Kuliah III. ProteinStruktur dan Fungsi

SEL: Arsitektur dan Senyawa dalam Sel

Air Karbohidrat Lipid Vitamin & Mineral Protein Asam Amino Asam Nukleat

Shape = Amino Acid Sequence

Proteins are made of 20 amino acids linked by peptide bonds

Polypeptide backbone is the repeating sequence of the N-C-C-N-C-C… in the peptide bond

The side chain or R group is not part of the backbone or the peptide bond

Polypeptide backbone

Amino AcidsNOTE: You need to know this table

HYDROPHILIC HYDROPHOBIC

Struktur Asam Amino

Protein-clasified by function

Make up about 15% of the cell, have many function in the cell:

1. ENZYME : catalytic activity and function2. TRANSPORT : bind & carry ligands3. STORAGE : ovalbumin, casein4. CONTRACTILE (MOTOR): can contract, change shape 5. STRUCTURAL : keratin of hair, feathers, & nails, fibroin

of silk & webs6. DEFENSIVE (PROTECT): antibody, snake venom7. REGULATORY (SIGNAL): hormones8. RECEPTORS (DETECT STIMULI): light & rhodopsin

Protein structure

Primary structure: amino acid sequence

Secondary structure: folding of single polypeptide chains

Tertiary structure: 3-dimensional shape of proteins

Quaternary structure: joining of polypeptide chains into proteins

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Peter J. Russell, iGenetics: Copyright © Pearson Education, Inc., publishing as Benjamin Cummings.

linear sequence of peptides

each peptide is several amino acids

frequently highly folded

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Struktur Primer:

Urutan asam-asam amino yang membentuknya, terikat satu sama lain dengan ikatan peptida.

The primary structure of a protein is its unique sequence of amino acids.

Lysozyme, an enzyme that attacks bacteria, consists on a polypeptide chain of 129 amino acids.

The precise primary structure of a protein is determined by inherited genetic information.

Protein Folding

The peptide bond allows for rotation around it and therefore the protein can fold and orient the R groups in favorable positions

Weak non-covalent interactions will hold the protein in its functional shape – these are weak and will take many to hold the shape

Non-covalent Bonds in Proteins

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

Protein Folding (continued)

Proteins shape is determined by the sequence of the amino acids

The final shape is called the conformation and has the lowest free energy possible

Denaturation is the process of unfolding the protein Can be down with heat, pH or chemical

compounds In the chemical compound, can remove and

have the protein renature or refold

Refolding

STRUKTUR SEKUNDER

Dibentuk dan dipertahankan oleh ikatan hidrogen antara C=O dengan NH pada ikatan peptida

Helix ά (3,6 asam amino), prolin (penyelang kesinambungan)

Lembaran β (R berganti-ganti diatas/dibawah tulang punggung).

Protein Folding

2 regular folding patterns have been identified – formed between the bonds of the peptide backbone

-helix – protein turns like a spiral – fibrous proteins (hair, nails, horns)

-sheet – protein folds back on itself as in a ribbon –globular protein

Beta-pleated sheet

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.

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)

Alpha-helix

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

Struktur Tersier Protein

Interaksi ion, hidrofobik, ikatan disulfida, ikatan kovalen

Protein fibrosa (serat-serat panjang, tongkat atau tali: kolagen, keratin)

Protein globuler (bulat, mudah larut dalam air/garam encer): Myoglobin, ribonuclease

KOLAGEN

Protein terbanyak dalam tubuh manusia high Glycine, Proline, & no Cysteine when

boiled makes gelatin 3 heliks kolagen: tropokolagen

Kolagen (lanjutan)

Keratin

Keratin ά : kulit, rambut, kuku high basic aa's (Arg, His, Lys), but with Cys Membentuk serat, tongkat yang panjang dapat diregang bila basah

Keratin ά

Keratin (lanjutan)

Silk Keratin β: sutera, paruh burung Bentuk lembaran bergelombang tidak dapat diregang bila basah

                     

Struktur Kuarterner

Penataan suatu rantai protein dengan protein lain dan dengan koenzim, tidak terikat secara kovalen

Hemoglobin, mioglobin, protein plasma, immunoglobulin, protein yang diperlukan untuk membawa Fe dan Cu

Hemoglobin & Immunoglobulin

PROTEIN KOMPLEK

lipoproteins –(+ lipids)blood, membrane, and   transport proteins

glycoproteins -  (+ carbohydrates)antibodies, cell surface proteins

nucleoproteins -  (+

nucleic acids) ribosomes & organelles

Denaturasi dan Renaturasi Protein

DENATURATION loss of 3-D conformation by heat, pH, organic solvents, detergents

RENATURATION - regaining of biological activity via self-assembly

Denature and Renature

Sickle cell anemia

Determinasi Struktur Protein

Molecular exclusion/gel filtration chromatography

Amino Acid Sequencing

Mass Spectrometry : detects exact MASS of small peptides.

X-Ray Crystallography : determines 3-D shape of molecules mathematically.

NMR Spectroscopy : magnetic signal indicate distances between atoms.           

The three-dimensional shapes of over 10,000 proteins have been determined using X-ray crystallograghy and NMR.

PEMISAHAN DAN DETEKSI PROTEIN

PEMISAHAN DAN DETEKSI PROTEIN

Determinasi Struktur Protein