Lecture 3: Proteins PDF

Lec. 3: Proteins Randa A. Zaghloul Faculty of pharmacy Mansoura University, Mansoura, Egypt 2024-2025 Biochemistry-1 1  So Far ! Recap ✓ What is Bioch...

Lec. 3: Proteins Randa A. Zaghloul Faculty of pharmacy Mansoura University, Mansoura, Egypt 2024-2025 Biochemistry-1 1  So Far ! Recap ✓ What is Biochemistry 1 all about ! ✓ carbohydrates? ✓ Proteins and amino acids? 2024-2025 Biochemistry-1 2  Learning objectives: to learn” Level of folding of the protein? Post translational modification? 2024-2025 Biochemistry-1 3  Classification of amino acids according: The nutritional value Glycine , Alanine Phenylalanine, tyrosine The biological value Valine, leucine, Isoleucine Tryptophan The Structure Threonine, serine Arginine lysine, Histidine the polarity of side Cysteine, methionine Glutamate, aspartate chains Proline Glutamine, asparagine 2024-2025 Biochemistry-1 4 Biologically active oligopeptides: Glutathione Oxytocin and Vassopressin Tripeptide chemically named Nona peptides hormones secreted from the posterior lobe of -Glutamyl-cysteinyl glycine pituitary gland It functions as antioxidant Oxytocin: contraction of smooth muscles of uterus → for induction of labor (Delivery of baby) Vasopressin (ADH) causes constriction of peripheral blood vessels leading to rise in blood pressure. 2024-2025 Biochemistry-1 5 2024-2025 Biochemistry-1 6 Hierarchical Structure of Proteins: ✓ Protein chain folds into a unique shape → stabilized by noncovalent interactions between regions in the linear sequence of amino acids. ✓ Spatial organization of a protein—its shape in 3D → key to understanding its function. ✓ Only when a protein is in its correct 3D structure, or conformation → able to function efficiently. ✓ Complexity of protein structure: by considering four organizational levels: 2024-2025 Biochemistry-1 7  I- Primary structure Def.: The sequence of amino acids in a protein Many genetic diseases result in proteins with abnormal amino acid sequences, which cause improper folding and loss or impairment of normal function. Imp.: If the primary structures of the normal & mutated proteins are known, this information may be used to diagnose or study the disease Bonds.: Amino acids are joined covalently by peptide bonds Molecular Weight of Proteins: The size of a protein or a polypeptide is reported as its mass in daltons (dalton = 1 atomic mass unit) or as its molecular weight (MW) 2024-2025 Biochemistry-1 8  II- Secondary structure Def.: forms regularly repeating structures termed the secondary structure. If proteins contained only primary structure, they would form long, spaghetti-like molecules. However, the polypeptide backbone of proteins Imp.: does not assume such a random structure, but instead the coils and folds forms secondary structure. Bonds.: H- bonds between repeating constituents of the polypeptide backbone Types: -helix, -pleated sheet -turns 2024-2025 Biochemistry-1 9 2024-2025 Biochemistry-1 10  A- -helix: a rod-like structure → side chains of the amino acids extending outward from the central axis of coiled polypeptide backbone. Hydrogen bonds extend down the spiral from carbonyl oxygen of one peptide linkage to the - NH- group of a peptide bond four residues ahead in the primary sequence (intra-chain). These hydrogen bonds are individually weak but collectively are the major force stabilizing the helical structure. A very diverse group of proteins contains α -helices. 2024-2025 Biochemistry-1 11  fibrous proteins Ex1: structure is nearly entirely α -helical → major component of tissues [as hair keratins & skin] → their rigidity is determined by number of disulfide bonds between constituent polypeptide chains. EX2: globular proteins Myoglobin The structure is also highly α -helicals.  Amino acids that disrupt an α-helix: disrupts an α-helix → its secondary -NH2 → not geometrically compatible Proline with the right-handed spiral of α -helix. Instead, it inserts a kink in the chain, which interferes with the smooth, helical structure. ↑↑↑ of charged amino acids (Ex:, glutamate, aspartate, histidine, lysine, or charged arginine) → disrupt helix by forming ionic bonds, or electrostatically amino acids repelling each other. Such as tryptophan, or valine or isoleucine → branch at β -carbon (the first amino acids with bulky carbon in the R-group, next to α -carbon) can interfere with formation of the side chains α -helix if they are present in large number 2024-2025 Biochemistry-1 13  B- The -pleated sheet: In some proteins, the polypeptide chains line up side by side to form sheets of molecules, Surfaces appear “pleated”, called the -pleated sheet. All of peptide bond components are involved in H- bonds. In globular proteins, β-sheets→ always have a right-handed curl, or twist, when viewed along the polypeptide backbone→ often form core. The structure is stabilized by hydrogen bonds Alignment: with N-terminal & C- terminal ends of β-strands Antiparallel alternating Parallel with all N- terminal of β-strands aligned together. 2024-2025 Biochemistry-1 14  The H-bonds could be: interchain H- bonds intrachain H- bonds formed in different polypeptide. formed in same polypeptide. Comparison of a β-sheet & an α-helix: 2024-2025 Biochemistry-1 15  C- The -bends (turns): It reverses the direction of a polypeptide chain, forming sharp bends that redirect the polypeptide backbone back toward the interior, to form a compact, globular shape. Found usually on surface of protein & often include charged residues. They often connect successive strands of antiparallel β-sheets. Generally composed of three or four amino acids.→ one of which: Proline →causes a “kink” Glycine →with smallest R-group→ frequently found in β-bends. Β-bends (U-shaped secondary structures) are stabilized by the formation of H- & ionic bonds. 2024-2025 Biochemistry-1 16  III- Tertiary structure of proteins Def.: The overall 3D-shape of an entire protein molecule Formation or folding of polypeptides into domains (basic units of structure & function), Imp.: and the final arrangement of domains within a protein. Bonds: By interactions between R groups, rather than between backbone constituents. Hydrogen bonds: Ionic interactions: side chains containing loosely bound hydrogens, such as Negatively Charged (COO¯) can interact with in the alcohol groups of serine and threonine, positively charged groups, such as the -amino (NH3+) They can form H-bonds with electron-rich atoms such as of lysine forming ionic bond (salt bridge). N-atoms of histidine or C=O of -COOH groups, CONH groups, & peptide bonds. 2024-2025 Biochemistry-1 17  Hydrophobic interactions: Covalent cross-linkages: a.a. with Non-polar side chains tend to fold Disulfide bond → covalent bond between into interior of the protein molecule → (-SH) of 2 cysteine residues, → formation of associate with other hydrophobic amino acids. cystine. 2 cysteines may be separated from each other In contrast, a.a. with polar or charged side by many amino acids in the primary sequence chains tend to be located on the surface of or even be located on two different polypeptide the molecule in contact with water molecules chains; of the solvent. Folding of the polypeptide chain(s) brings cysteine residues into proximity and permits covalent bonding of their side chains. it contributes to the stability of 3D shape of the protein molecule & prevents it from becoming denatured in the extracellular environment. 2024-2025 Biochemistry-1 18  Globular proteins Fibrous proteins Types such as collagen. such as myoglobin. Most proteins: are roughly spherical shape, consisting of variable amounts of coils with no regular structure. The fundamental functional and 3D structural units of polypeptides. Polypeptide chains > 200 amino acids in length generally consist of 2 or more domains. Core of a domain → combinations of supersecondary structural elements (motifs). Domain Folding of the peptide chain within a domain usually occurs independently of folding in other domains → Therefore, each domain has the characteristics of a small, compact globular protein that is structurally independent of the other domains in the polypeptide chain 2024-2025 Biochemistry-1 19  IV- Quaternary protein structure Formed of many proteins (subunits) (two or more) → each made up of multiple polypeptide chains Def.: These subunits: the same (as in a homodimer) or different (as in a heterodimer). The quaternary structure refers to how these protein subunits interact with each other and arrange themselves to form a larger aggregate protein complex. The final shape of the protein complex is once again stabilized by various interactions, Bonds: including H-bonding, disulfide-bridges & salt bridges. Hemoglobin is a globular protein Collagen is a fibrous protein consisting of Ex: consisting of 4 polypeptides: three polypeptides coiled like a rope. two alpha + two beta chains. 2024-2025 Biochemistry-1 20  Post-translational modifications of amino acids 2024-2025 Biochemistry-1 21  Nearly every protein in a cell is chemically modified after its synthesis on a ribosome. Such modifications may alter the activity, life span, or cellular location of proteins. These modifications may entail the linkage of a chemical group to the free –NH2 or –COOH group at either end of a protein or to a reactive side chain group in an internal residue. 1. Acetylation: addition of long lipid-like groups. Residues at or near the termini of some How The addition of an acetyl group (CH3CO) to the membrane proteins are chemically modified by amino group of the N-terminal residue the addition of long lipid-like groups = Importance hydrophobic “tails. most common form of chemical modification. Controlling life span of proteins within cells to anchor proteins to the lipid bilayer, constitutes one way that cells localize certain because nonacetylated proteins are rapidly proteins to membrane. degraded by intracellular proteases. 2024-2025 Biochemistry-1 22  3-Phosphorylation of amino acids 4. Glycosylation: Glycosylation of side chains of asparagine, Phosphorylation of serine, threonine, tyrosine, How serine, & threonine → attachment of linear & and histidine residues. branched carbohydrate chains. Importance In Many secreted & membrane proteins to: Certain proteins whose activity is regulated by Promotes folding of some proteins. reversible phosphorylation and Stabilizes the structure of proteins. dephosphorylation such as enzymes. Important in cell-cell adhesion 2024-2025 Biochemistry-1 23  5. Hydroxylation of proline and lysine residues in collagen How Hydroxylation of: Proline → Hydroxyproline this requires O2, Fe2+, & reducing agent vitamin C. Lysin → hydroxylysine Importance For the formation and stabilization of the triple helix of collagen. Deficiencies of these elements: hydroxylating enzymes [prolyl hydroxylase & lysyl hydroxylase] are unable to function. 6. Methylation of histidine residues in membrane receptors 7. Υ-carboxylation of glutamate in prothrombin, an essential blood-clotting factor: 2024-2025 Biochemistry-1 24  9. Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes: The life span of intracellular proteins varies from: In proteosomes: a chemical modification of a lysine side chain by the addition of ubiquitin, a 76-residue polypeptide, followed by degradation of the ubiquitin-tagged protein by a specialized proteolytic machine. The process of ubiquitinoylation is repeated many times, with each subsequent ubiquitin molecule being added How to the preceding one. The resulting polyubiquitin chain is recognized by a proteasome. The numerous proteasomes dispersed throughout the cell cytosol proteolytically cleave ubiquitin-tagged proteins in an ATP dependent process that yields short (7- to 8-residue) peptides and intact ubiquitin molecules. 2024-2025 Biochemistry-1 25  9. Ubiquitin Marks Cytosolic Proteins for Degradation in Proteasomes: for Eukaryotic cells have several intracellular proteolytic pathways for degrading misfolded or denatured proteins, normal proteins whose concentration must be decreased, and extracellular proteins taken up by the cell. Importance Cellular proteins degraded by the ubiquitin-mediated pathway fall into one of two general categories: (1) Native cytosolic proteins whose life spans are tightly controlled (2) proteins that become misfolded in the course of their synthesis in the endoplasmic reticulum (ER). Both contain sequences recognized by the ubiquitinating enzyme complex 2024-2025 Biochemistry-1 26 2024-2025 Biochemistry-1 27 2024-2025 Biochemistry-1 28  Learning objectives: to learn” Level of folding of the protein? Post-translational amino acids? 2024-2025 Biochemistry-1 29  Thanks 2024-2025 Biochemistry-1 30