AP Biology Unit 6: Gene Expression and Regulation – Study Notes

Gene Expression and Regulation

DNA & RNA as Heritable Information

Genetic information is stored and transmitted through nucleic acids, primarily DNA and, in some cases, RNA. The structure and organization of these molecules enable the faithful inheritance of traits from one generation to the next.

• DNA Structure: DNA is a double helix composed of two antiparallel strands of nucleotides. Each nucleotide consists of a deoxyribose sugar, a phosphate group, and a nitrogenous base (adenine, thymine, cytosine, guanine). Base-pairing rules: A pairs with T, C pairs with G.

• RNA Structure: RNA is typically single-stranded and contains ribose sugar. Uracil replaces thymine as a base.

• Hereditary Information: DNA stores genetic information in the sequence of its bases. During cell division, DNA is replicated and passed to daughter cells.

• Chromosomal Structure: Eukaryotic chromosomes are linear and associated with histone proteins, forming chromatin. Prokaryotic chromosomes are usually circular and lack histones.

• Plasmids: Small, circular DNA molecules found in prokaryotes and some eukaryotes; can carry additional genes and be transferred between cells.

Example: The bacterial plasmid pBR322 is commonly used in genetic engineering to introduce new genes into bacteria.

Transcription and RNA Processing

Transcription is the process by which genetic information in DNA is copied into RNA. In eukaryotes, the primary transcript (pre-mRNA) undergoes processing before translation.

• DNA vs. RNA: Both are nucleic acids, but DNA is double-stranded and stable, while RNA is single-stranded and more versatile in function.

• Types of RNA:

  • mRNA (messenger RNA): Carries genetic code from DNA to ribosomes.

  • tRNA (transfer RNA): Brings amino acids to ribosomes during translation.

  • rRNA (ribosomal RNA): Structural and catalytic component of ribosomes.

• Transcription Mechanism: RNA polymerase synthesizes RNA in the 5' to 3' direction using the DNA template (antisense) strand.

• Template Strand: Also called the non-coding, minus, or antisense strand.

• RNA Processing (Eukaryotes): Includes addition of a 5' cap, poly-A tail, and splicing to remove introns. Alternative splicing allows for multiple proteins from one gene.

Example: The human beta-globin gene undergoes alternative splicing to produce different mRNA variants.

Translation

Translation is the process by which the sequence of bases in mRNA is decoded to build a specific sequence of amino acids, forming a protein.

• Location: Occurs in the cytoplasm at ribosomes.

• Steps:

  • Initiation: Ribosome assembles around the start codon (AUG) on mRNA.

  • Elongation: tRNAs bring amino acids to the ribosome, matching codons in mRNA.

  • Termination: Occurs when a stop codon is reached; the completed polypeptide is released.

• Genetic Code: Each codon (three bases) specifies an amino acid. The code is redundant; some amino acids are encoded by more than one codon.

• Prokaryotes vs. Eukaryotes: In prokaryotes, transcription and translation are coupled; in eukaryotes, they are separated by the nuclear envelope.

• Retroviruses: Use reverse transcriptase to convert RNA into DNA, which integrates into the host genome.

Example: The HIV virus uses reverse transcriptase to replicate its genome inside host cells.

Regulation of Gene Expression and Cell Specialization

Gene expression is tightly regulated to ensure that the correct proteins are produced at the right time and place. This regulation underlies cell specialization and organismal development.

• Regulatory Sequences: DNA regions (e.g., promoters, enhancers) where regulatory proteins bind to control transcription.

• Transcription Factors: Proteins that bind to regulatory sequences to increase or decrease transcription.

• Positive and Negative Control: Activators enhance transcription; repressors inhibit it.

• Operons (Prokaryotes): Groups of genes regulated together (e.g., lac and trp operons).

• Regulation in Eukaryotes: Involves chromatin remodeling, transcription factors, and small RNAs (e.g., miRNA, siRNA).

• Epigenetic Inheritance: Heritable changes in gene expression not due to DNA sequence changes (e.g., DNA methylation, histone modification).

• Cell Differentiation: Results from differential gene expression; HOX genes are key regulators of body plan development.

• Environmental Influence: External stimuli can alter gene expression in mature cells.

Example: The lac operon in Escherichia coli is induced in the presence of lactose, allowing the bacteria to metabolize it.

Mutations

Mutations are changes in the DNA sequence that can affect genotype and phenotype. They are a primary source of genetic variation and can be subject to natural selection.

• Types of Mutations: Point mutations (substitutions), insertions, deletions, duplications, inversions, and chromosomal alterations.

• Effects: Mutations can be beneficial, harmful, or neutral depending on their impact on protein function and environmental context.

• Genotype to Phenotype: Changes in DNA can alter the type or amount of protein produced, leading to new traits.

• Chromosome Number Alterations: Errors in mitosis or meiosis can lead to aneuploidy (e.g., Down syndrome).

• Horizontal Gene Transfer (Prokaryotes):

  • Transformation: Uptake of naked DNA from the environment.

  • Transduction: Transfer of DNA by viruses (bacteriophages).

  • Conjugation: Direct transfer of DNA between cells via pili.

  • Transposition: Movement of DNA segments within the genome.

• Viral Recombination: Related viruses can exchange genetic material if they infect the same host cell.

Example: Sickle cell anemia is caused by a point mutation in the HBB gene, altering hemoglobin structure.

Biotechnology

Biotechnology involves the use of genetic engineering techniques to analyze and manipulate DNA and RNA for research, medicine, and industry.

• Electrophoresis: Technique to separate DNA, RNA, or proteins based on size and charge. Used for DNA fingerprinting and analysis.

• Restriction Enzymes: Proteins that cut DNA at specific sequences, enabling gene cloning and recombinant DNA technology.

• Plasmid-Based Transformation: Introduction of recombinant plasmids into cells to express new genes.

• Polymerase Chain Reaction (PCR): Amplifies specific DNA sequences exponentially for analysis.

• DNA Sequencing: Determines the exact order of nucleotides in a DNA molecule.

• Gene Expression Detection: Techniques such as RT-PCR and microarrays measure gene activity.

• Gene Editing: Technologies like RNA interference (RNAi) and CRISPR-Cas9 allow targeted modification of gene expression or sequence.

• Genomics and Proteomics: Study of entire genomes and proteomes to understand gene function and regulation.

Example: CRISPR-Cas9 is used to edit genes in model organisms and has potential for treating genetic diseases.

Table: Comparison of DNA and RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Strands	Double-stranded	Single-stranded
Bases	A, T, C, G	A, U, C, G
Function	Genetic information storage	Information transfer, catalysis, regulation

Key Equations and Concepts

• Central Dogma of Molecular Biology:

$\text{DNA} \xrightarrow{\text{transcription}} \text{RNA} \xrightarrow{\text{translation}} \text{Protein}$

• Genetic Code: Each codon (triplet of bases) codes for one amino acid.

• PCR Amplification: Number of DNA copies after n cycles:

$N = N_0 \times 2^n$

• Mutation Rate: Probability of mutation per base per generation.

Additional info: Some explanations and examples have been expanded for clarity and completeness based on standard college biology curricula.