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Protein Synthesis and Structure Section 2-4 Protein Functions: General Information • Proteins account for almost 50% of the dry mass of most cells • Proteins are the most structurally sophisticated molecules known • Each protein has a specific 3-diminsional shape, or “confirmation” that is vital to its function Protein Functions • • • • • • • • Enzymatic Structural Storage Transport Hormonal Receptor Contractile and motor Defensive Four Levels of Protein Structure Primary Structure • The unique sequence of amino acids that make up a polypeptide • Amino acids: • • • • An asymmetrical carbon An amino group (contains Nitrogen) A carboxyl group A side chain (R group) which makes each amino acid unique Primary Structure • Amino acids are linked together with dehydration reactions • Peptide bonds- the bonds between amino acids Primary Structure • The chain will have two ends: • An amino end- known as the Nterminus • A carboxyl end- known as the Cterminus • Primary structure is achieved through the processes of transcription and translation Secondary Structure • Refers to the coils and folds in the polypeptide chain due to hydrogen bonds between repeating areas on the polypeptide backbone Secondary Structure • Alpha helix (α helix)- a delicate coil held together by hydrogen bonding between every fourth amino acid • Beta pleated sheet (β pleated sheet)- two or more regions of a polypeptide chain lying side by side and connected by hydrogen bonds between the two parallel polypeptide back bones Tertiary Structure • Folding due to interactions between the amino acid side chains • Main causes of tertiary structure • Hydrogen bonds between polar R-groups • Hydrophobic interactions between nonpolar R groups causes them to clump together and form Van der Wall’s interactions • Dislufide bridges between two sulfhydryl groups Tertiary Structure: Main Causes • Hydrogen bonds between polar R-groups • Hydrophobic interactions between nonpolar R groups causes them to clump together and form Van der Wall’s interactions • Dislufide bridges between two sulfhydryl groups Quaternary Structure • Overall shape of the protein caused by the association of two or more polypeptide chains • NOT ALL PROTEINS HAVE QUATERNARY STRUCTURE Protein Synthesis General Information • Also called gene expression • DNA provides the blueprints for the building of proteins General Information • Involves two processes: • Transcription- copying DNA into mRNA • Translation- translates the code from nucleic acid into amino acid at the ribosome Evolutionary Advantage of Transcription and Translation • DNA is protected inside the nucleus • Using an RNA intermediate allows multiple copies of a protein to be made at once because many mRNA molecules can be made from one gene, then translated repeatedly Prokaryotes vs. Eukaryotes Prokaryotes • Only one compartment (no nucleus) • Transcription and Translation occur simultaneously Prokaryotes vs. Eukaryotes Eukaryotes • Transcription occurs in the nucleus • The primary transcript is then modified (RNA processing) before leaving the nucleus • Translation occurs in the cytoplasm at the ribosome The Genetic Code • Triplet Code- the flow if information from gene (DNA) to protein is written in the DNA as non-overlapping, threenucleotide segments • Template Strand: • The mRNA is complimentary to the template strand • The DNA is read in the 3’ to 5’ • The mRNA is synthesized and read from 5’ to 3’ The Genetic Code • Codons- each three base sequence on the mRNA strand • Each codon codes for a specific amino acid Redundant but not Ambiguous • Redundant- multiple codons can code for the same amino acid • Not Ambiguous- no codon codes for more than one amino acid Special Codons • AUG= start • UAA, UAG, UGA= stop Transcription Initiation • RNA polymerase binds to the promoter • The promoter is a specific sequence that tells the RNA polymerase where to bind and determines what DNA strand will serve as the template • In eukaryotes, specific proteins called transcription factors assist the RNA polymerase in binding and forming the transcription initiation complex Initiation Elongation • RNA polymerase adds nucleotides to the 3’ end of the growing RNA molecule • Complimentary base pairing occurs • The new RNA molecule peals away from the DNA template and the DNA reforms Termination • In prokaryotes, the RNA polymerase detaches after the termination signal is transcribed • In eukaryotes, the RNA polymerase transcribes the polyadenylation signal sequence then the mRNA is cut off of the RNA polymerase RNA Processing EUKARYOTIC CELLS ONLY Altering of the Ends of the mRNA • 5’ cap- modified guanine molecule added on the 5’ end • Poly-A-tail- 50-250 adenine nucleotides are added to the 3’ end • • • • Functions: Facilitate export from the nucleus Protect the mRNA from degradation by enzymes Assist the ribosomes in attaching in the cytoplasm RNA Processing RNA Splicing • Removal of large portions of the mRNA • snRNPs (“snurps”) recognize and cut out areas of the mRNA • Introns- the portions of the mRNA that are removed • Exons- the portions of the mRNA that exit the nucleus Translation Transfer RNA, tRNA • Translates nucleotides into amino acids • One end has an anticodon, complementary to the mRNA codon • The other end is bound to an amino acid • Excellent example of how structure fits function Ribosomes • Contain three sites for holding tRNA: • P site- holds the growing polypeptide chain • A site- holds the tRNA that is carrying the next amino acid in the chain • E site- where the tRNA leaves the ribosome • Exit Tunnel= where the polypeptide leaves the ribosome Translation- The Process Initiation • Small ribosomal subunit binds the mRNA and the initiator tRNA • Subunit scans the mRNA until it reaches the start codon, establishing the correct reading frame as the tRNA hydrogen bonds to the start codon Initiation • Translation initiation complex forms- the large ribosomal subunit attaches with the assistance of initiation factors and an expenditure of energy Elongation Elongation • The ribosome reads the mRNA in the 5’ to 3’ direction • Anticodon of the incoming tRNA hydrogen bonds to the mRNA codon in the A site • The peptide bond forms between the amino acid on the tRNA of the A site and the growing polypeptide chain in the P site • Translocation of the tRNA shifts the A site tRNA to the P site and the P site tRNA to the E site so it can exit Termination • Release factor: • Added when stop codon is reached • Causes the addition of a water molecule to the end of the polypeptide • The polypeptide is released Forming a Functional Protein Protein Folding • Folding occurs as the protein is being synthesized • Folding is dependent on • The properties of the peptide chain • The physical and chemical properties of the environment WHY MIGHT THIS BE A PROBLEM??? Chaperonins • Proteins that assist in the proper folding of other proteins by shielding them form the cell environment Post-Translational Modification • Chemical modification by the attachment of sugars, lipids, phosphate groups, or other components • Enzymes may remove one or more amino acids from the Nterminus • Single polypeptides may by cut into two or more smaller pieces Denaturation • The changes in a protein’s native conformation that renders it biologically inactive • • • • Factors that cause denaturation: Change in the environment Change in temperature Change in pH Changes in Environment • If moved from an aqueous environment to a nonpolar organic solvent, the protein will turn inside out • Chemicals can disrupt disulfide and hydrogen bonds that stabilize secondary and tertiary structure Changes in Temperature • Excessive heat can cause movement to overpower sensitive hydrogen bonds • Excessive cold will slow the protein down substantially Changes in pH • All proteins have an optimal pH at which they function • Optimal pH is not necessarily 7