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Chapter 10, Genes control phenotypic traits through the expression of…

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    - - 20 AAs
  - - - Viruses that infect bacteria
  - - - Nucleic acids
      - Monomers
        
        Polymers
        
        Polynucleotides
        
        2 types
        
        DNA (deoxiribose)
        
        Adenine (A)
        
        Thymine (T)
        
        1 more item...
        
        Double Helix
        
        Structure and function
        
        DNA ligase
        
        Enzyme that links or ligates, into a single DNA strand
        
        RNA (ribose)
        
        Adenine (A)
        
        Uracil (U)
        
        1 more item...
        
        Nucleotides
        
        Sugar-phosphate backbone
- - - - DNA polymerases
        
        The enzymes that link DNA nucleotides to a growing daughter strand
      - Technique by which a specific segment of a DNA molecule can be targeted and quickly amplified in the laboratory
        
        Primers
        
        Chemically synthesized single-stranded DNA molecules with sequences that are complementary to sequences at each end of the target sequence
    - - The scientific analysis of evidence for crime scene investigations and other legal proceedings
    - - A method that separates macromolecules on the basis of size, electrical charge, or other physical properties
    - - Short tandem repeat (STR)
        
        STR analysis
        
        Method of DNA profiling that compares the lengths of STR sequences at specific sites in the genome
        
        The repetitive DNA used in DNA profiles consists of short sequences repeated many timesin a row
      - Consists of nucleotide sequences that are present in multiple copies in the genome
  - - - Chromosome structure and chemical modifications can affect a gene expression
        
        Differentiation
        
        Cells must become specialized in structure and function , with each step type of cell fulfilling a distinct role.
        
        Chemical modifications and epigenetic inheritance
        
        Epigenetic inheritance
        
        Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
        
        X inactivation
        
        X chromosome inactivation
        
        Initiated early in embryonic development, when one of the two X chromosomes in each cell is inactivated at random
        
        Barr body
        
        The inactive X in each cell of a female condenses into a compact object
        
        DNA packing
        
        Nucleosome
        
        Histones + DNA
        
        Histones
        
        A crucil aspect of DNA packing is the association of the DNA with this small proteins
      - Eukaryotes usually use activators
        
        Transcription factors
        
        Eukaryotic RNA polymerase requires the assistance of proteins
        
        Enhancers
        
        The first step in iniating gene transcription is the binding of activator proteins to DNA control sequences
        
        Most genes off
      - Alternative RNA splicing
        
        An organism can produce more than one type of polypeptide from a single gene
        
        Breakdown of mRNA
        
        Regulatory proteins for translation
        
        Protein processing
      - Junk DNA ----> Functional RNAs
        
        micro RNAs (miRNAs)
        
        small interfering RNAs (siRNAs)
        
        RNA interference (RNAi)
        
        The blocking of gene expression by siRNAs
        
        RNA interfere of translation
        
        Formation of centromere
        
        Methylation for gamete formation
        
        Degrade complementing mRNAs
        
        Block translation of partially complementing mRNAs
      - Animal development controlled by series of RNAs and proteins
        
        Homeotic genes
        
        Control other genes in body part formation
        
        regulates other genes to produce body parts
      - Researchers can monitor the expression of specific genes
        
        Nucleic acid hybridization
        
        The base pairing of one strand of a nucleic acis to a complementary sequence on another strand
        
        DNA microarray
        
        Consists of tiny amounts of a large number of different single-stranded DNA fragments
      - Signal transduction pathways convert messages received at the cell surface to responses within the cell
    - - Plants
        
        Clone
        
        an organism produced through asexual reproduction from a single parent
        
        Topitotent
        
        Capable of producing every kind of specialized cell in the organism
        
        Regeneration
        
        The regrowth of lost body parts
      - Animals
        
        Nuclear transplantation
        
        Replacinf the nucleus of an egg cell or zygote with a nucleus from an injected adult somatic cell
        
        Reproductive cloning
        
        If the animal being cloned is a mammal, the blastocyst is then implanted into the uterus of a surrogate mother. The cloned animal will be genetically identical to the donor of the nucleus
      - Therapeutic cloning can produce stem cells with great medical potential
        
        Therapeutic cloning
        
        Adult stem cell
        
        Embryonic stem cells (ES cells)
    - - Oncogene
        
        Cause cancer when present in a single copy in the cell
      - Photo-oncogene
        
        A normal cellular gene that has the potential to become an oncogene
      - Tumor-suppressor genes
        
        The development of a malignant tumor is paralleled by a gradual accumulation of mutations that convert photo-oncogenes and knock out tumor-suppressor normal products inhibit cell division
      - Carcinogens
        
        Agents that alter DNA and make cells cancerous
  - - - A harmaless variant (mutant) or derivate of a pathogen that is used to stimulate the immune system to mout a lasting defense against that pathogen.
    - - If a gene is trnaplanted from one organism into another, typically of another species, the recombinant organism would be called transgenic organism
    - - Alteration of a diseased individual's genes for therapeutic purposes
  - - - The application of computational methods to the storage and analysis of biological data
      - Proteomics
        
        A systematic study of the full protein sets (proteomes) encoded by genomes
    - - The study of complete sets of genes (genomes)
      - Human genome project (HGP)
        
        A massive publically funded scientific endeavor to determine thae nucleotide sequence of all DNA in the human genome and indentify the location and sequence of every gene
      - Whole genome shotgun
        
        Cloning and sequencing of DNA fragments from randomly cut DNA derives from the entire genome
  - - - DNA technology
        
        GMOS
        
        Recombinant DNA
        
        Comes from multiple different sources
        
        Genetic engineering
        
        Genetically modified organisms
        
        Organisms that have acquired one or more genes by artifitial means
        
        Manipulation of DNA
      - The manipulation of organisns or their components to make useful products
    - - Copies of a particular gene
      - Clone
    - - Bacterial plasmid
        
        Vector
        
        Delivery mechanisms
      - DNA cloning
      - DNA ligase
        
        connects sugar phosphate backbones
    - - Restriction enzyme cuts sugar-phosphate backbones
      - DNA fragments added from another molecule cut by the same enzyme. Base pairing occurs
      - Restriction site
        
        Biologists identified hundreds of different restriction enzymes, each of which recognizes a particular short DNA sequence
    - - Molecule that is used to find a specific gene of other mucleotide sequence within a mass of DNA
- - - - HIV
        
        Retrovirus
        
        An RNA virus that reproduces by means of a DNA molecule (replication)
        
        They reverse the usual DNA ---> RNA flow of genetic information
        
        Reverse transcriptase
        
        Catalyzes reverse transcription: the synthesis of DNA on an RNA template
        
        Complementary DNA (cDNA)
        
        represent only the subset of genes that had been transcribed into mRNA in the starting cells.
        
        Helps in the making of genes for cloning
      - Aids
  - - - Viral DNA replication occurs without destroying the host cell
      - Prophage
        
        Viral DNA is inserted into the bacterial chromosome. Once inserted, the phage DNA is referred to a prophageand most of its genes are inactives
  - - - The transfer of bacterial genes by a phage
      - Conjugation
        
        Physical union of two bacterial cellsand the DNA transfer between them
        
        F factor
        
        Plasmid
        
        R plasmids
        
        Plasmids that carry genes that can affect the survival of the cell
        
        A small circular DNA molecule
        
        F for fertility
- - - - Missense mutation
        
        Results in an amino acid substitution
      - Nonsense mutation
        
        Substitutes a stop codon for an amino acid
      - Silent mutation
        
        Has no effect on the protein sequence
      - Frameshift mutation
        
        Insertion
        
        May result in a shift in the reading frame or insertion of a stop codon
        
        Deletion
      - Any change in the genetic information of a cell or virus
      - Mutagens
        
        Mutations that are caused by physical or chemical agents
- - - - Genetic code
  - - - Terminator
        
        Signals the end of the gene
      - It's a nucleotide sequence that acts as a binding site for RNA polymerase and determinates where trancription starts.
      - RNA polymerase adds RNA nucleotides until it reaches a sequence of DNA bases called the terminator
    - - Operator
        
        DNA control sequence
        
        Operon
        
        Repressor
        
        Activator
        
        Cluster of genes with related functions, along with the control sequences
        
        They turn off when lactose is absent
      - The Iac operon
  - - - The newly formed RNA strand grows. As synthesis continues. the growing RNA molecule peels away from its DNA template, allowing the two separated DNA strands to come back together in the region already transcribed.
      - Termination
        
        When RNA polymerase reaches the terminator DNA (which signals the end of the gene), the polymerase molecule detaches from the newly made RNA strand and the gene
        
        Messenger RNA (mRNA)
        
        Encodes amino acid sequences
        
        Introns
        
        Most genes of plants and animals include internal noncoding regions (intervening sequences)
        
        Exons
        
        The coding regions (the parts of genes that are expressed)
        
        RNA splicing
        
        Before the RNA leaves the nucleus, the introns are removed, and the exons are joined to produce and mRNA molecule with a continuous coding sequence
- - - - Special triplet of bases. It's a complementary to a codon triplet on mRNA
  - - - A ribosome consists of two subunits, a large sub unit and a small sub unit, each made up of proteins and a kind of RNA
  - - - Start codon
        
        ...where tranlation is to begin on the mRNA molecule. The initiator tRNA carries the amino acid methionine (Met); its anticodon, UAC, base pairs with the start codon, AUG
    - - P site
        
        Holds the growing polypeptide. Amino acids are added one by one to the growing chain of amino acids
    - - The anticodon of an incoming tRNA molecule, carrying its amino acid, pairs with the mRNA codon in the A site of the ribosome
      - The polypeptide separated from the tRNA in the P site and attaches by a new peptide bond to the amino acid carried by the tRNA in the A site. The ribosome catalyzes the formation of the peptide bond, adding an amino acid to the growing polypeptide chain, which snakes out of the ribosome via a tunnel through the molecule
      - The P site tRNA leaves the ribosome, and the ribosome translocates the remaining tRNA from the A site to the P site. The codon and anticodon remain hydrogen-bonded, and the mRNA and tRNA move as a unit. This brings into the A site the next mRNA codon to be translated
      - Elongation continues until a...
        
        Stop codon
        
        ...reaches the ribosome's A site
      - Termination
        
        The completed polypeptide is freed from the last tRNA, and the ribosome splits back into its separate subunits