Cellular Proteins and Regulation Quiz

Metabolic Regulation

• Metabolic pathways involve thousands of different reactions catalyzed by 30,000 proteins in a typical cell.
• Metabolites are shared by one or more pathways.
• Approximately 12% of all genes encode regulatory proteins (4,000 genes).
• Receptors, regulators of gene expression, and 500 different protein kinases are involved in metabolic regulation.
• Interlocking metabolic processes are regulated simultaneously in cells.
• The right product, concentration, and time are essential for proper regulation.

Metabolism - the feat!

• Cells regulate interlocking metabolic processes simultaneously, despite external changes.
• Cells generate no leftovers during metabolic processes.
• Time scale for response to hormone or growth factors is hours; catalytic activity changes can happen in seconds to hours.

Factors affecting enzyme activity

• Extracellular signals, transcription factors, mRNA degradation, mRNA translation on ribosomes, protein degradation, and enzyme sequestration in subcellular organelles (e.g. endoplasmic reticulum) affect enzyme activity.
• Enzymes combine with regulatory proteins, undergo phosphorylation/dephosphorylation and bind to ligands affecting enzyme activity.

Alteration of enzyme activity

• Enzyme activity can change in response to hormones or growth factors.
• Rates of synthesis and degradation (time scale: hours to days) impact enzyme activity.
• Allosteric control (seconds to hours) and covalent modification (seconds to hours) modify catalytic activity.

Time Scales of Regulatory Mechanisms

• Availability of substrates: minutes
• Allosteric activation/inhibition of enzymes: minutes
• Covalent modification of enzymes: minutes to hours
• Synthesis of new enzyme molecules: hours to days

Insulin Regulated Genes

• Insulin regulates expression of various genes involved in pathways like glycolysis, gluconeogenesis, pentose phosphate pathway, and fatty acid synthesis.
• Increased expression of genes such as Hexokinase II, Phosphofructokinase-1, and Glucose-6-phosphate dehydrogenase is observed in response to insulin.

Insulin Regulation

• More than 150 genes are regulated by insulin.
• Insulin response elements (REs/IREs), involving specific transcription factors, mediate insulin's effect on gene expression.

Regulatory Input Into Genes

• The regulatory input into genes is complex, involving multiple transcription factors and response elements (e.g., HNF-4α, SREBP-1, PPARγ2, FOXO1, CREB, etc.) for specific genes.

ATP Maintenance

• Maintaining a constant supply and concentration of ATP (5-10 mM) is crucial for cell function.
• The ratio of ATP/ADP, NADH/NAD+, and NADPH/NADP+ are pivotal for reactions using these cofactors.
• AMP is a sensitive indicator of the cell's energy status, and AMP levels less than 0.1 mM indicate low energy within the cell

Adenine Nucleotides and Metabolic Regulation

• Many ATP-using enzymes have Km values between 0.1–1 mM.
• ATP concentration in a typical cell is ~5 mM.
• A drop in intracellular ATP concentration impacts numerous cellular reactions.

AMP-activated Protein Kinase (AMPK)

• Many regulatory processes are linked to AMP regulation, with AMPK playing a key role.

AMPK Signaling Pathway

• AMPK is activated by elevated AMP and/or decreased ATP.
• AMPK regulates metabolism through phosphorylation of target proteins, shifting metabolism from energy-consuming to energy-generating reactions.

General Regulatory Mechanisms

• Glycolysis and gluconeogenesis, operating in opposite directions, must be regulated to prevent futile cycles.
• Metabolites are partitioned among pathways (e.g., glycolysis and pentose phosphate pathway).
• Cells utilize fuel (e.g., glucose, fatty acids, glycogen, amino acids) best suited for immediate needs.
• Biosynthetic pathways are shut down when product accumulates.

Coordinated Regulation of Pathways (Glycolysis and gluconeogenesis)

• In futile cycles, both glycolysis and gluconeogenesis operate simultaneously consuming ATP without net reactions.
• Cells coordinate regulations of these two processes to avoid wasteful cycles.

Allosteric Regulation

• Allosteric regulation is very rapid (milliseconds).
• Allosteric regulation is triggered locally by changes in metabolite concentrations (substrate, product, or cofactors).

Covalent Modification

• Common mechanisms involve phosphorylation and dephosphorylation catalyzed by kinases and phosphatases.
• Phosphorylation alters enzyme activity through electrostatic changes, inhibitor movement, protein interactions and conformational changes.

Isoenzymes

• Isoenzymes (different forms of an enzyme) exhibit differing kinetic or regulatory proprieties, cofactor usage, subcellular distribution, and amino acid sequences.
• Isoenzyme variations are regulated by development stages, tissue location, metabolic patterns, and response to allosteric modifications.
• Examples include hexokinase and lactate dehydrogenase (LDH).

Compartmentation

• Physical separation of metabolic processes (e.g., fatty acid synthesis and degradation) within different cellular compartments is crucial.
• Compartmentation increases metabolite concentrations.
• Compartmentation reduces diffusion barriers allowing different environments(e.g pH and potential gradients for oxidative phosphorylation), assists metabolic control.

Location-Dependent Functions of Metabolic Enzymes

• Metabolic enzymes can fulfill non-metabolic functions based on their subcellular location (e.g. regulating gene expression, histone acetylation, substrate localization).