RNA/DNA Structure & Function

 

Nucleic Acids - Structure

Components and structure of the nucleic acids. Polymerization occurs through the condensation of the phosphate on the 5' carbon and OH on the 3' carbon linkage.

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Nucleic Acids - Bases and Nomenclature

Structure and nomenclature of the five nitrogenous bases that form parts of DNA and RNA-thymine, adenine, cytosine, guanine, and uracil.

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Nucleic Acids - Polymerization

Polymerization occurs by formation of phosphodiester bonds in the 5' to 3' direction. Synthesis must always add to the 3' end of the growing chain of DNA or RNA.

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Double Helix and Base Complementarity

Base pairing (A/T; C/G) is determined by structure and size of the bases and hold by hydrogen bonds. Structure and size of the anti-parallel double helix.

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RNA Double Helix

A look at the stability of the RNA "hairpin" or double helix, wih comparison to the DNA double helix.

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Transforming Principle - Griffith's Experiment

Griffith's historical experiments with bacteria that led to the discovery of DNA as the hereditary material.

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Structure of DNA

Detailed review of the structure - sugar, bases, and phosphates - and polymerization of DNA.

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Genetic Material - Avery's Experiment

Historical experiments that used bacterial phage to confirm DNA as the hereditary material. Radioactively labeling DNA and protein and determine that viruses only inject DNA into bacteria.

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Avery's Experiment isolating DNA as further proof of genetic material.

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The Double Helix - Watson and Crick

Watson and Crick's historical discovery of base pairing and the double helical structure of DNA.

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DNA Replication - Components and Direction

DNA replication is a form of polymerization that requires nucleotides, DNA template, complementary primers, and DNA polymerase. Polymerization occurs in the 5' to 3' direction.

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DNA Replication - Leading and Lagging Strands and Enzymes

Leading and lagging strands during DNA replication. Primase makes primers and ligase joins the strand made off of the lagging strand. Topoisomerase cuts and unwinds the circular bacterial DNA.

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DNA Replication - Fidelity

Fidelity of DNA replication depends on the low mistake rates of DNA polymerase, and proofreading and mismatch repair enzymes.

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Base pair recognition and endonuclease are responsible for high replication fidelity. Movie showing endonuclease action.

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Transcription

Transcription is the process that uses the template strand of DNA to make mRNA based on base pairing. Transcription starts at the promoter and stops at the stop signal.

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A look at the chemical/informational process of transcription and the macromolecules that assist the process.

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Translation I and II

Translation is the process that uses mRNA as a template to make protein based on triplet codes. Crick discovered tRNA as the adaptor molecule during translation. Translation starts at the start codon (AUG) and ends at the stop codon.

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Post-Transcriptional Modifications

In eukaryotes, immature mRNAs are processed post transcription - introns are spliced out and a 5' G-cap and a 3' poly-A tail are added.

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Alternative Splicing

Alternative splicing and domain swapping in eukaryotes results in different proteins from the same gene. Bacteria might have selected out introns under evolutionary pressure.

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DNA - Overview

Overview of DNA-nucleotide structure, polymerization, polarity, base pairing, and the double helix.

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Genes

Definition, major properties, locations and functions of a gene.

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Genetic Material - Griffith's Experiment

Griffith's experiment that proved DNA was the genetic material. Also known as the "Transforming principle.".

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DNA Content - Chargaff's Experiment

DNA content varied in different organisms, but remained constant in all tissues within an organism. In all organisms, A and T, and C and G percentages were consistent. Led to the idea of base pairing.

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DNA Structure - Watson and Crick I and II

Structure of DNA deduced from X-ray crystallography, base pairing/interaction, and Chargaff's rule.

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Meselson-Stahl Experiment

Semi-conservative replication of DNA based on experiments with nucleotides with different nitrogen isotopes.

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DNA Replication - DNA Polymerase

Length of DNA and accuracy of replication. DNA polymerase and mechanism of nucleotide polymerization. Movie showing DNA replication.

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DNA Replication - Replication Fork

DNA polymerization from 5' to 3'. Opening at the replication fork allow simultaneous replication of both leading and lagging strands; need for RNA primers and DNA ligase.

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DNA Repair

Repair mechanism and mismatch repair during DNA replication. Movie showing DNA repair protein.

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Discusses the various ways DNA gets proofread and repaired after errors or mutagenic damage.

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DNA Replication - Initiation

Origin of replication in E. coli and replication forks as the initiation of replication.

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Information Storage in DNA

Information encoded in DNA, RNA, and proteins; storage capacity of DNA.

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DNA to Protein

Historical theories on how DNA encoded protein.

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Messenger RNA (mRNA)

Differences between DNA and RNA. Use of mRNA as an intermediate between DNA and protein.

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Transfer RNA (tRNA) and Codons

tRNA as the adaptor molecule between mRNA and protein during translation.

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Genetic Code

Cracking the genetic code. Historical approach of determining which amino acid matched each codon. Properties of the genetic code - degeneracy, start and stop codons, and universality.

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Protein Synthesis

Ribosomes and types of RNA involved in translation and peptide bond formation.

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The Central Dogma

Brief summary of the Central Dogma - replication, transcription, and translation - the information flow from DNA to RNA to proteins.

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RNA Splicing

Loops within mRNA/DNA hybrids suggested coding and non-coding information in the DNA. Discovery of RNA splicing. Eukaryotic pre-mRNA contains exons and introns.

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RNA Splicing - Examples

Factor VIII and Dystrophia as examples of splicing. Demonstrates length of exons and alternative splicing.

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Ribozyme

RNA catalyzes its own splicing. Discovery of enzymatic functions of RNA.

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Nucleic Acids - DNA and RNA

Nucleotide structure and components - sugar, phosphate group, and bases. Formation of DNA/RNA from monomeric nucleotides through phosphodiester bonds. Hydrogen bonds and base pairing results in the double helical structure of DNA.

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Nucleic Acids - Overview

A discussion of the components of nucleic acids: Dibose and deoxyribose, nitrogenous bases, and phosphate groups, as well as a look at the polymerization of nucleotides.

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The RNA Molecule

RNA's structure, function, and evolution.

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Gene and RNA Classes

A discussion of the various types of genes and resulting RNA products.

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Problems in Transcription

Challenges faced by RNA in carrying out transcription, and the role of promoters in solving these challenges.

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mRNA and Initiation of Translation

Parts of a mature mRNA: 5'Gcap, polyA tail, the 5' UTR (untranslated region), and the start codon (AUG). Initiation of translation occurs when the ribosome binds to the 5'Gcap and 5'UTR. tRNA brings a methionine to the AUG start codon.

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Elongation and Termination of Translation

Mechanism of elongation of protein. Charged tRNA brings amino acid to the mRNA and ribosome. Codon and anti-codon match, and adjacent amino acids join by forming peptide bonds. Termination of the protein chain occurs when the ribosome reaches a stop codon. Polypeptide chain falls off to terminate translation.

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Genetic Code and Amino Acid Structures

Table containing the genetic code and amino acid structure at pH 7.0.

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Nucleotide Structure and Base Pairing

Purines and pyrimidines. Base pairing and hydrogen bonds that form the double helix.

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Single Stranded DNA

Structure and replication of single stranded DNA.

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Proofreading and Editing of DNA

Proofreading and repair mechanisms during DNA replication. Effects of defective DNA polymerase.

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Transcription, Translation, and Mutations I and II

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Products of transcription and translation. DNA mutations that affect the protein product.

Products of transcription and translation. tRNA mutations that affect the protein product. Comparison between bacterial and human genes.

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DNA Replication - Example

Problem on DNA replication that asks about primers, and leading and lagging strands during replication.

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Central Dogma - Example II

Problem on the Central Dogma that tests transcription and translation.

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DNA as Genetic Material

Griffith's and other's experiments determined that DNA carried the genetic material.

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Replication

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Components of DNA replication, the replication fork and base pairing, phosphodiester bonds, and polymerase.

True or false questions about the process of DNA replication.

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Representations of DNA

Various forms used to represent DNA structure, genes, and mutations.

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The Central Dogma - Summary

Table summarizing enzyme, building blocks, start, end, direction, template, and pairings involved in the processes of replication, transcription, and translation.

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Central Dogma - Enzymes, Location, and Modifications

Identify enzymes, other components and cellular location of DNA replication, transcription, and translation.

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DNA Replication

Replication fork, primers, direction of replication, and enzymes involved in replication.

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Translational Inhibitors

Effect of translational inhibitors on the protein product.

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DNA Structure - Experimental Data

Using Griffith, Avery, Chargaff, and Mendelson and Stohl's experiments as basis, determine the structure of alien DNA based on given data.

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Transcription and Translation - Example

Definition, location, and products of transcription and translation.

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Mutations and Proteins

Effect of mutations in the gene and tRNAs on the protein product.

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Untranslated Gene Regions

Identify and compare regions of the gene that do not encode protein.

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