Week 2: Building Life: Macromolecules

Note: This document outlines the major concepts for the week and is intended as a basis for
structuring your study. The questions listed following this page are only intended to guide
your understanding of the week’s content and not as example/practice questions. Answers
will not be provided.

Learning Outcomes for this week:

1. Determine how organic macromolecules which include proteins, nucleic acids,
carbohydrates and lipids, are built from simpler units.
● Explain why carbon is the backbone of organic molecules.
● Distinguish between the monomers that make up macromolecules, and the
bonds that link monomers.
● Distinguish between major macromolecules based on their chemical structure.

2. Identify biologically important macromolecules and their functions within a cell or

organism.
● List the roles of the major groups of macromolecules in organisms.
● Define a nucleotide and give examples of biologically important nucleotides.
● Describe the chemical composition and structure of DNA and explain how this
structure facilitates its biological role.

3. Apply theoretical knowledge of chemical bonding to the form and function of

proteins.
● Define the primary, secondary, tertiary and quaternary structure of proteins.
● Identify the chemical interactions that lead to the four levels of protein
structure
● Deduce how the environment of the protein may affect the structure of
proteins

4. Explain how enzymes speed up and drive chemical reactions, and provide factors that
can affect enzyme function.

● Distinguish between an endergonic and exergonic reaction.

● Describe the effect of enzymes on chemical reactions.
 ● Explain how the cell can regulate the activity of enzymes, both positively and
negatively.
● Explain the main factors that impact the function of enzymes.

Suggested Skeleton Notes:

Note: The following will help indicate the specific concepts, key terms (bolded) and useful
diagrams to construct for this week’s learning outcomes. You can use the weekly material,
including the workshop, to make your notes on the following topics. It will also contain hints
on note taking for the semester. As the semester progresses, the notes will become more
‘bare bones’ and require more structure from you.

LO1. Determine how organic macromolecules which include proteins, nucleic acids,
carbohydrates and lipids, are built from simpler units.

Additional key terms: amino acid, condensation reaction (dehydration reaction), fatty acid,
glycosidic bond, monosaccharide, peptide bond, phosphodiester bond, phospholipid, purine,
pyrimidine, polypeptide, polysaccharide

● Explain why carbon is the backbone of organic molecules. What type of bonds to
carbon atoms form? What other properties does carbon have that enables it to form a
diversity of molecules?

Carbon is the backbone of organic molecules due to its ability to form up to four covalent
bonds, allowing for diverse molecular structures. These bonds include single, double, or triple
bonds, enabling carbon to create long chains, branches, and rings.

● What is the difference between a monomer and a polymer?

A monomer is a single unit that serves as the building block for larger molecules called
polymers. Monomers undergo polymerization to form polymers, which consist of repeated
monomeric units.

● Describe the monomers that make up proteins, nucleic acids and carbohydrates.
Sketch an example of the chemical structure of each.

- Proteins: Monomers are amino acids, consisting of an amino group, a carboxyl group, a
hydrogen atom, and a side chain (R group).
- Nucleic acids: Monomers are nucleotides, consisting of a pentose sugar, a phosphate group,
and a nitrogenous base.
- Carbohydrates: Monomers are monosaccharides, simple sugars with a general formula of
(CH2O)n.

● For each of these macromolecules, what are the bonds that link these monomers to
enable a polymer to form?
- Proteins: Formed by peptide bonds between amino acids via condensation reactions.
- Nucleic acids: Formed by phosphodiester bonds between nucleotides via condensation
reactions.
- Carbohydrates: Formed by glycosidic bonds between monosaccharides via condensation
reactions.

● Explain how lipids are different to the other macromolecules with regards to
polymerisation? Describe how lipids are structured and sketch an example of their
chemical structure.

Lipids differ from other macromolecules as they don't form polymers. They include fats, oils,
phospholipids, steroids, and waxes. Lipids are typically composed of glycerol and fatty acids,
forming structures like triglycerides. They are hydrophobic due to their nonpolar nature.

LO2. Identify biologically important macromolecules and their functions within a cell or
organism.
Additional key terms: Cellulose, complementary bases, disaccharide, double helix, fructose,
galactose, glucose, glycogen, lactose, ribose, starch, sucrose, triglyceride, sugar phosphate

● List the roles of the major groups of macromolecules in organisms. How are they used
within a cell/organism? Provide examples of each.

Macromolecule General cellular functions Examples of these

functional
macromolecules

Carbohydrates - Carbohydrates serve as a Glucose (Used for

primary source of energy for cells cellular respiration to
and organisms. Glucose, fructose, produce ATP, the
and galactose are simple sugars energy currency of
used for energy production. cells), cellulose
- Carbohydrates contribute to the (Provides structural
structural integrity of cells and support in plant cell
organisms. Cellulose forms the walls), glycogen, starch
cell walls of plants, providing
rigidity and support.
- Glycogen (in animals) and
starch (in plants) store excess
glucose.

Lipids - Lipids serve as a concentrated Triglycerides (Store

source of energy storage in energy in adipose tissue
organisms. Triglycerides store and provide insulation),
energy in adipose tissue. phospholipids, steroids.
 - Lipids, especially adipose tissue,
provide thermal insulation to help
maintain body temperature.

-Phospholipids form the main

structural component of cell
membranes, providing a barrier
between the cell and its
environment.

Proteins - Proteins act as biological - Enzymes: Examples

catalysts, facilitating biochemical include amylase, which
reactions within cells. Enzymes breaks down
speed up chemical reactions carbohydrates, and
without being consumed. proteases, which break
-Proteins provide structural down proteins.
support to cells and tissues. - Collagen: Found in
Collagen is a fibrous protein skin, tendons, and
found in connective tissues, bones, providing
providing strength and elasticity. structural support and
- Proteins such as hemoglobin elasticity.
transport molecules such as - Hemoglobin:
oxygen and carbon dioxide in the Transports oxygen in
bloodstream. red blood cells.

Nucleic Acids - Nucleic acids store genetic - DNA: Stores genetic

information in the form of DNA information in the
(deoxyribonucleic acid) and RNA nucleus of cells,
(ribonucleic acid). encoding instructions
- Nucleic acids play a crucial role for protein synthesis.
in protein synthesis. DNA serves - RNA: Various types
as a template for RNA, which, in of RNA, including
turn, guides the synthesis of messenger RNA
proteins. (mRNA), transfer RNA
- Some nucleic acids, such as (tRNA), and ribosomal
certain types of RNA, are RNA (rRNA),
involved in cellular participate in different
communication and regulation. stages of protein
synthesis.
 ● Outline the differences between unsaturated and saturated fats.

- Saturated Fats:
- No double bonds between carbon atoms.
- Solid at room temperature.
- Found in animal products.
- Associated with increased risk of cardiovascular diseases.

- Unsaturated Fats:
- Have one or more double bonds between carbon atoms.
- Liquid at room temperature.
- Found in plant-based oils.
- Consuming in moderation can lower cholesterol and reduce heart disease risk.

● Define a nucleotide, and what are the differences between the structure of DNA and
RNA? Draw a diagram of each annotating where these differences are.

Nucleotide: Building block of nucleic acids, composed of a sugar, phosphate group, and
nitrogenous base.

- Differences:
- Sugar: DNA has deoxyribose; RNA has ribose.
- Bases: DNA has thymine (T); RNA has uracil (U).
- Structure: DNA usually double-stranded; RNA often single-stranded.

● Explain how the chemical composition and structure of DNA facilitates its biological
role.

- DNA's sequence of bases stores genetic information accurately during replication and
protein synthesis.
- Double-stranded helix structure protects genetic material from damage.
- DNA structure allows controlled access for processes like transcription and replication.
- DNA's structure allows for genetic variation, evolution, and adaptation to changing
environments.

LO3. Apply theoretical knowledge of chemical bonding to the form and function of proteins.
Additional key terms: α-helix, β-pleated sheet
  Explain how the various R-groups of amino acids influence amino acids. How can this
affect a protein?

The diverse R-groups of amino acids influence protein structure and function:
- Hydrophobic R-groups tend to cluster together in the protein core, stabilizing the structure.
- Polar R-groups participate in hydrogen bonding, influencing folding and stability.
- Charged R-groups can form ionic interactions, affecting protein folding and function.
- Disulfide bonds between cysteine residues contribute to structural stability.

● Define the primary structure, secondary structure, tertiary structure and quaternary
structure of proteins. Sketch a diagram of each type.
- Primary Structure: Linear sequence of amino acids.
- Secondary Structure: Local folding patterns, such as α-helices and β-pleated sheets.
- Tertiary Structure: Overall 3D folding of the polypeptide chain.
- Quaternary Structure: Arrangement of multiple polypeptide subunits (if present).

● Describe how environmental factors such as temperature and pH may affect protein
structure.
- Temperature: High temperatures denature proteins, while low temperatures affect
flexibility.
- pH: Changes in pH affect ionization of amino acid side chains, impacting interactions.
- Ionic Strength: Alters electrostatic interactions, influencing protein stability and
structure.

LO4. Explain how enzymes speed up and drive chemical reactions, and provide factors that
can affect enzyme function.
Additional key terms: activation energy, allosteric, ATP, chemical energy, coenzyme,
cofactor, energetic coupling, enzyme-substrate complex, Gibbs free energy, substrate

● Explain what is meant by potential and kinetic energy.

- Potential Energy: Energy stored within an object due to its position or state. Examples
include chemical energy stored in bonds and gravitational potential energy.
- Kinetic Energy: Energy possessed by an object due to its motion. Examples include the
energy of moving objects like a rolling ball or a flowing river.

● Define an endergonic and an exergonic reaction. Explain how they differ from each
other. You may like to include an annotated diagram to help explain this.

- Endergonic Reaction: A reaction that absorbs energy from its surroundings to proceed. The
products have higher energy than the reactants, and the change in Gibbs free energy (∆G) is
positive. Endergonic reactions are non-spontaneous under standard conditions.
- Exergonic Reaction: A reaction that releases energy to its surroundings as it proceeds. The
products have lower energy than the reactants, and the change in Gibbs free energy (∆G) is
negative. Exergonic reactions are spontaneous under standard conditions.
● Describe the effect of enzymes on chemical reactions.
- Enzymes act as biological catalysts, speeding up chemical reactions by lowering the
activation energy required for the reaction to occur.
- They achieve this by bringing reactants (substrates) into close proximity and orienting them
favorably for bond formation, forming an enzyme-substrate complex.
- Enzymes provide an alternative pathway for the reaction, reducing the energy barrier and
facilitating the conversion of substrates into products.

● Explain how the cell can regulate the activity of enzymes, both positively and
negatively.

- Positive Regulation: Enzyme activity can be enhanced by activators that bind to the
enzyme, leading to conformational changes that increase catalytic activity. For example,
allosteric activators.
- Negative Regulation: Enzyme activity can be inhibited by inhibitors that bind to the
enzyme, blocking the active site or inducing conformational changes that reduce catalytic
activity. For example, competitive and non-competitive inhibitors.

● List the main factors that impact the function of enzymes and describe this impact.

- pH: Changes in pH can affect enzyme activity by altering the ionization state of amino acid
residues in the enzyme's active site, affecting substrate binding and catalysis.
- Temperature: Enzyme activity typically increases with temperature up to an optimal point,
beyond which high temperatures can denature the enzyme and reduce activity.
- Substrate Concentration: Increasing substrate concentration initially increases enzyme
activity until all active sites are saturated, leading to a plateau in the reaction rate.
- Cofactors and Coenzymes: Some enzymes require cofactors (inorganic ions) or coenzymes
(organic molecules) for optimal activity. Their presence or absence can influence enzyme
function.
- Enzyme Concentration: Higher enzyme concentrations generally result in increased reaction
rates until substrate becomes limiting, beyond which further increases in enzyme
concentration do not affect the rate.
- Inhibitors: Competitive inhibitors compete with the substrate for the enzyme's active site,
while non-competitive inhibitors bind to allosteric sites, altering enzyme conformation and
reducing activity.
- Allosteric Regulation: Allosteric modulators can bind to regulatory sites on enzymes,
inducing conformational changes that affect enzyme activity either positively or negatively.