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 typically 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 used in genetic engineering to clone genes.

Transcription and RNA Processing

Transcription is the process by which genetic information in DNA is copied into RNA. In eukaryotes, the primary transcript 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 an mRNA molecule is used to direct the synthesis of a protein. This process occurs in the cytoplasm at the ribosome.

• Location: In prokaryotes, translation occurs in the cytoplasm. In eukaryotes, it occurs in the cytoplasm or on the rough endoplasmic reticulum.

• Steps of Translation:

  • Initiation: Ribosome assembles around the mRNA and the first tRNA.

  • Elongation: tRNAs bring amino acids to the ribosome, and the polypeptide chain grows.

  • Termination: The ribosome reaches a stop codon and releases the completed polypeptide.

• Genetic Code: Each codon (three nucleotides) codes for a specific 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 in 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 such as promoters and enhancers interact with regulatory proteins to control transcription.

• Transcription Factors: Proteins that bind to promoter regions 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). Inducers and repressors modulate their activity.

• Regulation in Eukaryotes: Multiple stages can be regulated, including chromatin structure (epigenetics), transcription, RNA processing, and translation.

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

• Small RNAs: Such as miRNA and siRNA, can regulate gene expression post-transcriptionally.

• Cell Differentiation: Results from differential gene expression, often regulated by transcription factors and environmental cues.

• HOX Genes: Homeobox genes that control body plan and cell fate during development.

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

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 the environment.

• 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 is trisomy 21).

• Horizontal Gene Transfer (Prokaryotes): Includes transformation (uptake of naked DNA), transduction (virus-mediated), conjugation (direct transfer), and transposition (movement of DNA segments).

• 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.

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 or cloning. Equation for PCR amplification after n cycles: $N = N_0 \times 2^n$

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

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

• 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, regulation, and interaction.

Example: CRISPR-Cas9 is used to edit genes in model organisms and has potential for gene therapy in humans.

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
Location	Nucleus (eukaryotes), cytoplasm (prokaryotes)	Nucleus, cytoplasm, ribosome
Function	Genetic information storage	Information transfer, catalysis, regulation

Table: Types of Mutations and Their Effects

Type of Mutation	Description	Possible Effect
Point Mutation	Change in a single nucleotide	Silent, missense, or nonsense mutation
Insertion	Addition of one or more nucleotides	Frameshift, altered protein
Deletion	Loss of one or more nucleotides	Frameshift, altered protein
Duplication	Repeat of a DNA segment	Gene dosage effects
Chromosomal Alteration	Change in chromosome structure or number	Genetic disorders, aneuploidy

Additional info:

• Epigenetic modifications such as DNA methylation and histone acetylation can be inherited and affect gene expression without altering the DNA sequence.

• Alternative splicing increases protein diversity in eukaryotes.

• Horizontal gene transfer is a major source of genetic diversity in prokaryotes.