BIOCHEMISTRY – VERASTIGUE

Amino Acid: Building block of Protein

 Contains the ff. chemical groups attached to α-carbon:
a. Amino group
b. Carboxyl group
c. Side chain group (R) – gives the identity to amino acid
 All amino acids (except glycine) have at least one stereocenter
(α-C) and are chiral (stereoisomers)
 Two stereoisomers:
a. L- and D-amino aid
b. majority of α-amino acids are in L-configuration at the α-C
 General Structure of Amino Acid

Classification of Amino Acid

According to type of side chain/r group

- Neutral
- Acidic
- Basic
According to Polarity
- Uncharged nonpolar
- Unchanged polar
- Changed polar
According to Nutritional Requirements
- Essential : acquired from food/s we intake
- Non-essential : Produce by the body
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Common Amino Acids

NEUTRAL
Aliphatic Sulfur-containing Hydroxyl Aromatic Amide
(PA-GiV-IsoLe) (CysMeth) (PTT) G(ami)ng-(de)N
Proline Cysteine Serine Phenylalanin Asparagine
e
Alanine Methionine Threonine Tryptophan Glutamine
Glycine Tyrosine
Valine
Isoleucine
Leucine

BASIC ACIDIC ADDITIONAL INFO/S:

LAH Aspartic Tryptophan – Amino group containing Indole Grp
Lysine Glutamic Tryptophan is also the precursor of
Arginine neurotransmitter serotinin
Histidine Phenylalanine – Precursor of tyrosine
Aliphatic – with hydrocarbons compound joining a
straight chain; increasing number of C in
hydrocarbon chain
Classification of Amino Acid

According to type of side chain/r group

- Neutral UNCHARGED NP UNCHARGED P CHARGED
POLAR
- Acidic
Alanine (A) Glycine (G) Lycine (K)
- Basic
Valine (V) Cysteine (C) Arginine (R)
According to Polarity
Leucine (L) Serine (S) Histidine (H)
- Uncharged nonpolar : A, V, L, I, M, F, P, W
Isoleucine (I) Threonine (T) Aspartic (D)
- Unchanged polar : G, C, S, T, Y, N, Q,
Methionine (M) Tyrosine (Y) Glutamic (E)
- Changed polar : K, R, H, D, E
Phenylalanine (F) Asparagine (N)
According to Nutritional Requirements
Proline (P) Glutamine (Q)
- Essential : PVT TIM HALLS
Tryptophan (W)
- Non-essential
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NON-ESSENTIAL
ESSENTIAL
Proline
Valine
Alanine
Tryptophan
Asparagine
Threonine
Arginine
Isoleucine
Glutamine
Methionine
Aspartic Acid
Histidine
Cysteine
Arginine Acid
Glutamic
Lysine
Glycine
Leucine
Phenylalanine
Serine
Tyrosine

AMINO ACID  A compound that contains both an

amino group and a carboxyl group
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 a-Amino Acid: An amino acid in
which the amino group is on the
carbon adjacent to the carboxyl
group.
 Note: Although amino acids are
commonly written in the unionized
form they are more properly written
in the zwitterion (internal salt)
form.

CHIRALITY OF a-AMINO ACIDS
 With the exception of glycine, all
protein-derived amino acids have at
least one stereocenter (the a-
carbon) and are chiral.
 The vast majority of a-amino acids
have the L-configuration at the a-
carbon
 turning it into a positive ion.
 A comparison of the configuration of
L-alanine and D-glyceraldehyde (as
Fischer projections):
 NH3+ group to the base turning the
PROTEIN-DERIVED a-AMINO
ACIDS
1) For 19 or the 20, the a-amino group
is primary; for proline, it is secondary
2) With the exception of glycine, the
a-carbon of each is a stereocenter.
3) Isoleucine (Left) and the Threonine
(Right) contain a second
stereocenter.
IONIZATION Vs. Ph
The net charge of an amino acid depends on
the pH of the solution in which it is
dissolved.
 If an amino acid is dissolve in water,
it is present in the aqueous solution
as its ZWITTERION
 If a strong acid is added (e.g. HCl) to
bring the pH of the solution to 0.0,
the the strong acid donates a proton
to the -COO- of the zwitterion
 If a strong base is added (e.g. NaOH)
to the solution and bring its pH to
14, a proton is transferred from the
zwitterion into a negative ion.
ISOELECTRIC POINT (pI)
 Isoelectric point, pI: The pH at which
molecules of a compound in solution
have no net charge.
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CYSTEINE
 The -SH (sulfuhydryl) group of cysteine is
easily oxidized to an -S-S- (disulfide).
  Peptide bond (peptide linkage):
PHE, TRP, TYR
- The amino acids phenylalanine,
tryptophan, and tyrosine have aromatic
rings on their side chains.
- Tryptophan is the precursor of
neurotransmitter serotonin
TYR AND PHE
 Phenylalanine and Tyrosine are
precursors of norepinephrine and
epinephrine, both which are stimulatory
neurotransmitters.

OTHER AMINO ACIDS
 Hydroxylation (oxidation) of proline,
lysine, and tyrosine, respectively and
iodination for tyrosine, give these
uncommon amino acids.
PEPTIDES
Emil Fischer (1902) proposed that proteins
are long chains of amino acids joined by
AMIDE BONDS.
Special name given to the amide
bond between a-carboxyl group of
one amino acid and the a-amino
group of another.
 Peptide: short polymer of amino
acids joined by peptide bonds; they
are classified by the number of
amino acids in chain.
 Dipeptide: Contains 2 amino acids
joined by peptide bond
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 Tripeptide: Contains 3 amino acids
joined by peptide bond
 Polypeptide: macromolecule
containing many amino acids (>30)
 Protein: Biological macromolecule
containing 30 to 50 amino acids
joined by peptide bonds.
 RESIDUES: individual amino acid
units
PEPTIDE BOND
 A typically written as carbonyl group
bonded to an N-H Group. Linus Pauling
discovered 40% double bond between 2
amino acids is planar (explained using
concept of resonance)
 chains, its pI is 4.9
WRITING PEPTIDES
 Peptides are written from left to right,
beginning with the free -NH3+ group and
ending with the free -COO- group.
 C-Terminal A.A.: end of the chain
having the free -COO- group
 N-Terminal A.A.: end of the chain
having the free -NH3+ group
 Alternatively, referred as C-
Terminus and N-Terminus
PEPTIDES
 Small peptide showing the direction of
peptide chain (N-terminal to C-Terminal)
PEPTIDES AND PROTEINS
 Proteins have Zwitterions
 Proteins have an Isoelectric point
 At its isoelectric point, protein has no
charge
 At any pH above (> basic than) its pI, it
has net negative charge
 At any pH below (> acidic than) its pI, it
has net positive charge
 Hemoglobin, has equal no. of acidic
and basic side chains, its pI is 6.8
 Serum Albumin, has more acidic side
 Proteins- soluble in water at their
isoelectric points; can be precipitated
from solution when pH = pI.
PROTEINS
Proteins serve many functions, including
the following:
1. Structure: Collagen and keratin are the
chief constituents of skin, bone, hair, and
nails.
2. Catalysts: Virtually all reactions in living
systems are catalyzed by proteins called
enzymes.
3. Movement: Muscles are made up of
proteins called myosin and actin.
4. Transport: Hemoglobin transports
oxygen from the lungs to cells, other
proteins transport molecules across cell
membranes.
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5. Hormones: Many hormones are
proteins, among them insulin, oxytocin,
and human growth hormone.
6. Protection: Blood clotting involves the
protein fibrinogen; the body used proteins
called antibodies to fight disease.
7. Storage: Casein in milk and ovalbumin
in eggs store nutrients for newborn infants
and birds. Ferritin, a protein in the liver,
stores iron.
8. Regulation: Certain proteins not only
control the expression of genes, but also
control when gene expression takes place.
LEVEL OF STRUCTURE
a. Primary structure: The sequence of
amino acids in a polypeptide chain.
Read from the N-terminal amino acid to
the C-terminal amino acid.
b. Secondary structure: Conformations of
amino acids in localized regions of a
polypeptide chain. Examples are a-
helix, b-pleated sheet, and random coil.
c. Tertiary structure: The complete three-
dimensional arrangement of atoms of a
polypeptide chain.
d. Quaternary structure: The spatial
relationship and interactions between
subunits in a protein that has more
than one polypeptide chain.
PRIMARY STRUCTURE
 The number peptides possible from the
20 protein-derived amino acids is
enormous.
• There are 20 x 20 = 400 dipeptides
possible.
• There are 20 x 20 x 20 = 8000
tripeptides possible.
• The number of peptides possible for a
chain of n amino acids is 20n.
• For a small protein of 60 amino acids,
the number of proteins possible is 2060 =
1078, which is possibly greater than the
number of atoms in the universe!
 The hormone insulin consists of two
polypeptide chains, A and B, held
together by two disulfide bonds.
 How important is the exact amino acid
sequence?
 Human insulin consists of two
polypeptide chains having a total of
51 amino acids; the two chains are
connected by two interchain disulfide
bonds.
 Differences between four types of
insulin.
 Vasopressin and oxytocin are both
nonapeptides but have quite different
biological functions.
 Vasopressin is an antidiuretic hormone.
 Oxytocin affects contractions of the
uterus in childbirth and the muscles of
the breast that aid in the secretion of
milk.
 The structures of vasopressin an
oxytocin.
SECONDARY STRUCTURE
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 The most common types of
secondary structure are a-helix and
b-pleated sheet.
a. a-Helix: A type of secondary
structure in which a section of
polypeptide chain coils into a
spiral, most commonly a right-
handed spiral.
b. b-Pleated sheet: A type of
secondary structure in which two
polypeptide chains or sections of
the same polypeptide chain align
parallel to each other; the chains
may be parallel or antiparallel.
 2˚ of proteins is hydrogen-bonded
arrangement of backbone of the
protein
 Two bonds have free rotation:
- Bond between a-carbon and amino
nitrogen in residue
- Bond between the a-carbon
and carboxyl carbon of residue
 THE a-HELIX
 In a section of a-helix
 There are 3.6 amino acids per turn
of the helix.
 The six atoms of each peptide
bond lie in the same plane.
 The N-H groups of peptide bonds
point in the same direction,
roughly parallel to the axis of the
helix.
 The C=O groups of peptide bonds
point in the opposite direction,
also roughly parallel to the axis of
the helix.
 The C=O group of each peptide
bond is hydrogen bonded to the N-
H group of the peptide bond four
amino acid units away from it.
 All R- groups point outward from
the helix.
 Several factors can disrupt an a-helix
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 proline creates a bend because of (1) the  B-Bulge - a common non-repetitive

restricted rotation due to its cyclic structure irregular 2˚ motif in anti-parallel
and (2) its -amino group has no N-H for structure
hydrogen bonding
 strong electrostatic repulsion caused by the
proximity of several side chains of like
charge, e.g., Lys and Arg or Glu and Asp
 steric crowding caused by the proximity of
bulky side chains, e.g., Val, Ile, Thr

b-PLEATED SHEET
 Structure or Reverse Turns
- Glycine found in reverse turns
-Spatial (steric) reasons
-Polypeptide changes direction
-Proline also encountered in reverse
turns. Why?

 In a section of b-pleated sheet;

 The six atoms of each peptide bond of a
b-pleated sheet lie in the same plane.
 The C=O and N-H groups of the 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- groups on any one chain
alternate, first above, then below the a-Helices and b -sheets
plane of the sheet, etc
- Supersecondary structures: the
combination of a- and b-sections, as for
example
- b-a-b unit: two parallel strands of b-
sheet connected by a stretch of a-helix
- a-a unit: two antiparallel a-helices
- b-meander: an antiparallel sheet
formed by a series of tight reverse turns
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connecting stretches of a polypeptide
chain
- Greek key: a repetitive supersecondary
structure formed when an antiparallel
sheet doubles back on itself
- b-barrel: created when b-sheets are
extensive enough to fold back on
themselves
- Many globular proteins contain all three
kinds of secondary structure in different parts
of their molecules: a-helix, b-pleated sheet,
and random coil
- Schematic structure of the enzyme
carboxypeptidase. The b-pleated sheet
sections are shown in blue, the a-helix
portions in green, and the random coils as
orange strings.
THE COLLAGEN TRIPLE HELIX
- consists of three polypeptide chains
wrapped around each other in a
ropelike twist to form a triple helix
called tropocollagen; MW approx.
300,000
- 30% of amino acids in each chain are
Pro and Hyp (hydroxyproline);
hydroxylysine also occurs
- Every third position is Gly and
repeating sequences are X-Pro-Gly
and X-Hyp-Gly
- Each polypeptide chain is a helix but
not an a-helix
- The three strands are held together
by hydrogen bonding involving
hydroxyproline and hydroxylysine
- With age, collagen helices become
cross linked by covalent bonds formed
between Lys and His residues
TWO TYPES OF PROTEINS
1. Fibrous proteins: contain polypeptide
chains organized approximately parallel
along a single axis.
They
• consist of long fibers or large sheets
• tend to be mechanically strong
• are insoluble in water and dilute salt
solutions
• play important structural roles in
nature
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Examples :
• keratin of hair and wool
• collagen of connective tissue of animals
including
• cartilage, bones, teeth, skin, and blood
vessels
2. Globular proteins: proteins which are
folded to a more or less spherical shape
• they tend to be soluble in water and
salt solutions
• most of their polar side chains are on
the outside and interact with the aqueous
environment by hydrogen bonding and ion-
dipole interactions
• most of their nonpolar side chains are
buried inside
• nearly all have substantial sections of a-
helix and b-sheet
TERTIARY STRUCTURE
 The 3-dimensional arrangement of
atoms in the molecule.
 In fibrous protein, backbone of protein
does not fall back on itself, it is important
aspect of 3˚ not specified by 2˚ structure.
 In globular protein, more information
needed. 3k structure allows for the
 The arrangement of polypeptide chains into
determination of the way helical and
pleated-sheet sections fold back on each
other.
 Interactions between side chains also
plays a role.
 Tertiary structure: the overall
conformation of an entire polypeptide
chain.
 Tertiary structure is stabilized in four
ways:
 Covalent bonds as for example, the
formation of disulfide bonds
between cysteine side chains.
 Hydrogen bonding between polar
groups of side chains, as for example
between the -OH groups of serine
and threonine.
 Salt bridges, as for example, the
attraction of the -NH3+ group of
lysine and the -COO- group of
aspartic acid.
 Hydrophobic interactions, as for
example, between the nonpolar side
chains of phenylalanine and
isoleucine.
QUATERNARY STRUCTURE
a noncovalently bonded aggregation.
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• The individual chains are held together by  Integral membrane protein of

hydrogen bonds, salt bridges, and hydrophobic rhodopsin, made of a-helices.
interactions.

Hemoglobin
 Adult hemoglobin: Two alpha chains of 141
amino acids each, and two beta chains of
146 amino acids each.
 Fetal hemoglobin: Two alpha chains and
two gamma chains. Fetal hemoglobin has
a greater affinity for oxygen than does
adult hemoglobin.
 Each chain surrounds an iron-containing
heme unit.  An integral membrane protein from
the outer mitochondrial membrane
forming a b-barrel from eight b-
pleated sheets.

 Integral membrane proteins form
quaternary structures in which the outer
surface is largely nonpolar (hydrophobic)
and interacts with the lipid bilayer.
DENATURATION
 Denaturation: The process of
destroying the native conformation
of a protein by chemical or physical
means.
 Some denaturations are reversible,
while others permanently damage
the protein.
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DENATURATION AND REFOLDING

 Noncovalentinteractions that stabilize
proteins areweak and can be disrupted.
 Denaturation: the loss of 3˚
structuralorder… ”Unfolding”

DENATURATION AGENTS
 Heat: Heat can disrupt hydrogen bonding;
in globular proteins, it can cause unfolding
of polypeptide chains with the result that
coagulation and precipitation may take
place.
 6 M aqueous urea: Disrupts hydrogen
bonding.
 Surface-active agents: Detergents such as
sodium dodecylbenzenesulfate (SDS)
disrupt hydrogen bonding.
 Reducing agents: 2-Mercaptoethanol
(HOCH2CH2SH) cleaves disulfide bonds by
reducing -S-S- groups to -SH groups.
 Heavy metal ions: Transition metal ions
such as Pb2+, Hg2+, and Cd2+ form water-
insoluble salts with -SH groups; Hg2+ for
example forms -S-Hg-S-.
 Alcohols: 70% ethanol penetrates bacteria
and kills them by coagulating their
proteins. It is used to sterilize skin before
injections.