2.

4 PROTEINS
Essential Idea: Proteins have a very wide range of functions in living organisms

NOS: Looking for patterns, trends and discrepancies – most but not all organisms
assemble proteins from the same amino acid
Peptide bond
2.4.U1 Amino acids are linked together by condensation to form polypeptides
2.4.S1 Drawing molecular diagrams to show formation of peptide bond

• RECALL the structure of an amino acid

• RECALL the formation of a peptide bond

• Several amino acids (monomer) linked

together via condensation form a long
chain of polypeptide (polymer)
• This is catalysed by ribosomes in the
cell = site of protein synthesis
• The polypeptides will then be further
modified into a protein
 20 Different Amino Acids
2.4.U2 There are 20 different amino acids in polypeptides synthesized on ribosomes

• There are 20 different kinds of amino acids

• With different side chain (R group in the amino
acid)
• Which is universal to all living organisms
• Meaning all organisms uses the same 20 types
of amino acids
• The R group may be non-polar, polar, positively
charged or negatively charged
* there are two more which are found in only certain organisms
(selenocysteine & pyrrolysine)
OMG, do I have to
remember all of
these?

Chill, you don’t.

You just need to
be aware there
are different
amino acids with
different side
chains which may
be polar, non-
polar, and
charged
Sequence of Amino Acids
2.4.U3 Amino acids can be linked together in any sequence giving a huge range of possible polypeptides

Most polypeptide chains range from

about 50 – 2000 amino acids long.

If there are 50 amino acids in a

polypeptide, the possible
combination of sequence of amino
acids in a polypeptides will be 2050 =
1.1259 x 1065

Since a polypeptide can be of any length, of any possible combination of the 20 different
types of amino acids, there are almost infinite possible different combination/sequence
of amino acids to form an infinite number of different polypeptides.
The Central Dogma of Genetics
2.4.U4 The amino acid sequence is coded for by genes

1. Amino acid sequence is coded by genes (DNA) which is stored in the nucleus
2. A strand of mRNA (messenger RNA) copies the sequence of DNA bases (ATCG) ”code” in
the nucleus
3. Floats out of the nucleus & binds to the ribosome
4. And instruct the ribosome how to assemble the polypeptides
5. Sequence of amino acid  based on the sequence of DNA (genes)
*Most organisms use the same 20 amino acids in the same genetic code because the genetic code is also
universal (although there are some exceptions) – all organisms uses same DNA code to code for proteins
 Genome
2.4.U8 Every individual has a unique proteome

• GENOME = total amount of DNA ( coding & non-

coding DNA) and is the same in all the cells
• Genes = DNA that codes for a protein – which
instructs the production of proteins/ proteome
• PROTEOME = all the proteins produced by a cell
 Proteome
• Different proteins are produced
depending on location of cell, function
of cell, cell differentiation &
environment of cell
• Specific genes are turned on/off in A single gene = mRNA & polypeptides can be spliced,
modified etc to produce different proteins
different cell according to required
function of proteins
• Eg: insulin only produced in pancreas
• Pigment proteins (rhodopsin) only
produced in eye
https://www.proteinatlas.org/humanproteome/tissue
https://www.youtube.com/watch?v=hok2hyED9go
Protein Levels of Structure
2.4.U5 A protein may consist of a single polypeptide or more than one
polypeptide linked together

There are four levels of protein structure:

1. Primary structure = polypeptide chain

• The order of amino acid will determine the
future structures

2. Secondary structure = when hydrogen bonds

between the N-H group and C=O group of
different amino acid forms
• Two possible shapes: ⍺ - helix &
β – pleated sheet
• Most fibrous proteins have secondary
structure (eg: collagen & keratin)
 7.3.U8 The secondary structure is their formation of alpha helices
7.3.U7 The sequence and number of amino acid in the and beta pleated sheets stabilised by hydrogen bonding
polypeptide is the primary structure
H- bonds form
H-bonds form between carbonyl and
adjacent turns of the amino groups backbone
helix/ every 4th of laterally aligned
amino acid polypeptide chain
 How proteins fold: https://www.youtube.com/watch?v=Pjt1Q2ZZVjA&t=43s
Tertiary structure
2.4.U6 The amino acid sequence determines the
3D conformation of a protein

• Further bonds formed between the R

group side chains folds the proteins into
a complex 3D structure
• Eg: H-bonds, disulphide bonds, ionic
bonds and hydrophobic interactions
• This structure is common in globular
proteins and maybe important for
function (eg: specific active site shape for
enzymes)
• Order of amino acids seq  determine
3D shape of proteins
7.3.U9 The tertiary structure is the further folding of the polypeptide stabilised by interaction between R groups
Quaternary
Structure
7.3.U10 The quaternary structure exists in proteins with more than one polypeptide chain
• Forms when multiple polypeptides
interact together (haemoglobin is
composed of four polypeptide chains)
• Or interact with inorganic prosthetic
group (eg: Fe – haem group in
haemoglobin)
• Can be fibrous or globular proteins

• Fibrous proteins = structural role (part of a

structure) = eg: collagen, spider silk https://www.na
ture.com/article
s/s41586-021-0
• Globular proteins = functional role = 3819-2
perform a certain function = eg: enzyme
Proteins are commonly described as either being fibrous or globular in nature. Fibrous proteins
have structural roles whereas globular proteins are functional (active in a cell’s metabolism).
Denaturation of Proteins
2.4.A2 denaturation of proteins by heat or by deviation of pH from the optimum

• The 3D shape of proteins are held by

intermolecular forces of H-bonds & bonds
between R group side chains which are
relatively weak
• When these bonds are broken and causes a
change in the shape of the protein =
denaturation
• Some denaturation are reversible but some are
permanent
• Heat can break intermolecular H-bonds
• pH can cause changes in charges, thus
breaking/changes ionic bonds
Amino Acids: https://www.youtube.com/watch?v=He1zHW7Vydo
Primary & Secondary: https://www.youtube.com/watch?v=a56ChCHTa3w
Tertiary & Quaternary: https://www.youtube.com/watch?v=1Fl_rSgQ5_8
Globular Proteins: https://www.youtube.com/watch?v=i7CFjX9d81o
Fibrous Proteins: https://www.youtube.com/watch?v=MHMH21uTOZU
Protein & Lipids Test: https://www.youtube.com/watch?v=VqnMTtzEP1o
Proteins Range of Functions
2.4.U7 Living organisms synthesize many different proteins with a wide range of functions
RuBisCO
2.4.A1 Rubisco, insulin, immunoglobins, rhodopsin, collagen and spider silk as examples of the range of protein
functions

• enzyme= RIBULOSE BIOPHOSPHATE

CARBOXYLASE (globular protein)
• Found in chloroplasts – in green leaves &
algal cells
• Catalyse the reaction that fixes carbon
dioxide from the atmosphere in light
independent stage – Calvin cycle (more in
8.3 Photosynthesis)
• Provide source of carbon
 INSULIN
• Hormone produce by the β cells in
the pancreas
• Signal the cells in liver to convert
glucose to glycogen
• Signal body cells to absorb glucose
• To reduce blood glucose
concentration
• Affected cells have receptors on
the membrane surface that can
bind to insulin
• Globular protein
 IMMUNOGLOBIN
• Also known as antibodies
• Two binding site that binds to antigen
• Antigen = surface molecule on pathogen
that invoke immune response
• Binding sites vary greatly (many
immunoglobin with different binding sites
that can target many different kinds of
pathogen)
• Can also act as a marker to signal
phagocytes to engulf pathogen
• Bilaterally symmetrical
 RHODOPSI
N
• Membrane protein in rod cells of
retina
• Pigment that absorbs light –
photoreceptor
• Detects very low light intensity
(monochrome – b/w)
• Changes shape when absorb
photon of light & generate a
nerve impulse to the brain
• Globular protein
 COLLAGEN
• Connective tissue in humans (structural)
• Rope-like – made of 3 polypeptides wound
together
• Form mesh fibres in skin and blood vessels
that resist tearing
• Gives strength to tendon, ligaments, skin,
blood vessels,
• forms part of teeth and bones – helps prevent
cracks and fractures
• a quarter of protein in human body is made up
of collagen
• Based on your knowledge, can collagen skin
care products help to improve skin?
 SPIDER
SILK
• Different types of silk with
different structural functions
• Dragline silk is stronger than
Kevlar (synthetic fiber) &
steel (by weight)
• Can be stretched &
extendible without breaking
• Made with regions of β –
pleated sheet connected
together
• Fibrous protein
Denaturation Experiment
2.4.Egg white/albumin solution can be used in denaturation experiment

• Refer to handout