Protein

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)