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Chapter 16 - 17 (The Flow of Genetic Information ~ Gene Expression:…

- - - - Ribozymes: RNA enzymes that catalyze certain biochemical reactions, such as in the aminotransferase activity of the ribosome and in the cleavage (or ligation) of its own or another RNA.
        
        They are also observed to participate in viral replication.
      - The Functional and Evolutionary Importance of Introns
        ~ Alternative RNA splicing: a regulated process during gene expression that results in a single gene coding for multiple proteins.
        ~ Domains: a conserved part of a given protein sequence and tertiary structure that can evolve, function, and exist independently of the rest of the protein chain.
        
        Each domain forms a compact three-dimensional structure and often can be independently stable and folded.
  - - - The Structure and Function of Transfer RNA
        ~ Key: Translating a genetic message into a specific amino acid sequence is the fact that each tRNA molecule enables the translation of a given mRNA codon into a certain amino acid.
        
        ~ Anticodon: A sequence of three adjacent nucleotides located on one end of transfer RNA.
        
        It bounds to the complementary coding triplet of nucleotides in messenger RNA during translation phase of protein synthesis.
        
        ~ aminoacyl-tRNA synthetases: also called tRNA-ligase, is an enzyme that attaches the appropriate amino acid onto its tRNA.
        
        It does so by catalyzing the esterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA.
        
        ~ Wobble: flexible base pairing at a codon position.
      - The Structure and Function of Ribosomes
        ~ ribosomal RNAs (rRNA): a molecular component of a ribosome, the cell's essential protein factory.
        
        Strictly speaking, ribosomal RNA (rRNA) does not make proteins. It makes polypeptides (assemblies of amino acids) that go to make up proteins.
        
        ~ P site: the second binding site for tRNA in the ribosome.
        ~ A site: (aminoacyl), which is the first binding site in the ribosome
        ~ E site: (exit), the third.
    - - Ribosome Association and Initiation of Translation
        ~ Start Codons: AUG - signals for translation; establishes as a start codon for mRNA, reading frame.
        
        A small ribosomal subunit binds to both the mRNA and a specific initiator tRNA, which carries amino acid methionine.
        
        Bacteria: A small subunit can bind the 2 in either order; binds the mRNA at a specific RNA sequence, upstream of the AUG codon.
        
        Eukaryotes: a small subunit, the initiator tRNA already bound to the 5' cap of the mRNA and then moves/scans, downstream along the mRNA until it reaches the start codon.
      - Elongation of the Polypeptide Chain
        ~ This stage, amino acids at the C-terminus of the growing chain.
        
        each addition, elongation factors, occurs in the 3-step cycle.
        
        ~ takes less than a 10th of a second in bacteria and is repeated as each amino acid is added until the polypeptide is complete.
      - Termination of Translation
        
        ~ Stops until it reaches the A site.
        
        UAG, UAA, and UGA (written in 5' to 3') do not cde for amino acids but instead act as signals to stop translation.
    - - Protein Folding and Post-Translational Modification
        ~ During the synthesis of the polypeptide chain, it begins to coil and fold; forming a 3D molecule with secondary and tertiary structure.
        
        Enzymes may remove one or more amino acids from leading end.
      - Targeting Polypeptides to Specific Locations
        ~ Bound ribosomes make proteins secreted from the cell, such as insulin.
        ~ Signal Peptide: a short peptide (usually 16-30 amino acids long) present at the N-terminus of the majority of newly synthesized proteins that are destined.
        ~ Signal-recognition particle (SRP): an abundant, cytosolic, universally conserved ribonucleoprotein (protein-RNA complex) that recognizes and targets specific proteins to the endoplasmic reticulum in eukaryotes and the plasma membrane in prokaryotes.
  - - - RNA Polymerase Binding and Initiation of Transcription
        ~ Starting Point: the nuclceotide where mRNA polymerase actually begins synthesis of the mRNA.
        
        ~ Transcription Factors: a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.
        ~ Transcription Initation Complex: the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA).
        ~ TATA Box: a DNA sequence that indicates where a genetic sequence can be read and decoded. It is a type of promoter sequence, which specifies to other molecules where transcription begins.
      - Elongation of the RNA Strand
        
        ~ The enzymes add the nucleotides to the 3"' end of the growing RNA molecule as it continues along the double helix.
      - Termination of Transcription
        ~ Bacteria:
        
        Proceeds through a terminator sequnce in the DNA.
        
        causing polymerase to detach from the DNA and release the transcript.
        
        ~ Eukaryotes:
        
        RNA polymerase II transcribes a sequence on the DNA.
  - - - Substitutions
        ~ Nucleotide-pair substitutions: A type of mutation involving replacement or substitution of a single nucleotide base with another in DNA or RNA molecule. Supplement.
        
        This type of mutation occurring in noncoding sequences often does not result in an altered amino acid sequence during translation.
        
        ~ Silent Mutation: a change in the sequence of nucleotide bases that constitutes DNA, without a subsequent change in the amino acid or the function of the overall protein.
        ~ Missense Mutations: a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid.
        
        It is a type of nonsynonymous substitution.
        
        ~ Nonsense Mutation: A form of point mutation resulting in a nonsense codon that does not code for amino acid and leads to a protein product that is early truncated.
      - Insertions and Deletions
        ~ Frameshift Mutation: a genetic mutation caused by indels of a number of nucleotides in a DNA sequence that is not divisible by three.
        
        Due to the triplet nature of gene expression by codons, the insertion or deletion can change the reading frame, resulting in a completely different translation from the original.
  - - - Nutritional Mutants in Neurospora: Scientific Inquiry
        ~ Standford University; bread mold experiment by Beadle and Edward Tatum.
        
        The Product of Gene Expression: A Developing Story
        Colleagues - Adrian and Norman investigated a biochemical pathway for arginine synthesis.
        
        Final deduction: the function of gene is to dictate the production of a specific enzyme.
    - - Codons: Triplets of Nucleotides
        
        the smallest units of uniform length that can be code for all the amino acids.
        
        triplet code: the normal version of the genetic code in which a sequence of three nucleotides codes for the synthesis of a specific amino acid.
        
        ~ Template Strand: the term that refers to the strand used by DNA polymerase or RNA polymerase to attach complementary bases during DNA replication or RNA transcription, respectively; either molecule moves down the strand in the 3' to 5' direction, and at each subsequent base, it adds the complement of the current.
        
        Codons: a sequence of three DNA or RNA nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis.
        
        Coding Strand: the DNA strand whose base sequence corresponds to the base sequence of the RNA transcript produced
      - Cracking the Code
        ~ 1960s: Molecular biologists cracked the genetic code of life when a series f elegant experiments disclosed the amino acids translations of each of the RNA codons.
        
        Decifered by Marshall Nirenberg (1961), the discovery of the poly-U mRNA.
        
        ~ Reading Frame: a way of dividing the sequence of nucleotides in a nucleic acid (DNA or RNA) molecule into a set of consecutive, non-overlapping triplets.
      - Evolution of the Genetic Code
        
        ~ A language shared by all living things must have been operating very early in the history of life.
    - - ~ Translation: the process of translating the sequence of a messenger RNA (mRNA) molecule to a sequence of amino acids during protein synthesis.
        
        The genetic code describes the relationship between the sequence of base pairs in a gene and the corresponding amino acid sequence that it encodes.
        
        ~ Ribosome: A sphere-shaped structure within the cytoplasm of a cell that is composed of RNA and protein and is the site of protein synthesis.
      - ~ Primary Transcript: the single-stranded ribonucleic acid product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation.
- - - - ~ Semiconservative Model: relating to or being genetic replication in which a double-stranded molecule of nucleic acid separates into two single strands each of which serves as a template for the formation of a complementary strand that together with the template forms a complete molecule.
    - - Getting Started
        ~ Origins of Replication: a particular sequence in a genome at which replication is initiated.
        
        This can either involve the replication of DNA in living organisms such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses, such as double-stranded RNA viruses.
        
        ~ Replication Fork: the area where the replication of DNA will actually take place.
        
        There are two strands of DNA that are exposed once the double helix is opened.
        
        One strand is referred to as the leading strand, and the other strand is referred to as the lagging strand.
        
        ~ Helicases: An enzyme that utilizes energy from nucleoside triphosphate (e.g. ATP) hydrolysis in order to unwind the two annealed nucleic acid strands.
        ~ Single-Strand Binding Proteins: a protein found in E. Coli bacteria, that binds to single-stranded regions of deoxyribonucleic acid (DNA).
        
        Single-stranded DNA is produced during all aspects of DNA metabolism: replication, recombination, and repair.
        
        ~ Topoisomerase: A class of enzymes that break, swivel, and rejoin double-stranded DNA.
        
        Topoisomerase type I cuts one strand.
        
        Topoisomerase type II cuts both strands of the DNA to relax the coil and extend the DNA molecule.
      - Synthesizing a New DNA Strand
        ~ DNA cannot initiate the synthesis of a polynucleotide; they can only add DNA nucleiotides to the emd of an already existing chain that is base-paired with template strand.
        
        Primer: a short nucleic acid sequence that provides a starting point for DNA synthesis.
        
        Primase: an enzyme that synthesizes short RNA sequences called primers. These primers serve as a starting point for DNA synthesis.
        
        DNA Polymerase: an enzyme that synthesizes DNA molecules from deoxyribonucleotides, the building blocks of DNA.
      - Antiparallel Elongation
        ~ 2 ends of a DNA strand are different, giving each strand directionally.
        
        5' to 3' or/and 3' to 5'.
        
        ~ Leading Strand: it is replicated continuously in the 3' to 5'.
        
        DNA Pol III synthesize all leading strand.
        
        ~ Lagging Strand: replicated continuously in the 5' to 3'.
        
        synthesized discontinuouslly, as a series of fragments.
        
        ~ Okazaki Fragments: short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA replication.
      - The DNA Replication Complex
        
        Various proteins that participate in DNA replication actually form a single large complex.
        
        DNA replication complex may not move along the DNA; rather, the DNA may move through the complex during the replication process.
      - Proofreading and Repairing DNA
        ~ Initial pairing errors between incoming nucleiotides and those in the templates strand occur at a rate of 1 in 10^5 nucleiotides.
        
        polymerase removes the nucleiotide and then resume synthesis.
        
        ~ Mismatch Repair: A system within the cell for correcting errors in DNA that works by detecting and replacing bases in the DNA that are wrongly paired (mismatched bases).
        
        ~ Nulease: an enzyme that is responsible for breaking the bonds between nucleotides in nucleic acids. nucleotides, are the small subunits that make up large nucleic acids, such as DNA and RNA.
        ~ Nulceotide Excision Repair: a process that repairs damage to one strand of the DNA, particularly from UV irradiation, which distorts the DNA helix.
        
        The DNA flanking the damage site is cleaved to generate a single-stranded gap that is repaired by copying the undamaged strand to restore an intact helix.
  - - - ~ Nucleosomes: a fundamental unit of DNA packaging in eukaryotes, consisting of a segment of DNA wound in sequence around eight histone protein cores.
        
        This structure is often compared to thread wrapped around a spool.
        
        ~ 30-nm fiber: the beads-on-a-string structure in turn coils into a 30 nm diameter helical structure.
        ~ Looped domains (300-nm fiber): scaffold composed of proteins; rich in topoisomerase.
        ~ Metaphase chromosome: a compacted chromosome. (X)
  - - - Transformation: the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s).
    - - ~ Virus: a small infectious agent that replicates only inside the living cells of an organism.
        
        Viruses can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.
      - 1952, Martha Chase and Alfred Hershey performed experiments showing that DNA is the genetic material of a phage known as T2.
      - Additional Evidence That DNA is the Genetic Material
        ~ DNA: A polymer of nucleotides; a nitrogenous base, a pentose sugar (deoxyribose), and a phosphate group.
        
        ~ 1950: Chargaff reported that each base composition varies from one species to another.
        
        Chargaff's Rules
        
        DNA base composition varies between species.
        
        Each species has T and A bases, roughly equal %, as are those of G and C bases.
    - - Base Pairings
        ~ Purines and Pyrimidines
        
        Purines have 2 rings
        
        Guanine and Adenine
        
        Pyrimidines have 1 ring
        
        Thymine and Cytosine
        
        ~ Thymine - Adenine
        ~ Guanine - Cytosine