A presentation on topic 2.1. "Molecules to Metabolism" of the IB Biology curriculum

1. 2.1. Molecules to Metabolism
Miltiadis-Spyridon Kitsos
Platon IB Diploma
http://www.edupic.net/Images/Mitosis/prometaphase.png

2. The official IB Diploma Biology guide
Essential idea: Living organisms control their composition by a complex web of chemical reactions.
https://ibpublishing.ibo.org/server2/rest/app/tsm.xql?doc=d_4_biolo_gui_1402_1_e&part=8&c
hapter=1

3. Introduction to Molecular Biology
Molecular biology explains living processes in terms of the chemical substances involved.
http://dataphys.org/list/wp-content/uploads/2014/12/Watson-Crick-
DNA-model.jpg
In 1953 Watson and Crick suggested a model on the
structure of DNA and this completely revolutionized our
understanding of biological processes which can be
looked through the “molecular” glass
Later one Watson proposed the Central Dogma of
Molecular Biology which safely connected the production
of proteins, a diverse group of molecules with DNA, the
genetic material of most organisms.
https://upload.wikimedia.org/wikipedia/commons/thumb/6/68/Central_Dogma_of_Molecular_Biochemistry_with_Enzymes.jpg/256
px-Central_Dogma_of_Molecular_Biochemistry_with_Enzymes.jpg
Other molecules are also important for living
organism. Can you name some of them?

4. Molecular biologists have a reductionist approach
Molecular biology explains living processes in terms of the chemical substances involved.
System’s biology approach
Looking at the interactions and
dynamics between the
components.
Benefits
Looks at the emerging properties
arising from the interactions
among the components.
Reductionist approach
Looking at the components
Benefits
Effective process, may yield
useful information by breaking
down complex processes into
simpler parts.
Biological system/Organism
In 1966 Francis Crick said that “The ultimate aim of the modern movement in biology is to explain all
biology in terms of physics and chemistry”. This statement is the epitome of the reductionist approach
in biology. Can you think of examples where this approach may not be appropriate?
Read more https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1299179/Reductionism and complexity in molecular biology

5. Carbon compounds
Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.
C
6 2
4
Carbon
12.0107
Carbon is the 15th most abundant element on earth but can be used to create
a diverse group of compounds which contribute to a diverse palette of
structures and functions.
Chemical properties of carbon
• May create four covalent bonds (strongest bonds) with other atoms.
Remember that covalent bonds result from the sharing of pairs of
electrons by two adjacent atoms. Look at the CH4 molecule
https://upload.wikimedia.org/wikipedia/c
ommons/thumb/2/29/Electron_shell_006
_Carbon.svg/558px-
Electron_shell_006_Carbon.svg.png
Carbon electron configuration
Carbon in the
period table
https://upload.wikimedia.org/wikipedia/commons/thumb/1/17/Covale
nt.svg/334px-Covalent.svg.png
covalent bond Biological significance
• The large number of covalent bonds
leads to the development of complex
structures either with other carbon
atoms (carbon chains)
https://upload.wikimedia.org/wikipedia/commons/thumb/3/31/Linoleic_acid_
shorthand_formula.PNG/800px-Linoleic_acid_shorthand_formula.PNG
• or with other chemical elements
https://upload.wikimedia.org/wiki
pedia/commons/thumb/8/88/D-
Phenylalanine.svg/228px-D-
Phenylalanine.svg.png
Bonds between carbon
atoms and other
chemical elements may
be single or double or
even triple
https://qph.ec.quoracdn.net/main-qimg-
d3f0d78f8981ac6da4fea003c673aa07?convert_to_webp=true

6. Groups of carbon compounds
Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
Carbohydrates
• Composed of C, H and O
• General chemical formula (CH2O)x
• Used as fast-access energy storage molecules
• Glucose, fructose and galactose are
monosaccharides, that is, monomers used to
build more complex carbohydrates like starch or
glycogen (polysaccharides)
Macromolecules
• Molecules of large molecular
weight composed of simpler
organic compounds, known as
monomers, chemically bonded
among each other.
http://stopdiabetesmellitus.com/wp-
content/uploads/2015/01/Glucose.png
Glucose and other
monosaccharides are usually
found in ring structure
Fructose
http://www.wpclipart.com/science/atoms_mol
ecules/molecules/fructose.png
http://chemistry.gravitywaves.com/CHE452/images/Glycogen.gifGlycogen
http://img.medscapestatic.com/pi/meds/ckb/75/43975tn.jpg

7. Groups of carbon compounds
Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
Lipids
• Composed of C, H and O
• Include steroids, waxes fatty acids and
triglycerides
• Distinguished in fats (solids) and oils (liquid)
• Diverse group of molecules
https://upload.wikimedia.org/wikipedia/commons/b/be/Fat_triglyceride_shorthand_formula.PNG
Triglycerides
https://courses.washington.edu/conj/membrane/fattyacid.png
fatty acids
Saturated
Unsaturated
Polyunsaturated Saturated fatty acids contain no double bonds
in the carbon chain
Monounsaturated fatty acids contain one
double bond in the carbon chain
Polyunsaturated fatty acids contain many
double bonds in the carbon chain
Phospholipids
http://figures.boundless-cdn.com/18565/full/figure-05-01-03a.jpeg
Steroids
http://www.chem.latech.edu/~deddy/chem121/
Image195.gif

8. Groups of carbon compounds
Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
Proteins
• Composed of C, H, O, N (some may include sulphur)
• Proteins is a diverse group of macromolecules with
numerous functions within the cell.
• Proteins are macromolecules composed of simpler
monomers called amino acids.
Remember the numerous roles of the membrane proteins
http://www.nature.com/scitable/content/ne0000/ne0000/ne0000/ne0000/14706234/U3CP1-
4_MemProteinFunction_ksm.jpg
They also act as biocatalysts,
catalysing numerous
biochemical reactions.
http://4.bp.blogspot.com/-
T0SV3qOTFLI/UjToYXUpapI/AAAAAAAAACg/4EEjhi_pP-
g/s1600/catalase.gif
http://www.medicalnewstoday.com/content/images/articles/262/262881/collagen.jpg
Proteins may also have a structural role
Collagen
Antibodies are proteins participating in
specific immunity
https://www.amgenscience.com/static/files/amgenscience/img/episodes
/the-shape-of-drugs-to-come/monoclonal-antibodies/1.png

9. Groups of carbon compounds
Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.
Nucleic acids
• Composed of C, H, O, N
• Nucleic acids are macromolecules
composed of monomers called nucleotides.
• Each nucleotide has three components: a
pentose sugar, a phosphate group and a
nitrogenous base.
• There are two main types of nucleic acids
DNA and RNA which differ on the type of
sugar and composition of nitrogenous
bases.
http://ib.bioninja.com.au/_Media/nucleotide_med.jpeg
A nucleotide
Nucleotides joined together via covalent
bonds form polynucleotide chains.
Two polynucleotide chains form the molecule
of DNA which is a double helix.
http://www.mhhe.com/biosci/ap/ap_prep/cem1s9_3.jpg
On the other hand, the RNA
molecule is single-stranded
http://www.wiley.com/legacy/college/boyer/0470003790/structur
e/tRNA/trna_diagram.gif

10. Ribose
Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised
amino acid.
C
CC
C
C
O
Ribose is a pentose (has 5 carbons) forming a
ring of four carbons with a side chain (5th)
• Draw the ring of the molecule.
• Add the side chain.
• Number the atoms starting with number
one on the right.
• Add the –OH (hydroxyl) and H groups. Take
care of the order.
C
CC
C
C
O OH
H
H
OH
H
OH
H
H2OH
http://www.biotopics.co.uk/jsmol/ribose.html

11. Glucose
Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised
amino acid.
Glucose is a hexose (has 6 carbons) forming a
ring of five carbons with a side chain (6th)
• Draw the ring of the molecule
• Add the side chain
• Number the atoms starting with number
one on the right.
• Add the –OH (hydroxyl) and H groups. Take
care of the order
C
CC
C
C O
C
1
23
4
5
6
H
OH
H
OH
OH
H
H
H2OH
C
CC
C
C O
C
1
23
4
5
6
OH
http://www.biotopics.co.uk/jsmol/alphabetaglucose.html
http://www.biotopics.co.uk/jsmol/alphabetaglucose.html alpha-D-glucose

12. Fatty acids
Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised
amino acid.
Any fatty acid has a long unbranched carbon
chain with single bonds.
• Draw the carbon chain
• Add the carboxyl group (R-COOH).
Remember this is an extra carbon atom
• Add the H atoms
Butyric acid
C C C C
O
OH
Carboxyl group
C C C C
O
OH
Methyl group
H H H
H H H
H
http://www.raw-milk-facts.com/images/FatTrio.gif
http://www.biotopics.co.uk/jsmol/fattyacids.html#
Stearic acid

13. Amino acids
Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised
amino acid.
amino group carboxyl group
The R is the functional group of each amino acid
and may correspond to different chemical groups
http://web.chem.ucla.edu/~harding/IGOC/A/amino_acid01.
png
carboxyl group
amino group
http://study.com/cimages/multimages/16/valine.png
Valine
https://upload.wikimedia.org/wikipedia/commons/6/62/Alanine.png
Alanine

14. Amino acids
Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised
amino acid.
There are twenty one different amino acids participating in the structure of proteins with each one having a
different functional group.
Amino acids are grouped according to the properties of the functional groups.
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a9/Amino_Acids.svg/2000px-
Amino_Acids.svg.png

15. Amino acids
Skill: Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalised
amino acid.
There are twenty one different amino acids participating in the structure of proteins with each one having a
different functional group.
Amino acids are grouped according to the properties of the functional groups.
http://upload.wikimedia.org/wikipedia/commons/thumb/a/a9/Amino_Acids.svg/2000px-
Amino_Acids.svg.png

16. Identifying molecules
Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.
Identify the following molecules
Molecule 1
Molecule 2
Molecules 3
Molecule 4 Molecule 5
Molecule 6

17. Identifying molecules
Identification of biochemicals such as sugars, lipids or amino acids from molecular diagrams.
Identify the following molecules
Molecule 1
Molecule 2
Molecules 3
Molecule 4
Molecule 5 Molecule 6
Amino acid
 Amino group
 Carboxyl group
Polyunsaturated fatty acid
 Long carbon chain with double bonds
 Carboxyl group
Monosaccharide
 C, H and O
 Five carbons in a
ring and a side
chain
Monosaccharide
 C, H and O
 Five carbons in a
ring and a side
chain
Monounsaturated fatty acid
 Long carbon chain with one double bond
 Carboxyl group
Glycerol
(triglycerides)

18. The discovery of urea and the falsification of vitalism
Falsification of theories—the artificial synthesis of urea helped to falsify vitalism
In 1828 the German chemist Friedrich Wöhler synthesized urea
artificially using silver isocyanate and ammonium chloride
https://upload.wikimedia.org/wikipedia
/commons/thumb/3/32/Friedrich_Wöhl
er_Litho.jpg/800px-
Friedrich_Wöhler_Litho.jpg
http://www.evolution-
textbook.org/content/free/figures/04_EVOW_A
rt/05_EVOW_CH04.jpg
Till then, urea was known as a product of the kidneys and a
component of urine. Moreover, it was believed that living
organisms had a vital principle which among others, was giving
them the ability to produce organic compounds. This perception
was known as vitalism
Wöhler’s accidental discovery refuted the theory of vitalism and
proved that the synthesis or urea and other organic compounds
in living organisms is governed by the same basic principles of
chemistry and physics as in non-living matter.
Read more
https://www.sciencebasedmedicine.org/the-death-and-rebirth-of-
vitalism/
Please remember that there are still processes in living
organisms that have not been replicated in vitro. One of them is
the synthesis of the polypeptide chains in the ribosomes.

19. The natural and artificial synthesis of urea
Application: Urea as an example of a compound that is produced by living organisms
but can also be artificially synthesized.
Production in humans
• A series of enzymatically catalysed
reactions.
• Produced in the liver when there is
an excess of proteins / amino acids.
• Component of urine.
• Transported to the kidneys to be
filtered out and exit the body by
urine.
Artificial production
• Chemical reactions are not catalyzed
by enzymes.
• Over 100 million tones produced
annually.
• Used as a fertilizer.
• End product identical to naturally
produced.
https://s-media-cache-
ak0.pinimg.com/736x/fb/c9/f6/fbc9f62d6bdad037c9b4de249845d6f6.jpg
http://www.essentialchemicalindustry.org/images/stories/520_Urea/Urea_04.JPG

20. Metabolism
Metabolism is the web of all the enzyme-catalysed reactions in a cell or organism
Biochemical reactions happening within cells are catalyzed by globular proteins called enzymes
(revisited later in 2.5).
Most biochemical reactions are linked together in pathways where the products of one reaction
are the reactants of the next one. In this manner a molecule is gradually converted to another in
a series of small steps.
A + B ------> C + D ------> E
Enzyme 1 Enzyme 2
There is an immense number of
biochemical reactions which are
interconnected and form a dense
network (may look like a metro map)
which is commonly known under the
term metabolism

21. Anabolism vs Catabolism
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.
Anabolism
Purpose: The synthesis of macromolecules from
smaller ones.
Main type of reactions: Condensation reactions
Energetics: Energy consumption
Examples: Photosynthesis, protein and DNA
synthesis
Catabolism
Purpose: Break down of macromolecules
into simpler ones.
Main type of reactions: Hydrolysis
reactions
Energetics: Energy yield
Examples: Cellular respiration, digestion of
molecules in the intestine
Coupling of energy an matter

22. Condensation vs Hydrolysis
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.
The purpose of condensation reactions is to join monomers and bind them via covalent
bonds. A by-product of the process is water.
http://www.cengage.com/biology/discipline_content/animations/reaction_types.htm
l
Covalent bond
This is a condensation reaction
between two amino acids
https://upload.wikimedia.org/wikipedia/commons/thumb/6/6b/AminoacidCondensation.svg
/576px-AminoacidCondensation.svg.png
And this is a condensation reaction
between two monosaccharides
http://www.old-ib.bioninja.com.au/_Media/glycosidic-linkage_med.jpeg

23. Condensation vs Hydrolysis
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.
The purpose of the hydrolysis reactions is to break down polymers into simpler monomers
This is the hydrolysis reaction of a dipeptide into two amino acids
And this is a hydrolysis reaction of a disaccharide
into two monosaccharides
H2O
enzyme
https://figures.boundless-cdn.com/30381/large/hydrolysis%20reaction%20amino%20acids.png
http://figures.boundless-cdn.com/18550/full/figure-03-01-02.jpeg
http://www.cengage.com/biology/discipline_content/animations/reaction_types.htm
l

24. Condensation vs Hydrolysis
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.

25. http://www.stepsinbiology.com