Molecular Biology (.ppsx)

Molecular Biology

Molecular BiologyTodays TopicsThe Structure of DNADNA ReplicationDNA TranscriptionDNA TranslationThe Central DogmaProteomicsEpigenetics

Chapter 9

BIO156Paradise Valley Community College#

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Its about the code, not the chemistry!TGCA

The single-letter codes can now be read into a computer to create the genome database.

AGTCCATTACGAAAATCGACTATCGAAGGGTAAAGGCTTATAAGCCATAGTCAGGTAATGCTTTTAGCTGATAGCTTCCCATTTCCGAATATTCGGTATC


Genetic Determinism

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1249,250,621492,449,994690,472,424881,626,7001,062,541,9601,233,657,0271,392,795,6901,539,159,7121,680,373,1431,815,907,8901,950,914,4062,084,766,3012,199,936,1792,307,285,7192,409,817,1112,500,171,8642,581,367,0742,659,444,3222,718,573,3052,781,598,8252,829,728,7202,881,033,2863,036,303,8463,095,693,981Cumulative Base Pairs the Human Genome(Draft)

mt16,569Y59,373,566X155,270,5602251,304,5662148,129,8952063,025,5201959,128,9831878,077,2481781,195,2101690,354,75315102,531,39214107,349,54013115,169,878Chr#Base Pairs 12133,851,89511135,006,51610135,534,7479141,213,4318146,364,0227159,138,6636171,115,0675180,915,2604191,154,2763198,022,4302243,199,3731249,250,621Chr#Base Pairs Percent of non-coding DNA: 98%Number of genes: 19,000 to 20,000

Source: Modified from schoolbag.info/biology/living/75.html. 2016.


Size of the Human GenomeAGTCCATTACGAAAATCGACTATCGAAGGGTAAAGGCTTATAAGCCATAGACATAGATAACTACCTTAGGAATATCAGTACGATTAAATGCCCATGAATCGAATTGGACCATAGCTAAGATCAGATCTAGTATCGAATGCTTATAGCCCATGGATACGATCAGATCAGATACGATAGTACATGCAATGGATCACCTAGATGGATCGATTAGGAATCCACCCATGTGGCATACCTAATTTGAAGAAAGACTACCTTAGGAATATCAGTACGATTAAATGGCCCATGAATCGAATTGGACGAATCGAATGCTTATAGCCCATGGATAAt the rate these bases are appearing, it would take 5 years of watching this to see the complete human genome.


Self-explanatory4

Fame and Glory

1916-2004

1905-2002Erwin ChargaffDiscovered the relationships between DNA bases, A, T, G, C.Rosalind Franklin & Maurice WilkinsDiscovered the basic structure of DNA by x-ray crystallographyJames Watson andFrancis CrickBuilt the first accurate model of a DNA molecule

1920-1958

1916-2004

1928-

1962

1962

1962

1949Photo 51


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3/17/2017Paradise Valley Community CollegeChapter 6 - DNA Structure and Function

A DNA molecule consists of two strands of nucleotide monomers running in opposite directions and coiled into a double helix(a twisting staircase).Three parts of a DNA nucleotideOne nitrogen-containing base(Adenine, Thymine, Guanine, or Cytosine) A five-carbon sugar (pentose, deoxyribose))Three phosphate groupsThe Double Helix

Credit: Modified from Chris Bickel, spectrum.ieee.org. 2017.CytosineSource: Modified from commons.wikimedia.org. 2017.


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The Double HelixTwo double-helix strands are held together by hydrogen bonds between nucleotide bases.Base-Pairing Rules (Chargaff) A pairs with T C pairs with G [A] ~ [T] [C] ~ [G]

Source: Modified from undsci.berkeley.edu. 2015.Guanine (G) Cytosine (C)Adenine (A) Thymine (T)

CGTA


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Paired DNA Strands


Patterns of Base Pairing The DNA sequence varies among species and among individualsEach species has characteristic DNA sequencesDNA sequenceThe order of nucleotide bases in a strand of DNABase pairs:TGTTCTATGTTTACTTAGTACCTCTTTAACAAGATACAAATGAATCATGGAGAAAT


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DNA Replication and RepairDNA helicaseUnwinds double-stranded DNADNA polymeraseDNA replication enzyme; assembles a new strand of DNA based on sequence of a DNA templateDNA ligaseEnzyme that seals breaks in double-stranded DNA


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DNA ReplicationThe two strands of a DNA molecule are complementary.Their nucleotides match up according to base-pairing rules(G to C, T to A).Each strand is labelled to indicate directionality.five-prime to three-primethree-prime to five-prime

5533TGATAGCTGACACTATCGACTG


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DNA ReplicationSource: interactMedical.com. 2017.


DNA Replication in Action

ChromosomeOriginal DNAReplication ForkFreeNucleotidesFree NucleotidesDNA PolymeraseDNA PolymeraseLeading StrandLagging StrandSource: Modified from philschatz.com. 2016.

Helicase


Semiconservativereplication

TGATAACTATThe base sequences of both DNA molecules is identical.Each parent strand becomes a template for a new DNA strand.Free nucleotides match their opposite on each strand.As replication startsDNA unwinds.parentparentnewnewCGTTTTAAAA


DNA Repair Mechanisms


MutationsUncorrected errors in DNA replication may become mutations.Mutation: A permanent change in DNA sequence

Source: Modified from biology-igcse.weebly.com. 2017.parentcorrectcopyparentmutantcopy


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DNA, RNA, & Protein Synthesis

Replication: DNA to DNA (Not part of protein synthesis)Occurs before mitosis & meiosis ONLYDuplication of DNA during S stage of InterphaseTranscription: DNA to RNADNA blueprint of gene is decodedResult: RNATranslation: RNA to ProteinRNA decoded & reconstructed (mRNA)Result: ProteinTheCentralDogma


DNA Replication


TelomeresTelomeres contain thousands of repeatsof the 6-nucleotidesequence T T A G G G

Source: www.nih.gov. 2015.

Elizabeth H. BlackburnCarol W. Greiderand Jack W. Szostak2009AATCCCAATCCCAATCCCAATCCCTTAGGGTTAGGGTTAGGGTTAGGG

ChromosomeTelomeres

Source: www.health-for-you.biz. 2015.


Telomeres protect the end of the chromosome from deterioration or from fusion with neighboringchromosomes.The Hayflick Limit: Cells die afterabout 100 cell divisions.

Chromosome

Telomeres: end caps thatprotect the chromosome


ChromosomesA eukaryotic chromosome is a molecule of DNA together with associated proteins.

ChromosomeStructure made of DNAand associated proteinsCarries a part of a cellsgenetic information

Source: www.beltina.org. 2015.


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DNA Packaging

DNA Packaging


30 nm solenoidBeads-on-a-stringNucleosomesCondensed sectionof chromatinExtended form of chromosomeStructureProteins organize DNA structurally.Histones allow chromosomesto pack tightly. Histone octomersType of protein that structurally organizes eukaryotic chromosomesNucleosomeA length of DNAwound around a spool of histone proteins

Chromosome(metaphase)

Naked DNA

Source: www.ncbe.reading.ac.uk. 2015.


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Chromosome NumberA eukaryotic cells DNA is divided into a characteristic number of chromosomes.Chromosome numberSum of all chromosomesA human body cell has 23 pairsDiploidCells having two of each type of chromosome characteristic (2n)

Source: www.washington.edu. 2015.


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Examples of Chromosome NumberSpecies# Chrom.Fruit fly8Amoeba13Garden Pea14Frog26Cat38Human46Species# Chrom.Potato48Pineapple50Cow60Dog78Vizcacha rat102Horsetail216Adders Tongue1,260


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Examples of Chromosome Number

Source: www.flickr.com. 2015.

Source: www.highlanddiary.co.uk. 2015.Adders tonguefern (1,260)Vizcacha rat (102)

Source: www.planet-mammiferes.org. 2015.

Horsetail (216)A living fossilSource: en.wikipedia.org. 2015.


KaryotypeThe karyotype of an organism reveals characteristics of an organisms chromosomes.

KaryotypeImage of an individualscomplement of chromosomes arrangedbysize,length,shape, andcentromere location12345678910111213141516171819202122

Source: fineartamerica.com. 2015.



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Types of ChromosomesTwo types of eukaryotic chromosomes:autosomes and sex chromosomesAutosomesPaired chromosomes with same length,shape, centromere location, and genes Any chromosome other than a sexchromosome Sex chromosomesMembers of a pair of chromosomesthat differ between males and femalesLooking at the chromosomes,Which one is the Y chromosome?Which one is the X chromosome?



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Karyotyping

5 mLvenousblood

Spread cellson slideDigest withtrypsinand stain

Analyzemetaphasespread

Karyogram

Addcolchicine(stops mitosisat metaphase)Digitize orphotograph

Add toculture medium(3 days @ 37C)

MitosisinducedSource: S. Belliappa. Modified from slideshare.com. 2017.


Sex Determination in HumansDiploid cells (2n)MeiosisHaploid cells (n)EggsSpermGametesZygotes


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Replication: DNA to DNA (Not part of protein synthesis)Occurs before mitosis & meiosis ONLYDuplication of DNA during S stage of InterphaseTranscription: DNA to RNADNA blueprint of gene is decodedResult: RNATranslation: RNA to ProteinRNA decoded & reconstructed (mRNA)Result: ProteinDNA, RNA, & Protein SynthesisTheCentralDogma


Transcription: DNA to mRNA


The Genetic CodeWe have 4 different letters within DNA.We have 20 different amino acids in a protein.How can 4 letters code for 20 amino acids?Possible combinations of 4 letters:44 = 256 combinations

GUUGUCGUAGUGAla A

UCAGUCAGUUUUUCUUAUUGPhe FLeu L

CUUCUCCUACUGLeu L

AUUAUCAUAAUGIle IMet M

GUUGUCGUAGUGVal V

UCUUCCUCAUCGSer S

CCUCCCCCACCGPro P

ACUACCACAACGThr T

UAUUACUAAUAGTyr YStop Stop

CAUCACCAACAGHis H Gln Q

AAUAACAAAAAGAsn NLys K

UGUUGCUGAUGGCys CStopTyr W

CGUCGCCGACGGArg R

AGUAGCAGAAGGSer SArg R

GGUGGCGGAGGGGly G

GAUGACGAAGAGAsp DGlu E

UCGAUCGAUCGAUCGASecond LetterFirst LetterThird LetterAUGUACGUACUACAUAAUGAGGUUCUAUGUUUACUUAGUACCUCUUUAUGA35 L N N E V L C L L S T L L * VYM


Why All the Colors?

ATCUGCGATTACTAGCGACTCCGACTTATCUGCGATTACTAGCGACTCCGACTT


Replication: DNA to DNA (Not part of protein synthesis)Occurs before mitosis & meiosis ONLYDuplication of DNA during S stage of InterphaseTranscription: DNA to RNADNA blueprint of gene is decodedResult: RNATranslation: RNA to ProteinRNA decoded & reconstructed (mRNA)Result: ProteinDNA, RNA, & Protein SynthesisTheCentralDogma


TranscriptionCentral Dogma of Molecular Biology

TranslationDNARNAProteinGenetic Determinism

MakesMakes

Gene Product


Translation: mRNA to Protein


The finished polypeptide

Codons-Anticodons

METHIONINEUACssDNALMHImRNA

ISOLEUCINEUAAGUA

HISTIDINEUAC

LEUCINEUAA

STOP

tRNA aa

CODON

ANTICODON3 TACTAAGTACTATAAAATGA 55 AUGAUUCAUGAUAUUUUACU 3


eukaryotes & ProkaryotesProkaryotesLack nucleusRNA transcription and protein translation are simultaneousNo RNA post-processing eventsGene expression is regulated at the transcriptional levelEukaryotesNucleus (DNA within)RNA transcription occurs prior to protein translation in the nucleusMany RNA post-processing eventsGene expression is regulated at many levelsGene Expression (Protein Synthesis)


PlasmamembraneDNA

mRNAGene Expression (Protein synthesis)Prokaryotes

ProteinRibosomes


Gene Expression (Protein synthesis)

NucleusDNACytosol

ProteinMaturemRNA

Pre-mRNARibosomes

Eukaryotes


Introns removedEnd-capping

Nuclear membrane

Eukaryotic Gene RegulationGene regulation is the process of turning genes on and off. Transcription rates altered byTranscription factorsEnhancer proteinsSilencers (DNA sequences)Insulators (DNA sequences)Promoters (TATA boxes)End-capping andremoval of introns is crucial.Golgi apparatus responsible for finishing protein and tagging it for delivery.

TranscriptioncontrolPreRNAsynthesiscontrolRNAtransportcontrolTranslationcontrolmRNAPrimarytranscript

ProteinDNAgeneTranscriptionTranslation


ProteomicsLocated on Chromosome 7The primary structure1,485 amino acidsThe secondary structure5 domainsThe tertiary structureGate for chloride ion transport

MQKTEKASIFSQSREEEVQDTRL

From the primary structure wecan deduce the mRNA and DNA of the gene.

CFTR: Cystic Fibrosis Transmembrane conductance Regulator


MQKTPLEKASIFSQIFFSWTKPILWKGYRQRLELSDIYQIHPGDSADNLSERLEREWDREVATSKKNPKLINALKRCFFWKFLFYGILLYLGEVTKAVQPLLLGRIIASYDRDNEHERSIAYYLAIGLCLLFVVRMLLLHPAIFGLHHIGMQMRIAMFSLIYKKTLKLSSKVLDKISTGQLVSLLSNNLNKFDEGLALAHFVWIAPLQVLLLMGLLWDLLQASAFCGLGFLIILALFQAWLGRMMMKYRDKRAGKINERLVITSQIIENIQSVKAYCWENAMEKIIETIRETELKLTRKAAYVRYFNSSAFFFSGFFVVFLSIVPHLLLDGISLRKIFTTISFSIVLRMAVTRQFPWAVQTWYDSLGVINKIQEFLQKEEYKSLEYNLTTTEVAMENVSASWDEGIGEFFEKAKLEVNGGNISNEDPSAFFSNFSLHVAPVLRNINFKIEKGQLLAIAGSTGAGKTSLLMMIMGELEPSAGKIKHSGRISFSPQVSWIMPGTIKENIVFGVSYDQYRYLSVIKACQLEEDISKFPEKDNTVLGEGGITLSGGQRARISLARAVYKDADLYLLDSPFSYLDLFTEKEIFESCVCKLMANKTRILVTSKVEQLKKADKVLILHEGSCYFYGTFSELQDQRPEFSSHLIGFDHFNAERRNSIITETLRRCSIDSDPTGVRNEVKNKSFKQVGDFSEKRKSSIINPRKSSRKFSVMQKSQPQMSGIEEEDVPAVQGERKLSLVPESDQGEASLPRSNIFNTGPTFQARRRQSVLNLMTRTSISQGSNAFATRKTSVRKMSVSSYSNSSFEVDIYNRRLSQDSILEVSEDINEEDLKECFLDDTDSPSTTTTWNTYLRFLTAHKNFIFILVFCIVIFLAEVVASSAGLWVLKSNAPVINTTSNGNGSEISDTLSVIVTHTSFYYVFYIYVGVVDSLLALGIFRGLPLVHSLISVSKVLHKKMLHAILHAPMSTFNTMRAGRILNRFSKDTAILDDILPLSIFDLTQLVLIVIGAITVVSLLEPYIFLATVPVIVAFILLRSYFLHTSQQLKQLESEARSPIFAHLITSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYLSTLRWFQMTIEMIFVIFFIAVSFISIATSGAGEEKVGIVLTLAMNIMNTLQWAVNASIDVDSLMRSVSRIFRFIDLPVEELINENKNKEEQLSEVLIYENDYIKKTQVWPSGGQMTVKNLSANYIDGGNTVLENISFSLSPGQRVGLLGRTGSGKSTLLSAFLRLLSTQGDIQIDGVSWQTIPLQKWRKAFGVIPQKVFIFSGSIRKNLDPYGKWSDEELLKVTEEVGLKLIIDQFPGQLDFVLLDGGCVLSHGHKQLVCLARSVLSKAKILLLDEPSAHLDPITFQIIRKTLKHAFADCTVILSEHRLEAMLECQRFLVIEDNTVRQYDSIQKLVNEKSFFKQAISHSDRLKLFPLHRRNSSKRKSRPQISALQEETEEEVQDTRLProteomicsLDLFTELeu - Asp - Leu-Phe - Thr - Glu5055065075085095101,485 amino acids

LDLFTE1-letter code for each aa:3-letter code for each aa:This is only the primary structure.At this point we have no idea what the DNA will look like.Amino Acid Sequence for CFTR protein


Deciphering the Protein

UUUUUAUUGCUUCUCCUACUGUUAGAUUUAUUUACGGAAUUGGACUUGUUCACAGAGCUUCUUACCCUCCUCACUCUACUACUGCUGctagatcttt ttacagaa53

5,952 possible RNA sequencesGAAACACUUGAUUUAUUAUUGCUUCUCCUACUGTTAGATCTTTTTACAGAADNA ContigAll possible codons

LDLFTELeu-Asp-Leu-Phe-Thr-Glu505506507508509510


Molecular Biology


Science

Molecular Biology (.ppsx)