Biochemistry: Protein Folding and Modifications
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Questions and Answers

What are post translational modifications primarily responsible for?

  • Modifying proteins after translation (correct)
  • Creating peptide bonds in proteins
  • Initiating transcription of DNA
  • Catalyzing the synthesis of amino acids

    • Which type of bonds predominantly assist proteins in maintaining their shape during folding?

  • Metallic bonds
  • Hydrogen bonds (correct)
  • Covalent bonds
  • Ionic bonds

    • Which amino acid property influences their orientation during protein folding?

  • Hydrophobicity only
  • Frequency of occurrence
  • Molecular weight
  • Charge and polarity (correct)

    • What is the effect of polar amino acid side chains in protein structures?

    <p>They lie on the outside to interact with water. (B)</p> Signup and view all the answers

    Which process is NOT considered a post translational modification?

    <p>Transcription (D)</p> Signup and view all the answers

    What characterizes the noncovalent bonds that help proteins fold?

    <p>They are weaker than covalent bonds. (B)</p> Signup and view all the answers

    How do long polypeptide chains contribute to protein folding?

    <p>They provide numerous possibilities for folding configurations. (D)</p> Signup and view all the answers

    Which of the following modifications is a form of proteolytic processing?

    <p>Cleavage of peptide bonds (D)</p> Signup and view all the answers

    What type of linkage is formed when myristoyl is attached to a protein?

    <p>Amide linkage to an N-terminal glycine residue (A)</p> Signup and view all the answers

    What distinguishes prenylation from acylation in protein modifications?

    <p>Prenylation adds isoprenoid groups, acylation adds fatty acyl groups (D)</p> Signup and view all the answers

    Which statement about GPI anchors is true?

    <p>They are attached to the C-terminus of proteins (B)</p> Signup and view all the answers

    What happens to Ras proteins that lose their palmitoyl group?

    <p>They are targeted to the Golgi membrane instead of the plasma membrane (A)</p> Signup and view all the answers

    Which fatty acyl group is more commonly attached to C-terminal cysteines?

    <p>Palmitic acid (A)</p> Signup and view all the answers

    What characterizes farnesylation in protein modifications?

    <p>It is linked via a thioether bond to a cysteine residue (C)</p> Signup and view all the answers

    How does the presence of the carbohydrate moiety affect GPI-anchored proteins?

    <p>It directs them to the cell surface via the secretory pathway (B)</p> Signup and view all the answers

    What is the primary function of the lipid modifications of proteins discussed?

    <p>To regulate subcellular localization of proteins (A)</p> Signup and view all the answers

    What happens to the immature glycoprotein after it is synthesized?

    <p>It is modified in the Golgi apparatus. (C)</p> Signup and view all the answers

    Which type of glycoconjugate modification may involve the addition or removal of monosaccharides?

    <p>Glycosylation (A)</p> Signup and view all the answers

    Which of the following modifications can alter protein function?

    <p>Phosphorylation (D)</p> Signup and view all the answers

    Which domains specifically recognize acetylated lysines?

    <p>Bromodomains (A)</p> Signup and view all the answers

    What are the residues that are primarily phosphorylated in proteins?

    <p>Serine, threonine, and tyrosine (C)</p> Signup and view all the answers

    Which modification is fundamental in JAK-STAT signaling?

    <p>Phosphorylation of tyrosine residues (D)</p> Signup and view all the answers

    What kind of proteins are JAKs in the context of the JAK-STAT pathway?

    <p>Kinases that activate signaling (C)</p> Signup and view all the answers

    What is the overall effect of ligand binding in the JAK-STAT pathway?

    <p>Cytokine receptor chain oligomerization (D)</p> Signup and view all the answers

    What type of bond forms between adjacent cysteine side chains?

    <p>Covalent disulfide bond (C)</p> Signup and view all the answers

    In bacteria, which oxidoreductase is responsible for catalyzing disulfide bond formation?

    <p>DsbA (C)</p> Signup and view all the answers

    Where do sulfhydryl oxidoreductases, such as protein disulfide isomerases (PDIs), primarily operate in eukaryotic cells?

    <p>Endoplasmic reticulum (A)</p> Signup and view all the answers

    What is the role of DsbB in the disulfide bond formation process in bacteria?

    <p>It reoxidizes DsbA (A)</p> Signup and view all the answers

    What do sorting motifs in proteins serve to identify?

    <p>Targeting proteins to their proper localization (D)</p> Signup and view all the answers

    Which option describes a feature of sorting motifs?

    <p>They can be located at either the N- or C-terminus of a protein (B)</p> Signup and view all the answers

    Which of the following processes facilitates the transfer of reducing equivalents to oxygen during aerobic growth in bacteria?

    <p>Transfer from coenzyme Q to respiratory chain (B)</p> Signup and view all the answers

    Which proteins are responsible for reducing PDIs in yeast during disulfide bond formation?

    <p>Ero1p and Erv2p (C)</p> Signup and view all the answers

    What is the role of ubiquitin in protein degradation?

    <p>It marks proteins for proteolytic degradation. (C)</p> Signup and view all the answers

    Which enzyme is responsible for the ATP-dependent attachment of ubiquitin to the ubiquitin-activating enzyme (E1)?

    <p>Ubiquitin-activating enzyme (E1) (C)</p> Signup and view all the answers

    Which part of the ubiquitin protein forms the peptide bond with the lysine side chain of the target protein?

    <p>C-terminal glycine (A)</p> Signup and view all the answers

    What is the role of chaperone proteins during protein translocation?

    <p>To assist in unfolding the protein if it is already folded (D)</p> Signup and view all the answers

    How does the nuclear localization sequence (NLS) facilitate nuclear import?

    <p>By being recognized by soluble nuclear import receptors (C)</p> Signup and view all the answers

    What distinguishes different types of polyubiquitin chains?

    <p>The lysine side chain in ubiquitin used for attachment (B)</p> Signup and view all the answers

    What potential effects do post-translational modifications have on proteins?

    <p>They can affect activity, stability, localization, and interactions. (B)</p> Signup and view all the answers

    What initiates the release of the imported protein from the nuclear import receptor?

    <p>GTP hydrolysis stimulated by the Ran protein (A)</p> Signup and view all the answers

    What is required for proteins to exit the nucleus?

    <p>Binding of an export receptor to nuclear export signal (NES) (B)</p> Signup and view all the answers

    Which of the following is NOT a type of post-translational modification mentioned?

    <p>Hydroxylation (A)</p> Signup and view all the answers

    What happens during ubiquitin chain elongation?

    <p>Additional ubiquitins are added to lysines on the target or on ubiquitin. (C)</p> Signup and view all the answers

    Which process is involved in making some polypeptides biologically active?

    <p>Post-translational cleavage (D)</p> Signup and view all the answers

    What is the main function of the proteasome in the context of ubiquitin?

    <p>It degrades ubiquitinated proteins. (D)</p> Signup and view all the answers

    What role does Ran-GTP play in the export of proteins from the nucleus?

    <p>It stimulates the release of the exported protein from the receptor (A)</p> Signup and view all the answers

    What happens to the protein during its translocation through the translocon?

    <p>It is often translated while being translocated (C)</p> Signup and view all the answers

    What is the significance of the signal sequence in protein translocation?

    <p>It is recognized by translocon, facilitating the protein's movement (A)</p> Signup and view all the answers

    Flashcards

    Post-Translational Modification (PTM)

    Changes made to a protein after its translation by ribosomes is complete. These modifications are catalyzed by enzymes and can include adding functional groups, proteolytic processing, and folding processes.

    What are some examples of PTMs?

    Examples include phosphorylation, neddylation, ubiquitination, proteolytic processing, and protein folding.

    What are the components of a protein?

    Proteins are made up of amino acids connected by peptide bonds, forming a polypeptide chain.

    What are peptide bonds?

    Peptide bonds are the links between amino acids in a protein.

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    Why are proteins flexible?

    The peptide bonds in proteins allow for rotation of the atoms, giving them flexibility.

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    What are noncovalent bonds?

    Weak bonds that help proteins fold and maintain their shape. They include hydrogen bonds, electrostatic interactions, and van der Waals attractions.

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    How do protein folds depend on amino acids?

    The distribution of polar and nonpolar amino acids influences protein folding. Polar amino acids tend to be on the outside of the protein, while nonpolar amino acids tend to be on the inside.

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    What is the significance of protein folding?

    Proper protein folding is crucial for their function. Misfolded proteins can be inactive or even harmful.

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    Disulfide Bond

    A covalent bond formed between two cysteine amino acid side chains.

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    Disulfide Bond Formation

    The process of creating a disulfide bond between cysteine residues.

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    DsbA

    An oxidoreductase in bacteria that catalyzes disulfide bond formation in the periplasm.

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    DsbB

    An oxidoreductase in bacteria that reoxidizes DsbA, allowing it to continue catalyzing disulfide bond formation.

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    PDIs

    Sulfhydryl oxidoreductases in eukaryotes that catalyze disulfide bond formation in the endoplasmic reticulum.

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    Ero1p and Erv2p

    FAD-dependent oxidases in yeast that reduce PDI, allowing it to continue catalyzing disulfide bond formation.

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    Sorting Motif

    A specific sequence of amino acids within a protein that directs it to a particular cellular location.

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    What does a sorting motif do?

    Sorting motifs direct proteins to the correct cellular compartment, ensuring proper function and localization.

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    Protein Translocation

    The movement of a protein across a biological membrane, from one cellular compartment to another.

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    Translocon

    A protein channel embedded in a membrane that facilitates the passage of proteins across the membrane.

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    Nuclear Localization Sequence (NLS)

    A specific amino acid sequence that signals proteins to be transported into the nucleus.

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    Nuclear Import Receptor

    A protein that binds to the NLS and guides proteins through the nuclear pore complex.

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    Ran Protein

    A small GTP-binding protein involved in nuclear transport, regulates the release of proteins at their destination.

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    Nuclear Export Signal (NES)

    An amino acid sequence that targets proteins for export out of the nucleus.

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    Polypeptide Cleavage

    The removal of a portion of a polypeptide chain to activate a protein.

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    What is acylation?

    Acylation is the process of attaching a fatty acyl group (like myristoyl or palmitoyl) to a protein.

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    Glycoprotein Modification

    The process of adding or removing monosaccharides from a glycoprotein in the Golgi apparatus, usually involving various enzymes.

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    Where does acylation occur?

    Acylation happens at the N-terminus (beginning) or C-terminus (end) of a protein.

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    N-acetyl-glucosamine

    A sugar molecule represented by a yellow hexagon, commonly found in glycoproteins.

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    Mannose

    A sugar molecule represented by a blue hexagon, often present in glycoproteins.

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    What is prenylation?

    Prenylation adds an isoprenoid group (like farnesyl or geranylgeranyl) to a protein.

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    Glucose

    A sugar molecule represented by a red hexagon, sometimes part of glycoproteins.

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    Where does prenylation occur?

    Prenylation usually occurs at the C-terminus (end) of a protein.

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    What's a GPI anchor?

    A GPI anchor is a complex molecule composed of carbohydrates and lipids that attaches to a protein.

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    Protein Phosphorylation

    The addition of a phosphate group to a protein, often regulated by kinases, which can alter its function.

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    What's the role of a GPI anchor?

    GPI anchors tether proteins to the cell membrane and direct them to the cell surface.

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    Protein Acetylation

    The attachment of an acetyl group to a protein, usually on side chains or the amino terminus.

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    Protein Methylation

    The addition of a methyl group to a protein, often on specific side chains.

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    What are the main types of protein lipid modifications?

    The main types of protein lipid modifications are acylation, prenylation, and GPI anchoring.

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    SH2 domain

    A protein domain that specifically recognizes and binds to phosphorylated tyrosine residues.

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    What's the importance of protein lipid modifications?

    Protein lipid modifications affect where a protein is located inside the cell and its function.

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    Ubiquitin

    A small protein that acts as a tag for proteins destined for degradation by the proteasome. It's attached to target proteins through a process called ubiquitination.

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    Proteasome

    A large protein complex responsible for breaking down (degrading) proteins marked with ubiquitin tags. It's like a cellular recycling center.

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    Ubiquitination

    The process of attaching ubiquitin molecules to a target protein. It involves a series of enzymatic steps including E1, E2, and E3 enzymes.

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    E1, E2, E3 Enzymes

    Enzymes involved in ubiquitination: E1 activates ubiquitin, E2 conjugates it to the target protein, and E3 facilitates the process.

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    Polyubiquitin Chain

    A chain of multiple ubiquitin molecules linked together. The type of chain determines the fate of the target protein, such as degradation or other functions.

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    Phosphorylation

    A common PTM where a phosphate group is added to a protein, often affecting its activity.

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    Ubiquitination vs. Phosphorylation

    Both are PTMs, but ubiquitination tags proteins for degradation, while phosphorylation can modulate protein activity.

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    Study Notes

    Post Translational Process

    • Post-translational modifications (PTMs) are changes to a protein after its translation by ribosomes is complete.
    • These modifications are catalyzed by enzymes.
    • PTMs include adding functional groups to a protein covalently.
    • Examples of PTMs include phosphorylation, neddylation, ubiquitination, proteolytic processing, and folding.
    • These processes are essential for a protein to mature functionally.

    Post Translational Modifications (PTM)

    • Proteins are made of amino acids linked together.
    • Amino acids have side chains that give them unique characteristics.
    • Some side chains are nonpolar and hydrophobic (repel water).
    • Other side chains are polar or charged (interact with water).

    Protein Folding

    • Long polypeptide chains are flexible, and can fold in numerous ways.
    • Noncovalent interactions maintain the folded shape: hydrogen bonds, electrostatic attractions, and van der Waals forces.
    • Polar amino acid side chains tend to lie towards the outside of proteins where they interact with water.
    • Nonpolar amino acid side chains are inside the protein to avoid water interactions.
    • Chaperones assist proper folding by preventing premature folding, aiding in correctly folding, and assisting in the unfolding of proteins if they fold incorrectly.
    • Co-translational folding is assisted by ribosome-associated chaperones, such as Hsp70 (DnaK) and Hsp60 (GroES + GroEL).

    Disulfide Bond Formation

    • Disulfide bonds (S-S bonds) are covalent bonds that form between two cysteine residues.
    • These bonds are critical for protein folding and stabilization.
    • They can link parts of the same polypeptide chain or different polypeptide chains.

    Protein Sorting Motifs

    • Protein localization is determined by unique amino acid sequences (sorting motifs or sorting signals).
    • Sorting motifs direct proteins to their proper locations within the cell.
    • Sorting motifs can be located at the N-terminus, C-terminus, or both of a protein.

    General Protein Translocation Mechanism

    • Sorting motifs can be recognized by receptors, often during or after protein synthesis.
    • If necessary, proteins are unfolded by chaperones to allow movement through the membrane.
    • The protein is then threaded through the translocon in the membrane or pulled across by chaperones.

    Protein Transport in/out of the Nucleus

    • The nuclear localization sequence (NLS) directs proteins into the nucleus.
    • Nuclear import receptors bind to NLS and transport the protein across the nuclear pore complex.
    • GTP hydrolysis by Ran protein facilitates release of the imported protein from the receptor.
    • Export receptors and nuclear export signals (NES) direct proteins out of the nucleus.

    Post-translational Cleavage of Polypeptide Chain

    • Some polypeptides need to be cleaved to become active.
    • Enzymes (like proteases) cleave polypeptides at specific amino acid locations.
    • Examples include chymotrypsin, which is initially produced as the inactive precursor chymotrypsinogen.
    • Self-excising domains (inteins) can be removed from proteins.

    Lipid Modifications of Protein

    • Covalent attachment of lipid groups targets proteins to membranes.
    • Examples include acylation (attachment of fatty acyl groups), prenylation (attachment of isoprenoid groups), and glycosylphosphatidylinositol (GPI) anchoring.

    Glycosylation of Proteins

    • Glycosylation is the addition of carbohydrate groups (glycans) to proteins.
    • Glycosylation can alter protein solubility, stability, and interactions with other molecules.
    • Glycosylation sites are often on the outside of proteins in contact with the cell environment.

    Protein Phosphorylation, Acetylation, and Methylation

    • Phosphorylation, acetylation, and methylation are covalent modifications to proteins that alter their activity and function.
    • Phosphorylation involves attaching phosphate groups to serine, threonine, or tyrosine residues.
    • Acetylation involves adding an acetyl group to lysine residues.
    • Methylation involves adding methyl groups to lysine or arginine residues.
    • Specific domains are recognized for each modification type.

    Ubiquitination of Proteins

    • Ubiquitination is the covalent attachment of ubiquitin proteins to target proteins.
    • This can mark proteins for degradation, regulation, or other cellular functions.
    • Different types of ubiquitin modifications can lead to different cellular outcomes.
    • Ubiquitination steps involve enzymes E1, E2, and E3.

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    Post Translational Process Lecture 8 PDF

    Description

    This quiz covers key concepts related to protein folding and post-translational modifications. Test your understanding of the bonds and forces that dictate protein structure and function. Delve into the mechanisms of protein folding and various types of modifications that occur after translation.

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