1. HBC1011 Biochemistry I
Trimester I, 2018/2019
Lecture 6 – Protein structure and
function
Ng Chong Han, PhD
MNAR1010, 06-2523751
chng@mmu.edu.my
2. Overview
• Protein function and functional group
• Amino acid: Chemical and Physical properties,
Types
• Polypeptide and peptide bond
• Primary structure
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3. Protein function
• Protein – large biological molecules, consisting of one or more
long chains of amino acid residues.
• Functions
– catalysts
– transport and store other molecules such as oxygen
– provide mechanical support and immune protection
– generate movement
– transmit nerve impulse
– control growth and differentiation.
• Proteins differ in their sequence of amino acids, which is dictated
by the nucleotide sequence of their genes, and which usually
results in folding of the protein into a specific three-dimensional
structure that determines its activity.
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4. The four levels of protein structure - 1
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• Proteins are linear polymers built of monomer units called amino
acids, which are linked end to end.
• Primary structure - the sequence of linked amino acids
• Secondary structure - 3D structure formed by H bonds between
a.a. near one another
5. The four levels of protein structure - 2
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• Tertiary structure - is formed by long-range interactions between a.a.
• Quaternary structure - the three-dimensional structure of a multi-
subunit protein and how the subunits fit together. Protein function
depends directly on this three-dimensional structure
6. Protein – Functional group
• Contains wide range of functional groups (on the side chains of
the a.a.)
e.g.: alcohol, thiol, thioether, carboxylic acids, carboxamides
• Chemically reactive
• Aid in the protein’s 3-D structure formation
• Contribute to the protein’s function
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7. Protein properties
• Proteins can interact with one another and with other
biological macromolecules to form protein complex.
– Examples : DNA replication machinery
• Rigid: in cytoskeleton/in connective tissue
• Flexibility: hinges, spring, lever structures in macromolecular
assembly
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Protein complex
8. Protein – 20 amino acids as building blocks
• Amino acids (a.a.) are amino derivatives of carboxylic acids, in
which amino (-NH2) and carboxyl (-COOH) functional groups,
along with a distinctive side-chain (R) specific to each amino acid
are bonded to the same carbon atom (α-carbon atom).
• The elements of an a.a. - carbon (C), hydrogen (H), oxygen (O),
and nitrogen (N), and other elements found in the side-chains (R).
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α
side
chain
α-amino
group
α-carboxyl group
9. Non standard amino acids
• Pyrrolysine - found in methanogenic organisms and other
eukaryotes.
• Selenocysteine - present in many noneukaryotes as well as most
eukaryotes, not coded directly by DNA.
• N-formylmethionine (fMet) – is often the initial amino acid of
proteins in bacteria, mitochondria and chloroplast.
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N-formylmethionine
10. Stereoisomerism
• 19 of the 20 a.a. - are chiral, or asymmetric molecule since 4
different groups bonded to it except for glycine whose R is H atom.
• Stereoisomers – compounds that have the same molecular formula
but differ in the arrangement or configuration
• A.a. may appear in the form of L (Latin laevus, left) or D (Latin
dexter, right) isomers, which comes from the ability of optically
active compounds to rotate polarized light to the left or the right.
.
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D-Alanine and L-Alanine
are nonsuperimposable
mirror images.
11. Stereoisomerism
• Most a.a. are in L-amino acids. A simple mnemonic for correct L-
form is "CORN": when the Cα atom is viewed with the H in the
back, the residues read "CO-R-N" in a anti-clockwise direction.
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12. Zwitterion
• Zwitterion is a neutral molecule with both positive and
negative electrical charges.
• Under the physiological pH range (6.8-7.4), a.a. are zwitterions, or
dipolar ions. The amino group is protonated (-NH3
+) because the
pKa is close to 9 while the carboxyl group is deprotonated/ionized
(-COO-) because the pKa is below 3.
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NH2RCHCO2H NH3
+RCHCO2
−
un-ionized zwitterion
13. Ionization state of amino acid
• Ionization state of an a.a varies with pH
• In acid solution, a.a.’s amino group protonated (-NH3
+) & carboxyl group is not
dissociated (-COOH), predominantly positively charged.
• pH raised: carboxylic acid group give out a proton. (Zwitterionic form – both
charges)
• Until pH ~9: protonated amino group loses a proton , predominantly negatively
charged.
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Predicting a.a. electrical
charges at a particular
pH is important since it
affects structure and
function.
14. pKa of amino acid
• pK1 = proton dissociation from the
carboxyl group
• pK2 = proton dissociation from the
amino group
• pKR (for some a.a. with R ionizable
group) = proton dissociation from the
R group
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• Because a.a contain acidic & basic
functional group, they can be titrated.
Titration curve for
Alanine (R=CH3)
15. Ionic forms of alanine
Dissociation of the carboxyl group: At a low pH, both of these
groups are protonated. As the pH of the solution is raised, the –
COOH group of Form I can dissociate by donating a proton, H+ to
the medium. The release of a proton results in the formation of
the carboxylate group, –COO–. This structure is Form II, which is a
zwitterion, is the isoelectric form of alanine with a net charge of
zero.
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H+ + H+ +
16. Ionic forms of alanine
Dissociation of the amino group: The second titratable group of
alanine is the amino (– NH3
+) group. Release of a proton from the
protonated amino group of Form II results in the fully
deprotonated form of alanine, Form III.
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H+ + H+ +
18. Isoelectric point (pI)
• The isoelectric point (pI) - the pH at which a molecule carries no
net electrical charge.
• The net charge on the molecule is affected by pH and can
become more positively or negatively charged due to the gain or
loss, respectively, of protons (H+).
• The pI value can affect the solubility of a molecule at a given pH.
They have minimum solubility in water or salt solutions at the pH
that corresponds to their pI and often precipitate out of solution.
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19. Isoelectric point (pI)
• At pH values between the two pKa values, the zwitterion
predominates, but coexists in equilibrium with small amounts of
net negative and net positive ions.
• At the exact midpoint between the two pKa values, the amount
of net negative and net positive ions balance, so that average net
charge of all forms present is zero.
• For amino acids such as alanine that possess monocarboxylic
acid and monoamino groups, pK1 and pK2 represent pKCOOH and
pKAmino respectively.
• For amino acids with charged side-chains, the pKa of the side-
chain is involved.
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20. Isoelectric point (pI)
• For amino acids with
charged side-chains, the
pKa of the side-chain is
involved.
• The isoelectric points
reflect the nature of
ionizing R groups present.
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21. Types of amino
acids
A.a. can be
categorized
based on the
properties of side
chains (R):
• Polar
(hydrophilic)
or Non-polar
(hydrophobic)
• Acidic or Basic
R group is
important for
protein function.
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24. Non polar side chain (Hydrophobic) -1
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• Aliphatic hydrocarbon group (the absence of a benzene ring)
• Glycine, Alanine, Branched-chain amino acids (Valine,
Leucine and Isoleucine)
25. Non polar side chain (Hydrophobic) - 2
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• Aliphatic cyclic group
• Proline (more conformationally restricted than the other amino acids,
influence protein architecture)
• Aromatic side group
• Phenylalanine
• Tryptophan
• Sulfur-containing group
• Methionine (almost always the first amino acid in a protein)
26. Non polar side chain
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• In proteins found in aqueous solutions––a
polar environment––the side chains of the
nonpolar amino acids tend to cluster
together in the interior of the protein.
• This phenomenon, the hydrophobic effect, is
the result of the hydrophobicity of the
nonpolar R-groups.
• The nonpolar R-groups fill up the interior of
the folded protein and help give it its 3D
shape.
• However, for proteins that are located in a
hydrophobic environment, such as a
membrane, the nonpolar R-groups are
found on the outside surface of the protein,
interacting with the lipid environment.
27. Proline – Structural support
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• Proline differs from other amino acids in that proline’s side chain
and α-amino N form a rigid, five-membered ring structure.
• Proline has a secondary amino group. The unique geometry of
proline contributes to the formation of the fibrous structure of
collagen, and often interrupts the α-helices found in globular
proteins.
28. Polar side chain (Hydrophilic) - 1
Electrically neutral (uncharged) at neutral pH
• Hydroxyl group
– Serine and Threonine have –OH group attached to an aliphatic side chain
– Tyrosine has –OH group attached to an aromatic ring
• Thiol group
– Cysteine has –SH which can react with other thiol group to forms disulfide
(-S-S-) bridges in protein in an oxidation reaction. Important for protein
structure, metal ion binding, antioxidant
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29. Disulfide bonds by oxidation of cysteine
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• Reversible formation of a disulfide bond by the
oxidation of two molecules of cysteine.
• Disulfide bonds between Cys residues stabilize the
structures of many proteins, may act as redox sensor.
30. Side chains as sites of attachment for other
compounds
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• The polar hydroxyl group of
serine, threonine, and, rarely,
tyrosine, can serve as a site of
attachment for structures such
as a phosphate group.
• In addition, the amide group of
asparagine, as well as the
hydroxyl group of serine or
threonine, can serve as a site of
attachment for oligosaccharide
chains in glycoproteins.
31. Polar side chain (Hydrophilic) - 2
• Amide group
– derived from carboxyl groups, in their side chains.
– Amide bonds do not usually ionize in the range of pH
encountered in biochemistry.
– Glutamine and asparagine can be considered derivatives of the
glutamic acid and aspartic acid, respectively.
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32. Acidic side chain
• Aspartic acid and glutamic acid,
have carboxyl groups in their side
chains in addition to the one
present in all amino acids.
• A carboxyl group can lose a proton,
forming the corresponding
carboxylate anion, glutamate and
aspartate, respectively.
• They are negatively charged at
neutral pH.
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33. Basic side chain
• Histidine, lysine and arginine
have basic side chains, and the
side chain is positively
charged at neutral pH.
• Lysine is capped by a primary
group and arginine by a
guanidinium group.
• Histidine contains an
imidazole group, which can
bind and release protons
during enzymatic reaction.
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34. Essential amino acid
• Essential amino acid - an amino acid that cannot be
synthesized de novo (from scratch) by the organism
being considered, and therefore must be supplied in its
diet.
• If they are not taken through diet, they will not be
available for protein synthesis. In addition, some a.a. are
considered conditionally essential. Under certain
conditions like illness or stress the body might not be
able, or might be limited in the ability, to synthesize
them.
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36. Polymerization of amino acids generates
protein
• Peptides are short chains of amino acid monomers linked by
covalent peptide (amide) bonds.
• The shortest peptides are dipeptides, consisting of 2 amino acids
joined by a single peptide bond, followed by tripeptides,
tetrapeptides, etc. A polypeptide is a long, continuous, and
unbranched peptide chain.
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Constant
backbone
Variable side chain
38. Polypeptides chain
• A polypeptide chain consists of :
• Main chain or backbone: regularly repeating part
• Distinctive side chain: variable part
• Backbone: rich in H-bonding potential
• Carbonyl group (C=O): good H-bond acceptor
• N-H group: good H-bond donor
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Constant
backbone
Variable side chain
39. Peptide bonds formation
• Formed by linking the α-carboxyl group of one a.a to α-amino
group of another a.a via peptide bond/amide bond, causing the
release of H2O, hence it is a (dehydration) condensation reaction
and usually occurs between amino acids.
• The resulting C(O)NH bond is called a peptide bond, and the
resulting molecule is an amide. The four-atom functional group -
C(=O)NH- is called a peptide link.
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40. Peptide bonds hydrolysis
• The equilibrium of reaction favor the side of hydrolysis rather
than synthesis
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Reaction favor left side (reactant).
But hydrolysis rate is extremely slow.
• Synthesis of protein primary structure require input of free
energy
• Peptide bond: kinetically stable, lifetime of 1000 yrs in the
absence of catalyst
41. Primary structure
• Proteins – most natural polypeptide chains contain between
50 and 2000 amino acid residues.
• The mean molecular weight of an a.a. is 110 g mol-1, and so
the m.w. of most proteins are between 5500 and 220000 g
mol-1.
• The mass of protein – expressed in units of dalton, one
dalton is equal to one atomic mass unit.
– Eg a protein with a m.w. of 50,000 g mol-1 has a mass of 50,000 daltons
or 50 kd (kilodaltons)
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42. 42
• Each a.a. unit in a
polypeptide is called
residue.
• A polypeptide chain has
polarity because its ends
are different: an α-amino
group is present at one
end and an α-carboxyl
group at the other.
43. 43
• The sequence of a.a. in
a polypeptide chain is
written starting with
the amino-terminal
(N-terminal) residue,
ending with the
carboxyl-terminal
(C-terminal residue)
Tyr-Thr-Gln-Trp-Ile is
different from
Ile-Trp-Gln-Thr-Tyr with
different chemical
properties.
44. Amino acid sequence
• In 1953, Frederick Sanger: a.a. seq. of insulin
• Landmark in biochemistry: protein has a precisely
defined a. a seq. consisting only the L-amino acid linked
by peptide bonds
• 2,000,000 protein seq. are known now
• Each protein has a unique, precisely defined a. a seq.
• Amino acid sequence a protein is referred to as primary
structure
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45. Amino acid sequence of bovine insulin, sequenced by Frederick Sanger in 1959
Biochemist and molecular biologist
Dr. Frederick Sanger, two time
Nobel Prize winner.
46. The study of amino acid sequence
1. To elucidate the mechanism of action
– i.e. catalytic mechanism of an enzyme
2. To determine the 3-D structures of protein
– Uncovering the rules that govern the folding of
polypeptide chains
3. To study molecular pathology
– Severe/fatal disease resulted from a change in a
single a. a within the protein
4. To determine evolutionary history
– To trace molecular event in evolution from amino acid
sequence
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47. Study questions
1. What are protein, peptide and polypeptides?
2. What is the difference between amine and amide?
3. What is a zwitterion?
4. Describe the classification of amino acid based on the side
chain properties.
5. Draw the basic structure of dipeptide with N- and C-terminal
end
6. How does peptide bond form?
7. What is isoelectric point?
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