PROTEIN & ASAM AMINO

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Modified by Prof Sismindari

Pendahuluan
Sebagian besar makromolekul yang penting dalam sistem biologi berupa Polimer yang disebut sebagai biopolimer Biopolymers ada 3 kelas :

proteins,
polysaccharides (carbohydrates), dan nucleic acids.

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Proteins
Makromolekul yang sangat penting Melakukan sebagian besar fungsi biologis dalam sel Terdapat berbagai macam protein yang berbeda
Mempunyai struktur 3 dimensi spesifik Mempunyai fungsi yang spesifik

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Proteins
Tersusun dari rangkaian asam amino Terdapat 2 bentuk asam amino :
Netral (dengan gugus -NH2 and COOH) zwitterionic (dengan gugus -NH3+ and -COO-).

A zwitterion mempunyai mempunyai muatan negatif dan positif dalam 1 molekul. Terdapat 20 jenis asam amino dalam sebagian besar protein.
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Abbreviations and Codes

Alanine A, Ala Arginine R, Arg Asparagine N, Asn Aspartic acid D, Asp Cysteine C, Cys Glutamine Q, Gln Glutamic Acid E, Glu Glycine G, Gly Histidine H, His Isoleucine I, Ile
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Leucine L, Leu Lysine K, Lys Methionine M, Met Phenylalanine F, Phe Proline P, Pro Serine S, Ser Threonine T, Thr Tryptophan W, Trp Tyrosine Y, Tyr Valine V, Val

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Fungsi Protein
Structural Movement Transport Storage Hormone Protection Enzymes
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Collagen; bones, tendons, cartilage Keratin; hair, skin, wool, nails, feathers

Myosin & Actin; muscle contractions

Hemoglobin; transports O2 Lipoproteins; transports lipids

Casein; in milk. Albumin; in eggs

Insulin; regulates blood glucose Growth hormone; regulates growth

Immunoglobulins; stimulate immunity Snake venom; plant toxins; Sucrase; catalyzes sucrose hydrolysis Pepsin; catalyzes protein hydrolysis
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General structure of amino acid

-carboxyl group

-amino group
-carbon Side chain
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Sifat asam basa dari asam amino Gugus karboksil sbg asam, donating a proton dalam larutan air. pKa gugus karoboksil normally 2 to 5. sehingga pH saat asam tsb terionisasi 50%: R-COOH R-COO- + H+
pH= [less than 2] [above 5]

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 Gugus Amino sebagai basa, menerima proton. pKa gugus amino around 9 10. sehingga pada pKa tsb groups are 50% ionized: R-NH3+ R-NH2 + H+
pH= [below 8]

[above 9]

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 Even though both acids and amines are present in the same molecule, they mostly behave as though they were separate entities:

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 Summary: At low pH, proton concentration [H+]is high. Therefore, both amines and carboxylic acids are protonated. (-NH3+ & -COOH) At high pH, proton concentration is low. Therefore, both amines and carboxylic acids are deprotonated. (-NH2 & -COO-) At neutral pH, amines are protonated(-NH3+) and carboxylates are deprotonated(-COO-)
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 Zwitter Ions: Ions yang mempunyai dua muatan disebut zwitter ions oleh ilmuwan German; the name still applies today, especially for amino acids at neutral pH:

+H N 3
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CH2 COO
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Acid-Base Properties of Amino Acids Sebagai contoh structures dari glycine:

(Non-existent form:) H2N CH2 - COOH

pH=1:

pH=7:

pH=12:
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Acid-Base Properties of Amino Acids Sebagai contoh structures dari glycine:

(Non-existent form:) H2N CH2 - COOH

pH=1:

+H N 3

CH2 - COOH

pH=7:

pH=12:
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Acid-Base Properties of Amino Acids Sebagai contoh structures dari glycine:

(Non-existent form:) H2N CH2 - COOH

pH=1:

+H N 3

CH2 - COOH CH2 COO-

pH=7:

+H N 3

pH=12:
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Acid-Base Properties of Amino Acids Sebagai contoh structures dari glycine:

(Non-existent form:) H2N CH2 - COOH

pH=1:

+H N 3

CH2 - COOH CH2 COO-

pH=7:

+H N 3

pH=12:
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H2N CH2 COO17

Klasifikasi asam amino

Dibagi dalam 5 grup tergantung pad substitusi pada R :
Nonpolar, aliphatic (7) Aromatic (3) Polar, uncharged (5) Positively charged (3)

Negatively charged (2)

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Klasifikasi Amino Acids

Nonpolar (hydrophobic) with hydrocarbon side chains. Polar (hydrophilic) with polar or ionic side chains. Acidic (hydrophilic) with acidic side chains. Basic (hydrophilic) with NH2 side chains.
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Nonpolar

Polar

Acidic Basic

Copyright 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Copyright 2007 by Pearson Education, Inc.Publishing as Benjamin Cummings

Nonpolar Amino Acids Nonpolar amino acid mempunyai R group alkyl group (7), atau aromatic (2).
Nonpolar asam amino

Glysin (Gly)

Alanin (Ala)

Valin (Val)

Leucine (Leu)

Isoleucine (Ile)

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Phenylalanine (Phe)

Methionine (Met) Proline (Pro) Modified by Prof Sismindari

Tryptophan (Trp)

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Polar Amino Acids

Polar amino acid mempunyai R group alcohol, thiol, atau amide (5), aromatik (1).
Polar asam amino (netral)

Serine (Ser)

Threonine (Thr)

Tyrosine (Tyr)

Cysteine (Cys)

Aspargine (Asn)

Glutamine (Glu)

Copyright 2007 by Pearson Education, Inc.

Publishing as Benjamin Cummings 9/24/2013

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Copyright 2007 by Pearson Education, Inc.Publishing as Benjamin Cummings

Asam dan Basa Asam Amino

Asam R group carboxyl (COO). Basa R group amino (NH3+).
Asam amino asam Asam amino Basa Basic Amino Acids

Aspartic acid (Asp)

Glutamine (Glu) Histidine (His) Lysine (Lys) Arginine (Arg)

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Tryptophan dan tyrosine mengabsorbsi sinar ultraviolet. Absorbance maximal sekitar panjang gelombang 280 nm. Kontribusi Phenylalanine pada umumnya sangat sedikit pada panjang gelombang tsb.

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Prolin banyak berpengaruh terhadap arsitektur protein karena strukturnya yang lebih konformatif rotasi terbatas

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Proteins
Bagaimana asam amino bisa terangkai menjadi pipeptida?
Reaksi Dehydrasi
(removal of water molecule)

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Formation of Peptide Bonds by Dehydration Amino acids are connected head to tail NH2

COOH
Carbodiimide

NH2

COOH

Dehydration
-H2O

O NH2
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C N

COOH
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Juang RH (2004) BCbasics

H
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Making a polypeptide chain

Ser

Phe

Cys
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9/24/2013 Modified by Prof Sismindari Copyright 2005 Pearson Education, Inc., publishing as Benjamin Cummings

Making a polypeptide chain

R groups

Ser

Phe

Cys
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linear chain or array of amino acids

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Definition:

Amino acid polymers of 50 amino acids are called

polypeptides, peptides, oligopeptides, etc. Amino acids polymer of >50 amino acids are called proteins.

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 Contoh dari dipeptide sweetener Aspartame. Other names include:

NutraSweet Equal Tri-Sweet Sanecta

IUPAC Name:
N-L- Aspartyl-L-phenylalanine 1-methyl ester

Abbreviated Structure:

Asp Phe - OCH3

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 Cross links antara rantai peptide:

Disulfide linkages antara individual cysteines are called cystines:

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 Insulin merupakan prot terkecil dengan 51 amino acids dalam dua rantai yang diikatkan oleh cystine (disulfide) :

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Peptida yg aktif secara dan polypeptides yang terjadi secara cepat dlm jumlah yang besar

Oxytocin: nine amino acid residues, secreted by the posterior pituitary and stimulates uterine contractions. Glucagon: 29 residues, a pancreatic hormone, opposing the action of insulin.

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Panjang protein sangat bervariasi

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Protein yang berbeda mempunyai komposisi asam amino yang berbeda

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Some proteins contain chemical groups other than amino acids

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Levels structure dalam proteins

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Primary Structure

Unique sequence of amino acids Linear arrangement of amino acids

Met-Lys-Val-Phe-Gly-Arg-Cys-Glu-Leu-Ala...
amino terminus N-terminus
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carboxyl terminus C-terminus

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Primary Structure
Overall structure depends upon:
number of amino acids (length of protein) specific composition of amino acids (number of amino acids of each type)

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Struktur Primer protein: Lysozyme

129 amino acids in length with 20 amino acids, many

possible proteins with a length of 129 amino acids

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Struktur Protein Sekunder

Certain segments of amino acid sequence take on a regular structure or folded pattern Alpha helix Beta pleated sheet
both are stabilized by Hydrogen bonds

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Secondary structure of a protein

Lysozyme
See p82

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Struktur Protein Tertier

Overall 3-D shape of the entire polypeptide
Held together by various bonds and interactions Hydrogen bonds Ionic bonds Disulfide bridges (two Cysteines) Hydrophobic interactions (including van der Walls interactions)

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Contoh ikatan/interaksi yang berperan dlm membentuk struktur tertier protein

two cysteine side chains

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Copyright 2005 Pearson Education, Inc., publishing as Benjamin Cummings

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Struktur 3D lysozyme

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 Sekuen ribonuclease:

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Protein Quarternary Structure

Applies only to proteins consisting of more than one polypeptide chain (or subunit) Refers to the arrangement of the subunits relative to each other

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Quaternary structure of proteins

4 subunits of a tetrameric protein

Collagen
triple helix

Hemoglobin

and chains with heme

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9/24/2013 Modified by Prof Sismindari Copyright 2005 Pearson Education, Inc., publishing as Benjamin Cummings

Normal vs. Sickle-cell Hemoglobin

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Glu acidic Val nonpolar

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Protein Structure
Protein conformation can change in response to environment of protein
temperature, pH, salt concentration, etc. may disrupt H-bonds, ionic bonds, etc.

Denaturation is the unfolding of the protein Renaturation is the refolding of the protein back
to its normal functional shape
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 Anfinson chose the enzyme, ribonuclease, for his experiments. This enzyme hydrolyzes RNA and is composed of a single polypeptide chain with 124 amino acids. Four disulfide (cystine) linkages are observed in the active enzyme that stabilize the 3-D (3) shape of the enzyme. The enzyme functions only when its 3demention structure is properly aligned.
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Anfinson used two chemicals to disrupt the enzymes 3 structure [DENATURATION ]

1. urea - disrupts hydrogen bonds 2. -mercaptoethanol reduces disulfide bonds

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Anfinsons Experiment:

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