Exam 2 Review Chapter 3 Central dogma Fig 3 3 order of information processing o Level of mRNA is elevated effect on gene transcription as opposed to an increase in protein translation Basic building blocks of DNA Fig 3 4 o Base Deoxyribose sugar Phosphate group DNA structure 4 bases adenine thymine cytosine guanine Differences between purines and pyrimidines purines two rings A G pyrimidines one ring T C Phosphodiester bond Covalent bond that connect sugars in the backbone of Connects 3 carbon of one nucleotide to 5 carbon of the DNA next Polarity of DNA strands One end differs from the other 5 versus 3 5 end free 5 phosphate 3 end free 3 hydroxyl Double strands are anti parallel Complementary base pairing based on H bonding Major groove minor groove A to T two hydrogen bonds C to G three hydrogen bonds You can skip topoisomerase chromatin structure 3 9 3 10 skip RNA World 3 11 Transcription Differences between DNA and RNA bases ribose etc o Ribose sugar uracil instead of thymine Template versus non template strand in transcription but individual genes can be on either one o Template strand is transcribed by RNA polymerase o Adds nucleotides to 3 end grows 5 to 3 Promoters regions of base pairs where RNA polymerase binds to DNA o TATA box TATA sequence is present o General transcription factors 6 attract RNA polymerase and associated proteins to site o RNA polymerase II responsible for transcription of protein coding genes o Mediator complex and activators transcriptional activator proteins bind to enhancers recruit a mediator complex of proteins interacts with Pol II complex Initiation of transcription depends on availability of transcriptional activator proteins Be able to draw a map of a typical gene and the primary RNA transcript Primary transcript messenger RNA mRNA carries genetic info from Glucocorticoid receptor GR as a transcription activator acting on DNA to ribosome enhancer sequences o When GR is bound receptor moves to nucleus and acts as activators RNA polymerase as a molecular machine o Channels for DNA input output o Nucleotide input RNA output o Features that disrupt DNA double helix stabilize RNA DNA duplex allow DNA double helix to reform Polymerization of mRNA new nucleotides added as triphosphate bases fig 3 19 RNA processing converts primary transcript into finished mRNA o 5 cap added to 5 end addition of special nucleotide Without the cap ribosome would not attach the mRNA translation would not occur Stabilize RNA transcript Stabilize RNA transcript o 3 polyadenylation poly A tail transcription termination o RNA splicing intron removal catalyzed by spliceosome o Alternative splicing primary transcripts from different genes spliced in different ways to yield different mRNAs proteins Chapter 4 Protein Structure o Glycine and Alanine hydrophobic o Peptide bond between carboxyl group amino group water formed o Secondary hydrogen bonds form between carbonyl group and amide group folding alpha helix beta sheet o Tertiary 3D spatial distribution of hydrophilic hydrophobic side chains bonding ionic hydrogen van der Waals o Quaternary made up of two or more identical or different polypeptide subunits How are these structures stabilized bonding Denaturation loss of tertiary structure unfolding lose functional activity See also how do we make proteins worksheet Translation o General structure of ribosome Large subunit three binding sites for tRNA o A aminoacyl o P peptidyl o E exit Small subunit o tRNA brings corresponding anticodon to mRNA o Codon non overlapping group of three adjacent nucleotides o Anticodon complementary nucleotides for codon o Reading frames ribosome can begin at any of three possible positions there is only one correct position o Genetic code redundancy of codons for amino acids o Aminoacyl tRNA synthetases connect specific amino acids to specific tRNA molecules One tRNA synthetase for each amino acid o Charged correct amino acid attached to tRNA o Steps of translation Initiation AUG codon is recognized Met established as first amino acid Elongation successive amino acids added one by one Termination completed polypeptide chain released from ribosome Cycloheximide protein synthesis inhibitor Blocks translocation step in elongation Lactimidomycin protein synthesis inhibitor Antiproliferative effect on tumor cell lines Blocks translocation step in elongation Interpret cycloheximide inhibition figure panel worksheet Chapter 6 6 1 Classification of organisms 6 2 Energy 6 4 Reactions o ATP chemical energy in the bonds used to drive cellular processes o Gibbs free energy amount of energy available to do work o G free energy of products free energy of reactants Positive energy required Negative energy released o Exergonic negative G proceed spontaneously o Endergonic positive G not spontaneous o ATP hydrolysis ATP H2O ADP Pi o Coupling of endergonic reactions to ATP hydrolysis 6 5 Enzymes o Role as catalysts speed up reaction o Transition state and activation energy o Lower activation energy Ea o Enzymes form transitional complexes with reactants o Allosteric effects activation and inhibition ways to control enzyme pathways Chapter 7 7 1 Know 4 stages of cellular respiration o Oxidation loss of electrons o Reduction gain of electrons higher energy o Carbon atoms in glucose become oxidized electrons partially removed o CO2 as a product o Oxygen final e acceptor forms H2O o along the way energy is harvested in multiple steps o Electron carriers NAD NADH o ATP generation Pi ADP ATP Reverse is ATP hydrolysis o Substrate level phosphorylation phosphate donated to ADP glycolysis and citric acid cycle o Oxidative phosphorylation ETC and H ion transport provide energy for ATP synthesis 7 2 Glycolysis Cytoplasm Begins with glucose partial breakdown of glucose initial steps use ATP Products two 3 carbon pyruvates 2 ATP 2 NADH Low efficiency but fast pathway for ATP production Anaerobic pyruvate must be fermented to reduced lactic acid 7 3 Acetyl coA synthesis Pyruvate transported into mitochondria Partially oxidized CO2 reduced NADH Acetyl groups 2 carbon conjugated to coenzyme A Other food molecules eg fatty acids can be metabolized to acetylcoA 7 4 Citric acid cycle o Begins with acetylcoA 2 carbon acetyl group with coA o Carbons are oxidized to CO2 products o Electrons energy transferred to e carriers NAD NADH FAD FAH2 o Some ATP production substrate level o Products 2 CO2 1 ATP 3 NADH 7 5 Electron Transport Chain ETC inner membrane of mitochondria o NADH
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