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DNA (Molecular Basis of Inheritance (Key Proteins (Getting started…

- - - - A-T ; 2 Hydrogen bonds
      - C-G ; 3 HYdrogen bonds
      - Adenine and Guanine are purines with two organic rings
      - Cytosine with Thymine are pyridines with singe organic ring
      - Equal amounts of each base complementary to the match
    - - Double-stranded by Hydrogen bonds b/w bases
      - Helical
      - Sugar-phosphate backbones ; Phosphate facing out and nitrogenous bases facing in
        
        Anti-parallel ; parallel with different orientations
    - - Genes are parts of chromosomes and chromosomes are made of DNA and protein
      - DNA was conclude to be the genetic material by testing bacteria infecting viruses, bacteriophages
      - information from DNA directs biochemical anatomical, physiological, and some behavioral traits
      - By transformation , external DNA assimilation changed the genes
      - DNA: polymer of nucleotides ; Adenine, guanine, Cytosine, and Thymine
      - Chargaff's rules
        
        DNA bases vary from specie
        
        A T bases equal and C G bases are equal
  - - - Helicase : untwist the double helix at replication forks and separating the two strands to become available
      - Single-strand binding proteins: bind to unpaired DNA strands
      - Topoismoerase: the untwisting at the fork causes strain and this enzyme breaks, swivels, and rejoins DNA strands
      - Replication of chromosomal DNA begins at origins of replication (short stretches of DNA)
        Protein separates the strands to replicate.
      - At end of replication bubble, there’s a replication fork, y shaped region parental strands are unwound.
    - - Primase starts a complementary RNA. Enzyme DNA Polymerases catalyze synthesis by adding nucleotides.
      - Each nucleotide is made of a sugar attached to a base and three phosphate groups. (d(deoxyribise)ATP) --> dATP
      - The initial nucleotide made in replication is a short strand of RNA. This RNA is a primer synthesized by the enzyme primase.
      - DNA pol I: remove RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides adde to 3' end of adjacent fragment
      - DNA pol II: synthesized new DNA strand by adding nucleotides to RNA primer or pre-existing DNA strand
    - - Leading strand: the new DNA strand along the template strand following the 5’  3’ direction.
      - Lagging strand: goes opposite of leading in segments and make the other template strand.
        Strands are called Okazaki fragments
      - DNA polymerase can only add nucleotides to the 3’ strand never 5’.
      - DNA ligase joins the sugar-phosphate backbone of all Okazaki fragments into one DNA strand
    - - DNA polymerase removes wrong nucleotide and proofreads while replication.
      - Nuclease cuts a segment of the damaged strand and polymerase and DNA ligase fills the spot.
    - - telomerase catalyzes lengthening of telomeres, restoring original length
      - Telomeres are nucleotide sequences of multiple repetitions .
        
        Protective functions; 1. prevent staggered ends from activating the systems for monitoring DNA damage; 2. buffer zone that provides protection from gene shortening
  - - - Deoxyribonucleic acid
      - nucleic acid molecule,; double-helix with strands of nucleotide monomers, A T C and G, bases. Able to be replicated to determine inheritance .
      - in nucleus entwined with proteins
      - In coiled form it is chromatin
    - - complex of DNA and protein that makes eukaryotic chromosomes, that fits into the nucleus
      - When not dividing chromatin is dispersed as very long thin fibers
      - Unwound DNA
      - Found throughout interphase
      - DNA IS being used for macromolecule synthesis
    - - cellular structure of one DNA molecule with protein molecules. a cell can have multiple chromosomes line up in the nucleus.
      - Tightly packed DNA
      - found only during cell division
      - DNA not being used for macromolecule synthesis
- - - - First stage in the central dogma
    - - elongation: polymerase moved downstream unwinding DNA and elongating RNA transcript; DNA strands reform double helix
      - termination: RNA transcript released and polymerase detaches
      - initiation: RNA polymerase binds to promoter and unwinds DNA; polymerase starts RNA synthesis at start point on template strand
    - - in the nucleus; mRNA transported to cytoplasm
    - - mRNA copied from DNA by unzipping the strand using the RNA polymerase and entering the complementary RNA strand.
      - as one side is transcribed, the nucleotides will be paired to make pre-mRNA
      - sequences called introns are removed and eons are spliced together
      - mRNA leaves nucleus to translate in ribosomes
  - - - within cell nucleus
    - - after transcription and before translation
    - - split genes and RNA splicing
        
        noncoding regions are introns and coding regions are eons which are expressed
        
        pre-mRNA splicing done spliceosome
        
        RNA splicing: RNA removed and remaining reconnected
        
        spliceosome catalyzes splicing reaction
      - Ribozymes
        
        ribozymes, RNA molecules that works as enzymes
        
        intron RNA functions as enzyme and does its own excision
        
        3 properties enable top be enzyme
        
        some bases have functional groups that work in catalysis
        
        ability to hydrogen bond adds specifitivity to catalytic activity
        
        RNA is single strand and pair
      - alteration fo mRNA ends
        
        5'. end modified by 5' cap
        
        at 3' end, enzyme adds A nucleotides making a poly-A tail
        
        help protect degradation by hydrolytic enzymes
        
        help ribosomes attach to 5' end in cytoplasm
        
        facilitate export of mRNA
  - - - proteins synthesized from mRNA by ribosomes that read from a codon (triplet code)
      - transfer RNAs guided by ribosome transfer amino acids from cytoplasms to amino acids in poly[peptide chain
      - ribosome adds amino acids from tRNA to chain
      - tRNA has 2 recognitions
        
        once it binds to codon, carries amino acid to ribosome
        the matching is done by the enzyme aminoacyl-tRNA synthetases
        
        pairing of tRNA anticodon with mRNA codon some can bind to more than one codon by versatile called a wobble due to the bases uracil binding to A or G
      - Ribosomes
        
        large and small subunit made of protein and ribosomal RNAs
        made in nucleus
        rRNA transcribed and exported to cytoplasm
        
        3 binding sites
        
        P site; holds tRNA carrying growing chain
        
        A site; holds tRNA carrying next amino acid to be added to chain
        
        E site; tRNA and mRNA close to be added to carboxyl end
        
        ribosomal DNA is responsible for structure and function of ribosome
      - 3 stages
        
        elongation; a. codon recognition; codon pairs w/ anticodon; b. peptide bond formation; c. translocation
        
        termination: ribosome reaches stop codon; hydrolyze polypeptide and tRNA in P site; 2 subunits dissacociate
        
        initiation: starting codon starts translation; ribosomal units bind to mRNA and tRNA ; large subunit attaches to make translation initiation complex; initiator tRNA sits in P site and A site is vacant
      - completing and targeting functional protein
        
        protein folding and modifications
        
        targeting polypeptides to specific locations
    - - In ribosomes ; complexes that facilitate linking of amino acids into polypeptide chains.
    - - after RNA processing