BIOCHEM

LECTURE
COMMON AMINO ACIDS
St. Mary’s College of Tagum Inc. | Ian John Hardee
• Proteins are like recipes made from different ingredients.
• All proteins are made from a basic set of 20 ingredients called
PROTEINS "common amino acids."

SPECIALIZED INGREDIENTS: MODIFIED AMINO ACIDS

I. PROTEIN COMPOSITION
• Sometimes, chefs (nature in this case) add a twist to the
recipe.
• They modify the common amino acids to create new flavors
(or functions).

PROTEIN
WHAT MODIFICATIONS LOOK LIFE
• These are precisely defined sequences of amino acids
(residues) linked through peptide bonds to form polymers • These modifications can be like adding special spices or
(hundreds or thousands of molecules combined to produce a ingredients.
single macromolecule. • It includes things like adding extra parts (functional groups)
or connecting certain parts within the amino acid.

LABELED AS “DERIVED” OR “MODIFIED”

• When amino acids get these special modifications, we call

them "derived" or "modified" amino acids.
• These changes happen after the amino acids are already part
of the protein.

SIMPLE TERMS

Figure 1. Chain of Amino Acids / Protein structure • Think of common amino acids as your basic ingredients.
• Modified amino acids are like adding a little extra flavor to the
recipe.
PEPTIDE • It's what makes each protein unique and interesting.

• A molecule formed by linking together a small number of

amino acids (from two to a dozen) through peptide bonds;
both peptides and proteins usually have a free amine group
on one end of the molecule (the N- terminal residue) and a
free carboxyl group on the other end of the molecule (the C-
terminal residue.

Figure 3. Small Peptide of Six Amino Acids

ADDITIONAL INFORMATION: Proteins are like long chains of beads, with hundreds or
even thousands of beads linked together. These chains are made of tiny units called
amino acids, which are connected by special links called 'peptide bonds’.

Just like a necklace, proteins have a starting point and an ending point. At one end, you
usually find an 'amine group,' which is like a bead with a plus sign (+). At the other end,
Figure 2. Polypeptide chain you usually find a 'carboxyl group,' which is like a bead with a minus sign (-).

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So, proteins are like long bead necklaces made up of amino acid beads, and they have • The fourth substituent, the side chain (indicated by R), varies
these special beads with plus and minus signs at each end."
and confers distinctive chemical properties to each amino acid

• In standard nomenclature for amino acids, the carbons of the

ABBREVIATION OF AMINO ACIDS
R group are labeled with Greek letters, starting with B for the
• The names of the 20 common amino acids are usually written first carbon attached to a carbon; for example, in glutamic acid
as a three-letter abbreviation with first letter capitalized or as (three linear carbons in the R group), the carbons are labeled
a single capital letter designation. ẞ, y, and 8, with the 8 carbons being the final carboxyl carbon
in this R group.

Figure 4. Abbreviation of Glycine (Gly, G)

Figure 5. Abbreviation of 20 common amino acids

Figure 6. Chemical structures of 20 common amino acids

amino acids contain central carbon (C)CALLED α carbon, to which four

substituents are bound: an amine group (NH2), a carboxylic acid group
(-COOH), a hydrogen atom (H), and a group unique to each amino
• Amino acids may be categorized according to the functional
acid is called the side chain or R group
groups and chemical properties of their side chains; some
amino acids groups fit more than one classification
• valine, leucine, and isoleucine have longer aliphatic side chains
that are hydrophobic; they tend to congregate in structures
that enable them to avoid water
• Cysteine and methionine, the two sulfur-containing amino
acids, are hydrophobic

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 (1) Two cysteine residues can bond via their thiol (-SH) groups
to form the derived amino acid cystine

THE IMPORTANCE OF IONIZATION

• Ionization is the process of gaining or losing charged

particles (ions).
• For amino acids, ionization is crucial because it
influences their behavior in biological systems.

Figure 7. Bonds of two cysteine via thiol

IONIZATION STATES OF AMINO ACIDS

1. Neutral State
• Serine and threonine have side chain hydroxyl group that • At a certain pH (around pH 7), amino acids exist in
makes them both hydrophilic and chemically reactive their neutral or zwitterionic form.
• The amino group is NH3+, and the carboxyl group
• The acidic amino acids aspartate and glutamate are is COO-.
dicarboxylic, monobasic amino acids because they have two • Net charge = 0.
carboxyl groups (one bound to a carbon and one in the acid
chain) but only one amine group (bound to a carbon); the
carboxyl groups of both amino acids and negatively charged 2. Acidic State
at physiologic pH (7.4) • At low pH (acidic conditions), amino acids lose a
proton from the amino group.
• Amino acids with basic side chains are lysine, arginine, and • The amino group becomes NH2.
histidine • The carboxyl group remains COO-.
• Net charge = -1.
• (1) The side chain amine group makes these amino acids
extremely polar and hydrophilic; at physiologic pH, both lysine
and arginine have positively charged amine groups
3. Basic State
• (2) At physiologic pH, the imidazole ring in histidine exists • At high pH (alkaline conditions), amino acids lose a
primarily in the uncharged form because the imidazole ring proton from the carboxyl group.
has a pk'a of approximately 6 • The amino group remains NH3+.
• The carboxyl group becomes COO.
• Asparagine and glutamine, the two amino acids that contain • Net charge = +1.
an amide group in the side chain, are not charged at
physiologic pH
WHY IONIZATION MATTERS

The ionization state affects:

AMINO ACIDS: THE BUILDING BLOCKS OF LIFE • Solubility: Ionized amino acids are more soluble in
water.
• Amino acids are fundamental molecules in • Structure: It influences the folding of proteins.
biochemistry.
• Reactivity: Ionization states are critical for chemical
• They are the building blocks of proteins, which are reactions in biology.
essential for life

PH AND AMINO ACID BEHAVIOR

THE STRUCTURE OF AMINO ACIDS
• The pH (acidity or alkalinity) of the environment
Amino acids have a specific structure:
determines the dominant ionization state of amino
• An amino group (NH2) acids.
• A carboxyl group (COOH) • Living organisms carefully regulate pH to control
• A side chain (R group) that varies among different amino amino acid behavior.
acids.

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SUMMARY • Peptide bonds form when the carbon from one amino acids
COOH group joins with the nitrogen from the NH2 group of
• Amino acids can exist in different ionization states the next amino acid. This bonding process also releases a
depending on pH water molecule.
• Ionization is vital for understanding protein structure • These peptide bonds are rigid and flat, and they serve as the
and function in biochemistry. protein's backbone.
• It plays a central role in the chemistry of life. • Other bonds within amino acids allow more flexibility and
rotation.

II. LEVELS OF PROTEIN STRUCTURE

PRIMARY STRUCTURE

• The primary structure of a protein is simply the specific order

and number of amino acids linked together by these peptide
bonds.
• When we write down the primary structure, we list the amino
WHAT MAKES UP PROTEIN? acids in order from left to right.
• The very first amino acid (called the N-terminal amino acid)
1. Primary Structure
has a free amino group (NH2), and its carboxyl group
• This is like the unique order of letters in a word. For
(COOH) is involved in forming the first peptide bond.
proteins, it's the specific order of building blocks called
• The following amino acids are listed to the right of the N-
amino acids.
terminal amino acid, and all of them are connected by peptide
2. Secondary Structure
bonds at their amino and carboxyl groups.
• Think of this as folding and twisting the protein chain,
• The last amino acid in the chain (called the C-terminal amino
like folding a piece of paper to make different shapes.
acid) has a free carboxyl group (COOH).
3. Tertiary Structure
• Imagine the final, 3D shapes of a paper origami. That's
what tertiary structure is for proteins.

MORE COMPLEXITY FOR SOME PROTEINS?

SECONDARY STRUCTURE
• Some proteins work together like a team.
• When this happens, they have an extra level called • Secondary structure is the next level of organization in
quaternary structure. proteins.
• It's like teamwork because multiple protein chains • It's created by the interactions of amino acids within the
come together. protein's primary structure.
• These interactions are mostly due to hydrogen bonding
between different parts of the protein.
DIFFERENT TEAM SIZES

• Some proteins are like a solo act, made of just one chain. We TYPE OF SECONDARY STRUCTURE
call these monomer (e.g., amino acid)
• Others are like a group performance, with two or more chains. There are three main types:
These are called oligomers. • alpha helix (α helix)
• We give them names based on the number of chains:
• beta pleated sheet (β sheet)
Two chains: Dimers
• collagen triple helix
Three chains: Trimers
Four chains: Tetramers
And so on...
ALPHA HELIX (α Helix)

• Found in many proteins, it's like a twisted rod.

• Formed by hydrogen bonds between an oxygen atom in one
AMINO ACID LINKAGE amino acid and a hydrogen atom in another amino acid
(specifically, between the carboxyl group oxygen and the
• Proteins are made up of building blocks called amino acids.
amine hydrogen).
• Amino acids are connected to each other through
• The helix has approximately 3.6 amino acids per turn.
something called a "peptide bond."

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 • Amino acids that are close together in the primary structure
are spatially close in the alpha helix.
• Some amino acids favor alpha helix formation, while others • Some proteins are composed of more than one polypeptide
tend to disrupt it. chain. Each polypeptide chain in such protein is called sub-
units.
• The quaternary structure refers to interaction between these
sub-units to form a large final 3D structure.
BETA PLEATED SHEET (β Sheet)

• Found in proteins like silk.

• Formed by hydrogen bonds between adjacent protein chains.
• Can be parallel (chains go in the same direction) or
antiparallel (chains go in opposite directions).
• Proteins with beta pleated sheets have an extended structure.

COLLAGEN TRIPLE HELIX

Figure 9. quaternary structure
• Abundant in connective tissues like bone and tendon.
• It's a triple helix, like three intertwined ropes.
• Held together by hydrogen bonds.
• Contains a lot of proline and glycine, with every third amino
III. TECHNIQUES FOR STUDYING PROTEINS
acid being glycine.
• There are about 3.3 amino acids per turn.
• The high concentration of glycine keeps the interior from
getting crowded.
• The amino acid composition of a protein can be discerned by
cleaving all the peptide bonds by separating and identifying
the constituent amino acids
Simply, secondary structure is how amino acids in a protein arrange
• The amino acids sequence of a protein can be discerned by
themselves due to hydrogen bonds. The alpha helix is like a twisted
using various methods to cleave only selected peptide bonds
rod, the beta pleated sheet is like a folded sheet, and collagen is like
• Protein is also identified and characterized by spectroscopy,
three ropes twisted together. These structures help give proteins their
ultracentrifugation, chromatography, and electrophoresis
unique shapes and functions.
• More sophisticated aspect of protein characterization is
accomplished by X-ray diffraction, circular dichroism
spectroscopy, nuclear magnetic resonance spectroscopy and
mass spectroscopy

• The Tertiary structure is one individual sub-unit. Refers to the

overall folding of a polypeptide chain to form a final three-
dimensional structure.

DEFINITION

• Amino acid sequence refers to the specific order in which

amino acids are linked together in a protein.

Figure 8. tertiary structure

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FUNCTION After determining the amino acid composition of a protein, the
determination of the structure includes identifying the N-terminal
The composition of Amino Acids determines a protein's chemical residue and C-terminal residue.
properties, such as its solubility , pH sensitivity, and ability to bind to
other molecules

• The first stage of determining the amino acid composition of

a protein, all the peptide bonds are hydrolyzed by an acid.
• In the second stage of determining the amino acid
composition of a protein, the hydrolyzed amino acids are
separated, identified, and quantitated.
• Amino acids can be separated by thin layer, chromatography, Proteins with multiple subunits, or quaternary structures, are composed
or liquid chromatography, which is the separation of molecules of individual subunits each having a unique amino acid sequence.
on a solid support according to their physical or chemical
Denaturation is a process where these proteins lose their secondary,
properties.
tertiary, and quaternary structures due to changes in temperature, pH,
• Amino acids can be identified and quantitated by reacting
or exposure to certain chemicals both in vivo and in vitro. However, the
them with reagents that produce a colored or fluorescent
primary structure remains intact.
product, the intensity of which is proportional to the
concentration of amino acid present. This loss of structure leads to the loss of normal biochemical activity
rendering the proteins nonfunctional. Additionally, disulfide bonds within
the proteins can be disrupted by reducing agents like mercaptoethanol
NINHYDRIN or dithiothreitol, leading to further denaturation

• A reagent that turns blue when reacted with amino acids and
yellow when reacted with amino acids (proline), is sensitive
to microgram quantities of amino acid.

1. The presence of protein and its integrity can be detected by

spectroscopy, a technique for identifying and quantitating unknown
molecules by their interaction with light.

Figure 10. Ninhydrin • Absorption Spectroscopy - Identifies peptide bonds and

certain functional groups by measuring the absorbance of
different wavelengths of visible light (UV)
• Fluorescence Spectroscopy - A more sensitive measurement
than visible spectroscopy detects the presence and quantity
FLUORESCAMINE of a protein.

• A reagent that reacts with the amine group to produce a 2. Ultracentrifugation separates proteins according to size.
fluorescent derivative, more sensitive than Ninhydrin;
3. Gel filtration chromatography (also called size exclusion
Fluorescamine can detect nanogram quantities of amino acids.
chromatography) separates proteins according to size.

4. Ion exchange chromatography separates proteins based on their

charge.

5. Affinity chromatography separates proteins that bind specifically with

certain chemical groups.

6. Electrophoresis, separation of charged molecules by their movement

on a solid support while exposed to an electric field. Aids in the
Figure 11. Fluorescamine separation of different proteins.

7. Isoelectric focusing separates proteins on the basis of their isoelectric

points.

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 NUCLEAR MAGNETIC RESONANCE (NMR) SPECTROCOPY

• NMR is like using tiny magnets to explore sculpture.

• It reveals details about specific atoms in the protein.
• Scientists learn about its shape and how it functions in its
DISCOVERING THE SHAPES OF PROTEIN environment.
• Think of proteins as tiny, intricate sculptures.
• Scientists use special tools to figure out how these sculptures
are shaped.

X-RAY DIFFRACTION

• One tool is like shining a super-bright flashlight on the

sculpture.
• It's called X-ray diffraction.
• It helps scientists see the protein's 3D structure, like
understanding the shape of a puzzle piece.

Figure 14. Nuclear Magnetic Resonance (NMR) Spectroscopy

MASS SPECTOMETRY (MS)

• MS is like weighing the protein.

• It's super precise and can tell us about tiny amounts of protein.
• We use it to figure out the protein's structure.

Figure 12. X-ray diffraction

CIRCULAR DICHROISM (CD) SPECTROSCOPY

• Imagine shining colorful lights on the sculpture.

• CD spectroscopy checks the colors the protein reflects.
• It tells us how the protein folds and twists, its secondary
structure.

Figure 15. Mass Spectrometry (MS)

Figure 13. Circular dichroism (CD) spectroscopy

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