AP Bio Unit 6 Study Guide

DNA Replication

• The process begins at specific locations on the DNA molecule known as "origins of replication."

• Helicase unwinds the double helix, creating replication forks.

• Single-strand binding proteins stabilize the unwound DNA, preventing it from re-annealing.

• Primase synthesizes short RNA primers that provide a starting point for DNA polymerase.

• DNA polymerase adds nucleotides to the growing DNA strand in a 5' to 3' direction. Leading and lagging strands are formed during replication, with the leading strand synthesized continuously and the lagging strand synthesized in short segments known as Okazaki fragments.

• Ligase rejoins the leading and lagging strands, and rejoins the okazaki fragments.

Protein Synthesis

Transcription

• Transcription factors mediate the binding of RNA Polymerase to initiate transcription at the Promoter region (TATA Box)

• The newly formed RNA is “capped” during polyadenylation, which adds a 5' cap and a poly-A tail to the RNA molecule, enhancing its stability and facilitating its export from the nucleus.

Translation

• During translation, the mRNA is decoded by ribosomes to synthesize proteins, where transfer RNA (tRNA) molecules bring specific amino acids to the ribosome according to the sequence of codons in the mRNA.

• Anti-codons pair with mRNA codons, ensuring that the correct amino acids are added to the growing polypeptide chain.

• The A-Site (Aminoacyl site) is where the new tRNA carrying an amino acid enters, the P-Site (Peptidyl site) holds the tRNA with the growing polypeptide chain, and the E-Site (Exit site) is where empty tRNA molecules exit the ribosome.

• The C-terminus of the polypeptide chain is formed when the last amino acid is added, completing the protein synthesis process. (COOH)

Gene Expression

Gene Mutations

• Silent Mutations: Have no effect on the resulting amino acid, purely a substitution

• Missense Mutations: Result in a different amino acid than originally intended

• Nonsense Mutations: Lead to a premature stop codon, resulting in a truncated and often nonfunctional protein.

• Frameshift Mutation: Involves the insertion or deletion of nucleotides in the DNA sequence, which shifts the reading frame and alters the entire amino acid sequence downstream

Expression

• Regulatory Sequences: create regulatory proteins that can enhance or inhibit the transcription of specific genes, and controlling gene expression levels.

• Operators are the “on/off switch” of DNA, positioned within the promoter region. The operon is a cluster of genes under the control of a single promoter, allowing for coordinated regulation of gene expression in response to environmental changes.

• Repressible Operons: Usually on, binding with a repressor protein prevents transcription when a specific inducer molecule is present, effectively turning off the gene expression in response to that molecule. (Lac)

• Inducible Operons: Typically off, these operons are activated when an inducer molecule binds to the repressor, allowing transcription to occur and enabling gene expression in response to specific environmental signals. (Trp)

Epigenetics and Biotechnology

Epigenetics

• Epigenetics: Refers to heritable changes in gene expression that do not involve alterations to the underlying DNA sequence.

• Histones: Proteins around which DNA is tightly coiled, playing a crucial role in the regulation of gene expression and chromatin structure.

• Nucleosomes: DNA wound twice around 8 histones, 2 of each type (H2A, H2B, H3, H4)

• Histone Acetylation: The process by which acetyl groups are added to the amino acids of histone proteins, resulting in a more relaxed chromatin structure that facilitates transcription and gene expression.

• DNA Methylation: The addition of methyl groups to DNA, typically at cytosine bases, which can inhibit gene expression by causing the DNA to be more tightly packed and less accessible for transcription.

Biotechnology

• Restriction Enzymes: Enzymes that cut DNA at specific sequences, allowing for the manipulation and cloning of genes.

• Restriction Fragments: Pieces of DNA that result from the action of restriction enzymes, which can be analyzed for various applications in genetic engineering and molecular biology.

• Sticky Ends: Short single-stranded overhangs that are created when restriction enzymes cut DNA in an offset manner, facilitating the ligation of DNA fragments by providing complementary base pairing.

• Gel Electrophoresis: A technique used to separate DNA fragments by size, utilizing an electric field to move negatively charged DNA through a gel matrix, allowing for visualization and analysis of the fragments.

• Polymerase Chain Reaction (PCR): A widely used method in molecular biology to amplify specific DNA sequences, generates millions of copies of a targeted segment for analysis and experimentation.