Cell Biology Exam 1 Study Notes: Cell Structure, Gene Regulation, Protein Structure, and Membranes

Chapter 1 – Cells

Cell Theory

The cell theory is a foundational concept in biology, stating that all living organisms are composed of cells, and that the cell is the basic unit of life. All cells arise from pre-existing cells.

• Key Points:

  • All organisms are made of one or more cells.

  • The cell is the structural and functional unit of life.

  • Cells arise only from pre-existing cells by division.

Cell Structure

Cells contain specialized structures called organelles that perform distinct functions. The structure and composition of cells differ between prokaryotes and eukaryotes, and between animal and plant cells.

• Organelles: Membrane-bound compartments such as the nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, and (in plants) chloroplasts.

• Eukaryotic vs. Prokaryotic Cells:

  • Eukaryotic cells have a nucleus and membrane-bound organelles (e.g., animal, plant, fungi, protists).

  • Prokaryotic cells lack a nucleus and most organelles (e.g., bacteria, archaea).

• Animal vs. Plant Cells:

  • Plant cells have a cell wall, chloroplasts, and large central vacuole.

  • Animal cells lack a cell wall and chloroplasts, but have centrioles and lysosomes.

Metazoan Evolution

Metazoans are multicellular animals that evolved from unicellular ancestors. Their evolution involved the development of specialized cell types and complex body plans.

• Key evolutionary steps include cell differentiation, cell adhesion, and communication.

Differentiation and Genomic Identity

Although all cells in a multicellular organism share the same genome, they can differentiate into various cell types by regulating gene expression.

• Differentiation: The process by which cells become specialized in structure and function.

• Regulation occurs through epigenetic mechanisms and transcriptional control.

Chromatin Structure and Gene Regulation

Chromatin is the complex of DNA and proteins (mainly histones) that packages genetic material in the nucleus. Its structure influences gene expression.

• DNA Methylation: Addition of methyl groups to cytosine bases, often leading to gene silencing.

• Histone Modification: Chemical modifications (e.g., acetylation) of histone proteins affect chromatin structure and gene accessibility.

• Chromatin Remodeling: ATP-dependent complexes reposition or restructure nucleosomes to regulate access to DNA.

Example: Acetylation of histone tails by histone acetyltransferases (HATs) generally leads to a more open chromatin structure and increased gene expression.

Eukaryotic Gene Regulation Basics

• Gene expression is controlled at multiple levels: chromatin structure, transcription, RNA processing, translation, and post-translational modification.

• Transcription factors and regulatory elements (enhancers, silencers) play key roles.

Experimental Design and Data Interpretation

Understanding how to interpret experimental data and design experiments is crucial. Focus on identifying variables, controls, and critiquing experimental design.

• Be able to analyze figures, understand why specific techniques are used, and propose experiments for novel scenarios.

Techniques in Cell and Molecular Biology

• Transient Transfection: Temporary introduction of foreign DNA into cells to study gene function.

• In Situ Hybridization: Technique to detect specific nucleic acid sequences within fixed tissues or cells using labeled probes.

• Immunohistochemistry/Immunocytochemistry: Use of antibodies to detect specific proteins in tissues (histochemistry) or cells (cytochemistry).

• Fluorescence Activated Cell Sorting (FACS): Technique to separate and analyze cells based on fluorescent labeling.

• Chromatin Immunoprecipitation (ChIP): Method to study protein-DNA interactions by immunoprecipitating DNA-bound proteins.

• Reverse Transcriptase PCR (RT-PCR): Technique to detect and quantify RNA by converting it to cDNA and amplifying specific sequences.

Chapters 2 and 3 – Protein Structure & Function

Bonds in Proteins

Proteins are polymers of amino acids linked by peptide bonds. Their structure is stabilized by various interactions:

• Peptide Bonds: Covalent bonds between amino acids.

• Hydrogen Bonds: Stabilize secondary and tertiary structures.

• Disulfide Bonds: Covalent bonds between cysteine residues.

• Ionic Interactions: Between charged side chains.

• Hydrophobic Interactions: Nonpolar side chains cluster away from water.

Amino Acid Classes

Amino acids are classified based on the properties of their side chains:

• Nonpolar (hydrophobic): e.g., alanine, valine, leucine

• Polar uncharged: e.g., serine, threonine, asparagine

• Polar charged (acidic): e.g., aspartic acid, glutamic acid

• Polar charged (basic): e.g., lysine, arginine, histidine

Protein Levels of Structure

• Primary Structure: Linear sequence of amino acids.

• Secondary Structure: Local folding into α-helices and β-sheets, stabilized by hydrogen bonds.

• Tertiary Structure: Overall 3D shape of a single polypeptide chain.

• Quaternary Structure: Association of multiple polypeptide chains.

Protein Functions

• Enzymes (catalysis)

• Structural proteins (e.g., actin, tubulin)

• Transport proteins (e.g., hemoglobin, membrane channels)

• Signaling proteins (e.g., hormones, receptors)

• Regulatory proteins (e.g., transcription factors)

Molecular Complementarity

Molecular complementarity refers to the precise fit between molecules, which determines the specificity and affinity of protein interactions.

• Shape, charge, and hydrophobic/hydrophilic properties contribute to complementarity.

• High specificity and affinity are essential for enzyme-substrate and receptor-ligand interactions.

Chapter 10 – Membranes & Membrane Proteins

Membrane Structure

Biological membranes are composed of a phospholipid bilayer with embedded proteins. The structure is often described by the fluid mosaic model.

• Phospholipids: Amphipathic molecules with hydrophilic heads and hydrophobic tails.

• Cholesterol: Modulates membrane fluidity.

• Proteins: Integral (span the membrane) and peripheral (associated with membrane surface).

Membrane Function

• Selective barrier for ions and molecules.

• Compartmentalization of cellular processes.

• Cell signaling and communication.

• Transport of substances via channels, carriers, and pumps.

Membrane Proteins

• Integral proteins: Span the membrane; often function as channels or receptors.

• Peripheral proteins: Loosely attached to membrane surface.

• CFTR (Cystic Fibrosis Transmembrane Conductance Regulator): An example of a membrane protein functioning as a chloride channel; mutations cause cystic fibrosis.

Amino Acids and Membrane Association

• Hydrophobic amino acids enable proteins to insert into the membrane.

• Hydrophilic regions interact with the aqueous environment or other proteins.

• Protein domains determine interactions with other membrane proteins (e.g., syntaxin in SNARE complexes).

Experimental Design and Data Interpretation (Membrane Proteins)

• Understand how to interpret data from experiments involving membrane proteins, such as clustering and mobility studies.

• Be able to critique experimental design and propose new experiments.

Techniques in Membrane Biology

• FRAP (Fluorescence Recovery After Photobleaching): Measures the mobility of membrane proteins by bleaching a fluorescently labeled area and monitoring recovery.

• Transfection: Introduction of foreign DNA to study protein function.

• Domain Mutagenesis: Mutating specific protein domains to assess their role in processes like clustering or mobility.

Summary Table: Key Techniques in Cell Biology

Technique	Main Purpose	Application Example
Transient Transfection	Introduce foreign DNA temporarily	Study gene/protein function in cultured cells
In Situ Hybridization	Detect specific nucleic acid sequences	Visualize mRNA expression in tissues
Immunohistochemistry/Immunocytochemistry	Detect specific proteins using antibodies	Localize proteins in cells/tissues
FACS	Sort and analyze cells by fluorescence	Isolate cell populations based on markers
ChIP	Study protein-DNA interactions	Identify transcription factor binding sites
RT-PCR	Quantify RNA expression	Measure gene expression levels
FRAP	Measure protein mobility	Analyze membrane protein dynamics
Domain Mutagenesis	Assess function of protein domains	Determine role in clustering/mobility

Additional info:

• For experimental design, always identify independent/dependent variables, controls, and possible confounding factors.

• Be prepared to interpret data from figures, even if the specific proteins or pathways differ from those discussed in class.