General Biology: Core Concepts and Practice Questions

Membrane Structure and Transport

Simple Diffusion Across Membranes

Cell membranes are selectively permeable barriers composed primarily of a phospholipid bilayer. The ability of molecules to cross the membrane depends on their size, polarity, and charge.

• Nonpolar small molecules (e.g., O2, CO2) diffuse most easily through the lipid bilayer.

• Polar or charged molecules (e.g., ions, glucose) require transport proteins to cross the membrane.

• Phospholipids are amphipathic: they have hydrophilic (polar) heads and hydrophobic (nonpolar) tails, forming a bilayer that allows small nonpolar molecules to diffuse through.

Example: Oxygen gas (O2) diffuses directly through the membrane, while sodium ions (Na+) require ion channels.

Cell Structure and Function

Eukaryotic Cell Compartments

Eukaryotic cells contain membrane-bound organelles, each with specialized functions. Nucleic acids (DNA or RNA) are found in the nucleus, mitochondria, and chloroplasts, but not in the Golgi apparatus.

• Nucleus: Contains most of the cell's DNA.

• Mitochondria and Chloroplasts: Contain their own DNA, supporting the endosymbiotic theory (these organelles originated from prokaryotes engulfed by ancestral eukaryotic cells).

• Golgi Apparatus: Involved in protein sorting and modification; does not contain DNA or RNA.

Unique Features of Eukaryotic Cells

• Internal membrane-bound compartments (organelles) are present in eukaryotes but not in prokaryotes.

• Ribosomes are present in both cell types, but only eukaryotes have a complex cytoskeleton and organelles like the nucleus, mitochondria, and Golgi apparatus.

Protein Trafficking in the Endomembrane System

Proteins destined for export or for certain organelles are synthesized by ribosomes on the rough endoplasmic reticulum (ER), then transported via vesicles to the Golgi apparatus for further modification and sorting.

1. Rough ER (site of synthesis for secreted/membrane proteins)

2. Vesicle (transports protein)

3. Golgi apparatus (modification and sorting)

4. Vesicle (final transport to destination)

Macromolecules: Structure and Function

Amino Acids and Proteins

Amino acids are the building blocks of proteins. Their side chains (R groups) determine their properties:

• Polar R groups (e.g., serine, asparagine) are hydrophilic and often found on protein surfaces or in contact with aqueous environments.

• Nonpolar R groups (e.g., phenylalanine, leucine) are hydrophobic and often found in the interior of proteins or membrane-spanning regions.

Biomolecule Identification

Major classes of biomolecules include:

• Lipids: Nonpolar molecules, e.g., steroids.

• Amino acids: Contain amino and carboxyl groups, central carbon, and R group.

• Carbohydrates: Sugars and polymers of sugars.

• Nucleotides: Composed of a phosphate group, sugar, and nitrogenous base.

Bioenergetics: Photosynthesis and Cellular Respiration

Photosynthesis

• Light reactions occur in the thylakoid membrane of chloroplasts, generating a proton gradient across the thylakoid membrane (high [H+] in the thylakoid lumen).

• ATP is produced as protons flow back into the stroma through ATP synthase.

• Oxygen is generated by the oxidation of water by Photosystem II (P680).

Cellular Respiration

• During the electron transport chain (ETC), energy is used to pump H+ into the mitochondrial intermembrane space, creating a proton gradient.

• Oxygen is the final electron acceptor in aerobic respiration, forming water.

Enzyme Structure and Regulation

Enzyme Inhibition and Regulation

• Permanent inhibition: Achieved by covalently binding a molecule to the enzyme's active site.

• Kinases add phosphate groups (phosphorylation), which can inhibit or activate enzymes.

• Phosphatases remove phosphate groups (dephosphorylation), reversing the effect.

Enzyme Structure Levels

• Primary structure: Amino acid sequence (not affected by pH changes).

• Secondary and tertiary structures: Maintained by non-covalent interactions; can be disrupted by changes in pH.

Cell Signaling

Signal Transduction Pathways

Cell signaling often involves a ligand (signal molecule), receptor, and second messenger. Mutations in early steps of a pathway can block downstream effects.

• Non-conservative missense mutations can alter protein function and decrease pathway output (e.g., decreased glycogen catabolism).

Cell Division and Genetics

Meiosis and Genetic Variation

• Meiosis I: Homologous chromosomes pair and separate, generating genetic diversity through crossing over and independent assortment.

• Result: Four genetically unique daughter cells.

Mendelian Genetics

• Autosomal recessive traits: Both parents must carry at least one recessive allele for an offspring to express the trait.

• Dominant and recessive alleles: Dominant alleles mask the effect of recessive alleles in heterozygotes.

• Epistasis: One gene can mask the effect of another gene (e.g., coat color in Labrador retrievers).

Sex-Linked Inheritance

• X-linked traits: Males are hemizygous (one X chromosome), so recessive alleles are expressed if present.

Molecular Biology: Gene Expression and Regulation

Transcription and RNA Processing

• Transcription factors are required for RNA polymerase II to initiate transcription in eukaryotes.

• Alternative splicing allows a single gene to encode multiple proteins.

• DNA sequence encodes information for protein sequence, regulatory signals, and replication templates.

Gene Structure

• Promoter: Region where RNA polymerase binds to initiate transcription.

• Terminator: Signals RNA polymerase to stop transcription.

• Exons: Coding regions included in mRNA and translated into protein.

• Introns: Non-coding regions spliced out during RNA processing.

• UTRs (Untranslated Regions): Present in mRNA but not translated into protein.

RNA Polymerase vs. DNA Polymerase

• RNA polymerase does not require a primer to initiate synthesis; DNA polymerase does.

Mutations

• Missense mutation: Changes one amino acid to another (e.g., serine to cysteine).

• Nonsense mutation: Introduces a premature stop codon, truncating the protein.

• Non-conservative missense: Substitutes an amino acid with different properties, likely altering protein function.

Gene Regulation Levels

Level	Examples
Chromatin arrangement	Histone methylation/acetylation
Transcriptional control	Promoters, transcription factors
Post-transcriptional control	Poly-A tail, 5' cap, splicing, microRNA degradation
Post-translational control	Glycosylation, phosphorylation, proteolysis

DNA Technology and Molecular Genetics

PCR and DNA Sequencing

• PCR primers must be complementary to the ends of the target sequence (forward and reverse primers).

• Sanger sequencing uses fluorescently labeled dideoxynucleotides (ddNTPs) to identify terminal bases.

Gene Families and RFLP Analysis

• Gene duplication is required for the formation of gene families.

• RFLP (Restriction Fragment Length Polymorphism): Used to visualize genotypes at specific loci by fragment length after restriction enzyme digestion.

Evolutionary Biology

Mechanisms of Evolution

• Darwin and Wallace: Natural selection acts on individuals; populations evolve.

• Lamarck: Proposed inheritance of acquired characteristics (now disproven).

• Heterochrony: Evolutionary change in the timing of developmental events.

Hardy-Weinberg Equilibrium

• Allele and genotype frequencies remain constant if no selection, mutation, migration, genetic drift, or non-random mating occurs.

• Equilibrium does not require allele frequencies to be 50/50.

Tables and Diagrams

Example: Eye Color and Size in Drosophila Crosses

Eye Phenotype	Female Genotypes	Male Genotypes
Normal size, red	XO+XO+ SS+SS+	XO+Y SS+
Normal size, orange	XO+XO SS+SS+	XOY SS+
Small size, red	XO+XO+ SSSS	XO+Y SS
Small size, orange	XO+XO SSSS	XOY SS

Additional info: Table inferred from the provided genotype/phenotype mapping in the Drosophila cross problem.

Summary

• This set of questions and annotated answers covers foundational topics in General Biology, including cell structure, macromolecules, metabolism, genetics, gene expression, molecular biology techniques, and evolution.

• Understanding these core concepts is essential for success in introductory biology courses and for building a foundation for advanced study in the life sciences.