Transcription Factors

General vs Specific Transcription Factors

Transcription factors are proteins that regulate gene expression by binding to DNA. General transcription factors are required for the transcription of all genes, while specific transcription factors regulate particular genes.

• General transcription factors: Form the basic transcription machinery, such as TFIID, and are necessary for RNA polymerase to initiate transcription.

• Specific transcription factors: Bind to unique DNA sequences to activate or repress the transcription of specific genes.

• Example: The transcription factor NF-κB is specific and regulates immune response genes.

Cis vs Trans Regulation

Gene regulation can occur through elements located on the same DNA molecule (cis) or through factors that act from elsewhere (trans).

• Cis elements: DNA sequences such as promoters and enhancers located near the gene they regulate.

• Trans factors: Proteins or RNAs that bind to cis elements to influence gene expression.

Activators vs Repressors

• Activators: Increase transcription by facilitating RNA polymerase binding.

• Repressors: Decrease transcription by blocking RNA polymerase or recruiting silencing complexes.

Binding Sites

• Transcription factors recognize specific DNA sequences called binding sites.

• These sites are often found in promoters or enhancers.

Operons

Concept of Operons

An operon is a cluster of genes under the control of a single promoter, commonly found in prokaryotes.

• Allows coordinated expression of genes with related functions.

• Example: The lac operon in Escherichia coli controls lactose metabolism.

Repressible vs Inducible Operons

• Repressible operons: Usually active but can be turned off (e.g., trp operon).

• Inducible operons: Usually off but can be turned on in response to a substrate (e.g., lac operon).

Operon Logic

• Operons use regulatory proteins to sense environmental conditions and adjust gene expression accordingly.

Epigenetics

Histones

Histones are proteins that package DNA into chromatin, affecting gene accessibility.

• Histone modifications (e.g., acetylation, methylation) regulate gene expression.

Heterochromatin vs Euchromatin

• Heterochromatin: Densely packed, transcriptionally inactive.

• Euchromatin: Loosely packed, transcriptionally active.

DNA Methylation

• Adding methyl groups to DNA (usually cytosine) silences gene expression.

• Important for development and cell differentiation.

Studying Gene Function

Knockdown vs Knockout vs Overexpression

• Knockdown: Reduces gene expression, often using RNA interference.

• Knockout: Completely removes or inactivates a gene.

• Overexpression: Increases gene expression beyond normal levels.

• Uses: To study gene function, disease models, and drug targets.

Reporters

• Luciferase: Produces light, used to measure gene expression.

• GUS: Produces a color change, used in plant studies.

• GFP: Fluorescent protein, used to visualize gene expression in live cells.

• Promoter analysis: Measures activity of gene regulatory regions.

• Protein analysis: Measures abundance or localization of proteins.

Organelles vs Cell Structures

Overview

Cells contain various structures and organelles, each with specific functions. Some are found in all cells, others only in eukaryotes or prokaryotes.

• Actin & motors: Cell movement, muscle contraction.

• Microtubules & motors: Chromosome movement, vesicle transport.

• Intermediate filaments: Structural support.

Membrane Transport

Diffusion and Concentration Gradients

• Diffusion: Movement of molecules from high to low concentration.

• Concentration gradient: Difference in concentration across a membrane.

Passive vs Active Transport

• Passive transport: No energy required (e.g., simple diffusion, facilitated diffusion).

• Active transport: Requires energy (usually ATP).

Primary vs Secondary Active Transport

• Primary: Direct use of ATP (e.g., Na+/K+ pump).

• Secondary: Uses energy from another gradient (e.g., glucose/Na+ co-transport).

Co-transporter vs Counter-transporter vs Uniporter

• Co-transporter (symporter): Moves two substances in the same direction.

• Counter-transporter (antiporter): Moves two substances in opposite directions.

• Uniporter: Moves one substance.

Exocytosis and Phagocytosis

• Exocytosis: Release of substances from the cell.

• Phagocytosis: Uptake of large particles by the cell.

Cell Signaling

Reception, Transduction, Response

• Reception: Cell detects a signal molecule.

• Transduction: Signal is relayed inside the cell.

• Response: Cell changes activity (e.g., gene expression, metabolism).

Sources of Signals

• Signals can come from hormones, neurotransmitters, environmental cues.

Types of Responses

• Responses include changes in gene expression, enzyme activity, cell movement.

Enzymes

What Enzymes Are and What They Do

• Enzymes: Biological catalysts that speed up chemical reactions.

• Lower activation energy without being consumed.

Reversibility

• Some enzyme-catalyzed reactions are reversible, others are not.

Cofactors

• Non-protein helpers (e.g., metal ions, vitamins) required for enzyme activity.

Inhibitors

• Substances that decrease enzyme activity (competitive or non-competitive).

Metabolism

Catabolism vs Anabolism

• Catabolism: Breakdown of molecules to release energy.

• Anabolism: Synthesis of molecules, requires energy.

Reading Biochemical Pathways

• Pathways are sequences of enzyme-catalyzed reactions.

• Arrows indicate direction; intermediates and products are shown.

Glucose Metabolism

Glycolysis

• Investment phase: Uses ATP to phosphorylate glucose.

• Payoff phase: Produces ATP and NADH.

• Summary: 1 glucose → 2 pyruvate + 2 ATP + 2 NADH

Fermentation

• Occurs when oxygen is absent.

• Regenerates NAD+ for glycolysis.

• Example: Lactic acid fermentation in muscle cells.

Respiration

• Citric Acid Cycle: Cyclic pathway that oxidizes acetyl-CoA to CO2, producing NADH and FADH2.

• Inputs: Acetyl-CoA, NAD+, FAD, ADP

• Outputs: CO2, NADH, FADH2, ATP

• Electron Transport Chain: Transfers electrons from NADH/FADH2 to O2, creating a proton gradient.

• ATP synthase: Uses proton gradient to make ATP.

• Oxygen: Final electron acceptor; necessary for aerobic respiration.

• ATP yield: Complete oxidation of glucose yields ~30-32 ATP.

Summary Equations

• Glycolysis:

• Cellular Respiration:

Photosynthesis

Summary Equation

Pigments

• Chlorophyll: Main pigment, absorbs red and blue light.

• Carotenoids: Accessory pigments, absorb other wavelengths.

• Anthocyanins: Pigments with protective roles.

Light Harvesting Complex & Photosystem

• Photosystems are protein complexes that capture light energy.

• Light harvesting complexes funnel energy to reaction centers.

Light Reactions/Electron Transport Chain

• Light excites electrons, which move through an electron transport chain, creating a proton gradient.

• Water is necessary as the electron donor; produces O2 as a byproduct.

• Outputs: ATP, NADPH, O2

• Inputs: Light, water, ADP, NADP+

Calvin Cycle

• Uses ATP and NADPH to fix CO2 into sugars.

• Outputs: Glucose (after 6 turns), ADP, NADP+

• Inputs: CO2, ATP, NADPH

• Must run 6 times to produce one molecule of glucose.