BIOCHEM REVIEWER
Amino acids and Proteins Repetition of the reaction produces polypeptides
and proteins.
What Are the Structures and
Properties of Amino Acids?
A typical Amino Acids Contain a Central
Tetrahedral Carbon Atom
Central to this structure is the tetrahedral alpha (a)
carbon (Ca), which is covalently linked to both the
amino group and the carboxyl group.
Also bonded to this a-carbon are a hydrogen and
a variable side chain.
All 20 of the common amino acids are a-amino acids.
They have a carboxyl group and an amino group
bonded to the same carbon atom (the a-carbon)
They differ from each other in their side chains, or
R groups, which vary in structure, size, and electric
charge, and which influence the solubility of the
In neutral solution (pH 7), the carboxyl group exists amino acids in water.
as -COO(-) and the amino group as -NH3(+).
Because the resulting amino acid contains one
positive and one negative charge, it is a neutral
molecule called a zwitterion.
Amino acids are also chiral molecules. With four
different groups attached to it, the a-carbon is said
to be asymmetric.
Amino Acids Can Join via Peptide Bonds
The amino and carboxyl groups of amino acids can
react in a head-to-tail fashion, eliminating a water
molecule and forming a covalent amide linkage,
which, in the case of peptides and proteins, is
typically referred to as a peptide bond.
REFERENCES: Garrett, R., & Grisham, C. M. (2008). Biochemistry (4th ed.) Australia: brooks/Cole, Cengage Learning
Nelson, D. L., Cox, M. M., & Lehninger, A. L. (2008). Lehninger principles of biochemistry (5th ed.) NewYork
BIOCHEM REVIEWER
The Polypeptide Backbone Is Relatively
Polar
Peptides Can Be Classified According to
How Many Amino Acids They Contain
Each unit is called an amino acid residue, the
word residue denoting what is left after the release
of H2O when an amino acid forms a peptide link
upon joining the peptide chain.
Dipeptides have two amino acid residues,
tripeptides have three, tetrapeptides four, and
so on.
Oligopeptides- peptide chains of more than
12 and less than about 20 amino acid residues
Polypeptide- when the chain exceeds several
dozen amino acids in length
What Architectural Arrangements
Characterize Protein Structure?
Proteins fall into Three Basic Classes
According to Shape and Solubility
Fibrous proteins
- Have relatively simple, regular linear
structures.
- serve structural roles
- Insoluble in water or in dilute salt solutions
Globular proteins
- Roughly spherical in shape
- Compactly folded so that hydrophobic amino
acid side chains are in the interior of the
molecule and the hydrophilic side chains are
on the outside exposed to the solvent, water.
- Very soluble in aqueous solutions
-
REFERENCES: Garrett, R., & Grisham, C. M. (2008). Biochemistry (4th ed.) Australia: brooks/Cole, Cengage Learning
Nelson, D. L., Cox, M. M., & Lehninger, A. L. (2008). Lehninger principles of biochemistry (5th ed.) NewYork
BIOCHEM REVIEWER
Membrane proteins a-helix:
- For interaction with the nonpolar phase within
membranes
- Insoluble in aqueous solutions
- Have fewer hydrophilic amino acids than
cytosolic proteins
Protein Structure Is Described in
Terms of Four Levels of Organization
PRIMARY STRUCTURE: simply the
sequence of amino acids The helix can be viewed as a stacked array of peptide
planes hinged at the a-carbons and approximately
Primary structure dictates the structure and parallel to the helix.
function of the proteins.
B-pleated sheet:
Example: Met-Thr-Ser-Val-Asp-Lys
SECONDARY STRUCTURE: Localized
conformation of the chain.
Proteins starts to twists within the main chain
in accordance with chemical forces.
The amine groups’ hydrogen and the carboxyl
Antiparallel- amino-terminal of the strand
groups’ oxygen form hydrogen bonds that
positioned next to the carboxyl-terminal of the
stabilize the secondary structure.
other strand.
Parallel- N- and C- strand positioned in the
Hydrogen Bonds Are Formed Whenever same direction
Possible
TERTIARY STRUCTURE: Complete
a-helix (alpha-helix) - polypeptide backbone folding pattern.
is wound tightly around an imaginary axis
drawn longitudinally through the center of the Interaction through Hydrogen bonding, ionic
helix, and the side chain of amino acid bonding, dipole-dipole interactions and
residue protrudes outward from the helical London-dispersion forces contribute to
backbone. tertiary structure.
B-pleated sheet (beta-pleated sheet)-
polypeptide chain backbone is extended into a The overall 3-D conformational arrangement
zigzag structure. There are two forms of B- of all atoms in protein is due to the
pleated sheet structure, the parallel and interactions between the amino acid side
antiparallel. chains (r-group)
REFERENCES: Garrett, R., & Grisham, C. M. (2008). Biochemistry (4th ed.) Australia: brooks/Cole, Cengage Learning
Nelson, D. L., Cox, M. M., & Lehninger, A. L. (2008). Lehninger principles of biochemistry (5th ed.) NewYork
BIOCHEM REVIEWER
Tertiary structure: Keep in mind: In quaternary structure,
subunits are not covalently bound, instead,
they make only electrostatic interactions.
SUMMARY OF PROTEIN STRUCTURE:
Additionally, much stronger linkages
between sulfur-containing R groups of
cysteine referred to as disulfide bonds also
contribute to tertiary structure keeping the
polypeptide firmly attached to one another.
Disulfide bond (Cys-Cys):
Protein denaturation and Folding
Denaturation refers to the loss of the 3D
QUATERNARY STRUCTURE- structure of a protein enough to lose its
Interactions of subunits function.
Proteins comprise two or multiple separate
Most proteins are denatured by heat, chemical
polypeptides chains known as subunits. The
reagents like acid base (extreme pH), organic
arrangement of these subunits when joined
solvents, detergents and other denaturing
together comprise the quaternary structure.
solvents.
High level of structural proteins is classified
into two major groups: FIBRIOUS and Denature process for some proteins can be
GLOBULAR reversed where primary structure is still intact
and may be re-folded into its functional form
once returned to its normal environment.
REFERENCES: Garrett, R., & Grisham, C. M. (2008). Biochemistry (4th ed.) Australia: brooks/Cole, Cengage Learning
Nelson, D. L., Cox, M. M., & Lehninger, A. L. (2008). Lehninger principles of biochemistry (5th ed.) NewYork
BIOCHEM REVIEWER
What Are the Many Biological THINGS YOU SHOULD
Functions of Proteins? REMEMBER:
1. Structure - many proteins are used as
supporting filaments, wires or sheets to offer Amino acids are building blocks of proteins
biological structures stability or protection.
Amino acids have four functional groups;
2. Catalysis - Catalytic activity in almost all Amino, Carboxyl, R group and H atom
chemical reactions in the body is the function of
Amino acids are asymmetric or chiral except for
Enzymes.
glycine
3. Movement - protein constitutes a big protein of
There are 20 major amino acids that are needed
muscle fiber and helps move components of our
to make up protein
bodies.
Proteins are synthesized through the process of
4. Transport - these proteins make it possible to
translation
move substances to their destinations
Amino acids are covalently joined together by
5. Hormones- these proteins help regulate cell
peptide bonds
growth
Proteins have four levels of structure which is
6. Protection - proteins involved in the immune
crucial for proper protein function
system, which helps defend the body from foreign
invasion, thus, protecting the body from injury.
Proteins have many functions: structure,
catalysis, movement, transport, storage,
7. Storage- these proteins help store other
regulation, protection, hormone and more
substances in the organism. An example of
storage protein includes ovalbumin (a component
of protein of egg white) and ferritin (stored iron).
8. Regulation- these proteins mediate cellular and
physiologic activities.
Protein Biosynthesis
Protein biosynthesis is achieved through the
translation process which takes place in five
stages:
1. Activation of amino acid
2. Initiation
3. Elongation
4. Termination of Ribosome recycling
5. Folding and posttranslational processing
Guys, watch niyo nalang protein biosynthesis sa YT para d
kayo mahirapan iimagine hahaha.
The purpose of translation is to produce
specific protein by putting together specific
amino acids.
REFERENCES: Garrett, R., & Grisham, C. M. (2008). Biochemistry (4th ed.) Australia: brooks/Cole, Cengage Learning
Nelson, D. L., Cox, M. M., & Lehninger, A. L. (2008). Lehninger principles of biochemistry (5th ed.) NewYork
