Lecture 1-2 Protein Structure and Function

• The four building blocks of cells are sugar, fatty acids, amino acids, and nucleotides.
• Macromolecules are produced by both condensation and hydrolysis reactions.
• Condensation reactions are when two molecules combine to form a single molecule, removal of water.
• Hydrolysis reactions use water to break down molecules, releasing energy.
• Cells couple hydrolysis and condensation reactions because hydrolysis reactions release energy and that energy is used to start a condensation reaction.
• An amino acid consists of an alpha carbon that has an amino acid, carboxyl group, hydrogen and a side chain/R group.
• In pH7, free amino acids exist in ionized form, meaning the amino group accepts a proton and the carboxyl group donates a proton.
• N-terminus is the amino acid group; first amino acid in the polypeptide chain.
• C-terminus is the carboxyl group; last amino acid in the polypeptide chain.
• Polar amino acids are hydrophilic and can form hydrogen bonds, they like water.
• Acidic polar have a negatively charged side chain.
• Basic polar have a positively charged side chain.
• Nonpolar amino acids are hydrophobic and cannot form hydrogen bonds.
• Covalent bonds help stabilize the backbone of proteins (outside of cell), form between amino acids linking them.
• Noncovalent interactions between polar amino acids influence the 3d shape of proteins (in the cell), including hydrogen bonds, electrostatic interactions, and van der waals interactions.
• Chaperones are proteins that help refold proteins.
• A ligand is any substance that is bound by a protein.
• Alpha helices and beta sheets are common structures in proteins because they rely on hydrogen bonding between N-H and C=O groups and proteins have amino and carboxyl groups on their chains.
• Chaperone proteins form an isolation chamber so that protein can fold without aggregating with other proteins.
• Proteins that are secreted by cell or attached to outer surface of plasma membrane have disulfide bonds.
• Disulfide bonds are covalent bonds between cysteines that stabilize protein structure or combine different polypeptide chains (that happen outside of the cell).
• Protein shape dictates protein function.
• Misfolding of proteins causes protein aggregation in a cell.
• Chaperone proteins can form an isolation chamber so that protein can fold without aggregating with other proteins.
• Hydrophobic interactions determine the shape of protein; nonpolar amino acids cluster in core
• Protein domains are regions in the polypeptide chain that can fold into stable structure and perform a function.
• Proteins use weak noncovalent bonds to bind specific ligands and other proteins.
• Protein denaturing is a change in protein shape that reduces the proteins activity.
• Chaperone proteins help refold proteins by looking for hydrophobic patches.
• The four different levels of protein structure are: Primary (sequence of amino acids), Secondary (hydrogen bonding that forms alpha helices and beta sheets), Tertiary (collection of secondary structure), and Quaternary (binding of different polypeptide chains (subunits)).
• Protein subunits are single polypeptide chains that come together to form larger protein complex.
• Refolding proteins allows them to have a function.
• Protein aggregation is when unfolded proteins hydrophobic part cluster together.
• The E1, E2, and E3 enzymes are involved in protein degradation.
• Heat shock proteins (Hsp) are chaperone proteins that refold proteins that have been denatured.
• Hsp70 binds extend releases until the protein is long enough to correctly fold.
• Transcriptional regulation, post-transcriptional regulation, post-translational regulation, and protein degradation are different strategies a cell can use to regulate protein activity.
• Protein phosphorylation is the attachment of a phosphate group to an amino acid side chain.
• Hsp60 and Hsp70 work together, with Hsp60 preparing unfolded or misfolded proteins for entry into the Hsp60 chaperonin complex.
• Hsp60 needs Hsp70 to bind and fold proteins after being synthesized by ribosomes.