Gene Expression and Regulation

Chapter 8: Gene Expression and Regulation

• Cell differentiation relies on the control of gene expression.
• Some proteins are common to all cell types, while others are unique.
• Gene expression responds to internal and external environmental changes.
• Gene expression is controlled at multiple levels, with transcriptional control being the most significant.
• Transcription regulators control gene expression by up or down regulating it.
• These regulators bind to regulatory DNA sequences, specifically at the Tata box where transcription initiates.

Prokaryotic Gene Regulation: Operons

• Operons are gene sets controlled by a single promoter, found only in prokaryotes.
• They are required for single cellular processes like tryptophan production or lactose breakdown.
• The operator is a sequence located in the promoter region.
• Transcriptional repressors are allosteric proteins activated by molecules
• Activated repressors bind to the operator and halt transcription.
• Transcriptional activators bind to DNA and increase transcription, and are also allosteric, needing to bind to activate.
• Activators and repressors work together in the Lac Operon, which contains genes for lactose breakdown and is both an activator and repressor.
• In the presence of lactose, the Lac repressor releases from DNA, otherwise it stops Lac Operon transcription when bound.
• The CAP activator binds to cyclic AMP to start Lac Operon transcription when bound to DNA
• CAP Activator produces cyclic AMP when glucose levels are low.
• An operon is active when glucose is absent and lactose is present.

Eukaryotic Gene Regulation

• Eukaryotic gene regulation is more complex due to diverse cell and tissue types.
• Eukaryotes do not have operons; each gene is regulated individually.
• Regulatory DNA sequences can be far from the gene.
• Enhancers are binding sites for eukaryotic transcription activators that increase expression.
• Silencers are binding sites for eukaryotic transcription repressors that halt expression.
• DNA folding allows interaction with the promoter region via a mediator.
• The mediator is a large protein complex and picks what is best.
• Activators and repressors can act before or after the gene by and either help or inhibit transcription factor binding.
• Regulators work together to control a gene through combinatorial control.
• The Lac operon resembles eukaryotic transcriptional control, with the mediator incorporating signals near the promoter.
• The mediator allows multiple activators and repressors to control gene expression.

Chapter 11: Coordinated Gene Expression and Cell Memory

• A single protein can coordinate expression by binding to different genes
• Binding of the protein to different genes alters their conformation when activated by one protein signal.
• Cortisol affects many processes within the body.
• Combined transcription regulators allow for unique combinations of gene expression
• Cells can change tissue type using only a few regulatory proteins.
• One regulatory protein can cause a precursor cell to divide into two.
• Cell memory describes daughter cells being similar to parent cells, achieved through epigenetics.
• Epigenetic inheritance involves changes not in the DNA sequence.
• Genetics refers to sequence changes, while inheritance occurs between cell generations
• A single transcription regulator can produce complex structures by regulating multiple genes and other regulators in an expression cascade.

Cell Memory and Epigenetics (Modification)

• Positive Feedback: A protein activates its own gene expression, ensuring it remains expressed once started.
• Methylation results in a methyl group added to cytosine and often blocks transcription (especially in CG patterns).

Histone Modification

• Covalent bonding of histone protein tails is a histone modification technique.
• Histone Modification results in turning on or off what you had in the parent cell
• Both patterns are copied into daughter cells and passed on.
• Post-transcriptional control occurs via regulatory, non-coding RNAs like:
  • MicroRNAs (miRNAs)
  • Short Interfering RNAs (siRNAs)
  • Long Non Coding RNAs (lnRNA)
• MicroRNAs (miRNAs):
  • Act rapidly.
  • Are transcribed from the genome.
  • Regulate mRNAs by being complementary to a target mRNA
  • Eventually leading to its degradation.
• Short interfering RNAs (siRNAs):
  • Originate from foreign double-stranded RNA (viruses) and are cut into pieces.
  • Pieces bind back to foreign RNA, resulting in its degradation.
  • Are not naturally produced by our bodies.
• RNA interference (RNAi) uses siRNAs and is a research tool to stop gene expression.
• Long noncoding RNA (lnRNA):
  • Is transcribed from the coding strand of genes.
  • Binds to and regulates mRNA
• Expression Cascade refers to a series of genes, with each gene regulating the next one (or several) in the series.

Proteins and Cell Membrane Structure

• Proteins attach to the cell membrane through lipid binding or protein-protein interactions.
• Many membrane proteins are amphipathic, possessing both hydrophilic (polar head) and hydrophobic (non-polar tail) regions.
• The hydrophobic part interacts with the lipid bilayer, often forming alpha-helices or beta-sheets.
• Backbone H+ bonds to itself inside the bilayer in a beta barrel is 2 sheets rolled up.
• The cell cortex, a meshwork of proteins, sugars, and molecules, provides structure to the cell membrane.
• It anchors proteins, supports cell structure, and changes cell shape to facilitate movement.
• Membrane proteins can move across the membrane but may be restricted to specialized function.
• Proteins can be bound to the cell cortex (inside), extracellular matrix (outside), or other cells.
• Barrier proteins physically block protein movement
• Alpha-helices and beta-sheets form in the lipid bilayer because backbone hydrogens bond to each other, nonpolar side chains face lipids, and polar side chains face the open channel.

Chapter 12: Membrane Transport

• Small, nonpolar molecules diffuse through the lipid bilayer down their concentration gradient.
• Most other molecules diffuse much less effectively.
• Diffusion follows the order: small nonpolar > small polar > large polar > ions.
• Ion concentrations differ between the inside and outside of the cell, maintained by transport proteins.
• Water preferentially travels into a cell (osmosis) to equalize solute concentration, increasing pressure.
• Cells expel water or resist pressure.
• The electrochemical gradient, combining charge (electrical) and solute concentration (chemical), determines passive transport.
• Passive transport moves molecules/ions down their electrochemical gradient.
• Active transport moves molecules/ions up their electrochemical gradient.
• At resting membrane potential, the electrochemical gradient is at equilibrium, with the cytosol slightly negative relative to the outside.

Membrane Transport Proteins

• Channels allow different molecules to pass based on size/charge, and are ONLY passive.
• Transporters exhibit highly specific binding to a molecule and can be passive or active.
• Ion channels are selective for specific ion types based on size and charge.
• They can open or close randomly or in response to a stimulus.
• Channels can be 1000 times faster than a transporter when open.
• Gated channels open/close due to a variety of stimuli, including voltage (membrane potential changes), ligand binding, or physical motion.
• Active transport works against the electrochemical gradient of the cell

Uniport and Pumps

• Uniport: Passive transporter that moves a single solute down its electrochemical gradient through specific binding (e.g., glucose transporter).
• Pumps: Active transporters that move solutes against their electrochemical gradient using energy from: -The electrochemical gradient of other solutes (Na+ or H+) - which are coupled pumps -ATP: Sodium-potassium pump -Light
• The sodium-potassium pump (Na+/K+ pump) produces a steep electrochemical gradient using ATP (Na+K+ATPase).
• It pumps 3 Na+ out and 2 K+ in, used to power other processes like alters membrane potential and helps set up the resting membrane potential.
• Potassium leak channels maintain resting membrane potential by opening and closing randomly, making the membrane more permeable to K+.
• Coupled pumps move two types of solutes by moving: -One solute down its electrochemical gradient and one solute up. -Using Na+ (in animals) or H+ (in plants, fungi, and bacteria) gradients.

Symport and Antiport

• Antiport: Transports two types of solutes in opposite directions across the membrane.
• Symport: Transports two types of solutes in the same direction across the membrane.
• Glucose symporter: Transports spontaneously, opening and closing only when empty or fully occupied.
• A sodium gradient is used to import glucose from the gut (Na+ moves down, glucose moves up).

Neurons and Action Potentials

• Neurons transmit signals through action potentials, which are moving changes in membrane potential.
• Action potentials are propagated by depolarization, which is when the membrane potential switches (negative outside, positive inside).
• Voltage-gated Na+ channels open, causing Na+ to move.
• After opening, the Na+ channel becomes inactive (refractory period), and is closed and insensitive to membrane potential.
• Repolarization returns the membrane potential to its resting state.
• Action potentials are propagated by Na+ influx, with the refractory period preventing backward signal movement.
• Synapses connect two cells
• At synapses neurons connect to other cells and communication can be electrical or chemical:
  • Electrical > Chemical -Action potentials open voltage-gated Ca+ channels. -Neurotransmitters are released into the synaptic cleft.
  • Chemical > Electrical -Nuerotrasmitters bind to ligan-gated ion channels.
  • Ions enter the postsynaptic cell.
  • The charge of these ions can be is either + or -
  • Positive charges are excitatory (start AP)
  • Negative charges are inhibitory (stop AP)
• Complexity of synaptic signaling is key to the human brain.