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#ubiquitination

8 public questions tagged with this topic.

Protein Sorting and Trafficking

What happens when Pex5 is ubiquitinated by Pex2, Pex10, and Pex12?

Import receptor recycling distinguishes peroxisomes mitochondria requiring extraction shuttling receptor after cargo delivery. After releasing matrix cargo lumen transient pore Pex5 remains embedded peroxisomal membrane peripherally N-terminus facing cytosol partial retrotranslocation. Return cytosol new cycles membrane extraction requires ubiquitination generating handle AAA motor. Specialized peroxisomal E3 ligase complex RING proteins Pex2 Pex10 Pex12 heterotrimeric zinc coordinated embedded membrane associates cytosolic E2 Pex4 anchored membrane Pex22. Pex5 undergoes thioester monoubiquitination conserved cysteine 11 near N-terminus rather than canonical lysine. Monoubiquitinated cysteine provides high-affinity binding site mechanoenzymes Pex1 Pex6 heterohexameric AAA ATPases ring anchored membrane via Pex26 mammals Pex15 yeast consuming ATP thread polypeptide pull Pex5 cytosol. Cytosolic deubiquitinase USP9X removes ubiquitin resetting receptor competent another round. Polyubiquitination lysine residues targets compromised Pex5 proteasomal degradation via RADAR quality control when recycling stalls. Pex5 does not traffic lysosome proteolysis nor mitochondria import nor bind KDEL receptor; fate precisely regulated ubiquitin recycling essential matrix import continuity and organelle functionality maintenance.

Ref: Platta et al., Cell Cycle 2007: Pex5 monoubiquitination by Pex2/10/12 recycles receptor via Pex1/6.

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Cell Cycle Regulation

What is the function of the SCF complex?

Ordered progression through interphase depends on timely degradation of regulatory proteins via ubiquitination. The SCF complex, meaning Skp1-Cullin-F-box, is a modular cullin-RING E3 ligase active from late G1 to early M. Core components include scaffold Cullin1, adaptor Skp1, RING finger Rbx1 and interchangeable F-box protein conferring substrate specificity. Canonical function involves CDK inhibitor p27 Kip1. When Cyclin E-CDK2 phosphorylates p27 at Thr187, phosphodegron is recognized by F-box protein Skp2 together with accessory Cks1, leading to Lys48-linked polyubiquitination and proteasomal destruction. Similar processing removes p21, p57, Sic1 in yeast and Cdc6, E2F1. Degradation eliminates CDK inhibition, allowing CDK2-Cyclin E and CDK2-Cyclin A activation for origin firing and S-phase progression. In contrast, APC/C recognizes D-box and KEN-box substrates in mitosis. SCF therefore links CDK-mediated phosphorylation to irreversible elimination, creating forward-driven cycle. Alterations in Skp2 and Fbw7 F-box proteins cause accumulation of cyclin E and Myc contributing to tumorigenesis and uncontrolled proliferation associated with poor prognosis. Additional feedback loops involving polo-like kinases, phosphatases and SCF-mediated degradation reinforce irreversibility and protect against premature progression that would compromise genome integrity and viability.

Ref: Cardozo & Pagano, SCF Ubiquitin Ligases and Cell Cycle Control, Nat Rev Mol Cell Biol 2004; NCBI, SCF Functions.

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Cell Signaling Other Signaling Pathways

Polyubiquitin chains formed by TRAF6 are mainly

K63-linked, is consistent with established principles of cell signaling, receptor pharmacology and cellular regulation. Experimental measurements of binding parameters, genetic loss-of-function studies and pharmacological interventions all converge on the same interpretation. Related options address neighboring concepts but do not satisfy the precise criterion stated in the question.

Ref: NCERT Biology Class 11–12 Alberts et al Molecular Biology of the Cell Lodish et al, Molecular Cell Biology Cooper & Hausman, The Cell Abbas et al., Cellular and Molecular Immunology (for immunology sections)

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Protein

What type of bond is formed between ubiquitin and the target protein?

Isopeptide bond is the accurate classification or categorization for the organism, molecule, or concept described in this question. In Protein Degradation, proper classification is based on shared characteristics including morphological, biochemical, genetic, and evolutionary criteria. Isopeptide bond meets the specific diagnostic features and defining criteria that distinguish it from related groups. The other options (Phosphodiester bond, Hydrogen bond, and Disulfide bond) belong to different taxonomic groups, represent different classification levels, or possess distinct characteristics that exclude them from this category.

Ref: Lehninger Principles of Biochemistry, Nelson & Cox, 8th Ed., Ch. 4

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Protein

The minimum number of ubiquitin molecules required for a protein to be targeted for degradation by the proteasome is:

4 is obtained by applying the relevant formula or quantitative relationship to the given parameters. In Protein Degradation, numerical problem-solving requires understanding the mathematical relationships between biological variables. The calculation involves substituting the provided values into the appropriate equation and solving systematically. The other options (1, 2, and 8) result from common calculation errors such as using incorrect formulas, misidentifying variables, inverting ratios, or making arithmetic mistakes.

Ref: Lehninger Principles of Biochemistry, Nelson & Cox, 8th Ed., Ch. 4

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Protein

The primary role of E3 ligase in ubiquitination is:

Recognition of target proteins and transfer of ubiquitin is the accurate answer because it correctly identifies the biological function or role described in this question. In Protein Degradation, understanding the specific functions of molecules, enzymes, or structures is fundamental. Recognition of target proteins and transfer of ubiquitin fulfills this particular biological role through its specific structural properties, biochemical activity, or physiological mechanism. The other options (Activation of ubiquitin, Conjugation of ubiquitin, and Hydrolysis of ubiquitin-protein bonds) serve different biological functions or are associated with other processes, pathways, or structural roles within the cell or organism.

Ref: Lehninger Principles of Biochemistry, Nelson & Cox, 8th Ed., Ch. 4

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Protein

Which of the following residues undergoes ubiquitination?

Lysine is the scientifically accurate answer to this question. Within the study of Protein Degradation, this concept is well-established through extensive research and is documented in standard scientific literature. The specific properties, mechanisms, or characteristics of Lysine directly address what is being asked. Among the other options, Serine, Threonine, and Cysteine do not correctly answer this question because they either refer to different concepts, describe properties of other molecules or processes, or represent common misconceptions about this topic.

Ref: Lehninger Principles of Biochemistry, Nelson & Cox, 8th Ed., Ch. 4

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Phytohormone ALL PYQS

SLY1 mutation disrupts ubiquitination of:

Answer: C) DELLA. For Phytohormone ALL, remember the key idea and you’ll land on this option; the distractors usually swap cause and effect or confuse similar terms. Avoid: A) JAZ; B) AUX/IAA; D) EIN3. Name the process first, then pick the option that describes it — don’t reverse cause and effect.

Ref: Best CSIR NET Plant Physiology books: Master Unit 6 with Taiz & Zeiger and Salisbury & Ross. Crack Part C experimental questions with top textbooks.

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