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Proteins

Protein Functions
– Proteins are extremely important macromolecules that are used by the cells of our body in many
different ways.

1. Provide structure
e.g.: keratin - found in our hair, nails and skin
entire cytoskeleton consists of different types of proteins (e.g.: actin)

2. Regulate body processes

e.g.: enzymes - speed up biochemical reactions

3. Transport materials
e.g.: Haemoglobin - O2 transporting protein found in our red blood cells.

4. Act as a messenger - Some proteins like hormones are messenger proteins, which help to
coordinate certain body activities.
e.g.: insulin - regulates glucose metabolism.

5. Protect the body

e.g.: antibodies are specialized proteins involved in defending the body from foreign
invaders.

Amino acids
– Amino acids are the monomers that make up proteins.
– There are 20 different amino acids commonly found in proteins.
– Amino acids share a basic structure, which consists of a central carbon atom, also known as the
a-carbon, bonded to an amino group, a carboxylic group, a H atom, and a R group (side chain).

General structure of an a-amino acid At physiological pH

– At physiological pH (pH 7.0 – 7.4), the amino group is typically protonated while the carboxyl
group is typically deprotonated.
– The R group determines the identity of amino acids.
– The amino acids can be categorized into 5 main classes based on the properties of their R groups.

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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1. Nonpolar, Aliphatic R Groups

– Proline has an aliphatic side chain with a distinctive cyclic structure.

– Methionine – a sulfur containing amino acid.
– The side chains of alanine, valine, leucine and isoleucine tend to cluster together within proteins,
stabilizing protein structure by means of hydrophobic interactions.

2. Aromatic R Groups

– Relatively non-polar (hydrophobic) amino acids because of the aromatic side chain.
– All can participate in hydrophobic interactions, and the hydroxyl group of Tyr can form H- bonds.
– Tyr and Trp are more polar than Phe.
– These amino acids can absorb UV light, and accounts for the characteristic absorbance of light by
most proteins at a wavelength of 280 nm (used in the characterization of proteins).

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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3. Polar, Uncharged R Groups

– Contain functional groups that can form H-bonds with water.

– Therefore, more soluble in water than non-polar amino acids.
– Cys has the ability to form disulphide bonds.
– Disulfide bonds play a special role in the structure of many proteins by forming covalent links
between parts of a protein molecule or between 2 polypeptide chains.

4. Positively Charged (Basic) R Groups

– The R group is basic.

– The most hydrophilic R groups are those that are either positively or negatively charged.

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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– In many enzyme-catalyzed reactions, a His residue facilitates the reaction by serving as a proton
donor or acceptor.

5. Negatively Charged (Acidic) R Groups

– The R group is acidic.

– Has a net negative charge at pH 7.0.

Stereoisomers of amino acids

– For all the common amino acids except glycine, the a-carbon is bonded to 4 different groups.
– The a-C is thus a chiral center.
– Because of the tetrahedral arrangement of the bonding orbitals around the a-carbon atom, the
4 groups can have 2 unique spatial arrangements, and therefore 2 possible stereoisomers.
– They are non-superimposable mirror images of each other and represent a class of stereoisomers
called enantiomers.
– Molecules with a chiral center are optically active, that is they rotate plane polarized light.
– The absolute configuration of amino acids are specified by D,L system (similar to what we used
for monosaccharides).

– In these formulas, the carbons are lined up vertically, with the chiral atom in the center.
– When presented in this way, the R group of the amino acid is always below the a-carbon.
– L-amino acids are those with the a-amino group on the left, and D-amino acids have the a-amino
group on the right.
– The amino acid residues in protein molecules are exclusively L-stereoisomers.

Essential amino acids

– Amino acids that cannot be synthesized in our body are called essential amino acids.
– These amino acids must be obtained through our diet.
– the best sources of essential amino acids are animal proteins like meat, eggs and poultry.

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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e.g.: histidine
isoleucine
leucine
lysine
methionine
phenylalanine
threonine
tryptophan
valine

Conditionally essential amino acids

– These are considered essential only under specific circumstances such as illness or stress.
e.g.: although arginine is considered non-essential, our body can’t meet demands when
fighting certain diseases like cancer.

Non-essential amino acids

– These amino acids can be synthesized in our body in sufficient amounts.
e.g.: alanine
arginine *
asparagine
aspartic acid
cysteine *
glutamic acid
glutamine *
glycine *
proline *
serine
tyrosine *
(* can be conditionally essential)

Roles of essential amino acids

o Histidine: used to produce histamine, a neurotransmitter that is vital to immune
response, digestion, sleep-wake cycles.
o Isoleucine: involved in muscle metabolism. Also important for immune function,
haemoglobin production and energy regulation.
o Leucine: critical for protein synthesis and muscle repair. Also helps regulate blood sugar
levels, stimulates wound healing and produces growth hormones.
o Lysine: plays major roles in protein synthesis, hormone and enzyme production and the
absorption of calcium. Also important for energy production, immune function and the
production of collagen and elastin.

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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o Methionine: plays an important role in metabolism and detoxification. Also necessary for
tissue growth and the absorption of zinc and selenium.
o Phenylalanine: a precursor for the neurotransmitters like dopamine. Involved in the
production of other amino acids like Tyr.
o Threonine: a principal part of structural proteins such as collagen and elastin. Also plays
a role in fat metabolism and immune function.
o Tryptophan: maintain proper nitrogen balance and is a precursor to serotonin, a
neurotransmitter that regulates your appetite, sleep and mood
o Valine: helps stimulate muscle growth and regeneration and is involved in energy
production.

Peptide bond
– Two amino acid residues can be covalently joined through a linkage termed a peptide bond, to
yield a dipeptide.
– A peptide bond is formed by removal of a water molecule from the a-carboxyl group of one
amino acid and the a-amino group of another.

Amino terminal Carboxyl terminal

(N-terminal) (C-terminal)

The peptide bond (has a

partial double bond
character)

– 3 amino acids can be joined by 2 peptide bonds to form a tripeptide.

– When a few amino acids are joined in this manner, the structure is called an oligopeptide.
– When many amino acids are joined, the product is called a polypeptide or a protein.
– Proteins may have hundreds or sometimes thousands of amino acid residues.
– In a peptide, the amino acid residue at the end with a free a-amino group is the amino terminal
(or N-terminal) residue.
– The residue at the other end is the carboxyl terminal (C-terminal) residue.
– By convention, peptide sequences are written N-terminus to C-terminus.

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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Protein structure
– Proteins are polymers of amino acids.
– Individual amino acids are joined by peptide bonds to form linear polypeptide chains.
– The linear polypeptide chain is folded into specific structural conformations.
– A protein can have up to 4 levels of structural organization: primary, secondary, tertiary and
quaternary structures.

1. Primary structure
– Simply the sequence of amino acids in the polypeptide chain or chains if the protein consists of
more than one polypeptide chain.
– The amino acid sequence is written from the N-terminus to the C-terminus.

e.g.: Gly-Ile-Val-Glu-Cys-Cys-Ala-Ser-Val-Cys-Ser-Leu……

– The primary structure of a protein determines the other levels of structural organizations (2ry, 3ry
and 4ry).
– The primary structure is mainly stabilized by peptide bonds.

2. Secondary structure
– Refers to local folded structures that form within a polypeptide due to interactions between
atoms of the backbone (polypeptide chain apart from the R groups – 2ry structure does not
involve R group atoms).
– The most common types of 2ry structures are the a-helix and b-conformation.
– Both a-helix and b-conformation are held in shape by hydrogen bonds, which form between the
carbonyl O of one amino acid and the amino H of another amino acid.

a-helix
– The carbonyl O of one amino acid is hydrogen bonded to the amino H of an amino acid that is 4
residues away.
e.g: the carbonyl of amino acid 1 (n) would form a H-bond to the N-H of amino acid 5 (n+4).

– This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a
curled ribbon, with each turn of the helix contains 3.6 amino acids.
– The R group of the amino acids point outward from the a-helix, where they are free to interact.
– The a-helix is very common in proteins because it makes optimal use of internal H-bonds.

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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5.4 Å
3.6 residues

– Some polypeptides cannot form a stable a-helix.

– The interaction between the amino acid side chains can stabilize or destabilize the a-helix.
– if polypeptide chain has a long stretch of glutamic acid residues, this segment of the chain will
not form an a-helix.
– The negatively charged carboxyl group of the adjacent Glu residues repel each other strongly so
that they prevent the formation of the a-helix.
– Similarly, a polypeptide rich in Pro will not form an a-helix.
– In Pro, the N atom is part of a rigid ring and rotation about the N-Ca bond is not possible.
– Also, the N atom of a Pro residue in a peptide linkage has no substituent H to participate in H-
bonds with other residues.
– Thus, Pro introduces a destabilizing kink in the polypeptide and hence Pro is very rarely found in
a-helix.

b-conformation
– This is a more extended conformation of polypeptide chains.
– In the b-conformation, the backbone of the polypeptide chain is extended into a zigzag rather
than helical structure.
– The zigzag polypeptide chains can be arranged side by side to form a structure resembling a series
of pleats.
– This arrangement is called a b-sheet.
– In a b-sheet H-bonds are formed between adjacent segments of a polypeptide chain but can also
be quite distant from each other in the linear sequence of the polypeptide, they may even be
segments in different polypeptide chains.
– The R groups of adjacent amino acids protrude from the zigzag structure in opposite directions.
– The adjacent polypeptide chains in a b-sheet can be either parallel or antiparallel (having the
same or opposite amino-to-carboxyl orientations).
– When 2 or more b-sheets are layered close together within a protein, the R groups of the amino
residues on the touching surfaces must be relatively smaller (Gly and Ala are better).

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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C N N N
↑ ↓ ↓ ↓
N C C C

Antiparallel Parallel

b turns
– The b turns are very common in proteins, when the peptide makes a turn a loop (where the
polypeptide chain reverses direction).
– In globular proteins, nearly one third of the amino acid residues are b turns.
– The b turns are the connective elements that link successive runs of polypeptide chain.
– The b turn connects the ends of 2 adjacent segments of anti-parallel b sheets.
– The b turn structure is a 180° turn involving 4 amino acid residues.
– The carbonyl oxygen of the first residue forms a hydrogen bond with the amino group hydrogen
of the fourth amino acid in the turn.
– Glycine and Proline residues frequently occur in b turns.
o Glycine - due to its very small size (R=H) allows b turns.
o Proline - in the peptide bond proline residue assumes a cis configuration, which is
very amenable to tight turns.

3. Tertiary structure
– The overall 3-dimensional arrangement of all atoms in a protein is referred to as the tertiary
structure.
– This describes the folding of its secondary structural elements and specifies the positions of each
atom in the protein, including those of its side chains.
– Tertiary structure in a protein is stabilized by both covalent and non-covalent interactions
between the R groups of the amino acids.

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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o Covalent - disulphide bonds (between 2 cysteine residues)
o Non-covalent - hydrogen bonds
o Ionic bonds
o Dipole-dipole interactions.
o Van der Walls interactions.
o Hydrophobic interactions.

4. Quaternary structure
– Some proteins contain 2 or more separate polypeptide chains or subunits which may be identical
or different.
– The arrangement of protein subunit in 3-dimentional complexes in a multi-subunit protein is
called the quaternary structure.
– Interaction that stabilize quaternary structure include:
o Hydrophobic interactions (among non-polar side chains at the contacting regions of
the subunits)
o Electrostatic interaction (ionic bonds)
o Hydrogen bonds

– haemoglobin (oxygen carrier protein in blood) has 4 subunits (2a and 2b).
– DNA polymerase (enzyme that synthesize new strands of DNA) has 10 subunits.

Proteins can be classified into 2 major groups based on their higher-level structure

1. Fibrous proteins 2 Globular proteins

§ Polypeptide chains are arranged in long § polypeptide chains folded into a

strands or sheets.
§ usually consist of a single type of
secondary structure.
§ provide support, shape and external
protection to vertebrates.
spherical or globular shape
§ often contain several types of
secondary structure.
§ most enzymes and regulatory proteins
are globular proteins.

e.g.: e.g.:
- a-keratin - provide strength - found in - Myoglobin - oxygen binding protein in
hair, nails muscle cells
- collagen - provide strength - found in - Cytochrome C - component of the
connective tissues such as respiratory chain of mitochondria.
tendons/cartilage - Lysozyme - an enzyme abundant in egg
- silk fibroin - the protein in silk - produced white and human tears.
by insects and spiders

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)

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Protein Denaturation
– Each protein has its own unique shape.
– If the temperature or pH of a protein’s environment is changed, or if it’s exposed to chemical,
the interactions holding the protein may be disrupted.
– This will cause the protein to lose its three-dimensional structure and turn into an unstructured
string of amino acids.
– When a protein loses its higher-order structure, but not its primary sequence, it is said to be
denatured.
– Denatured proteins are usually non-functional.
– For some proteins, denaturation can be reversed.
– Since the primary structure of the polypeptide is still intact, it may be able to refold into its
functional form if it is returned to its normal environment.
– Other times, denaturation is permanent.
e.g.: the albumin protein in egg white becomes opaque and solid as it’s denatured by heat
and will not return to its original even when cooled down.

Dr. R.K. Ahinsa, B.Sc. (Perad), Ph.D. (Michigan State, USA)