2.

4 Proteins
Understandings:
■ Amino acids are linked together by condensation to form polypeptides
■ There are 20 different amino acids in polypeptides synthesised on ribosomes
■ Amino acids can be linked together in any sequence giving a huge range of possible
polypeptides
■ The amino acid sequence of polypeptides is coded for by genes
■ A protein may consist of a single polypeptide or more than one polypeptide linked
together
■ The amino acid sequence determines the three-dimensional conformation of a
protein
■ Living organisms synthesise many different proteins with a wide range of functions
■ Every individual has a unique proteome
Applications & Skills
Applications: Skills:

■ Rubisco, insulin, ■ Drawing molecular diagrams to

immunoglobulins, rhodopsin, show the formation of a peptide
collagen and spider silk as bond
examples of the range of protein
functions

■ Denaturation of proteins by heat

or by deviation of pH from the
optimum
Amino Acids
Proteins are comprised of long chains of Amino acids all share a common basic
recurring monomers called amino acids structure, with a central carbon atom
bound to:

■ An amine group (NH2)

■ A carboxylic acid group (COOH)

■ A hydrogen atom (H)

■ A variable side chain (R)

Amino Acids
There are 20 different amino acids which
are universal to all living organisms
■ A further two – selenocysteine and
pyrrolysine – are modified variants
found only in certain organisms
Amino acids are joined together on the
ribosome to form long chains called
polypeptides, which make up proteins.
Each type of amino acid differs in the
composition of the variable side chain.
Side Chains
These side chains will have distinct
chemical properties (e.g. charged, non-
polar, etc.) and hence cause the protein
to fold and function differently
according to its specific position within
the polypeptide chain.
As most natural polypeptide chains
contain between 50 – 2000 amino acid
residues, organisms are capable of
producing a huge range of possible
polypeptides
Peptide Bond
Amino acids can be covalently joined
together in a condensation reaction to
form a dipeptide and water.

The covalent bond between the amino

acids is called a peptide bond and, for
this reason, long chains of covalently
bonded amino acids are called
polypeptides.

Polypeptide chains can be broken

down via hydrolysis reactions, which
requires water to reverse the process.
Peptide bonds are formed
between the amine and carboxylic
acid groups of adjacent amino
acids

■ The amine group loses a

hydrogen atom (H) and the
carboxylic acid loses a
hydroxyl (OH) – this forms
water (H2O)
Protein Structure
Amino acids are covalently joined via peptide bonds to form long chains called
polypeptides

The order of the amino acid sequence is called the primary structure and determines
the way the chain will fold

■ Different amino acid sequences will fold into different configurations due to the
chemical properties of the variable side chains
Helices
Amino acid sequences will commonly
fold into two stable configurations, called
secondary structures
■ Alpha helices occur when the amino
acid sequence folds into a coil /
spiral arrangement
Both α-helices and β-pleated sheets
result from hydrogen bonds forming
between non-adjacent amino and
carboxyl groups
■ Where no secondary structure
exists, the polypeptide chain will
form a random coil

■ Beta-pleated sheets occur when the

amino acid sequence adopts a
directionally-oriented staggered
strand conformation
Tertiary Structure
The overall three-dimensional
configuration of the protein is referred to
as the tertiary structure of the protein
The tertiary structure of a polypeptide
chain will be determined by the
interactions between the variable side
chains
■ These interactions may include
hydrogen bonds, disulphide
bridges, ionic interactions, polar
associations, etc.
The affinity or repulsion of side chains
will affect the overall shape of the
polypeptide chain and are determined
by the position of specific amino acids
within a sequence
■ Hence, the order of the amino acid
sequence (primary structure)
determines all subsequent levels of
protein folding
Certain proteins possess a fourth level
of structural organisation called a
quaternary structure

Quaternary structures are found in

proteins that consist of more than one
polypeptide chain linked together

Alternatively, proteins may have a

quaternary structure if they include
inorganic prosthetic groups as part of
their structure

Not all proteins will have a quaternary

structure – many proteins consist of a
single polypeptide chain
Quaternary Structure
An example of a protein with a quaternary structure is
hemoglobin (O2 carrying molecule in red blood cells)

■ Hemoglobin is composed of four polypeptide chains

(two alpha chains and two beta chains)

■ It is also composed of iron-containing heme groups

(prosthetic groups responsible for binding oxygen
Denaturation
Denaturation is a structural Denaturation of proteins can usually be caused
change in a protein that by two key conditions – temperature and pH
results in the loss (usually
permanent) of its biological
properties

■ Because the way a

protein folds determines
its function, any change
or abrogation of the
tertiary structure will
alter its activity
Temperature
■ High levels of thermal energy may
disrupt the hydrogen bonds that hold
the protein together

■ As these bonds are broken, the protein

will begin to unfold and lose its capacity
to function as intended

■ Temperatures at which proteins

denature may vary, but most human
proteins function optimally at body
temperature (~37ºC)
pH
■ Amino acids are zwitterions, neutral molecules
possessing both negatively (COO–) and positively
(NH3+) charged regions

■ Changing the pH will alter the charge of the

protein, which in turn will alter protein solubility
and overall shape

■ All proteins have an optimal pH which is

dependent on the environment in which it
functions (e.g. stomach proteins require an
acidic environment to operate, whereas blood
proteins function best at a neutral pH)
Effect of pH on Protein Structure
Gene → Polypeptide
A gene is a sequence of DNA
which encodes a polypeptide
sequence
A gene sequence is converted into a polypeptide
sequence via two processes:
■ Transcription – making an mRNA transcript
based on a DNA template (occurs within the
nucleus)
■ Translation – using the instructions of the
mRNA transcript to link amino acids together
(occurs at the ribosome)
Genes
Typically, one gene will code for one polypeptide – however
there are exceptions to this rule:

■ Genes may be alternatively spliced to generate multiple

polypeptide variants

■ Genes encoding tRNA sequences are transcribed but

never translated

■ Genes may be mutated (their base sequence is changed)

and consequently produce an alternative polypeptide
sequence
Proteome
The proteome is the totality of proteins The proteome is always significantly
expressed within a cell, tissue or larger than the number of genes in an
organism at a certain time individual due to a number of factors:

■ The proteome of any given ■ Gene sequences may be

individual will be unique, as protein alternatively spliced following
expression patterns are determined transcription to generate multiple
by an individual’s genes protein variants from a single gene

■ Proteins may be modified (e.g.

glycosylated, phosphorylated, etc.)
following translation to promote
further variations
 Protein Functions
Proteins are a very diverse class of compounds and may serve a number of different
roles within a cell, including:

■ Structure – e.g. collagen, spider silk

■ Hormones – e.g. insulin, glucagon

■ Immunity – e.g. immunoglobulins

■ Transport – e.g. haemoglobin

■ Sensation – e.g. rhodopsin

■ Movement – e.g. actin, myosin

■ Enzymes – e.g. Rubisco, catalase

Structure & Hormones
The following are specific examples of the Hormones
different functions of proteins:
■ Insulin: Protein produced by the
Structure pancreas and triggers a reduction
in blood glucose levels
■ Collagen: A component of the
connective tissue of animals (most ■ Glucagon: Protein produced by the
abundant protein in mammals) pancreas that triggers an increase
in blood glucose levels
■ Spider silk: A fiber spun by spiders and
used to make webs (by weight, is
stronger than kevlar and steel)
Immunity & Transport
Immunity Transport

■ Immunoglobulins: Antibodies ■ Haemoglobin: A protein found in

produced by plasma cells that are red blood cells that is responsible
capable of targeting specific antigens for the transport of oxygen

■ Cytochrome: A group of proteins

located in the mitochondria and
involved in the electron transport
chain
Sensation, Movement & Enzymes
Sensation Enzymes
■ Rhodopsin: A pigment in the ■ Rubisco: An enzyme involved in the
photoreceptor cells of the retina that is
light independent stage of
responsible for the detection of light
photosynthesis

Movement

■ Actin: Thin filaments involved in the

contraction of muscle fibres

■ Myosin: Thick filaments involved in the

contraction of muscle fibres