Honors Biology Reading Guide Chapter 10 v Fredrick Griffith Ø When he killed bacteria and then mixed the bacteria remains with living harmless

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1 Honors Biology Reading Guide Chapter 10 v Fredrick Griffith Ø When he killed bacteria and then mixed the bacteria remains with living harmless bacteria some living bacteria cells converted to disease causing form all of the descendants of transformed bacteria inherited ability to cause disease Ø Some chemical component of the dead bacteria could act as a transforming factor that brought about a heritable change in live bacteria v Hershey and Chase Ø Worked with bacteriophages Ø Marked the DNA and the protein in T2 with radioactive tracers Ø Proved that it is the viral DNA that contains the instructions for making phages and that DNA is the molecule of heredity v Watson and Crick Ø Three major fundamental principles discovered DNA s shape is a double helix Individual structures of the bases dictate pairing Sugar and phosphate backbone Purines are paired with pyrimidine v Chargaff s rules Ø A always pairs with T Ø G always pairs with C Ø Amount of A is equal to the amount of T and the amount of G is equal to the amount of C v Rosalind Franklin Ø Produced an X- ray crystallographic image Ø Helping Watson and Crick As a result they discovered that DNA had a double helix and the shape of the DNA v Archibald Garrod Ø Genes dictate phenotypes through enzymes, an inherited disease reflects persons inability to make a particular enzyme and he was right v George Beadle and Edward Tatum Ø They proposed the one gene one protein hypothesis Ø The idea that the function of a gene is to dictate the production of a specific enzyme v DNA and RNA are polymers Ø Basic structure They are covalently bonded Nucleic acids Polymers nucleotides Polynucleotide Have sugar phosphate and nitrogenous base

2 v Bases Ø Pyrimidine Single strand Cytosine (C) Thymine (T) Ø Purines Double strand Adenine (A) Guanine (G) v Comparing DNA and RNA Ø DNA G, T, A, C Deoxyribose sugar

3 Ø RNA G, U, A, C Ribose sugar v Watson and Crick discovered how DNA appears the major structural components are Ø Sugar phosphate Ø Nitrogenous bases v Chromosome theory of inheritance says that these influence phenotype Gene Chromosome v The double helix is held together through hydrogen bonds v Base pairing explains how DNA is replicated the three main steps are as follows Ø Two strands of DNA separate Ø Nucleotides line up one at a time along the template strand in accordance to base pairing rules Each becomes template assembly of complimentary strand from a supply of free nucleotides always in the nucleus Ø Enzymes link nucleotides to form new DNA strands v Semiconservative model of DNA duplication Ø Types of DNA replication in which the replicated double helix consists of one old strand derived from the old molecules and one newly made strand Ø Half of the parent DNA molecule is conserved while half of the DNA molecule is new v Replication of DNA begins in a place called the origins of replication - short stretches of DNA with specific sequence

4 Ø Here nucleotides then proteins attach to DNA and separate strands Ø Replication then proceeds in both directions Ø On the parent DNA replication bubbles are formed v In eukaryotes there can be hundreds and thousands of replication bubbles at a time Ø The more bubbles that are present the faster the replication time v The process of DNA replication differs on the two strands Ø The names oft h two ends of the DNA backbone is 3 prime and 5 prime Ø How they are different Prime refers to the carbon atoms of the nucleotide sugars 3 carbon attached to an OH- group 5 carbon attacked to phosphate groups Opposite sides o the DNA molecules

5 v DNA polymerase inks nucleotides in the growing daughter strands v The enzymes add nucleotides only to the 3 end of the DNA v Daughter strands grow in the 5 à 3 direction v One of the daughter strands can be synthesized in one continuous piece by a DNA polymerase working toward the forking point of the parental DNA but to make other daughter stand polymerase molecules must work outward from the forking point any way this can be accomplished if a new strand is synthesized in short pieces as fork opens up, Okazai fragments v DNA ligase links of ligates pieces together into a single DNA strand

6 v Other functions of polymerase and ligase Ø Polymerase: proofreading step removes nucleotides that have base paired incorrectly during replication Ø Both: also repairing DNA damages by harmful radiation (X- rays and UV light) or toxic chemicals from the environment v How does DNA (genotype) determine physical traits (phenotypes) Ø Proteins are links between the genotypes and the phenotypes gene doesn t build a protein directly protein dispatches instructions to form RNA which programs protein synthesis v Central dogma Ø Molecular chain of command is form DNA in the nucleus of the cell RNA to protein synthesis in the cytoplasm two main stages are transcription and the synthesis of RNA under the direction of DNA and translation, the synthesis of protein under the direction of RNA

7 v Beadle and Tatum discovered the one gene to one enzyme hypothesis, the idea that the function of a gene is to dictate the production of a specific enzyme Ø Expansion Includes all proteins Functions of genes is to dictate the production of a polypeptide v The chemical language of the DNA is translated into the chemical language of proteins because the bridge between DNA and protein synthesis is nucleic acid RNA, DNA transcribed into RNA which is translated into a protein DNA à RNA à protein v Transcription Ø The synthesis of RNA under the direction of DNA Ø DNA is the template to create the RNA strand v Translation Ø The synthesis of proteins under the direction of RNA v Codon Ø A 3 nucleotide sequence in mrna that specifies a particular amino acid or polypeptide termination signal the basic unit of the genetic code v Triplet code: Ø A set of 3 nucleotide long words that specify the amino acids for polypeptide chains v Genetic code Ø Amino acids are specified by codons There is no ambiguity although there is redundancy Signal polypeptide chain to start and stop Complimentary relationship to codons in DNA/RNA Genetic code is mostly universal v Transcription process Ø Occurs in the nucleus of a eukaryotic cell Ø Three steps

8 Initiation attachment of RNA polymerase to the promoter and the start of the RNA synthesis Elongation RNA grows longer as RNA synthesis continues the RNA strands peel away from the DNA template allowing the two separated DNA strands to come back together in the region already transcribed Termination RNA polymerase reached a sequence of bases in the DNA template called a terminator this sequence signals the end of the genes at that point in time polymerase molecule detaches form the RNA molecule and that gene v Messenger RNA (mrna) Ø Conveys genetic messages form DNA to the translation machinery of the cell Ø Eukaryotic transcripts are modified or processed Addition extra nucleotides ends of RNA transcript additions include a small cap at one end and a long tail at the other end, cap and tail facilitates the export of the mrna from nucleus protect the mrna from attack by cellular organisms and help ribosomes bind to the mrna capital not translated into protein Non coding stretches of nucleotides that interrupt the nucleotides that actually code for amino acids internal noncoding regions called introns (intervening sequences) coded regions that are expressed are called exons introns are removes an the exons are joined to produce an mrna molecule with a continuous coding sequence RNA splicing provides means to produce multiple polypeptides from single gene v Transfer RNA (trna) Ø Converts words nucleic acids (codons) to the amino acid words of proteins a cell employs trna Ø trna knows which amino acids to pick up form the cytoplasm because Recognizing appropriate codons in the mrna with unique structure trna Ø Twisting upon itself trna forms several double stranded regions in which short stretches RNA base pair with other stretches via Hydrogen bonds Ø Single stranded loop at one end folded molecule contains special triplet bases called anticodon Ø Anticodon complementary to a codon triplet on mrna during translation anticodon recognize particular codon on mrna by using base pairing rules Ø Other end of the trna molecule is a site where one specific kind of amino acid can attack Ø Each amino acid is joined to the correct trna by a specific enzyme each enzyme specifically binds one types of amino acid to all trna molecules that coded for that amino acid Use ATP to drive action Ø Resulting trna amino acid complex then add amino acid to goring polypeptide chain

9 v Ribosomal RNA (rrna) Ø The type of ribonucleic acid that together with proteins makes ribosomes the most abundant RNA in most cells

10 v Translation Ø Initiation brings together the mrna at RNA bearing the first amino acid and the two subunits of a ribosome Establishes exactly where translation will begin ensuring that the mrna codons are translated into the correct sequence of amino acids An mrna molecule bonds to a small ribosomal subunit A special initiator trna binds to a specific codon called the start codon where translation is to begin on the mrna molecule initiator trna garries th amino acid its anticodon binds to the start codon Large ribosomal subunit bings to the small one creating a continual ribosome initiator trna fits into one of that of trna binding sites on the ribosome this site called the P site will bold the growing polypeptide the other trna binding site called he A site is vacant and ready for the next amino acid bearing trna Ø Elongation Codon recognition the anticodon of an incoming trna molecule carrying its amino acid pairs with the mrna codon in the A site of the ribosome Peptide bond formation - The polypeptide separates from the trna in the P site and attaches by a new peptide bond to the amino acid carried by the trna in the A site the ribosome catalyzes formation of the peptide bond adding one more amino acid to the growing peptide chain Translocation the P site trna now leaves the ribosome and the ribosome translocate (moves) the remaining trna in the A site with the growing polypeptide to the P site the codon and the anticodon remain hydrogen bonded and the mrna and the trna move as a unit this movement brings into the A site the next mrna codon to be translated and the process can start again with the codon recognition Ø Termination Elongation continues until a stop codon reaches the ribosomes site stop codons don not code for amino acids but as signals to stop translation completed polypeptide is freed from the last trna and ribosome splits back into its separate subunits v Polypeptides can be made in under a minute v When the polypeptide structure is made it coils and folds assuming a 3- D shape its tertiary structure, several polypeptides may come together forming a protein with quaternary structure v Proteins in an organism determine the appearance and the capabilities of the cell and the organism v Mutation Ø A change in the nucleotide sequence of an organism s DNA the ultimate source of genetic diversity can also occur in the DNA or RNA of a virus v Silent mutation Ø A mutation in a gene that changes a codon to one that encodes for the same amino acid as the original codon the amino acid sequence of the resulting polypeptide is thus unchanged

11 v Missense mutation Ø A change in the nucleotide sequence of a gene that alters the amino acid sequence of the resulting polypeptide, a codon is changed from encoding one amino acid to encoding a different amino acid v Nonsense mutation Ø A change in the nucleotide sequence of a gene that converts an amino acid encoding codon to a stop codon this results in a shortened peptide v Reading frame Ø The way a cell s mrna translating machinery groups the mrna nucleotides into codons v Insertion Ø The addition of one or more nucleotides form a gene my a mutation v Deletion Ø The loss of one of more nucleotides from a gene by mutation v Substitution Ø Replacement of one nucleotide and its base pairing partner with another pair of nucleotides v Mutagen Ø A chemical or physical agent that interacts with DNA and causes a mutation High energy X- rays UV light v The mutations that have disastrous effects are Ø Deletion/insertion Because mrna is read as a series of nucleotide triplets (codons) during translation adding/subtracting nucleotides may alter reading frame all nucleotides down stream insertion/deletion will be regrouped into different codons, result is nonfunctional peptide v Mutagenesis Ø Production of mutations Ø Spontaneous mutations are due to errors that occur during DNA replication or recombination v Mutations always harmful? Ø No Cause diversity in genes Makes evolution and natural selection possible Essential tool genetics create different alleles needed for genetic research