BSC 315 Final Review Topics PDF

Part 1: Mendelian Genetics Punnett Squares and Probabilities: Understand how to use Punnett squares to predict the genotypes and phenotypes of offspring from different crosses. Practice calculating probabilities of specific genotypes and phenotypes using the product rule and the sum...

Part 1: Mendelian Genetics Punnett Squares and Probabilities: Understand how to use Punnett squares to predict the genotypes and phenotypes of offspring from different crosses. Practice calculating probabilities of specific genotypes and phenotypes using the product rule and the sum rule. Monohybrid and Dihybrid Crosses: Be able to analyze monohybrid crosses, which involve a single trait, and dihybrid crosses, which involve two traits. Understand the expected phenotypic ratios for different types of inheritance patterns, including complete dominance, incomplete dominance, and codominance. Ratios: Familiarize yourself with the classic Mendelian ratios and what they signify. For instance: ○ 3:1 phenotypic ratio in the F2 generation of a monohybrid cross with complete dominance. ○ 9:3:3:1 phenotypic ratio in the F2 generation of a dihybrid cross with complete dominance. ○ 1:2:1 phenotypic ratio in the F2 generation of a monohybrid cross with incomplete dominance. Pedigrees and Probabilities: Practice interpreting pedigrees to determine the mode of inheritance of a trait. Calculate probabilities of individuals inheriting specific genotypes or phenotypes based on pedigree information. Key Concepts and Terms: Make sure you understand the definitions and applications of the following: ○ Pure breeding: Organisms that produce offspring with the same phenotype when self-fertilized or crossed with another pure-breeding organism for the same trait. ○ Genotype: The genetic makeup of an individual, represented by the combination of alleles. ○ Phenotype: The observable characteristics of an individual, determined by the genotype and environmental factors. ○ Law of independent assortment: Different pairs of alleles segregate independently during gamete formation. ○ Test Cross: A cross between an individual with an unknown genotype and an individual homozygous recessive for the trait of interest. Part 2: Chromosomes and DNA Cell Cycle and Stages of Mitosis and Meiosis: Know the different stages of the cell cycle, including interphase (G1, S, and G2 phases), mitosis, and meiosis I and II. Understand the key events that occur during each stage. Given the ploidy of an organism, be able to determine the number of chromosomes and chromatids present in each stage of the cell cycle. Crossing Over and Recombination: Understand when and how crossing over occurs during meiosis. Relate crossing over to the generation of recombinant chromosomes and increased genetic diversity.  Genetic Linkage and Linkage Mapping: Grasp the concept of genetic linkage and how the frequency of recombination between genes can be used to construct genetic maps. Remember these key points: ○ Map unit = centimorgan = recombination frequency expressed as a percentage. ○ Recombination frequency provides a measure of the genetic distance between genes. ○ Genes with a recombination frequency greater than 50% are considered to assort independently. Sex-Linked Genes and Pedigrees: Be able to analyze pedigrees to determine the mode of inheritance of sex-linked traits. Recall that in humans, males are typically XY and females are XX. Therefore, males are hemizygous for X-linked genes, meaning they have only one copy of the gene on their single X chromosome. Females can be homozygous or heterozygous for X-linked genes. DNA Structure: Review the basic structure of DNA, including its composition of nucleotides, the complementary base pairing rules (A with T, and G with C), and the distinction between purines (A and G) and pyrimidines (C and T). Nucleotide Sequence and Genetic Information: Understand that the sequence of nucleotides in DNA is the basis of genetic information. DNA Replication: Know the mechanism of DNA replication, including that it is a semi-conservative process (each new DNA molecule consists of one original strand and one newly synthesized strand), the directionality of DNA synthesis (5' to 3'), and the role of dNTPs as building blocks and energy sources for DNA polymerization. Complementation Mapping: Understand how complementation tests are used to determine if mutations are in the same gene or different genes. Mutations: Be familiar with different types of mutations and their effects, including substitutions (transitions and transversions), insertions, and deletions. Part 3: Central Dogma of Molecular Biology Central Dogma: Understand the flow of genetic information from DNA to RNA to protein (DNA → RNA → protein) and the polarity between DNA, RNA, and the amino acid chain. Gene Expression: Understand the process of gene expression, which involves the transcription of DNA into RNA and the translation of RNA into protein. The Genetic Code: Review the genetic code and its use in translating mRNA codons into amino acids. Remember that there are 64 possible codons: 61 codons specify amino acids, and 3 are stop codons that signal the termination of translation. Transcription: Know the stages of transcription (initiation, elongation, and termination) and the differences in transcription between prokaryotes and eukaryotes. ○ Prokaryotic Transcription: Occurs in the cytoplasm, uses a single RNA polymerase, and does not involve extensive RNA processing. ○ Eukaryotic Transcription: Occurs in the nucleus, utilizes three different RNA polymerases, and involves extensive RNA processing, including the addition of a 5' cap, a 3' poly-A tail, and the splicing out of introns. Proteins Involved in Transcription: Be familiar with the key proteins involved in transcription, such as RNA polymerase and transcription factors.  Translation: Understand the stages of translation (initiation, elongation, and termination) and the differences between prokaryotic and eukaryotic translation. ○ Prokaryotic Translation: Can begin while transcription is still in progress; utilizes a Shine-Dalgarno sequence in the 5' untranslated region (UTR) of the mRNA for ribosome binding; the first amino acid is a modified methionine (fMet). ○ Eukaryotic Translation: Begins after the mRNA has been transported from the nucleus to the cytoplasm; the small ribosomal subunit binds to the 5' cap of the mRNA and scans for the first AUG codon; the first amino acid is methionine. Ribosomes: Review the structure and function of ribosomes, the sites of protein synthesis. Ribosomes are composed of a small subunit and a large subunit. They have three tRNA binding sites: ○ A site: The aminoacyl (acceptor) site, where the incoming charged tRNA carrying the next amino acid binds. ○ P site: The peptidyl site, where the tRNA carrying the growing polypeptide chain is located. ○ E site: The exit site, from which the uncharged tRNA leaves the ribosome after donating its amino acid. Mutations in the Coding Sequence: Understand how different types of mutations in the coding sequence of a gene can affect the amino acid sequence of the protein. For example, a missense mutation can change a single amino acid, a nonsense mutation can introduce a premature stop codon, and a frameshift mutation can alter the reading frame, leading to a completely different amino acid sequence. Part 4: Gene Regulation Chromosome Structure and Compaction: Understand how DNA is packaged into chromosomes, the role of histone proteins in DNA compaction, the structure of nucleosomes, and the levels of chromosome organization. Chromosomal Packaging and Gene Expression: Understand how the packaging of DNA into chromatin can affect gene expression. ○ Euchromatin: Less condensed, transcriptionally active regions of chromosomes. ○ Heterochromatin: Highly condensed, transcriptionally inactive regions of chromosomes. Histone Modifications: Be familiar with the major types of histone modifications, such as acetylation and methylation, and their effects on chromatin structure and gene expression. Chromosomal Rearrangements: Know the different types of chromosomal rearrangements, including deletions, duplications, inversions, and translocations, and their potential consequences. Transposable Elements: Understand the nature of transposable elements, their classification (retrotransposons and DNA transposons), and their mechanisms of mobilization. Aneuploidy and Polyploidy: Define aneuploidy (changes in the number of individual chromosomes) and polyploidy (changes in the number of complete sets of  chromosomes). Know examples of aneuploidy, such as monosomy (2n-1) and trisomy (2n+1), and polyploidy, such as triploidy (3n) and tetraploidy (4n). Homology: Understand the concept of homology in genes and how homologous genes can arise through gene duplication events. Differentiate between orthologs (homologous genes in different species that arose from a common ancestral gene) and paralogs (homologous genes within a single species that arose from gene duplication). Bacterial Genetics: Understand the key features of bacteria, including auxotrophs (nutritional mutants), prototrophs (wild-type bacteria), and pathogenic bacteria. Be familiar with horizontal gene transfer and conjugation as mechanisms for transferring genetic material in bacteria. Prokaryotic Gene Regulation: Understand the concept of an operon, a cluster of genes that are transcribed together and regulated as a unit. Be familiar with the lac operon as a classic example of prokaryotic gene regulation and the roles of cis-acting elements (DNA sequences that regulate the expression of nearby genes, like the operator) and trans-acting factors (proteins that can bind to DNA and regulate gene expression, like the repressor). Positive and Negative Regulation: Understand how both positive regulators (activators) and negative regulators (repressors) can control gene expression. Part 5: DNA Technology and Development This section covers the material from Lectures 27-30. The review slides provide an overview of the key concepts from this portion of the course. Chapter 20: Epigenetics DNA Methylation: Understand the role of DNA methylation in gene silencing and its inheritance through mitotic cell divisions. Focus on how methylation patterns can alter gene expression without changing the DNA sequence. Chromatin Structure: Review how chromatin structure influences transcription. Recall that euchromatin is more accessible to the transcriptional machinery, while heterochromatin is generally transcriptionally silent. Imprinting: Grasp the concept of genomic imprinting, where the expression of a gene depends on whether it was inherited from the mother or the father. Imprinted genes are often silenced by DNA methylation. Chapter 22: Genes and Development Model Organisms: Understand the rationale for using model organisms, such as Drosophila melanogaster, to study developmental processes. Genetic Screens: Appreciate how mutant screens help identify genes involved in a specific developmental process. This involves isolating mutants with defects in the process of interest and then characterizing the mutated genes. Gene Expression Analysis: Know the techniques used to study the temporal and spatial expression of genes during development, including: ○ In situ hybridization to detect mRNA. ○ Antibody staining or green fluorescent protein (GFP) tagging to detect protein products.  Genetic Hierarchy in Drosophila Development: Understand the hierarchical control of gene expression during anterior-posterior body plan development in Drosophila, focusing on: ○ Maternal effect genes (morphogens): These genes are expressed in the mother and their mRNA or protein products are deposited in the egg, establishing gradients that influence early embryonic development. For example: Bicoid: A maternal effect gene that establishes the anterior end of the embryo. Nanos: A maternal effect gene that establishes the posterior end of the embryo. Caudal: A maternal effect gene that is uniformly distributed in the egg initially but is repressed by Bicoid protein, resulting in a posterior-to-anterior gradient. ○ Zygotic segmentation genes: These genes are expressed in the embryo and act downstream of maternal effect genes to establish the segmentation pattern of the embryo. They are categorized into: Gap genes: Expressed in broad domains and define large regions of the embryo. Pair-rule genes: Expressed in alternating stripes and define the boundaries of segments. Segment polarity genes: Expressed in a repeated pattern within each segment and determine the anterior-posterior polarity of each segment. ○ Homeotic genes: These genes act after the segmentation genes and specify the identity of each segment, determining the type of structures that will develop in each segment. Chapters 10 and 12: DNA Technology Restriction Enzymes: Understand how restriction enzymes are used to fragment DNA. Remember that restriction enzymes recognize specific DNA sequences and cut the DNA at those sites. Sticky Ends and Blunt Ends: Be able to distinguish between restriction enzymes that generate DNA fragments with sticky ends (single-stranded overhangs) and those that generate blunt-ended fragments. Sticky ends can be useful for joining DNA fragments together because complementary sticky ends can base pair. Molecular Cloning: Understand the steps involved in cloning DNA fragments, including the use of restriction enzymes to cut DNA, DNA ligase to join DNA fragments together, vectors (such as plasmids) to carry the DNA into a host cell, and the selection and screening of transformed cells. Polymerase Chain Reaction (PCR): Know the steps of PCR (denaturation, annealing, and extension) and the role of each step in amplifying a specific DNA region. DNA Sequencing: Understand the principles of DNA sequencing: ○ Sanger sequencing: Review the mechanism of Sanger sequencing, which involves the use of dideoxynucleotides (ddNTPs) to terminate DNA synthesis at specific nucleotides. Be able to interpret a sequencing chromatogram to determine the DNA sequence.  ○ Next-generation sequencing (NGS): Understand the basics of NGS, which allows for high-throughput sequencing of millions or billions of DNA fragments simultaneously. Appreciate the advantages of NGS over traditional Sanger sequencing, including its speed, cost-effectiveness, and ability to sequence entire genomes or specific regions of interest. Genome Sequencing Strategies: Be familiar with the two main genome sequencing approaches: ○ Whole-genome sequencing: Sequencing the entire genome of an organism. ○ Shotgun sequencing: Breaking the genome into random fragments, sequencing those fragments, and then assembling the sequence using overlapping fragments. Bioinformatics: Understand the role of bioinformatics in analyzing and interpreting the vast amounts of data generated by DNA sequencing projects. Chapter 21: Genome Manipulation Methods Transgenic Organisms: Understand the process of creating transgenic organisms, which involves introducing foreign DNA into an organism's genome. CRISPR/Cas9: Understand how the CRISPR/Cas9 system can be used for targeted genome editing. This system allows for the introduction of precise changes into a genome, including: ○ Gene knockouts: Disrupting a gene's function. ○ Gene knockins: Introducing a specific mutation or adding a new gene. Exam-Focused Notes on Mendelian Genetics, Chromosomes, and Gene Expression Mendelian Principles of Heredity ​ Mendel's Law of Segregation [1, 2]: The two alleles for each trait separate during gamete formation, and two gametes, one from each parent, unite randomly at fertilization. ​ Example: In a monohybrid cross between two heterozygous individuals (Aa), the phenotypic ratio of the offspring will be 3:1, with 3/4 of the offspring showing the dominant phenotype and 1/4 showing the recessive phenotype. ​ Mendel's Law of Independent Assortment : Different pairs of alleles segregate independently during gamete formation. ​ Example: In a dihybrid cross between two individuals heterozygous for two traits (AaBb), the phenotypic ratio of the offspring will be 9:3:3:1. This ratio arises from the independent assortment of the alleles for the two traits. ​ Test Crosses [1, 2]: Used to determine the genotype of an individual with a dominant phenotype. The individual is crossed with a homozygous recessive individual. ​ Example: If a plant with purple flowers (dominant phenotype) is crossed with a plant with white flowers (homozygous recessive), the offspring will all have purple flowers if the purple-flowered parent is homozygous dominant (PP). If the purple-flowered parent is heterozygous (Pp), half of the offspring will have purple flowers and half will have white flowers. ​ Branched-line Diagrams [4-6]: Useful for visualizing all possible progeny genotypes and phenotypes, particularly in dihybrid and multihybrid crosses. ​ Example: A branched-line diagram for a dihybrid cross between two individuals heterozygous for two traits (AaBb) would show all 16 possible genotypes and their corresponding phenotypes. ​ Probability Rules: The product rule and the sum rule can be used to calculate the probabilities of specific genotypes and phenotypes in crosses. ​ Product rule: The probability of two independent events occurring together is the product of their individual probabilities. ​ Sum rule: The probability of either of two mutually exclusive events occurring is the sum of their individual probabilities. Extensions to Mendel for Single-Gene Inheritance ​ Complete Dominance: The hybrid resembles one of the two parents. ​ Incomplete Dominance: The hybrid resembles neither parent. ​ Example: In a cross between red-flowered and white-flowered snapdragons, the F1 generation will have pink flowers. ​ Codominance: The hybrid shows traits from both parents. ​ Example: In human blood type, the A and B alleles are codominant. ​ Multiple Alleles: Some genes have more than two alleles. [8, 9] ​ Example: The ABO blood group system in humans has three alleles: A, B, and O. ​ Pleiotropy: One gene can affect multiple traits. ​ Example: The gene responsible for cystic fibrosis affects multiple organ systems. ​ Recessive Lethal Alleles: Some alleles are lethal when homozygous recessive. ​ Example: The allele for yellow coat color in mice is lethal when homozygous. ​ Penetrance: The proportion of individuals with a specific genotype that exhibit the expected phenotype.  ​ Expressivity: The degree to which a phenotype is expressed in an individual with a specific genotype. Extensions to Mendel for Two-Gene Inheritance ​ Epistasis: The interaction between genes where the phenotype of one gene masks the phenotype of another gene. [11, 12] ​ Example: In Labrador retrievers, coat color is determined by two genes. One gene determines whether the dog will have black or brown pigment, and the other gene determines whether the pigment will be deposited in the hair. ​ Locus Heterogeneity: A phenotype can be caused by mutations in different genes. ​ Complementation: Two mutations that produce the same phenotype can be in different genes. ​ Example: If two white-flowered plants are crossed and produce offspring with colored flowers, the mutations are in different genes. Chromosomes and Inheritance ​ Chromosomes: The carriers of genes. ​ Somatic Cells: Diploid (2n) cells that make up the body of an organism. ​ Gametes: Haploid (n) cells (sperm and egg) that are involved in sexual reproduction. ​ Zygotes: Diploid (2n) cells formed by the fusion of a sperm and egg. ​ Homologous Chromosomes: Chromosomes that carry the same genes but may have different alleles. ​ Sister Chromatids: Two identical copies of a chromosome that are joined together at the centromere. ​ Mitosis: Cell division that preserves chromosome number. [14-16] ​ Interphase: Period of cell growth and chromosome duplication. ​ Prophase: Chromosomes condense and the nuclear envelope breaks down. ​ Metaphase: Chromosomes align at the metaphase plate. ​ Anaphase: Sister chromatids separate and move to opposite poles of the cell. ​ Telophase: Nuclear envelopes reform and chromosomes decondense. ​ Cytokinesis: The cytoplasm divides, producing two daughter cells. [17, 18] ​ Meiosis: Cell division that halves chromosome number, producing haploid gametes. [19, 20] ​ Meiosis I: Homologous chromosomes separate. ​ Meiosis II: Sister chromatids separate. ​ Sex Chromosomes: Chromosomes that determine sex. [14, 21] ​ In humans: XX = female, XY = male. ​ Sex Linkage: Genes located on the sex chromosomes. ​ Example: The gene for red-green color blindness is located on the X chromosome. Gene Linkage and Recombination ​ Gene Linkage: Genes located on the same chromosome tend to be inherited together. [22, 23] ​ Recombination: The exchange of genetic material between homologous chromosomes during meiosis. [22, 23] ​ Crossing Over: The physical exchange of chromosome segments between homologs. ​ Recombination Frequency: The proportion of offspring that have recombinant genotypes. [24, 25] ​ Used to map genes: The closer two genes are on a chromosome, the lower their recombination frequency. [24, 25]  ​ Parental Gametes: Gametes that contain the same combination of alleles as the parent. [22, 23] ​ Recombinant Gametes: Gametes that contain a different combination of alleles than the parent. [22, 23] DNA Structure ​ DNA: Deoxyribonucleic acid. A double helix composed of two antiparallel strands of nucleotides. ​ Nucleotides: The building blocks of DNA. Composed of a sugar (deoxyribose), a phosphate group, and a nitrogenous base. [27, 28] ​ Nitrogenous Bases: Adenine (A), guanine (G), cytosine (C), and thymine (T). [28, 29] ​ Base Pairing: A pairs with T, and G pairs with C. ​ Antiparallel Strands: The two strands of DNA run in opposite directions. [30, 31] ​ Phosphodiester Bonds: Covalent bonds joining adjacent nucleotides in a DNA strand. ​ Hydrogen Bonds: Weak bonds that hold the two strands of DNA together. DNA Replication ​ Semiconservative Replication: Each new DNA molecule consists of one original strand and one newly synthesized strand. [32-34] ​ DNA Polymerase: Enzyme that catalyzes the addition of nucleotides to a growing DNA strand. [31, 34] ​ DNA polymerase III: Primary enzyme in DNA replication. [35, 36] ​ DNA polymerase I: Fills in gaps between Okazaki fragments. ​ Primers: Short RNA sequences that provide a starting point for DNA synthesis. [31, 35, 36] ​ Leading Strand: The strand of DNA that is synthesized continuously. ​ Lagging Strand: The strand of DNA that is synthesized discontinuously as Okazaki fragments. ​ Okazaki Fragments: Short DNA fragments that are synthesized on the lagging strand. [35, 36] ​ DNA Helicase: Enzyme that unwinds the DNA double helix. ​ Single-Stranded Binding Proteins: Proteins that keep the DNA strands separated during replication. ​ Primase: Enzyme that synthesizes RNA primers. ​ Ligase: Enzyme that joins Okazaki fragments together. [36, 37] ​ Topoisomerase: Enzyme that relaxes supercoils in DNA. [36, 37] ​ Telomeres: Repetitive DNA sequences at the ends of chromosomes. [34, 38] ​ Protect chromosomes from degradation. Mutations and Gene Function ​ Mutations: Changes in the DNA sequence. ​ Somatic Mutations: Mutations that occur in body cells. ​ Germ-Line Mutations: Mutations that occur in gamete-producing cells. ​ Types of Mutations: ​ Point Mutations: Changes in a single nucleotide. ​ Insertions: Addition of one or more nucleotides. ​ Deletions: Removal of one or more nucleotides. ​ Effects of Mutations: ​ Silent Mutations: Do not change the amino acid sequence. ​ Missense Mutations: Change one amino acid in the protein.  ​ Nonsense Mutations: Create a premature stop codon. ​ Frameshift Mutations: Shift the reading frame of the gene, altering the amino acid sequence. ​ DNA Repair: Cells have mechanisms to repair DNA damage. ​ Proofreading: DNA polymerase can correct errors during replication. Proteins and Gene Expression ​ Central Dogma: The flow of genetic information from DNA to RNA to protein. [43, 44] ​ Transcription: DNA is copied into RNA. ​ Translation: RNA is used to synthesize a protein. ​ RNA: Ribonucleic acid. A single-stranded molecule composed of nucleotides. ​ Messenger RNA (mRNA): Carries the genetic information from DNA to the ribosomes. ​ Transfer RNA (tRNA): Carries amino acids to the ribosomes during translation. [47, 48] ​ Ribosomal RNA (rRNA): A structural component of ribosomes. ​ Genetic Code: The set of rules that relate the sequence of nucleotides in mRNA to the sequence of amino acids in a protein. ​ Codons: Three-nucleotide sequences in mRNA that specify an amino acid. [48, 50] ​ Transcription: ​ Promoter: A DNA sequence that signals the start of a gene. [45, 51] ​ RNA Polymerase: Enzyme that catalyzes transcription. [51, 52] ​ Template Strand: The strand of DNA that is used as a template for RNA synthesis. [46, 53] ​ RNA-Like Strand: The strand of DNA that has the same sequence as the RNA transcript, except that T is replaced with U. [46, 53] ​ RNA Processing (Eukaryotes): ​ 5' Cap: A modified guanine nucleotide added to the 5' end of mRNA. ​ 3' Poly-A Tail: A string of adenine nucleotides added to the 3' end of mRNA. ​ Splicing: The removal of introns from pre-mRNA. [44, 54-57] ​ Introns: Noncoding sequences that are removed from pre-mRNA. [44, 57] ​ Exons: Coding sequences that are joined together to form mature mRNA. [44, 57] ​ Translation: ​ Ribosomes: The sites of protein synthesis. ​ Anticodon: A three-nucleotide sequence on tRNA that is complementary to a codon on mRNA. ​ Initiation: The ribosome binds to mRNA and the first tRNA carrying methionine (Met) binds to the start codon (AUG). ​ Elongation: Amino acids are added to the growing polypeptide chain one at a time. ​ Termination: The ribosome reaches a stop codon (UAA, UAG, or UGA) and translation stops. Gene Regulation in Prokaryotes ​ Operon: A cluster of genes that are transcribed together and controlled by a single promoter. [60, 61] ​ lac Operon: An operon in E. coli that controls the metabolism of lactose. [60, 61] ​ Structural Genes: lacZ, lacY, and lacA, which encode enzymes involved in lactose metabolism. ​ Operator: A DNA sequence near the promoter that can be bound by a repressor protein. ​ Repressor: A protein that binds to the operator and prevents transcription.  ​ Inducer: A molecule that binds to the repressor and causes it to release from the operator, allowing transcription to occur. ​ Allolactose is the inducer of the lac operon. ​ Positive Regulation: A regulatory protein activates transcription. ​ Negative Regulation: A regulatory protein inhibits transcription. Gene Regulation in Eukaryotes ​ Chromatin Structure: Chromatin structure can affect gene expression. ​ Heterochromatin: Highly condensed chromatin that is generally transcriptionally inactive. ​ Euchromatin: Less condensed chromatin that is generally transcriptionally active. ​ Transcription Factors: Proteins that bind to DNA and regulate transcription. ​ Enhancers: DNA sequences that can enhance transcription. [63, 65, 66] ​ Silencers: DNA sequences that can repress transcription. ​ RNA Interference (RNAi): A mechanism of gene regulation that involves small RNA molecules. ​ MicroRNAs (miRNAs): Small RNA molecules that can bind to mRNA and inhibit translation. Epigenetics ​ Epigenetics: Heritable changes in gene expression that do not involve changes in the DNA sequence. ​ DNA Methylation: The addition of a methyl group to a cytosine base in DNA. ​ Can silence genes. ​ Histone Modification: The addition or removal of chemical groups to histone proteins. ​ Can affect chromatin structure and gene expression. ​ Genomic Imprinting: The expression of a gene depends on the parent from which it was inherited. [68-70] Genes and Development ​ Model Organisms: Organisms that are used to study biological processes. [71, 72] ​ Examples: Drosophila melanogaster (fruit fly), Caenorhabditis elegans (nematode), Mus musculus (mouse). ​ Maternal Effect Genes: Genes that are expressed in the mother and whose products affect the development of the embryo. [72, 73] ​ Morphogens: Proteins that establish concentration gradients in the embryo and influence cell fate. [72, 73] ​ Bicoid and Nanos: Maternal effect genes that establish the anterior-posterior axis in Drosophila embryos. [74, 75] ​ Zygotic Genes: Genes that are expressed in the embryo. [73, 74] ​ Segmentation Genes: Genes that control the development of body segments. [72-74] ​ Gap Genes: Define broad regions of the embryo. [76, 77] ​ Pair-Rule Genes: Define alternating segments. ​ Segment Polarity Genes: Define the anterior-posterior polarity of each segment. ​ Homeotic Genes: Genes that specify the identity of body segments. [72, 73, 78] ​ Mutations in homeotic genes can cause transformations of body parts. DNA Technology ​ Restriction Enzymes: Enzymes that cut DNA at specific sequences. [79, 80] ​ Used to fragment DNA.  ​ Gel Electrophoresis: A technique for separating DNA fragments by size. [80, 81] ​ Molecular Cloning: The process of inserting a DNA fragment into a vector and amplifying it in a host cell. [81, 82] ​ Vectors: DNA molecules that can carry foreign DNA into a host cell. ​ Plasmids: Small, circular DNA molecules that are commonly used as vectors. [82, 83] ​ Bacterial Artificial Chromosomes (BACs): Large vectors that can carry large DNA inserts. ​ Yeast Artificial Chromosomes (YACs): Even larger vectors than BACs. ​ Genomic DNA Libraries: Collections of clones that contain the entire genome of an organism. ​ Polymerase Chain Reaction (PCR): A technique for amplifying a specific DNA sequence. [84-86] ​ Requires primers: Short DNA sequences that are complementary to the target sequence. ​ DNA Sequencing: The process of determining the order of nucleotides in a DNA molecule. [87, 88] ​ Sanger Sequencing: A classic method of DNA sequencing that uses dideoxynucleotides (ddNTPs). [89-93] ​ Next-Generation Sequencing (NGS): High-throughput sequencing technologies that can sequence millions or billions of DNA fragments in parallel. [94-96] ​ Genome Sequencing: The process of determining the entire DNA sequence of an organism's genome. [96, 97] ​ Bioinformatics: The science of using computational tools to analyze biological data. ​ Transgenic Organisms: Organisms that have been genetically modified by the introduction of foreign DNA. ​ CRISPR/Cas9: A gene editing tool that can be used to make precise changes to the DNA sequence. Ploidy ​ Ploidy: The number of chromosome sets in a cell. [100, 101] ​ Haploid (n): One set of chromosomes. ​ Diploid (2n): Two sets of chromosomes. ​ Polyploid: More than two sets of chromosomes. ​ Aneuploidy: An abnormal number of chromosomes. ​ Monosomy: One chromosome is missing. [100, 102] ​ Trisomy: One extra chromosome is present. [100, 102] Genome Architecture and Evolution ​ Syntenic Blocks: Conserved segments of chromosomes in different species. ​ Gene Families: Groups of genes that are related by sequence and function. ​ Homologs: Genes that are related by descent from a common ancestor. ​ Orthologs: Homologous genes in different species. ​ Paralogs: Homologous genes within the same species. ​ Exon Shuffling: The rearrangement of exons during evolution, leading to new combinations of protein domains. ​ De Novo Genes: Genes that arise from noncoding DNA sequences. Prokaryote Genetics ​ Bacteria: Prokaryotic organisms that lack a nucleus and membrane-bound organelles. [104, 105] ​ Bacterial Genomes: Typically circular and smaller than eukaryotic genomes. ​ Core Genome: Genes that are shared by all strains of a bacterial species. ​ Pangenome: The core genome plus all genes that are found in some strains. ​ Plasmids: Small, circular DNA molecules that can replicate independently of the bacterial chromosome. ​ Can carry genes that confer antibiotic resistance. ​ Gene Transfer in Bacteria: ​ Transformation: The uptake of foreign DNA from the environment. ​ Transduction: The transfer of DNA by bacteriophages (viruses that infect bacteria). ​ Conjugation: The transfer of DNA from one bacterium to another through direct contact. [104, 107] ​ F Plasmid: A plasmid that can integrate into the bacterial chromosome and transfer genes by conjugation. [104, 108] ​ Transposable Elements: DNA sequences that can move from one location to another in the genome. ​ Insertion Sequences (IS elements): Simple transposable elements. [104, 108] ​ Transposons (Tn elements): More complex transposable elements that can carry genes.