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Chapter 3

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Kim Dej

Chapter 3- Protein Structure and Function - Proteome: entire protein complement of an organism 3.1 Hierarchial Structure of Proteins - A protein chain folds into a shape stabilized by noncovalent interactions between regions of the linear sequence. - Function is derived from 3D structure and structure is derived by amino acid sequence. Primary Structure - Linear arrangement of amino acids. - Linked by peptide bonds. - Backbone exhibits directionality. - Size of a protein or polypeptide is reported as its mass in daltons or molecular weight (MW). Secondary Structure - Spatial arrangements resulting from the folding of localized parts of a polypeptide chain. - In the absence of stabilizing noncovalent interactions, a polypeptide assumed a random coil structure. - Alpha helices and beta sheets are the major internal supportive elements in proteins. The α Helix - The carbonyl oxygen atom of each peptide bond is hydrogen-bonded to the amide hydrogen atom of the amino acid four residues toward the C-terminus. - Confers a directionality on the helix - The arrangement holds the backbone in a rodlike cylinder from which the side chains point outward. The β Sheet - Consists of laterally packed B strands - Hydrogen bonding between backbone atoms in adjacent B strands, within either the same polypeptide chaon or between different polypeptide chains, forms a B sheet. - Have a directionality defined by the orientation of the peptide bond. Turns - Composed of 3 or 4 residues, turns are located on the surface of a protein, forming sharp bends that redirect the polypeptide backbone back toward the interior. - They are stabilized by a hydrogen bond between their end residues. - Glycine and proline are commonly present in turns. - A polypeptide may also contain larger bends, or loops. Tertiary Structure - Overall conformation of a polypeptide chain. - Stabilized by hydrophobic interactions between the nonpolar side chains, hydrogen bonds between polar side chains, and peptide bonds. - Tertiary structure is not rigidly fixed. - The simplest way to represent 3D structure is to trace the course of the backbone atoms with a solid line. Motifs - Particular combinations of secondary structures. - Build up the tertiary structure of a protein. - The helix-loop-helix is a Ca2+ binding motif – oxygen atoms in the invariant residues bind a Ca2+ ion through ionic bonds. - The zinc finger motif- an a helix and two B strands with an antiparallel orientation, form a fingerlike bundle help together by a zinc ion. - Coiled coil- each polypeptide chain contains a-helical segments in which the hydrophobic residues are in a regular pattern- a repeated heptad sequence. - The overall helical structure is amphipathic. Structural and Functional Domains - EGF, epidermal growth factor is a domain. - It Is a small soluble peptide hormone that binds to cels in the embryo and in skin and connective tissue in adults causing them to divide. Members of protein families have a common evolutionary ancestor - 3D structures of myoglobin and the α, β subunits of hemoglobin are similar. - Many identical or chemically similar residues are found in identical positions throughout primary structures of both proteins. - Proteins that have a common ancestor are called homologs. - Can trace their lineage by comparing their sequences. 3.2 Folding, Modification and Degradation of proteins - Assembly of amino acids is dictated by Mrna. - The cell has error-checking processes - Misfolded proteins are degraded Information for folding is encoded in the sequence - All molecules adopt a native state conformation (most stable form) - In vitro protein folding is a self-directed process. Folding of proteins in vitro is promoted by chaperones - Cells require a faster, more efficient mechanism for folding proteins into their correct shapes. - Two general families of chaperones: o Molecular chaperones: bind and stabilize unfolded or partly folded proteins, thereby preventing these proteins from aggregating and being degraded.  Consist of Hsp70 in cytosol, BiP in ER and DnaK in bacteria.  When bound to ATP Hsp70-like proteins assume an open form in which an exposed hydrophobic pocket transiently binds to exposed hydrophobic regions of the unfolded target protein.  Hydrolysis of the bound ATP causes molecular chaperones to assume a closed form in which a target protein can undergo folding. o Chaperonins: directly facilitate the folding of protein.  Formed fron two rings of oligomers.  Eukaryotic chaperonin- TriC  Bacterial, mitochondrial, chloroplast chaperonin- GroEL  In bacteria, a partly folded or misfolded polypeptide is inseted into the cavity of GroEL, where it binds to the inner wall and folded into its native conformation  In an ATP- dependent step, GroEL undergoes a conformational change and releases the folded protein, a process assisted by a co-chaperonin, GroES , which caps the ends of GroEL. Many proteins undergo chemical modification of amino acid residues - Acetylation: the attachment of these hydrophobic tails which function to anchor proteins to the lipid bilayer, constitutes one way that cells localize certain proteins to membranes. - Phosphorylation - Glycosylation - Hydroxylation - Methylation - Y-carboxylation Peptide segments sometimes removed after synthesis - After synthesis, some proteins undergo irreversible changes that do not entail changes in individual amino acid residues. o Sometimes called processing - Most common form is enzymatic cleavage of a backbone peptide bond by proteases. - Proteolytic cleavage is a common mechanism for activating enzymes. - Protein self-splicing takes place in bacteria and some eukaryotes. o An internal segment of a polypeptide is removed and the ends of the polypeptide are rejoined. - The excised peptide appears to eliminate itself from the protein by a mechanism similar to that used in the processing of some RNA molecules. Ubiquitin marks cytosolic proteins for degradation in proteasomes - The activity of a cellular protein depends on the amount present, which reflects the balance between its rate of synthesis and rate of degradation in the cell. - Eukaryotic cells have several intracellulalar proteolytic pathways for degrading misfolded or denatured proteins, normal proteins whose concentration must be decreased and extracellular proteins taken up by the cell. o One major pathway is degradation by enzymes within lysosomes  Directed primarily toward extracellular proteins taken up by the cell and aged or defective organelles of the cell. o There are also cytosolic mechanisms for degrading proteins. o Chemical modification of ubiquitin, followed by degradation of the ubiquitin-tagged protein by a specialized proteolytic machine Ubiquitination is a 3 step process 1. Activation of ubiquitin-activating enzyme (E1) by the addition of a ubiquitin molecule- requires ATP. 2. Transfer of this ubiquitin molecule to a cysteine residue in ubiquitin-conjugating enzyme(E2) 3. Formation of a peptide bond between the ubiquitin molecule bound to E2 and a lysine residue in the target protein, a reaction catalyzed by ubiquitin ligase. (E3) - This process is repeated many times, with each subsequent ubiquitin molecule being added to the preceding one. - The resulting polyubiquitin chain is recognized by a proteasome which cleaves in an ATP dependent process that yields short peptides and intact ubiquitin molecules. - Cellular proteins degraded by the ubiquitin-mediated pathway fall into one of the two general categories: o Native cytosolic proteins whose life spans are tightly controlled o Proteins that become misfolded in the course of their synthesis in the ER - Both contain sequences recognized by the ubiquinating enzyme complex. - Cyclins are cytosolic proteins whose amount are tightly controlled throughout the cell cycle. - The misfolding of proteins in the ER exposes hydrophobic sequences. These are transported to the cytosol where ubiquitinating enzymes recognize the exposed hydrophobic sequences. Digestive proteases degrade dietary proteins - The major extracellular pathway for protein degradation is the system of digestive proteases that breaks down ingested proteins into peptides and amino acids in the intestinal tract. - Three classes of proteases: o Endoproteases: attack selected peptide bonds within a chain. Ex: pepsin o Exopeptidases: sequentially remove residues from the N-terminus or C-terminus of a protein. o Peptidases: split oligopeptides containing as many as about 20 amino acids into di and tripeptides and individual amino acids. Alternatively folded pr
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