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Unit 3 - Coggle Diagram

- - - - His experiments lead to the later discovery of bacteriophage- a virus that infects bacteria (Hershey and Chase)
  - - - Polynucleotides: A polymer made up of many nucleotide monomers covalently bonded together
        
        Sugar-phosphate backbone: In a polynucleotide, the alternating chain of sugar to phosphate to which nitrogenous bases attach
        
        DNA (deoxyribonucleic acid): A double-stranded helical nucleic acid molecule the consitis of nucleotide Monomers adenine (A), cytosine (C), guanine (G), an thymine (T)
        
        In RNA, the sugar is a ribose, and instead of having thymine, it has uracil (U)
      - CHAPTER CONNECTION: Types of bonding and functional groups
  - - - C complements G and vise-a-versa, A complements T and vise-a-versa (IN DNA COMPLEMENTARY STRANDS)
  - - - CHAPTER ONE CONNECTION: Structure and function (shown in the double helix of DNA)
  - - - DNA Ligase then links the pieces (called Okazaki fragments) together into a single strand of DNA
  - - - There are 2 main stages of this process, transcription (the synthesis of RNA under the direction of DNA), and translation (the synthesis of protein under the direction of RNA)
  - - - Triplet code: a set of 3 nucleotides specify the amino acids for polypeptide chains
        
        the group of three nucleotides is called a codon
  - - - aka, each codon of mRNA is matched to an amino acid to make a specific amino acid sequence
  - - - Promoter: is a specific binding site for RNA polymerase that determines where transcription starts
        
        Terminator: a specific sequence of nucleotides in DNA that marks the end of a gene
  - - - RNA splicing is the removal of introns and joining of exons in eukaryotic RNA, forming and mRNA molecule (happens in the nucleus)
  - - - An anticodon is the sequence of nucleotide that is complementary to a codon triplet on mRNA
  - - - Ribosomal RNA (rRNA): A type of ribonucleic acid that works with proteins to make ribosomes
        
        A ribosome holds mRNA and tRNAs together and connects amino acids from the tRNAs to the growing polypeptide chain.
        
        CHAPTER 4.6 connection- Ribosomes make proteins for use in the cell and for export
  - - - The process of initiation brings together the mRNA, a tRNA bearing the first amino acid
      - STEP 1: an mRNA molecule binds to a ribosomal subunit and a start codon starts the process
        
        STEP 2- a large ribosomal subunit binds to a small subunit, creating a ribosome. The cite where this happens is called the P site. The vacant rRNA binding site is the A-site
  - - - 2- The polypeptide separates from the tRNA in the P site and attaches by a new peptide bond to he amino acid. One more amino acid is added through ribosome catalyzes
        
        3- Then, the P site tRNA leaves the ribosome, and the ribosome translocates the remaining tRNA from the A site to the P site, elongating the cell. This process continues until a stop codon reaches the A site
  - - - DNA doesn't participate directly in translation
  - - - Silent mutation: a mutation in a gene that changes a codon to one that codes of the same amino acid, resulting in an unchanged polypeptide
        
        Missense mutation: a change in the nucleotide sequences of a gene that alters the amino acid sequence of the resulting polypeptide. A codon is changed from encoding one amino acid to encoding a different amino acids
        
        Nonsense mutation: a change in the nucleotide sequence of a gene that converts and amino-acid-encoding codon to a stop codon. They result in shortened polypeptides
        
        Frameshift mutation: a change in the genetic material that involves the insertion/deletion of one or more nucleotides in a gene, resulting in a change in the triplet grouping
        
        Mutagens: A chemical or physical agent that interacts with DNA and causes mutations
  - - - They have two life cycles, the lytic cycle, and the lysogenic cycle
        
        Lytic cycle results in the breaking open of the host cell and releasing viruses into the host
        
        In the lysogenic cycle, viral DNA replication occurs without destroying the host cell.
        
        Prophage is phage DNA that has inserted by genetic recombination into the DNA of a bacterial chromosome
  - - - The genetic material of these viruses is RNA, which is replicated inside the host cell by special enzymes encoded by the virus. The viral genome (or its complement) serves as mRNA for the synthesis of viral proteins.
  - - - EX: HIV is the virus that causes AIDS
        
        Three processes contribute to the emergence of viral diseases: mutation, contact among species, and spread from isolated populations.
  - - - Retroviruses are RNA viruses that reproduce by means of a DNA molecule (the reverse the usual DNA → RNA flow of genetic information)
        
        They have an enzyme called reverse transcriptase, which catalyzes reverse transcription
  - - - They have no nucleic acid
  - - - Transduction: The transfer of bacterial genes from one bacterial cell to another by a phage
        
        Conjugation: The union of two bacterial cells of protist cells and the transfer of DNA between the two cells
  - - - Plasmid: a small ring of independently replicating DNA separate from the main chromosome(s). They are found in prokaryotes and yeasts
        
        R plasmid: A bacterial plasmid that carries genes for enzymes that destroy particular antibodies, thus making the bacterium resistant to the antibodies
- - - - He had many theories to explain genetics, but we now know that there are many issues with his theory like: The reproductive cells are not composed of particles from somatic (body) cells, and changes in somatic cells do not influence eggs and sperm
  - - - Genetics is the scientific study of heredity, and modern genetics began with a study on garden peas conducted by Gregor Mendel
        
        He discovered that there are characters (alleles) that are the heritable features that vary among individuals (ex. Flower color)
        
        Variants in character are called traits
        
        True-breeding varieties only produce the same variety as the parent plants
        
        Hybrids are offspring of two different varieties
        
        Genetic crossing is cross-fertilizing species to see what their offspring look like
        
        P= Parental generation
        
        F1= first generation, F2= second generation and so on
  - - - Theory 1: There are alternative versions of genes that account for variation in inherited characters. These alternative versions are called alleles
      - Theory 2: For each character, an organism inherits two alleles of a gene on from each parent
        
        i) An organism is homozygous is the two genes are identical
        ii) An organism is heterozygous is the two genes are different
      - Theory 3: If the two alleles of an inherited pair differ, then the one that determines the organism appearance is called the dominant allele. The one that has no noticeable effect on appearance is called the recessive allele
      - Theory 4: A sperm or egg carries only one allele for each inherited character because alleles segregation from each other during the production of gametes (Law of Segregation)
    - - Phenotype: The expressed traits of an organism.
      - Genotype: The genetic makeup of an organism
  - - - Two alleles can found on the same part of homologous chromosomes by be either dominant or recessive ( Capital or Lowercase)
  - - - Mendel’s Law of Independent Assortment: when gametes form during meiosis, each pair of alleles for a particular character segregate independently of each other
  - - - The test can be used to determine the unknown genotype
  - - - Rule of addition: the probability that an event can occur in two or more alternative ways is the sum of the separate probabilities of the different ways
  - - - It can be used to determine genotypes of mating that have already occurred
  - - - There are many recessive disorders that humans can have that range from relatively mild, to fatal. Most ppl who have recessive disorders are born to “normal” parents who are both heterozygotes
        
        This means that they are carriers (heterozygous for a recessively inherited disorder and who therefore doesn’t show symptoms of that disorder but can pass it to offspring)
        
        There are also multiple human disorders that are caused by dominant alleles like being polydactyly, dwarfism, and Huntington's disease
  - - - Fetal Testing is genetic testing before birth and it requires fetal cells
        
        Amniocentesis is performs in weeks 14-16 of a pregnancy and a needle through the abdomen and into the uterus to gather amniotic fluid to later culture and test
        
        Chorionic villus sampling (CVS) is when a physician extracts a sample of chorionic villus tissue from the placenta by inserted through the vagina. It is later karyotypes and tested. This is faster than Amniocentesis
        
        Both of these are invasive and hold risks such as miscarriage, premature birth, and maternal bleeding
  - - - Incomplete dominance: the phenotype of a heterozygote is a mix of the two types of homozygotes
  - - - EX: the ABO blood group involves three alleles of a single gene
        
        Matching compatible blood types is critical for safe blood transfusions. If a donor’s blood cells have a carbohydrate that is foreign to the recipient, then the immune system produces antibodies
  - - - EX: Sickle-cell anemia
        
        Sickle-cell is codominant: Codominance means that both traits are expressed; a carrier for the sickle-cell allele produces both normal and abnormal hemoglobin.
  - - - CHAPTER ONE CONNECTION: INTERACTION- a polygenic trait can result from the interactions of many smaller genes
  - - - Many characters result from a combination of heredity and environment
        
        CHAPTER ONE CONNECTION: life responds to environment
  - - - CHAPTER EIGHT CONNECTION- Cell division (mitosis/ meiosis)
  - - - wild-type is the version of a charter that most commonly occurs in nature
        
        mutant is the version of a character that occurs less frequently in nature than the wild-type
        
        Recombinant frequency: the percentage of recombinant offspring
  - - - Linkage map: An ordered list of the realtive locations of genes along a chromosome, as determined by recombination frequencies
  - - - Sex Chromosomes: a chromosome that determines whether an individual is male or female (X and Y in humans)
  - - - X-linked genes: display unique pattern of inheritance b/c males only have on X where females have 2
- - - - however, when the term is used today, they are usually referring to DNA technology, modern laboratory techniques for studying and manipulating genetic material
        
        Recombinant DNA is formed when scientists combine pieces of DNA from two different sources—often different species
        
        Today, recombinant DNA technology is widely used for genetic engineering, the direct manipulation of genes for practical purposes.
        
        To manipulate genes in the laboratory, biologists often use bacterial plasmids
        
        because plasmids are easily manipulated to carry virtually any genes, they are key tools for DNA cloning, the production of many identical copies of a target segment of DNA.
        
        In molecular biology, a vector is a piece of DNA that is used to move genes from one cell to another
        
        When DNA cloning involves a gene-carrying segment of DNA, it is called gene cloning
  - - - after a restriction enzyme binds to its restriction site, it cuts both strands of the DNA at precise points within the sequence, creating pieces of DNA called restriction fragments.
  - - - The probe molecules bind to and label DNA only from the cells containing the gene of interest, which has a complementary DNA sequence.
  - - - 2- Single-stranded DNA transcripts are made from the mRNA using reverse transcriptase
        
        3 Another enzyme is added to break down the mRNA,
        
        4- DNA polymerase
        
        The DNA that results is called complementary DNA (cDNA), nd it represents only the subset of genes that had been transcribed into mRNA in the starting cells
  - - - Gene cloning exactly copies a gene, while the CRISPR-Cas9 system modifies the gene.
        
        Cas9 is guided with an RNA molecule. The result is that Cas9 cuts both strands of an RNA sequence that is complementary to the guide RNA.
  - - - Mammals as provide the cells of choice for making some gene products as many proteins that mammalian cells secrets are glycoproteins and only mammalian cells can attach the sugars correctly
  - - - Treating diseases: Two products made using recombinant cells are human insulin and human growth hormone. Genetic engineering has allowed scientists to make lab-grown insulin and growth hormone
        
        Diagnosing: through DNA analysis, many inherited diseases can be identified in an individual before the onset of symptoms, even before birth
        
        Preventing: DNA technology is helping medical researchers develop vaccines
        
        A vaccine is a harmless variant (mutant) or derivative of a pathogen used to stimulate the immune system to mount a lasting defense against that pathogen, thereby preventing disease
  - - - If a gene is transplanted from one organism into another, typically of another species, the organism is called transgenic
        
        GMOS are used to make food more nutrient dense, more pest-resistant, and more
        
        A common vector used to introduce new genes into plant cells is a plasmid from the soil bacterium
  - - - Scientists and the public need to weigh the possible benefits of GMOs versus the risks on a case-by-case basis
        
        the best scenario would be to proceed with caution, basing our decisions on sound scientific information rather than on either irrational fear or blind optimism.
        
        UNIT ONE CONNECTION: the public plays a role in scientific research/ findings
  - - - Bone marrow cells are a good target for gene therapy treatment as they multiply throughout a person’s life and contain stem cells that give rise to different kinds of blood cells.
  - - - DNA profiling, the analysis of DNA samples to determine whether they came from the same individual.
        
        If two samples have an identical match, it is safe to say the samples came from the same person
  - - - PCR is a repeated three-step cycle that acts as a chain reaction that doubles the population of identical DNA molecules during each round
        
        The key to amplifying one particular segment of DNA and no others is the use of primers
        
        Primers: chemically synthesized single-stranded DNA molecules with sequences that are complementary to sequences at each end of the target sequence
  - - - negatively charged phosphate groups of the DNA are attracted to the positive pole; longer fragments are more restricted by the tangle of fibers in the gel than are shorter fragments.
  - - - The repetitive DNA used in DNA profiles consists of short sequences repeated many times in a row; such a series of repeats is called a short tandem repeat (STR)
        
        STR analysis is a method of DNA profiling that compares the lengths of STR sequences at specific sites in the genome.
  - - - A DNA profile can prove with near certainty that a sample of DNA does or does not come from a particular individual
  - - - However, researchers are also able to directly determine the sequences of DNA samples.
        
        “next-generation sequencing” technique Third-generation sequencing works with a single long DNA molecule
        
        Third-generation sequencing works with a single long DNA molecule
  - - - larger genomes don't always coordinate to more genes/ a more advanced organism
  - - - The potential benefits of having a complete map of the human genome are enormous. For instance, hundreds of disease-associated genes have been identified
  - - - this method is is fast and relatively inexpensive, but it is just one of several sequencing methods now used by researchers
  - - - Proteomics: the study of whole sets of proteins and their interactions
        
        this is beneficial because it is proteins that carry out the actual work of the cell, and one gene may produce multiple proteins.
  - - - Similarities in gene sequences correlate with evolutionary relatedness; greater genetic similarities reflect a more recent shared ancestry.
- - - - Gene expression: the process where gene info flows from genes to proteins (the flow of genetic info from the genotype to the phenotype)
        
        Promoter: control sequence is a promoter where the transcription enzyme, RNA polymerase, attaches and initiates transcription
        
        Operator: determines whether RNA polymerase can attach to the promoter and start transcribing the genes.
        
        Operon: A unit of genetic regulation common prokaryotes; a cluster of genes with related functions, along with the promoter and operator
        
        Repressor: a protein that turns off transcription
        
        Regulatory gene: codes for a protein that controls transcription of another gene or group of genes
        
        Activators (trp): a proteins switched on a gene or group of genes
      - UNIT ONE CONNECTION: response to environment
  - - - Histones: A small protein molecule important in DNA packing in the eukaryotic chromosome
        
        Epigenetic inheritance: inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome
        
        X-chromosome inactivation: in female mammals the inactivation of one X chromosome in each somatic cell. The inactive X-chrom. then condenses into a compact object called a Barr body
  - - - Step one is to initiate gene transcription in the binding of activator proteins to DNA control sequences called enhancers
        
        Next, a DNA-bending protein twists the DNA strand, bringing the bound activators closer to the promoter
        
        Once the DNA is bent, the bound activators interact with other transcription factor proteins which then bind to a gene's promoter
  - - - Alternative RNA splicing: multiple mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns
  - - - TWO: Initiation of Translation
        
        THREE: Protein Processing
        
        After translation is complete, eukaryotic polypeptides often require alterations before they become functional
        
        The process of translating an mRNA into a polypeptide also offers opportunities for regulation
      - Enzymes in the cytoplasm break down molecules of mRNA, and the timing of this event is an important factor regulating the amounts of various proteins that are produced in the cell
  - - - siRNA: a small, single-stranded RNA molecule that associates with one+ proteins in a complex that can degrade/ prevent translation
  - - - We can test this on fruit flies by putting a homeotic gene for a leg where a head should be grown, and in there, the leg will replace the head or grow alongside it
  - - - These can be studied using a DNA microarray that consists of tiny amounts of different single-stranded DNA fragments. Each fragment is attached to a well in a glass slide that are arranged in a tightly spaced array. Ideally, these fragments represent all the genes in the genome of an organism.
        
        We can learn which genes are active (transcribed) in a particular sample of cells
  - - - Signal transduction pathways are crucial to many cellular functions
  - - - The joining of yeast cells is like "sex" because the process results in the creation of a diploid cell that is a genetic blend of two parental haploid cells.
        
        CHAPTER FOUR CONNECTION: haploid versus diploid cells
  - - - Totipotent cells can give rise to all of the different types of cells w/in an organism
        
        an organism produced through asexual reproduction from a single parent is called a clone and plant cloning is used very often in agriculture
        
        researchers wondered if artificial cloning is possible in animals, and a good indication that differentiation doesn't need to impair an animals cell's genetic power is regeneration (the regrowth of body parts from pieces of an organism)
  - - - Dolly the sheep was the first cloned mammal and it hundreds of failures to achieve a single success with Dolly. Such experimentation with humans raises ethical questions.
  - - - Because adult stem cells are farther along the road to differentiation than ES cells, they can give rise to only a few related types of cells
  - - - A proto-oncogene is a normal gen that through mutation can be converted to a cancer-causing gene
        
        A tumor suppressor gene is a gene whose product inhibits cell division, thereby preventing uncontrollable cell growth
  - - - mutant tumor-suppressor gene encodes a defective protein unable to function in a pathway that normally inhibits cell division.
  - - - Tobacco is one of the most common carcinogens in america