Protein Synthesis and Structure
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Transcript of Protein Synthesis and Structure
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Protein Synthesis and StructureSection 2-4
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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
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Protein Functions• Enzymatic• Structural• Storage• Transport• Hormonal• Receptor• Contractile and motor• Defensive
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Four Levels of Protein Structure
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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
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Primary Structure• Amino acids are linked together with
dehydration reactions
• Peptide bonds- the bonds between amino acids
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Primary Structure• The chain will have two ends:• An amino end- known as the N-
terminus
• A carboxyl end- known as the C-terminus
• Primary structure is achieved through the processes of transcription and translation
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Secondary Structure• Refers to the coils and folds in the polypeptide chain due to
hydrogen bonds between repeating areas on the polypeptide backbone
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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
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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
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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
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Quaternary Structure• Overall shape of the protein caused by the association of two
or more polypeptide chains• NOT ALL PROTEINS HAVE QUATERNARY STRUCTURE
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Protein Synthesis
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General Information• Also called gene
expression
• DNA provides the blueprints for the building of proteins
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General Information• Involves two processes:
• Transcription- copying DNA into mRNA
• Translation- translates the code from nucleic acid into amino acid at the ribosome
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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
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Prokaryotes vs. Eukaryotes
Prokaryotes
• Only one compartment (no nucleus)• Transcription and
Translation occur simultaneously
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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
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The Genetic Code• Triplet Code- the flow if information from gene (DNA) to
protein is written in the DNA as non-overlapping, three-nucleotide 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’
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The Genetic Code• Codons- each three base sequence on the mRNA strand• Each codon codes for a specific amino acid
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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
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Special Codons• AUG= start
• UAA, UAG, UGA= stop
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Transcription
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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
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Initiation
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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
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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
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RNA Processing
EUKARYOTIC CELLS ONLY
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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
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RNA Processing
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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
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Translation
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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
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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
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Translation- The Process
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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
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Initiation• Translation initiation complex forms- the large ribosomal
subunit attaches with the assistance of initiation factors and an expenditure of energy
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Elongation
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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
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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
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Forming a Functional Protein
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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???
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Chaperonins• Proteins that assist in the proper folding of other proteins by
shielding them form the cell environment
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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 N-terminus
• Single polypeptides may by cut into two or more smaller pieces
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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
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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
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Changes in Temperature• Excessive heat can cause movement to overpower sensitive
hydrogen bonds
• Excessive cold will slow the protein down substantially
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Changes in pH• All proteins have an optimal pH at which they function
• Optimal pH is not necessarily 7