Biochemistry: Enzyme Function and Regulation

Allosteric Enzymes

• Regulated by molecules binding to sites other than the active site
• Binding causes conformational changes that activate or inhibit enzyme activity

Enzyme Inhibitors

• Decrease enzyme activity
• Block the active site or allosteric site

Enzyme Activators

• Increase enzyme activity
• Enhance enzyme function

Agonist

• Activates a receptor
• Mimics the natural signal

Antagonist

• Blocks the receptor
• Prevents activation

Endoplasmic Reticulum

• Largest internal membrane of a cell
• Contains the cisternal space
• Rough ER synthesizes proteins and adds carbohydrates to proteins to make glycoproteins
• Smooth ER synthesizes carbohydrates and lipids
• Smooth ER stores calcium, keeping intracellular calcium concentration low so calcium can function as a signaling molecule

Golgi Apparatus

• Sorts, packs, and distributes molecules within and outside the cell
• Modifies carbohydrates and/or adds them to proteins

Vacuole

• Makes up approximately 90% of the internal volume of a plant cell
• Stores waste products
• Maintains the internal structure of the cell

Chemical Reactions

• Reactants: What goes into the reaction (A+B)
• Product: What comes out of the reaction (AB)
• Yields: Symbol for the reaction going from reactants to product (→)
• Coefficients: Numbers in front of each reactant or product indicating the proportional amount
• Subscripts: Numbers after each element indicating the number of atoms of that element in the molecule

Energy

• The capacity of something to do work (force operating on an object over a distance)
• Biochemistry: energy is the capacity for change in chemical composition and molecular properties

Potential Energy

• Stored energy of a state or position

Kinetic Energy

• Energy of movement

Passive Transport Proteins

• Do not require chemical-bond energy for substance movement
• Movement occurs due to a concentration gradient
• Examples: channel proteins, carrier proteins

Active Transport Proteins

• Require energy from ATP to move molecules against a concentration gradient
• Primary Active Transport: Carrier proteins directly utilize ATP to move molecules
• Example: Sodium/Potassium pump
• Secondary Active Transport: Carrier proteins indirectly utilize ATP via proton pumps
• Example: Glucose uptake in the intestines

Cell Junctions:

• Additional membrane connecting structures forming after initial cell-cell binding
• Communicating junctions: Permit diffusion of small molecules or ions between cells to communicate with one another (Gap junctions, Plasmodesmata)
• Septate junctions: Prevent leakage of water and solutes between cells and form barriers (Tight junctions)
• Adhesive junctions: Mechanically attach cytoskeletons of cells to one another (Desmosomes)

Bulk Transport:

• Endocytosis: Cells engulf materials into the cell by forming vesicles from the plasma membrane
• Phagocytosis: "Cell eating" where large particles like bacteria are engulfed
• Pinocytosis: "Cell drinking" where fluids and dissolved solutes are taken in
• Receptor-mediated endocytosis: Specific molecules are ingested after binding to cell surface receptors
• Exocytosis: Cells expel materials out of the cell by fusing vesicles with the plasma membrane, releasing their contents to the extracellular space.

Chemical Signaling Systems:

• Autocrine: Cells release signaling molecules that act on themselves
• Juxtacrine: Occurs through direct contact between neighboring cells, where the signal molecule remains attached to the signaling cell's membrane and interacts with receptors on adjacent cells
• Paracrine: Cells release signaling molecules that act on nearby cells within a close range

Dissociation Constant (Kd):

• Measure of the affinity between two binding molecules (ligand and protein)

Classes of Signaling Receptors:

• Ligand-gated Ion Channels: Open or close in response to ligand binding, allowing ions to pass through the membrane
• Protein Kinase Receptors: Ligand binding activates their intrinsic kinase activity, which phosphorylates target proteins to trigger cellular responses
• G Protein-Coupled Receptors: Ligand binding activates an associated G protein, which then triggers downstream signaling pathways inside the cell.

Catalysts

• Speed up chemical reactions
• Do not determine whether a reaction occurs, only the rate of reaction
• Example: Enzymes

Transition States

• The point in which a molecule(s) are reactive
• Energy input is called activation energy (Ea)

Equilibrium

• A stable system where no reaction is taking place

Enzyme Classes

• Oxidoreductases: Transfer electrons between molecules
• Transferases: Transfer groups of atoms (functional groups) between molecules
• Hydrolases: Add water to covalent bonds to breakdown molecules
• Lyases: Catalyze breaking of non-hydrolytic bonds (splitting chemicals into smaller molecules without using water)
• Isomerases: Rearrangement of atoms within a molecule
• Ligases: Join two molecules together

Saturation Point

• The point in which all enzymes are bound to a substrate

Activation Energy

• The energy barrier that must be overcome for a reaction to proceed

Substrates

• The reactant or part that physically attaches to the enzyme protein which is then catalyzed by the enzyme

Glycolysis

• Input: Glucose, ATP (x2)
• Output: Pyruvate (x2), ATP (x2 net), NADH (x2)

Citric Acid Cycle

• Input: Acetate, water, GDP, NAD+, FAD
• Output: Carbon Dioxide, NADH, FADH2, GTP

Electron Transport Chain

• Input: NADH, FADH2, O2, H+ (protons), ADP, Phosphate
• Output: ATP, NAD+, FAD+, H2O

Oxidation

• Loss of electrons
• Happens during glycolysis when NAD+ becomes NADH and during the Citric Acid Cycle during steps 3, 4, 6, and 8

Reduction

• Gain of electrons
• Happens during fermentation when NADH becomes NAD+

Chemiosmosis

• Process where ATP is formed by combining a free-roaming phosphate group with a molecule of ADP, through the use of the enzyme ATP synthase.
• ATP synthase is powered by the passive diffusion of protons (H+) into the F0 unit.
• The F1 unit spins, mashing the ADP and phosphate group together.
• This process is done on the inner mitochondrial membrane.
• Utilizes the proton gradient from the intermembrane space of the mitochondria.

Receptor Antagonists vs. Agonists

• Antagonists: Block receptors, preventing activation
• Agonists: Activate receptors by mimicking natural ligands, triggering a biological response