Asam Amino dan Protein

Protein

Molekul yg sangat vital untuk

organisme terdapt di semua sel
Polimer disusun oleh 20 mcm
asam amino standar
Rantai asam amino dihubungkan dg
iktn kovalen yg spesifik
Struktur & fungsi ditentukan oleh
kombinasi, jumlah dan urutan asam
amino
Sifat fisik dan kimiawi dipengaruhi
oleh asam amino penyusunnya

Fungsi Protein

Reaksi kimia enzymes

Immune system antibodies
Mechanical structure tendons
Generation of force muscles
Nerve conduction ion channels
Vision eye lens
Pengatur pertumbuhan dan diferensiasi
Transport dan penyimpanan
. . . and much more!

Asam Amino

merupakan unit penyusun

protein
Struktur:
satu atom C sentral yang
mengikat secara kovalent:
gugus amino,
gugus karboksil,
satu atom H dan
rantai samping (gugus R)

 Gugus R rantai samping yang berbeda-beda pada

setiap jenis asam amino
Gugus R yang berbeda-beda tersebut menentukan:
-. Struktur
-. Ukuran
-. Muatan elektrik
-. Sifat kelarutan di dalam air
-. Siafat-sifat lain

Asam amino standar

Asam amino yang menyusun

protein organisme ada 20 macam
disebut sebagai asam amino
standar
Diketahui asam amino ke 21
disebut selenosistein (jarang
ditemukan) Terdapat di beberapa
enzim seperti gluthatione
peroxidase
Selenenosistein mempy kode
genetik: UGA biasa utk stop
kodon tjd pd mRNA dgn
struktur 2nd yg banyak.

Klasifikasi Asam amino

Diklasifikasikan berdasar gugus R (rantai samping)

Biasanya sifat-sifat seperti: hidrofobik/hidrofilik, polar/non
polar, ada/tidaknya gugus terionisasi

AROMATIK
NON
POLAR

Asam amino

BASIC (+)

ACIDIC (-)

POLAR

Asam amino non polar

Memiliki gugus R alifatik

Glisin, alanin, valin, leusin, isoleusin dan prolin
Bersifat hidrofobik. Semakin hidrofobik suatu a.a spt
Ile (I) biasa terdapat di bagian dlm protein.
Prolin berbeda dgn a.a siklis. Tapi mempunyai
byk kesamaan sifat dgn kelompok alifatis ini.
Umum terdapat pada protein yang berinteraksi
dengan lipid

Asam amino polar

Memiliki gugus R yang tidak bermuatan

Serin , threonin, sistein, metionin, asparagin,
glutamin
Bersifat hidrofilik mudah larut dalam air
Cenderung terdapat di bagian luar protein
Sistein berbeda dgn yg lain, karena ggs R terionisasi
pada pH tinggi (pH = 8.3) sehingga dapat
mengalami oksidasi dengan sistein membentuk
ikatan disulfide
(-S-S-) sistin (tdk tmsk dlm a.a. standar karena
selalu tjd dari 2 buah molekul sistein dan tidak
dikode oleh DNA)

Asam amino dengan gugus R

aromatik

Fenilalanin, tirosin dan triptofan

Bersifat relatif non polar hidrofobik
Fenilalanin bersama dgn V, L & I a.a plg
hidrofobik
Tirosin gugus hidroksil , triptofan cincin indol
Sehingga mampu membentuk ikatan hidrogen
penting untuk menentukan struktur ensim
Asam amino aromatik mampu menyerap sinar UV
280 nm sering digunakan utk menentukan kadar
protein

Asam amino dengan gugus R

bermuatan positif

Lisin, arginin, dan histidin

Mempunyai gugus yg bsft basa pd rantai
sampingnya
Bersifat polar terletak di permukaan protein dapat
mengikat air.
Histidin mempunyai muatan mendekati netral (pd
gugus imidazol) dibanding

lisin gugus amino

arginin gugus guanidino

Krn histidin dpt terionisasi pada pH mendekati pH

fisioligis sering berperan dlm reaksi ensimatis yg
melibatkan pertukaran proton

Asam amino dengan gugus R

bermuatan negatif

Aspartat dan glutamat

Mempunyai gugus karboksil pada rantai
sampingnya bermuatan (-) / acid pada pH 7

Asam amino non standar

Merupakan asam amino

diluar 20 mcm as. Amino
standar
Terjadi karena modifikasi
yang terjadi setelah suatu
asam amino standar
menjadi protein.
Kurang lebih 300 asam
amino non standar
dijumpai pada sel

modifikasi serin yang

mengalami fosforilasi
oleh protein kinase

 modifikasi prolin dlm proses

modifikasi posttranslasi, oleh
prokolagen prolin hidroksilase.
Ditemukan pada kolagen untuk
menstabilkan struktur

Dari modifikasi Glu oleh vit K.

karboksi glutamat mampu
mengikat Ca penting utk
penjendalan darah.
Ditemukan pd protein protombin

 Modifikasi lisin. Terdapat di kolagen dan miosin (protein

kontraksi pd otot) dan berperan untuk sisi terikatnya
polisakarida
Beberapa ditemukan asam amino nonstandar yang tidak
menyusun protein merupakan senyawa antara
metabolisme (biosintesis arginin dan urea)

Bentuk Zwitterionic dari amino

Dalam kondisi sel normal asam amino
berada dalam bentuk zwitterions (dipolar
ions):
Amino group =

-NH3+

Carboxyl group =

-COO-

Memunculkan sifat amfoter : bisa

berlaku asam atau berlaku sebagai
basa.
pH saat asam amino berupa ion zwitter
= TITIK ISOELEKTRIK (pHI atau pI)

Prentice Hall c2002

Chapter 3

19

AminoAcidChemistry
R

amino

NH2 C

acid

COOH

H
The free amino and carboxylic acid groups have pKas

NH3+

NH2

COOH

pKa ~ 9.4

COO-

pKa ~ 2.2

R
NH3 C

COO-

H
At physiological pH, amino acids are zwitterions

Titration curve for alanine

Titration curves
are used to
determine pKa
values
pK1 = 2.4
pK2 = 9.9
pIAla = isoelectric
point
Prentice Hall c2002

Chapter 3

21

Ionization of Histidine

(a) Titration curve

of histidine
pK1 = 1.8
pK2 = 6.0
pK3 = 9.3

Prentice Hall c2002

Chapter 3

22

Table
3.2
pKa values of
amino acid
ionizable groups

Prentice Hall c2002

Chapter 3

23

Sintesis Protein
DNA: deoxyribonucleic acid
RNA: ribonucleic acid
Transcription

Protein
transportation

Translation
rRNA
tRNA

Transcription

RNA forms base

pairs with DNA

C-G
A-U

Primary transcriptlength of RNA that

results from the
process of
transcription

TRANSCRIPTION
ACGATACCCTGACGAGCGTTAGCTATCG
UGCUAUGGGACU

Translation

Second stage of protein production

mRNA is on a ribosome

Ribosomes

2 subunits, separate in cytoplasm until they

join to begin translation

Large
Small

Contain 3 binding sites

E
P
A

Translation

Second stage of protein production

mRNA is on a ribosome
tRNA brings amino acids to the ribosome

tRNA

Transfer RNA
Bound to one amino
acid on one end
Anticodon on the
other end
complements mRNA
codon

tRNA Function

Amino acids must be in the correct order for

the protein to function correctly
tRNA lines up amino acids using mRNA code

Reading the DNA code

Every 3 DNA bases pairs with 3 mRNA bases

Every group of 3 mRNA bases encodes a
single amino acid
Codon- coding triplet of mRNA bases

How many bases code for

each amino acid?

1 base = 1 amino acid

2 bases = 1 amino acid

41 =

42 =

3 bases = 1 amino acid

43 =

The Genetic Code

ACGATACCCTGACGAGCGTTAGCTATCG
UGCUAUGGGACUG

Asam amino berikatan

dengan asam amino lain
membentuk Protein

 Peptide bond - linkage between amino acids

is a secondary amide bond
Formed by condensation of the -carboxyl of
one amino acid with the -amino of another
amino acid (loss of H2O molecule)
Primary structure - linear sequence of
amino acids in a polypeptide or protein
Prentice Hall c2002

Chapter 3

37

Peptide bond between

two amino acids

Prentice Hall c2002

Chapter 3

38

Planar peptide groups in a

polypeptide chain
Rotation around C-N bond is restricted due to the
double-bond nature of the resonance hybrid form
Peptide groups (blue planes) are therefore planar

Prentice Hall c2002

Chapter 3

39

Fig. 4.7 Trans and cis

conformations
of a peptide group

Nearly all peptide groups in proteins are

in the trans conformation

Prentice Hall c2002

Chapter 3

40

4.1 There Are Four Levels of Protein

Structure
Primary structure - amino acid linear sequence
Secondary structure - regions of regularly
repeating conformations of the peptide chain, such
as -helices and -sheets
Tertiary structure - describes the shape of the fully
folded polypeptide chain
Quaternary structure - arrangement of two or
more polypeptide chains into multisubunit molecule
Prentice Hall c2002

Chapter 3

41

Levels of Structure in Protein

Primary: A description of all covalent bonds. The

sequence of AA residues
Secondary: particularly stable arrangements of AA
giving rise to recurring structural patterns.
Tertiary: All aspects of the 3D folding of a polypeptide.
Quaternary: The spatial arrangement of multisubunits
protein

Fig. 4.10
The helix

Prentice Hall c2002

Chapter 3

43

Fig. 4.11 Stereo view of right-handed

helix
All side chains project outward from helix axis

Prentice Hall c2002

Chapter 3

44

Fig. 4.13 Horse liver alcohol

dehydrogenase
Amphipathic
helix (blue ribbon)
Hydrophobic
residues (blue)
directed inward,
hydrophilic (red)
outward

Prentice Hall c2002

Chapter 3

45

Fig 4.15 -Sheets (a) parallel, (b)

antiparallel

Prentice Hall c2002

Chapter 3

46

Fig. 4.19
Common
motifs

Prentice Hall c2002

Chapter 3

47

Fig. 4.23
Common
domain folds

Prentice Hall c2002

Chapter 3

48

4.8 Quaternary Structure

Refers to the organization of subunits in a

protein with multiple subunits (an oligomer)
Subunits (may be identical or different) have a
defined stoichiometry and arrangement
Subunits are held together by many weak,
noncovalent interactions (hydrophobic,
electrostatic, van der Waals)
Prentice Hall c2002

Chapter 3

49

Fig 4.25 Quaternary structure of

multidomain proteins

Prentice Hall c2002

Chapter 3

50

Fig. 4.42 Hemoglobin tetramer

(a) Human oxyhemoglobin (b) Tetramer schematic

Prentice Hall c2002

Chapter 3

51

Proline has a nitrogen in the

aliphatic ring system
Proline (Pro, P) - has a three
carbon side chain bonded to
the -amino nitrogen
The heterocyclic pyrrolidine
ring restricts the geometry of
polypeptides (collagen)

Prentice Hall c2002

Chapter 3

53

Learning Check P3
Identify the level of protein structure
1. Primary2. Secondary
3.
Tertiary
4. Quaternary
A.
B.
C.
D.
E.

Beta pleated sheet

Order of amino acids in a protein
A protein with two or more peptide chains
The shape of a globular protein
Disulfide bonds between R groups
55

Solution P3
Identify the level of protein structure
1. Primary
2. Secondary
3. Tertiary
4. Quaternary
2 Beta pleated sheet
B.
1 Order of amino acids in a protein
C.
4 A protein with two or more peptide
chains
D. 3 The shape of a globular protein
E. 3 Disulfide bonds between R groups
A.

56

Protein Hydrolysis

Break down of peptide bonds

Requires acid or base, water and
heat or proteolytic enzyme
Gives smaller peptides and
amino acids
Similar to digestion of proteins
using enzymes
Occurs in cells to provide amino
acids to synthesize other
proteins and tissues
57

Hydrolysis of a Dipeptide
OH
CH3 O

CH 2 O

H2O, H
+
H3N CH C N CH C OH
heat
H

OH
CH 2 O

CH3 O

+
H3N CH COH

+
H3N CH C OH
58

Denaturation
Disruption of secondary, tertiary and quaternary protein structure by
heat/organics
Break apart H bonds and disrupt hydrophobic attractions
acids/ bases
Break H bonds between polar R groups and
ionic bonds
heavy metal ions
React with S-S bonds to form solids
agitation
Stretches chains until bonds break

59

Applications of
Denaturation

Hard boiling an egg

Wiping the skin with alcohol swab for
injection
Cooking food to destroy E. coli.
Heat used to cauterize blood vessels
Autoclave sterilizes instruments
Milk is heated to make yogurt

60