IPostTransW11 - Protein Processing & Function Protein...

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Unformatted text preview: Protein Processing & Function Protein Shape Determines Function • Post-translation modification – polypeptide Æ functional protein • Specific 3-D shape • Shape is critical to function Protein Structure A protein’s specific function depends on its shape and distribution of functional groups. • Denaturation = loss of shape Ë loss of function DNA polymerase: its active site fits DNA Levels of Protein Structure ÿPrimary lysozyme Primary structure of protein: the amino acid sequence ÿPolypeptide sequence ÿSecondary ÿFolding coils & pleats ÿTertiary ÿComplete 3-D shape Primary structure is due to strong covalent peptide bonds joining amino acids together. ÿQuarternary ÿCombining polypeptides lysozyme Primary Structure & Protein Trafficking Leading sequence of amino acids in a polypeptide being synthesized determines its fate: cytosolic , membrane-bound, nuclear, or secreted. 1 Polypeptide synthesis begins on a free ribosome in the cytosol. 2 An SRP binds to the signal peptide, halting synthesis momentarily. 3 The SRP binds to a receptor protein in the ER membrane. This receptor is part of a protein complex (a translocation complex) that has a membrane pore and a signal-cleaving enzyme. 4 The SRP leaves, and the polypeptide resumes growing, meanwhile translocating across the membrane. (The signal peptide stays attached to the membrane.) 5 The signalcleaving enzyme cuts off the signal peptide. 6 The rest of the completed polypeptide leaves the ribosome and folds into its final conformation. Ribosome mRNA Signal peptide Signalrecognition particle (SRP) SRP receptor CYTOSOL protein Signal peptide removed ER membrane Protein Modification of primary structure • Chemical alteration of amino acid side groups – Methylation; hydroxylation; etc. – E.g.: • N-terminal methyl- methionine fi protects peptide from amino-peptidases. • Collagen contains many hydroxy -prolines & hydroxy lysines fi allows condensation with oligosaccharides Translocation complex Figure 17.21 Heyer 1 Protein Processing & Function Modification of primary structure • Cleavage of polypeptide chain – – – Zymogens: • inactive pre-enzyme minus fragment Æ active enzyme Secondary structure: group of amino acids folded repetitively to make a discrete shape. Isolation of fragments within a protein: • Insulin polypeptide folds over to be cross-linked with itself, and is then cleaved into two polypeptides due to hydrogen bonds between amino acids’ backbones. Multiple products: • Pro- opio melano cortin (POMC) — translated polypeptide cleaved into fragments: 1. Endorphin ( opioid ) 2. Melanocyte stimulating hormone 3. Corticotropin stimulating hormone Tertiary structure: the overall 3-d conformation of a polypeptide. lysozyme Tertiary Structure (Salt bridge) Tertiary structure involves several kinds of bonds between side groups of amino acids at various locations along the polypeptide backbone. Covalent disulfide bonds between cystine residues are the strongest and most stable. Quaternary Structure Most proteins are hydrophilic outside, hydrophobic inside. Tertiary structure is maintained by amino acids interacting with other amino acids and with water. Heyer Multiple polypeptides joined to make a single protein. (May be the same or products of separate genes) 2 Protein Processing & Function Quaternary Structure Hemoglobin Genes and Gene Products 2 b-chain polypeptides 2 a-chain polypeptides collagen hemoglobin Hemoglobin Gene Product Production Yolk sac Liver Spleen Bone marrow http://www.mun.ca/biology/desmid/brian/BIOL3530/DB_Ch09/fig9_24.jpg Prosthetic groups Non-amino acid groups added to a polypeptide. • Carbohydrate fi glycoprotein HbF : 2α and 2γ HbE : 2ζ and 2ε HbA1 : 2α and 2β HbA2 : 2α and 2δ • Lipid fi lipoprotein • Nucleic acid fi nucleoprotein • Phosphate fi phosphoprotein • “activated” protein • Metal ion fi metalloprotein Mehta, A. B., and A. V. Hoffbrand . 2000. Haematology at a glance, Blackwell Science, Malden, Mass. Hemoglobin Molecule Heyer • Heme (organic porphyrin ring with an iron core) fi hemoprotein Cytochrome C Cytochrome An electron carrier 3 Protein Processing & Function Protein Shape Determines Function How Proteins Fold v A protein’s function depends on its folding. • How do proteins get folded into the required conformation? DNA polymerase: its active site fits DNA DNA polymerase: its active site fits DNA HbA – ß chain HbS – ß chain val glu Hemoglobin Electrophoresis hydrophobic Homozygous HbS Sickle Cell Hemoglobin: folding depends on primary structure How Proteins Fold v A protein’s function depends on its folding. v There may be more than 1 way for a big polypeptide to fold. Heyer Heterozygous HbS Normal adult Normal neonate HbSC http:// themedicalbiochemistrypage .org/hemoglobin-myoglobin.html Protein folding: Is it all downhill? Ribonuclease can renature itself. This makes it an unusually tough protein. 4 Protein Processing & Function Designing a protein to fold Structure of an artificial protein predicted observed —hydrophobic amino acid residues Understanding protein structure is important Nutlin, a tumorsuppressing drug that mimics the shape of protein p53 (transcription factor). How Proteins Fold v A protein’s function depends on its folding. v There may be more than 1 way for a big polypeptide to fold. v Some proteins can fold on their own, but many require help. v Chaperonins are proteins that help fold other proteins. A Chaperonin unfolded folded Unfolded or incompletely folded proteins may be destroyed. Provides a “safe folding environment” — Probably binds to polypeptide, to induce the correct folding conformation Heyer 5 Protein Processing & Function Proteins the Molecular Machines v Incorrectly folded proteins don’t work, and they clump together (they become insoluble). v If not refolded or destroyed, they can accumulate and cause problems. ß Eg., excess accumulated misfolded proteins (plaques) in neural tissue Æ ßParkinson disease ßAlzheimers disease ßMad cow disease Prion Basics v Prions are an unusual kind of misfolded protein. Prions infectious p rotein a gents v Prions can cause CNS diseases like mad cow, scrapie, kuru, and Creutzfeldt-Jakob disease. v Prions can be transmitted from one individual to another. Prion Basics Prion Basics v Everybody has prion proteins (PrP). v Everybody has prion proteins (PrP). v PrP comes in 2 forms: good and bad. Prion protein structure is conserved. Heyer normal & p rion versions of P r P of 6 Protein Processing & Function Prion Basics v Everybody has prion proteins (PrP). v PrP comes in 2 forms: good and bad. v Bad PrP catalyzes the misfolding of good PrP, changing good PrP to bad. Prion Original prion Many prions Normal protein New prion Misfolded bad PrP catalyzes the misfolding of good PrP. Figure 18.13 Prion Basics Prion Disease: Open Questions v Everybody has prion proteins (PrP). v What does good PrP normally do? v PrP comes in 2 forms: good and bad. v How specifically does bad PrP convert good PrP? v Bad PrP catalyzes the misfolding of good PrP, changing good PrP to bad. v Consuming bad PrP can turn all your good PrP bad (chain reaction). • Transmitted by food, transfusions, transplants, brain extracts. Other Protein Folding Research v Can conversion be blocked? v Why isn’t PrP digested/destroyed when eaten? v How does bad PrP get to the brain? v How does bad PrP cause disease? Accumulations of misfolded proteins v Alzheimer’s disease is completely different from prion diseases. v Prion disease: misfolded protein catalyzes more misfolding. v However, both are caused by accumulations of misfolded proteins. v Alzheimer’s: cause of misfolding unknown, but failure of “unfolded protein response” pathway is key. Alzheimer’ s Heyer Creutzfeldt-Jakob Alzheimer’ s Creutzfeldt-Jakob 7 ...
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This note was uploaded on 09/02/2011 for the course BIOL 6B taught by Professor Heyer during the Spring '10 term at DeAnza College.

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