2.

1 Molecules to metabolism

By Chris Paine
https://bioknowledgy.weebly.com/
2.1 Molecules to metabolism

Essential idea: Living organisms control their composition

by a complex web of chemical reactions.

The background is just a small part of the IUBMB-Sigma-Nicholson Metabolic Pathways

Chart aims to show all the metabolic pathways found in eukaryote cells. The chart in it's
entirety shows how complex the chemicals reactions needed to support life in a single cell
unit.

By Chris Paine
https://bioknowledgy.weebly.com/
Understandings
Statement Guidance
2.1.U1 Molecular biology explains living processes in
terms of the chemical substances involved.
2.1.U2 Carbon atoms can form four covalent bonds
allowing a diversity of stable compounds to exist.
2.1.U3 Life is based on carbon compounds including Sugars include monosaccharides and
carbohydrates, lipids, proteins and nucleic acids. disaccharides. Only one saturated fat is
expected and its specific name is not
necessary. The variable radical of amino acids
can be shown as R. The structure of individual
R-groups does not need to be memorized.
2.1.U4 Metabolism is the web of all the enzyme-catalysed
reactions in a cell or organism.
2.1.U5 Anabolism is the synthesis of complex molecules
from simpler molecules including the formation of
macromolecules from monomers by condensation
reactions.
2.1.U6 Catabolism is the breakdown of complex molecules
into simpler molecules including the hydrolysis of
macromolecules into monomers.
Applications and Skills
Statement Guidance
2.1.A1 Urea as an example of a compound that is
produced by living organisms but can also be
artificially synthesized.
2.1.S1 Drawing molecular diagrams of glucose, ribose, a Only the ring forms of D-ribose, alpha–D-
saturated fatty acid and a generalized amino acid. glucose and beta-D-glucose are expected in
drawings.
2.1.S2 Identification of biochemicals such as sugars, lipids Students should be able to recognize from
or amino acids from molecular diagrams. molecular diagrams that triglycerides,
phospholipids and steroids are lipids.
Drawings of steroids are not expected.
Proteins or parts of polypeptides should be
recognized from molecular diagrams showing
amino acids linked by peptide bonds.
2.1.U1 Molecular biology explains living processes in terms of the
chemical substances involved.

The structure of DNA was discovered

in 1953 – Watson & Crick
Molecular Biology  our
understanding of living processes

https://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg
2.1.U1 Molecular biology explains living processes in terms of the
chemical substances involved.

Organic molecules, especially

proteins, are very complex and
varied.
What we know so far is still only the
tip of the iceberg!

What do you think the approach used

by molecular biologists?
Reductionist or System approach?

https://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg
 In reductionist view, the behavior of biological systems can be
explained by the properties of components.

The reduction of complex systems to simpler components that are more

manageable to study

The system oriented approach insisted that biological systems have

emergent properties that only can have a system as a whole and not
its constituent parts.
Explores emergent properties by
complementing reductionism with the analysis of the
interaction of parts within a biological system

https://quizlet.com/62026170/reductionism-vs-systems-biology-flash-cards/
www.sciencedirect.com/science/article/pii/S1319562X15001485
TOK Discussion
To what extent is reductionist and system approach
useful in Biology?

See if you can provide an example from real life

before applying to an example in biology (from our
Topic 1) to illustrate your point(s).
Problem with the approach:
Molecules can have dual roles (e.g. Melanin is the
pigment that colors both skin and eyes) and also
may interact with each other in ways that a
reductionist approach overlooks.
2.1.U2 Carbon atoms can form four covalent bonds allowing a
diversity of stable compounds to exist.
Despite only being the 15th most abundant element Carbon atoms contain four
on the planet carbon forms the backbone of every electrons in their outer shell
single organic molecule. allowing them to form four
covalent bonds with potential
four other different atoms, e.g.
Covalent bonds are the strongest type of
methane (CH4).
bond between atoms.
= Stable molecules

The result of these properties is

an almost infinite number of
different possible molecules
involving carbon.

http://commons.wikimedia.org/wiki/File:Carbon-atom.jpg
http://www.ks.uiuc.edu/images/ofmonth/2002-11/titin.jpg
http://upload.wikimedia.org/wikipedia/commons/3/3e/Methane-2D-dot-cross.png
Titin is the largest known protein
Chemical formula C169723 H270464
N45688 O52243 S912.)
2.1.U2 Carbon atoms can form four covalent bonds allowing a
diversity of stable compounds to exist.
2.1.U3 Life is based on carbon compounds including
carbohydrates, lipids, proteins and nucleic acids.

There are four types of biological macromolecules

• Carbohydrates
• Lipids
• Proteins
• Nucleic acids
2.1.U3 Life is based on carbon compounds including
carbohydrates, lipids, proteins and nucleic acids.

Carbohydrates
Glucose – a hexose
• Made of C, H, and O in the ratio of (6 carbon) monomer
1:2:1
• Monomers are commonly ring
shaped molecules
• Polymers made up of monomers
• Functions:
– precursors (building blocks) of
polysaccharides, nucleotides and amino
acids
– Animals: Glucose (A source of energy
which can be broken down to form ATP
via cellular respiration)
- Plants: Cellulose (Used by plant cells as a
strengthening component of the cell
wall)
http://www.doctortee.com/dsu/tiftickjian/cse-img/biology/chemistry/polysaccharides.jpg
2.1.S1 Drawing molecular diagrams of glucose, ribose, a
saturated fatty acid and a generalized amino acid.

Try drawing by hand (or on

eMolecules online drawing tool eMolecules) the following
molecules:
• Glucose
• Ribose
• A generalised saturated fatty
acid
• A generalised amino acid
• An example saturated fatty
acid e.g. Butyric acid (the
simplest)

n.b. you also need to test yourself

15 mins, 1 day and one week later
to make sure you remember

http://www.emolecules.com/
Guiding question:
• If fat is so bad, then why is it a part of us (literally)?
2.1.U3 Life is based on carbon compounds including
carbohydrates, lipids, proteins and nucleic acids.

Lipids
• Lipids are a group of organic molecules that are insoluble in water but
soluble in non-polar organic solvents
• Common lipids include triglycerides (fats – solid at room temperature
and oils – liquid at room temperature), phospholipids and steroids

http://hyperphysics.phy-astr.gsu.edu/hbase/organic/imgorg/lipid.gif
Triglycerides
2.1.S2 Identification of biochemicals such as sugars, lipids or
amino acids from molecular diagrams.
General structural formula for a fatty* acid

http://www.eufic.org/article/pt/nutricao/gorduras/expid/23/
One saturated fatty acid example
 Steroids
• Structure: Four carbon rings with no fatty acid tails
• Functions:
• Component of animal cell membranes
• Modified to form sex hormones
Steroids
Can you list the different functions of lipid for your
body?
2.1.U3 Life is based on carbon compounds including carbohydrates,
lipids, proteins and nucleic acids.
Proteins
• Contain carbon, hydrogen, oxygen and nitrogen (sulfur present only in cysteine and
methionine)
• Proteins are large organic compounds made of amino acids arranged into one or more
linear chains

Glycine – an amino acid

2.1.S2 Identification of biochemicals such as sugars, lipids or
amino acids from molecular diagrams.
The R group is like x in an equation. It is a
variable that stands in for a bunch of different
side chains

Look out for this structure

2.1.S2 Identification of biochemicals such as sugars, lipids or
amino acids from molecular diagrams.

The amine and acid groups

could be at opposite ends, the
R could be on top, bottom or
side depending on orientation.
2.1.S2 Identification of biochemicals such as sugars, lipids or
amino acids from molecular diagrams.

Alanine Arginin Leucine

e

Here are three of

the twenty amino
acids found in
eukaryotes.

http://commons.wikimedia.org/wiki/File:Alanine.png
http://commons.wikimedia.org/wiki/File:Arginine.png
http://commons.wikimedia.org/wiki/File:Leucine.png
2.1.S2 Identification of biochemicals such as sugars, lipids or
amino acids from molecular diagrams.
2.1.S2 Identification of biochemicals such as sugars, lipids or
amino acids from molecular diagrams.

Or it could be represented differently:

Stay calm, you only need to know the
GENERAL FORMULA
http://commons.wikimedia.org/wiki/File:Amino_Acids.svg
2.1.S2 Identification of biochemicals such as sugars, lipids or
amino acids from molecular diagrams.
2.1.S2 Identification of biochemicals such as sugars, lipids or
amino acids from molecular diagrams.
2.1.U3 Life is based on carbon compounds including carbohydrates, lipids,
proteins and nucleic acids.

Nucleic acids
• Contain carbon,
RIBOSE DEOXYRIBOSE
hydrogen, oxygen,
nitrogen and
phosphorus CH2OH O OH CH2OH
O OH
• Chains of sub-units
called nucleotides C C
C C
• Nucleotides consist of
base, sugar and H H H H H H H H
phosphate groups
covalently bonded C C C C
together
• If the sugar is ribose OH OH OH H
then the nucleic acid
formed is RNA if the
sugar is deoxyribose
then DNA is formed
 Nucleic acids consists of phosphate, sugar and organic base

The sugar, the phosphate and one of the bases combine to form a nucleotide

PO4
adenine

sugar
Nucleotide structure in terms of sugar (deoxyribose), base and phosphate
2.1.S2 Identification of biochemicals such as sugars, lipids or
amino acids from molecular diagrams.
2.1.U4 Metabolism is the web of all the enzyme-catalysed
reactions in a cell or organism.

Revisit the essential idea of this topic.

Explore the IUBMB-Sigma-Nicholson Metabolic Pathways Chart and realise that most cells
use the majority of the pathways and that every path is controlled by a different enzyme. The
metabolism as a concept is the sum of all the pathways used in a particular cell.

Metabolism: The sum of all enzyme-mediated

chemical reactions within an organism

Thus, what are the main functions of metabolism?

1) Synthesis of energy for cellular activities (e.g.?)

2) Synthesis or breaking down of metabolic compounds to be
assimilated (e.g.?)
2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the
formation of macromolecules from monomers by condensation reactions.
2.1.U5 Catabolism is the breakdown of complex molecules into simpler molecules including the
hydrolysis of macromolecules into monomers.
2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the
formation of macromolecules from monomers by condensation reactions.
2.1.U5 Catabolism is the breakdown of complex molecules into simpler molecules including the
hydrolysis of macromolecules into monomers.
http://ib.bioninja.com.au/standard-level/topic-2-molecular-
biology/21-molecules-to-metabolism/organic-polymers.html
Maltose (two glucose units) is present in germinating
seeds.
2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the
formation of macromolecules from monomers by condensation reactions.

Examples of anabolism by condensation Enzyme?

Maltose
What synthase
does it do?condenses two
molecules of glucose into
What is the
maltose name
forming of the
a glycosidic
bond?
bond
Product?

What synthesizes the

dipeptide?
A ribosome condenses two
amino
What acids
is the into of
name a dipeptide
the bond?
forming a peptide bond
Product?

The bonds formed are types of covalent

bonds.

Bonding monomers together creates a

polymer (mono = one, poly = many)

http://commons.wikimedia.org/wiki/File:Peptidformationball.svg
2.1.U5 Catabolism is the breakdown of complex molecules into simpler molecules including the
hydrolysis of macromolecules into monomers.

Examples of catabolism by hydrolysis

Enzyme?
A protease hydrolyses a
What dipeptide
does it do?
into two amino
What acids
is thebreaking
name ofthethe bond?
peptide
bond
Product?

Enzyme?
Lactase hydrolyses Lactose
What does it do?
into Glucose and Galactose
What is the name of the bond?
breaking the glycosidic bond
Product?

http://commons.wikimedia.org/wiki/File:Lactose_hydrolysis.svg
http://commons.wikimedia.org/wiki/File:Amino_acid4.png
Is this anabolism or catabolism?

Enzyme?
- Enzymes are too complicated
What-does
It is ita set
do?of reactions
- name
What is the Ester bonds
of the bond?
Product? - Triglycerides
http://ib.bioninja.com.au/standard-level/topic-2-molecular-
biology/21-molecules-to-metabolism/organic-polymers.html
 - Enzyme?
- What does it do?
- What is the name
http://ib.bion of the bond?
inja.com.au/s - Product?
tandard-
level/topic-2-
molecular-
biology/21-
molecules-to-
metabolism/o
rganic-
polymers.htm
l
2.1.A1 Urea as an example of a compound that is produced by
living organisms but can also be artificially synthesized.
Nature of Science: Falsification of theories—the artificial synthesis of
urea helped to falsify vitalism. (1.9)

- Vitalism  Living organisms has vital force, differentiating them from

non-living.
- Wöhler in 1828 accidentally synthesised urea, whilst attempting to
prepare ammonium cyanate without the need of living tissue.
- Vitalism in terms of organic matter can only be produced by
organism is thus falsified since Wöhler provide evidence that organic
chemicals can be produced synthetically.

In essence, vitalism proposes that

there is an unknown factor that we
may not yet be able to explain, that is
essential in explaining life.
Vitalism on this premise is both
unscientific and unfalsifiable.
Most of the time, it is a matter of time
and accumulation knowledge.

Source: http://en.wikipedia.org/wiki/File:Friedrich_woehler.jpg Source: http://www.biog1445.org/demo/08/nitrogenouswastes.html

For more on vitalism, you can read the article by William Betchel

https://mechanism.ucsd.edu/teaching/philbio/vitalism.htm

What other theory was falsified? (Re: chapter 1)

http://ib.bioninja.com.au/standard-level/topic-2-molecular-
biology/21-molecules-to-metabolism/falsifying-vitalism.html
Outline condensation and hydrolysis reactions using a
different example for each. [5]
Bibliography / Acknowledgments

Jason de Nys

Click4Biology