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PROTEIN
Elements: C, H, O, N, (S, P)
Kuliah ke-4 BIOKIMIA
FAKULTAS PETERNAKAN
UNIVERSITAS BRAWIJAYA
Prof. Dr.sc.agr. Ir. Suyadi, MS.
INTRODUCTION: PROTEIN
• Elements: C, H, O, N, and sometimes S.
• Function: Enzymes, structural proteins,
storage proteins, transport proteins,
hormones, proteins for movement,
protection, and toxins.
Introduction
• The subunits of a protein are amino acids or to
be precise amino acid residues.
• An amino acid consists of:
– a central carbon atom (the alpha Carbon Calpha)
and an amino group (NH2),
– a hydrogen atom (H),
– a carboxy group (COOH) and
– a side chain (R) which are bound to the Calpha.
Gugus amino dan karboksil
Gugus asam amino
Figure : Peptide bond linking two amino acids
Jenis Protein: Primer, sekunder, tertier, Quarter
General Structure
• Proteins are made from several amino acids,
bonded together. It is the arrangement of the
amino acid that forms the primary structure of
proteins. The basic amino acid form has a
carboxyl group on one end, a methyl group
that only has one hydrogen in the middle, and
a amino group on the other end. Attached to
the methyl group is a R group.
General Structure
• Proteins are made from several
amino acids, bonded together. It is
the arrangement of the amino acid
that forms the primary structure of
proteins.
• The basic amino acid form has a
carboxyl group on one end, a
methyl group that only has one
hydrogen in the middle, and a
amino group on the other end.
• Attached to the methyl group is a R
group.
Macam asam amino
General
Structure
There are 20+ amino acids, each differing only in the composition of the R groups. An R
group could be a sulfydrl, another methyl, a string a methyls, rings of carbons, and
several other organic groups. Proteins can be either acidic or basic, hydrophilic or
hydrophobic. The following table shows 20 amino acids that common in proteins.
Proteins play key roles in a living
system
• Three examples of protein functions
Alcohol
dehydrogenase
oxidizes alcohols
to aldehydes or
ketones
– Catalysis:
Almost all chemical reactions in a living
cell are catalyzed by protein enzymes.
– Transport:
Some proteins transports various
substances, such as oxygen, ions, and so
on.
Haemoglobin
carries oxygen
– Information transfer:
For example, hormones.
Insulin controls
the amount of
sugar in the
blood
Amino acid: Basic unit of protein
R
NH3
+
C
Amino group
H
Different side chains,
R, determin the
COO properties of 20
Carboxylic
acid group
amino acids.
An amino acid
20 Amino acids
Glycine (G)
Alanine (A)
Valine (V)
Isoleucine (I)
Leucine (L)
Proline (P)
Methionine (M)
Phenylalanine (F)
Tryptophan (W)
Asparagine (N)
Glutamine (Q)
Serine (S)
Threonine (T)
Tyrosine (Y)
Cysteine (C)
Lysine (K)
Arginine (R)
Histidine (H)
Asparatic acid (D) Glutamic acid (E)
White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic
Proteins are linear polymers of amino
acids
R1
NH3＋
C
R2
COOー
＋
NH3＋
H
H
H 2O
A
R2
R3
C
CO
NH
C
CO
NH
C
H
Peptide
bond
H
Peptide
bond
H
F
G
N
S
T
D
K
G
S
A
＋
A carboxylic acid
condenses with an amino
group with the release of a
water
H 2O
R1
NH3＋
COOー
C
CO
The amino acid
sequence is called as
primary structure
Amino acid sequence is encoded by
DNA base sequence in a gene
DNA
molecule
＝
・
G
C
G
C
T
T
A
A
G
C
G
C
・
・ DNA base
C
G sequence
C
G
A
A
T
T
C
G
C
G
・
Amino acid sequence is encoded by
DNA base sequence in a gene
T
T
A
G
Phe
Leu
Leu
Ile
Met
Val
TCT
TCC
TCA
TCG
CCT
CCC
CCA
CCG
ACT
ACC
ACA
ACG
GCT
GCC
GCA
GCG
Ser
Pro
Thr
Ala
TAT
TAC
TAA
TAG
CAT
CAC
CAA
CAG
AAT
AAC
AAA
AAG
GAT
GAC
GAA
GAG
G
Tyr
Stop
His
Gln
Asn
Lys
Asp
Glu
TGT
TGC
TGA
TGG
CGT
CGC
CGA
CGG
AGT
AGC
AGA
AGG
GGT
GGC
GGA
GGG
Cys
Stop
Trp
Arg
Ser
Arg
Gly
T
C
A
G
T
C
A
G
T
C
A
G
T
C
A
G
Third letter
First letter
C
TTT
TTC
TTA
TTG
CTT
CTC
CTA
CTG
ATT
ATC
ATA
ATG
GTT
GTC
GTA
GTG
C
Second letter
A
Gene is protein’s blueprint, genome is
life’s blueprint
DNA
Genome
Gene
Protein
Gene Gene Gene Gene
Gene
Gene
Gene
Gene
Gene
Gene
Gene Gene Gene
Gene
Protein
Protein
Protein
Protein
Protein Protein
Protein
Protein
Protein
Protein Protein
Protein
Protein
Protein
Gene is protein’s blueprint, genome is
life’s blueprint
Glycolysis network
Genome
Gene Gene Gene Gene
Gene
Gene
Gene
Gene
Gene
Gene
Gene Gene Gene
Gene
Protein
Protein
Protein
Protein
Protein Protein
Protein
Protein
Protein
Protein Protein
Protein
Protein
Protein
In 2003, Human genome sequence
was deciphered!
•
•
•
•
•
Genome is the complete set of genes of a living thing.
In 2003, the human genome sequencing was completed.
The human genome contains about 3 billion base pairs.
The number of genes is estimated to be between 20,000 to 25,000.
The difference between the genome of human and that of
chimpanzee is only 1.23%!
3 billion base pair => 6 G letters
&
1 letter => 1 byte
The whole genome can be recorded in
just 10 CD-ROMs!
Each Protein has a unique structure
Amino acid sequence
NLKTEWPELVGKSVEE
AKKVILQDKPEAQIIVL
PVGTIVTMEYRIDRVR
LFVDKLDNIAEVPRVG
Folding!
Basic structural units of proteins:
Secondary structure
α-helix
β-sheet
Secondary structures, α-helix and βsheet, have regular hydrogen-bonding
patterns.
Three-dimensional structure of
proteins
Tertiary structure
Quaternary structure
Hierarchical nature of protein
structure
Primary structure (Amino acid sequence)
↓
Secondary structure （α-helix, β-sheet）
↓
Tertiary structure （Three-dimensional structure
formed by assembly of secondary structures）
↓
Quaternary structure （Structure formed by more than
one polypeptide chains）
Close relationship between protein
structure and its function
Example of enzyme reaction
substrates
enzyme
A
enzyme
B
Matching
the shape
to A
enzyme
A
Binding to A
Digestion
of A!
Hormone receptor
Antibody
Protein structure prediction has remained
elusive over half a century
“Can we predict a protein structure from
its amino acid sequence?”
Now, impossible!
Protein Classification
• Proteins can be described as having several layers of structure. At the
lowest level, the primary structure of proteins are nothing more that the
amino acids which compose the protein, and how those proteins are
bonded to each other. The bonds between proteins are called peptide
bonds, and they can have either single bonds, double bonds, triple bonds,
or more holding the amino acids into a protein molecule.
• At the next level, the secondary structure of proteins, proteins show a
definite geometric pattern. One pattern that the protein can take is a
helical structure, similar to a spiral staircase. Hair has such a secondary
structure. When examined closely, you can see the turns in the proteins of
hair molecules. A second geometric pattern is the pleated sheet, where
several polypeptide chains go in several different directions. I think of a
sheet of paper, or a length of fabric. When viewed closely, silk fibronin, the
silk protein, forms such a shape. Skin, although made of more than just
proteins, provides another example of a protein with a sheet structure.
The following figure shows the pleated sheet secondary structure of silk.
Contoh struktur protein
• Skin fibroin
• Next, we find a tertiary structure to proteins.
Here, we find the three-dimensional structure of
the globular proteins, where disulfide bridges
puts kinks and bends in the secondary structure.
Again thinking about hair, some people have
straight hair, some have wavy hair, and some
have curly hair. The links and bends in the
secondary structure causes the curls in hair. Curly
hair has more kinks and bends that wavy hair,
and straight hair has very few, if any bends
Contoh struktur protein
• Psoriasin
• At the last, we see the quaternary structure of
proteins. This the the form taken by complex
proteins formed from two or more smaller,
polypeptide chains. The polypeptide chains
form pieces of a jigsaw puzzle, that when put
together form a single protein. Hemoglobin
provides a good example, being made from
four polypeptide chains.
Contoh struktur protein
• Hemoglobin
PENJELASAN STRUKTUR DAN
FUNGSI PROTEIN
Protein Function in Cell
1. Enzymes
•
Catalyze biological reactions
2. Structural role
•
•
•
Cell wall
Cell membrane
Cytoplasm
Protein Structure
Protein Structure
Model Molecule: Hemoglobin
Hemoglobin: Background
• Protein in red blood cells
Hemoglobin: Background
• Protein in red blood cells
• Composed of four subunits, each
containing a heme group: a ringlike structure with a central iron
atom that binds oxygen
Red blood cell
Heme Groups in Hemoglobin
Hemoglobin: Background
• Protein in red blood cells
• Composed of four subunits, each
containing a heme group: a ring-like
structure with a central iron atom that
binds oxygen
• Picks up oxygen in lungs, releases it in
peripheral tissues (e.g. muscles)
Hemoglobin – Quaternary Structure
Two alpha subunits and two beta subunits
(141 AA per alpha, 146 AA per beta)
Hemoglobin – Tertiary Structure
One beta subunit (8 alpha helices)
Hemoglobin – Secondary Structure
alpha helix
Structure Stabilizing Interactions
• Noncovalent
– Van der Waals forces (transient, weak electrical
attraction of one atom for another)
– Hydrophobic (clustering of nonpolar groups)
– Hydrogen bonding
Hydrogen Bonding
• Involves three atoms:
– Donor electronegative atom (D)
(Nitrogen or Oxygen in proteins)
– Hydrogen bound to donor (H)
– Acceptor electronegative atom (A) in close
proximity
D–H
A
D-H Interaction
• Polarization due to electron withdrawal
from the hydrogen to D giving D partial negative
charge and the H a partial positive charge
• Proximity of the Acceptor A causes further charge
separation δ- δ+
δ-
D–H
A
D-H Interaction
• Polarization due to electron withdrawal from the
hydrogen to D giving D partial negative charge
and the H a partial positive charge
• Proximity of the Acceptor A causes further charge
separation
δ-
• Result:
δ+
D–H
δ-
A
– Closer approach of A to H
– Higher interaction energy than a simple van der Waals interaction
Hydrogen Bonding
And Secondary Structure
alpha-helix
beta-sheet
Structure Stabilizing Interactions
• Noncovalent
– Van der Waals forces (transient, weak electrical
attraction of one atom for another)
– Hydrophobic (clustering of nonpolar groups)
– Hydrogen bonding
• Covalent
– Disulfide bonds
Disulfide Bonds
• Side chain of cysteine contains highly reactive
thiol group
• Two thiol groups form a disulfide bond
Disulfide Bridge
Disulfide Bonds
• Side chain of cysteine contains highly reactive
thiol group
• Two thiol groups form a disulfide bond
• Contribute to the stability of the folded state by
linking distant parts of the polypeptide chain
Disulfide Bridge –
Linking Distant Amino Acids
Hemoglobin – Primary Structure
-Val-His-Leu-Thr-Pro-Glu-GluLys-Ser-Ala-Val-Thr-Ala-Leu-TrpGly-Lys-Val-Asn-Val-Asp-Glu-ValGly-Gly-Glu-…..
NH2
beta subunit amino acid sequence
Protein Structure - Primary
• Protein: chain of amino acids joined by
peptide bonds
Protein Structure - Primary
• Protein: chain of amino acids joined by
peptide bonds
• Amino Acid
– Central carbon (Cα) attached to:
•
•
•
•
Hydrogen (H)
Amino group (-NH2)
Carboxyl group (-COOH)
Side chain (R)
General Amino Acid Structure
H
H 2N
α
C
R
COOH
General Amino Acid Structure
At pH 7.0
H
+H3N
α
C
R
COO-
General Amino Acid Structure
Amino Acids
• Chiral
Chirality: Glyceraldehyde
D-glyderaldehyde
L-glyderaldehyde
Amino Acids
• Chiral
• 20 naturally occuring; distinguishing side
chain
20 Naturally-occurring Amino Acids
Amino Acids
• Chiral
• 20 naturally occuring; distinguishing side
chain
• Classification:
• Non-polar (hydrophobic)
• Charged polar
• Uncharged polar
Alanine:
Nonpolar
Serine:
Uncharged Polar
Aspartic Acid
Charged Polar
Glycine
Nonpolar (special case)
Peptide Bond
• Joins amino acids
Peptide Bond Formation
Peptide Chain
Peptide Bond
• Joins amino acids
• 40% double bond character
– Caused by resonance
Peptide bond
• Joins amino acids
• 40% double bond character
– Caused by resonance
– Results in shorter bond length
Peptide Bond Lengths
Peptide bond
• Joins amino acids
• 40% double bond character
– Caused by resonance
– Results in shorter bond length
– Double bond disallows rotation
Protein Conformation Framework
• Bond rotation determines protein
folding, 3D structure
Bond Rotation Determines Protein
Folding
Protein Conformation Framework
• Bond rotation determines protein
folding, 3D structure
• Torsion angle (dihedral angle) τ
– Measures orientation of four linked
atoms in a molecule: A, B, C, D
Protein Conformation Framework
• Bond rotation determines protein
folding, 3D structure
• Torsion angle (dihedral angle) τ
– Measures orientation of four linked atoms
in a molecule: A, B, C, D
– τABCD defined as the angle between the
normal to the plane of atoms A-B-C and
normal to the plane of atoms B-C-D
Ethane Rotation
A
D
B
C
A
D
B
C
Protein Conformation Framework
• Bond rotation determines protein
folding, 3D structure
• Torsion angle (dihedral angle) τ
– Measures orientation of four linked atoms
in a molecule: A, B, C, D
– τABCD defined as the angle between the
normal to the plane of atoms A-B-C and
normal to the plane of atoms B-C-D
– Three repeating torsion angles along
protein backbone: ω, φ, ψ
Backbone Torsion Angles
Backbone Torsion Angles
• Dihedral angle ω : rotation about the peptide bond,
namely Cα1-{C-N}- Cα2
Backbone Torsion Angles
Backbone Torsion Angles
• Dihedral angle ω : rotation about the peptide
bond, namely Cα1-{C-N}- Cα2
• Dihedral angle φ : rotation about the bond
between N and Cα
Backbone Torsion Angles
Backbone Torsion Angles
• Dihedral angle ω : rotation about the peptide
bond, namely Cα1-{C-N}- Cα2
• Dihedral angle φ : rotation about the bond
between N and Cα
• Dihedral angle ψ : rotation about the bond
between Cα and the carbonyl carbon
Backbone Torsion Angles
Backbone Torsion Angles
• ω angle tends to be planar (0º - cis, or 180 º - trans)
due to delocalization of carbonyl π electrons and
nitrogen lone pair
Backbone Torsion Angles
• ω angle tends to be planar (0º - cis, or 180 º trans) due to delocalization of carbonyl pi
electrons and nitrogen lone pair
• φ and ψ are flexible, therefore rotation occurs
here
Backbone Torsion Angles
Backbone Torsion Angles
• ω angle tends to be planar (0º - cis, or 180 º trans) due to delocalization of carbonyl pi
electrons and nitrogen lone pair
• φ and ψ are flexible, therefore rotation occurs
here
• However, φ and ψ of a given amino acid residue
are limited due to steric hindrance
Steric Hindrance
• Interference to rotation caused by spatial
arrangement of atoms within molecule
• Atoms cannot overlap
• Atom size defined by van der Waals radii
• Electron clouds repel each other
Backbone Torsion Angles
• ω angle tends to be planar (0º - cis, or 180 º trans) due to delocalization of carbonyl pi
electrons and nitrogen lone pair
• φ and ψ are flexible, therefore rotation occurs
here
• However, φ and ψ of a given amino acid residue
are limited due to steric hindrance
• Only 10% of the {φ, ψ} combinations are generally
observed for proteins
• First noticed by G.N. Ramachandran
Sequence Similarity
• Sequence similarity implies structural,
functional, and evolutionary commonality
Homologous Proteins:
Enterotoxin and Cholera toxin
Enterotoxin
Cholera toxin
80% homology
Sequence Similarity
• Sequence similarity implies structural,
functional, and evolutionary commonality
• Low sequence similarity implies little
structural similarity
Nonhomologous Proteins:
Cytochrome and Barstar
Cytochrome
Barstar
Less than 20% homology
Sequence Similarity
• Sequence similarity implies structural,
functional, and evolutionary commonality
• Low sequence similarity implies little
structural similarity
• Small mutations generally well-tolerated by
native structure – with exceptions!
Sequence Similarity Exception
• Sickle-cell anemia resulting from one residue
change in hemoglobin protein
• Replace highly polar (hydrophilic) glutamate
with nonpolar (hydrophobic) valine
Sickle-cell mutation in hemoglobin
sequence
Normal Trait
• Hemoglobin molecules exist as single,
isolated units in RBC, whether oxygen
bound or not
• Cells maintain basic disc shape, whether
transporting oxygen or not
Sickle-cell Trait
• Oxy-hemoglobin is isolated, but deoxyhemoglobin sticks together in
polymers, distorting RBC
• Some cells take on “sickle” shape
Sickle-cell
RBC Distortion
• Hydrophobic valine replaces hydrophilic glutamate
• Causes hemoglobin molecules to repel water and be
attracted to one another
• Leads to the formation of long hemoglobin filaments
Hemoglobin Polymerization
Normal
Mutant
RBC Distortion
• Hydrophobic valine replaces hydrophilic glutamate
• Causes hemoglobin molecules to repel water and be
attracted to one another
• Leads to the formation of long hemoglobin filaments
• Filaments distort the shape of red blood cells
(analogy: icicle in a water balloon)
• Rigid structure of sickle cells blocks capillaries and
prevents red blood cells from delivering oxygen
Capillary Blockage
Sickle-cell Trait
• Oxy-hemoglobin is isolated, but deoxyhemoglobin sticks together in
polymers, distorting RBC
• Some cells take on “sickle” shape
• When hemoglobin again binds oxygen,
again becomes isolated
• Cyclic alteration damages hemoglobin
and ultimately RBC itself
Protein: The Machinery of Life
NH2-Val-His-Leu-Thr-Pro-Glu-GluLys-Ser-Ala-Val-Thr-Ala-Leu-TrpGly-Lys-Val-Asn-Val-Asp-Glu-ValGly-Gly-Glu-…..
“Life is the mode of existence of proteins, and this mode
of existence essentially consists in the constant selfrenewal of the chemical constituents of these
substances.”
Friedrich Engles, 1878
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• The subunits of a protein are amino acids or to
be precise amino acid residues.
• An amino acid consists of:
• a central carbon atom (the alpha Carbon
Calpha) and an amino group (NH2),
• a hydrogen atom (H),
• a carboxy group (COOH) and
• a side chain (R) which are bound to the Calpha.