Biochemistry

Protein
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Group 2 Biochemistry Reporting

By:

Mary Kirsten Barolo

Miguel Ronaldo Beluso

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PROTEINS
Proteins are the most important of all
biological compounds. The very word
”protein” is derived from the Greek
proteios, meaning “of first importance
and the scientists who named these
compounds more than 100 years up
chose an appropriate term.
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 Proteins have multiple functions,

THE including: acting as enzymes and

FUNCTIONS hormones, maintaining proper fluid and

acid-base balance, providing nutrient
OF transport, making antibodies, enabling
wound healing and tissue regeneration,
PROTEIN and providing energy when carbohydrate
and fat intake is inadequate.
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AMINO ACIDS

Amino acids are the

building blocks or
monomers of proteins. It
contains a basic amine
functional group and
a carboxylic group.
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There are 20 naturally

occurring amino acids in protein
that differ in the alkyl group (R)
attached to the alpha C atom. These
amino acids are called alpha amino
acids.

The amino acids are represented by

a three-letter notation such as gly for
glycine and phe for phenylalanine or
the one capital letter notation such
as G for glycine or F for
phenylalanine.
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Because of the different

electronic characteristics of
the functional R groups,
amino acids are classified as
non-polar aliphatic,
aromatic, polar negatively
charged or acidic, and polar
positively charged or basic
amino acids.
z AMINO ACIDS
EXIST AS
ZWITTERIONS

An amino acid has both a basic

amine group and an acidic
carboxylic acid group. There is an
internal transfer of a hydrogen ion
from the -COOH group to the -
NH2 group to leave an ion with both
a negative charge and a positive
charge. This is called a zwitterion.
AMINO
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ACIDS COMBINE TO
FORM PROTEIN
When two or more amino acids
link together, they form a peptide.
The links between amino acids are
called peptide bonds. When many
amino acids link together, the
structure is called a
polypeptide. When polypeptides
come together, they form a
protein.
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AMINO ACID CHARACTERISTICS

Each amino acid has unique characteristics arising from the size,
shape, solubility, and ionization properties of its R group. As a
result, the side chains of amino acids exert a profound effect on the
structure and biological activity of proteins. Although amino acids
can be classified in various ways, one common approach is to
classify them according to whether the functional group on the side
chain at neutral pH is nonpolar, polar but uncharged, negatively
charged, or positively charged.
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UNCOMMON AMINO ACIDS

In addition to the 20 common

amino acids, there are two
nonstandard, or non-canonical
amino acids found in
nature, selenocysteine (Sec or U)
present in many prokaryotes as
well as most eukaryotes, and
pyrrolysine (Pyl or O), found in
some archaea and one bacterium.
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PROTEIN
PROPERTIES
Physical Properties of Proteins

 Proteins are colorless and usually

tasteless. These are homogeneous
and crystalline.

 The proteins range in shape from

simple crystalloid spherical
structures to long fibrillar
structures. Two distinct patterns
of shape
have been recognized :
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GLOBULAR
PROTEIN

These are spherical in

shape and occur mainly in
plants, especially, in seeds
and in leaf cells. These are
bundles formed by folding
and crumpling of protein
chains.
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FIBROUS
PROTEIN

These are thread-like or

ellipsoidal in shape and occur
generally in animal muscles.
Most of the studies regarding
protein structure have been
conducted using these
proteins.
 PROTEIN
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PRIMARY STRUCTURE

The protein‘s primary structure is the amino acid sequence in its

polypeptide chain. A protein‘s primary structure is the sequence in
which various shapes and varieties of popped maize are strung together.
PROTEIN
z SECONDARY
STRUCTURE

The alpha helix is a common structural motif

or secondary structure found in proteins. It is
characterized by a helical or spiral shape
formed by a polypeptide chain's backbone.
This helical structure is stabilized by
intramolecular hydrogen bonds between the
carbonyl oxygen of one amino acid residue and
the amide hydrogen of an amino acid residue
located four positions away in the sequence.
This repeating pattern of hydrogen bonds gives
rise to the helical conformation.
BETA PLEATED
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SHEETS
Beta-sheets are characterized by a specific
arrangement of amino acid residues within a
protein's polypeptide chain that forms a
sheet-like structure. This arrangement is
stabilized by hydrogen bonds between
adjacent strands of the polypeptide chain.
 PROTEIN
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TERTIARY STRUCTURE

The tertiary structure of a protein refers to the three-dimensional arrangement of atoms

in the entire polypeptide chain of the protein. It is the highest level of protein structure
and is essential for understanding the protein's function.
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COVALENT BOND

Covalent bonds are a type of chemical bond that forms when two atoms share electrons
to achieve a stable electron configuration. In a covalent bond, atoms come together to
share pairs of electrons, creating a strong electrostatic attraction between the positively
charged atomic nuclei and the negatively charged shared electrons. Covalent bonds are
common in molecules and contribute to the formation of various chemical compounds.
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HYDROGEN BONDING

Hydrogen bonding is a type of intermolecular force that occurs when a hydrogen atom,
covalently bonded to a highly electronegative atom (usually nitrogen, oxygen, or
fluorine), is attracted to another electronegative atom in a different molecule. Hydrogen
bonds are relatively strong compared to other intermolecular forces and play a
significant role in the properties and behavior of molecules.
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SALT BRIDGES

Typically found in ionic compounds or within a protein's three-dimensional structure.

Salt bridges play important roles in various chemical and biological processes.
 HYDROPHOBIC
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INTERACTIONS

Hydrophobic interactions are non-covalent interactions between nonpolar molecules or

nonpolar regions of molecules in the presence of a polar solvent, such as water. These
interactions play a crucial role in the structure and behavior of biological molecules,
particularly in proteins, lipid membranes, and the self-assembly of various biomolecules.
 METAL
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ION COORDINATION

Metal ion coordination refers to the arrangement and binding of metal ions with specific
ligands or atoms in a molecule or complex. This coordination plays a critical role in
various chemical and biological processes, and it is essential for the stability and function
of metalloenzymes, metalloproteins, and metal-containing biomolecules.
PROTEIN
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QUARTERNARY STRUCTURE

The quaternary structure of a protein refers to the arrangement of multiple

protein subunits (polypeptide chains) into a functional, multi-subunit complex.
This level of protein structure is relevant for proteins that consist of two or more
individual polypeptide chains, known as subunits, and it describes how these
subunits interact with each other to form a larger, biologically active unit.
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PROTEIN DENATURATION

Protein denaturation is a process in which a protein loses its

native three-dimensional structure and, as a result, its biological
activity. This disruption of the protein's structure can occur due
to various factors, including changes in temperature, pH,
exposure to chemicals, or mechanical forces. When a protein
becomes denatured, it typically loses its ability to perform its
biological function effectively.
Causes of Denaturation:
•HEAT: Elevated temperatures can disrupt the weak non-covalent interactions
(hydrogen bonds, van der Waals forces, etc.) that maintain a protein's folded structure.
Extreme heat can lead to the unfolding of the protein.

•pH: Altering the pH of the environment can affect the charges on amino acid residues
in a protein. This can disrupt electrostatic interactions and change the protein's shape.

•CHEMICALS: Certain chemicals, such as strong acids, bases, organic solvents, and
chaotropic agents (substances that disrupt the structure of water), can denature
proteins by breaking bonds or interfering with non-covalent interactions.

•MECHANICAL STRESS: Agitation, shearing forces, or physical manipulation can

disrupt a protein's structure.
 True or False
1. Amino acids are the building blocks of Proteins?
2. Proteins came from the Green word proteios?
3. The zwitterion is a molecule that has at least two functional groups?
4. Globular Protein are made up of polypeptide chains that are elongated and fibrous in nature or
have a sheet like structure?
5. The alpha helix is a common structural motif or secondary structure found in proteins.
6. The globular protein is a protein that us water-soluble and shaped like a sphere or a globe upon
folding.
7. Peptide is formed by linking two or more amino acids.
8. Proteins have limited functions.
9. Protein’s primary structure is the amino acid sequence in its polypeptide chain.
10. Proteins are the most important of all biological compounds.
11. In some cases, Chaperone molecules may reverse denaturation.
12. Secondary and tertiary structures stabilize the native conformations of proteins.
13. The precise fit of polypeptide subunits into the aggregated whole is called the Primary Structure.
14. Many amino acids form a polypeptide chain.
15. The symbol for isoelectric point is pE.
11. In some cases, Chaperone molecules may reverse denaturation.
12. Secondary and tertiary structures stabilize the native conformations of proteins.
13. The precise fit of polypeptide subunits into the aggregated whole is called the Primary Structure.
14. Many amino acids form a polypeptide chain.
15. The symbol for isoelectric point is pE.
1. Which of the following is part of the 20 Amino Acids Commonly found in Proteins.
a. Alanine
b. Proline
c. valine
d. all of the above
2. is the three-dimensional conformation of the protein molecule?
e. Primary Structure
f. Secondary Structure
g. Tertiary Structure
d. Quaternary Structure
3. Giant molecules made of amino acids linked together by peptide bonds.
a. Hemoglobin
b. Protein
c. Keratin
d. Hydrogen
4. Molecules that has the ability to reverse protein denaturation
e. Keratin
f. Hemoglobin
g. Chaperone
h. Collagen
5. The precise fit of polypeptide subunits into the aggregated whole is called the?
a. Primary Structure
b. Secondary Structure
c. Tertiary Structure
d. Quaternary Structure
 ANSWERS
1. TRUE 11. TRUE
2. TRUE 12. TRUE
3. TRUE 13. FALSE
4. FALSE 14. TRUE
5. TRUE 15. FALSE
6. TRUE 16. D
7. TRUE 17. C
8. FALSE 18. B
9. TRUE 19. C
10. TRUE 20. D