Principles of Genetics
Principles of Genetics BIOL 3130
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This 17 page Class Notes was uploaded by Colby Frami on Monday October 12, 2015. The Class Notes belongs to BIOL 3130 at Georgia Southern University taught by John Harrison in Fall. Since its upload, it has received 78 views. For similar materials see /class/222026/biol-3130-georgia-southern-university in Biology at Georgia Southern University.
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Date Created: 10/12/15
CHAPTER 9 o Terms to know o DNA o Gene o Chromosome o Allele o Four essential characteristics to function as the molecule of heredity o FIG 91 o Capable of being replicated o Why You can t give yours away Then you ll have none left o Store information o What type Proteins o Make use ofthe information expression o transcription o translation o Capable of change variation through mutation o Significance Changing environment population variation o Structure Function o Once the importance of DNA in genetic processes was realized in 1944 work intensified with the hope of discerning not only the structural basis of this molecule but also the relationship of its structure to its function pg 182 o Everyone knew that they could not understand how DNA could function as the blueprint for life until they understood the chemical structure o DNA and RNA Structure DNA and RNA are types ofgolynucleotides Nucleotide nucleoside phosphate Nucleoside nitrogenous base pentose sugar o Nucleotides o 5 carbon pentose sugar o Nitrogenous base o Fig 97 o Pyrimidine ring single ring o Purine ring double ring o Phosphate Group o Fig 99 o Polynucleotides Nucleotides covalently bond 39 39 quot bondl o Fig 910 o 5 amp 3 o Refers to the direction of the molecule based on which end of the molecule has 5 carbons and which has 3 o 5 is up and 3 is down o DNA occurs as stable double helix 2 polynucleotide strands Strands run antigarallel to each other o Strandsjoined by hydrogen bonds between nitrogenous bases Nucleotide pairing follows rules of complementation based on hydrogen bonding o Hydrogen bonds are very weak but since DNA is held together by SO many of them together they are very strong o RNA typcaosingle stranded no double helix structure o Complementary to some region of DNA genes o Several functional types of RNA messenger RNA Gm RNAD carries blueprint for proteins what most people think of as genes o transfer RNA tRNA carry amino acids to ribosomes o ribosomal RNA ara structural component of ribosomes o Composition of total cellular RNA o mRNA 5 o tRNA 15 o rRNA 80 CHAPTER 10 DNA Replication o Review Concepts o DNA molecule is a double helix where the strands are antiparallel o Nucleotide pairing follows rules of complementation based on hydrogen bonding o Complementations rules allow each strand of a double helix o DNA Replication o semiconservative each parent strand acts as a template for a new strand o each new molecule keeps half of the parent molecule o The parent strand and the new strand form a new double helix through hydrogen bonding o Fig 102 o Important Enzymes amp Proteins o DNA replication is a complex and cooperative effort of several enzymes and other proteins o DNA Polymerase o General category of enzymesthat build DNA polymers from nucleotides monomers Functions 5 to 31 l L Comment 3 limitation ofmis molecule it can only build a new molecule from the 5 to the o 3 to 5 exonuclease activity Comment 4 Figure 107 amp 108 o 5 to 3 exonuclease activity o Proofreading o Helicase o Category of enzymes that break hydrogen bonds and separate denature the two strands of a double helix Functions o Help initiate Origin of Replication o Extend the Replication Fork o SingleStranded Binding Proteins SSBP s o Proteins that stabilize the singlestranded structure produced bythe helicase o DNA Topoisomerase o Category of enzymes that prevent the double helix from coiling too tightly o Work by cutting and reattaching DNA strand to release tension o m important topoisomerase in DNA replication o RNA Polymerase o General category of enzymes that build M polymers from nucleotide monomers Primase a type of RNA Polymerase that produces a small starter molecule primer that DNA Polymerase can add to o DNA Ligase o Enzyme that forms covalent bonds phosphodiester bonds between unattached nucleotides in a DNA polymer DNA Replication Bacteria o Chromosomes o Prokaryotic chromosome Typically double stranded DNA Typically circular N Typically one small chromosome J Associated with structural proteins but not tightly packed o Bacterial Genomes are circular Requires only one origin of replication and two replication forks o Good simple model of how DNA replication works o Several types of DNA polymerase exist each with slightly different functions o DNA polymerase III is the most essential for replication Table 102 Propertiw of Bacterial DNA Polymerases d l I II a l Properties I II III Initiation of chain synthesis 5 3 polymerization 35 exonuclease activity 53 exonuclease activity Molecules of polymerasecell 400 15 Unwindinglquot DNA and the Origin of o Proteins bind to specific sequences 9mers and initiate unwinding o Helicase entersthe replication bubble and extends the replication fork in both directions lnitiationl of I quot quot o Primase an RNA polymerase synthesizes a short molecule of RNA called a M Antiparallel Elongation o How does the antiparallel structure of the double helix affect replication o DNA polymerases add nucleotides only to the free 339 end of a growing strand Along the leading strand DNA polymerase can synthesize a complementary strand continuously moving toward the replication fork o To elongate the lagging strand the other new strand of DNA DNA polymerase must work in the direction away from the replication fork Lagging strand replication must occur in short segments Okazaki Fragments with a separate primer for each fragment o Leading strand replication can occur continuously from one primer o Figure 1013 o As elongation occurs RNA Primers must be removed and replaced with DNA nucleotides o DNA Polymerase I typically performsthis task o Exonuclease activity o Polymerase activity DNA ugas Yuvmscuva em bundsbelwaen Okazakmaumems nun mpucalnn Eukarm cmu man n Repeated nucllnlnml and Inllnal 51mm Packaued andcumensed DNA cannmbe vephcaled unvanscnbed cmum TVmEa vephcaled metaphasa chvumusume s11 Mme ach ham h sme UH The enusmeac av we makes a may cmumam meve an chmmaud DNA R39Ephcahunr Eukarvu 25 m ueneva mudg uhEphcauun stN swmuavbelwaen pvukawmes and eukawmes o Differences in replication are related to 1 Linear vs circular chromosomes 2 More DNA per cell in eukaryotes o Eukaryotes must copy large amounts of DNA quickly 100 s to 1000 s of origins of replication exist per chromosome Specific arrangements of nucleotides called autonomously replicating sequences ARS o figure 1014 Proteins recognize and bind to ARS origin recognition complex ORC 3 Proteins associated with eukaryotic chromosomes 4 Different polymerases Table 105 Properties of Eukaryotic DNA Polymerases Polymerase a 3 5 g V C Location Nucleus Nucleus Nucleus Nucleus Mitochondria Nucleus 3 5 No No Yes Yes Yes No Exonuclease Activity Essential to Yes No Yes Yes No No uclear replication a polymerase Synthesizes RNA and DNA primers Limited to synthesizing small fragments 5 polymerase Takes over after a polymerase o Synthesizes leading and lagging strand 5 to 3 o exonuclease and proofreading abilities o a polymerase lethal to organism if mutated or not present o functions not fully understood similarto 6 pol B and Cpolymerases function in DNA repair 5 Telomeres o The ends of eukaryotic chromosomes telomere have unique structures and important protective functions o Telomeres are characterized by repeated nucleotide sequences 5 TTAGG3 in humans o Problem the end of the lagging strand cannot be completely replicated FIGURE 1016 o Telomeras solved the problem enzyme unique to eukarvotes Comment 7 enzyme that deals with replicating ulomeres o An RNA protein complex ribonucleoprotein that can synthesize DNA repeats without a tem plate FIGURE 1017 o Adds repeats of TTGGGG which form a hairpin turn the G s bond to each other imperfect world This creates a new 3 end to continue to copy from o Only active in your reproductive organs Biotechnology Side Note Polymerase Chain Reaction PCR o Important technology developed from knowledge of how replication works o Replication in a test tube o Even in the 1980 s genetic research was limited in most organisms o It was hard to get enough DNA to work with o PCR is a technique by which a short segment of a gene can be replicated almost exponentially o Kary Mullis developed the idea 19831985 o Most of the tasks performed by enzymes and other proteins could be accomplished by adding heat other enzymes with work in a test tube o Double stranded DNA denatures to single stranded at 9095 C etc o Problem The necessary enzymes polymerase will also break down at high tem peratures o Bacteria Themus aquatcus discovered living in hot springs 90 C Harvest polymerase problem solved Polymerase Chain Reaction PCR o PCR involves three basic steps involving rapid changes in temperature and polymerase function o Put 4 main things in a little test tube DNA Template dNTP s Primers and Taq Polymerase 1 Denaturation of template DNA 90 C 2 Anneal complementary primers 5060 C 3 Polymerization 72 C by polymerase 4 REPEAT Comment 9 youtnbe com CHAPTER 12 Transcrpton and the Genetic Code o Drawing 1 o Allows us to control when products are produced o Transcription allows us to make MASSIVE amounts of RNA o Say you eat a hamburger You need more than one digestive enzyme to digest it right Transcription o Figure 121 o Transfers information from DNA to an RNA molecule o Messenger RNA mRNA carries the genetic code to produce proteins Rules of complementation allow DNA to act as a template for RNA synthesis The Genetic Code o mRNA is organized into nucleotide triplets called codons o Codons code for amino acids during translation o There are 64 codons and 20 amino acids o Figure 127 o The code is degenerate redundant but NOT ambiguous Wobble Hypothesis 3rd nucleotide most degenerate o 3rd position degeneracy and wobble Table 124 o Relates to flexibility in pairing rules between mRNA and tRNA during translation o Approximately 50 types of tRNA but 64 codons in eukaryotes o Possible buffer against mutations o Really important for translation o AUG start or initiator codon o Amino acid methionine met the first amino acid in all polypeptides tells the ribosomes to start translation o In prokaryotes the initial methionine must be fmet Stop Codons l Comment 11 memonze o Three stop codons UAA UAG UGA o not recognized by any tRNA molecules do not code for amino acids Signal to terminatetranslation NOT a signal fortranscription o Mutations that insert early stop codons typically bad news o Is the genetic code universal Yes with exceptions Table 125 o Mitochondrial genomes have a slightly different code o Mitochondrial genomes also have their own tRNA s and ribosomes o Differences found in some bacteria rare and protozoans The Transcription Process o RNA polymerase primary enzyme involved in mRNA synthesis o figure 128 o there are several types of RNA polymerase o composed of several subunits each with a function o uses DNA as a template to synthesize a single stranded RNA molecule in the 5 to 3 direction The Transcription Procws Prokaryotes Promoter o Specific sequences on the template DNA strand where RNA polymerase binds Extremely important for regulation of transcription o Located upstream from the site where transcription begins o Contain critical conserved sequences 10 region and 35 region o Sigma subunit of RNA Polymerase recognizes promoters o RNA Polymerase binding allows initiation of transcription addition ofthe first 5 nucleotide at the transcription initiation site 1 site o No primer is necessary Elongation proceeds synthesizing an RNA molecule in the 5 to 3 direction that is complementary to the template DNA strand Termination o specific sequences termination sequence downstream from the gene signal for RNA Polymerase to stop transcription o Figure 128 o In bacteria groups of genes can be transcribed in one mRNA molecule Polycistronic mRNA o Transcription of all genes are under the regulation of the same promoter Q Below you will find A a DNA molecule showing only the codons for a gene and B the amino acid sequence of the protein that should be produced after transcription and translation of this gene Connect the concepts of 1 DNA structure double stranded complementary base pairing antiparallel etc and 2 the process of transcription to explain why only one strand of a DNA molecule is transcribed to produce the correct protein DNA Molecule 5 ATGGTGTTGTGA3 3 TACCACAACACT5 Protein Molecule MetValLeu A RNA does not recognize the start codon It recognizes the Promotor RNA Polymerase is going to read the DNA strand in the 3 to 5 direction and build in the 5 to 3 Top Strand 5 UCACAACACCAU3 which makes sergln Bottom Strand 5 AUGGUGUUGUGA3 which makes metvalleu Therefore the RNA polymerase can only synthesize RNA from the template strand which is usually the complementary strand of DNA o The Transcription Procas Eukaryotes o Occurs in the nucleus mRNA then transported to the ribosomes o More complicated chromosome structure chromatinproteins more complicated process to make DNA available to RNA polymerase Regulation of transcription is more complicated promoters enhancers transcription factors binding proteins o RNA molecule must be modified RNA processing before translation can occur o A consequence of Gene Structure o More Terminology for Transcription Regulatory Elements leisacting elementsl lrequlatorv 39 entd of DNA 39 39 39 which reside pm omre DNA molecule within the template strand o 10 box TATA box 35 box etc in prokaryotes Speed39mp39msm dom o Eukaryotes TATA box at 35 CAAT box 80 to 100 o Enhancers csacting elements that enhance speed up rate of transcription o Unique more common in eukaryotes o Can reside upstream downstream orwithin the gene transaction factors molecules usually proteins that typically bind to cs Comment 14 outside ofthe DNA molecule elements to promote or inhibit transcription o Transcription factors a class of proteins required for RNA 39 to required in eukaryotes for RNA to be able to and function in eu karyotes recognize and bind to the promotorin aDNA strand o Initiation of Eukaryotic Transcription TATA binding protein TBP a transcription factor binds to the TATA box within the promoter Several other transcription factors then bind to TBP forming a transcription must form before transcription process can start 3 RNA polymerase can then bind and transcription begins N o Eukaryotes possess three types of RNA Polymerases o Table 126 o Elongation and Termination of Eukaryotic Transcription o Very similarto the process in Prokaryotes Posttranscriptional Processing o A major difference between prokaryotic and eukaryotic transcription Eukaryotic mRNA has to be transported from the nucleus to the cytoplasm o structures are added to help with transport and protect the molecule during transport from the nucleus to the cytoplasm and ribosomes M Eukaryotic genes contain introns and exons o Figure 1211 Exons o Region of the gene that includes codons and other elements 5 UTRl etc found in the final mRNA molecule Comment 17 Untmnslated Region found on the 5 end ofthe RNA Where the Codons are contained molecule a erthepximerandbefoxe the Start Codon that tells the n39bosome to make protein 1 lntrons o transcribed but by the time it all gets to the ribosomes they are not found in final mRNA o Do not contain codons noncoding DNA o Why are they there Buffer against mutation this is where you find a lot of your csacting elements o major portion of the eukaryotic genome Posttranscriptional Processing After transcription RNA molecules in the nucleus hnRNA s heterogeneous nuclear RNA or pre RNA o Figure 129 2 A 5 cap is added o A modified nucleoside o protection and transport o required for translation 3 3 cleavage 4 Several to hundreds of adenine nucleotides are added to the 3 end 1 PolyA tail 2 protection and transport 5 ntrons out out and removed splicing 6 Exons are ligated together 1 Now ready to be taken to a ribosome and translated into a protein Chapter 13 Translation and Protein o Protein Basics o What is a protein o W sequence of amino acidsl that make Polypeptide chains o Polypeptide chain of amino acids primary structure o Figure 1315 o All amino acids have the same base structure o Amino and Carboxyl Groups o Figure 1316 Important in peptide bond formation Important in secondary structure of proteins o Figure 1317 o RGroups 1 Unique Rgroup for each of the 20 amino acids M4 2 Amino acids are categorized into one of four chemical groups based on the Rgroup 1 Nonpolar hydrophobic 2 Polar hydrophilic 3 Polar Basic positively charged 4 Polar Acidic negatively chargedl o RGroups 3 Extremely important fortertiary and quaternary structure of the protein tertiary and quaternary structure usually determine functionality Structure Function o Reading Frame AUG CTA CGG ll Protein Basics o Review Protein Structure o Primary structure sequence order of amino acids function Very important Figure 1315 Correct Reading Frame o Secondary Structure repeated pattern of folding due to hydrogen bonding Tertiary Structure 3D structure resulting from specific folding patterns o In essence ifthe shape isn t right that protein will NOT function properly o Every Iproteinl has a 39 tertiary structure structure function o Important Rgroup interactions 1 Hydrophobicinteractions 2 Hydrophilic interactions Polar Hydrophilic molecules prefer to interact with water than each other hydration shell 3 Ionic bonds salt bridges 4 Disulfide Bridged Very Important Disulfide covalent bonds o bysteind cys C is the only amino acid whose Rgroup will form covalent bonds Quaternary Structure Several polypeptides in tertiary structure join to form a functional protein structure function o Figure 13 19 o Rgroups are important o Called oligomeric proteins o Not all proteins are oligomeric o Each polypeptide is a subunit of that protein o What proteins have we talked about recently that have subunits o All polymerases RNApolymerase etc End of 138 END OF UNIT ONE Comment 21 Proteins are the work force of any biological We think of as the anchors ofprotein stxucture Strong Covalent bonds Memorize II
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