Chapter 3 Replication 03 23 2014 2 exact copies of DNA before cell division Parental strands template for daughter strands RNA vs DNA Life evolved from an RNA based world Chemical o Sugar in RNA Ribose carries OH on 2 carbon Additional OH group RNA less stable than DNA o Uracil instead of thymine o 5 end triphosphate instead of monophosphate Physical o RNA molecules shorter smaller than DNA very large RNA molecules single stranded folds back on itself enhances stability The Central Dogma RNA DNA transcription RNA translation Protein Polymer of nucleotides linked by phosphodiester bonds RNA strand polarity determined by which end of chain carries 3 OH Transcription transcript DNA double helix unwinds one strand is used as a template for DNA template strand runs 3 5 RNA transcript strand grows 5 3 Promoters region where transcription is initiated o 5 TATAAA 3 TATA box first nucleotide to be transcribed is usually about 25 base pairs from the TATA box o Bacteria promoter recognition mediated by protein sigma factor associates with RNA polymerase helps bind to specific promoters o Eukaryotes General transcription factors at least 6 proteins attracts RNA polymerase Pol II to promoter Transcriptional activator proteins binds to enhancer specific DNA sequence Transcriptional activator proteins attracts mediator complex which interacts with Pol II Transcription bubble Within the Pol II RNA transcript paired with template strand creates RNA DNA duplex Bacteria length of bubble is 14 base pairs length of duplex is 8 base pairs Ribonucleotides paired with nucleotides 3 OH of growing strand attacks high energy phosphate bond innermost phosphate phosphate bond of incoming ribonucleotide provides energy to drive reaction 2 phosphates of incoming ribonucleotide released as pyrophosphate Terminators region where transcription stops Transcript produced by polymerization of ribonucleoside of triphosphates Translation Primary transcript RNA transcript that comes off the template DNA strand contains genetic information of gene transcribed mRNA messenger RNA RNA molecule that combines with the ribosome to direct protein synthesis Prokaryotes primary transcript is the mRNA o Translation begins before transcription is complete no nucleus to spatially separate o Polycistronic mRNA contain genetic information for synthesis of 2 or more different proteins Eukaryotes Transcription in nucleus translation in the cytoplasm o RNA processing complex chemical modification of primary transcript converts primary transcript into finished mRNA which can then be translated by the ribosome 3 major chemical modifications 5 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 cap Polyadenylation addition of about 250 consecutive A bearing ribosomes to 3 end forming poly A tail Cap and tail protect 2 ends of transcript and increase stability of RNA transcript until translated in cytoplasm RNA splicing intron removal process introns excision of certain sequences from transcript exons what is left intact spliceosome complex of RNA and protein that catalyzes process Specific sequences near ends of intron undergo base pairing with RNA molecules in spliceosome Spliceosome enables reaction cuts one end of the intron and connects it to a nucleotide near the other forms a loop and tail lariat The exon on one end of intron is brought next to exon at the other end Exons are joined and introns are released Lariat making up intron breaks down into nucleotides 90 of human genes contain an intron Alternative 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 genes Chapter 4 Amino Acid Structure 03 23 2014 Amino group carboxyl group H r group side chains Tetrahedral Amino acids in a protein listed in order from left to right starting at amino end carboxyl end o Hydrophilic basic acidic polar one side of the chain is slightly more negatively charged than the other o Hydrophobic hard to make hydrogen bonds o Glycine r group is hyrdrogen increases flexibility of o Proline r group linked back to amino group kink bend in polypeptide backbone polypeptide backbone o Cystenine t cystenine side chains s s disulfide bond can connect different parts of same different proteins Peptide bonds o bond formed between 2 amino acids o carboxyl reacts with amino of next water released o R groups of each amino acid point in different directions o C O group in bond is carbonyl group N H group is amide o Amino end and carboxyl end of peptide o Polypeptide amino acids connected together Polypeptide protein especially when chain folds into stablility Amino acid residues amino acids that are incorporated into a protein Sequence o Primary structure sequence of amino acids determines how a o Secondary structure results from hydrogen bonding in protein folds polypeptide backbone Pauling and Corey discovered 2 types of secondary structures using x ray crystallography alpha helix and beta sheet stabilized by hydrogen bonding along peptide backbone Beta sheets can run parallel or antiparallel antiparallel is more stable b c of favorable hydrogen bonding o Tertiary structure 3D shape of the protein results from interactions between amino acid side chains Can be shown 3 different ways ball stick model emphasizes atoms in amino acid chain ribbon model space filling model emphasizes secondary structures shows overall shape and contour of folded protein o Quaternary structure results from interactions of polypeptide subunits may be identical or different Denatured unfolded state Chaperones evolved proteins that help protect slow folding or denatured proteins until reaching 3D structure Translation Ribosomes complex structures of RNA and protein bind with mRNA translation takes place on ribosomes o Consists of a small subunit and large subunit both composed of RNA and protein o Eukaryotic ribosomes larger than prokaryotic ribosomes o Large subunit has 3 binding sites for transfer RNA tRNA A aminoacyl site P peptidyl site E exit site o Major 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 tRNA o actual translation of each codon in mRNA into one amino acid in the polypeptide o small RNA molecules 70 90
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