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Peptides to
Proteins
What are PROTEINS?
Proteins are large, complex molecules
that serve diverse functional and
structural roles within cells.
Proteins are the ACTION FORCE
in the cell.
Enzyme
Defense
Protease
Antibody
Fights
Viruses
Degrades
Protein
Proteins can be functionally classified.
Motion
Actin
Transpor
t
Hemoglobin
Contracts Muscle Fibers
Carries O2
Regulation
Insulin
Controls Blood Glucose
Support
Keratin
Forms Hair
and Nails
Proteins are chains of amino acids.
O
C
OH
N
H
H
Short chains of amino acids are called
peptides.
Proteins are polypeptide molecules that
contain many peptide subunits.
N
H
H
Amino acids have an amino group,
carboxyl group, R group and hydrogen.
R
NH2
C
H
Amino Acid 1
COOH
Each amino acid has unique chemical
properties.
Glycine
Histidine
Glutamine
Glutamate
Lysine
Cysteine
Aspartate
Asparagine
Arginine
Isoleucine
Methionine
Serine
Leucine
Proline
Alanine
Threonine
Tryptophan
Phenylalanine
Valine
Tyrosine
Peptide bonds form by
dehydration synthesis
R
R
NH2
C
H
Amino Acid 1
H N
C
O
OH
H
C
COOH
H
Amino Acid 2
H2O
R
R
C
COOH
NH2
C
H
Amino Acid 1
H
Amino Acid 2
Peptide bond
 A protein is a linear sequence of amino acids
linked together by peptide bonds. The peptide bond
is a covalent bond between the -amino group of one
amino acid and the -carboxyl group of another.
 The peptide bond has partial double bond
character and is nearly always in the trans
configuration.
 The backbone conformation of a polypeptide is
specified by the rotation angles about the Cα–N
bond (phi, φ) and Cα–C bond (psi, ψ) of each of its
amino acid residues.
The sterically allowed values of φ and ψ
are visualized in a Ramachandran plot.
When two amino acids are joined by a
peptide bond they form a dipeptide.
Addition of further amino acids results in
long chains called oligopeptides and
polypeptides.
Gene
3’
Nucleus
Messenger
Ribonucleic Acid
(mRNA)
Trp
tRNA
Ala
tRNA
Met
Met
Large
Subunit
Ribosome
Met
5’
Amino Acidtransfer
RNA
tRNA
Ala
Empty tRNA
Trp
Empty tRNA
A
U
G
G
C
C
U
G
G
U
A
G
Small Subunit
Cytoplasm
Ribonucleotides
Codon 1
A
U
G = Methionine
Codon 3
U
G
G = Tryptophan
Codon 2
G
C
C
Codon 4
U
A
G = Stop
= Alanine
A
G
C
U
is the synthesis of proteins in the cell.
Primary
There are 4 basic
Secondary
Tertiar
y
Quaternary
L
V
M
H
G
I
Q
Y
P
S
E
C
K
T
F
The primary structure is the
sequence of amino acids.
N
R
A
P
D
Primary structure
• The linear sequence of amino acids
joined together by peptide bonds is termed
as the primary structure of the protein.
• The position of covalent disulfide bonds
between cysteine residues is also included
in the primary structure.
The secondary structure is primarily composed of
alpha helices and beta-pleated sheets.
Folding Back and
Coiling
Alpha Helix
Primary Structure
Beta-Pleated Sheet
Secondary structure
• Secondary structure in a protein refers to the regular
folding of regions of the polypeptide chain.
• The two most common types of secondary structure
are the -helix and the -pleated sheet.
• The -helix is a cylindrical, rod-like helical
arrangement of the amino acids in the polypeptide
chain which is maintained by hydrogen bonds
parallel to the helix axis.
• In a -pleated sheet, hydrogen bonds form
between adjacent sections of polypeptides
that are either running in the same
direction (parallel -pleated sheet) or in the
opposite direction (antiparallel -pleated
sheet).
• Turns reverse the direction of the
polypeptide chain and are often found
connecting the ends of antiparallel pleated sheets.
The tertiary structure is the protein’s 3D
shape.
Tertiary structure
•Tertiary structure in a protein refers to the
three-dimensional arrangement of all the
amino acids in the polypeptide chain.
•This biologically active, native
conformation is maintained by multiple
noncovalent bonds.
The quaternary structure is the assembly
of folded subunits.
Quaternary structure
• If a protein is made up of more than one
polypeptide chain it is said to have
quaternary structure.
• This refers to the spatial arrangement of
the polypeptide subunits and the nature of
the interactions between them.
Summary
• Proteins are biological workhorses that
carry out most of the functions within
the cell.
• Proteins are large biological molecules
that serve diverse functional and
structural roles within cells.
• Proteins are synthesized during the
translation process.
Summary cont’d…
• Proteins are composed of amino acids
that are covalently linked by peptide
bonds.
• Proteins have four basic levels of
structure. However, proteins must fold
correctly in order to function properly.
The four levels of structure in proteins. (a) Primary
structure (amino acid sequence),
(b) secondary structure (-helix), (c) tertiary
structure, (d) quaternary structure