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Questions and Answers
Enzymes function effectively at the high pH found inside the lysosome.
False
Proteins can be labeled for degradation by a process called polyubiquitination.
True
The proteasome is a hollow, barrel-shaped complex containing protease activity.
True
Polypeptide chains cannot be modified after translation.
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Proteolytic cleavage is a process that activates zymogens.
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Each word of DNA consists of 3 nucleotides, which codes for 2 amino acids.
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Phosphorylation of proteins is an unregulated process.
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The genetic code is universal and applies to all species.
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A single amino acid can be coded for by multiple different codons.
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Steroid hormone receptors undergo a conformational change upon ligand binding.
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Tyrosine phosphorylation has the least important effects among the amino acids mentioned.
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An insertion of nucleotides causes a frame-shift mutation, which does not affect the remaining sequence.
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Huntington's disease can occur due to amplification of a codon between generations.
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The ribosome is a complex of protein and rRNA.
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A missense mutation in the β-globin gene involves a single nucleotide substitution that converts a glutamic acid codon to a valine codon.
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The P site of the ribosome binds incoming aminoacyl tRNA.
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TRNA molecules fold into a straight-line structure.
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Elongation involves the addition of amino acids to the amino end of the growing chain.
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Francis Crick proposed that there must be an adaptor molecule for nucleic acids to interact with amino acids.
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The ribosome moves along the mRNA in a 5’ to 3’ direction during translation.
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The initiator tRNA is located in the A site during the initiation of translation.
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The 'wobble' position refers to the first base in a codon.
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There are approximately 61 codons that code for amino acids and about 50 tRNAs.
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Peptide bond formation is catalyzed at the peptidyl transferase centre.
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GTP is required for the final assembly of the ribosome.
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The ribosome is composed solely of protein.
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The exit site (E site) contains aminoacyl tRNA.
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Aminoacyl-tRNA is formed when an amino acid is added to the 5' end of the tRNA molecule.
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Serine is coded by the codon UCC.
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Elongation involves the addition of amino acids to the amino end of the growing chain.
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The ribosome translocation moves by one codon along the mRNA.
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The peptidyl transferase activity of ribosome is responsible for the termination of protein synthesis.
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The empty tRNA moves into the A site after the peptide bond formation.
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A release factor recognizes a stop codon in the A site during termination.
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An Open Reading Frame (ORF) can start and end at random positions within a sequence of nucleotides.
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The genetic code is non-overlapping, meaning it is read as a continuous sequence from a fixed starting point.
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Each ‘word’ of DNA consists of 4 nucleotides and codes for 1 amino acid.
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Frame-shift mutations can occur due to insertions or deletions of nucleotides.
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Huntington's disease is caused by the deletion of codons in the genetic code.
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The genetic code translates nucleic acid sequences to amino acid sequences, where a codon consists of 4 nucleotides.
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In the translation process, termination factors are essential for the proper completion of protein synthesis.
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MRNA is not required for the process of translation.
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An insertion of nucleotides typically leads to a frame-shift mutation, which can significantly affect the protein's function.
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Phosphorylation of proteins can affect their activity, localization, and function.
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The ribosome is solely composed of ribosomal proteins without any RNA components.
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The process of elongation in translation involves the addition of amino acids to the carboxyl end of the growing polypeptide chain.
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Codons can specify more than one amino acid, making the genetic code ambiguous.
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The third base in a codon is known as the 'wobble' position.
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Aminoacyl-tRNA is formed when an amino acid is added to the 5' end of the tRNA molecule.
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Ribosomes are exclusively composed of RNA.
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There are approximately 50 different tRNA types that correspond to 61 codons coding for amino acids.
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Transfer RNA molecules have a straight-line structure.
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Francis Crick suggested that nucleic acids interact with amino acids through a unique structure of adaptor molecules.
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The amino-acid addition process to tRNA is catalyzed by ribosomal RNA.
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Serine is encoded by the codon UCC according to the genetic code.
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The carboxyl end of the growing polypeptide chain is where amino acids are added during elongation.
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The P site of the ribosome is where incoming aminoacyl tRNA is first accepted.
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The initiator tRNA is located in the E site during the initiation of translation.
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During translation, the ribosome moves along the mRNA in the 3’ to 5’ direction.
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Recognition of the start codon by the tRNA is essential for the initiation of translation.
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GTP is not required during the initiation of translation.
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The ribosome has a specific site known as the decoding center for accepting tRNAs.
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During elongation, after forming a peptide bond, the ribosome translocates three nucleotides in the 5’ direction.
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During ribosome translocation, the peptidyl chain is moved to the A site.
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Peptidyl transferase activity involves the formation of peptide bonds at the P site.
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Termination of translation occurs when a release factor binds to the A site.
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The path through the ribosome for each tRNA is A – E – P sites.
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Each elongation step involves the binding of a new aminoacyl tRNA in the P site.
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The lysosome contains degradative enzymes that specifically target proteins only.
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Regulating protein activity solely relies on the protein synthesis process, without any involvement of degradation.
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Cyclins are examples of proteins that undergo rapid turnover to control the cell cycle progression.
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Protein levels, protein location, and post-translational modification are the only methods used by a cell to regulate protein activity.
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Protein degradation is an unnecessary process and does not contribute to cellular homeostasis.
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The proteasome is found exclusively in the nucleus and cannot be located in the cytoplasm.
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Proteins can undergo various covalent modifications after translation, including glycosylation.
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Steroid hormone receptors require a conformational change to release their inhibitory subunits.
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Reversible phosphorylation can occur on all amino acid residues in a protein equally.
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Zymogens are active forms of enzymes that do not require activation by cleavage.
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The ratio of phosphorylated serine to threonine to tyrosine residues is approximately 10:1:100.
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Ligand binding to a protein does not alter the protein's shape or its active conformation.
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Proteolytic cleavage does not play a role in the processing of insulin from its precursor form.
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An Open Reading Frame (ORF) is a set of codons that runs continuously and always begins with a stop codon.
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The genetic code is redundant, meaning multiple codons can code for the same amino acid.
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A single nucleotide insertion in a DNA sequence will always create a frame-shift mutation.
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The phenomenon of codon amplification can lead to increased severity of diseases such as Huntington's disease.
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The genetic code is specific and applies only to a limited number of species.
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The A site of the ribosome binds deacylated tRNA during translation.
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During elongation, peptide bonds are formed between adjacent amino acids at the P site.
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Recognition of the start codon by the tRNAmet molecule is crucial for the initiation of translation.
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The ribosome moves along mRNA in a 3’ to 5’ direction during translation.
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Initiation factors are not required for the ribosome to recognize the start of translation.
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The 60S ribosomal subunit assembles with the 40S subunit during the final assembly of translation.
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Elongation involves moving the ribosome three nucleotides at a time along the mRNA.
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The decoding center ensures that only tRNAs with anticodons that match the codon are rejected.
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The tRNA molecules typically have a cloverleaf secondary structure.
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There are 61 tRNA molecules that correspond to the 61 different coding codons.
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The anti-codon loop of tRNA pairs with mRNA codons based on non-specific rules.
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A single tRNA species can recognize only one specific codon.
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The aminoacyl-tRNA is formed by the addition of an amino acid to the 3' end of the tRNA molecule.
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Francis Crick theorized that there would be 20 different types of transfer RNA molecules due to the 20 amino acids.
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Transfer RNA does not undergo any post-transcriptional modifications.
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The ribosome is involved solely in the synthesis of nucleic acids.
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Study Notes
Lysosomes
- Enzymes within lysosomes function optimally at a low pH.
Proteasome
- Proteins targeted for degradation are labelled with a polyubiquitin tag.
- The proteasome recognizes this tag and degrades the protein.
- The proteasome is a multiprotein complex with protease activity.
Post-Translational Modification
- Modifications occur after translation to form mature functional proteins.
- Proteolytic cleavage removes sections of a protein, for example, in the processing of insulin and activation of trypsinogen.
- Covalent modifications include disulfide bond formation, phosphorylation, glycosylation, farnesylation, and GPI anchoring.
Ligand Binding
- Ligands can induce conformational changes in proteins, activating them, releasing inhibitory subunits, or altering their cellular location.
- Steroid hormone receptors undergo conformational change upon binding to their steroid ligand.
- This change allows the receptor to dimerize and enter the nucleus.
Proteolytic Cleavage
- Zymogens are inactive 'pro-enzymes' activated by proteolytic cleavage.
- Enterokinase is an example of an enzyme that activates zymogens.
- Proteolytic cascades, like the clotting cascade, involve a series of sequential proteolytic cleavage events.
Reversible Phosphorylation
- Phosphorylation of proteins on serine, threonine, and tyrosine residues is a tightly regulated process.
- Kinases add phosphate groups, while phosphatases remove them.
- Tyrosine phosphorylation plays a critical role in cellular signaling and regulation.
The Genetic Code
- The genetic code is non-overlapping, meaning codons are read in a continuous sequence.
- The 'reading frame' is defined by the start codon, and only one open reading frame (ORF) in a sequence contains functional information.
- Insertions or deletions within a sequence can cause 'frame-shift' mutations.
The Genetic Code: Properties
- Specific: Each codon always codes for the same amino acid.
- Universal: The code is largely the same across all species.
- Redundant: Multiple codons can code for the same amino acid.
- Non-overlapping: The code is read as a continuous sequence of bases, three at a time.
Disease and Coding Sequence Changes
- Huntington's disease results from the amplification of CAG codons in the HTT gene, causing an increased number of glutamine residues in the protein.
- Sickle Cell Disease (SCD) is caused by a single nucleotide substitution in the beta-globin gene, changing a glutamic acid codon to a valine codon.
tRNA
- tRNA molecules serve as adaptor molecules, translating the genetic code.
- These molecules fold into an L-shaped structure with a specific 3-dimensional shape.
- Aminoacyl-tRNA synthetases attach amino acids to the 3' end of tRNA, forming aminoacyl-tRNAs.
- The anticodon loop on tRNA interacts with codons in mRNA through base-pairing.
Wobble Position
- The third base in a codon is called the wobble position, allowing for flexibility in codon-anticodon matching.
- A single tRNA can often recognize multiple codons for the same amino acid.
Ribosomes
- Ribosomes are essential for protein synthesis.
- They consist of ribosomal RNA (rRNA) and proteins.
- Ribosomes bring mRNA and tRNA together during translation.
Ribosome Structure
- The ribosome has three sites: A site for aminoacyl tRNA, P site for the growing polypeptide chain, and E site for exiting tRNA.
- The decoding center ensures only codons matching tRNA anticodons enter the A site.
- Peptidyl transferase activity catalyzes peptide bond formation.
Translation Initiation
- Initiation requires the assembly of ribosomal subunits, mRNA, initiator tRNA (tRNAmet), GTP, and initiation factors.
- Recognition of the start codon by the tRNAmet molecule is crucial.
- The 60S ribosomal subunit joins the 40S subunit to complete the complex.
Translation Elongation
- Amino acids are added to the growing polypeptide chain in the carboxyl-terminal direction.
- The ribosome moves along the mRNA in the 5' to 3' direction.
- Elongation involves three steps:
- Delivery of the next aminoacyl-tRNA to the A site.
- Peptide bond formation between adjacent amino acids.
- Ribosome translocation to the next codon.
Translation Termination
- Termination occurs when a stop codon enters the A site.
- Release factors bind to the stop codon, causing:
- Release of the newly synthesized polypeptide chain.
- Dissociation of the ribosomal subunits and mRNA.
Information Flow
- The Central Dogma of Molecular Biology describes the flow of genetic information from DNA to RNA to protein.
- Coined by Francis Crick in 1956.
Overview of Translation
- Translation is the process of converting the information in mRNA into amino acids, resulting in protein synthesis.
- Consists of three stages: initiation, elongation, and termination.
Translation Requirements
- Template: mRNA carries the genetic code.
- Catalyst: Ribosome, composed of ribosomal proteins and rRNA, facilitates the process.
- Activated Precursors: Aminoacyl-tRNA, tRNA molecules coupled to amino acids via energy-rich bonds.
- Release/Termination Factors: Assist in terminating the translation process.
The Genetic Code
- The genetic code is the dictionary for translating DNA sequences into amino acids.
- Each three-nucleotide sequence (codon) in mRNA corresponds to a specific amino acid.
- The code is unpunctuated, meaning it's read continuously without gaps.
Reading Frames
- Open Reading Frame (ORF): A continuous sequence of codons beginning with a start codon and ending with a stop codon.
- The 'reading frame' is determined by the position of the start codon.
- In protein synthesis, only one ORF is essential for information.
- Insertions or deletions of nucleotides can cause "frame-shift" mutations, altering the reading frame and potentially changing the encoded protein.
The Genetic Code: Specific, Universal, Redundant, Non-Overlapping
- Specific: Each codon always codes for the same amino acid.
- Universal: Applies to all species, conserved from early evolution.
- Redundant: A given amino acid can be specified by several codons.
- Non-Overlapping: The code is read continuously as a sequence of bases, taken three at a time.
Changes in Coding Sequence and Disease
- Huntington's Disease: Caused by amplified codons, leading to extra amino acids and altered protein structure, potentially accumulating in the cell.
- Sickle Cell Disease (SCD): A missense mutation in the β-globin gene, a single nucleotide substitution resulting in an amino acid change from glutamic acid to valine.
tRNA: The Adaptor Molecule
- tRNA acts as an adaptor molecule, bridging the gap between nucleic acids and proteins.
- Proposed by Francis Crick, with 20 different adaptors for each amino acid.
- tRNA folds into an L-shaped structure due to base-pairing between nucleotides.
- The amino acid is added to the 3' end of the tRNA molecule to give an aminoacyl-tRNA by aminoacyl-tRNA synthetase.
- The anticodon loop on tRNA recognizes codons within the mRNA through base-pairing.
The Wobble Position
- The third base in a codon (first in the anticodon) is known as the "wobble position". Provides flexibility in codon recognition allowing a single tRNA to match multiple codons.
Ribosome: The Protein Synthesis Factory
- Ribosomes are complexes of proteins and rRNA, essential for protein synthesis.
- They bind tRNA and mRNA together to translate the nucleotide sequence of mRNA into the amino acid sequence of a protein.
Ribosome Structure
- A (aminoacyl) site: Binds incoming aminoacyl-tRNA.
- P (peptidyl) site: Contains tRNA with the growing polypeptide chain.
- E (exit) site: Holds deacylated tRNA before release.
- Decoding center: Ensures only matching tRNAs are accepted.
- Peptidyl transferase center: Catalyzes peptide bond formation.
Initiation of Translation
- Requires the assembly of components: 40s ribosomal subunit, mRNA, tRNAmet (initiator tRNA), GTP, and initiation factors.
- Recognition of the start codon by tRNAmet.
- Addition of the 60s ribosomal subunit to complete the assembly.
Elongation of Translation
- Involves adding amino acids to the carboxyl end of the growing chain.
- The ribosome moves along the mRNA in the 5' to 3' direction.
- Requires aminoacyl-tRNA delivery to the A site, peptide bond formation by peptidyl transferase, and ribosome translocation to the next codon.
Termination of Translation
- Occurs when a stop codon reaches the A site.
- Recognized by a release factor that binds to the A site, causing the release of the newly synthesized protein and detaching the ribosome from the mRNA.
Disassembly of the tRNA-ribosome-mRNA complex
- Ribosomal subunits, mRNA, tRNA and protein factors can be recycled and used to make additional proteins.
Regulation of Protein Activity
- Many key functions that occur in cells are dependent on the activities of proteins.
- Regulating protein activity is essential for maintaining cellular function.
Regulation of Protein Activity: Mechanisms
- Protein Levels: Regulating the amount of protein produced.
- Protein Location: Controlling where a protein is located within the cell.
- Post-translational Modification: Modifying proteins after translation to alter their activity.
Balancing Protein Synthesis with Degradation
- Protein turnover is a natural process.
- "Housekeeping" proteins are damaged and need to be replaced.
- Some proteins involved in cellular processes are degraded for tight control over their levels.
- Rapid turnover of some proteins allows for changes in their levels.
Protein Degradation Mechanisms
-
Lysosomal Degradation: Lysosomes are membrane-bound organelles containing degradative enzymes.
- These enzymes degrade proteins, other molecules, organelles, microbes, and materials delivered to the lysosome.
- Enzymes function optimally in the low pH environment of the lysosome.
-
Proteasomal Degradation: Proteins can be tagged for degradation by polyubiquitination.
- Polyubiquitinated proteins are recognized by the proteasome and degraded.
- Proteasome: A multiprotein, hollow, barrel-shaped complex containing protease activity.
- Found in the nucleus and cytoplasm.
- Protein "caps" on the proteasome recognize tagged proteins and feed them into the proteasome for degradation.
Polypeptide Chain Modifications After Translation
-
Proteolytic Cleavage: Processing of proteins from immature to mature forms.
- Example: Processing of insulin from pre-pro insulin to mature insulin.
- Example: Trypsinogen to trypsin.
-
Covalent Modifications: Modifications that alter the protein's structure and function.
- Disulfide Bond Formation: Stabilizes protein structure.
- Phosphorylation: Often activates or inactivates proteins. Important control mechanism.
- Glycosylation: Often found in extracellular proteins.
- Farnesylation and GPI Anchoring: Target proteins to membranes.
Ligand Binding
- Ligands bind to proteins and induce conformational changes.
- This allows for activation, inhibition, or relocation of proteins.
- Example: Steroid hormone receptors bind their ligands, undergo conformational changes, dimerize, and enter the nucleus.
Proteolytic Cleavage
- Zymogens: Inactive precursor forms of enzymes (pro-enzymes).
- Activated by proteolytic cleavage.
- Example: Enterokinase activates trypsinogen to trypsin.
- Proteolytic cascades: Series of proteolytic cleavages, often involved in complex processes like blood clotting.
Reversible Phosphorylation of Proteins
- Phosphate groups can be added to serine, threonine, and tyrosine residues.
- Tightly regulated process.
- Kinases add phosphate groups, phosphatases remove them.
- Ratio of phosphorylated serine:threonine:tyrosine is approximately 100:10:1.
- Tyrosine phosphorylation often has significant effects on protein activity.
Genetic Code: Introduction
- The genetic code specifies the relationship between codons (three-nucleotide sequences) and amino acids.
- If one nucleotide coded for one amino acid, there would be 4 possibilities.
- Two nucleotides would provide 16 possibilities (4 x 4).
- Three nucleotides provide 64 possibilities (4 x 4 x 4).
- Each "word" of DNA consists of three nucleotides/bases, which code for one amino acid.
The Genetic Code: Properties
-
Unpunctuated: Reading frames determine the sequence of amino acids.
- Open Reading Frame (ORF): A continuous set of codons starting with a start codon and ending with a stop codon.
- The reading frame is determined by the position of the start codon.
- Only one ORF contains useful information for protein synthesis.
-
Specific: A specific codon always codes for the same amino acid.
-
Universal: The code applies to all species. Conserved from early evolution.
-
Redundant: A given amino acid can be coded for by several different codons.
-
Non-overlapping: The code is read from a fixed starting point as a continuous sequence of bases, taken three at a time.
Genetic Code and Disease: Huntington's Disease
- Codon amplification can occur between generations.
- Each extra codon copy leads to an extra copy of the amino acid in the protein.
- This can alter protein structure and lead to accumulation and deposition of the protein in the cell.
Genetic Code and Disease: Sickle Cell Disease (SCD)
- Missense mutation in the β-globin gene.
- A single nucleotide substitution (A to T) in the codon for amino acid 6.
- Converts a glutamic acid codon (GAG) to a valine codon (GTG).
- Autosomal recessive inheritance.
tRNA: The Adaptor Molecule
- Nucleic acids and proteins are structurally different.
- Francis Crick proposed "adaptor molecules" to bridge this gap: These molecules would bind to amino acids and recognize specific codons in mRNA.
- tRNA is the adaptor molecule.
tRNA Properties
- tRNA molecules fold into L-shaped structures.
- Secondary structure: "Cloverleaf" shape due to base pairing.
- Tertiary structure: L-shaped three-dimensional shape.
- Post-transcriptional modifications occur in tRNA molecules.
- Amino acid is added to the 3' end of the tRNA molecule by aminoacyl-tRNA synthetase.
- Specificity derives from the 3D structure of the tRNA.
- The "anticodon loop" of tRNA recognizes codons in mRNA through base pairing following Watson-Crick rules.
- ~80 nucleotides in length.
- About 50 different tRNA molecules exist.
tRNA Anticodon and mRNA Codon Pairing
- tRNA anticodons pair with mRNA codons following Watson-Crick base pairing rules.
- Example: UCC codes for Serine.
The "Wobble" Position
- The 3rd base in a codon is the "wobble" position.
- Allows for flexibility in codon-anticodon pairing.
- A single tRNA species can recognize multiple codons.
The Ribosome
- Ribosomes are the protein synthesis machinery.
- Composed of protein and ribosomal RNA (rRNA).
- rRNA has extensive secondary structuring, similar to tRNA.
- Brings tRNA and mRNA together to translate the nucleotide sequence of mRNA into the amino acid sequence of a protein.
Ribosome Structure
- A site: Aminoacyl site, binds incoming aminoacyl-tRNA.
- P site: Peptidyl site, holds the tRNA containing the growing polypeptide chain.
- E site: Exit site, where the deacylated tRNA exits the ribosome.
- Decoding center: Ensures only tRNAs with the correct anticodon are accepted into the A site.
- Peptidyl transferase center: Catalyzes peptide bond formation between amino acids.
Initiation of Translation: Requirement
-
Assembly of components for protein synthesis:
- 40S ribosomal subunit
- mRNA to be translated
- tRNA specified by the first codon in the mRNA (tRNAmet)
- GTP (energy source)
- Initiation factors (help the ribosome recognize the start of translation)
-
Recognition of the start codon by tRNAmet.
-
Addition of the 60S ribosomal subunit to complete the ribosome assembly.
Initiation of Translation: Steps
- Step 1: Initial assembly of components.
- Step 2: Recognition of the start codon.
-
Step 3: Final assembly of the ribosome.
- The initiator tRNA is in the P site.
Elongation: Building the Polypeptide Chain
-
Elongation involves adding amino acids to the carboxyl end of the growing polypeptide chain.
-
Ribosome moves along the mRNA in the 5' to 3' direction.
-
Step 1: The next required aminoacyl-tRNA is delivered to the A site (with help of elongation factors).
-
Step 2: Peptide bond formation between adjacent amino acids, catalyzed by peptidyltransferase.
-
Step 3: Translocation: Ribosome moves three nucleotides in the 3' direction to the next codon.
- The growing chain moves to the P site.
- The uncharged tRNA moves to the E site and is released.
- The A site is free to accept the next tRNA.
-
Note: The P site initially contains the initiator tRNA.
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This quiz explores the functions of lysosomes and proteasomes in cellular processes, including details on enzyme activity, protein degradation, and post-translational modifications. Test your understanding of how ligand binding affects protein functionality and cellular localization.
