First Exams 2025

B1.2 Proteins
Theme: Form and Function

Level of Organisation: Molecules

SL and HL
Combined Content
SL and HL Content
From
IB Guiding Questions the IB

What is the relationship between amino acid sequence

and the diversity in form and function of proteins?
How are protein molecules affected by their chemical
and physical environments?
SL and HL Content
From
SL & HL Content: B1.2 Proteins the IB

B1.2.1: Generalized structure of an amino acid

B1.2.2: Condensation reactions forming dipeptides and longer chains of
amino acids
B1.2.3: Dietary requirements for amino acids
B1.2.4: Infinite variety of possible peptide chains
B1.2.5: Effect of pH and temperature on protein structure
SL and HL Content

SL & HL Key Terms

Amino acid Polypeptide

Amine Group
Carboxylic Acid Group
Side Chain (R Group)
Condensation Reaction
Dipeptide
Peptide Bond
Essential Amino Acids
Non-Essential Amino Acids
Genetic Code
Denaturation
SL and HL Content
From
B1.2.1: Generalized structure of an amino acid the IB

Students should be able to draw a diagram of a generalized amino acid

showing the alpha carbon atom with amine group, carboxyl group, R-
group and hydrogen attached.
SL and HL Content

Proteins are Composed of Amino Acids

❓ Outline the
generalized
structure of
amino acids.
SL and HL Content

Generalized Structure of Amino Acids

All amino acids have the same general structure including:

Hydrogen attached to a central alpha carbon

Amine Carboxyl
Group (- group
NH2) (-COOH)

Side chain (R
Group) Students
attached to a should be able
central alpha Amino Acid Structure to draw an
carbon amino acid.
SL and HL Content

Twenty Amino Acids

All organisms use the same twenty amino acids to build their proteins.
All twenty amino acids will have an amine group (-NH 2) and a carboxylic
acid group (-COOH).
Each amino acid has a different R group. The R group determines the
chemical properties and behavior of the amino acid.
IB students are not expected to know the names or specific structures of
amino acids, but if you are interested in the different R groups, see the
linked article.
SL and HL Content
From
B1.2.2: Condensation reactions forming the IB
dipeptides and longer chains of amino acids

Students should be able to write the word equation for this reaction and
draw a generalized dipeptide after modelling the reaction with
molecular models.
SL and HL Content

Formation of Dipeptides
Amino acids undergo condensation reactions to form dipeptides.

Amino Amino
+ Dipeptide + Water
Acid Acid

Students are expected to recall the word equation for the formation of a
dipeptide.
SL and HL Content

Formation of Dipeptides
A peptide bond forms between

the carbon of the and the amine group of

carboxylic acid group of the second amino acid.
one amino acid
SL and HL Content

Formation of Dipeptides

-OH and -H are removed from the amino acids, to form water.
SL and HL Content

Formation of Dipeptides
A peptide bond is present between the two amino acids, forming a dipeptide.

+ + H 2O
Peptide
Bond
Students are expected to be able to draw a diagram of a dipeptide.
Students should model the reaction using molecular models.
If the school does not have molecular models, Molview can be used to
create virtual models of amino acids and dipeptides.
SL and HL Content

Amino Acid Models

The amino acid structural diagram and model were created using
Molview.
SL and HL Content

Polypeptides
A polypeptide is a long chain of amino acids.
Polypeptides are formed by many condensation reactions at a ribosome
during the process of translation
❓ Identify the peptide bonds on the short polypeptide below:

The peptide bond is always between the C and N of neighbouring amino

acids.
SL and HL Content
From
B1.2.3: Dietary requirements for amino acids the IB

Essential amino acids cannot be synthesized and must be obtained from

food.
Non-essential amino acids can be made from other amino acids.
Students are not required to give examples of essential and nonessential
amino acids.
Vegan diets require attention to ensure essential amino acids are
consumed.
SL and HL Content

Proteins and Our Diet

Proteins are part of
a healthy human
diet.
Proteins are broken
down to amino
acids by the
digestive system.
These amino acids
are then used to
synthesize proteins
for the body.
SL and HL Content

Essential Amino Acids

Humans require 20 amino acids to produce all of the proteins.
Humans can synthesize eleven of the amino acids, which are known as non-
essential amino acids
The other nine amino acids that humans require are known as essential
amino acids, and must be consumed in the diet.
Proteins are present in a range of foods including meat, dairy products,
beans, and tofu.
Meat and animal products are considered complete proteins, as they contain
all nine of the essential amino acids.
Most plant sources of protein do not provide all of the essential amino acids.
SL and HL Content

Vegan Diets and Amino Acids

Vegans need to ensure

that their daily diet
includes a range of protein
sources to ensure that
they consume all of the
essential amino acids.
Read the linked article on
sources of plant proteins.

Plant based protein sources

SL and HL Content
From
B1.2.4: Infinite variety of possible peptide chains the IB

Include the ideas that 20 amino acids are coded for in the genetic code,
that peptide chains can have any number of amino acids, from a few to
thousands, and that amino acids can be in any order.
Students should be familiar with examples of polypeptides.
SL and HL Content

Proteins and the Genetic Code

Genes on DNA code for polypeptide chains,
which form proteins.
The genetic code of DNA is transcribed to mRNA.
mRNA is translated by ribosomes into a
polypeptide chain.
Polypeptides in proteins can have any number of
amino acids. Human polypeptides range from 51
amino acids in insulin to 34000 in titin.
Amino acids can occur in any order in a
polypeptide, meaning that the variety of possible Genetic code for amino acids

polypeptides is infinite.
SL and HL Content
From
the IB
B1.2.5: Effect of pH and temperature on protein
structure

Include the term “denaturation”.

SL and HL Content

Protein Denaturation

Denaturation is a
conformational
change in the shape
of a molecule, such
as a protein,
resulting in the loss
of function.
SL and HL Content

Protein Denaturation

All proteins have a specific

shape which determines
the function of the
Temperature
protein.
pH
Proteins can be denatured
by extreme changes in pH
and temperature. Functional Protein Denatured Protein
Protein denaturation
SL and HL Content

Review and Discuss: SL & HL Key Terms

Amino acid Polypeptide

Amine Group Essential Amino Acids
Carboxylic Acid Group Non-Essential Amino Acids
Side Chain (R Group) Genetic Code
Condensation Reaction Denaturation
Dipeptide
Peptide Bond
SL and HL Content
From
B1.2 Proteins - IB Linking Questions the IB

How do abiotic factors influence the form of molecules?

What is the relationship between the genome and the proteome of an
organism?
Additional HL
Content
HL Content Only
From
Additional HL Content: B1.2 Proteins the IB

B1.2.6: Chemical diversity in the R-groups of amino acids as a basis for

the immense diversity in protein form and function
B1.2.7: Impact of primary structure on the conformation of proteins
B1.2.8: Pleating and coiling of secondary structure of proteins
B1.2.9: Dependence of tertiary structure on hydrogen bonds, ionic
bonds, disulfide covalent bonds and hydrophobic interactions
B1.2.10: Effect of polar and non-polar amino acids on tertiary structure of
proteins
HL Content Only
From
Additional HL Content: B1.2 Proteins the IB

B1.2.11: Quaternary structure of non-conjugated and conjugated proteins

B1.2.12: Relationship of form and function in globular and fibrous
proteins
HL Content Only

HL Only Key Terms

Hydrophobic Tertiary Protein Structure

Hydrophilic Quaternary Protein Structure
Polar Conjugated Protein
Nonpolar Prosthetic Group
Denature Globular Protein
Primary Protein Structure Fibrous Protein
Secondary Protein Structure
HL Content Only
From
B1.2.6: Chemical diversity in the R-groups of the IB
amino acids as a basis for the immense
diversity in protein form and function

Students are not required to give specific examples of R-groups.

However, students should understand that R-groups determine the
properties of assembled polypeptides.
Students should appreciate that R groups are hydrophobic or hydrophilic
and that hydrophilic R-groups are polar or charged, acidic or basic.
HL Content Only

R Groups

The 20 amino acids found in living things

all have the same general structure, but
they have different side chains, R groups.
The R groups determine the chemical
properties of an amino acid.
The R groups can be:
● Hydrophobic - repelled by water
General Amino Acid Structure
● Hydrophilic - attracted to water
HL Content Only

R Groups
The hydrophilic R groups are:

● Polar or charged
● Acidic or basic

The chemical interactions of the R

groups in polypeptides determine the
shape of proteins.
The shape of proteins determines
their function.
Twenty Amino Acid R-Groups
HL Content Only

Protein Structure
Read the
linked article
on protein
structure

❓ Explain
the four
levels of
structure
in
proteins.
HL Content Only

Protein Structure

Levels of Protein Structure

HL Content Only
From
B1.2.7: Impact of primary structure on the the IB

conformation of proteins

Students should understand that the sequence of amino acids and the
precise position of each amino acid within a structure determines the
three-dimensional shape of proteins. Proteins therefore have precise,
predictable and repeatable structures, despite their complexity.
HL Content Only

Primary Proteins Structure

The primary protein
structure is the
number and
sequence of amino
acids in a
polypeptide.
The primary protein
structure is
determined by the
nucleotide base
sequence of a gene.
HL Content Only

Primary Protein Structure

The amino acids in a
polypeptide are joined
together by peptide bonds
through condensation
reactions.
The precise sequence of
amino acids in a polypeptide
determines the shape of the
polypeptide, due to
interactions between R
groups. Primary Protein Structure
HL Content Only

Protein Folding Problem

Proteins have precise
predictable shapes
based on their amino
acid sequence.
Scientists are working
on being able to
predict the shapes of
proteins based on the
sequence of amino
acids in polypeptides.
HL Content Only
From
B1.2.8: Pleating and coiling of secondary the IB

structure of proteins

Include hydrogen bonding in regular positions to stabilize alpha helices

and beta-pleated sheets.
HL Content Only

Secondary Protein Structure

Secondary
protein structure
is the folding of
the polypeptide
to form alpha
helices and beta
pleated sheets.
HL Content Only

Secondary Protein Structure

Alpha helices and beta

pleated sheets form due to
hydrogen bonding between
C=O of one amino acid and
N-H of a second amino acid.
The hydrogen bonds occur at
regular intervals adding
stability to the protein.

Secondary protein structure - alpha helices and beta pleated sheets

HL Content Only
From
B1.2.9: Dependence of tertiary structure on the IB

hydrogen bonds, ionic bonds, disulfide covalent

bonds and hydrophobic interactions

Students are not required to name examples of amino acids that

participate in these types of bonding, apart from pairs of cysteines
forming disulfide bonds.
Students should understand that amine and carboxyl groups in R-groups
can become positively or negatively charged by binding or dissociation
of hydrogen ions and that they can then participate in ionic bonding.
HL Content Only

Tertiary Structure of Proteins

The tertiary
protein structure
is the further
folding of the
polypeptide due
to interactions
between the R
groups.
HL Content Only

Tertiary Structure of Proteins

Interactions between R groups cause a polypeptide to fold into a specific
shape.
Interactions include:
● Ionic bonds between charged R Groups - amine and carboxyl groups in
R-groups can become positively or negatively charged by binding or
dissociation of hydrogen ions, allowing the formation of ionic bonds.
● Covalent bonds forming between R groups, including disulfide bonds.
● Hydrogen bonding between R groups.
● Hydrophobic and hydrophilic interactions of R groups, as proteins
found in organisms are surrounded by water.
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Tertiary Protein Structure - Disulfide Bonds

Disulfide bridges are bonds that form

between the R groups of two cysteine
amino acids in a polypeptide.

Cysteine is an amino acid with sulfur

within its R group.
If the R groups of two cysteine amino acids
are in close proximity, a covalent bond
forms between the sulfurs.
Tertiary Protein Structure
HL Content Only
From
B1.2.10: Effect of polar and non-polar amino the IB

acids on tertiary structure of proteins

In proteins that are soluble in water, hydrophobic amino acids are

clustered in the core of globular proteins. Integral proteins have regions
with hydrophobic amino acids, helping them to embed in membranes.
HL Content Only

Tertiary Protein Structure and Water

Many proteins are water
soluble.
Hydrophobic amino acids, with
nonpolar R groups, cluster in a
core of globular proteins.
Hydrophilic amino acids, with
polar or ionic R groups, are
located on the outside of the
protein.
Hydrophobic and hydrophilic interactions of proteins
HL Content Only

Integral Proteins in Membranes

Integral proteins are permanently attached to a
membrane.

Integral proteins are embedded within the phospholipid

bilayer.
The portion of the integral protein in the middle of the
bilayer, surrounded by hydrophilic fatty acid tails, is
hydrophobic due to the presence of non-polar R groups.
The portion of the integral protein exposed to water
(cytoplasm inside the cell, and tissue fluid outside the cell)
is hydrophilic due to polar and charged R groups.
HL Content Only
From
B1.2.11: Quaternary structure of non- the IB

conjugated and conjugated proteins

Include insulin and collagen as examples of non-conjugated proteins and

haemoglobin as an example of a conjugated protein.
Nature of Science: Technology allows imaging of structures that would
be impossible to observe with the unaided senses.
For example, cryogenic electron microscopy has allowed imaging of
single-protein molecules and their interactions with other molecules.
HL Content Only

Quaternary Protein Structure

Many proteins are

composed of more
than one
polypeptide chain.
The quaternary
structure exists in
proteins composed
of more than one
polypeptide.
HL Content Only

Quaternary Protein Structure

The polypeptides are held together

due to the R groups on each
polypeptide such as
● hydrogen bonds
● covalent bonds such as disulfide
bridges
● Ionic bonds
● Hydrophilic and hydrophobic
interactions Quaternary Protein Structure
HL Content Only

Conjugated Proteins
A conjugated protein is a protein attached to a
non-polypeptide group, known as a prosthetic Β chain Β chain

group.
Adult haemoglobin is an example of a globular
conjugated protein. Heme
Group

Haemoglobin is composed of: 𝞪 chain 𝞪 chain

● Two alpha polypeptide chains Haemoglobin

● Two beta polypeptide chains

The function of haemoglobin is to
● Four haem groups (which are not carry oxygen within red blood cells.
polypeptides)
HL Content Only

Insulin is a Non-Conjugated Protein

Non-conjugated proteins are composed of only polypeptides.
Insulin is an example of a non-conjugated protein.

Insulin is a globular protein composed of two

polypeptide chains linked by two disulfide
bridges.
Insulin is a hormone that helps to regulate
blood glucose levels, by causing the liver to
remove glucose from the blood.

Insulin
HL Content Only

Collagen is a Non-Conjugated Protein

Collagen is a non-conjugated protein.

Collagen is a fibrous protein composed of three

polypeptide chains that are tightly coiled
together into a triple helix structure

Collagen is the main structural protein found in

connective tissues such as skin, cartilage, and
bones. Collagen
The fibrous nature of collagen provides
strength, support, and elasticity to tissues.
HL Content Only

Cryogenic Electron Microscopes

Nature of Science
Technological developments allow scientists to view structures that are
impossible to see without technology.

Cryogenic electron microscopy has allowed imaging of single-protein

molecules and their interactions with other molecules, which is not
possible with light or electron microscopes.
Biologists have developed a better understanding of protein structure
and function since the development of the cryogenic electron
microscope.
HL Content Only
From
A1.2.12: Relationship of form and function in the IB

globular and fibrous proteins

Students should know the difference in shape between globular and

fibrous proteins and understand that their shapes make them suitable
for specific functions.
Use insulin and collagen to exemplify how form and function are related.
HL Content Only

Globular and Fibrous Proteins

Read the section on
globular and fibrous
proteins in the linked
article.

❓ Compare and
contrast, using
examples, globular
proteins and
fibrous proteins.
HL Content Only

Insulin and Collagen: Similarities

Proteins can be classified as globular proteins or fibrous proteins based
on their general shape.

Insulin is a globular protein and collagen is a fibrous protein.

Similarities include:

● They are composed of amino acids joined by peptide bonds during

the process of translation on ribosomes.
● They have a quaternary structure with more than one polypeptide.
HL Content Only

Insulin and Collagen: Differences

Differences include:

Insulin Collagen
Classification Globular Protein Fibrous Protein
Shape Spherical Long and narrow
Irregular amino acid
Repetitive amino acid
Amino Acids sequence with hydrophobic
sequence
amino acids in the core.
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Insulin and Collagen: Differences

Insulin Collagen
Solubility Soluble in water Insoluble in water
Number of Two polypeptides held Three polypeptides held
polypeptides together by disulfide bonds together by hydrogen bonds
Structural Functional
Insulin is a hormone with a The three polypeptides in
specific globular shape, with collagen form flexible fibres
Function a binding site for receptors on with high tensile strength and
target cells. elasticity which provides
Insulin is soluble and can be structural support to body
transported in the blood. tissues.
HL Content Only

HL Only Key Terms

Hydrophobic Tertiary Protein Structure

Hydrophilic Quaternary Protein Structure
Polar Conjugated Protein
Nonpolar Prosthetic Group
Denature Globular Protein
Primary Protein Structure Fibrous Protein
Secondary Protein Structure
SL and HL Content
From
B1.2 Proteins - IB Linking Questions the IB

How do abiotic factors influence the form of molecules?

What is the relationship between the genome and the proteome of an
organism?
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