2.

1 Molecules to Metabolism

Topic 2: Molecular Biology


2.1 Essential Idea:
Living organisms control their
composition using a complex web of
chemical reactions.
Understandings:
● Outline the role of molecular biology in explaining how
chemical substances are involved in living processes.
● Describe how carbon atoms can form four covalent bonds,
allowing a diversity of stable compounds to exist.
● State that life is based on carbon compounds, including
carbohydrates, lipids, proteins and nucleic acids.
● Outline metabolism as the web of all the enzyme-catalysed
reactions in a cell or organism.
● Outline anabolism as the synthesis of complex molecules
from simpler molecules, including the formation of
macromolecules from monomers by condensation reactions.
● Outline catabolism as the breakdown of complex molecules
into simpler molecules, including the hydrolysis of
macromolecules into monomers.
● Describe urea as an example of a compound that is produced
by living organisms, but can also be artificially synthesised.
● State the main application of artificially produced urea.
● Draw the molecular diagrams of glucose, ribose, a saturated
fatty acid and a generalised amino acid.
● Identify biochemicals, such as sugars, lipids or amino acids
from molecular diagrams.

Lesson 1
Organic Molecules & Living Processes
Kognity 2.1.0, 2.1.1, 2.1.2
Cambridge Pg. xx-xx
● Outline the role of molecular biology
in explaining how chemical
substances are involved in living
processes.
● Describe how carbon atoms can form
four covalent bonds, allowing a
diversity of stable compounds to
exist.
● State that life is based on carbon
compounds, including carbohydrates,
lipids, proteins and nucleic acids.
● Draw the molecular diagrams of
glucose, ribose, a saturated fatty acid
and a generalised amino acid.
● Identify biochemicals, such as sugars,
lipids or amino acids from molecular
diagrams.
Why are we called
“carbon-based
lifeforms?”
Big Picture

Everything that happens in cells (and living things) is

determined by a network of chemical reactions
DNA, molecules, membranes, organelles, and other
cellular structures are the result of and carry out
biochemical reactions
Metabolism: the web of all the enzyme-catalysed
reactions in a cell or organism
Understanding the metabolism allows us to solve
chemical imbalances in the body with targeted treatment
Carbon-Based Organic Molecules

● Organic compounds: chemical substances made in and

used by living organism; mostly carbon-based
○ Examples: carbohydrates, lipids, proteins, nucleic acids

● Not all carbon containing compounds are organic (Ex.

carbon dioxide, carbon monoxide, carbonates and
hydrogen carbonates)
Why Carbon?

● 4 electrons in the outer shell = 4 covalent bonds

● Allows carbon to form 4 stable bonds with other
carbons or different elements → can form a wide
variety of diverse stable structures!
● Carbon can form long chains and ring structures
Examples of Stable Carbon Arrangements

Note that there are 4

lines (4 covalent
bonds) attached to
each carbon
Macromolecules

● Macromolecules: large (macro) organic molecules that

make up living things
● Made up of smaller monomers joined by chemical bonds
to make polymers
● 4 kinds: carbohydrates, lipids, proteins, and nucleic acids
● All contain carbon, oxygen, and hydrogen atoms
● Additional elements present depending on the molecule
(Ex. nitrogen, phosphorus)
Drawing Organic Molecules

You will need to be able to draw:

● Alpha-D-glucose
● Beta-D-glucose
● Fatty acids
● Amino acid (general structure)
● Ribose
See the examples on the following slides, and try drawing one of each on paper.
Carbohydrates (Sugars)

Carbohydrates are macromolecules composed of three elements: carbon, hydrogen and oxygen
The ratio of hydrogen to oxygen is 2:1.
Monomer: Glucose
Examples of carbohydrates:
● Alpha-D-glucose: used in the production of ATP in cells
● Beta-D-glucose: used to build cells walls in plants
● Starch: used as long-term storage in plants
● Ribose: used as a component in DNA in RNA (sugar-phosphate backbone)
Drawing: Alpha-D-glucose & Beta-D-glucose

Start by drawing a hexagon with the oxygen

atom at the top right corner.
Then there should be 5 carbon atoms
clockwise, where the last C atom (number 6)
is a CH2OH group attached to carbon atom
number 5.
Then, draw the -OH groups in their correct
positions (alpha-D-glucose: OH on top;
beta-D-glucose: OH on bottom)
Lipids

Diverse group of organic compounds including steroids (e.g. cholesterol), waxes,

phospholipids and triglycerides
Monomer: fatty acids
Examples of lipids:
● Triglycerides: Used as long-term storage in adipose tissue in animals
● Steroids: Used as chemical messengers in the body, have a distinctive ring shape
● Phospholipids: Major component of plasma membranes
Drawing: Fatty Acids
Check the functional groups:
Presence of -COOH attached to a long hydrocarbon chain implies the monomer is a fatty
acid.
You may draw a saturated fatty acid simply as CH3(CH2)16COOH, as in the figure below.
Keep the total number of carbon atoms in the molecule between 8 and 12.
Proteins

Proteins consists of amino acids that are arranged in long chains.

Monomer: amino acids
Examples of Proteins:
● Structural proteins: Proteins such as keratin and collagen form the structural framework
of many parts of the body.
● Enzymes: Metabolic proteins that speed up chemical reactions in the body.
● Polypeptides: A sequence of amino acids that may make up a protein, or a series of
polypeptides can also make up a protein.
Drawing: Amino Acids

Check the functional groups:

Presence of -COOH, also called a carboxyl group and -NH2,
also called an amine group, implies the monomer is an amino
acid.
“R” represents the many possible structures of the 20
different amino acids, and is a placeholder
Nucleic Acids

Nucleic acids are also chains but formed by nucleotides.

Monomer: Ribose
Examples of Nucleic Acids:
● DNA: Used to store genetic information
● RNA: Used to create proteins at ribosomes using the
information stored in DNA.
Drawing: Ribose

Check whether the number of hydrogen and

oxygen atom is in the ratio of 2:1; this implies the
monomer is a sugar. You then count the number of
carbon atoms to identify whether it is ribose (5
carbon) or glucose (6 carbon).
Practice:
Kognity 2.1 Molecules to Metabolism
Lesson 1 Review Questions

Please complete for next class


Lesson 2
Metabolism, anabolism, and catabolism
Kognity 2.1.3, 2.1.4
Cambridge Pg. xx-xx
● Outline metabolism as the web of all the
enzyme-catalysed reactions in a cell or
organism.
● Outline anabolism as the synthesis of
complex molecules from simpler
molecules, including the formation of
macromolecules from monomers by
condensation reactions.
● Outline catabolism as the breakdown of
complex molecules into simpler
molecules, including the hydrolysis of
macromolecules into monomers.
● Describe urea as an example of a
compound that is produced by living
organisms, but can also be artificially
synthesised.
● State the main application of artificially
produced urea.
Review!

Draw the basic structure of:

● Glucose
● Fatty Acid
● Ribose
● Amino Acid
 Metabolism, Anabolism, & Catabolism
Metabolism: all of the enzymatic reactions that take place inside a living organism.
Anabolism Catabolism
Definition the synthesis of complex the breakdown of macromolecules into
macromolecules from monomers monomers
Energy use requires input of energy energy is released in the process
Type of Condensation reactions Hydrolysis
reactions

Examples Ex. Amino acids form proteins, glucose Ex. The breakdown of sugars (including
forms starch glycolysis) or fats to release energy
Hydrolysis and Condensation Reactions

Hydrolysis: the breaking of

chemical bonds by the addition of
water molecules
Hydrolysis and Condensation Reactions

Condensation Reaction: reaction in which

two smaller organic molecules combine to
form a larger molecule with the accompanied
formation of water or some other simple
molecule
Urea

● Urea is an organic compound with the formula CO(NH2)2

● Used by the human body to excrete nitrogen because it is

non-toxic and highly soluble
○ Question: why would non-toxicity and solubility matter?

● Also widely used as a nitrogen fertiliser → led to its

artificial synthesis on a large scale
Synthesis of Urea

● In 1828, Friedrich Wöhler demonstrated

(accidentally) that a by-product of life could
be artificially synthesised

● First experiment to show that the synthesis

of an organic compound from two inorganic
molecules was achievable → provided
evidence that contradicted the theory of
vitalism
Vitalism

● According to the theory of vitalism, organic

compounds could only be synthesised by living
organisms
● Living things possessed an 'element' that non-living
things did not have → “divine principle” or “life
spark”
● Artificial synthesis of urea from inorganic chemicals
in the laboratory helped to falsify the theory of
vitalism
Let’s make some models!

Build the basic structure of:

● *Glucose
● Fatty Acid
● Ribose
● *Amino Acid
● Urea
Also: Model a hydrolysis reaction between two glucose or amino acids
Practice:
Kognity 2.1 Molecules to Metabolism
Lesson 2 Review Questions

Read: Kognity 2.2.0, 2.2.1, 2.2.2

Please complete for next class