Comprehensive Study Guide: Foundations of Biology Final Exam

Unit 1 – Biomolecules and Cells

Cell Structure: Prokaryotic vs. Eukaryotic Cells

• Prokaryotic cells (e.g., bacteria, archaea) lack membrane-bound organelles and a nucleus. Their DNA is found in a nucleoid region.

• Eukaryotic cells (e.g., plants, animals, fungi, protists) have a nucleus and various membrane-bound organelles (e.g., mitochondria, endoplasmic reticulum, Golgi apparatus).

• Phospholipid bilayer forms the fundamental structure of all cell membranes, with hydrophilic (water-attracting) heads facing outward and hydrophobic (water-repelling) tails facing inward.

• Hydrophobic areas are the fatty acid tails in the interior of the bilayer; hydrophilic areas are the phosphate heads on the exterior surfaces.

• Biomolecules in cells:

  • Proteins: Embedded in membranes (as channels, receptors), in cytoplasm, and as enzymes.

  • Lipids: Main component of membranes, energy storage (e.g., triglycerides).

  • Carbohydrates: Attached to proteins/lipids on cell surface (glycoproteins/glycolipids), energy storage (glycogen, starch).

  • Nucleic acids: DNA in nucleus (eukaryotes) or nucleoid (prokaryotes), RNA throughout cell.

• Polar regions of molecules interact with water; non-polar regions interact with other non-polar molecules or are buried within membranes.

• Transmembrane proteins have hydrophobic regions spanning the membrane and hydrophilic regions exposed to the aqueous environment.

• Difference in phospholipid bilayers: Eukaryotic cells may have sterols (e.g., cholesterol) for membrane fluidity; some organelles have unique lipid compositions.

• Organelle functions:

  • Nucleus: Stores genetic material.

  • Mitochondria: ATP production via cellular respiration.

  • Chloroplasts (plants/algae): Photosynthesis.

  • Endoplasmic reticulum (ER): Protein and lipid synthesis.

  • Golgi apparatus: Protein modification and sorting.

  • Lysosomes/peroxisomes: Degradation of macromolecules.

• Transport across membranes:

  • Polar molecules (e.g., ions, glucose) require transport proteins (channels, carriers) due to the hydrophobic core of the bilayer.

  • Non-polar molecules (e.g., O2, CO2) can diffuse directly through the membrane.

Unit 2 – Bioenergetics and Cell Signaling

Energy Transfer in Cells

• Glycolysis: Occurs in the cytoplasm of all cells. Converts glucose to pyruvate, producing ATP and NADH.

• TCA (Krebs) Cycle: Occurs in the mitochondrial matrix (eukaryotes). Acetyl-CoA adds carbon; outputs include CO2, NADH, FADH2, and ATP/GTP.

• Electron Transport Chain (ETC): Located in the inner mitochondrial membrane (eukaryotes) or plasma membrane (prokaryotes). Uses NADH/FADH2 to create a proton gradient, producing water and ATP.

• ATP Synthase: Powered by the flow of H+ down its gradient; synthesizes ATP from ADP and Pi.

  • Equation: $\text{ADP} + \text{P}_i \rightarrow \text{ATP}$

• Photosynthesis (plants):

  • Light reactions: Occur in thylakoid membranes; inputs: light, H2O; outputs: O2, ATP, NADPH.

  • Calvin cycle: Occurs in stroma; inputs: CO2, ATP, NADPH; outputs: glucose (or G3P).

• H+ concentration: Highest in the intermembrane space (mitochondria) and thylakoid lumen (chloroplasts).

• Link between mitochondria and chloroplasts: Both use electron transport chains and chemiosmosis to generate ATP; products of one process (e.g., O2 from photosynthesis) are substrates for the other (cellular respiration).

Cell Signaling

• Signal reception: Occurs at the cell membrane (for polar molecules) via receptors.

• Signal transduction: Intracellular signaling cascades relay and amplify the signal.

• Cellular response: Changes in gene expression, metabolism, or cell behavior.

• Phosphate groups: Added by kinases (phosphorylation) to activate/inactivate proteins; removed by phosphatases. G protein-coupled receptors (GPCRs) use GTP/GDP binding for on/off states.

Unit 3 – Cell Cycle and Genetics

Mitosis vs. Meiosis

• Mitosis: Occurs in somatic cells for growth and repair; produces two genetically identical diploid cells.

• Meiosis: Occurs in germ cells to produce gametes; results in four genetically unique haploid cells.

Dihybrid Crosses and Chromosome Behavior

• Dihybrid cross: Involves two genes; can be independently assorting, sex-linked, or linked.

• Key cues: Look for inheritance patterns, parental genotypes, and phenotypic ratios.

• Chromosome drawing: Homologous pairs (same genes, possibly different alleles) vs. gametes (haploid, one copy of each gene).

Unit 4 – Making Proteins

Transcription and Translation

• Gene: A DNA sequence that codes for a functional product (protein or RNA).

• Relationship: Genes are segments of DNA, organized into chromosomes; DNA is transcribed into RNA, which is translated into protein.

• DNA structure: Double helix with antiparallel strands (5' to 3' and 3' to 5').

• Regulatory regions: Sites where transcription factors (TFs) and general transcription factors (GTFs) bind to control gene expression.

• RNA polymerase: Enzyme that synthesizes RNA from a DNA template, reading 3' to 5' and synthesizing 5' to 3'.

• mRNA processing: In eukaryotes, includes addition of 5' cap, poly-A tail, and splicing of introns.

• Translation: Initiates at the start codon (AUG), ends at a stop codon; ribosome reads mRNA 5' to 3'.

• DNA mutations: Point mutations can be silent, missense, nonsense, or frameshift, affecting protein structure/function.

• Gene expression regulation: Controlled at transcriptional, post-transcriptional, translational, and post-translational levels.

• Differentiation: Process by which cells become specialized; linked to development via differential gene expression.

• Biotechnology techniques: Used for gene cloning, sequencing, expression analysis, and genetic modification; all involve manipulation or analysis of nucleic acids.

Overarching Concepts and Critical Thinking

• Origin of cells: Chemical properties of biomolecules and early Earth conditions enabled formation of protocells; modern cells have complex metabolic and genetic processes.

• Endosymbiotic theory: Mitochondria and chloroplasts originated from engulfed prokaryotes; supported by double membranes, own DNA, and similarities to bacteria.

• ATP formation: Cells convert chemical energy from food or light into ATP, the universal energy currency.

• Source of energy and carbon: Energy for ATP bonds comes from sunlight (photosynthesis) or chemical bonds (respiration); carbon in glucose and other biomolecules originates from atmospheric CO2 (photosynthesis).

• Genetic diversity: Sexual reproduction (meiosis, recombination, independent assortment) and mutation create diversity, essential for evolution and species survival.

• Central dogma: Information flows from DNA → RNA → Protein.

• Differential gene expression: Determines cell function; regulated by transcription factors, epigenetic modifications, and signaling pathways.

• Biological analysis: Techniques measure DNA, RNA, or protein to reveal gene expression, mutations, or cellular state.

Sample Table: Comparison of Mitosis and Meiosis

Feature	Mitosis	Meiosis
Cell type	Somatic	Germ (sex cells)
Number of divisions	1	2
Number of daughter cells	2	4
Genetic composition	Identical to parent	Genetically unique
Chromosome number	Diploid (2n)	Haploid (n)

Additional Info

• For diagrams, practice labeling all structures and processes from memory.

• Critical thinking questions often require integrating knowledge across topics (e.g., linking cell structure to function, or genetics to evolution).