BIOL-L211 Lecture 38 Outline of Last Lecture I. Molecular CloningOutline of Current Lecture I. ReviewCurrent LectureReview!What is the structure of DNA?DNA forms a double helix structure with a major groove and a minor groove. It is a series of deoxyribonucleotides linked by a phosphate group. There are four possible nitrogenous bases: Adenine, Guanine (purines), Thymine, and Cytosine (pyrimidines).Describe a nucleotide.A nucleotide is an organic molecule containing a phosphate group, a sugar backbone, and a nitrogenous base (AGTC or U in RNA)What is the relationship between the four nucleotides that comprise DNA? What is Chargaff's rule?Purines pair with pyrimidines; specifically: A pairs with T, G pairs with C with two and three hydrogen bonds between them respectively. Chargaff's rule describes/defines that specific bonding. Note: there will thus be the same number of A's as T's, and the same number of G's as T's in DNA.What is the semi-conservative model of replication?The semi-conservative model of replication (correctly) suggests that DNA unzips and each strand serves as a separate template for replication.What is a replication origin? Replication bubble? Replication fork?A replication origin is the location where DNA replication begins (the two strands are melted apart and the replication bubble forms here). A replication bubble unzips DNA in both directionsstarting at the replication origin. The replication fork zooms in on one half of the replication bubble where the DNA is actively unzipping.Describe DNA polymerase.DNA polymerase is like a hand. It has fingers (which position the correct nucleotides to be added), a palm (which catalyzes DNA synthesis), and a thumb (which helps prevent DNA polymerase from letting go of the template strand).These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.Describe how DNA polymerase synthesizes DNA.DNA polymerase reads DNA 3' to 5' and then synthesizes it 5' to 3'.What is the difference between the leading and lagging strands of DNA?The leading strand is synthesized in one long stretch while the lagging strand must be synthesized in short (Okazaki) fragments.What is the end replication problem?In a linear chromosome, there is no way to finish the end of the lagging strand, so each time replication proceeds, the end of the chromosome (telomere) shortens. The problem is solved bytelomerase, but telomerase action decreases with age.What is the structure of RNA?RNA is generally single stranded. It uses ribose as its sugar backbone. It can interact with itself to form secondary structures including bulges, stem loops (hairpins), junctions, and internal loopsDescribe a ribonucleotide.A ribonucleotide contains a phosphate group, a ribose sugar, and one of four nitrogenous bases:Adenine, Uracil, Guanine, or CytosineWhat are the different types of RNA? What are their purposes?rRNA: found in ribosome; helps in translationmRNA: serves as template for translationtRNA: brings correct amino acid for polypeptide chain formationWhat is a promoter? Consensus sequence? Gene? Operon?A promoter is the location where transcription begins. In prokaryotes, sigma factors find the promoter. In eukaryotes, the pre-initiation complex forms at the promoter. RNA polymerase is recruited there. A consensus sequence is a sequence recognized by some protein/enzyme/complex. The degree to which a sequence is close/similar to consensus increases the degree to which it will be bound. A gene is a specific stretch of DNA that codes for a certain product (protein). An operon is found in prokaryotes and occurs when one promoter controls the transcription of multiple genes.What is the role of sigma factor?Sigma factors help RNA polymerase find the promoter by recognizing a consensus sequence.What is the role of the preinitiation complex?The preinitiation complex helps recruit RNA polymerase in eukaryotic transcription.Describe abortive synthesis.Abortive synthesis occurs before RNA polymerase escapes the promoter region.Describe how RNAP/Pol II synthesizes RNA.Pol II synthesizes RNA 5' to 3'What is transcriptional termination?Transcriptional termination is when the mRNA transcript is cleaved and released and Pol II dissociates from the template strand.What is a regulatory binding site? Activator? Repressor?A regulatory binding site is a location bound by transcriptional regulators such as activators and repressors. Activators bind a sequence away from the promoter and help recruit Pol II. Repressors bind operators (in prokaryotes) and other locations (not overlapping the promoter) in eukaryotes and inhibit transcription.What is an alternative sigma factor?Alternative sigma factors recognize different consensus sequences and thus can increase the transcription of different genes under certain cellular conditions.What role does the phosphorylation of the Pol II CTD play?The phosphorylation of the Pol II CTD tail helps facilitate promoter escape.What are histone modifications and how do they relate to transcriptional regulation?Histone modifications are reversible alterations to histones performed by histone modifying proteins. These modifications do not alter the DNA sequence or DNA but instead loosen or tighten DNA on a histone. Histone acetyltransferases add an acetyl group with a negative chargethat loosens DNA allowing for increased transcription. Histone deacetylases remove acetyl groups and tighten chromatin.What is an amino acid?An amino acid is a component of a protein that contains an amino group, a carboxyl group, a proton, and a side chain (R group)What is a peptide bond?A peptide bond is the bond formed between the amino group of one amino acid and the carboxyl group of another. The formation of this bond releases water as a side product.What are the four levels of protein structure?Primary, secondary, tertiary, and quaternaryWhat is meant by the genetic code being degenerate?The genetic code is degenerate because although there are 64 possible combinations of bases (codons), there are only 20 amino acids. Thus, multiple different codons can code for the same amino acid.What is an open reading frame?An open reading frame is defined by the start and stop codons and is the series of codons that code for a single protein.What is a ribosome?A ribosome is composed of protein and rRNA. It facilitates translation. It has a large and small subunit. The peptidyl