For Further Exploration
NOVA. 2018. Gene Sequencing Speeds Diagnosis of Deadly Newborn Diseases. NOVA, March 7, 2018. Accessed January 31, 2023. http://www.pbs.org/wgbh/nova/next/body/newborn-gene-sequencing/.
Zimmer, Carl. N.d. “Carl Zimmer’s Game of Genomes.” STATnews. Accessed January 31, 2023. https://www.statnews.com/feature/game-of-genomes/season-one/.
Illumina. 2016. “Illumina Sequencing by Synthesis.” YouTube.com, October 5, 2016. Accessed January 31, 2023. https://www.youtube.com/watch?v=fCd6B5HRaZ8.
Aartsma-Rus, Annemieke, Ieke B. Ginjaar, and Kate Bushby. 2016. “The Importance of Genetic Diagnosis for Duchenne Muscular Dystrophy.” Journal of Medical Genetics 53 (3): 145–151.
Acuna-Hidalgo, Rocio, Joris A. Veltman, and Alexander Hoischen. 2016. “New Insights into the Generation and Role of De Novo Mutations in Health and Disease.” Genome Biology 17 (241): 1–19.
Albert, Benjamin, Susanna Tomassetti, Yvonne Gloor, Daniel Dilg, Stefano Mattarocci, Slawomir Kubik, Lukas Hafner, and David Shore. 2019. “Sfp1 Regulates Transcriptional Networks Driving Cell Growth and Division through Multiple Promoter-Binding Modes.” Genes & Development 33 (5–6): 288–293.
Almathen, Faisal, Haitham Elbir, Hussain Bahbahani, Joram Mwacharo, and Olivier Hanotte. 2018. “Polymorphisms in Mc1r and Asip Genes Are Associated with Coat Color Variation in the Arabian Camel.” Journal of Heredity 109 (6): 700–706.
Ballester, Leomar Y., Rajyalakshmi Luthra, Rashmi Kanagal-Shamanna, and Rajesh R. Singh. 2016. “Advances in Clinical Next-Generation Sequencing: Target Enrichment and Sequencing Technologies.” Expert Review of Molecular Diagnostics 16 (3): 357–372.
Baranovskiy, Andrey G., Vincent N. Duong, Nigar D. Babayeva, Yinbo Zhang, Youri I. Pavlov, Karen S. Anderson, and Tahir H. Tahirov. 2018. “Activity and Fidelity of Human DNA Polymerase Alpha Depend on Primer Structure.” Journal of Biological Chemistry 293 (18): 6824–6843.
Brezina, Paulina R., Raymond Anchan, and William G. Kearns. 2016. “Preimplantation Genetic Testing for Aneuploidy: What Technology Should You Use and What Are the Differences?” Journal of Assisted Reproduction and Genetics 33 (7): 823–832.
Bultman, Scott J. 2017. “Interplay Between Diet, Gut Microbiota, Epigenetic Events, and Colorectal Cancer.” Molecular Nutrition & Food Research 61 (1):1–12.
Cutting, Garry R. 2015. “Cystic Fibrosis Genetics: From Molecular Understanding to Clinical Application.” Nature Reviews Genetics 16 (1): 45–56.
D’Alessandro, Giuseppina., and Fabrizio d’Adda di Fagagna. 2017. “Transcription and DNA Damage: Holding Hands or Crossing Swords?” Journal of Molecular Biology 429 (21): 3215–3229.
De Craene, Johan-Owen, Dimitri L. Bertazzi, Séverine Bar, and Sylvie Friant. 2017. “Phosphoinositides, Major Actors in Membrane Trafficking and Lipid Signaling Pathways.” International Journal of Molecular Sciences 18 (3): 1–20.
Deng, Lian, and Shuhua Xu. 2018. “Adaptation of Human Skin Color in Various Populations.” Hereditas 155 (1): 1–12.
Dever, Thomas E., Terri G. Kinzy, and Graham D. Pavitt. 2016. “Mechanism and Regulation of Protein Synthesis in Saccharomyces Cerevisiae.” Genetics 203 (1): 65–107.
Eme, Laura, Anja Spang, Jonathan Lombard, Courtney W. Stairs, and Thijs J. G. Ettema. 2017. “Archaea and the Origin of Eukaryotes.” Nature Reviews Microbiology 15 (12): 711–723.
Gomez-Carballa, Alberto, Jacobo Pardo-Seco, Stefania Brandini, Alessandro Achilli, Ugo A. Perego, Michael D. Coble, Toni M. Diegoli, et al. 2018. “The Peopling of South America and the Trans-Andean Gene Flow of the First Settlers.” Genome Research 28 (6): 767–779.
Gvozdenov, Zlata, Janhavi Kolhe, and Brian C. Freeman. 2019. “The Nuclear and DNA-Associated Molecular Chaperone Network.” Cold Spring Harbor Perspectives in Biology 11 (10): a034009.
Harkins, Kelly M., and Anne C. Stone. 2015. “Ancient Pathogen Genomics: Insights into Timing and Adaptation.” Journal of Human Evolution 79: 137–149.
Jackson, Maria, Leah Marks, Gerhard H. W. May, and Joanna B. Wilson. 2018. “The Genetic Basis of Disease.” Essays in Biochemistry 62 (5): 643–723.
Lenormand, Thomas, Jan Engelstadter, Susan E. Johnston, Erik Wijnker, and Christopher R. Haag. 2016. “Evolutionary Mysteries in Meiosis.” Philosophical Transactions of the Royal Society B 371: 1–14.
Levy, Shawn E., and Richard M. Myers. 2016. “Advancements in Next-Generation Sequencing.” Annual Review of Genomics and Human Genetics 17: 95–115.
Lindo, John, Emilia Huerta-Sánchez, Shigeki Nakagome, Morten Rasmussen, Barbara Petzelt, Joycelynn Mitchell, Jerome S. Cybulski, et al. 2016. “A Time Transect of Exomes from a Native American Population Before and After European Contact.” Nature Communications 7: 1–11. https://doi.org/10.1038/ncomms13175.
Lu, Mengfei, Cathryn M. Lewis, and Matthew Traylor. 2017. “Pharmacogenetic Testing through the Direct-to-Consumer Genetic Testing Company 23andme.” BMC Medical Genomics 10 (47): 1–8.
Ly, Lundi, Donovan Chan, Mahmoud Aarabi, Mylene Landry, Nathalie A. Behan, Amanda J. MacFarlane, and Jacquetta Trasler. 2017. “Intergenerational Impact of Paternal Lifetime Exposures to Both Folic Acid Deficiency and Supplementation on Reproductive Outcomes and Imprinted Gene Methylation.” Molecular Human Reproduction 23 (7): 461–477.
Ma, Wenxiu, Giancarlo Bonora, Joel B. Berletch, Xinxian Deng, William S. Noble, and Christine M. Disteche. 2018. “X-Chromosome Inactivation and Escape from X Inactivation in Mouse.” Methods in Molecular Biology 1861: 205–219.
Machiela, Mitchell J., Weiyin Zhou, Eric Karlins, Joshua N. Sampson, Neal D. Freedman, Qi Yang, Belynda Hicks, et al. 2016. “Female Chromosome X Mosaicism Is Age-Related and Preferentially Affects the Inactivated X Chromosome.” Nature Communications 7: 1–9. https://doi.org/10.1038/ncomms11843.
Mahdavi, Morteza, Mohammadreza Nassiri, Mohammad M. Kooshyar, Masoume Vakili-Azghandi, Amir Avan, Ryan Sandry, Suja Pillai, Alfred K. Lam, and Vinod Gopalan. 2019. “Hereditary Breast Cancer; Genetic Penetrance and Current Status with BRCA.” Journal of Cellular Physiology 234 (5): 5741–5750.
McDade, Thomas W., Calen P. Ryan, Meaghan J. Jones, Morgan K. Hoke, Judith Borja, Gregory E. Miller, Christopher W. Kuzawa, and Michael S. Kobor. 2019. “Genome-Wide Analysis of DNA Methylation in Relation to Socioeconomic Status During Development and Early Adulthood.” American Journal of Physical Anthropology 169 (1): 3–11.
Migeon, Barbara R. 2017. “Choosing the Active X: The Human Version of X Inactivation.” Trends in Genetics 33 (12): 899–909.
Myerowitz, Rachel. 1997. “Tay-Sachs Disease-Causing Mutations and Neutral Polymorphisms in the Hex A Gene.” Human Mutation 9 (3): 195–208.
Onufriev, Alexey V., and Helmut Schiessel. 2019. “The Nucleosome: From Structure to Function through Physics.” Current Opinion in Structural Biology 56: 119–130.
Quillen, Ellen E., Heather L. Norton, Esteban J. Parra, Frida Lona-Durazo, Khai C. Ang, Florin M. Illiescu, Laurel N. Pearson, et al. 2019. “Shades of Complexity: New Perspectives on the Evolution and Genetic Architecture of Human Skin.” American Journal of Physical Anthropology 168 (67): 4–26.
Raspelli, Erica, and Roberta Fraschini. 2019. “Spindle Pole Power in Health and Disease.” Current Genetics 65 (4): 851–855.
Ravinet, M., R. Faria, R. K. Butlin, J. Galindo, N. Bierne, M. Rafajlovic, M. A. F. Noor, B. Mehlig, and A. M. Westram. 2017. “Interpreting the Genomic Landscape of Speciation: A Road Map for Finding Barriers to Gene Flow.” Journal of Evolutionary Biology 30 (8): 1450–1477.
Regev, Aviv, Sarah A. Teichmann, Eric S. Lander, Ido Amit, Christophe Benoist, Ewan Birney, Bernd Bodenmiller, et al. 2017. “The Human Cell Atlas.” Elife 6e27041: 1–30. https://doi.org/10.7554.eLife.27041.
Roberts, Andrea L., Nicole Gladish, Evan Gatev, Meaghan J. Jones, Ying Chen, Julia L. MacIsaac, Shelley S. Tworoger, et al. 2018. “Exposure to Childhood Abuse Is Associated with Human Sperm DNA Methylation.” Translational Psychiatry 8 (194): 1–11.
Roger, Andrew J., Sergio A. Muñoz-Gómez, and Ryoma Kamikawa. 2017. “The Origin and Diversification of Mitochondria.” Current Biology 27 (21): R1177–R1192. https://www.sciencedirect.com/scienc...9X?via%3Dihub#!
Ségurel, Laure, and Céline Bon. 2017. “On the Evolution of Lactase Persistence in Humans.” Annual Review of Genomics and Human Genetics 18: 297–319.
Sheth, Bhavisha P., and Vrinda S. Thaker. 2017. “DNA Barcoding and Traditional Taxonomy: An Integrated Approach for Biodiversity Conservation.” Genome 60 (7): 618–628.
Skloot, Rebecca. 2010. The Immortal Life of Henrietta Lacks. New York: Crown Publishing Group.
Snedeker, Jonathan, Matthew Wooten, and Xin Chen. 2017. “The Inherent Asymmetry of DNA Replication.” Annual Review of Cell and Developmental Biology 33: 291–318.
Sullivan-Pyke, Chantae, and Anuja Dokras. 2018. “Preimplantation Genetic Screening and Preimplantation Genetic Diagnosis.” Obstetrics and Gynecology Clinics of North America 45 (1): 113–125.
Szostak, Jack W. 2017. “The Narrow Road to the Deep Past: In Search of the Chemistry of the Origin of Life.” Angewandte Chemie International Edition 56 (37): 11037–11043.
Tessema, Mathewos, Ulrich Lehmann, and Hans Kreipe. 2004. “Cell Cycle and No End.” Virchows Archiv European Journal of Pathology 444 (4): 313–323.
Tishkoff, Sarah A., Floyd A. Reed, Alessia Ranciaro, Benjamin F. Voight, Courtney C. Babbitt, Jesse S. Silverman, Kweli Powell, et al. 2007. “Convergent Adaptation of Human Lactase Persistence in Africa and Europe.” Nature Genetics 39 (1): 31–40.
Visootsak, Jeannie, and John M. Graham, Jr. 2006. “Klinefelter Syndrome and Other Sex Chromosomal Aneuploidies.” Orphanet Journal of Rare Diseases 1:42. https://doi.org/10.1186/1750-1172-1-42.
Wolfe, George C., dir. 2017. The Immortal Life of Henrietta Lacks. HBO Films, April 22, 2017. TV Movie.
Yamamoto, Fumi-ichiro, Henrik Clausen, Thayer White, John Marken, and Sen-itiroh Hakomori. 1990. “Molecular Genetic Basis of the Histo-Blood Group ABO System.” Nature 345 (6272): 229–233.
Zlotogora, Joël. 2003. “Penetrance and Expressivity in the Molecular Age.” Genetics in Medicine 5 (5): 347–352.
Zorina-Lichtenwalter, Katerina, Ryan N. Lichtenwalter, Dima V. Zaykin, Marc Parisien, Simon Gravel, Andrey Bortsov, and Luda Diatchenko. 2019. “A Study in Scarlet: MC1R as the Main Predictor of Red Hair and Exemplar of the Flip-Flop Effect.” Human Molecular Genetics 28 (12): 2093-2106.
Zwart, Haeh. 2018. “In the Beginning Was the Genome: Genomics and the Bi-Textuality of Human Existence.” New Bioethics 24 (1): 26–43.
Figure 3.2: Two cells drawn with openings so the inside organelles can be viewed and labeled. The eukaryotic cell is square shaped with a thick cell membrane around the outside. DNA is inside a circular membrane-enclosed nucleus. Labeled arrows point to different shaped membrane-enclosed organelles and ribosomes (represented by small dots). The prokaryotic cell has a capsule shape and a flagellum (tail). The thick cell wall is labeled, as is the cell membrane underneath it. DNA is loosely coiled in the nucleoid, ribosomes are represented by small dots.
Figure 3.3: Two cells are depicted with different shaped organelles inside them. The plant cell is square with a thick cellulose cell wall outside the cell membrane. The cytoplasm inside holds many chloroplasts (green ovals), two mitochondrion (brown ovals with wavy lines inside), and a circular nucleus containing loose DNA strands. A large permanent vacuole (empty space) is shown. The animal cell is round, with a thin cell wall. The cytoplasm holds different shaped organelles including a few mitochondria and a circular nucleus containing loose DNA strands.
Figure 3.4: The phospholipid bilayer is constructed of two sheet-like layers of lipid molecules. The individual lipid molecules have hydrophobic tails and hydrophilic heads. The tail-side of the two sheets form the middle of the bilayer, with the heads forming the outsides of the bilayer.
Under the bilayer are filaments of the cytoskeleton (drawn as thick wavy lines). Imbedded in the phospholipid bilayer are:
- Glycoproteins: proteins with carbohydrate attached,
- Glycolipid: lipid with carbohydrate attached,
- Peripheral membrane proteins (fit in only one layer),
- Integral membrane proteins (that extend all the way through the bilayer),
- Cholesterol (small molecules in only one layer), and
- Protein channels (hat extend all the way through the bilayer)
Figure 3.5: A three-dimensional cell is partly opened to expose various labeled organelles. These include:
- A sphere shaped nucleus containing a smaller sphere shaped nucleolus,
- Ribosomes depicted as small dots,
- Rough endoplasmic reticulum shown as long thin membranes outside of the nucleus,
- Smooth endoplasmic reticulum near the rough ER,
- Mitochondria shown as small oval organelles with a wavy membrane inside. Some have microtubules (lines) extending from them.
- Tube like centrioles,
- Golgi body appearing as a stacked membrane, and
- Lysosomes appear as small dots outside the nucleus.
Figure 3.9: The DNA double helix is shown wound around nucleosomes. Each nucleosome is made of clustered spherical histones and the DNA wraps around it twice. The DNA wound around nucleosomes resembles “beads on a string.” Many wrapped and condensed nucleosomes form chromatin fiber, which are further wound into an X-shaped chromosome.
Figure 3.12: Original (template) DNA extends from an X shaped chromosome, and its two strands are separated at the replication fork by helicase (an enzyme depicted as a triangle). The bottom original template strand has DNA polymerase moving away from the replication fork to create a new lagging strand DNA by adding free nucleotides. On the upper strand of original DNA, DNA polymerase works toward the replication fork, adding free nucleotides to build the leading strand.
Figure 3.15: This pie chart shows the proportion of time spent in each cell phase. The shortest phases are the mitotic phases (mitosis followed by cytokinesis) which lead to the formation of two daughter cells. This is followed by a long cell growth (G1, interphase), DNA synthesis (S, interphase), and cell growth (G2, interphase), before returning to the mitotic phase.
Figure 3.17: Image depicts protein synthesis as divided into three phases, and shows the molecules involved at each phase, and that are used to help create the following document. First, in transcription, DNA (double stranded) is used as a template to create pre-mRNA (single stranded). Second, in RNA processing (also called splicing), pre-mRNA is modified to form a shorter mature mRNA. Lastly, in translation, mature mRNA is used as instructions to link together spherical amino acids in a chain, or protein.
Figure 3.18: The single-stranded structure of RNA is shown with a backbone of sugar-phosphates in a helical shape and nucleobases are shown as rungs on a ladder. On the left side of the figure, the chemical structure of each nucleobase is depicted: cytosine (C), guanine (G), adenine (A), and uracil (U).
Figure 3.19: A stretch of double stranded DNA is depicted in the process of transcription. The two strands are pulled apart in the middle, the top strand forms the template strand. RNA polymerase (a bubble shaped enzyme) sits on the template strand and adds free nucleotides to a growing RNA transcript. The DNA template strand reads ATGACGGATCAG… and the RNA strand is complementary and contains uracil (U; UACUGCCUAGUC…).
Figure 3.20: At the top of the diagram, sections of a gene (DNA) are labeled: a promoter region followed by alternating sections of exons (filled in with horizontal lines) and introns (vertical lines). In the middle of the diagram, the pre mRNA transcription contains copies of the alternating exon and intron portions with lines drawn in. The bottom strand (mature mRNA) shows the introns removed and the exons (all horizontal lines) connected.
Figure 3.21: A roughly circular ribosome sits on a mRNA strand and facilitates the transfer of amino acids (dots) carried by tRNA to a growing amino acid (peptide) chain. Amino acids appear as different colored dots on a string. Their abbreviations and full names are listed.
- alanine— ala
- arginine— arg
- asparagine— asn
- aspartic acid— asp
- cysteine— cys
- glutamine— gln
- glutamic acid— glu
- glycine— gly
- histidine— his
- isoleucine— ile
- leucine— leu
- lysine— lys
- methionine— met
- phenylalanine— phe
- proline— pro
- serine— ser
- threonine— thr
- tryptophan– trp
- tyrosine— tyr
- valine— val
Figure 3.22: Accessible full text RNA codon to amino acid table
Figure 3.26: Grid illustration of the pollen of a purple-flowered pea plant (heterozygous genotype of capital B and lowercase b) mixing with the pistol (also a heterozygous genotype of capital B and lowercase b) could create combinations of genotypes: two capital B alleles (purple flower), capital B and lowercase B alleles (purple flower), or two lower case b alleles (white flower).
Figure 3.28: A grid format uses images of circles for the red blood cells, covered with smaller shapes, to depict antigens on blood types. Shapes that fit against the antigen shapes like puzzle pieces depict antibodies that can bind antigens.
For ABO blood types:
- A has circular (A) antigens on the cell, and V-shaped antibodies capable of binding B antigens.
- B has triangular (B) antigens on the cell, and moon-shaped antibodies capable of binding A antigens.
- AB has circular (A) and triangle (B) antigens. No corresponding antibodies.
- O has no antigens, and both V-shaped and moon-shaped antibodies capable of binding A and B antigens.
For Rh Blood types:
- Rh+ has rectangular (Rh) antigens on the cell. No corresponding antibodies.
- Rh- has no specific antigens, and box-shaped antibodies capable of binding Rh antigens.
Figure 3.29: A 3×3 Punnett-square grid showing the genotypes that result when the different ABO blood type alleles come together. A, B, and O constitute both the row and column headers. The cells are the resulting genotype (two combined alleles).
Top row: AA, AB, AO
Middle row: AB, BB, BO
Bottom row: AO, BO, OO
Figure 3.34: Two images each show DNA wrapped around a series of histones. The top image shows DNA wrapped around seven tightly clustered histones. Many methyl groups (small dots) are on the DNA and on histone tails. A portion of the DNA tucked between two histones is highlighted as a gene and labeled “DNA inaccessible, gene inactive”. Text reads: Methylation of DNA and histones causes nucleosomes to pack tightly together. Transcription factors cannot bind the DNA, and genes are not expressed. The bottom image shows DNA wrapping around three widely spaced histones, with a highlighted active gene (where the DNA is accessible between two histones). Acetyl groups are attached to histone tails. Text reads: Histone acetylation results in loose packing of nucleosomes. Transcription factors can bind the DNA and genes are expressed.