Protein KKNI 2019

Chapter 3
Protein
By Dewi Yuliani
Structure and Function of Biomolecule 1

Outline
• Protein Introduction
• Properties and Structure of amino
acid
• Protein structure

Protein Introduction

Light from the Hemoglobin (Hb) an Skin, horns, nails,

enzyme, Luciferase, oxygen binding hair, claws, and
that uses a chemical protein feathers, all different
reaction to produce forms of keratin, a
light. structural protein.
David L. Nelson & Michael M. Cox, Lehninger Principles of Biochemistry 4th,Ed, Page 76.

♫ Proteins are polymers of amino acids linked together by

what is called “ Peptide bond” (see latter).
♫ There are about 300 amino acids occur in nature. Only

20 of them occur in proteins.
♫ Amino acid polymers of ≤50 amino acids are called

“polypeptides, peptides, oligopeptides, etc.”
♫ Amino acids polymer of >50 amino acids are called

“proteins.”

General Structure of Amino Acid Amino acid
Karp, page 50 Structure and Function of Biomolecule 7

Carbon Numbering System Amino acid

Amino acid
• Alpha (α) are on the

carbon adjacent to the
Carbon Numbering System
carboxyl group.
• Beta (β) on the 2nd

carbon.
• Gama (γ) are on the 3rd

carbon from the
carboxyl group.

Amino acid
mirror
Stereoisomer of the α-amino acid
L-α-amino acid D-α-amino acid

Amino acid
Occurs naturally Mirror Image

Stereoisomer of the α-amino acid
In Fact, …
All of the amino acids incorporated by organism into proteins are
of the L form.

Amino Acid Code Amino acid
Margaret Oakley Dayhoff

(1925-1983)

Amino Acid Code Amino acid

Amino Acid Structure
methionine isoleucine valine leucine glycine alanine
Proline glutamine
phenylalanine tyrosine tryptophan Aspartic acid
asparagine
threonine
lysine arginine histidine Glutamic acid
serine cysteine
+
2
+
3

Amino Acid Form Amino acid
When amino acid is dissolved in water, it is exist in solution as

dipolar ion or zwitterion.
Lehninger, page 81 Structure and Function of Biomolecule 15

Amino acid
At a particular pH, the

Zwitterion Form of Amino Acid
amino acid carries no

net charge and is
called a zwitterion.
pH, at which the

amino acid has a net
charge of zero is
called the isoelectric
point (pI).
Zwitterion can act as

acid and base.

Amino acid
Zwitterion can
act as acid
(donor proton)
Acid Base of Amino Acid
Zwitterion can
act as base
(acceptor
proton)
Lehninger, page 81
Acid Base of Amino Acid Amino acid
Even though both acids and amines are present in the same
molecule, they mostly behave as though they were separate entities

Structure and Function of Biomolecule

19
Titration Curve of Glycine

pI 
2
1
pK1  pK2 
Amino acid
20
David L. Nelson & Michael M. Cox, Lehninger Principles of Biochemistry 4th,Ed, Page 83
Titration Curve of Glycine
pI 
2
1
pK1  pKR   3,22

Amino acid
21
David L. Nelson & Michael M. Cox, Lehninger Principles of Biochemistry 4th,Ed, Page 83
AA Properties
Amino Acid Classification
NON POLAR POLAR
ALIPHATIC AROMATIC CHARGE UNCHARGE
Gly (G) Ser (S)

Phe (F) Thr (T)
Ala (A) Tyr (Y) Cys (C)
Val (V) Trp (W) Asn (N)
Leu (L) Gln (Q)
Ile (I) POSITIVE NEGATIVE
Pro (P) Lys (K) Asp (D)
Met (M) Arg (R) Glu (E)
His (H)
Nonpolar, Aliphatic R Side AA Properties

AA Properties
Nonpolar, Aromatic R Groups
Nonpolar, Aromatic R Side

AA Properties
• Tryptophan and
tyrosine, and to a
much lesser extent
phenylalanine,
absorb ultraviolet
light.
• This accounts for

the characteristic
strong absorbance
of light by most
proteins at a
wavelength of 280
nm.
Image taken from: http://slideplayer.com/slide/4617706/15/images/37/The+ultraviolet+absorption+spectra+of+the+aromatic+amino+acids+at+pH+6.jpg

AA Properties
Polar, uncharged R Groups
Polar, Uncharge R Side
Disulfide bridge
Lodish, page 38

AA Properties
Negatively Charged R Group
Polar, Charge R Side
NEGATIVE POSITIVE

AA Properties
Non Protein Amino Acid
O-phosphoserine
Gamma-carboxyglutamic
acid
4-Hydroxyproline Trogia venenata Zhu L

AA Properties
Application of biochemical engineering process:

CURLING & REBONDING

AA Properties
Peptide Bond Formation
The portion of each

amino acid remaining in
the chain is called an
amino acid residue.

AA Properties
Peptide Bond Characteristic

AA Properties
Image taken from:

http://plantcellbiology.masters.grkraj.org/html/Plant_Cell_Biochemistry_ Image taken from: http://3.bp.blogspot.com/-
And_Metabolism1-Proteins_And_Enzymes_files/image013.gif sV3G_ihcBvw/TdpLKfTqeWI/AAAAAAAAAD0/O
RaILfo47Z8/s1600/figure3.jpg
• Peptide bonds have partial double bond character due to resonance

that limits rotation about this bond.

AA Properties
Image taken from:

http://isite.lps.org/sputnam/AdvancedChem/Ch%2018%20Notes_files/primary_bondangles.jpg
Rotation is allowed in the surrounding of N–C and C–C=O bonds.

Rotation angle in the N–C bond is called  (phi).
Rotation angle in the C–C=O bond is called  (psi).

AA Properties

AA Properties
Atom C Atom H
Atom O R group
Image taken from:
http://oregonstate.edu/instruct/bb450/450material/stryer7/2/figure_02_20.jpg

AA Properties
Atom C
Atom O
Pengecualian untuk urutan X-Pro, dimana X adalah asam
amino lain selain Pro  Konformasi cis lebih disukai. Atom H
Image taken from: R group
http://oregonstate.edu/instruct/bb450/450material/stryer7/2/figure_02_20.jpg

AA Properties
Ramachandran Plot

AA Properties
Ramachandran Plot
Ramachandran Plot showed steric
contour diagram.
For example:
Glisil residue in polipeptida

AA Properties
Ramachandran Plot
Ramachandran Plot, example: Alanil residue in polipeptida
Image taken from: http://oregonstate.edu/instruct/bb450/450material/stryer7/2/figure_02_23.jpg

Protein Definition
• Protein are not just polypeptides.
• Every protein has a defined order of amino acids

residues.
• Level protein structure: primary, secondary, tertiary,

and quaternary.

Protein Sequence
MKGKKWTALALTLPLAASLSTGVDAETVHKGKAPTADKNGVFYEVYVNSFYDA
NKDGHGDLKGLTQKLDYLNDGNSHTKNDLQVNGIWMMPVNPSPSYHKYDVTDY
YNIDPQYGNLQDFRKLMKEADKRDVKVIMDLVVNHTSSEHPWFQAALKDKNSK
YRDYYIWADKNTDLNEKGSWGQQVWHKAPNGEYFYGTFWEGMPDLNYDNPEVR
KEMINVGKFWLKQGVDGFRLDAALHIFKGQTPEGAKKNILWWNEFRDAMKKEN
PNVYLTGEVWDQPEVVAPYYQSLDSLFNFDLAGKIVSSVKAGNDQGIATAAAA
TDELFKSYNPNKIDGIFLTNHDQNRVMSELSGDVNKAKSAASILLTLPGNPYI
YYGEEIGMTGEKPDELIREPFRWYEGNGIGQTSWETPVYNKGGNGVSVEAQTK
QKDSLLNHYREMIRVRQQHEELVKGTLQSISVDSKEVVAYSRTYKGKSISVYH
NISNQPVKVSVAAKGNLIFASEKGAKKVKNQLVIPANRTVLIK

Primary Structure
Primary Structure
Ser-Gly-Tyr-Ala-Leu or SGYAL

Primary Structure
Amino acid
H3N+-- C G D
G I V E
W
I
C P
Y F H A
L
I
A T
N S
I Q Q K
The primary structure of a polypeptide is the specific linear sequence of amino

acids that constitute the chain.

Secondary Structure
Results from hydrogen bond formation between hydrogen of –NH

group of peptide bond and the carbonyl oxygen of another peptide
bond.
According to H-bonding there are two main forms of secondary

structure:
Alpha helix
Beta sheet
Beta Turn

Secondary Structure
Alpha Helix: Bridge Inspiration
Image taken from: http://www.e-architect.co.uk/images/jpgs/singapore/helix_bridge_w100810_cfj1.jpg

Secondary Structure
Alpha Helix: Staircase Inspiration
Image taken from: http://cdn.trendhunterstatic.com/thumbs/stunning- Image taken from; http://s3-eu-west-

spiral-staircases-garvan-medical-institude-helix-stairs.jpeg 1.amazonaws.com/olafureliasson.net/objektimages_final/IMG_MDA100996_1600px.jpg

Secondary Structure
Alpha Helix: Characteristics

It is the most common confirmation.
Tightly packed coiled polypeptide backbone, with extending side chains.
The formation of the α-helix is spontaneous.
It is spaced four residues apart. It is stabilized by H-bonding between

amide hydrogens and carbonyl oxygens of peptide bonds.
This orientation of H-bonding produces a helical coiling of the peptide

backbone such that the R-groups lie on the exterior of the helix and
perpendicular to its axis.

Secondary Structure
3.6 AA
5.4 Å

Secondary Structure
Alpha Helix: Formation
• Some amino acids have high helix forming tendencies. They include
methionine, alanine, leucine, uncharged glutamate, and lysine.
• Others, such as prolin, glycine, and negatively charged aspartate, disfavor its
formation.

Secondary Structure
Alpha Helix: Ramachandran Plot
David L. & Michael Cox. Lehninger, page 122.
Image taken from: http://oregonstate.edu/instruct/bb450/450material/stryer7/2/figure_02_26.jpg

Secondary Structure
Alpha Helix: Keratin in Our Hair

Secondary Structure
Beta Sheet: Structure
0.7 nm
Image taken from:

https://wikispaces.psu.edu/download/t
humbnails/48201939/image-
3.jpg?version=1&modificationDate=125
1298688000&api=v2
The formation can be in parallel or antiparallel configuration.

Secondary Structure
Beta Sheet: Antiparalel Structure
Atom C
Atom O
Atom H
R group
NC

Secondary Structure
Beta Sheet: Paralel Structure
Atom C
Atom O
Atom H
R group

Secondary Structure
Beta Sheet: Ramachandran Plot
Image taken from:

http://oregonstate.edu/instruct/bb4
50/450material/stryer7/2/figure_02
_29.jpg

Secondary Structure
Beta Turn: Formation
♫ Beta turn occur frequently

whenever strands in beta sheets
change the direction.
♫ The 180 turn is accomplished

over four amino acids.
♫ The turn is stabilized by

hydrogen bond from a carbonyl
oxygen to amide proton three
residues down the sequence.
Image taken from:
http://oregonstate.edu/instruct/bb450/450material/s
tryer7/2/figure_02_36.jpg

Secondary Structure

Secondary Structure

Secondary Structure

Tertiary Structure
Struktur yang dibentuk akibat rotasi pada ikatan tunggal disebut

konformasi.
Karena protein memiliki banyak ikatan tunggal, maka banyak

sekali konformasi yang mungkin dibentuk.
One or more polypeptides precisely twisted, folded and coiled

into a molecule of unique shape (conformation).
Tetapi ... Secara termodinamika hanya ada satu konformasi yang

akhirnya akan dibentuk, yaitu native structure.
This conformation is essential for some protein function.

Tertiary Structure
Enzyme enables a protein

to recognize and bind
specifically to another
molecule e.g.
hormone/receptor;
enzyme/substrate and
antibody/antigen.
Image taken from:

https://publications.nigms.nih.gov/biobeat/12-
02-16/12-02-16-4.jpg

Tertiary Structure
Tertiary Structure and Functional Diversity : Different Folding
for Different Functions
http://oregonstate.edu/instruction/bi314/fall12/figure_04_17.jpg
Image taken from:

Tertiary Structure
… FOLDING…

Tertiary Structure
… FOLDING…
Gaya dorong utama dalam folding
protein adalah interaksi
hidrofobik yang terjadi antar
gugus non-polar dari rantai
samping polipeptida sebagai
upaya untuk meminimalisasi
kontak dengan molekul air.
Hydrophobic group
Hydrophilic group
Image taken from:

https://upload.wikimedia.org/wikipedia/commons/c/c5/Protein_folding_schematic.png

Tertiary Structure
Structure and Function of Biomolecule Karp, page

66 54
Tertiary Structure
Proteins with similar 1° structure also have similar 3° structure
Image taken from: http://image.slidesharecdn.com/chapter4part2-protein3-dstructure-3edand4thstructureandproteinfolding-141101094335-conversion-

gate02/95/chapter-4-part-2-protein-3d-structure-3ed-and-4th-structure-and-protein-folding-3-638.jpg?cb=1416159888

Tertiary Structure
Protein: Domain
 Proteins have various
molecular weight (MW).
 Strat from small up to large

protein.
 Protein with MW > 20000 (>

200 amino acid residues)
sometimes have
independent globular units.
 It is called domain.
Image taken from:
http://www.topsan.org/@api/deki/files/7395/=GE15694A
-domains-labeled_(1).png?size=webview

Quaternary Structure
∞ The quaternary structure is consist of two or more

polypeptide chains and are held together by noncovalent
interaction.
∞ Each polypeptide is called subunit.
∞ Subunit either function independently or may co-

operatively.
∞ Dimer – 2 polypeptides, Trimer – 3 polypeptides, so on.
∞ Protein function will be lost if the subunit dissociate.

Quaternary Structure
Image taken from: https://swissmodel.expasy.org/static/course/images/IMG00143.GIF

For example: Chaperonin
GroEL (homo-multimer).
Chaperon consist of 7
subunit called heptamers.

Protein Function
Protein involved in almost everything….. !
Enzymes (pepsin, DNA polymerase)

Structure (keratin, collagen)
Carriers & Transport (hemoglobin, aquaporin)
Cell communication
signals (insulin & other hormones)
receptors
Defense (antibodies)
Movement (actin & myosin)
Storage (bean seed proteins)

Image taken from: https://upload.wikimedia.org/wikipedia/commons/2/28/Hexokinase_3O08.png
Protein Function
72
Hexokinase

Protein as enzyme
Image taken from: https://upload.wikimedia.org/wikipedia/commons/0/0d/InsulinHexamer.jpg
Protein Function
73
Insulin

Protein as signal
Image taken from: https://crystallography365.files.wordpress.com/2014/03/myaglobin.jpg
Protein Function
74
Myoglobin
Protein as carrier & transport
Image taken from: https://upload.wikimedia.org/wikipedia/commons/b/ba/Hemoglobin_t-r_state_ani.gif
Protein Function
75
Hemoglobin
Protein as carrier & transport
Image taken from: http://absoluteantibody.com/wp-content/uploads/2014/03/ProteinAG.png
Protein Function
76
Protein as defense
Image taken from: https://upload.wikimedia.org/wikipedia/commons/d/d3/Actin_with_ADP_highlighted.png
Protein Function
77
Actin

Protein as movement
Image taken from: http://www.bio.miami.edu/tom/courses/protected/MCB6/ch19/19-22.jpg
Protein Function
78
Collagen

Protein as structural
Protein Case
Protein Malfunction: Sickle cell anaemia

Protein Analysis
• Qualitative test for amino acid and protein analysis :

Ninhydrin, Biuret, Xantoproteic acid, Millon’s,
Sulphur test, and Hopkins Cole test.
• Quantitative test for amino acid and protein analysis:

Biuret, Lowry and Kjeldhal method.
• Protein Separation: SDS-PAGE electrophoresis.

Protein Analysis
SDS PAGE (Sodium Dodecyl Sulfate Polyacrylamide gel

electrophoresis)
Image taken from: http://www.bio-

rad.com/webroot/web/images/lsr/products/electrophoresis/category_overlay_content/global/mptetra_family_shot.jpg

Protein Analysis
Image taken from: http://www.bio-
rad.com/webroot/web/images/lsr/solutions//
technologies/protein_electrophoresis_blottin
g_and_imaging/protein_electrophoresis/tech
nology_detail/pet11_img3.jpg
Image taken from: https://upload.wikimedia.org/wikipedia/commons/4/46/SDS-PAGE_Electrophoresis.png

Protein Analysis
-
Electrophoresis:
separation of
protein based on
the their mobility
through a solid
support. The
separation is based
on charge or
molecular mass.

Protein Analysis

References
• Engelbert Buxbaum, (2007): Fundamentals of Protein
Structure and Function, Springer, New York.
• Matthew & van Holde. (1996): Biochemistry 2nd Edition, The
Benjamin/Cummings Publishing Company, Inc., New York.
• David L. Nelson & Michael M. Cox. 2000. Lehninger Principles
of Biochemistry 4th Edition, W.H. Freeman, New York.
• Chapter 25. Amino acids, Peptides and Proteins.
https://www.google.co.id/url?sa=t&rct=j&q=&esrc=s&source
=web&cd=1&cad=rja&uact=8&ved=0ahUKEwjo6f2Cs5PPAhX
GkJQKHd3wAOgQFggaMAA&url=http%3A%2F%2Fas.vanderb
ilt.edu%2Fchemistry%2FRizzo%2FChem220b%2FCh25.ppt&u
sg=AFQjCNEvhUzSM96X1L0bJnHfoFWRWEQ2Tw&sig2=GF1Z
_aLkoXpZZypRaLc7oA&bvm=bv.133178914,d.dGo, accessed
September 12, 2016.

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Chapter 3

Structure and Function of Biomolecule 1

Structure and Function of Biomolecule 2

Structure and Function of Biomolecule 3

Light from the Hemoglobin (Hb) an Skin, horns, nails,

Structure and Function of Biomolecule 5

♫ Proteins are polymers of amino acids linked together by

♫ There are about 300 amino acids occur in nature. Only

♫ Amino acid polymers of ≤50 amino acids are called

♫ Amino acids polymer of >50 amino acids are called

Structure and Function of Biomolecule 6

Karp, page 50 Structure and Function of Biomolecule 7

Structure and Function of Biomolecule 8

• Alpha (α) are on the

• Beta (β) on the 2nd

• Gama (γ) are on the 3rd

Structure and Function of Biomolecule 9

L-α-amino acid D-α-amino acid

Structure and Function of Biomolecule 10

Occurs naturally Mirror Image

Structure and Function of Biomolecule 11

Margaret Oakley Dayhoff

Structure and Function of Biomolecule 12

Structure and Function of Biomolecule 13

lysine arginine histidine Glutamic acid

Structure and Function of Biomolecule 14

When amino acid is dissolved in water, it is exist in solution as

Lehninger, page 81 Structure and Function of Biomolecule 15

At a particular pH, the

amino acid carries no

pH, at which the

Zwitterion can act as

Structure and Function of Biomolecule 16

Structure and Function of Biomolecule 18

Structure and Function of Biomolecule

Structure and Function of Biomolecule

Structure and Function of Biomolecule

Amino Acid Classification

NON POLAR POLAR

ALIPHATIC AROMATIC CHARGE UNCHARGE

Gly (G) Ser (S)

Structure and Function of Biomolecule 24

Structure and Function of Biomolecule 25

• This accounts for

Image taken from: http://slideplayer.com/slide/4617706/15/images/37/The+ultraviolet+absorption+spectra+of+the+aromatic+amino+acids+at+pH+6.jpg

Structure and Function of Biomolecule 26

Structure and Function of Biomolecule 27

Structure and Function of Biomolecule 28

Non Protein Amino Acid

4-Hydroxyproline Trogia venenata Zhu L

Structure and Function of Biomolecule 29

Application of biochemical engineering process:

Structure and Function of Biomolecule 30

The portion of each

Structure and Function of Biomolecule 31

Peptide Bond Characteristic

Structure and Function of Biomolecule 32

Peptide Bond Characteristic

Image taken from:

• Peptide bonds have partial double bond character due to resonance

Structure and Function of Biomolecule 33

Peptide Bond Characteristic

Image taken from: