L8: Posttraslational modification of proteins

Question 1

What are post-translational modifications (PTMs), and what is their role in regulating proteins?

Answer 1

-covalent changes made to proteins after translation
- They modify protein activity, stability, folding, and localization.
- They are used to activate, inactivate, or degrade proteins, contributing to the control of gene activity

Question 2

Are post-translational modifications reversible, and what enzymes are involved?

Answer 2

• Most PTMs reversible
• Kinases, phosphatases, transferases, ligases, & proteases add/remove functional groups.
• Phosphatases remove phosphates added by kinases.
• Proteases cleave peptide bonds

Question 2

List some common types of post-translational modifications and provide examples

Answer 2

• Phosphorylation: Addition of a phosphate group (e.g., serine, threonine, tyrosine).
• Example: Protein kinases
• Methylation: Addition of a methyl group (–CH3) to lysines. Example: Histone modifications.
• Acetylation: Addition of an acetyl group (COCH3) to lysines. Example: Histone acetylation.
• Ubiquitination: Attachment of a ubiquitin polypeptide to a protein. Example: Proteasomal degradation.
• Proteolysis: Cleavage of protein to remove inhibitory regions. Example: Activation of enzymes.
• Lipidation: Addition of lipids. Example: Myristylation.

-Glycosylation: Addition of sugars. Example: N-linked glycosylation

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Question 2

What are the two broad classes of covalent modifications of proteins, and what do they involve?

Answer 2

1 enzyme-assisted covalent addition/elimination of chemical groups
2 covalent cleavage of peptide fragments by proteases
- they can activate/repress protein activity, degrade proteins, or change their location

Question 3

What are the functions of post-translational modifications in terms of gene expression control and cellular regulation?

Answer 3

• PTMs contribute to controlling protein folding, stability, activity, and targeting
• also play roles in signal transduction, cell division, differentiation, survival & gene expression
• they increase protein diversity in the cell

Question 4

Provide an example of post-translational modification through proteolytic cleavage.

Answer 4

• Proteins can be produced as inactive forms, like proenzymes
• Cleavage of additional AAs activates them.

Examples: Pepsinogen → Pepsin (stomach protease),
Prothrombin → Thrombin (blood clotting),
Preproinsulin → Insulin (pancreatic hormone).

Question 5

Explain the process of protein phosphorylation and its significance in regulating gene expression.

Answer 5

• involves adding a phosphoryl group (PO32-) to specific AAs like serine, threonine, or tyrosine
• can activate/inactivate protein/enzyme activity
• Kinases add phosphates, phosphatases remove them
• used in signal transduction pathways to control cellular responses

Question 6

Give an example of a signaling pathway involving protein phosphorylation.

Answer 6

• MAP kinase cascade
• Epinephrine/glucagon signals glycogen breakdown. cAMP activates protein kinase A (PKA)
• which phosphorylates glycogen synthase & phosphorylase kinase → glycogen degradation

Question 7

What are receptor tyrosine kinases (RTKs), and how do they regulate cellular responses?

Answer 7

• transmembrane proteins.
• contain tyrosine kinase domains.
• ligand binding induces dimerization of RTKs.
• dimerization activates kinase domains.
• activated kinase domains initiate intracellular signaling cascades.
• these cascades regulate cellular responses like proliferation, differentiation, and survival.

Question 8

Describe the MAP kinase cascade and its role in cellular signalling

Answer 8

• MAP kinase cascade is a phosphorylation cascade
• GTP → Ras → Raf → MEK → ERK. Active ERK acts as a TF, regulating gene expression.
• this cascade amplifies signals & coordinates multiple processes, like cell division, differentiation & survival

Question 9

Describe Regulation of Post-Translational Modification by Ubiquitination

Answer 9

• Ubiquitination involves adding ubiquitin molecules to lysine residues.
• Ubiquitin is an 8kD protein with 76 amino acids.
• Monoubiquitination = adds a single ubiquitin molecule, affecting protein location.
• Polyubiquitination = adds chains of ubiquitin → protein degradation.
• Ubiquitin ligases add ubiquitin, de-ubiquitinating enzymes remove it.
• Ubiquitination regulates protein activity during cell division.

Question 10

Describe Ubiquitination Machinery

Answer 10

• Ubiquitin activating enzyme (E1) transfers ubiquitin to ubiquitin conjugation enzyme (E2).
• Ubiquitin ligase (E3) identifies target proteins and catalyzes ubiquitin transfer.
• E2 bound to ubiquitin transfers ubiquitin to the target protein.
• Multiple ubiquitin molecules target proteins to the 26S proteasome

Question 11

What are the roles of Ubiquitination?

Answer 11

• Mono-ubiquitination: Single ubiquitin recruits downstream effector proteins.
• Linked poly-ubiquitin chains: Different ubiquitin-binding proteins (UBP) direct proteins to proteasome.
• Ubiquitin regulates cell division and cell cycle progression.
• Cyclins control cell cycle stages and are degraded through ubiquitination

Question 12

Describe the regulation of Post-Translational Modification by Methylation

Answer 12

• Methylation: Addition of methyl groups to lysine or arginine residues
• Methylation can change protein conformation & function
• reversible

Question 13

Describe the regulation of Post-Translational Modification by Acetylation

Answer 13

• Acetylation: Addition of acetyl groups to lysine or N-terminus.
• Acetylation neutralizes protein charge, regulating activity
• reversible

Question 14

what does epigenetic control refer to?

Answer 14

refers to gene expression control via protein modifications (e.g. acetylation & methylation)

Question 15

histones commonly regulated by what?

Answer 15

methylation and acetylation

Question 16

Describe Regulation of Post-Translational Modification by Lipidation

Answer 16

• Lipidation adds lipids to proteins, directing targeting or activation.
• Myristoylation and palmitoylation promote plasma membrane association.
• GPI-anchor anchors extracellular proteins to plasma membrane.
• Lipid addition anchors proteins, allows interactions, and targets vesicles

Question 17

Describe the regulation of Post-Translational Modification by Glycosylation

Answer 17

• glycosylation adds sugars/glycans to proteins
• More than 50% of the human proteome is glycosylated
• Glycosylation ensures protein folding, resistance, interaction, and localization.
• Glycans: involved in cell communication, trafficking, and organism-related roles.
  Examples: Proteoglycans, GPI-anchored glycoproteins, glycoproteins, glycosphingolipids, O-GIcNAc, and blood group glycans
• N-linked and O-linked glycosylation are common types.

(- Glycosylation is crucial for protein, cell, and organism function)

Question 18

What are the roles for Glycosylation?

Answer 18

• Glycosylation helps proteins fold & interact
• Specific glycosylation patterns change protein activity.
• Glycosyltransferases add different sugars, producing diverse patterns.
• Disorders of glycosylation can lead to cancer & immune disorders