Replication2 exact copies of DNA before cell divisionParental strands template for daughter strandsRNA vs DNALife evolved from an RNA based worldChemicalSugar in RNA Ribose, carries –OH on 2’ carbonAdditional –OH group RNA less stable than DNAUracil instead of thymine5’ end triphosphate (instead of monophosphate)PhysicalRNA molecules shorter (smaller) than DNA (very large)RNA molecules single stranded folds back on itself, enhances stabilityThe Central DogmaDNA transcription RNA translation ProteinRNAPolymer of nucleotides linked by phosphodiester bondsRNA strand polarity determined by which end of chain carries 3’-OHTranscriptionDNA double helix unwinds one strand is used as a template for transcriptDNA template strand runs 3’ 5’RNA transcript strand grows 5’ 3’Promoters: region where transcription is initiated5’-TATAAA-3’ TATA box: first nucleotide to be transcribed is usually about 25 base pairs from the TATA boxBacteria: promoter recognition mediated by protein sigma factor associates with RNA polymerase, helps bind to specific promotersEukaryotesGeneral transcription factors: at least 6 proteins, attracts RNA polymerase (Pol II) to promoterTranscriptional activator proteins: binds to enhancer (specific DNA sequence)Transcriptional activator proteins: attracts mediator complex which interacts with Pol IITranscription bubbleWithin the Pol IIRNA transcript paired with template strand creates RNA - DNA duplexBacteria: length of bubble is 14 base pairs, length of duplex is 8 base pairsRibonucleotides paired with nucleotides3’-OH of growing strand attacks high-energy phosphate bond (innermost phosphate-phosphate bond) of incoming ribonucleotide provides energy to drive reaction2 phosphates of incoming ribonucleotide released as pyrophosphateTerminators: region where transcription stopsTranscript produced by polymerization of ribonucleoside of triphosphatesTranslationPrimary transcript: RNA transcript that comes off the template DNA strand, contains genetic information of gene transcribedmRNA: messenger RNA, RNA molecule that combines with the ribosome to direct protein synthesisProkaryotes: primary transcript is the mRNATranslation begins before transcription is complete, no nucleus to spatially separatePolycistronic mRNA: contain genetic information for synthesis of 2 or more different proteinsEukaryotes: Transcription in nucleus, translation in the cytoplasmRNA processing: complex chemical modification of primary transcript, converts primary transcript into finished mRNA, which can then be translated by the ribosome, 3 major chemical modifications5’ cap: 5’ end of primary transcript modified by addition of a modified nucleotide called 7-methylguanosine attached by 5’ to 5’ phosphate linkage, ribosomes recognize mRNA by 5’ capPolyadenylation: addition of about 250 consecutive A-bearing ribosomes to 3’ end, forming poly(A) tailCap and tail protect 2 ends of transcript and increase stability of RNA transcript until translated in cytoplasmRNA splicing: intron removal process, introns: excision of certain sequences from transcript, exons: what is left intact, spliceosome: complex of RNA and protein that catalyzes processSpecific sequences near ends of intron undergo base pairing with RNA molecules in spliceosomeSpliceosome enables reaction cuts one end of the intron and connects it to a nucleotide near the other, forms a loop and tail: lariatThe exon on one end of intron is brought next to exon at the other end. Exons are joined and introns are releasedLariat making up intron breaks down into nucleotides90% of human genes contain an intronAlternative splicing: presence of multiple introns, primary transcripts from same gene can be spliced in different ways to yield different mRNAs different protein products more than 80% human genesAmino Acid StructureAmino group, carboxyl group, H, r group/side chainsTetrahedralAmino acids in a protein listed in order from left to right starting at amino end carboxyl endHydrophilic: basic, acidic, polar, one side of the chain is slightly more negatively charged than the otherHydrophobic: hard to make hydrogen bondsGlycine: r group is hyrdrogen, increases flexibility of polypeptide backboneProline: r group linked back to amino group, kink/bend in polypeptide backboneCystenine: t cystenine side chains s-s disulfide bond, can connect different parts of same/different proteinsPeptide bonds:bond formed between 2 amino acidscarboxyl reacts with amino of next, water releasedR groups of each amino acid point in different directionsC=O group in bond is carbonyl group, N-H group is amideAmino end and carboxyl end of peptidePolypeptide: amino acids connected togetherPolypeptide=protein, especially when chain folds into stablilityAmino acid residues: amino acids that are incorporated into a proteinSequencePrimary structure: sequence of amino acids, determines how a protein foldsSecondary structure: results from hydrogen bonding in polypeptide backbonePauling and Corey discovered 2 types of secondary structures using x-ray crystallography alpha helix and beta sheet: stabilized by hydrogen bonding along peptide backboneBeta sheets can run parallel or antiparallel, antiparallel is more stable b/c of favorable hydrogen bondingTertiary structure: 3D shape of the protein, results from interactions between amino acid side chainsCan be shown 3 different waysball & stick modelemphasizes atoms in amino acid chainribbon modelemphasizes secondary structuresspace-filling modelshows overall shape and contour of folded proteinQuaternary structure: results from interactions of polypeptide subunits, may be identical or differentDenatured: unfolded stateChaperones: evolved proteins that help protect slow folding or denatured proteins until reaching 3D structureTranslationRibosomes: complex structures of RNA and protein, bind with mRNA, translation takes place on ribosomesConsists of a small subunit and large subunit, both composed of RNA and proteinEukaryotic ribosomes larger than prokaryotic ribosomesLarge subunit has 3 binding sites for transfer RNA (tRNA)A (aminoacyl) siteP (peptidyl) siteE (exit) siteMajor role of ribosome is to ensure sequence in mRNA coding for amino acids is read in successive, non overlapping groups of 3 nucleotides (establishing correct reading frame for codons)tRNAactual translation of each codon in mRNA into one amino acid
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