Amino Acids and Proteins

Introduction to General, Organic, and Biochemistry, 11th Edition by

Bettelheim, Brown, Campbell, Farrell, Torres
Organic Chemistry, 11th Edition by Solomons et.al.

Olivert M. Sitoy, M.Sc., R.Ch.

Chemistry Department
College of Arts and Sciences
Xavier University – Ateneo de Cagayan
 Proteins
Proteins: Naturally-occurring, unbranched polymer of Amino Acids.
▪ Provide nitrogen and sulfur for the diet
▪ Most abundant macromolecules in the cell
▪ Carry out most of the work of the cell
▪ Composed of at least 40 amino acid residues:
 Proteins
Proteins: Naturally-occurring, unbranched polymer of Amino Acids.
▪ Provide nitrogen and sulfur for the diet
▪ Most abundant macromolecules in the cell
▪ Carry out most of the work of the cell
▪ Composed of at least 40 amino acid residues:
 Proteins
Proteins: Naturally-occurring, unbranched polymer of Amino Acids.
▪ Structure: Collagen and keratin in skin, bone, hair, and nails.
▪ Catalyst: Reactions in living systems are catalyzed by proteins
(enzymes)
▪ Movement: Myosin and actin in the muscle.
▪ Transport: Hemoglobin for oxygen transport, and other
transport proteins (lipoproteins)
▪ Hormones: Insulin, oxytocin, and human growth hormones.
▪ Protection: Fibrinogen for blood clotting, and Antibodies to
fight diseases.
▪ Storage: Casein in milk and ovalbumin in eggs for storage of
nutrients, and ferritin in liver for iron storage.
▪ Regulation: Control of gene expression.
 Proteins
Proteins: Naturally-occurring, unbranched polymer of Amino Acids.
• Typically, 9000 different proteins is in a cell (10000 in humans)
• Can either be Fibrous or Globular:

Collagen: a fibrous protein

Hemoglobin: a globular protein

 Amino Acids
Amino Acids: compound that contains an amino and a carboxyl group.
▪ α-amino acid: amino acids in which the amino group and the
carboxyl group are attached to the α-carbon.

R = side chain – vary in size, charge, acidity, functional groups

present, hydrogen-bonding activity, and chemical reactivity.
 Amino Acids
Amino Acids: compound that contains an amino and a carboxyl group.
▪ Although α-amino acid are commonly written in the un-ionized
form, they are more properly written in the zwitterion (internal
salt form.

Unionized Form Zwitterion – a positive charge on one atom

and a negative charge on another atom
 Chirality of Amino Acids
Excluding glycine, all protein-
derived amino acids have at least
one stereocenter (the α-carbon)
and are chiral.
▪ Most of protein derived
amino α-amino acids have Naturally occurring Form
L-configuration at the α–
carbon.
▪ For example: a comparison
of stereochemistry of D-
Glyceraldehyde and L-
Alanine
Naturally occurring Form
 Protein-Derived Amino Acids
Non-polar Amino Acids: Contains non-polar (hydrophobic) side chains
 Protein-Derived Amino Acids
Polar Neutral Amino Acids: Contains polar, uncharged side chains
 Protein-Derived Amino Acids
Polar Acidic/Basic Amino Acids: Contains polar, charged side chains
 Protein-Derived Amino Acids
Amino Acids: compound that contains an amino and a carboxyl group.
▪ All 20 are α-amino acid
▪ For 19 of the 20 amino acids, the α-amino group is primary; for
proline, it is secondary
▪ Except glycine, the α-carbon of each is a stereocenter
▪ Isoleucine and threonine each contains a second stereocenter
 Ionization vs. pH
The net charge on amino acid depends on the pH of the solution.
▪ If an amino acid is dissolved in water (pH = 7.0), it exist as a
zwitterion.
▪ Adding a strong acid (e.g. HCl), pH becomes 2.0 or lower.
▪ The acid donates H+ to the COO- of the amino acid, turning the
zwitterion to a positively charged ion.
 Ionization vs. pH
The net charge on amino acid depends on the pH of the solution.
▪ If an amino acid is dissolved in water (pH = 7.0), it exist as a
zwitterion.
▪ Adding a strong base (e.g. NaOH), pH becomes 10.0 or higher.
▪ The NH3+ of the amino acid is transferred to the base, turning
the zwitterion to a negatively charged ion.
 Ionization vs. pH
The net charge on amino acid depends on the pH of the solution.
▪ If an amino acid is dissolved in water (pH = 7.0), it exist as a
zwitterion.
▪ The acid donates H+ to the COO- of the amino acid, turning the
zwitterion to a positively charged ion. (pH < 7.0)
▪ The NH3+ of the amino acid is transferred to the base, turning
the zwitterion to a negatively charged ion. (pH > 7.0)
 Isoelectric Point
Isoelectric point: pH where majority of molecules has no net charge.
Amino Acid Name Isoelectric point Amino Acid Name Isoelectric point
Alanine 6.01 Leucine 5.98
Arginine 10.76 Lysine 9.74
Asparagine 5.41 Methionine 5.74
Aspartic Acid 2.77 Phenylalanine 5.48
Cysteine 5.07 Proline 6.48
Glutamic Acid 3.22 Serine 5.68
Glutamine 5.65 Threonine 5.87
Glycine 5.97 Tryptophan 5.88
Histidine 7.59 Tyrosine 5.66
Isoleucine 6.02 Valine 5.97
 Cysteine: A Chemically Unique Amino Acid
Cysteine: An amino acid with –SH (sulfhydryl) group
 Amino Acids with Aromatic Side Chains
▪ Key precursor to neurotransmitters
▪ Tryptophan: Converted to serotonin (5-hydroxytryptamine)
 Amino Acids with Aromatic Side Chains
▪ Key precursor to neurotransmitters
▪ Tyrosine and Phenylalanine: Precursor to norepinephrine and
epinephrine (i.e. catecholamines)
 Uncommon Amino Acids
▪ Post-translational modification: modification of amino acids by
certain organism after biosynthesis.
▪ Hydroxylation (oxidation) of proline, lysine, and tyrosine.

Stabilization of collagen fibers

 Uncommon Amino Acids
▪ Post-translational modification: modification of amino acids by
certain organism after biosynthesis.
▪ Iodination of tyrosine.

▪ Animals and humans that exhibit

sluggishness and slow metabolism
are often given thyroxine to
help ramp up their metabolism
 Peptides
▪ Emil Fischer proposed that proteins are long chains of amino acids
joined by amide bonds (1902).
▪ Peptide Bond: Amide bond between the α-carboxyl group of one
amino acid and the α-amino group of another amino acid
 Peptides
▪ Peptide: A short polymer of amino acids joined by peptide bonds;
classified by the number of amino acid residues
▪ Dipeptide: A molecule compose of two (2) amino acids connected
by a peptide bond
 Peptides
▪ Peptide: A short polymer of amino acids joined by peptide bonds;
classified by the number of amino acid residues
▪ Tripeptide: A molecule compose of three (3) amino acids connected
by a peptide bond
 Peptides
▪ Peptide: A short polymer of amino acids joined by peptide bonds;
classified by the number of amino acid residues
▪ Polypeptide: A macromolecule compose of amino acids connected
by a peptide bond.
▪ Protein: A biological macromolecule containing at least 30 to 50
amino acids connected by a peptide bond.
 Writing Peptides
▪ Convention: Left to right, starting with free –NH3+ group and
ending with the free –COO- group.
▪ C-terminal amino acid: amino acid at the end of the chain bearing
the –COO- group.
▪ N-terminal amino acid: amino acid at the beginning of the chain
bearing the –NH3+ group.
 Peptides and Proteins
▪ Proteins behaves as zwitterion and have an isoelectric point.
▪ At isoelectric point (pI), proteins have no net charge.
▪ At any pH above (more basic than) the pI, it has a net negative
charge.
▪ At any pH below (more acidic than) the pI, it has a net positive
charge.
▪ Example: Hemoglobin has an almost equal number of acidic
and basic side chains; its pI is 6.8.
▪ Example: Serum albumin has more acidic side chains; its pI is
4.9.
▪ Proteins are least soluble in water at their isoelectric point and
can be precipitated from solution at this pH.
 Levels of Protein Structure

▪ Primary Structure: Sequence of amino acid in a polypeptide chain.

▪ Secondary Structure: Conformation of amino acids in localized
regions of a polypeptide chain (e.g., α-helix, β-pleated sheets and
random coils)
▪ Tertiary Structure: Complete three-dimensional arrangement of
atoms in a polypeptide chain.
▪ Quaternary Structure: the spatial relationship and interactions
between subunits in a protein that has more than one polypeptide
chain.
Levels of Protein Structure
Levels of Protein Structure
 Primary Structure of Proteins
Primary Structure: Sequence of amino acid in a polypeptide chain.
▪ Translation of information contained in the genes

The number peptides possible from the 20 protein-derived amino

acids is enormous.
▪ 400 possible dipeptides, 8000 possible tripeptides and so on.
▪ Rule of Thumb: 20n = number of peptides possible with n
number of amino acids
▪ For small proteins of 60 amino acids, the number of proteins
possible is 2060 = 1078, which is possible greater than the
number of atoms in universe.
 Primary Structure of Proteins
Primary Structure: Sequence of amino acid in a polypeptide chain.
▪ Translation of information contained in the genes
 Primary Structure of Proteins
Primary Structure: Sequence of amino acid in a polypeptide chain.
▪ Translation of information contained in the genes

Human insulin consist of two polypeptide chains having a total of 51

amino acids; the two chains are connected by two interchain disulfide
bonds.
 Primary Structure of Proteins
Primary Structure: Sequence of amino acid in a polypeptide chain.
▪ Translation of information contained in the genes
▪ Vasopressin and oxytocin are both nonapeptides but quite different
biological functions.
▪ Vasopressin is an antidiuretic hormone.
▪ Oxytocin affects contraction of the uterus in childbirth and the
muscle of the breast that aid in the secretion of milk.
 Primary Structure of Proteins
Primary Structure: Sequence of amino acid in a polypeptide chain.
▪ Translation of information contained in the genes
 Secondary Structure of Proteins
Secondary Structure: Conformation of amino acids in localized regions
of a polypeptide chain.
▪ Commonly α-helix and β-pleated
sheet.
▪ α-helix: a section of polypeptide
chain coils into spiral, most
commonly a right-handed spiral
▪ β-pleated sheet: two polypeptide
chains or sections of the same
polypeptide chain align parallel to
each other (can either be parallel
or antiparallel)
 Secondary Structure of Proteins
Secondary Structure: Conformation of amino acids in localized regions
of a polypeptide chain.
 Secondary Structure of Proteins
Secondary Structure: Conformation of amino acids in localized regions
of a polypeptide chain.
 Secondary Structure of Proteins
Secondary Structure: Conformation of amino acids in localized regions
of a polypeptide chain.

In α-helix:
▪ 3.6 amino acids per turn of the helix
▪ Six atoms of each peptide bond lie on the same plane
▪ N-H groups of amide bonds point in the same direction, roughly
parallel to the axis of the helix.
▪ C=O group of amide bonds point in the opposite direction, also
roughly parallel to the axis of the helix.
▪ Hydrogen bonding between C=O and N-H groups exist.
▪ All R- side chains points outward the helix
 Secondary Structure of Proteins
Secondary Structure: Conformation of amino acids in localized regions
of a polypeptide chain.
 Secondary Structure of Proteins
Secondary Structure: Conformation of amino acids in localized regions
of a polypeptide chain.

In β-pleated sheet:
▪ Six atoms of each peptide bond lie on the same plane.
▪ The C=O and N-H groups of peptide bonds from adjacent chains
point toward each other and are in the same plane so that
hydrogen bonding is possible between them.
▪ All R- side chains on any one chain alternate. First above, then
below the plane of the sheets, etc.
 Secondary Structure of Proteins
Secondary Structure: Conformation of amino acids in localized regions
of a polypeptide chain.
 Collagen Triple Helix
Tropocollagen: Three polypeptide chains wrapped around each other
forming a triple helix.
▪ Collagen: A structural protein of connective tissues (bone,
cartilage, tendon, blood vessels, skin)
▪ 30 amino acids in each are proline and L-hydroxyproline (Hyp);
L-hydroxylysine (Hyl) also occurs.
▪ Every third position is glycine and repeating sequence are X-Pro-
Gly and X-Hyp-Gly
▪ Each polypeptide chain is a helix but not α-helix.
▪ The three strands are held by hydrogen bonding between
hydroxyproline and hydroxylysine.
▪ During aging, collagen helices becomes cross-linked by covalent
bonds between the side chains of lysine.
 Collagen Triple Helix
Tropocollagen: Three polypeptide chains wrapped around each other
forming a triple helix.
Collagen Triple Helix
 Tertiary Structure of Proteins
Tertiary Structure: overall conformation of an entire polypeptide
chain.

Tertiary structure are stabilized in four ways:

▪ Covalent Bonds: disulfide bonds between cysteine side chains.
▪ Hydrogen Bonding: interaction between polar groups of the
side chains (e.g. –OH group of serine and threonine).
▪ Salt Bridges: attraction of the –NH3+ group of lysine and the
COO- group of aspartic acid.
▪ Hydrophobic Interaction: interaction between non-polar chains
(e.g. side chains of phenylalanine and isoleucine)
▪ Metal Interaction: interaction of same charged side chains with
a metal ion in between
 Tertiary Structure of Proteins
Tertiary Structure: overall conformation of an entire polypeptide
chain.
 Tertiary Structure of Proteins
Tertiary Structure: overall conformation of an entire polypeptide
chain.
 Tertiary Structure of Proteins
Tertiary Structure: overall conformation of an entire polypeptide
chain.
 Tertiary Structure of Proteins
Tertiary Structure: overall conformation of an entire polypeptide
chain.
 Quaternary Structure of Proteins
Quaternary Structure: arrangement of polypeptide chains into a non-
covalently bonded aggregation

Quaternary structure are stabilized in four ways:

▪ Hydrogen Bonding: interaction between polar groups of the
side chains (e.g. –OH group of serine and threonine).
▪ Salt Bridges: attraction of the –NH3+ group of lysine and the
COO- group of aspartic acid.
▪ Hydrophobic Interaction: interaction between non-polar chains
(e.g. side chains of phenylalanine and isoleucine)
 Quaternary Structure of Proteins
Quaternary Structure: arrangement of polypeptide chains into a non-
covalently bonded aggregation

In Hemoglobin:
▪ Adult Hemoglobin: two alpha chains of 141 amino acids each,
and two beta chains of 146 amino acids each.
▪ Each chain surrounds an iron-containing heme unit
▪ Fetal Hemoglobin: two alpha chains, and two gamma chains;
has greater affinity to oxygen relative to adult hemoglobin
 Quaternary Structure of Proteins
Quaternary Structure: arrangement of polypeptide chains into a non-
covalently bonded aggregation
 Hemoglobin

▪ Oxygen binds to heme in

hemoglobin; when one O2
bind, the binding of the
next O2 is easier.
▪ The first 2,3-bisphospho-
glycerate to leave
deoxyhemoglobin.
▪ During binding, shape
changes which favors more
reaction of oxygen
 Hemoglobin

▪ H+ from metabolizing cells

(low pH) favors oxygen
release from Hb.
▪ When the oxygen concentration is low, as in
the peripheral tissues, H is bound and O2 is
released.

▪ Higher pH in the lungs

favors binding of oxygen to
Hb.
▪ When the oxygen concentration is high, as in
the lungs, hemoglobin binds O2 and releases
protons
 Oxygen Transport: Mother-Fetus

▪ Fetal Hb is different from

adult Hb
▪ It does not bind to BPG and
has higher affinity to O2
 Oxygen Transport: Mother-Fetus

▪ Sickle cell hemoglobin (Hb

S) has a valine substituted
for glutamic acid in the
beta chain.
▪ Deoxy version clumping
and forming the
characteristic sickle cells
▪ Early death; sickle cell trait
= malaria resistance
 Quaternary Structure of Proteins
Quaternary Structure: arrangement of polypeptide chains into a non-
covalently bonded aggregation

1RSS = Ribosomal Protein S7 from

Thermus thermophilus

2AWK = Green Fluorescent Protein

(GFP) R96M mature chromophore

The 8 β strands in these eight structural

motifs associate in the center of the
molecule to form a so called β–barrel.
 Denaturation
Denaturation: destruction of native conformation of protein by
chemical or physical means.
▪ Some denaturation are reversible, while some are permanent.

Denaturation includes:
▪ Heat: disrupts hydrogen bonding; in globular proteins, it can
lead to unfolding of polypeptide chains which might results to
coagulation and precipitation.
▪ 6M aqueous urea: disrupts hydrogen bonding
▪ Surface-active agents: disrupts hydrogen bonding (e.g.
detergent)
▪ Reducing agents: cleavage of disulfide bonds through reduction
(e.g. 2-mercaptoethanol)
 Denaturation
Denaturation: destruction of native conformation of protein by
chemical or physical means.
▪ Some denaturation are reversible, while some are permanent.

Denaturation includes:
▪ Heavy metal ions: formation of water-insoluble salts with thiol
side chains (e.g., Pb2+, Hg2+, and Cd2+)
▪ Alcohol: sterilization of skin before injection due to complete
denaturation of proteins (e.g. 70% ethanol).
 Denaturation
Denaturation: destruction of native conformation of protein by
chemical or physical means.
▪ Some denaturation are reversible, while some are permanent.
 Protein Digestion and Diet
Digestion: degradation of proteins in the diet.
▪ Stomach: Facilitated by the enzyme, pepsin.
▪ Small Intestine: trypsin, chymotrypsin, elastase, etc.

Essential Amino Acids: Cannot be synthesized by humans

▪ Ile, Leu, Lys, Met, Phe, Thr, Try, Val, His*

Complete protein from animal provides essential AA in proper

proportions.

Imbalanced protein from vegetables sources must be balanced. (e.g.,

beans (Lys +Trp) and corn (Met))