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Chapters 16 and 17. Objectives Describe the data that led Watson and Crick to suggest their model of DNA structure

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  • Objectives

    • Describe the data that led Watson and Crick to suggest their model of DNA structure

    • Show how the double helix model of DNA conformed to prior observations of the chemistry of the molecule and, at the same time, suggested mechanisms for the roles of DNA in gene expression and chromosome replication

    • Define and explain the terms replication, transcription and translation


  • Define what is meant by semi-conservative DNA replication and describe the role of Okazaki fragments

  • Use the base-pairing rules to determine the nucleic acid sequences of new DNA strands, mRNA and tRNA from DNA sequences

  • Trace the steps of protein synthesis, including the locations of the processes, the involvement of complex molecular machinery and the requirement for inputs of energy

  • Explain why the DNA code must involve a reading frame of three bases


Introduction
Introduction and describe the role of Okazaki fragments

  • Many basics of molecular biology determined using viruses that infect bacteria

    • viruses composed of protein coat and internal genetic material (DNA or RNA)

      • not living-no cell structure, no metabolism, cannot self-replicate

    • Bacterial viruses called bacteriophages

      • logical choice for experiments


  • Early experiments showed DNA genetic material and describe the role of Okazaki fragments

  • 1928-Griffith

    • Streptococcus pneumonia is a bacteria that causes pneumonia in mammals

      • 2 strains: 1 pathogenic and 1 nonpathogenic

    • Mix heat killed pathogenic strain with living nonpath strain and some of these cells became pathogenic


Transformation
Transformation and describe the role of Okazaki fragments

  • Change in genotype and phenotype due to an assimilation of external DNA by the cell


1952 hershey and chase
1952-Hershey and Chase and describe the role of Okazaki fragments

  • Showed that viruses can infect bacteria


Dna is the genetic material
DNA is the Genetic Material and describe the role of Okazaki fragments

  • Prior to the 1950’s, it was already known that DNA is a polymer of nucleotides, each consisting of three components

  • Each monomer (nucleotide) composed of phosphate group, 5C sugar, and nitrogenous base

    • DNA-deoxyribose

    • RNA-ribose

  • Each polymer contains four nucleotides named for the nitrogenous bases

    • DNA

      • thymine-T, cytosine-C, adenine-A, and guanine-G

    • RNA

      • uracil-U replaces T


  • DNA and describe the role of Okazaki fragments

    • DNA is hereditary information is enclosed in the chemical language of DNA

    • DNA is the blue print and program that directs the development of many traits


    Watson and crick
    Watson and Crick and describe the role of Okazaki fragments

    • DNA is double-stranded helix

      • Watson-Crick model based on observations from many sources

        • chemical structure of bases

        • X-ray crystallographs from Rosalind Franklin

        • chemical analysis of DNA

          • A=T and G=C

        • ratios of A+T and G+C


    final model that fit observations is double helix with sugar backbones on outside and hydrogen-bonded bases on inside

    • twisted rope ladder

    • A always bonds with T and G always bonds with C

    • led to proposed mechanisms of DNA function


    Meselson backbones on outside and hydrogen-bonded bases on inside and Stahl demonstrated that DNA replication is semi-conservative, confirming the Watson-Crick model


    Dna replication
    DNA Replication backbones on outside and hydrogen-bonded bases on inside

    • Copying of the DNA is extremely fast and accurate

      • Prokaryotes= 5000 nuc per second

      • Errors occur in every 1 billion nuc

    • DNA replication depends on base pairing rules

      • requires accurate and complete copies of DNA

    • known as semi-conservative replication

      • each strand of DNA molecule acts as template for synthesis of new strand

      • bases added to growing strand using base-pairing rules



    3’ replication

    5’




    3’ end of leading strand has potential to get shorter with repeated replication

    • solved by two mechanisms

      • telomeres - non-coding repeated DNA sequences at ends of linear molecules

      • telomerases - catalyzes lengthening of telomeres

    • shortening of telomeres may represent cell life - limiting factor


    Chapter 16 check list
    Chapter 16 Check list repeated replication

    • What did Griffith do?

    • What did Hershey and Chase do?

    • Watson and Crick?

    • Meselson and Stahl?

    • What bases pair with each other?

    • DNA replication is _______?

    • Can stranded DNA have many replication sites?

    • What about circular DNA?

    • What are the enzymes that are used in replication, what do they do and what order do they occur in?

    • Define leading vs. lagging strands and the differences between them.

    • DNA synthesis starts with what kind of primer?


    Gene expression transcription and translation ch 17
    Gene Expression/Transcription and Translation(CH 17) repeated replication

    • Genotype expressed as proteins-basis of phenotypic traits

      • one gene-one polypeptide hypothesis

      • flow of information is from DNA to RNA (transcription) to polypeptide (translation)


    Genes specify proteins via transcription and translation
    Genes specify proteins via transcription and translation repeated replication

    • Evidence for this idea came from studies of metabolic defects

    • 1909, British physician Archibald Garrod was the first to dictate phenotypes through enzymes


    Nutritional mutants
    Nutritional Mutants repeated replication

    • Beadle and Tatum caused bread mold to mutate by using x-rays

      • Could not survive on minimal medium

    • Using genetic crosses they determined that their mutants fell into three classes, each mutated in a different gene


    Genetic information written as codons and translated into amino acids

    occurs in two stages:

    • transcription of DNA in nucleus into mRNA

    • translation of mRNA into amino acid sequence in cytoplasm


    two languages used by cell amino acids

    • nucleotides-five letters in alphabet (T or U, A, C, G)

    • amino acids-20 letters in alphabet

    • DNA= Code

    • MRNA=Codon

    • TRNA= Anticodon


    • smallest nucleotide word that can accommodate amino acid alphabet is a three-letter word

    • triplets of bases in nucleotides specify specific amino acids-known as codons

      • first codon deciphered was UUU-phenylalanine

    • forms the basis of the genetic code

      • universal

      • redundant but not ambiguous


    Evolution of genetic code
    Evolution of Genetic Code alphabet is a three-letter word

    • The genetic code is nearly universal and it is shared by organisms from the simplest bacteria to the most complex animals


    Transcription
    Transcription alphabet is a three-letter word

    • Makes copies of information in DNA molecule in form of messenger RNA

      • occurs in nucleus in eukaryotes and cytoplasm in prokaryotes

      • involves RNA polymerase

      • initiated at promoter region and elongation continues until terminated at terminator region

    • Two other types of RNA-rRNA and tRNA-also transcribed




    • https:// gene, are the site of RNA polymerase bindingwww.youtube.com/watch?v=WsofH466lqk


    • Eukaryotic mRNA’s are processed before leaving the nucleus gene, are the site of RNA polymerase binding

      • modified nucleotide G subunits added to 5’ end (cap) and a poly-A tail added to 3’ end

      • introns (non-coding sequences) excised from mRNA by spliceosomes and exons (coding sequences) linked together.

        • shuffling of exons contributes to protein diversity


    Function and evolution of introns
    Function and Evolution of Introns gene, are the site of RNA polymerase binding

    • The presence of introns allows for alternative RNA splicing

    • Proteins often have different structural and functional regions called domains

    • In many cases different exons code for the different domains


    Translation
    Translation gene, are the site of RNA polymerase binding

    • Occurs in cytoplasm

      • involves ribosomes, tRNA, mRNA enzymes and protein factors, and energy sources



    • Transfer RNA (tRNA) acts as interpreter gene, are the site of RNA polymerase binding

      • amino acids recognized by codons to anticodon match

      • tRNA-one for each amino acid-matches amino acid to codon

        • contains special region (anti-codon) that base-pairs with codon for its amino acid on mRNA

          • correct amino acid is bound to tRNA by enzyme complex (one for each tRNA-amino acid combination) using ATP


    Ribosomes gene, are the site of RNA polymerase binding

    • build polypeptides

    • composed of rRNA and protein in two subunits

    • provides stable platform for assembly of peptides

      • contains binding sites for mRNA, two tRNA-amino acid complexes and the growing polypeptide



    Translation divided into three phases
    Translation divided into three phases gene, are the site of RNA polymerase binding

    Initiation

    • initiation sequence helps bind mRNA to small subunit of ribosome

    • methionine-tRNA binds to start codon (AUG-also codes for methionine) via anticodon of tRNA

    • large subunit binds to small subunit so that methionine tRNA fits in P site of large subunit


    Elongation gene, are the site of RNA polymerase binding

    • involves three steps

      • anticodon of incoming tRNA-amino acid complex binds to codon in A site

      • peptide bond formed between polypeptide (attached to tRNA in P site) and new amino acid

      • P site tRNA leaves ribosome and A site tRNA-polypetide complex moves to P site


    • Termination gene, are the site of RNA polymerase binding

      • elongation continues until stop codon (UAA, UAG or UGA) reached

      • finished polypeptide released

      • ribosome splits into two subunits




    Proteins destined for membranes or export from cell are synthesized on rough ER

    • signal sequence at amino end of polypeptide triggers binding to ER

    • cytosolic polypeptides lack signal sequence and are synthesized by free ribosomes


    In prokaryotes, transcription synthesized on rough ERand translation can occur concurrently leading to the formation of “lampbrusharrays”


    Mutations
    Mutations synthesized on rough ER

    • Mutations change the meaning of genes

      • cause a change in nucleotide sequence of DNA

      • differences in inherited traits can be traced to mutations


    • two types of alterations to DNA sequence synthesized on rough ER

      • substitution-replacement of one nucleotide with another

        • usually results in replacement of one amino acid with another in polypeptide or no change if new codon codes for same amino acid

        • example-sickle cell anemia allele

          • single base change in DNA results in amino acid change in hemoglobin


    • insertion or deletion of bases in DNA sequence synthesized on rough ER

      • results in phase shift of three base reading frame

      • affects all codons after mutation

        • results in different amino acid sequence

      • almost always results in non-functional polypeptide

    • mutations can occur spontaneously or by physical (radiation) or chemical mutagens


    Check list
    Check list synthesized on rough ER

    • The flow of information is from…?

    • What is the codon, code and anticodon?

    • What nucleotides are in DNA and RNA?

    • Is the genetic code universal?

    • What is transcription? Describe the process.

    • What is translation? Describe the process.

    • What enzymes are involved in transcription?

    • What are the specific regions on DNA that indicate where transcription starts.

    • What are the types of DNA alterations?


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