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PROTEIN
Kuliah ke-4 BIOKIMIAFAKULTAS PETERNAKAN UNIVERSITAS BRAWIJAYA
Prof. Dr.sc.agr. Ir. Suyadi, MS.
Elements: C, H, O, N, (S, P)
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
– 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.
– Information transfer:For example, hormones.
Alcohol dehydrogenase oxidizes alcohols to aldehydes or ketones
Haemoglobin carries oxygen
Insulin controls the amount of sugar in the blood
Amino acid: Basic unit of protein
COO-NH3+ C
R
HAn amino
acid
Different side chains, R, determin the properties of 20 amino acids.
Amino group Carboxylic acid group
20 Amino acids
Glycine (G)
Glutamic acid (E)Asparatic acid (D)
Methionine (M)
Threonine (T)Serine (S)
Glutamine (Q)
Asparagine (N)
Tryptophan (W)Phenylalanine (F)
Cysteine (C)
Proline (P)
Leucine (L)Isoleucine (I)Valine (V)
Alanine (A)
Histidine (H)Lysine (K)
Tyrosine (Y)
Arginine (R)
White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic
Proteins are linear polymers of amino acids
R1
NH3+ C CO
H
R2
NH C CO
H
R3
NH C CO
H
R2
NH3+ C COO ー
H
+
R1
NH3+ C COO ー
H
+
H2OH2O
Peptide bond
Peptide bond
The amino acid sequence is called
as primary structure A AF
NGG
S TS
DK
A carboxylic acid condenses with an amino group with the release of a water
Amino acid sequence is encoded by DNA base sequence in a gene
・CGCGAATTCGCG・
・GCGCTTAAGCGC・
DNA molecule
=
DNA base sequence
Amino acid sequence is encoded by DNA base sequence in a gene
Second letterT C A G
First letter
T
TTTPhe
TCT
Ser
TATTyr
TGTCys
T
Third letter
TTC TCC TAC TGC CTTA
LeuTCA TAA
StopTGA Stop A
TTG TCG TAG TGG Trp G
C
CTT
Leu
CCT
Pro
CATHis
CGT
Arg
TCTC CCC CAC CGC CCTA CCA CAA
GlnCGA A
CTG CCG CAG CGG G
A
ATTIle
ACT
Thr
AATAsn
AGTSer
TATC ACC AAC AGC CATA ACA AAA
LysAGA
ArgA
ATG Met ACG AAG AGG G
G
GTT
Val
GCT
Ala
GATAsp
GGT
Gly
TGTC GCC GAC GGC CGTA GCA GAA
GluGGA A
GTG GCG GAG GGG G
Gene is protein’s blueprint, genome is life’s blueprint
Gene
GenomeDNA
Protein
Gene GeneGene
Gene
GeneGeneGeneGene
GeneGeneGeneGene
GeneGene
Protein Protein
ProteinProtein
Protein
ProteinProtein
Protein
Protein
Protein
Protein
ProteinProtein
Protein
Gene is protein’s blueprint, genome is life’s blueprint
Genome
Gene GeneGene
Gene
GeneGeneGeneGene
GeneGeneGeneGene
GeneGene
Protein Protein
ProteinProtein
Protein
ProteinProtein
Protein
Protein
Protein
Protein
ProteinProtein
Protein
Glycolysis network
3 billion base pair => 6 G letters &
1 letter => 1 byte
The whole genome can be recorded in just 10 CD-ROMs!
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%!
Each Protein has a unique structure
Amino acid sequence
NLKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAE
VPRVGFolding!
Basic structural units of proteins: Secondary structure
α-helix β-sheet
Secondary structures, α-helix and β-sheet, 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
enzyme
A
B
A
Binding to A
Digestion of A!
enzyme
Matching the shape to A
Hormone receptor AntibodyExample of enzyme reaction
enzyme
substrates
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 ring-like 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
D – H Aδ- δ+ δ-
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
• Result:– Closer approach of A to H– Higher interaction energy than a simple van der Waals interaction
D – H Aδ- δ+ δ-
Hydrogen BondingAnd 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
NH2-Val-His-Leu-Thr-Pro-Glu-Glu-Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp-Gly-Lys-Val-Asn-Val-Asp-Glu-Val-Gly-Gly-Glu-…..
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
Cα
H
R
COOHH2N
General Amino Acid StructureAt pH 7.0
Cα
H
R
COO-+H3N
General Amino Acid Structure
Amino Acids
• Chiral
Chirality: Glyceraldehyde
L-glyderaldehydeD-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 AcidCharged Polar
GlycineNonpolar (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
CB
DA
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
– 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 Cα
1-{C-N}- Cα2
Backbone Torsion Angles
Backbone Torsion Angles
• Dihedral angle ω : rotation about the peptide bond, namely Cα
1-{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 Cα
1-{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 de-oxyhemoglobin 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 de-oxyhemoglobin 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
“Life is the mode of existence of proteins, and this mode of existence essentially consists in the constant self-renewal of the chemical constituents of these substances.”
Friedrich Engles, 1878
NH2-Val-His-Leu-Thr-Pro-Glu-Glu-Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp-Gly-Lys-Val-Asn-Val-Asp-Glu-Val-Gly-Gly-Glu-…..
TUGAS
1. Menyusun Paper secara berkelompok tentang: PROTEIN – STRUKTUR DAN FUNGSI
2. Membuat materi presentasi ppt sebagai bahan diskusi kelompok minggu berikutnya
3. Paper dikumpulkan ke dosen paling lambat 2 mgg dari sekarang dalam bentuk soft copy (file) ke email : suyadi@ub.ac.id
• 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.
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