1. UNIVERSITAS BRAWIJAYA Prof. Dr.sc.agr. Ir. Suyadi, MS.
PROTEIN
Elements: C, H, O, N, (S, P)
Kuliah ke-4 BIOKIMIA
FAKULTAS PETERNAKAN
UNIVERSITAS BRAWIJAYA
Prof. Dr.sc.agr. Ir. Suyadi, MS.

2. 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.

3. 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.

4. Gugus amino dan karboksil

5. Gugus asam amino

7. Figure : Peptide bond linking two amino acids

8. Jenis Protein: Primer, sekunder, tertier, Quarter

9. 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.

10. 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.

11. Macam asam amino

12. 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.

13. 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

14. Amino acid: Basic unit of protein
COO-
NH3+ C R H
Different side chains, R, determin the properties of 20 amino acids.
Amino group
Carboxylic acid group
An amino acid

15. White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic
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)
Asparatic acid (D)
Glutamic acid (E)
Lysine (K)
Arginine (R)
Histidine (H)
White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

16. Proteins are linear polymers of amino acids
NH3＋ C
COOー ＋
NH3＋ C
COOー ＋ H H
A carboxylic acid condenses with an amino group with the release of a water
H2O
H2O R1 R2 R3
NH3＋ C CO NH C CO NH C CO H
Peptide bond H
Peptide bond H
The amino acid sequence is called as primary structure F T D A G S K A N G S

17. Amino acid sequence is encoded by DNA base sequence in a gene
DNA molecule
DNA base sequence ・ C G A T ＝

18. Amino acid sequence is encoded by DNA base sequence in a gene
Second letter T C A G
First letter
TTT
Phe
TCT
Ser
TAT
Tyr
TGT
Cys
Third letter
TTC
TCC
TAC
TGC
TTA
Leu
TCA
TAA
Stop
TGA
TTG
TCG
TAG
TGG
Trp
CTT
CCT
Pro
CAT
His
CGT
Arg
CTC
CCC
CAC
CGC
CTA
CCA
CAA
Gln
CGA
CTG
CCG
CAG
CGG
ATT
Ile
ACT
Thr
AAT
Asn
AGT
ATC
ACC
AAC
AGC
ATA
ACA
AAA
Lys
AGA
ATG
Met
ACG
AAG
AGG
GTT
Val
GCT
Ala
GAT
Asp
GGT
Gly
GTC
GCC
GAC
GGC
GTA
GCA
GAA
Glu
GGA
GTG
GCG
GAG
GGG

19. Gene is protein’s blueprint, genome is life’s blueprint
DNA
Genome
Gene
Gene
Protein
Protein

20. Gene is protein’s blueprint, genome is life’s blueprint
Glycolysis network
Genome
Gene
Protein

21. 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!

22. Each Protein has a unique structure
Amino acid sequence
NLKTEWPELVGKSVEEAKKVILQDKPEAQIIVLPVGTIVTMEYRIDRVRLFVDKLDNIAEVPRVG
Folding!

23. Basic structural units of proteins: Secondary structure
α-helix
β-sheet
Secondary structures, α-helix and β-sheet, have regular hydrogen-bonding patterns.

24. Three-dimensional structure of proteins
Tertiary structure
Quaternary structure

25. 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）

26. Close relationship between protein structure and its function
Example of enzyme reaction
Hormone receptor
Antibody
substrates A
enzyme
enzyme B
Matching the shape to A
Digestion of A!
enzyme A
Binding to A

27. Protein structure prediction has remained elusive over half a century
“Can we predict a protein structure from its amino acid sequence?”
Now, impossible!

28. 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.

29. Contoh struktur protein
Skin fibroin

30. Next, we find a tertiary structure to proteins
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

31. Contoh struktur protein
Psoriasin

32. At the last, we see the quaternary structure of proteins
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.

33. Contoh struktur protein
Hemoglobin

34. PENJELASAN STRUKTUR DAN FUNGSI PROTEIN

35. Protein Function in Cell
Enzymes
Catalyze biological reactions
Structural role
Cell wall
Cell membrane
Cytoplasm

36. Protein Structure

37. Protein Structure

38. Model Molecule: Hemoglobin

39. Hemoglobin: Background
Protein in red blood cells

40. 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

41. Heme Groups in Hemoglobin

42. 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)

43. Hemoglobin – Quaternary Structure
Two alpha subunits and two beta subunits
(141 AA per alpha, 146 AA per beta)

44. Hemoglobin – Tertiary Structure
One beta subunit (8 alpha helices)

45. Hemoglobin – Secondary Structure
alpha helix

46. Structure Stabilizing Interactions
Noncovalent
Van der Waals forces (transient, weak electrical attraction of one atom for another)
Hydrophobic (clustering of nonpolar groups)
Hydrogen bonding

47. Hydrogen Bonding D – H A 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

48. 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 A δ- δ+

49. D-H Interaction D – H A δ- δ+
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 A δ- δ+

50. And Secondary Structure
Hydrogen Bonding
And Secondary Structure
alpha-helix
beta-sheet

51. 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

52. Disulfide Bonds
Side chain of cysteine contains highly reactive thiol group
Two thiol groups form a disulfide bond

53. Disulfide Bridge

54. 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 

55. Disulfide Bridge – Linking Distant Amino Acids

56. 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

57. Protein Structure - Primary
Protein: chain of amino acids joined by peptide bonds

58. 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)

59. General Amino Acid StructureH
H2N Cα
COOH R

60. General Amino Acid Structure
At pH 7.0 H
+H3N Cα
COO- R

61. General Amino Acid Structure

62. Amino Acids
Chiral

63. Chirality: Glyceraldehyde
D-glyderaldehyde
L-glyderaldehyde

64. Amino Acids
Chiral
20 naturally occuring; distinguishing side chain

65. 20 Naturally-occurring Amino Acids

66. Amino Acids Chiral 20 naturally occuring; distinguishing side chain
Classification:
Non-polar (hydrophobic)
Charged polar
Uncharged polar

67. Alanine:
Nonpolar

68. Serine:
Uncharged Polar

69. Aspartic Acid Charged Polar

70. Glycine Nonpolar (special case)

71. Peptide Bond
Joins amino acids

72. Peptide Bond Formation

73. Peptide Chain

74. Peptide Bond Joins amino acids 40% double bond character
Caused by resonance

76. Peptide bond Joins amino acids 40% double bond character
Caused by resonance
Results in shorter bond length

77. Peptide Bond Lengths

78. Peptide bond Joins amino acids 40% double bond character
Caused by resonance
Results in shorter bond length
Double bond disallows rotation

79. Protein Conformation Framework
Bond rotation determines protein folding, 3D structure

80. Bond Rotation Determines Protein Folding

81. 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

83. 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

84. Ethane Rotation A A D D B B C C

85. 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

86. Backbone Torsion Angles

87. Backbone Torsion Angles
Dihedral angle ω : rotation about the peptide bond, namely Cα1-{C-N}- Cα2

88. Backbone Torsion Angles

89. 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

90. Backbone Torsion Angles

91. 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

92. Backbone Torsion Angles

93. 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

95. 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

96. Backbone Torsion Angles

97. 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

98. 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

99. 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

100. Sequence Similarity
Sequence similarity implies structural, functional, and evolutionary commonality

101. Homologous Proteins: Enterotoxin and Cholera toxin
80% homology

102. Sequence Similarity
Sequence similarity implies structural, functional, and evolutionary commonality
Low sequence similarity implies little structural similarity

103. Nonhomologous Proteins: Cytochrome and Barstar
Less than 20% homology

104. 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!

105. Sequence Similarity Exception
Sickle-cell anemia resulting from one residue change in hemoglobin protein
Replace highly polar (hydrophilic) glutamate with nonpolar (hydrophobic) valine

106. Sickle-cell mutation in hemoglobin sequence

107. 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

108. Sickle-cell Trait
Oxy-hemoglobin is isolated, but de-oxyhemoglobin sticks together in polymers, distorting RBC
Some cells take on “sickle” shape

109. Sickle-cell

110. 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

111. Hemoglobin Polymerization
Normal
Mutant

112. 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

113. Capillary Blockage

114. 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

115. Protein: The Machinery of Life
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-…..
“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

116. TUGAS
Menyusun Paper secara berkelompok tentang: PROTEIN – STRUKTUR DAN FUNGSI
Membuat materi presentasi ppt sebagai bahan diskusi kelompok minggu berikutnya
Paper dikumpulkan ke dosen paling lambat 2 mgg dari sekarang dalam bentuk soft copy (file) ke

119. 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.