BIOCHEM: PROTEINS

OVERVIEW:
• Characteristics of Proteins
- Amino Acids: The Building Block for Proteins
- Essential Amino Acids
- Chirality and Amino Acids
- Acid Base Properties of Amino Acids
- Cysteine: A chemically Unique Amino Acids
• Peptides
- Nature of Peptide Bond
- Peptide Bond
- Small Peptide Nuerotransmitters
• Protein functions
• General Structural Characteristics of Proteins
- Types of Conjugated Proteins
- Protein Structures

CHARACTERISTICS OF PROTEINS
- derived from the Greek word “prōteios”, meaning “holding first place”.
- Proteins are large, complex molecules that play many critical roles in the body. They do
most of the work in cells and are required for the structure, function, and regulation of the
body’s tissues and organs.
- A highly complex substance that is present in all living organisms.
- Proteins are of great nutritional value and are directly involved in the chemical process
essential for life.
- Proteins are naturally occurring, unbranched polymer in which the monomer units are
amino acids.
- All proteins contain the elements carbon, hydrogen, oxygen, nitrogen, and sulfur.
- Proteins are naturally occurring, unbranched polymer in which the monomer units are
amino.
Proteins are needed for the synthesis of enzymes, hormones, blood components, tissues and
sometimes for energy.
AMINO ACIDS : THE BUILDING BLOCK FOR PROTEINS
• Amino acid is an organic compound that contains both an amino group and carboxyl group.
• The amino acids found in proteins are always a-amino acids.
• An a-amino acid is an amino acid in which the amino group and the carboxyl group are
attached to the a-carbon atom.
• The R group present in an a-amino acid is called the amino acid side chain.
• Standard amino acid - is one of the 20 a-amino acids normally found in proteins.

Amino acids are grouped according to side-chain polarity. There are four (4) categories namely;
(1) Nonpolar amino acids - is an amino acid that contains one amino group, one carboxyl group,
and a nonpolar side chain. (Flash the structures)
(2) Polar neutral amino acid - is an amino acid that contains one amino group, one carboxyl
group, and a side chain that is polar but neutral. (Flash the structures)
(3) Polar acidic amino acid - is an amino acid that contains one amino group and two carboxyl
groups, the second carboxyl group being part of the side chain. (Flash the structures)
(4) Polar basic amino acid - is an amino acid that contains two amino group and one carboxyl
group, the second amino group being part of the side chain. (Flash the structures)

ESSENTIAL AMINO ACIDS

• Essential amino acid - is a standard amino acid needed for protein synthesis that must be
obtained from dietary sources because the human body cannot synthesize it in adequate amounts
from other substances.
• Complete dietary protein - is a protein that contains all of the essential amino acids in the same
relative amounts in which the body needs.
• Incomplete dietary protein - is a protein that does not contain adequate amounts of one or more
of the essential amino acids, relative to the body's needs. (Associated with the term incomplete
dietary protein is the liming amino acid).
• Limiting amino acids - is an essential amino acid that is missing in an incomplete dietary
protein, but present in inadequate amounts.
• Complementary dietary proteins - are two or more incomplete dietary proteins that, when
combined, it provide an adequate amount of all essential amino acids.
CHIRALITY and AMINO ACIDS
Chirality - or handedness, means that an object or molecule cannot be superimposed on its mirror
image by any translations or rotations.
Achiral - (absence of chirality) are those objects that are identical to their mirror image.

ACID-BASE PROPERTIES of AMINO ACIDS

•Amino acids are white crystalline solids with relatively high decomposition points.
•Most amino acids decompose before they melt.
•Most amino acids are not very soluble in water due to strong intermolecular forces within their
crystal structures.
Zwitterion - is a molecule that has a positive charge on one atom and a negative charge on
another atom, but has no net charge.
Isoelectric Points- is the pH at which an amino acid exists primarily in its zwitterion form.

CYSTEINE : A CHEMICALLY UNIQUE AMINO ACID

Cysteine - a chemical property that is unique among the standard amino acids. It is the only
standard amino acid that has a side chain that contains a sulfhydryl group.

PEPTIDES
Under proper conditions, amino acids can bond together to produce an unbranched chain of
amino acids. The length of the amino acid chain can vary from a few amino acids to many amino
acids. Such as chain of covalently linked amino acids is called a peptide
• Peptides - is an unbranched chain of amino acids, peptides are classified by the number of
amino acids present in the chain.
• Dipeptide - a compound containing two amino acids.
• Tripeptide - a compound containing three amino acids joined together in a chain.
• Oligopeptide - is loosely used to refer to peptides with 10 to 20 amino acids residues.
• Polypeptide - longer peptides, a long unbranched chain of amino acids.
NATURE OF PEPTIDE BOND
- The bonds that link amino acids together in a peptide chain a re called peptide bonds.
- The nature of the peptide bond becomes apparent by reconsidering a chemical reaction
previously encountered. The reaction between a carboxylic acid and an anime to produce
an amide was considered.

What is peptide bond?

Peptide bond is a covalent bond between the carboxyl group of one amino acid and yhe amino
group of another amino acid.
Amino acid residue - is the proportion of an amino acid structure that remains.

• Tripeptide contains the amino acids glycine, alanine, and serine, is (Gly-Ala-Ser). When we use
this abbreviated notation, by convention, the amino acid at the N-terminal end of the peptide is
always written on the left.
• The repeating sequence of peptide bonds and a-carbon —CH groups in a peptide is referred to
as the backbone of the peptide.

Peptide Nomenclature: Small peptides are named as derivatives of the C-terminal amino acid
that is present.
Isomeric peptides: Peptides that contain the same amino acids but in different order are different
molecules with different properties.
Small Peptide Hormones: The two best-known peptide hormones are oxytocin and vasopressin,
both produced by the pituitary gland.
Oxytocin: regulated uterine contractions and lactations, in the other hand..
Vasopressin: regulates the excretion of water by the kidneys, also affects the blood pressure.

SMALL PEPTIDE NUEROTRANSMITTERS

Enkephalin- are pentapeptide neurotransmitters produced by the brain itself that bind at receptor
sites in the brain to reduce pain.
The two best-known enkephalins are Met-enkephalin and Leu-enkephalin.
• Met-enkephalin: Tyr-Gly-Gly-Phe-Met
• Leu-enkephalin: Tyr-Gly-Gly-Phe-Leu
PROTEIN FUCTIONS
- Proteins are essential for life and are essential for wide range of cellular activities. Protein
enzymes catalyze the vast majority of chemical reactions that occur in the cell. Proteins
provide many of the structural elements of a cell, and they help to bind cells together into
tissues. Proteins, in the form of antibodies, protect animals from disease, and many
hormones are proteins. Furthermore, they control the activity of genes and regulate gene
expression.
- Proteins are made up of hundreds or thousands of smaller units called amino acids, which
are attached to one another in long chains. There are 20 different types of amino acids
that can be combined to make a protein. The sequence of amino acids determines each
protein’s unique 3-dimensional structure and its specific function. Amino acids are
coded by combinations of three DNA building blocks (nucleotides), determined by the
sequence of genes. Proteins can be described according to their large range of functions
in the body:

FUNCTION Description Example

Antibody Antibodies bind to specific Immunoglobulin
foreign particles, such as
viruses and bacteria, to help
protect the body.
Enzyme Enzymes carry out almost all Phenylalanine hydroxylase
of the thousands of chemical
reactions that take place in
cells. They also assist with
the formation of new
molecules by reading the
genetic information stored in
DNA.
Messenger Messenger proteins, such as Growth hormone
some types of hormones,
transmit signals to coordinate
biological processes between
different cells, tissues, and
organs.
Structural component These proteins provide Actin
structure and support for
cells. On a larger scale, they
also allow the body to move.
 Transport/storage These proteins bind and carry Ferritin
atoms and small molecules
within cells and throughout
the body.

GENERAL STRUCTURAL CHARACTERISTICS of PROTEINS

• A protein was defined simply as a naturally occurring, unbranched polymer in which the
monomer units are amino acidsm.
• Protein - is a peptide in which at least 40 amino acid residues are present
• Monomeric protein - is a protein in which only one peptide chain is present.
• Multimeric protein - is a protein in which more than one peptide chain is present.
• Simple protein - is a protein in which only amino acid residues are present
• Conjugated protein - is a protein that has one or mire peptide chains.
• Prosthetic group - is a non-amino acid group present in a conjugated protein.

TYPES OF CONJUGATED PROTEINS

- Hemoproteins
- Lipoproteins
- Glycoproteins
- Phosphoproteins
- Nucleoproteins
- Metalliproteins

• Primary Protein Structure is the order in which amino acids are linked together in a protein.
• Secondary Structure of Proteins s the arrangement in space adopted by the backbone portion of
a protein.

The two (2) most common types of secondary structure :

- alpha helix (a helix)
- beta pleated sheet (B pleated sheet)
Most proteins fold into unique 3d structures. The shape into which a protein naturally folds is
known as its native conformation. Although many proteins can fold unassisted, simply through
the chemical properties of their amino acids, others require the aid of molecular chaperones to
fold into their native states. Biochemists often refer to four distinct aspects of a protein’s
structure:
- Primary structure: the amino acid sequence. A protein is a polyamide.

- Secondary structure: regularly repeating local structures stabilized by hydrogen bonds.

The most common examples are the a-helix, B-sheet, and turns.

- Tertiary structure: the overall shape of a single protein molecule; the spatial
relationship of the secondary structures to one another. Tertiary structure is generally
 stabilized by nonlocal interactions, most commonly the formation of a hydrophobic core,
but also through salt bridges, hydrogen bonds, disulfide bonds, and even posttranslational
modifications. The term “tertiary structure” is often used as synonymous with the term
fold. The tertiary structure is what controls the basic function of the protein.

- Quaternary structure: the structure formed by several protein molecules (polypeptide

chains), usually called protein subunits, which function as a single protein complex.
 - Quinary structure: the signatures of protein surface that organize the crowded cellular
interior. Quinary structure is dependent on transient, yet essential, macromolecular
interactions that occur inside living cells.

CLASSES OF PROTEINS
Proteins can be informally divided into three main classes, which correlate with typical tertiary
structures:
• Globular proteins- In biochemistry, globular proteins or spheroproteins are spherical ("globe-
like") proteins and are one of the common protein types (the others being fibrous, disordered and
membrane proteins). Globular proteins are somewhat water-soluble (forming colloids in water),
unlike the fibrous or membrane proteins.
• Fibrous proteins- Fibrous proteins contain polypeptide chains organized approximately in
parallel along a single axis, producing long fibers or large sheets. Such proteins tend to be
mechanically strong and resistant to solubilization in water. Fibrous proteins often play a
structural role in nature.
• Membrane proteins- A membrane protein is a protein molecule that is attached to, or
associated with, the membrane of a cell or an organelle. Membrane proteins can be put into two
groups based on how the protein is associated with the membrane. Integral membrane proteins
are permanently embedded within the plasma membrane.

GROUP MEMBERS:
Reymond James Q. Lachica
Butch Geu Lupango
Winly Hainto
Ninya Guinoo
Hannah Interino
Kenneth Abrera Gasca
Marilou Galarza
Junne Wilson Infante