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.
 ● 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
Lesson 1 ●
compounds to exist.
State that life is based on
carbon compounds, including
Organic Molecules & Living carbohydrates, lipids, proteins
Processes and nucleic acids.
● Draw the molecular diagrams
Kognity 2.1.0, 2.1.1, 2.1.2 of glucose, ribose, a saturated
Cambridge Pg. xx-xx 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

 ● 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

Lesson 2 ●
from monomers by condensation
reactions.
Outline catabolism as the
breakdown of complex molecules
Metabolism, anabolism, and into simpler molecules, including
catabolism the hydrolysis of macromolecules
into monomers.
Kognity 2.1.3, 2.1.4 ● Describe urea as an example of a
Cambridge Pg. xx-xx 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
macromolecules from monomers into 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, Ex. The breakdown of sugars
glucose forms starch (including 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