BCOR 101 Week 1 Reading Notes
BCOR 101 Week 1 Reading Notes BCOR 101
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Date Created: 01/23/16
BCOR 101- CHAPTER 1: GENETICS ANALYSIS TEXTBOOK NOTES CHAPTER 1: THE MOLECULAR BASIS OF HEREDITY, VARIATION, AND EVOLUTION SECTION 1.1: MODERN GENETICS IS IN ITS SECOND CENTURY Three botanists: Carl Correns, Hugo de Vries, Erich von Tschermak- reached strikingly similar conclusions about the transmission of hereditary traits in plants o Results mirrored those of Mendel but they actually rediscovered an explanation of hereditary transmission published by Mendel 34 years prior; their announcement of these refindings allowed for the start of modern genetics Testing, verification, and expanding on the explanation of hereditary began immediately by biologists William Bateson read a publication about the appearance of the hereditary disease alkaptonuria in multiple members of unrelated families by Archibald Garrod o Bateson with the help of Garrod published the first documented source of a human hereditary disorder Walter Sutton and Theodore Boveri- used microscopy to observe chromosome movement during cell division in reproductive cells (gametes) o Saw the patterns of chromosome movement mirrored the transmission of the Mendelian hereditary units o Implied that hereditary units (genes) posited by Mendel are located on chromosomes Each chromosome carries many genes; homologs carry genes for the same traits in the same order on each member of the pair Bacteria and archaea- single celled organisms that do not have a true nucleus; usually have a singular circular chromosome Eukaryotes- nucleus which permanently contains multiple sets of chromosomes; almost most eukaryotes have haploid and diploid stages in their life o Ex: sperm and eggs are haploid and have one copy of each chromosome pair, eukaryotic genomes contains two copies of each gene (homologous pair) in diploid state o Plants and animals also contain DNA in mitochondria and chloroplasts (plants only) Present by the dozens in each cell and each one carries one or more copies of its own chromosome Produce proteins that work with protein produced by nuclear genes to perform essential functions in cells- ATP production in mitochondria which is principal energy source for cellular energy; chloroplasts are necessary for photosynthesis Transmitted in cytoplasm during cell division Have evolutionary history; descended from ancient parasitic bacterial invasion of eukaryotic cells Complete set of nuclear chromosomes transmitted during the cell-division process of mitosis which produce genetically identical cells; meiosis creates sexual cells which are haploid in diploid organisms Gene was seen as the physical unit of heredity and revealed relationships between the observable traits of the organism (phenotype) and the genetic constitution of the organism (genotype) 1914, Oswald Avery, Colin MacLeod, and Maclyn McCarthy- identified DNA as the hereditary material which began the “molecular era” in genetics th o Spanned he second half of the 20 century and lasts until today, began with the effort to discover the molecular structure of DNA James Watson, Francis Crick, Maurice Wilkins, and Rosalind Franklin- discovered the double helix structure of DNA in 1953 In 1958, common mechanism of DNA replication was found 1960s- basic mechanisms of DNA transcription and mRNA translation were laid out, and genetic code by which mRNA is translated into proteins was deciphered Last Universal Common Ancestor- all life is descended from a common ancestor o Divided into three domains: Bacteria, Eukarya, Archaea o Derived from model created by Carl Woese and colleagues in mid 1970s o Used morphology and molecular sequences to determine phylogenetic relationships between existing organisms and therefore trace the evolution of life Used the sequence of ribosomal RNA (rRNA) as the basis for comparison Species which are members of the same evolutionary lineage will share certain rRNA sequence changes that are not part of the species outside of the lineage Recognition of DNA as the hereditary material which stores and conveys genetic material, although certain viruses use RNA as hereditary material DNA has a double helix stranded structure DNA replication contains two steps: transcription and translation Three branches of modern genetics: transmission genetics, evolutionary genetics, and molecular genetics o Not rigidly differentiated and there is substantial cross-communication among all of them Vocab words: genes, chromosomes, homologous pairs, homologs, haploid, nucleoid, diploid, polyploidy, mitochondria, chloroplasts, cytoplasmic inheritance, mitosis, meiosis, gametes, phenotype, genotype, alleles, genomes, LUCA, Eukarya, Bacteria, Archaea, deoxyribose nucleic acid (DNA), ribonucleic acid (RNA), DNA double helix, DNA duplex, DNA replication, transcription, messenger RNA (mRNA), translation, ribosomes, transmission genetics, Mendelian genetics, Evolutionary genetics, Molecular genetics, (defined at the end of the notes) SECTION 1.2: THE STRUCTURE OF DNA SUGGESTS A MECHANISM FOR REPLICATION o Hereditary transmission is the process of dispersing genetic information from parents to offspring o Completed by the generation of reproductive cells in males and females, followed by the union of sperm and egg or pollen or spores at fertilization and then the development of an organism o Watson and Crick discovered the molecular structure of DNA as a double helix composed of two strands of DNA with an invariant sugar-phosphate backbone on the outside and nucleotide bases arrayed in complementary base pairs which orient themselves toward the center of the molecule o Weren’t the ones actively engaged in laboratory research; Rosalind Franklin was one of their principal sources Franklin used an early form of x-ray diffraction imagery to examine the crystal structure of DNA The pattern diffracted by the x-rays created a double helix o Watson and Crick also used research by Chargaff who had determined the percentages of the four DNA nucleotide bases and discovered that the percentages of adenosine and thymine are equal and cytosine and guanine are equal (all approximately) o Each strand of the double helix is composed of nucleotides which have three principal components: a 5 carbon deoxyribose sugar, a phosphate group, and one of four nitrogen-containing nucleotide bases o Nucleotides are linked together by a covalent phosphodiester bond o Nucleotide bases are hydrophobic o Hydrogen bonds form between the complementary base pairs o Strands are antiparallel o Vocabulary Words: Chargaff’s rule, complementary base pairs, DNA nucleotides, adenine, guanine, thymine, cytosine, phosphodiester bond, hydrogen bonds, strand polarity, antiparallel, semiconservative replication, parental strand, daughter strand SECTION 1.3: DNA TRANSCRIPTION AND MESSENGER RNA TRANSLATION EXPRESS GENES o Central dogma of biology summarizes the relationships between DNA, RNA, and proteins o Functional role of DNA- maintaining, directing, and regulating the expression of genetic information o RNA and proteins in gene function o Most important idea is that DNA does not code directly for proteins DNA makes up genome of an organism and is the permanent source of genetic information in the cell by directing gene expression through transcription of DNA to RNA and then to the production of proteins o Two forms of RNA which play a role in transcription but are not transcribed: ribosomal RNA (rRNA) and transfer RNA (tRNA) o Transcription- process by which information in DNA sequence is converted into RNA sequence o RNA composed of 4 nucleotides that are chemically very similar to DNA o Ribose sugar, phosphate group, one of four nitrogenous bases all identical to those in DNA except uracil which replaces thymine o Certain DNA sequences, most commonly promoters, bind RNA polymerase and other transcriptional proteins o Messenger RNA codons base pair with tRNA anticodons at the ribosome o Each tRNA carries a specific amino acid that is added to the growing polypeptide chain o Genetic code contains 61 codons that specify amino acids and 3 are stop codons o Genomics, proteomics, transcriptomics, and metabolomics are new investigative strategies that can help decipher complex problems of systems biology o Vocabulary words: central dogma of biology, ribosomal RNA (rRNA), transfer RNA (tRNA), amino acids, reverse transcription, template strand, coding strand, uracil, promoters, start of transcription, termination sequence, exons, introns, peptide bond, polypeptide, protein, codon, start codon, anticodon, stop codon, genetic code, genomics, megabases, transcriptomics, transcriptome, metabolomics, proteomics, proteome, systems biology SECTION 1.4: EVOLUTION HAS A MOLECULAR BASIS o Four processes- natural selection, migration, mutation, and genetic drift- drive the evolution of population and species o The evolution of adaptive morphological characters occurs through natural selection pressures exerted on species by their environment o Nonadaptive characters are neutral to natural selection evolve by other evolutionary processes o Modern synthesis of evolution is the name applied to the union of transmission genetics, molecular genetics, Darwinian evolution, and modern evolutionary genetics o Phylogenetic trees describe evolutionary relationships among modern species and trace their descent from common ancestors to identify the most likely pattern of evolution o Shared derived characteristics are molecular and morphological attributes that evolve in descendant species from ancient characters found in a common ancestor o Molecular phylogenies trace the evolution of nucleic acid or protein sequences from common ancestors to modern species o Vocabulary Words: evolution, natural selection, migration, mutation, genetic drift, modern synthesis, phylogenetic tree, cladistics, clades, monophyletic groups, shared derived characteristics, synaptomorphies, homology, paraphyletic group, homoplasmy, outgroup, ingroup VOCABULARY WORDS Genes: the physical unit of heredity, composed of a DNA sequence that is transcribed and encodes a polypeptide or another functional molecule Chromosomes: a structure composed of DNA and associated proteins that in total contain the genome of an organism Homologous pairs: Chromosomes that synapse (pair) during meiosis. Chromosomes with the same genes in the same order; also known as homologous chromosomes, or homologs Homologs: Homologous chromosomes that have the same genes and structure and pair with one another during meiosis Haploid: Possessing a single set of chromosomes (n); a cell or organism that possesses one-half the number of chromosomes found in diploid cells of the organism Nucleoid: the region of bacterial and archaeal cells (or mitochondria or chloroplasts) where the main chromosome resides Diploid: the characteristic number of chromosomes (2n) in somatic cell nuclei during the diploid phase of the eukaryotic life cycle. Equal to twice the haploid (n) number of chromosomes found in the nuclei of gametes of sexually reproducing diploid species Polyploidy: the presence of more than two complete sets of chromosomes in a genome Mitochondria: an organelle, bounded by a double membrane, encoding polypeptides that interact with nuclear gene polypeptides in oxidative phosphorylation to generate ATP. In many species, mitochondria also participate in other metabolic processes and biochemical reactions, including ion homeostasis and biosynthetic pathways Chloroplasts: an organelle, bounded by a double membrane, where photosynthetic reactions convert light energy and CO2 into fixed organic carbon Cytoplasmic inheritance: the random distribution of mitochondria and chloroplasts between daughter cells Mitosis: the process of cell division in somatic cells that produces genetically identical daughter cells through a single nuclear division Meiosis: the process of cell division occurring in germ-line cells. Produces four haploid gametes or spores through two successive nuclear divisions in diploid species Gametes: the reproductive cells produced by male and female reproductive structures; sperm or pollen in male animals and plants and eggs in females Phenotype: the observable physical characteristics or traits of an organism; the physical manifestation of a specific genotype Genotype: the genetic composition of an organism or a cell (ex. all of alleles of all the genes); the alleles of a single gene or a specified set of genes in a cell or organism Alleles: an alternative form of a gene Genomes: the entire complement of DNA sequences in a chromosome set of an organism LUCA: stands for last universal common ancestor Eukarya: one of the three domains of life; separate from Archaea and Bacteria Bacteria: one of the three domains of life: separate from Eukarya and Archaea Archaea: one of the three domains of life; separate from Bacteria and Eukarya Deoxyribose nucleic acid (DNA): the hereditary molecule of organisms. Composed of two complementary strands of nucleotides with purine bases adenine (A) and guanine (G) and pyrimidine bases thymine (T) and cytosine (C) Ribonucleic acid (RNA):a family of polynucleotides that are transcribed from DNA. RNAs are composed of nucleotides containing the sugar ribose, one or more phosphate atoms, and one of four nitrogenous bases (A,G, C, and U) DNA double helix: the two complementary strands of DNA arranged in antiparallel orientation also known as DNA duplex DNA replication: the synthesis of new DNA strands by complementary base pairing of nucleotides in a daughter strand to those in a template strand Transcription: the cellular processes that synthesizes RNA strands from a DNA template strand Messenger RNA (mRNA):a form of RNA transcribed from a gene and subsequently translated to produce a polypeptide or protein Translation: the process taking place a ribosomes to synthesize polypeptides. Complementary base pairing between mRNA codons and tRNA anticodons determines the order of amino acids composing the polypeptide Ribosomes: ribonucleoprotein particles, composed of rRNAs and numerous proteins, at which translation takes place Transmission genetics: the subfield of genetics concerned with assessment and analysis of gene transfer from parents to offspring. Synonym with Mendelian genetics Mendelian genetics: referring to genetic applications and analyses using the law of segregation and the law of independent assortment originally described through experiments and analysis by Gregor Mendel Evolutionary genetics: the study of evolution and evolutionary processes using genetic techniques and tools Molecular genetics: the subfield of genetics that studies hereditary transmission, variation, mutation, and evolution through the analysis of nucleic acids and proteins Chargaff’s rule: the observation that the percentage of adenine equals that of thymine and that guanine percentage equals cytosine percentage in DNA Complementary base pairs: the specific pattern of purine-pyrimidine pairing of nucleic acid strands. In DNA, G with C and A with T; in RNA, uses U instead of T DNA nucleotides: DNA building blocks composed of deoxyribose sugar, a nitrogenous base, and one or more phosphate groups Adenine: one of four nitrogenous nucleotide bases in DNA and RNA; one of the two types of purine nucleotides in DNA and RNA Guanine: one of four nitrogenous nucleotide bases in DNA and RNA; one of two types of purine nucleotides in DNA and RNA Thymine: one of four nitrogenous nucleotide bases in DNA; one of two types of pyrimidine nucleotides in DNA Cytosine: one of four nitrogenous nucleotide bases in DNA and RNA; one of two types of pyrimidine nucleotides in DNA and RNA Phosphodiester bond: a type of covalent bond formed between two nucleotides in a nucleic acid strain. Formed between the 5’ phosphate group of one nucleotide and the 3’ OH of the adjacent nucleotide Hydrogen bonds: weak electrostatic attraction formed by the sharing of a positively charged hydrogen atom by negatively charged oxygen and nitrogen atoms. Hydrogen bonds form between complementary nucleotides to hold nucleic acid strands together Strand polarity (5’ and 3’):the orientation of a nucleic acid strand indicating its 5’ phosphate and 3’ hydroxyl ends Antiparallel: opposite 5’ and 3’ orientations of two complementary nucleic acid strands Semiconservative replication: the established method of DNA replication in which each strand of a parental duplex acts as a template for daughter strand synthesis and each daughter duplex is composed of one parental strand and a complementary daughter strand Parental strand: the DNA strand acting as a template to direct the synthesis of a new(“daughter”) strand of DNA Daughter strand: a newly synthesized strand of DNA that is complementary to a template strand Central dogma of biology: the description of the functional relationship between DNA, RNA and proteins ( DNA to RNA to proteins) Ribosomal RNA (rRNA): a group of RNA molecules that compose part of the structure of ribosomes Transfer RNA (tRNA): a family of small RNA molecules that each bind a specific amino acid and convey it to the ribosome, where the anticodon sequence undertakes complementary base pairing with an mRNA codon during translation Amino acids: an aminocarboxylic acid that is a component of a polypeptide or a protein Reverse transcription: the process of DNA synthesis from an RNA template by the enzyme reverse transcriptase Template strand: the DNA strand serving as a template for synthesis of a complementary nucleic acid strand Coding strand: the nontemplate strand of DNA that has the same 5’-to-3’ polarity as its transcript and the same sequence, except for T in DNA and U in RNA Uracil: one of the four nitrogenous nucleotide bases in RNA; one of the two types of pyrimidine nucleotides in RNA Promoters: a regulatory sequence of DNA near the 5’ end of a gene that acts as the binding location of RNA polymerase and directs RNA polymerase to the start of transcription Start of transcription: the DNA location at which transcription begins Termination sequence: DNA sequences that serve to stop transcription, also known as transcription termination Exons: a nonintron segment of coding sequence of a gene. Joined together following intron splicing, exons correspond to the mRNA sequence that is coded into a polypeptide Introns: intervening sequences between the exons of many eukaryotic genes. Present in DNA and pre-mRNA, but spliced out during pre-mRNA processing Peptide bond: a type of covalent bond that joins amino acids in polypeptide chains. Formed between the amino end of one amino acid and the carboxyl end of the adjoining amino acid Polypeptide: a chain of amino acids joined by peptide bonds. Formed at ribosomes during translation Protein: a string of amino acids encoded during translation of mRNA and linked together by peptide bonds Codon: the nucleotide triplet of mRNA that encodes a single amino acid Start codon: most commonly AUG, encoding methionine, the first codon translate in polypeptide synthesis Anticodon: the nucleotide triplet sequence of transfer RNA that pairs with an mRNA codon sequence in translation Stop codon: one of three codons that bind a release factor instead a base- pairing with tRNA to initiate a series of events that stops translation Genetic code; the universal set of correspondences of mRNA codons to amino acids. Used in translation to synthesize polypeptides Genomics: the study of the structure, function, composition, and evolution of genomes Megabases: Equal to 1,000, 000 nucleotide bases. Refers to DNA or to RNA molecules or fragments Transcriptomics: the study of all the transcripts, collectively known as the transcriptome, within a cell, tissue, or organism Transcriptome: set of transcripts present in a cell, tissue, or organism Metabolomics: the study of proteins, processes, and interactions involved in the metabolism of organisms Proteomics: the study of all the proteins, collectively knowns as the proteome, within a cell, tissue, or organism Proteome: set of the proteins in a cell, tissue, or organism Systems biology: prediction of biological functions of genes based on correlations between different data sets Evolution: any change in the genetic characteristics of a population, strain, or species over time; the theory of all organisms are related by common ancestry and have diversified from common ancestors over time Natural selection: the evolutionary processes operating through differences in survival, fecundity, and relative fitness of organisms with different genotypes and phenotypes Migration: a process of evolution referring to the movement of organisms and genes between populations, also known as gene flow Mutation: an inherited change in DNA Genetic drift: a process of evolution referring to random changes in allele frequencies that result from sampling errors. Occurs in all populations but is strongest in small populations Modern synthesis: referring to the broad-based effort beginning in the middle of the 20 century to unite Mendelian genetics with Darwin’s theory of evolution by natural selection Phylogenetic tree: a diagram of evolutionary relationships among organisms or genes based on morphological or molecular characteristics Cladistics: the classification of organisms by characteristics that are unique to the group and distinguish it from other groups. Involves branching of new species from ancestral species Clades: in phylogenetics, a group of organisms defined by characteristics that are unique to the group and distinguish the group from others Monophyletic groups: a group of organisms with a single common ancestor Shared derived characteristics: characteristics or traits of organisms that evolve from more ancestral characteristics or traits found in ancestral organisms Synaptomorphies: similar to shared derived characteristics, shared between member of the same clade, molecular or morphological Homology: evolutionarily related, having descended from a common ancestor Paraphyletic group: a group of organisms that includes some but not all the members descended from a common ancestor Homoplasmy: the presence of one allele version of DNA in the organellar genomes of a cell Outgroup: a species related to members of a clade but outside the clade; used to root the clade Ingroup: a species within a clade used to compare to other members of the clade
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