DNA Replication and Transcription

• Lecture topic is Genetics, specifically DNA Replication and Transcription to mRNA.

Learning Objectives

• Understand the central dogma of biology.
• Recognize that DNA carries the instructions to create an organism.
• Be familiar with the basic structure of a DNA double helix, including the location of the 5' and 3' ends and the base pairing rules.
• Comprehend that DNA polymerase requires a template and a primer to function.
• Understand how DNA polymerase corrects incorrectly formed base pairs.
• Be able to sketch a bacterial chromosome during replication, indicating replication forks, leading and lagging strands, and the 5' and 3' ends.
• Know the functions of Helicase, Primase, DNA Polymerase III, Gyrase, DNA Polymerase I, and Ligase in DNA replication.
• Grasp the differences between DNA polymerase and RNA polymerase.
• Understand how a bacterial cell initiates gene transcription into mRNA, including why certain promoters are more easily recognized by RNA polymerase.
• Understand how alternate sigma factors allow a bacterium to regulate multiple genes concurrently.
• Be able to identify the template strand from a given double-stranded DNA sequence and promoter.

Vocabulary

• Central Dogma: The process by which DNA is transcribed into RNA, which is then translated into protein.
• Replication: The process of duplicating DNA.
• Transcription: The process of creating RNA from a DNA template.
• Reverse Transcription: The process of creating DNA from an RNA template.
• Translation: The process of creating a protein from an RNA template.
• Antiparallel Double Helix: DNA structure in which two strands run in opposite directions.
• Hydrogen Bonded Base Pair: Pairs of nucleotide bases linked by hydrogen bonds.
• Phosphodiester Bond: Covalent linkage connecting nucleotides.
• 5' Phosphate: The end of a DNA strand with a phosphate group attached to the 5' carbon atom.
• 3' Hydroxyl: The end of a DNA strand with a hydroxyl group attached to the 3' carbon atom.
• Pyrophosphate: A byproduct of DNA synthesis.
• Primer: A short strand of RNA or DNA that serves as a starting point for DNA synthesis.
• Template: The strand of DNA used to create a new strand during replication or transcription.
• Proofreading: The error-correcting process performed by DNA polymerase.
• Semiconservative: DNA replication in which each new DNA molecule consists of one original and one new strand.
• Bidirectional: Replication from a single origin that proceeds in two directions.
• Theta Replication: DNA replication in a circular chromosome to create a structure resembling the Greek letter theta.
• Replication Bubble: An unwound and open region of DNA where replication occurs.
• OriC/Ter: The origin and termination sites of replication.
• Leading Strand: The DNA strand synthesized continuously during replication.
• Lagging Strand: The DNA strand synthesized discontinuously in fragments during replication.
• Okazaki Fragment: Short DNA fragments synthesized on the lagging strand.
• Helicase: An enzyme that unwinds the DNA double helix.
• Gyrase: An enzyme that relieves strain during DNA replication.
• Primase: An enzyme that synthesizes RNA primers.
• Ligase: An enzyme that joins DNA fragments.
• DNA Polymerase III: The primary enzyme responsible for DNA replication.
• DNA Polymerase I: An enzyme that removes RNA primers and replaces them with DNA.
• RNA Polymerase: The enzyme responsible for RNA synthesis.
• Sigma Factor (Sigma Subunit): A protein that helps RNA polymerase bind to a promoter.
• Core Enzyme: The RNA polymerase enzyme without the sigma factor.
• Promoter: A DNA sequence where RNA polymerase binds to initiate transcription.
• Consensus Sequence: A sequence of DNA or RNA that represents the most common nucleotides at each position.
• -10/-35 Sites: Promoter regions recognized by sigma factors.
• Gene: A segment of DNA that codes for a protein.
• Template Strand: The DNA strand that is used as a template for RNA synthesis.
• Nontemplate Strand: The DNA strand that is not used as a template for RNA synthesis.
• Hairpin Loop Terminator: A structure in RNA that signals the end of transcription.

Central Dogma

• Replication: DNA is copied to make more DNA.
• Transcription: DNA is used as a template to synthesize RNA.
• Translation: RNA is used as a template to synthesize proteins.
• RNA polymerase catalyzes the synthesis of RNA during transcription.
• Ribosomes facilitate the translation of RNA into proteins.
• DNA polymerase facilitates replication.
• Reverse transcriptase is an enzyme that transcribes RNA to DNA.

Nucleic Acids - Nucleotides

• Nucleotides consist of a sugar, a phosphate group, and a nitrogenous base.
• The sugar in DNA is deoxyribose.
• The four nitrogenous bases in DNA are adenine, guanine, cytosine, and thymine.
• Adenine and guanine are purines, while cytosine and thymine are pyrimidines.

DNA Structure

• DNA is a double-stranded helix.
• The two strands are antiparallel, with one running from 5' to 3' and the other running from 3' to 5'.
• The two strands are complementary.
• Adenine pairs with thymine, and guanine pairs with cytosine.
• G:C pairs are stronger because they have three hydrogen bonds, while A:T pairs have only two.
• The sugar-phosphate backbone forms the structure of DNA.

DNA Synthesis

• DNA polymerase requires a template to copy.
• DNA polymerase reads the template strand from 3' to 5' and makes new DNA from 5' to 3'.
• DNA polymerase adds a new nucleotide to the existing 3'-OH group of the sugar molecule of a nucleic acid polymer; primer is used to get this started.
• Energy for DNA synthesis comes from splitting pyrophosphate from nucleoside triphosphate.
• DNA polymerase can proofread the DNA it synthesizes.

DNA Replication

• DNA replication is semiconservative: each new DNA molecule contains one original and one new strand.
• Replication is bidirectional, originating at a specific sequence (oriC) and ending at a specific sequence (ter).
• Helicase unwinds the DNA at the origin of replication.
• Primase synthesizes an RNA primer.
• DNA polymerase III catalyzes the synthesis of new DNA, using complementary base pairing.
• DNA gyrase relieves helical tension.
• Okazaki fragments are produced during discontinuous synthesis.
• DNA polymerase I removes the RNA primer and replaces it with DNA.
• DNA ligase seals the gaps.

Genes

• Genes contain DNA information that codes for proteins.
• Genes consist of coding sequences and regulatory regions.

Transcription

• DNA is transcribed into RNA.
• The minus strand serves as the template.
• RNA polymerase does not need a primer.
• In RNA, adenine pairs with uracil instead of thymine.
• Only genes are transcribed into mRNA.
• Transcription begins at a special DNA sequence called the promoter.
• E. coli has 4,000,000 base pairs and about 4,000 genes. Thus, each gene in bacteria is about 1,000 base pairs.
• RNA polymerase is the enzyme responsible for RNA synthesis.
• Prokaryotes have one enzyme that synthesizes all RNA molecules.
• Eukaryotes have three enzymes: RNA polymerase I (rRNA), RNA polymerase II (mRNA), and RNA polymerase III (tRNA).
• RNA polymerase sigma subunit binds to the promoter.
• The promoter is two consensus sequences separated by 15-17 base pairs.
• The direction of the promoter determines the DNA strand copied.
• Transcription is 5' to 3', so the template is read 3' to 5'.
• The promoter signals the beginning of a gene, and the hairpin loop signals the end of a gene.