Protein

Adelya Desi Kurniawati, STP., MP., M.Sc.

Tujuan Pembelajaran
1. Mahasiswa memahami terkait protein dan
fungsinya
2. Mahasiswa memahami terkait asam amino dan
struktur dasarnya
3. Mahasiswa memahami struktur protein
4. Mahasiswa memahami terkait denaturasi
protein
Proteins play key roles in a
living system
Alcohol
dehydrogenase
Three examples of protein oxidizes alcohols
to aldehydes or
functions ketones

Catalysis:
Almost all chemical reactions in a living
cell are catalyzed by protein enzymes. Haemoglobin
carries oxygen
Transport:
Some proteins transports various
substances, such as oxygen, ions, and
so on. Insulin controls
the amount of
Information transfer: sugar in the
blood
For example, hormones.
Amino acid:
Basic unit of protein
Carboxylic
COO- acid group

NH3+ C H
Amino group
Different side chains, R,
R determine the properties
An amino acid of 20 amino acids.
Amino acid: Gugus karboksilat

COO-

Cα
Amino acid: Gugus karboksilat

COO-
+NH
3 Cα

Amino
Amino acid: Gugus karboksilat

COO-
+NH
3 C H
α

Atom Hidrogen

Amino
Amino acid: Gugus karboksilat

COO-
+NH
3 C H
α

Atom Hidrogen

Amino
R
Side chain
CHIRAL (rantai samping)
Zwitterionic form of amino acids

- Carboxyl
COO group
+NH
3 C Hα
Amino
group
R
• Under normal cellular conditions amino acids are
zwitterions (dipolar ions):
 - Carboxyl
COO group
+NH
3 C Hα
Amino
group
R
• Under normal cellular conditions amino acids are
zwitterions (dipolar ions):
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
R
Amino Acid
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
H
Amino Acid
Glycine / Gly, G
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
CH3

Amino Acid
Alanine / Ala, A
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
CH
H3C CH3
Amino Acid
Valine / Val, V
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
CH2
CH
Amino Acid
H3C
Leucine / Leu, L CH3
Four aliphatic amino acid
structures
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
H C CH3
CH2
Amino Acid
Isoleucine / Ile, I CH3
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
CH2

Amino Acid
Phenilalanine/ Phe, F
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
CH2

Amino Acid
Tyrosine/ Tyr, Y
OH
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
CH2
CH2
Amino Acid
N
Tryptophan/ Trp, W
H
Aromatic amino acid
structures
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
CH2
SH
Amino Acid
Cysteine/ Cys, C
 - Carboxyl
COO group
+NH
3 C H α
Amino
group
CH2
CH2
Amino Acid
Methionine/ Met, M
S
CH
Methionine and Cystine
Formation of Cystine
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
H C OH
H
Amino Acid
Serine/ Ser, S
 - Carboxyl
COO group
+NH
3 C H
α
Amino
group
H C OH
CH3
Amino Acid
Threonine/ Thr, T
Atom
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

Peptide Linkage
 Proteins are linear
polymers of amino acids
R1 R2
NH3＋ C COO ＋ NH3＋ C COO ＋
ー ー
H H A carboxylic acid
H 2O condenses with an amino
H 2O
group with the release of a
R1 R2 R3 water

NH3＋ C CO NH C CO NH C CO
H Peptide H Peptide H
bond bond
The amino acid
F T D sequence is called as
A G N S K A
G S primary structure
Amino acid sequence is encoded
by DNA base sequence in a gene
DNA ・ ・ DNA base
G C
molecule C G sequence
G C
C G
T A
＝ T
A
A
T
A T
G C
C G
G C
C G
・ ・
Amino acid sequence is encoded
by DNA base sequence in a gene
Second letter
T C A G
TTT TCT TAT TGT T
Phe Tyr Cys
TTC TCC
Ser TAC TGC C
T
TTA Leu TCA TAA TGA Stop A
Stop
TTG TCG TAG TGG Trp G
CTT CCT CAT CGT T
His
CTC CCC CAC CGC C

Third letter
First letter

C Leu Pro Arg

CTA CCA CAA CGA A
Gln
CTG CCG CAG CGG G
ATT ACT AAT AGT T
Asn Ser
ATC Ile ACC AAC AGC C
A Thr
ATA ACA AAA AGA A
Lys Arg
ATG Met ACG AAG AGG G
GTT GCT GAT GGT T
Asp
GTC GCC GAC GGC C
G Val Ala Gly
GTA GCA GAA GGA A
Glu
GTG GCG GAG GGG G
Each Protein has a unique
structure

Amino acid sequence

NLKTEWPELVGKSVEE
AKKVILQDKPEAQIIVL
PVGTIVTMEYRIDRVR
LFVDKLDNIAEVPRVG

Folding!
Protein 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）
Primary structure
Glutamate

Glycine trans
orientation
Cysteine

Valine

Lysine
Secondary structure

Mostly a-helix: Mostly b-sheet:

Myohemerythrin Immunoglobulin, V2 domain
a-Helix
b-Sheet
 Tertiary structure

Four-helix bundle: Antiparallel b-barrel: Parallel b-barrel,

Myohemerythrin Immunoglobulin, V2 a/b:
domain
Pyruvate kinase,
domain 1
Tertiary structure: cofactors
myohemerythrin

cytochrome c
 Cofactors (coenzymes)
S
Cys 3

dx2-y2
1 Cys
S dz2
N N
Fe

N N
5 dxz , dyz
Iron-sulfur cluster 8

dxy

O O
-O -O

heme

Metals: Cu, Zn,

flavin Fe, Mg, Ca, Ni, Co
 Protein folding

Met Glu
Gly

Thr ?
Ser
Lys

Ala folded protein

Gly Phe
Quaternary structure
Structural Interactions in Proteins
Enzymes: Precision Catalysts
Inhibition of an Enzyme

Inhibitor

Allosteric Inhibition Competitive Inhibition

Protein structure prediction has
remained elusive over half a
century
“Can we predict a protein structure
from its amino acid sequence?”

No, impossible!
 Protein Denaturation
Denaturation is a process that changes the molecular structure
without breaking any of the peptide bonds of a protein

Denaturation can be brought about by a variety of agents, of which

the most important are heat, pH, salts, and surface effects.
 Protein Denaturation
• denaturation is nonreversible (mostly); however, there are some
exceptions, such as the recovery of some types of enzyme activity after
heating.

• The temperature
range in which
denaturation and
coagulation of most
proteins take place
is about 55–75 °C
Summary
• Proteins are key players in our living systems.
• Proteins are polymers consisting of 20 kinds of amino
acids.
• Each protein folds into a unique three-dimensional
structure defined by its amino acid sequence.
• Protein structure has a hierarchical nature.
• Protein structure is closely related to its function.
• Protein denaturation changes the molecular structure,
involves loss of biological activity and significant
changes in some physical or functional properties such
as solubility
.
 Spencer L Seager Karen C.
(2018), Timberlake (2019),
Chapter 18 Chapter 16
References and
Reading Material
This Presentation is Prepared by
“Adelya Desi Kurniawati, STP., MP., M.Sc.”