VPP3021 Veterinary Biochemistry - Protein Structure & Function PDF

# VPP3021 Veterinary Biochemistry ## **Protein: Structure & Functions** - **Mokrish Ajat PhD** - Department of Veterinary Preclinical Sciences - Faculty of Veterinary Medicine - Universiti Putra Malaysia - [email protected] ### **What to be discussed?** - Amino acids of proteins & Structure...

# VPP3021 Veterinary Biochemistry ## **Protein: Structure & Functions** - **Mokrish Ajat PhD** - Department of Veterinary Preclinical Sciences - Faculty of Veterinary Medicine - Universiti Putra Malaysia - [email protected] ### **What to be discussed?** - Amino acids of proteins & Structure - Protein Folding - General functions - Specific protein functions - Diseases caused by changes in protein structure ### **To be discussed** - Synthesis - Amino acids of proteins - Types of amino acids - Different structures - Protein folding - Conformational Diseases - Protein functions - Hemoglobins ## **Transcription & translation** - One strand of DNA directs the synthesis of messenger RNA (mRNA). - The base sequence of the transcribed RNA is complementary to that of the DNA strand. - The message is translated when transfer RNA (tRNA) molecules align with the mRNA complementary base pairing between three-nucleotide segments known as codons. - Each tRNA carries a specific amino acid. - These amino acids are covalently joined to form a protein. - The sequence of bases in DNA specifies the sequence of amino acids in a protein. ## **Amino acids building block of protein structure** | Primary structure | Secondary structure | Tertiary structure | Quaternary structure | |---|---|---|---| | Amino acid residues | a Helix | Polypeptide chain | Assembled subunits | - Primary structure of a peptide is a linear sequence of amino acids that will determine the functions of a protein. - A typical amino acid is a zwitterionic molecule that carries charged groups of opposite polarity. - Amino acids undergo condensation resulting to the formation of CO-NH, an amide linkage or peptide bond. - Polymerization of two, three, four, and many amino acids will be called dipeptides, tripeptides, oligopeptides and polypeptides respectively. ### **Amino acid characteristics** - **Nonpolar, aliphatic R groups**: * Glycine * Alanine * Proline * Valine * Leucine * Isoleucine * Methionine - **Polar, uncharged R groups**: * Serine * Threonine * Cysteine * Asparagine * Glutamine - **Aromatic R groups**: * Phenylalanine * Tyrosine * Tryptophan - **Positively charged R groups**: * Lysine * Arginine * Histidine - **Negatively charged R groups**: * Aspartate * Glutamate - **Non - standard amino acids**: * Primary Sequence ## **Non-standard amino acids** - Amino acid derivatives in proteins – unusual amino acids results from modification on the amino acid residues. - D-amino acids - bacterial polypeptides, peptide antibiotics (valinomycin, gramicidin A and actinomycin D. - Biologically active - maybe oxidized as metabolic fuels to provide energy or signaling molecules or messenger (GABA, dopamine = neurotransmitters), (Histamine = allergic reaction) and (Thyroxine = stimulate vertebrate metabolism). - Amino acid derivatives in proteins – unusual amino acids results from modification on the amino acid residues. ## **Primary sequence reveals the function of a protein** - Evolution conserves amino acids that are important to protein structure and function across species. - Sequence comparison of multiple "homologs" of a particular protein reveals highly conserved regions that are important for function. - Clusters of conserved residues are called "motifs". Motifs carry out a particular function or form a particular structure that is important for the conserved protein. ## **Secondary structure** - Two most common ones are alpha helices and beta sheets. - There are intermediates before being folded to tertiary structure. - Defined by the pattern of hydrogen bonds between amino hydrogen and carboxyl oxygen atoms in the peptide. - Fibrous proteins have repeating secondary structures. - Keratin (double helix) is a mechanically durable and relatively unreactive protein that occurs in all higher vertebrates. - It is the principal component of their outer epidermal (skin) layer and its related appendages, such as hair, horn, nails, and feathers. - Keratins have been classified as either alpha keratins, which occur in mammals, or beta keratins, which occur in birds and reptiles. Humans have more than 50 keratin genes that are expressed in a tissue-specific manner. - Collagen (triple helix) which occurs in all multicellular animals is the most abundant extracellular protein. These strong, insoluble fibers are the major stress-bearing components of connective tissues such as bone, teeth, cartilage, tendon, and the fibrous matrices of skin and blood vessels. ## **Tertiary structure protein** - The tertiary structure of a protein describes the folding of its secondary structural elements and specifies the positions of each atom in the protein including its side chains. - Information can be found in an online database via the internet. X-Ray crystallography and NMR spectroscopy determines the positions of atoms in proteins. ## **Quaternary structure proteins** - The quaternary structure of a protein contains multiple subunits, usually arranged symmetrically. ## **Protein Folding** - A folding protein follows a pathway from high energy and high entropy to low energy and low entropy. - Experiments showed that many proteins fold to their native confirmations in less than a few seconds. As proteins fold, its conformational stability increases sharply, which makes folding a one-way process. - A folding protein must proceed from a high-energy, high entropy state to a low energy, low entropy state. - Protein disulfide isomerase catalyzes disulfide bond formation. - A variety of molecular chaperones assist protein misfolding via an ATP-dependent bind-and-release mechanism. - The misfolded proteins form fibrils containing extensive beta structure. ## **Molecular chaperones assist protein folding ** - Molecular chaperones are essential proteins that bind to unfolded and partially folded polypeptide chains to disrupt the improper association of exposed hydrophobic segments that would otherwise lead to non-native folding as well as polypeptide aggregation and precipitation. - Many molecular chaperones were first described as heat shock proteins (Hsp) because their rate of synthesis is increased at elevated temperatures. - Presumably, the additional chaperones are required to recover heat-denatured proteins or to prevent misfolding under conditions of environmental stress. - Hsp70, trigger factor, chaperonins, Hsp90 ## **Protein Misfolding Diseases** - Most proteins in the body maintain their native conformations or, if they become partially denatured, are either renatured through the auspices of molecular chaperones or are proteolytically degraded. - However, at least 35 different—and usually fatal—human and animal diseases are associated with the extracellular deposition of normally soluble proteins in certain tissues in the form of insoluble fibrous aggregates known as amyloids. - **spongiform encephalopathy (BSE or mad cow disease)** seen in cattle and livestock and **Creutzfeldt-Jakob disease (CJD)** seen in humans. - **Alzheimer and Huntington disease** - **Sickle Cell Anemia** - single amino acid change in hemoglobin related to disease - **Osteoarthritis** - single amino acid change in collagen protein causes joint damage ## **Protein Functions** - **Myoglobin** - **Transport** - Hemoglobin - **Contractile function** - Myosin and Actin - **Defensive proteins** - Antibodies - **Catalysis** - enzymes - **Structural** - keratin - **Trans-membrane transport** - Na+/K+ATPases - **Toxins** - snake venoms, ricin - **Hormones** - insulin - **Storage proteins** - seeds and eggs ## **Hemoglobin** - **Structure** - quarternary globular protein (a2 and b2)subunits with four heme group - **Function** - major physiological role to facilitate oxygen transport and gives red blood cells colour ## **Myosin & Actin** - **Structure** - parallel bundles of myofibrils (actin and myosin) - **Function** - muscles contraction (read on the mechanism)