Protein Structure and Function 2012 Student

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Part IHierarchical Structure of Proteins

Protein Structure and FunctionChap. 3



Primary Structure

N-term. C-term.



Secondary Structure-alpha ( a ) helix



Secondary Structure-beta ( ) sheet



Tertiary Structure



Motifs-Regular Combinations of Secondary Structure



Protein Domains

3° Structureof HA



Modular Nature of Proteins



Quaternary Structure of Proteins



Macromolecular Assemblies



Transcription Initiation Machinery



Conservation of Protein Structure andFunction Throughout Evolution



Structural Similarities of the Different Globins



Part II

Folding, Modification, andDegradation of Proteins



Molecular Chaperone-Mediated Protein Folding

1. ATP-bound Hsp70 binds to unfolded protein

2. Hydrolysis of ATP to ADP (release of P i) promotes folding

3. Exchange of ATP for ADP releases folded protein



Chaperonin Mediated Protein Folding



Chemical Modification of Amino Acid Residues



Protein Degradation-Protein Life span varies from a few minutes to the life of the cell

-Several pathways for degradation of proteins




-Several pathways for degradation of proteins1. Lysosomal-membrane bound organelle

-Interior is highly acidic and containshydrolytic enzymes

-Primarily degrade extracellular proteins takenup by the cell



Pathways for Lysosomal Degradation of Proteins

Fig. 5-20




-Several pathways for degradation of proteins1. Lysosomal-membrane bound organelle

-Interior is highly acidic and containshydrolytic enzymes

-Primarily degrade extracellular proteins takenup by the cell

2. Proteasome-directed degradation-Macromolecular machinethat degrades proteins than have been poly-ubiquitinated

-Ubiquitin-76 amino acid polypeptide that is covalentely

attached to lysine residues-Polyubiquitin chain is recognized by the proteasome-Degrades proteins in an ATP-dependent manner intoshort (7-8 amino acid) peptides



Ubiquitination and Proteasome-mediated Protein Degradation



Part III

Enzymes and Chemical Work of Cells



Antibody-Antigen Interactions are Highly Specific



Enzymes

-Catalyze chemical alteration of their ligands

-Ligand=Substrate-Most chemical reactions in the cell are catalyzed byenzymes

-Enzymes do not alter the reaction

-Enzymes increase the reaction rate by lowering the

activation energyi.e.-accelerate the formation of products fromreactants without altering the value of G



G

Enzymes Accelerate the Reaction Rate



Enzyme Active Site Binds the Substrate

Kinase Core-240 Amino aciddomain of PKA

Protein Kinase A(PKA)



No Substrate bound Substrate binding causesconformational change tobring ATP and peptidebinding sites closer together

Conformational Change Caused by Substrate Binding

E Ki i



Enzyme Kinetics-Conversion of one substrate into a product using two differentenzyme concentrations and increasing substrate concentrations

E Ki i



Enzyme Kinetics-Conversion of one substrate into a product using constant enzymeconcentration and two substrates

-Enzyme has different affinity for the two substrates



Enzymes in Common Pathways

Diffusion of product to nextenzyme in the pathway

Scaffold-keepsenzymes closeto each other

Multifunctional Enzyme-enzymeencoded by a single gene that hasmore than one catalytic activity



Pyruvate Dehydrogenase Complex

P IV



Part IV

Mechanisms for RegulatingProtein Function



Cooperative Binding of O 2 to Hemoglobin



Ligand Binding Activates Protein Kinase A Catalytic Subunit

l d l 2+ d h



Calmodulin Functions as Ca 2+ Binding Switch Protein

GTP Bi di P t i F ti M l l S it h



GTP-Binding Proteins Function as Molecular Switches

Regulation of Protein Function by Phosphorylation/Dephosphorylation



Regulation of Protein Function by Phosphorylation/Dephosphorylation

Protein Structure and Function 2012 Student

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