Topic 1 Molecules, Transport

and Health
Chapter 1A – Proteins

▷ Introduction to Proteins
▷ Amino Acids
▷ Bonds in Proteins
▷ Protein Structure
▷ Fibrous and Globular Proteins
▷ Conjugated Proteins

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 Introduction to Proteins
▷ Proteins are organic molecules that have many importation functions
including:

❖ Structural roles
• Muscles
• Tendons
• Bones

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 Introduction to Proteins
▷ Proteins are organic molecules that have many importation functions
including:

❖ Metabolic Roles
• Enzymes

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 Introduction to Proteins
▷ Proteins are organic molecules that have many importation functions
including:

❖ Transport Roles
• Hemoglobin

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 Introduction to Proteins
▷ Like carbohydrates and lipids,
proteins are made up of carbon,
hydrogen and oxygen

▷ Proteins also contain other

elements
• They all contain nitrogen
• Many also contain sulfur

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 Amino Acids
▷ Amino acids are the building blocks used to make proteins
▷ They are monomers
▷ Protein is a polymer of amino acids

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 Amino Acids
▷ All amino acids have the same basic structure
▷ A central carbon bonded to carboxyl group
(COOH)
▷ An amino group (NH2)
▷ A hydrogen atom
▷ And R group

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 Amino Acids
▷ We have 20 naturally occurring
amino acids
▷ Each have a different R group
▷ Same structure, apart from the
R groups
▷ R groups can vary:
○ Size
○ Polarity
○

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 R groups
▷ R groups can vary in size

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 R groups
▷ R groups can vary in polarity

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 R groups
▷ R groups can vary in polarity

Alanine Cysteine

δ+ δ-

Polar
Non-Polar

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 Formation of Polypeptides
▷ Amino acids are monomers
▷ Building blocks of larger proteins
▷ Protein is a polymer of amino acids

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 Formation of Polypeptides
▷ Two amino acids are joined together by a condensation reaction to form a
dipeptide
▷ The condensation reaction occurs between the carboxyl group (-COOH)
and the amino group (-NH2) on adjacent amino acids
▷ A peptide bond joins the two amino acids together to form a dipeptide
Peptide bond

Condensation

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 Formation of Polypeptides
▷ Two amino acids join together to
create a dipeptide
▷ Many amino acids join together form
a polypeptide

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 Formation of Polypeptides
▷ A protein is formed when one or many polypeptide chains fold into a
specific shape
▷ This shape allows the polypeptide to perform a specific function

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 Peptide Bonds
▷ Many amino acids can be joined
together is a series of
condensation reactions to form a
polypeptide

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 Peptide Bonds
▷ Polypeptides can be broken down
into amino acids by a series of
hydrolysis reactions

Hydrolysis

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 Protein Structure
▷ Proteins can be described by
their structure
○ Primary
○ Secondary
○ Tertiary
○ Quaternary

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 Primary Structure

▷ Primary structure is simply the specific order of amino acids in a

polypeptide chain
▷ Long chains of different amino acids monomers joined together via
peptide bonds
▷ Different combinations of amino acids give different chains

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Secondary Structure
▷ Secondary structure of a polypeptide chain is
created is the curling and folding of the
polypeptide chain due to the formation of
hydrogen bonds
○ The O of the carboxyl group has a small
negative charge
○ The H of the amino group has a small positive
charge
▷ Hydrogen bonding between the two groups will
fold and twist the polypeptide into its secondary
structure 21
Secondary Structure
❖ Alpha Helix
❖ Beta pleated sheets

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Secondary Structure
❖ Alpha Helix
o In an a-helix, the polypeptide
chain coils with hydrogen
bonds keeping the coil stable

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Secondary Structure
❖ Beta Pleated sheets
o In beta-pleated sheets, the
chains form a zig-zag and fold
over themselves
o Most fibrous proteins have
this type of structure

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Tertiary Structure
▷ The polypeptide chain in addition to any α-
helices and β-pleated sheets folds further to
form complex 3D shapes
▷ Various types of bond, including between
the R groups of adjacent amino acids hold the
structure in place
○ Hydrogen bonds
○ Ionic bonds
○ Disulfide links
○ Hydrophilic and hydrophobic R groups 25
 Bonds in Proteins
▷ In addition to the peptide bonds made between amino acids, other bonds
can be formed to create 3D structures
▷ These bonds depend on the R group present on the amino acids
▷ Types of bonds:
○ Hydrogen Bonds
○ Disulfide Bonds
○ Ionic Bonds
○ Hydrophobic and hydrophilic interactions

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 Bonds in Proteins
▷ Types of bonds:
❖ Hydrogen Bonds
■ Tiny negative charge of oxygen
of the COOH and tiny positive
charge of the hydrogen on NH2
form a hydrogen bond

■ Hydrogen bonds tend to weak

and break easily if pH and
temperature conditions change
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 Bonds in Proteins
▷ Types of bonds:

❖ Disulfide Bonds
■ Sulfur atoms between the amino
acids can form a covalent bond

■ This a disulfide bond

■ Disulfide bonds are strong and
do not break easily
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 Bonds in Proteins
▷ Types of bonds:

❖ Ionic Bonds
■ Ionic bonds are found between amino acids with charged
R groups

■ Opposite charges attract each other and holds different

part of the polypeptide chain together

■ Broken in changes of pH
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 Bonds in Proteins
▷ Types of bonds:

❖ Hydrophobic and hydrophilic interactions

■ Hydrophobic: Amino acids orient
themselves towards the center of the
polypeptide to avoid water

■ Hydrophilic: Amino acids orient

themselves outward to be close to
the water

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Tertiary Structure
▷ Tertiary structure is critical for how a
protein functions
▷ Active site of the enzyme depends on
the protein forming a very specific tertiary
structure
▷ If we change the tertiary structure of an
enzyme (ex. heating it) then the shape of
the active site changes and the enzyme
can no longer function effectively

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 Polypeptide 1 Polypeptide 2
Quaternary Structure
▷ Quaternary structure is the specific 3D
shape of a protein that is determined by
the multiple polypeptide chains and/or
prosthetic groups bonded together

Prosthetic
groups

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 Polypeptide 1 Polypeptide 2
Quaternary Structure
▷ Quaternary structure is the 3D
arrangement of more than one tertiary
polypeptide held together by the same
bonds:
○ Hydrogen bonds
○ Ionic bonds
○ Disulfide bonds
▷ May also contain additional non-amino Prosthetic
acid derived groups known as prosthetic groups

groups 34
Fibrous Proteins

▷ Form repetitive amino acids sequences

▷ Form long rope-like molecules
▷ Fibrous proteins play a structural role
▷ Large portion of amino acids with hydrophobic R
groups making them insoluble in water

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Fibrous Proteins
▷ Collagen
• Provides strength to
tendons, ligaments,
bones and skin
• Its quaternary
structure has 3
polypeptide chains
• Often found together
in fibers to form
collagen fibers
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Globular Proteins

▷ A globular protein is a protein with a

spherical shape that is soluble in
water.
▷ Globular Proteins have tertiary and
quaternary structures
▷ Usually have a spherical shape due to
its tightly folded polypeptide chain

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Globular Proteins
▷ Globular proteins are soluble in water
▷ Some amino acids have R groups that
are hydrophilic. These are found on the
surface of a globular protein
▷ Hydrophilic R groups on globular
proteins make them soluble in water
▷ Hydrophobic R groups are found in the
center of the protein

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 Polypeptide 1 Polypeptide 2
Quaternary Structure
▷ Quaternary structure is the 3D
arrangement of more than one tertiary
polypeptide held together by the same
bonds.

▷ May also contain additional non-amino

acid derived groups known as prosthetic
groups
Prosthetic
groups

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Conjugated Proteins

▷ Protein molecules joined to another type

of molecule which is known in this context
as a prosthetic group

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Haemoglobin
▷ Haemoglobin is globular protein as well
as a conjugated protein
▷ Haemoglobin consist of 4 polypeptide
chains
▷ The quaternary structure of hemoglobin
shows how the individual subunits are
arranged to form a larger 3D structure
▷ Haemoglobin contains the prosthetic
group haeme which binds to oxygen

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Conjugated Proteins
▷ Proteins that are conjugated with lipids are called lipoproteins
○ Important in the transport of cholesterol
○ Lipid prosthetic groups allows it to connect with the lipid cholesterol
▷ Proteins that are conjugated with carbohydrate are called
glycoproteins

○ Carbohydrate prosthetic groups allows the glycoprotein to hold

water

○ Harder for proteases to break them down 44