimum.

Protein denaturation animations

Denaturation experiments by ScienceProject

Protein denaturation experiment by UKessays

Protein denaturation virtual lab by Labster

• Skill: Drawing molecular diagrams to show the formation of a peptide bond.

Animation of peptidic bonding

Animation of peptidic bonding 2


• Proteomics and the production of proteins by cells cultured in fermenters offer many opportunities for the food, pharmaceutical and other industries.

Human Proteome Project by KRG

Proteins at work – the fascinating world of proteomics by Ted

2.5 Enzymes

Nature of Science

Experimental design—accurate, quantitative measurements in enzyme experiments require replicates to ensure reliability. (3.2)

Theory of knowledge

Development of some techniques benefits particular human populations more than others. For example, the development of lactose-free milk available in Europe and North America would have greater benefit in Africa/Asia where lactose intolerance is more prevalent. The development of techniques requires financial investment. Should knowledge be shared when techniques developed in one part of the world are more applicable in another?

Why are people lactose intolerant? TedEd

Lactose intolerance statistics


• Enzymes have an active site to which specific substrates bind.

• Enzyme catalysis involves molecular motion and the collision of substrates with the active site.

How enzymes work animation by McGraw Hill

Enzymes by kScience

• Temperature, pH and substrate concentration affect the rate of activity of enzymes.

• Enzymes can be denatured.

• Immobilized enzymes are widely used in industry.

Applications and Skills

• Application: Methods of production of lactose-free milk and its advantages.

Making lactose free milk video

• Skill: Design of experiments to test the effect of temperature, pH and substrate concentration on the activity of enzymes.

Interactive enzyme diversity by JonDarkow

• Skill: Experimental investigation of a factor affecting enzyme activity. (Practical 3)

Virtual lab by Glecoe


Enzymes are extensively used in industry for the production of items from fruit juice to washing powder.

Experiment by Nuffield

2.6 Structure of DNA and RNA

Nature of Science
Using models as representation of the real world—Crick and Watson used model making to discover the structure of DNA. (1.10)


How diverse is the human genome? Ted

Theory of knowledge

• The story of the elucidation of the structure of DNA illustrates that cooperation and collaboration among scientists exists alongside competition between research groups. To what extent is research in secret ‘anti-scientific’? What is the relationship between shared and personal knowledge in the natural sciences?

Discovery of DNA Structure and Function: Watson and Crick. What did they actually discovered?


• The nucleic acids DNA and RNA are polymers of nucleotides.

• DNA differs from RNA in the number of strands present, the base composition and the type of pentose.

• DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs.

Play the DNA game link

DNA extraction virtual lab by LearnGenetics

Applications and Skills

• Application: Crick and Watson’s elucidation of the structure of DNA using model making.

How I discovered DNA Ted

• Skill: Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases.

Build a DNA molecular by Learngenetics

2.7 DNA replication, transcription and translation

Nature of Science

Obtaining evidence for scientific theories—Meselson and Stahl obtained evidence for the semi-conservative replication of DNA. (1.8)


Things you may not know about DNA Learngenetics


• The replication of DNA is semi-conservative and depends on complementary base pairing.

• Helicase unwinds the double helix and separates the two strands by breaking hydrogen bonds.

• DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as a template.

• Transcription is the synthesis of mRNA copied from the DNA base sequences by RNA polymerase.

• Translation is the synthesis of polypeptides on ribosomes.

• The amino acid sequence of polypeptides is determined by mRNA according to the genetic code.

• Codons of three bases on mRNA correspond to one amino acid in a polypeptide.

• Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA.

How do we read genes? by Learn.genetics

DNA replication by CrashCourse 

Applications and Skills

• Application: Use of Taq DNA polymerase to produce multiple copies of DNA rapidly by the polymerase chain reaction (PCR).

Virtual PCR by LearnGenetics

Play the PCR game Link

• Application: Production of human insulin in bacteria as an example of the universality of the genetic code allowing gene transfer between species.

• Skill: Use a table of the genetic code to deduce which codon(s) corresponds to which amino acid.

2.8 Cell Respiration

Nature of Science

Assessing the ethics of scientific research—the use of invertebrates in respirometer experiments has ethical implications. (4.5)


• Cell respiration is the controlled release of energy from organic compounds to produce ATP.

• ATP from cell respiration is immediately available as a source of energy in the cell.

• Anaerobic cell respiration gives a small yield of ATP from glucose.

• Aerobic cell respiration requires oxygen and gives a large yield of ATP from glucose.

ATP and cellular respiration by CrashCourse

Applications and Skills

• Application: Use of anaerobic cell respiration in yeasts to produce ethanol and carbon dioxide in baking.

Vitual lab by Pearson

• Application: Lactate production in humans when anaerobic respiration is used to maximize the power of muscle contractions.

• Skill: Analysis of results from experiments involving measurement of respiration rates in germinating seeds or invertebrates using a respirometer.

Respirometer virtual lab by Pearson

Cellular Respiration (Principles): Measure energy consumption during exercise By Labster

2.9 Photosynthesis

Nature of Science
Experimental design—controlling relevant variables in photosynthesis experiments is essential. (3.1)


• Photosynthesis is the production of carbon compounds in cells using light energy.

• Visible light has a range of wavelengths with violet the shortest wavelength and red the longest.

• Chlorophyll absorbs red and blue light most effectively and reflects green light more than other colours.

• Oxygen is produced in photosynthesis from the photolysis of water.

• Energy is needed to produce carbohydrates and other carbon compounds from carbon dioxide.


Illuminating photosynthesis by PBS

Travel Deep Inside a Leaf by California Academy of Sciences


• Temperature, light intensity and carbon dioxide concentration are possible limiting factors on the rate of photosynthesis.


Overview of photosynthesis


Wavelenghts of light and photosynthesis by Khan Academy

Applications and Skills

• Application: Changes to the Earth’s atmosphere, oceans and rock deposition due to photosynthesis.

Plants Affect the Atmosphere by PBS

• Skill: Drawing an absorption spectrum for chlorophyll and an action spectrum for photosynthesis.

• Skill: Design of experiments to investigate the effect of limiting factors on photosynthesis.

Virtual lab by Reading

Virtual lab by Glencoe

Virtual lab by Kscience

Virtual lab by Golabz

• Skill: Separation of photosynthetic pigments by chromatograph. (Practical 4)

Virtual lab by Pearson

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