BIOCHEMISTRY (LEC)

GROUPS OF AMINO ACIDS

AMINO ACIDS AND PROTEINS

PROTEIN

 Derived from a Greek word “Proteios” that means “of

first importance”
 Molecule consisting of one or more polypeptide
chains
 Are made of amino acids

a. According to the side chains present

According to the side chains present:

1. Sulfur Atoms

2. Acidic groups

AMINO ACIDS

α-Amino Acids

 Building blocks of proteins

 Amine group (NH2) is attached to the C atom next to
the carboxyl group
 The amino group is basic while carboxylic group is
acidic in nature.
 Soluble in water but insoluble in organic solvents
(chloroform, acetone, ether)
 All amino acids have chiral carbon, except Glycine
3. Basic groups

4. Aromatic Rings
5. Imino Acids

b. According to the polarity of their side chains

1. Hydrophobic (Nonpolar) Amino Acids

 is an amino acid that contains one amino

group, one carboxyl group, and a nonpolar
side chain
 Prefer contact with one another over contact Polar, Acidic Negatively Charged Amino Acids
with water
 Generally found buried in the interior of  Is an amino acid that contains one amino group and
proteins, where they can associate with one two carboxyl groups, the second carboxyl group being
another and remain isolated from water part of the side chain
 9 amino acids  At physiological pH, the side chain of a polar acidic
o Alanine amino acid bears a negative charge
o Valine  They are acidic amino acids because ionization of the
o Leucine carboxylic acid releases a proton
o Isoleucine  Examples:
o Tryptophan o Glutamate
o Proline o Aspartate
o Glycine
o Methionine
o Phenylalanine

Polar, Basic Positively Charged Amino Acids

 is an amino acid that contains two amino groups and

2. Hydrophilic (Polar) Amino Acids
one carboxyl group, the second amino group being
part of the side chain
 Attracted to polar water molecules
 At physiological pH, the side chain of a polar basic
 Are often found on the surfaces of proteins
amino acid bears a positive charge
 3 Classes:
 Are basic because the side chain reacts with water,
o Polar, neutral
picking up a proton and releasing a hydroxide anion
o Polar, Acidic (Negatively Charged)  Examples:
o Polar, Basic (Positively Charged) o Lysine
 Is an amino acid that contains one amino o Arginine
group, one carboxyl group, and a side chain o Histidine
that is polar but neutral
 At physiological pH, the side chain of a polar
neutral amino acid is neither acidic nor basic
 More soluble in water than the nonpolar
amino acids as, in each case, the r group
present can hydrogen bond to water

Polar, Neutral Amino Acids

 Is an amino acid that contains one amino group, one

carboxyl group, and a side chain that is polar but
neutral
 At physiological pH, the side chain of a polar neutral
amino acid is neither acidic nor basic
 More soluble in water than the nonpolar amino acids
as, in each case, the R group present can hydrogen NUTRITIONAL CLASSES OF AMINO ACIDS
bond to water
Two Classes: Classification of Peptides
 Essential Amino Acids
o Are those that cannot be synthesized by the 1. DIPEPTIDES
body and are required in the diet

 Nonessential Amino Acids

o Are those amino acids that can be
synthesized by the body and need not be
included in the diet

2. OLIGOPEPTIDES
 Composed of 3-10 amino acids linked
together through peptide bond.
 Examples:
o Tripeptide: 3 amino acids linked by
2 peptide bonds
o Tetrapeptide: 4 amino acids linked
by 3 peptide bonds

3. POLYPEPTIDES
 Composed of 11-100 amino acids linked
together by peptide bonds

4. PROTEINS
 Composed of more than 100 amino acids
linked together by peptide bonds
Dietary Proteins
Naming of Proteins
 A complete dietary protein is a protein that contains
all the essential amino acids in approximately the
same relative amounts in which the human body

needs them
PEPTIDES AND PROTEINS

Peptide
 any compound produced by amide formation between
a carboxyl group of one amino acid and an amino
group of another
 Peptide Bond
o Amide group that links amino acids
o Dipeptide – the molecule formed by
condensing two amino acids
o N-terminal amino acid – with a free N+H3
o C-terminal amino acid – with a free –COO-
group

CLASSES OF PROTEINS

Based on the Number of Peptide Chains

“Types of Protein Based on the Number of Peptide Chains”

 can bind and thereby initiate the effect that
1. MONOMERIC PROTEIN the messenger carries
 is a protein in which only one peptide chain  are often the molecules that bind to enzymes
is present (catalytic proteins), thereby turning them “on”
and “off,” and thus controlling enzymatic
2. MULTIMERIC PROTEIN action
 is a protein in which more than one peptide
chain is present
FUNCTION EXAMPLES
 peptide chains present in multimeric proteins
are called protein subunits Collagen; bones, tendons, cartilage
Structural
Keratin; hair, skin, wool, nails, feathers
Based on Function Movement or
Myosin & Actin; muscle contractions
Contractile
“Types of Protein Based on its Function” Hemoglobin; transports O2
Transport
Lipoproteins; transports lipids
1. CATALYTIC PROTEINS
Nutrient Casein; in milk. Albumin; in eggs
 Enzymes
 Are biological catalysts (speed up chemical Insulin; regulates blood glucose
Messenger
reaction) Growth hormone; regulates growth
 Examples: amylase, pepsin, trypsin, lipase Immunoglobulins; stimulate immunity
Defense
Snake venom; plant toxins;
2. IMMUNE FUNCTIONS (DEFENSE PROTEIN) Sucrase; catalyzes sucrose hydrolysis
Catalytic
 Defend organisms against invasion by other Pepsin; catalyzes protein hydrolysis
species or protect them
 Immunoglobulin or antibodies Based on Structure
o Are specific protein molecules
produced by specialized cells of the “Types of Protein Based on Structure”
immune system (plasma cells) in
response to foreign bodies 1. Primary Structure
(antigens)  Is the amino acid sequence of the protein
chain
3. TRANSPORT PROTEINS  It results from the covalent bonding between
 Carry materials from one place to another in the amino acids in the chain (peptide bonds)
the body  Are translations of information contained in
 Examples: lipoproteins, transferrin, genes
hemoglobin, myoglobin

4. MESSENGER PROTEINS
 These proteins transmit signals to coordinate
biochemical processes between different
cells, tissues, and organs
 Examples: protein hormones (GH, FSH,
Insulin)

5. STRUCTURAL PROTEINS
 Provide mechanical support to large animals
and provide them with their outer coverings
 Confer stiffness and rigidity to otherwise
fluid-like biochemical systems
 Example: collagen and keratin

6. MOVEMENT / CONTRACTILE PROTEINS

 Necessary for all forms of movements
 Examples: myosin and actin

7. NUTRIENT PROTEINS
 These proteins are particularly important in 2. Secondary Structure
the early stages of life from embryo to infant  Where the peptide chains are folded
 Serve as sources of amino acids for regularly
embryos and infants  Is the result of hydrogen bonding between
 Examples: albumin (egg) and casein (milk) the amide hydrogens and carbonyl oxygens
of the peptide bonds
8. STORAGE PROTEINS
 These proteins bind (and store) small
molecules for future use
 Example: Ferritin (iron storage protein) and
Myoglobin (oxygen storage protein in the
muscles)

9. REGULATORY PROTEINS
 These proteins are often found embedded in
the exterior surface of cell membranes
 They act as sites at which messenger
molecules, including messenger proteins
 4. Quaternary Structure
 is the organization among the various
peptide chains in a multimeric protein
 Hemoglobin
o With four individual globular peptide
subunits
o 2 identical alpha-subunits
1) ALPHA HELIX o 2 identical beta-subunits
 is a protein secondary structure in which o Heme group - iron portion
a single protein chain adopts a shape  Can bind four molecules of
that resembles a coiled spring (helix), oxygen
with the coil configuration maintained by
hydrogen bonds

2) BETA PLEATED SHEET

 is a protein secondary structure in which
two fully extended protein chain
segments in the same or different
molecules are held together by
hydrogen bonds

3. Tertiary Structure
 Three-dimensional structure
 Polypeptide chain with its regions of
secondary structure further folds on itself
 Interactions responsible for tertiary structure:
o Covalent disulfide bond
o Electrostatic attractions
o Hydrogen bonds  The primary structure of a protein is simply the amino
o Hydrophobic attractions acid sequence.

 The secondary structure of a protein describes how

segments of the peptide backbone orient into a
regular pattern.

 The tertiary structure describes how the entire protein

molecule coils into an overall three-dimensional
shape.

 The quaternary structure describes how different

protein molecules come together to yield
 Based on Molecular Length and Shape

1. Fibrous Proteins
 is a protein whose molecules have an
elongated shape with one dimension much
longer than the others
 Are tough, insoluble, and composed of fibers
and sheets
 When the axial ratio of length:width is more
than 10
 Examples: collagen, keratin, elastins,
myosins, fibrin

2. Globular Proteins
 is a water-soluble protein whose molecules
have peptide chains that are folded into
spherical or globular shapes
 When axial ratio of length:width is less than
10
 Examples: hemoglobin, myoglobin, insulin,
immunoglobulins

3. Membrane Proteins
 a protein that is found associated with a
Based on Solubility and Physical Properties
membrane system of a cell
1. Simple Proteins  Example: ion channels, receptor proteins,
and proteins that allow cells to connect to
 A protein composed of only of amino acid
each other
residues
 These are the proteins which on complete
hydrolysis yield only amino acids
 Examples:
o globulin
o albumin

2. Compound or Conjugated Proteins

 A protein that incorporates one or more non-
amino acid units in its structures
 Amino acid portion is called apoprotein and
non-amino acid portion which may be
organic or inorganic is called the prosthetic
group (define the characteristics of these
proteins)
 Name of the conjugated protein is derived
from the prosthetic group

3. Derived Proteins
 Proteins derived from simple or conjugated
proteins by physical or chemical means
 Isoelectric Point

 is the pH at which an amino acid solution has no net

charge because an equal number of positive and
negative charges are present
 At the isoelectric point, almost all amino acid
molecules in a solution (more than 99%) are present
in their zwitterion form

PHYSICAL AND CHEMICAL PROPERTIES OF PROTEINS

 Generally tasteless
 Mostly are colorless, few are colored and crystalline
 Insoluble in fat solvents and present varied degrees
of solubility in water, salt solution, dilute acids, and
alkalis
 Mostly are with high molecular weight
 Most of them form non-diffusible colloid solutions of
the emulsoid type
 Are amphoteric
 Most of them are labile and readily modified in
solution when subjected to alterations in pH, UV, heat,
and organic solvents
 Very reactive and highly specific

Amphoteric

 Can act as an acid or base (depends on the pH of the

medium)
Electrophoresis
 In acid solution it acts like a base
 In alkaline solution it acts like an acid
 is the process of separating charged molecules on
the basis of their migration toward charged electrodes
associated with an electric field
 If the acidity or alkalinity of the solution is made less
and less, a point will be reached when the amino acid
group tends to migrate equally on both directions this
pH is called the isoelectric point
 DENATURATION OF PROTEINS Detergents

 is the partial or complete disorganization of a protein’s  Have both a hydrophobic region and a polar or
characteristic three-dimensional shape as a result of hydrophilic region
disruption of its secondary, tertiary, and quaternary  When interacts with proteins, they disrupt the
structural interactions hydrophobic interactions, causing the protein chain to
unfold
FACTORS:
 Temperature Heavy Metals
 pH
 Organic Solvents  Mercury or Lead
 Detergents  May form bonds with negatively charged side chain
 Heavy Metals groups
 Mechanical Stress  This interferes with the salt bridges formed between
amino acid R group, resulting in loss of conformation

Mechanical Stress

 Stirring, whipping, or shaking can disrupt the weak

interactions that maintain protein conformation

Temperature

 As the temperature increases, it also increases the

rate of molecular movement within the solution and
the bonds within the proteins begin to vibrate more
violently
 Lose their characteristic 3-dimensional conformation
and become completely disorganized
 56-60 degrees Celsius
 Coagulation will occur as the protein molecules then
unfold and become entangled; they have aggregated
to become a solid

pH

 When the pH of a protein solution is above the pI, all

the protein molecules will have a net negative surface
charge
 Below the pI, they will have a net positive charge
 At the pI, the protein molecules no longer have a net
surface charge, as a result they no longer strongly
repel one another and are at their least soluble pH

Organic Solvents

 Polar organic solvents denature proteins by disrupting

hydrogen bonds within the protein, in addition to
forming hydrogen bonds the solvent, water
 IMMUNOGLOBULINS

 Antibodies
 Produced by plasma cells
 Highly specific
 Has a memory
 Can recognize “self” from “non-self”
 Contain 4 peptide chains that are connected by
disulfide bonds and arranged in a Y-shaped
quaternary structure