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Nucleic Acids

MCAT Central Dogma

TermDefinition
Nucleoide Sugar, Base (on C1), and Phosphate (C5)
Nucleoside Sugar and Base - NO Phosphate
Deoxyribose/Ribose Difference Deoxyribose H on C2 (dNTP) Ribose OH on C2 (NTP) - Makes RNA less stable due to increased reactivity of Oxygen
DNA/RNA directionality 5' to 3' - New bases add on C3
Purines 2 C rings (AG is 2 Pure) Adenine/Guanine
Pyrimidines 1 C ring (CUT the Py) Cytosine Uracil (RNA) Thymine(DNA)
DNA Base Pairing Held together by H bonding A-T (2 H bonds) G-C (3 H bonds)
Genome All DNA in Organism
Prokaryote Genome Characteristics Single Circular Genome, Haploid Use Methylation as protection from own restriction digest enzymes Supercoiling - DNA Gyrase Plasmids - Extrachromosomal circular dsDNA (give extra abilities, Not required for lifecycles)
Eukaryotic Genome Characteristics Several Linear chromosomes, Diploid Wrapped around Histones for protection Human: 46 Chromosomes (23 Pairs)
DNA + Histones Nucleosomes
Chromatin Packaged Nucleosomes
Chromatid Made of Chromatin
Chromosome Chromatid (or 2 Sister Chromatid if replicated
Euchromatin Unwound, Active, Light Stain Expressed
Heterochromatin Tightly Wound, Inactive, Dark Stain Hibernating
Centromere Region on chromosome where sister chromatid held together Mitotic spindle attaches
Telomeres Ends of Eukaryotic Linear Chromosomes Short repeat sequences that loop back to stabilize DNA
Central Dogma DNA transcribed to RNA Translated into Protein Violations: Reverse Transcription and Functional RNA
Codons to know AUG - Start - Met STOP - UAA, UGA, UAG
Introns/Exons Introns: Non coding regions removed from RNA Exons: are expressed in mature mRNA
Source of Mutations -DNA Polymerase -Endogenous Damage -Exogenous Damage -Transposons
Missense Mutation Codon for AA becomes Codon for new AA (Changes AA) Point mutation
Nonsense Codon for AA becomes STOP codon (Shortened Protein) Point Mutation
Silent Mutation Codon for AA becomes new codon for same AA (No effect) Point Mutation
Frameshift Mutation Insertions and deletions shift reading frame forward or back
DNA Polymerase Errors Point(Missense/Silent/Nonsense) and Frameshift Mutations
Endogenous Damage From Reactive Oxygen Species or Physical Damage Oxidized DNA Crosslinked bases - Covalent bond between bases (Inter/intra strand) ds/ss Strand Breaks
Exogenous Damage from Radiation or Chemicals UV rad (TT dimers), X rays (dsBreaks/Translocation), Chemicals (physical or intercalation - chemical slips in between bases)
Transposons Jumping genes Gene for transposase (enzyme to randomly cut and paste DNA) Sandwiched by inverted repeats recognized by transposase
Types of Transposons IS Element: Just transposase and repeats Complex: Genes and transposase inside inverted repeats Compound: Two IS elements bracketing a central region
Mismatch Repair Pathway During/shortly after replication -parent strand is methylated (daughter is not) -Endonuclease identifies daughter removes bad base -Polymerase adds correct base Repair without mutation
Base/Nucleotide excision Repair Any time in cell cycle Remove bad base and replace as in mismatch repair but Can't Identify correct strand (picked at random) Possibility for permanent mutation
Homology-Directed Repair After replication - sister chromatid is present Use Identical sister chromatid as template Should repair dsBreak without mutation
Non-homologous end joining Any time in Cell Cycle Clean broken ends of dsBreak Ligate broken ends together Mutagenic (lose bases and can translocate)
Rules for DNA replication Semiconservative:1 old strand/1 new strand 5' to 3' for the strand being made Requires a RNA primer Requires a DNA template
Enzymes for DNA replication Helicase - Unwind DNA Topoisomerase - Cuts DNA to relax supercoiling Primase - Make RNA primers DNA Polymerase - Replicates DNA (both at once) and removes primers Ligase - Link Okazaki Fragments
Okazaki Fragments DNA replication chunks in the lagging strand
Prokaryotic DNA replication Only one origin - Polymerase travels apart 5 Polymerases
Prokaryotic DNA polymerase 1 and 3 DNA replication both have 3' to 5' exonuclease Pol 3 - High processivity - (main replicating enzyme no DNA repair) Pol 1- Low processivity - (some DNA repair)
Prokaryotic DNA polymerase 2,4 and 5 DNA repair
Eukaryotic DNA replication Multiple origins called replication bubbles Several DNA polymerases
Telomerase enzyme that elongates telomeres Has internal RNA template it uses to add new bases
hnRNA Preprocessed mRNA Before introns are excised
mi/si RNA Micro/Small interfering RNA Used to prevent translation and mark mRNA for breakdown
Transcription Regulation Primary regulation point for translation Promoter: Strong/weak affinity for RNA pol DNA binding proteins: Repressor/Enhancer of transcription
tRNA loading of AA Aminoacyl tRNA synthetase needs 2 ATP
Wobble base pairing Occurs when there is a wobble base at the 5' end of the anticodon fewer tRNAs are needed
Ribosomes Prok: 50s and 30s = 70s Prok are odd Euk: 60s and 40s =80s Euk are even
Translation E site: Exit site for empty tRNA P site: Growing Protein held here A site: New Amino Acid added here Small subunit binds Met first at P site - then Large subunit binds
Translation Termination Stop codon signals release factor to bind and separate last AA from tRNA
Translation Energy Cost tRNA loading: 2 ATP per tRNA Initiation: 1 ATP A site binding: 1 ATP per tRNA Translocation to P site: 1 ATP per tRNA Termination: 1 ATP Total ATP = 4x AA
Post Translation Modification Protein folding Covalent bond formation Protein cleavage (zymogens - Pro-/-ogen)
RNA Polymerases rmt Pol 1 - rRNA Pol 2 - mRNA Pol 3 - tRNA
Created by: mnmoon
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