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Struktur dan fungsi protein
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STRUKTUR & FUNGSI
PROTEIN
Evi Umayah Ulfa
PROTEIN
Asal kata “PROTEIOS” = UTAMA
Makromolekul yang tersusun atas Asam Amino yang
disatukan oleh ikatan peptida
Monomer : Asam-Amino 20 macam
Human Insulin
ASAM-ASAM AMINO YANG TERDAPAT
DALAM PROTEIN
Asam amino rantai samping alifatik
Glisin (Gly) = G
Valin (Val) = V
Alanin (Ala) = A
Leusin (Leu) = L
Isoleusin (Ile) = I
Asam amino rantai samping gugus
hidrosil (OH)
Serin (Ser) = S
Treonin (Tgr) = T
Tirosin (Tyr) = Y
Asam amino rantai samping sulfur
Sistein (Cys) = C
Metionin (Met) = M
Asam amino rantai samping gugus asidik dan
amida
Asam aspartat (Asp) = D
Asparagin (Asn) = N
Asam glutamat (Glu) = E
Glutamin (Gln) = Q
Asam amino rantai samping gugus alkalis
Arginin (Arg) = R
Lisin (Lys) = K
Histidin (His) = H *
Asam amino rantai samping
mengandung cincin aromatika
Histidin (His) = H
Tirosin (Tyr) = Y *
Fenilalanin (Phe) = F
Triptofan (Trp) = W
Asam amino siklik
Prolin (Pro) = P
JENIS ASAM AMINO
1. ASAM AMINO ESENSIAL (INDISPENSABLE AMINO ACID)
ASAM AMINO YANG TIDAK DAPAT DISINTESIS
OLEH TUBUH, HARUS DIPEROLEH DARI LUAR (MAKANAN)
2. ASAM AMINO NON ESENSIAL (DISPENSABLE AMINO ACID)
ASAM AMINO YANG DAPAT DISINTESIS DI DALAM TUBUH,
DARI SUPLAI NITROGEN
3. ASAM AMINO SEMI ESENSIAL (CONDITIONALLY ESSENSIAL)
ASAM AMINO YANG PADA KONDISI TERTENTU TIDAK DAPAT
DIBENTUK OLEH TUBUH
JENIS ASAM AMINO
ESENSIAL NON ESENSIAL SEMI ESENSIAL
Histidin Alanin
Lisin Arginin Arginin
Leusin Asparagin
Isoleusin Asam aspartat
Methionin Asam Glutamat
Valin Glutamin Glutamin
Threonin Glisin
Venilalanin Serin
Triptofan Prolin
Sistein Sistein
Tyrosin Tyrosin
Berat Molekul
Dalton:
Unit masa yang nilainya sebanding
dengan atom hidrogen
Gly C2NO2H5 75
Ala C3NO2H7 89
Val C5NO2H11 117
Leu C6NO2H13 131
Ile C6NO2H13 131
Peranan Protein
PROTEIN
Motion
(myosin, actin)
Defense
(antibodies, toxins)
Replication and repairing
of genetic information
(DNA and RNA polymerases)
Metabolism
(enzymes)
Mechanical (Collagen)
Material transport (Hb)
Klasifikasi Protein
1.
KOMPOSISINYA
3.
FUNGSI BIOLOGIS
2.
BENTUKNYA
1. Komposisinya
Protein sederhana (simple) : bila hihidrolisis hanya menghasilkan asam amino
Protein konjugat (cojugated) : bila dihidrolisis tidak hanya menghasilkan asam amino saja, tetapi juga komponen organikatau anorganik lainnya (gugus prostetik)
Macam-macam protein konjugat
Macam protein Gugus prostetik
1. Nukleo protein (ribosom, Tobacco mosaic virus) RNA
2. Lipoprotein (plasma 1-lipoprotein) Phospholipid, kolesterol, lipid netral
3. Glikoprotein # Globulin# Plasma orosomucoid
Heksosamin, galaktosa, manosaGalaktosa, manosa, N-asetil-galaktosamin,
4. Phosphoprotein (Kasein) Phosphate
5. Hemo protein (Hemoglobin, sitokrom C dan Katalase )
Fe-protoporphyrin
6. Flavoprotein (suksinat dehidro genase, D-amino acid oxidase)
Flavin adenin dinukleotida (FAD)
7. Metalloprotein # Ferritin# Sitokrom oksidase# Alkohol dehidrogenase# Xanthine oxidase
Fe(OH)2
Fe dan CuZnMo dan Fe
2. Bentuknya
Fiber (Fibrous)
Rantai poli-peptida yg disusun secara paralel.
Secara fisik protein ini kuat, tidak larut dalamair, larut dalam larutan garam.
Globular
Rantai polipeptidanya dilipat-lipat dgn kuat
sehingga berbentuk seperti bulat bundar.
13
Fibrous proteins have a structural role
Source:http://www.prideofindia.net/images/nails.jpg
http://opbs.okstate.edu/~petracek/2002%20protein%20structure%20function/CH06/Fig%2006-12.GIF
http://my.webmd.com/hw/health_guide_atoz/zm2662.asp?printing=true
Collagen fibers are a major portion of
tendons, bone and skin. Alpha helices of
collagen make up a triple helix structure
giving it tough and flexible properties.
•Fibroin fibers make the silk spun by
spiders and silk worms stronger weight
for weight than steel! The soft and
flexible properties come from the beta
structure.
•Keratin is a tough insoluble protein that
makes up the quills of echidna, your hair
and nails and the rattle of a rattle snake.
The structure comes from alpha helices
that are cross-linked by disulfide bonds.
The globular proteins
Cell motility
Organic catalysts in biochemical reactions – enzymes
Regulatory proteins – hormones, transcription factors
+2 2
Insulin binds to cell membranes and this triggers the cells to absorb glucose for use or for storage as glycogen in the liver.
Myosin (red) and actin filaments (green) in
coordinated muscle contraction
The globular proteins
Cell motility – proteins link together to form filaments which make movement possible.
Organic catalysts in biochemical reactions –enzymes
Regulatory proteins – hormones, transcription factors
Membrane proteins – MHC markers, protein channels, gap junctions
Defense against pathogens – poisons/toxins, antibodies, complement
Transport and storage – hemoglobin and myosin
3. Fungsi Biologis
1 Enzim Alcohol dehydrogenase, lipase, DNA Pol
2 Protein simpan (storage)
- Ovalbumin (protein putih telur)- Casein (protein susu)- Zein (protein biji jagung)
3 Protein transport - Hemoglobin (transport O2 dlm darah)- Myoglobin (transport O2 dlm otot)- Serum albumin (transport AL dalam arah)
4 Protein gerak (kontraktil)
Myosin dan actin( prot gerak pada otot)
3. Fungsi Biologis
5 Protein perlindungan (protective)
- Antibodi- fibrinogen- thrombin
6 Hormon - insulin
- hormon tumbuh- represor
7 Protein Struktural -coat protein virus-Keratin-Collagen- Elastin
Anatomy of an amino acid
The R groups, also called side chains,
make each AA unique and distinctive.
R groups are different in their size, charge,
hydrogen bonding capability and chemical
reactivity.
Aas are grouped as (1) non-polar,
hydrophobic; (2) polar, neutral; (3) basic;
and (4) acidic.
R groups are
non-polar,
hydrophobi
c aliphatic
or aromatic
groups.
R groups are
uncharged.
AAs are
insoluble in
H2O.
Non-polar and hydrophobic AAs
Polar and uncharged AAs
R groups are polar:
-OH, -SH, and -NH2. R groups are highly
reactive.
R AAs are soluble in H2O, that is, hydrophilic.
R groups have one -
NH2.
R groups are
positively charged at
neutral pH (=7.0).
AAs are highly
hydrophilic.
Basic Aas/ Positively Charged AAs
Acidic AAs
R groups have –
COOH.
R groups are
negatively charged
at physiological pH
(=7.4).
AAs are soluble in
H2O.
Polypeptide
Backbone
Levels of Protein Structure
Primary structure
Two peptides of 21 and 30 AAs
Two inter-chain -S-S- bonds
One intra-chain -S-S- bond
Secondary Structure
The secondary structure of a
protein results from hydrogen
bonds at regular intervals
along the polypeptide
backbone.
Alpha helix
beta pleated sheets
Beta turn
Random coil
Hydrogen Bonds in Proteins
H-bonds form between 1) atoms involved in the peptide bond; 2) peptide bond atoms and R groups; 3) R groups
Helix
Formed by a H-bond between every 4th peptide bond – C=O to N-H
Usually in proteins that span a membrane
The helix can either coil to the right or the left
Can also coil around each other – coiled-coil shape – a framework for structural proteins such as nails and skin
Sheets
Core of many proteins is
the sheet
Form rigid structures with
the H-bond
Can be of 2 types
Anti-parallel – run in an
opposite direction of its
neighbor (A)
Parallel – run in the same
direction with longer looping
sections between them (B)
turns
• -turns allow the protein backbone to make abrupt turns.
• Again, the propensity of a peptide for forming -turns depends on its sequence.
The structural properties of silk are due to beta
pleated sheets.
The presence of so many hydrogen bonds makes each silk
fiber stronger than steel.
Tertiary Structure
Tertiary structure is determined by a variety of interactions among R groups and between R groups and the polypeptide backbone. These interactions
include hydrogen bonds among polar and/or charged areas, ionic bondsbetween charged R groups, and hydrophobic interactions and van der Waals interactions among hydrophobic R groups.
While these three interactions are relatively weak, disulfide bridges, strong covalent bonds that form between the sulfhydryl groups (SH) of cysteine monomers, stabilize the structure.
Quaternary Structure
Quarternary structure results
from the aggregation of two
or more polypeptide subunits.
Collagen is a fibrous protein of
three polypeptides that are
supercoiled like a rope.
This provides the structural strength
for their role in connective tissue.
Hemoglobin is a
globular protein
with two copies
of two kinds
of polypeptides.
Examples of other quaternary
structuresTetramer Hexamer Filament
SSB DNA helicase Recombinase
Allows coordinated Allows coordinated DNA binding Allows complete
DNA binding and ATP hydrolysis coverage of an
extended molecule
Example of quaternary structure -
Sir1/Orc1 heterodimer
Example is Sir1/Orc1 complex solved at UW: Hou, Bernstein, Fox, and Keck
(2005) Proc. Natl. Acad. Sci. 102, 8489-94.
A protein’s conformation can change in response to the physical and chemical conditions.
Changes in pH, salt concentration, temperature, or other factors can unravel or denature a protein.
These forces disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that maintain the protein’s shape.
Some proteins can return to their functional shape after denaturation, but others cannot, especially in the crowded environment of the cell.
Usually denaturation is permanent
SINTESIS PROTEIN
DNA
mRNA
Polipeptida/
Pre protein
Protein
Transkripsi
Translasi
Post Translasi
Prosesing mRNA
Eukariotik
• Capping ‘5
• Tailing ‘3
• Splicing
SINTESIS PROTEIN PD
PROKARYOT
TRANSKRIPSI DAN TRANSLASI
Transcription Units in the Genome
• People typically report a gene sequence as the DNA
sequence that would be the mRNA if the T’s were written
as U’s (the coding strand).
• Remember, the template strand will be complementary
and antiparallel to the coding strand.
Promoters
• The promoter of a gene is defined as the initial RNA polymerase
binding site. The transcription start site (defined as nucleotide +1) is
close to the promoter and upstream of the start (AUG) codon.
Bacterial RNA polymerase
• In bacteria, RNA polymerase has a simple four subunit structure
(2’), but a fifth subunit (the sigma factor) binds to the complex
and brings it to the promoter.
• Sigma factor leaves the holoenzyme after initiation, leaving the
core enzyme to elongate the transcript.
• Different sigma factors recognize different promoters.
Holoenzyme includes the Sigma Factor
The Core Enzyme Elongates the mRNA
Sigma Factors
• Bacteria typically contain multiple s factors, allowing the activation of different
sets of genes.
– For example, E. coli has s factors encoded by
• rpoH - heat shock s factor
• rpoS - stationary phase s factor
• ntrA - nitrogen metabolism s factor
• flbB - flagellar gene s factor
• and more…
– The complement of genes encoding s factors in bacterial genomes
varies quite a bit among bacterial species.
Transcription Termination• Bacteria have two types of terminators:
– rho (r) independent or intrinsic terminators - these sequences
have a stem-loop followed by a string of U’s.
• RNAP pauses after the U’s and the formation of the stem-loop may
cause a local denaturation of the AT-rich terminator, ending
transcription.
• rho (r) dependent terminators - r binds to rut (r utilization) site in
non-translated region. r travels along mRNA at same speed as RNAP.
RNAP pauses at a stem-loop and r catches up to it. r unwinds
DNA-RNA hybrid causing polymerase to fall off.
• r has DNA-RNA helicase activity.
palindrome
termination
An RNA Stem-Loop Structure
RNA polymerase
• RNA polymerase (RNAP) separates the strands of DNA and polymerases
RNA in a 5’ to 3’ direction:
– Bacterial RNA polymerase is relatively simple, with four main
subunits - [present twice], , ’ (and a fifth w subunit).
– Eukaryotes have three RNA polymerases that are much more
complex.
• RNA pol I - rRNA
• RNA pol II - mRNA and snRNA
• RNA pol III - tRNA, 5S rRNA, and snRNA
Komponen Transkripsi
RNA Polimerase
(RNA Pol 2)
Pisahkan double
heliks DNA
Copy DNA
template
menjadi mRNA
Satukan U=A,
G=C
PROKARYOTIC RNA POLYMERASE
Single enzyme with 5 subunits
, ’, , ’ s : Holoenzyme (Sigma subunit finds start point)
, ’, , ’ : Core enzyme (elongation of RNA chain)
4 rNTPS RNA + PPi
DNA template and
RNA polymerase
3’ 5’
5’ 3’
5’ 3’
36.5kD
70kD
151kD
155kD
11kD
36.5kD
E. coli RNA polymerase
Nelson & Cox, 2000, p. 982
E. coli RNA polymerase
Nelson & Cox, 2005, p. 999
Figure 30.8
Local unwinding of DNA caused by RNA polymerase
ENZYMATIC SYNTHESIS OF RNA
Differences/similarities with DNA polymerases
i. Substrate
ii. Template conservation (Sense strand = mRNA)
iii. Primer need
iv. Proof reading
Template recognition and copying by base pairing
direction of synthesis : 5’ - 3’
Initiation with A or G (Sigma factor also needed)
*Termination : U sequence + hairpin + r factor
* Prokaryotic system (ATP dependent)