DNA Replication, Transcription and Gametogenesis PDF

LESSON 2 "replication bubble," a region where the two DNA Polymerase - The enzyme responsible DNA strands have separated. for building new DNA strands. It adds free Replication Fork: Within the replication bubble nucleotides...

LESSON 2 "replication bubble," a region where the two DNA Polymerase - The enzyme responsible DNA strands have separated. for building new DNA strands. It adds free Replication Fork: Within the replication bubble nucleotides (the building blocks of DNA: are "replication forks," Y-shaped structures adenine, thymine, cytosine, and guanine) to where the DNA is actively being unwound. The the existing DNA strand, following the process proceeds in both directions away from base-pairing rules (A with T, and C with G). the origin. DNA Replication DNA Polymerase and Strand Synthesis: DNA -​ is a semi-conservative process, polymerase (the enzyme labeled at the top of meaning each new DNA molecule is the image) moves along each separated composed of one original (parental) strand, adding new nucleotides to build new strand and one newly synthesized complementary strands. Notice the arrows strand. indicating the direction of synthesis. This Process: synthesis is not simultaneous for both strands. DNA Polymerase: The enzyme responsible for Leading and Lagging Strands: One strand (the building new DNA strands. It adds free leading strand) is synthesized continuously in nucleotides (the building blocks of DNA: the 5' to 3' direction (meaning that nucleotides adenine, thymine, cytosine, and guanine) to are added to the 3' end). The other strand (the the existing DNA strand, following the lagging strand) is synthesized discontinuously base-pairing rules (A with T, and C with G). in short fragments called Okazaki fragments, Helicase: The enzyme that unwinds and because DNA polymerase can only build in the separates the original DNA double helix, 5' to 3' direction. To synthesize the lagging creating a replication fork—the point where the strand, the polymerase must work against the DNA is being unwound and copied. direction of the replication fork, therefore Leading Strand: The strand that's synthesized needing to start and stop multiple times. continuously in the 5' to 3' direction as the Completion: The bottom image shows the final DNA unwinds. result: two identical DNA molecules, each Lagging Strand: The strand that's synthesized consisting of one original (parental) strand and discontinuously in short fragments (Okazaki one newly synthesized strand fragments) because it's built in the opposite (semi-conservative replication). Each new direction of the replication fork's movement. molecule is completely double-stranded. Original (template) DNA: The existing DNA —----------------------------------------------------------- molecule that serves as a template for the new Original DNA (Parent DNA): The DNA strands being synthesized. Each strand double-stranded DNA molecule that's being of the original DNA serves as a template for a replicated. Note that the double helix is new complementary strand. unwound at a specific point. —----------------------------------------------------------- Helicase: The enzyme that unwinds the DNA Initial State: The topmost image shows a double helix. It's shown at the replication fork, double-stranded DNA molecule. This is the separating the two parental strands. original DNA that needs to be replicated. The Primase: This enzyme is crucial. It synthesizes text points out that in eukaryotes (organisms short RNA primers. These primers provide a with complex cells), there are multiple "origins starting point for DNA polymerase, as DNA of replication" along the DNA strand, meaning polymerase can't initiate DNA synthesis on its replication starts at several points own—it needs a 3'-OH group to add simultaneously. This is to speed up the nucleotides to. The image shows the RNA process given the much larger size of primers in place on both the leading and eukaryotic genomes. lagging strands. Replication Bubble Formation: The second DNA Polymerase: This enzyme adds image shows the beginning of replication. An nucleotides to the 3' end of the growing DNA enzyme called helicase unwinds the double strand, following the base-pairing rules (A with helix at the origin of replication. This creates a T, and C with G). The image shows DNA polymerase working on both the leading and Ligase: After the Okazaki fragments are lagging strands. synthesized, the enzyme ligase joins them Leading Strand: DNA synthesis occurs together to form a continuous strand. This is continuously in the 5' to 3' direction. Only one shown by the "ligase" label connecting the primer is needed. Okazaki fragments. Lagging Strand: DNA synthesis is 5' End Replication: The synthesis of Okazaki discontinuous, creating Okazaki fragments. fragments happens in a way that the new DNA Multiple RNA primers are needed because is added to 5' end of the previous Okazaki DNA polymerase works in the 5' to 3' direction, fragment. but the lagging strand runs in the opposite Primer-placed nucleotides: The newly added direction of the replication fork. Each Okazaki nucleotides to the 5' end of the each Okazaki fragment requires a new primer. fragments. Okazaki Fragments: Short, newly synthesized —----------------------------------------------------------- DNA fragments on the lagging strand. Simplified representation of the replication Topoisomerase: This enzyme isn't directly fork during DNA replication, focusing on involved in the synthesis but is crucial for the difference between leading and lagging relieving the torsional strain caused by strand synthesis: unwinding the DNA ahead of the replication Parental DNA: The original double-stranded fork. It prevents supercoiling. DNA molecule is shown at the top. The 5' and RNA Primers: Short RNA sequences that 3' ends of each strand are indicated. provide a starting point for DNA polymerase. Replication Fork: The Y-shaped structure These are later removed and replaced with where the DNA strands are separating is the DNA. replication fork. —----------------------------------------------------------- Leading Strand: This strand is synthesized Contrast between leading and lagging continuously in the 5' to 3' direction. The arrow strand synthesis during DNA replication: indicates the direction of synthesis, which is Top (Leading Strand): the same as the movement of the replication Continuous Replication: The leading strand is fork. synthesized continuously in the 5' to 3' Lagging Strand: This strand is synthesized direction. This means that DNA polymerase discontinuously in short fragments called can add nucleotides to the 3' end of the Okazaki fragments. The arrows indicate the growing strand without interruption as the direction of synthesis of each Okazaki replication fork moves along the DNA fragment (5' to 3'), which is opposite to the molecule. This is indicated by the continuous movement of the replication fork. line of new nucleotides. Okazaki Fragments: The short DNA fragments 3' End Replication: The continuous synthesis that make up the lagging strand are happens at the 3' end of the growing strand. highlighted. Bottom (Lagging Strand): —----------------------------------------------------------- Discontinuous Replication: The lagging strand 3 Models of DNA replication: is synthesized discontinuously. This is Conservative: The original parental DNA because DNA polymerase can only synthesize remains intact, and a completely new DNA in the 5' to 3' direction. As the replication fork molecule is synthesized. After two rounds, progresses, the lagging strand must be you'd have one original double helix and three synthesized in short fragments (Okazaki entirely new ones. fragments). Semi-conservative: Each new DNA molecule Okazaki Fragments: These are the short DNA consists of one original (parental) strand and fragments synthesized on the lagging strand. one newly synthesized strand. This is the Each fragment requires a separate RNA correct model. After two rounds, you have two primer (indicated by the small circles). molecules with one original strand and one RNA Primers: These are short RNA entirely new strand, and two molecules that sequences that provide a starting point for are entirely new. DNA polymerase. Dispersive: The parental DNA is dispersed the 5' to 3' direction, using the DNA throughout both new DNA molecules. After template strand as a guide. two rounds, the original DNA would be even -​ The RNA nucleotides are added more diluted in the new molecules. according to base-pairing rules (A —----------------------------------------------------------- pairs with U in RNA, and G pairs with Transcription C). The image shows the growing -​ is the first step in gene expression, RNA strand extending away from the where the information encoded in a DNA. DNA sequence is copied into a Termination: messenger RNA (mRNA) molecule. -​ Transcription ends when RNA DNA (Deoxyribonucleic Acid): This is the polymerase reaches a termination original genetic material. The image shows a sequence on the DNA. segment of DNA with a sequence of bases: -​ The RNA polymerase detaches from 3'-ATGAGTCCAAGT-5'. The complementary the DNA, and the newly synthesized strand is also shown: 5'-TACTCAGGTTCA-3'. RNA molecule is released. The DNA Note that in DNA, Adenine (A) pairs with double helix rewinds. The image Thymine (T), and Guanine (G) pairs with depicts the separation of the RNA Cytosine (C). transcript from the DNA template. Transcription: This is the process where the —----------------------------------------------------------- DNA sequence is used as a template to create Processing of pre-mRNA into mature an mRNA molecule. The enzyme RNA mRNA in eukaryotes. Several steps are polymerase is responsible for this. required before the pre-mRNA can be mRNA (Messenger Ribonucleic Acid): This is translated into a polypeptide: the RNA copy of the DNA sequence. The Transcription: The process begins with image displays the mRNA sequence produced transcription by RNA polymerase II, which from the DNA template: uses DNA as a template to synthesize a 5'-UACUCAGGUUCA-3'. Note that in RNA, pre-mRNA molecule. The pre-mRNA includes: Uracil (U) replaces Thymine (T), so A pairs -​ Promoter: A DNA region that signals with U. the start of transcription. Codons: These are three-nucleotide -​ Exons: Coding sequences that will be sequences in mRNA that specify particular part of the final mRNA. amino acids during protein synthesis -​ Introns: Non-coding sequences that (translation). The mRNA sequence is divided are interspersed between exons. into codons in the image. -​ 5' Untranslated Region (5' UTR): A —----------------------------------------------------------- region at the 5' end of the pre-mRNA 3 Stages of Transcription: that isn't translated into protein but Initiation: plays a role in translation initiation. -​ RNA polymerase, the enzyme -​ 3' Untranslated Region (3' UTR): A responsible for transcription, binds to a region at the 3' end of the pre-mRNA specific region of the DNA called the that isn't translated but is involved in promoter. The promoter signals the translation termination and mRNA starting point of transcription. stability. -​ The DNA double helix unwinds around 5' Capping: A 5' GTP cap is added to the 5' the promoter region, allowing RNA end of the pre-mRNA molecule. This cap polymerase access to the template protects the mRNA from degradation and strand. helps with ribosome binding during translation. Elongation: 3' Poly(A) Tail Addition: A poly(A) tail (a string -​ RNA polymerase moves along the of adenine nucleotides) is added to the 3' end. template strand of the DNA, This tail also protects the mRNA from synthesizing a complementary RNA degradation and aids in export from the molecule. The RNA molecule is built in nucleus. RNA Splicing: Introns are removed, and exons —----------------------------------------------------------- are joined together to form a continuous 3 types of RNA involved in protein protein-coding sequence. This process is synthesis: performed by a spliceosome. mRNA (messenger RNA): Depicted as a Mature mRNA: The resulting mRNA molecule single-stranded, linear molecule. Its function is contains only exons and the 5' cap and 3' to carry the genetic code from DNA to the poly(A) tail. It is now ready for translation. ribosome, encoding the sequence of amino Translation: The mature mRNA is transported acids in a protein. to the ribosomes where the protein-coding tRNA (transfer RNA): Illustrated as a sequence is translated into a polypeptide cloverleaf-shaped molecule. Its role is to act chain (protein). as an adapter between mRNA and amino —----------------------------------------------------------- acids. It carries a specific amino acid to the Translation ribosome based on the mRNA codon it Processes of transcription and translation, recognizes. fundamental steps in gene expression rRNA (ribosomal RNA): Shown as a more within a cell: complex, globular structure. rRNA forms the Transcription: structural and catalytic core of the ribosome, -​ This process occurs within the cell the molecular machine responsible for nucleus. assembling amino acids into polypeptide -​ RNA polymerase, an enzyme, chains (proteins). unwinds a segment of DNA. —----------------------------------------------------------- -​ The enzyme then uses one strand of Codon table - used to translate a the DNA as a template to synthesize a three-nucleotide mRNA sequence (a codon) complementary strand of messenger into the corresponding amino acid during RNA (mRNA). protein synthesis. -​ The mRNA molecule is then To use the table: transported out of the nucleus into the Find the first base of the codon in the "First cytoplasm. base in codon" column on the left. Translation: Find the second base in the top row ("Second -​ This process takes place in the cell base in codon"). cytoplasm. Find the third base in the "Last base in codon" -​ The mRNA molecule binds to a column on the right. ribosome, a complex molecular The amino acid corresponding to that codon is machine. found at the intersection of these three -​ The ribosome moves along the positions. mRNA, reading it in groups of three For example, the codon AUG codes for nucleotides called codons. Methionine (Met), and also serves as a start -​ Each codon specifies a particular codon. The codons UAA, UAG, and UGA are amino acid. stop codons, signaling the end of protein -​ Transfer RNA (tRNA) molecules, each synthesis. Each codon specifies a particular carrying a specific amino acid, amino acid (or a stop signal), and multiple recognize and bind to the codons on codons can often code for the same amino the mRNA. acid (redundancy in the genetic code). -​ The ribosome links the amino acids together to form a growing polypeptide chain. -​ As the ribosome moves along the mRNA, the polypeptide chain grows until a stop codon is reached. -​ The completed polypeptide chain is then released from the ribosome, and it folds into a functional protein.  LESSON 3 in the gametes (Combination 3 and Gametogenesis is the biological process of Combination 4). producing gametes (sex cells). This independent assortment of chromosomes 2 types: during meiosis is a major source of genetic Oogenesis: The production of female gametes variation. The different combinations of (ova). A diploid (2n) primary oocyte undergoes chromosomes in the gametes mean that meiosis I to produce a haploid (n) secondary offspring inherit unique combinations of genes oocyte and a polar body (which usually from each parent. This is in addition to other degenerates). The secondary oocyte then sources of variation, such as crossing over undergoes meiosis II resulting in a haploid (recombination) that occurs during meiosis. ovum and another polar body. —----------------------------------------------------------- Spermatogenesis: The production of male Spermatogenesis gametes (sperm). A diploid (2n) primary -​ the process of sperm production in the spermatocyte undergoes meiosis I to produce testes. two haploid (n) secondary spermatocytes. -​ Location: Spermatogenesis occurs Each secondary spermatocyte undergoes within the seminiferous tubules of the meiosis II to yield two haploid spermatids. testes. These spermatids mature into sperm. Key stages: Fertilization is the fusion of a haploid ovum Spermatogonium: Diploid stem cells located and a haploid sperm, restoring the diploid (2n) near the basement membrane of the chromosome number in the resulting zygote. seminiferous tubules. —----------------------------------------------------------- Primary Spermatocyte: Spermatogonium Sexual reproduction involves the fusion of undergoes mitosis to produce primary two gametes—a sperm (male gamete) and an spermatocytes, which are still diploid. egg (female gamete)—to form a zygote. The Meiosis I: The primary spermatocyte zygote is a single diploid cell that contains undergoes meiosis I, a reductional division, genetic material from both parents and is the producing two haploid secondary first stage of development of a new organism. spermatocytes. Fertilization is the process of the sperm and Secondary Spermatocyte: Each secondary egg fusing. spermatocyte undergoes meiosis II, an —----------------------------------------------------------- equational division producing two haploid Meiosis: The Foundation of Gametogenesis round spermatids. The image illustrates how meiosis Round Spermatid: These haploid cells contributes to genetic diversity during undergo spermiogenesis, a differentiation gametogenesis. process. Meiosis is a type of cell division that reduces Spermatozoa (Sperm): The mature sperm the chromosome number by half, producing cells, characterized by a head (containing the haploid gametes (sperm and egg cells). acrosome and nucleus), a midpiece (rich in The key point is that there are two equally mitochondria), and a flagellum (tail) enabling probable arrangements of homologous motility. chromosomes at Metaphase I. This leads to —----------------------------------------------------------- different combinations of chromosomes Spermiogenesis being passed to the gametes. -​ the final stage of spermatogenesis where spermatids transform into Possibility 1 shows one arrangement leading mature spermatozoa (sperm). to two different combinations of chromosomes Key changes during spermiogenesis: in the resulting gametes (Combination 1 and Golgi Apparatus Activity: The Golgi apparatus Combination 2). packages enzymes into the acrosomal vesicle. Possibility 2 shows the alternative Acrosome Formation: The acrosomal vesicle arrangement at Metaphase I, resulting in two forms the acrosome, a cap-like structure over more different combinations of chromosomes the nucleus containing enzymes essential for fertilization (penetrating the egg's outer -​ This image illustrates oogenesis, the layers). process of egg (ovum) formation, and Nuclear Condensation: The nucleus becomes its relationship to the ovarian cycle. highly condensed, reducing its volume and Ovarian Cycle: The ovarian cycle is divided increasing its density. into 3 phases: Flagellum Development: A flagellum develops Follicular Phase: This phase begins with the from the centriole, providing motility to the development of primordial follicles containing sperm. primary oocytes. These follicles mature into Mitochondria Aggregation: Mitochondria Graafian follicles, containing secondary aggregate in the midpiece, providing energy oocytes. The follicles produce estrogen. for the sperm's movement. Ovulation Phase: A mature Graafian follicle Excess Cytoplasm Shedding: Excess ruptures, releasing a secondary oocyte into cytoplasm is shed, streamlining the sperm's the fallopian tube (ovulation). structure for efficient movement. Luteal Phase: After ovulation, the ruptured The result is a mature spermatozoon with a follicle transforms into the corpus luteum, head (containing the acrosome and which secretes progesterone. If fertilization condensed nucleus), a midpiece (containing does not occur, the corpus luteum mitochondria), and a flagellum (tail). degenerates. —----------------------------------------------------------- Key stages: Hormonal Control of Spermatogenesis Primary Oocyte (2n): A diploid cell that begins Hypothalamus: Releases GnRH meiosis I. Only one mature ovum is produced (gonadotropin-releasing hormone). per cycle. Anterior Pituitary: GnRH stimulates the Meiosis I: The primary oocyte undergoes anterior pituitary to release FSH meiosis I, producing a secondary oocyte (n) (follicle-stimulating hormone) and LH and a first polar body (n). The first polar body (luteinizing hormone). usually degenerates. Testes: Secondary Oocyte (n) (Oocyte II): The -​ FSH: Acts on Sertoli cells in the secondary oocyte proceeds to meiosis II only if seminiferous tubules. Sertoli cells fertilization occurs. support spermatogenesis and produce Meiosis II: If fertilization occurs, the secondary ABP (androgen-binding protein). oocyte completes meiosis II, producing a -​ LH: Acts on Leydig cells in the testes, mature ovum (n) and a second polar body (n). stimulating testosterone production. The second polar body also typically Testosterone: Testosterone is essential for degenerates. If fertilization doesn't occur, spermatogenesis and also provides negative meiosis II stops. feedback to the hypothalamus and anterior Ovum (n): The mature haploid egg cell. pituitary, regulating hormone levels. Inhibin: Sertoli cells also produce inhibin, Compared to the key stages of which inhibits FSH release from the anterior spermatogenesis: pituitary, providing another level of feedback Primary Spermatocyte (2n): A diploid cell that control. begins meiosis I. In summary, this is a negative feedback loop. Meiosis I: The primary spermatocyte The hypothalamus, anterior pituitary, and undergoes meiosis I, producing two haploid testes interact through hormonal signals to secondary spermatocytes. maintain appropriate levels of testosterone Secondary Spermatocyte (n): Each secondary and to support spermatogenesis. Testosterone spermatocyte undergoes meiosis II. and inhibin regulate the release of GnRH, Meiosis II: Each secondary spermatocyte FSH, and LH. produces two haploid spermatids. —----------------------------------------------------------- Spermatid (n): These then differentiate into Oogenesis mature sperm. -​ The formation of eggs occurs in the Sperm (n): Mature haploid sperm cells. ovaries. Fertilization: The image shows that fertilization resulting in recombinant chromosomes. This involves the fusion of a haploid ovum and a shuffling of genetic material creates new haploid sperm, resulting in a diploid zygote combinations of alleles, increasing genetic (2n). The zygote contains genetic material diversity in the resulting gametes. from both parents. Note that only one ovum is Therefore, gametogenesis, through meiosis produced during each oogenesis cycle, while and crossing over, is crucial for genetic spermatogenesis produces four sperm. diversity within a population. This variation is —----------------------------------------------------------- essential for adaptation and evolution. Hormonal Control of Oogenesis —----------------------------------------------------------- Hypothalamus: Releases GnRH Gametogenesis in Human Health (gonadotropin-releasing hormone). Sperm Defects: The image shows various Pituitary Gland: GnRH stimulates the pituitary sperm abnormalities: gland to release LH (luteinizing hormone) and Head Defects: Abnormal head shapes can FSH (follicle-stimulating hormone). affect the sperm's ability to penetrate the egg. Ovary: LH and FSH stimulate the ovaries to Midpiece Defects: Defects in the midpiece produce estrogen and progesterone. (containing mitochondria) impair sperm Estrogen and Progesterone: These hormones motility. regulate the uterine lining and have feedback Tail Defects: Abnormal tails reduce or effects on the hypothalamus and pituitary eliminate sperm motility. gland. There is primarily negative feedback, Acrosomeless: Lack of an acrosome prevents except for a period of positive feedback the sperm from penetrating the egg. around days 12-14 of the cycle, which triggers These defects can lead to infertility. ovulation. Uterus: Estrogen and progesterone prepare Normal Karyotype: The image also shows a the uterus for potential implantation of a normal human karyotype (a complete set of fertilized egg. human chromosomes). This is used for In short, the hypothalamus, pituitary gland, comparison to highlight that normal and ovaries interact through hormonal signals gametogenesis results in a normal to regulate the menstrual cycle and oogenesis. chromosome complement in the gametes. The levels of estrogen and progesterone are Genetic abnormalities in gametes (aneuploidy, controlled by feedback mechanisms involving chromosomal translocations) can lead to LH, FSH, and GnRH. Positive feedback genetic disorders in offspring. around the time of ovulation leads to a surge In conclusion, proper gametogenesis is in LH and FSH, triggering the release of the crucial for reproductive health. Errors during egg. Negative feedback maintains hormonal gametogenesis can result in sperm defects balance throughout most of the cycle. and/or chromosomal abnormalities in the —----------------------------------------------------------- gametes, leading to infertility or genetic See sa pic yung comparison table ng disorders in offspring. spermatogenesis at oogenesis —----------------------------------------------------------- —----------------------------------------------------------- Gametogenesis in Other Organisms Significance of Gametogenesis It shows an example of cyclical Process of crossing over (recombination) parthenogenesis in an organism (likely an during meiosis: insect). Bivalents Develop: Homologous chromosomes Cyclical Parthenogenesis: This type of pair up to form bivalents. reproduction involves alternating generations Chiasmata Form: Chiasmata (points of of sexual and asexual reproduction. In the crossing over) form between non-sister example shown: chromatids of homologous chromosomes. During certain seasons (spring and summer), Chromosomes Break: At the chiasmata, the females produce eggs that develop into homologous chromosomes break. females through parthenogenesis (asexual Recombination Occurs: Segments of DNA are reproduction). These females are genetically exchanged between non-sister chromatids, identical to the parent. In other seasons (autumn), females produce Environmental Factors Affecting eggs that require fertilization by males to Gametogenesis develop. This leads to sexual reproduction and This image illustrates how environmental genetic recombination. factors can significantly impact Males are produced only during the autumn. gametogenesis. It uses the example of BPA (Bisphenol A) to demonstrate this: This cyclical pattern allows for periods of BPA Production and Release: BPA is rapid population growth through asexual produced in industrial settings and released reproduction combined with the benefits of into the environment through various genetic diversity through sexual reproduction. pathways, including manufacturing processes The image also indicates that other and the disposal of products containing BPA. organisms may have different mechanisms BPA Distribution: BPA contaminates various of sex determination, which is not explicitly environmental compartments, including water illustrated. Sex determination can be bodies (rivers, lakes) and soil. influenced by various factors, including BPA Biomagnification and Biotransformation: genetics, environmental cues, and social BPA can accumulate in living organisms factors, depending on the species. through biomagnification (increasing Therefore, while the basic principles of concentration as it moves up the food chain) gametogenesis are similar across many and undergo biotransformation (chemical organisms, the specific mechanisms and the alteration within organisms). overall reproductive strategies can vary Toxic Effects on Organisms: BPA exposure substantially. can have toxic effects on organisms, including —----------------------------------------------------------- humans, potentially disrupting endocrine Gametogenesis in Plants systems and impacting gametogenesis. Gametogenesis in Plants: The female Metabolic Pathways of Degradation: Some gametophyte (embryo sac) is shown, organisms, such as fungi, have metabolic containing: pathways to degrade BPA which can mitigate, Egg cell: The female gamete. but not eliminate, the effects. Polar nuclei: Two nuclei that fuse with a sperm —----------------------------------------------------------- cell. Research and Advancements Synergids: Two cells assisting fertilization. This image discusses research and Antipodals: Three cells at the opposite end of advancements in gametogenesis, focusing the embryo sac. on the potential of stem cells: Double Fertilization: The process is shown in The image shows a diagram illustrating the two stages: stages of gametogenesis in both males and Release of Sperm Cells: Two sperm cells are females. The stages are clearly depicted, released from a pollen tube. showing the progression from germ cells to Double Fertilization: One sperm cell fertilizes mature gametes. Specific features of oocyte the egg cell, forming a diploid zygote (2n), and sperm development are shown. which develops into the embryo. The other This research is relevant for: sperm cell fuses with the two polar nuclei, Infertility treatment: Stem cells could be used forming a triploid endosperm (3n), which to create functional gametes for individuals provides nourishment for the developing with infertility issues. embryo. Understanding gametogenesis: Studying stem Significance: Double fertilization is a defining cell differentiation into gametes can provide characteristic of flowering plants. It results in valuable insights into the mechanisms of the simultaneous formation of both the embryo gametogenesis itself. (diploid) and the endosperm (triploid), which is Disease modeling: Stem cell-derived gametes a nutritive tissue supporting embryo could serve as models for studying genetic development. diseases affecting gamete development. —----------------------------------------------------------- In summary, the image points towards the exciting possibilities of stem cell research in advancing our understanding and treatment of gametogenesis-related issues.  LESSON 4 In essence, genes (DNA) provide the What is Gametogenesis? instructions (transcription), which are then (read on lesson 3) used to build proteins (translation). These —----------------------------------------------------------- proteins then carry out the functions that From single cell to complex organism determine an organism's characteristics. The Early Embryonic Development: This section entire process is tightly regulated and shows the initial stages of development after integrated. fertilization: —----------------------------------------------------------- Fertilized egg: The single-celled zygote. Cell Specialization 2-cell stage: The first cell division. Stem Cells: The central element is a stem 4-cell stage: Second cell division. cell, a pluripotent cell capable of differentiating 8-cell stage: Third cell division. into various specialized cell types. 16-cell stage: Further cell divisions. Specialized Cells: The image shows several Blastocyst (70-100 cells): A hollow ball of cells, examples of specialized cells that develop marking the completion of cleavage. from stem cells: Foetal Development: This section shows the Sex cells (gametes): Sperm and egg cells, development of the foetus at different responsible for reproduction. gestational ages: Muscle cells: Cells responsible for movement. Foetus - 4 weeks: Early stages of Fat cells (adipocytes): Cells that store energy. organogenesis. Bone cells (osteocytes): Cells that form bone Foetus - 10 weeks: Major organs are tissue. developing. Immune cells: Cells involved in the immune Foetus - 16 weeks: Significant growth and response. differentiation of organs. Epithelial cells: Cells that form linings and Foetus - 20 weeks: Further growth and coverings in the body. development; many organs are functional. Nervous cells (neurons): Cells that transmit —----------------------------------------------------------- nerve impulses. Genes as Instruction Manuals: Genes are Blood cells: Cells that circulate in the blood, the functional units of heredity, containing the carrying oxygen and other substances. instructions for building and maintaining an Cell Specialization Process: The diagram organism. These instructions are written in the shows that early cells are similar, but as DNA sequence. development proceeds, they undergo The Central Dogma: The image illustrates the differentiation, acquiring specialized structures central dogma of molecular biology: and functions. This specialization is crucial for Transcription: DNA is transcribed into RNA. the formation of tissues, organs, and organ This step involves copying the genetic systems, creating a multicellular organism with information from the DNA sequence into a complex organization. The process is messenger RNA (mRNA) molecule. regulated by genes and signaling pathways. Translation: The mRNA is translated into —----------------------------------------------------------- proteins. This step involves using the Body Organization information encoded in the mRNA to assemble Levels of Organization: amino acids into a specific protein sequence. Cell: The basic unit of life. The image shows a Proteins are the workhorses of the cell, single cell as the starting point. carrying out a vast array of functions. Tissue: A group of similar cells performing a Biochemical Reactions: Proteins and enzymes specific function. The image shows epithelial catalyze biochemical reactions, transforming tissue as an example. chemicals from one form to another. These Organ: A structure composed of different reactions are essential for metabolism and all tissues working together to perform a specific cellular processes. Metabolites are the function. The stomach is used as an example. intermediate and end products of these Organ System: A group of organs working reactions. together to perform a complex function. The digestive system is shown as an example. Organism: A complete living thing, composed regulation ensures that genes are expressed of multiple organ systems. The image shows a only when and where they are needed. human body as the final level of organization. Normal Activity: A cell is depicted with a gene —----------------------------------------------------------- (Gene A) in its active state ("ON"). This Organizing the Body: Pattern Formation represents a normal level of gene expression, (Cellular Level) leading to normal cellular activity. Cleavage: The zygote (fertilized egg) Altered Activity: The same cell is shown with undergoes rapid cell division, called cleavage. Gene A in its inactive state ("OFF"). This This process increases the number of cells represents altered gene expression, potentially without a significant increase in overall size. due to various regulatory mechanisms. The The image shows the progression through result is altered cellular activity. various stages: Mechanisms of Gene Regulation: Many (see stages sa first part ng lesson 4) mechanisms control gene expression, —----------------------------------------------------------- including: Genes Make Proteins: The Workers of the Transcriptional regulation: Control of the Cell initiation of transcription (RNA synthesis from Protein Synthesis: The process is shown in 2 DNA). main stages: Post-transcriptional regulation: Control of Transcription (in the nucleus): mRNA processing, transport, and stability. Double-stranded DNA unwinds, and one Translational regulation: Control of protein strand serves as a template for the synthesis synthesis from mRNA. of messenger RNA (mRNA). The mRNA Post-translational regulation: Control of protein molecule carries the genetic code from the modification, activity, and degradation. DNA to the cytoplasm. —----------------------------------------------------------- Translation (in the cytoplasm): The mRNA Signals Between Cells molecule moves to a ribosome. Transfer RNA Chemical Signaling: The image focuses on (tRNA) molecules, each carrying a specific synaptic transmission between neurons as an amino acid, bind to the mRNA according to the example of chemical signaling. Cells genetic code. The ribosome links the amino communicate with each other using chemical acids together to form a polypeptide chain signals, not direct physical contact. (amino acid chain), which folds into a Synaptic Transmission: functional protein. Sending Cell (Presynaptic Neuron): A neuron Key Components: releases neurotransmitters (chemical DNA: The genetic material containing the messengers) into the synapse, the space instructions for protein synthesis. between two neurons. mRNA: Carries the genetic code from DNA to Neurotransmitter Release: Neurotransmitters the ribosome. are stored in vesicles and released into the tRNA: Brings amino acids to the ribosome for synapse. protein synthesis. Receiving Cell (Postsynaptic Neuron): The Ribosome: The site where protein synthesis neurotransmitters diffuse across the synapse takes place. and bind to specific receptors on the receiving Amino acids: The building blocks of proteins. neuron's membrane. Polypeptide chain: A chain of amino acids Signal Transduction: This binding initiates forming a protein. signal transduction, a series of events that —----------------------------------------------------------- ultimately alter the receiving neuron's activity. Turning Genes On and Off: Regulation Significance: Chemical signaling is essential Gene Regulation: Not all genes are active all for coordinating cellular activities and the time. Gene expression, the process by maintaining proper bodily function. It's crucial which the information encoded in a gene is for processes such as nerve impulse used to synthesize a functional gene product transmission, hormone action, and immune (usually a protein), is tightly regulated. This responses. Dysregulation of chemical signaling can lead to various diseases. The image emphasizes that communication DNA: The organism's genome containing the between cells is fundamental for the overall genetic instructions. functioning of multicellular organisms. Master control gene: A single gene that —----------------------------------------------------------- regulates the expression of several other Signal for Growth and Form genes. Signal Transduction a process by which cells Other genes: Genes that are regulated by the receive and respond to extracellular signals. master control gene. These genes control the These signals are crucial for growth and development of specific body segments or development. structures. 3 Main Steps: The arrows show that the master control gene Reception: A signal molecule (ligand) from the controls the expression of several downstream extracellular fluid binds to a receptor protein genes. These downstream genes are on the cell's plasma membrane. This binding responsible for building specific body parts initiates the signaling process. according to the body plan. Mutations in Transduction: The binding of the signal master control genes can lead to significant molecule triggers a cascade of intracellular developmental defects, such as the formation events, often involving a series of protein of body parts in the wrong location. modifications and interactions. This forms the In summary, master control genes are key signal transduction pathway. The image shows regulators of development, ensuring the a simplified representation of this pathway as proper spatial and temporal expression of a series of changes in a signaling molecule other genes necessary for establishing the within the cytoplasm. body plan in animals. They are essential for Response: The transduction pathway proper development and the formation of a ultimately leads to a cellular response, functional organism. activating specific cellular processes. This —----------------------------------------------------------- response can include changes in gene Studying How Genes Work: Finding the expression, metabolism, or cell movement, all Problem First contributing to growth and form. This image describes forward genetics, a Significance: Signal transduction is essential research approach used to understand gene for cell communication and coordination. It function. allows cells to respond to their environment Forward Genetics Steps: and regulate various cellular processes, Make random mutations: The process begins ultimately impacting growth, development, and by introducing random mutations into an overall function. Errors in signal transduction organism's genome. This can be done through can lead to various diseases. The image various methods, such as chemical highlights how extracellular signals are mutagenesis or radiation. converted into intracellular responses, driving Screen for phenotypic change: The mutated cellular processes essential for growth and organisms are then screened to identify development. individuals exhibiting a change in phenotype —----------------------------------------------------------- (observable characteristics), or a trait of Master Control Genes: Setting up the Body interest. Plan Identify gene underlying mutant phenotype: -​ also known as homeotic genes, in The gene responsible for the observed establishing the body plan of an phenotypic change is identified. This often animal. involves positional cloning or other genetic -​ Some genes act as "master mapping techniques. controllers," regulating the Forward Genetics Approach: Forward expression of many other genes. genetics starts with an observable phenotype These master control genes control and works backward to identify the gene(s) the development of body structures. responsible for that trait. It's a powerful tool for They ensure that the basic layout of uncovering the genetic basis of complex traits the animal is correct. and biological processes. The approach is particularly useful when little is known about image shows a process involving an RNA the genes involved in a particular trait. virus: —----------------------------------------------------------- Viral genome: The genetic material of the virus This image compares the old and new containing the gene of interest. paradigms of forward genetics, highlighting RT-PCR: Reverse transcription polymerase advancements in technology and efficiency. chain reaction is used to generate cDNA from Old Paradigm (Years): the viral RNA. Genetics: This stage involved mutagenesis Infectious Clone: The cDNA is cloned into a (creating mutations), gene knockout/RNAi plasmid, creating an infectious clone of the (silencing genes), and mutation mapping virus. This clone can be used to introduce the (locating genes on chromosomes). These gene into cells. steps were time-consuming. Transfection: The infectious clone is Genomics: This stage relied on introduced into a cell line. reference/model organisms and Sanger The resulting phenotypic effects are then sequencing (a relatively slow DNA sequencing analyzed to determine the function of the method). Analysis of genomic data also took a gene. By altering or inactivating the gene, significant amount of time. researchers can observe the resulting Transcriptomics: This involved microarray changes in the organism's traits or analysis (measuring gene expression) and characteristics. This approach allows for a cDNA sequencing (sequencing direct test of gene function, unlike forward complementary DNA). These methods were genetics, which starts with a phenotype and also time-consuming compared to modern works backward to find the responsible genes. techniques. Reverse genetics is a powerful tool for New Paradigm (Weeks): understanding gene function in a targeted Genetics: This stage includes manner. hypothesis-driven strain selection and the —----------------------------------------------------------- generation of novel phenotypes. This is faster Steps of Reverse Genetics because it is targeted. This image contrasts forward and reverse Genomics: This stage leverages genetics approaches. advancements in technology. It uses any Forward Genetics: This approach starts with organism, multiple samples, genome a known phenotype (observable sequences, and digital transcriptomes for characteristic). Researchers then use methods analysis. This allows for high-throughput like mutagenesis (introducing mutations), QTL analysis and faster results. mapping (mapping quantitative trait loci), Key Differences: The main difference is the positional cloning (identifying a gene based on time scale. The old paradigm took years to its location on a chromosome), etc., to complete the forward genetics process, while discover the underlying gene responsible for the new paradigm, with advancements in that phenotype. genomics and transcriptomics, reduces this Reverse Genetics: This approach starts with time to weeks. The new paradigm also allows a known gene. Researchers then use researchers to study a wider range of techniques such as ectopic expression organisms and generate larger datasets. The (expressing the gene in an unusual location), shift from hypothesis-free to hypothesis-driven gene silencing (reducing gene expression), approaches also contributes to the increased gene targeting (altering a specific gene), efficiency. TILLING (Targeting Induced Local Lesions IN —----------------------------------------------------------- Genomes), etc., to alter the gene and observe Studying How Genes Work: Messing w/ a the resulting phenotype. This helps determine Gene First the gene's function. This image illustrates reverse genetics, a Comparison: The image illustrates that method used to determine gene function. forward genetics moves from phenotype to Reverse Genetics Steps: Reverse genetics gene, while reverse genetics moves from gene starts with a known gene sequence. The to phenotype. Both approaches are valuable for understanding gene function, but they use Dicer: An enzyme that cleaves the dsRNA or different starting points and strategies. shRNA into smaller fragments called small Forward genetics is useful for identifying interfering RNAs (siRNAs). genes involved in a particular trait, while Ago (Argonaute): An enzyme that binds to the reverse genetics is useful for confirming a siRNA. Ago is part of the RNA-induced gene's function and determining its role in a silencing complex (RISC). biological process. RISC (RNA-induced silencing complex) —----------------------------------------------------------- Formation: The siRNA bound to Ago forms the CRISPR-Cas9 System: CRISPR (Clustered RISC. Regularly Interspaced Short Palindromic siRNA/mRNA Complex: The RISC complex Repeats) is a gene-editing tool that uses a then binds to a complementary messenger guide RNA molecule to target a specific DNA RNA (mRNA) molecule. sequence. The Cas9 enzyme acts as mRNA Slicing: The RISC complex cleaves molecular scissors, cutting the DNA at the (cuts) the mRNA molecule. targeted location. Gene Silencing: The sliced mRNA is Mechanism: degraded, preventing protein synthesis, which Target DNA: The DNA sequence to be edited. leads to gene silencing. Guide RNA: A short RNA molecule designed In Summary, RNAi is a powerful gene to be complementary to the target DNA regulation mechanism that uses small RNA sequence. It guides the Cas9 enzyme to the molecules to target and degrade specific correct location. mRNAs, effectively silencing the expression of PAM (Protospacer Adjacent Motif): A short the corresponding genes. This image DNA sequence located adjacent to the target illustrates the key steps in this process, from sequence. Cas9 requires the PAM sequence the initial dsRNA or shRNA to the final to bind and cut the DNA. silencing of the target gene. Cas9: A nuclease enzyme (an enzyme that —----------------------------------------------------------- cuts DNA). It is guided to the target DNA by Hox Genes: Segment Identity Genes the guide RNA and cuts both strands of the Hox Genes: Hox genes are a group of DNA at the target site. homeobox-containing genes that play a crucial DNA Cut: The cut DNA can then be repaired role in animal development. They are arranged by the cell's natural DNA repair mechanisms. in clusters, and the order of the genes in the These mechanisms can be used to introduce cluster corresponds to their expression along specific changes to the gene. For example, a the anterior-posterior axis. new DNA sequence can be inserted into the Hox Clusters: The image shows four Hox gene cut site through homologous recombination. clusters (HOXA, HOXB, HOXC, and HOXD) in How does it work? humans. Each cluster contains multiple genes. CRISPR-Cas9 is a precise tool for making Gene Order: The genes within each cluster specific changes to genes. Its ability to target are arranged in a specific order, with the order specific DNA sequences has revolutionized reflecting the spatial expression pattern along gene editing technology, with applications in the body axis. Genes at the 3' end of the various fields, including medicine, agriculture, cluster are expressed in the anterior (head) and biotechnology. region, while genes at the 5' end are —----------------------------------------------------------- expressed in the posterior (tail) region. RNA interference (RNAi), a mechanism for Temporal Expression: The genes are also silencing genes. expressed temporally, with genes at the 3' end RNAi Process: being expressed earlier in development than dsRNA or shRNA: The process begins with those at the 5' end. double-stranded RNA (dsRNA) or short hairpin Body Plan: The color-coded segments of the RNA (shRNA). These are introduced into the human figure represent the body regions cell, either naturally or experimentally. where each Hox gene is expressed. The sequential expression of Hox genes along the anterior-posterior axis defines the identity of different body segments. Mutations in Hox regulation has been maintained throughout genes can lead to major developmental evolution, highlighting its importance in abnormalities, such as the formation of body establishing the body plan. parts in the wrong locations. Drosophila HOM-C: Shows the arrangement of In Summary, The image illustrates the Hox genes in the fruit fly, with their expression colinearity of Hox genes—their spatial regions along the body shown above. arrangement in the genome mirrors their Ancestral HOM-C: Represents a hypothetical expression along the anterior-posterior body ancestral Hox gene cluster. axis. This precise spatial and temporal Human Hox genes: Shows the four human regulation of Hox genes is essential for the Hox gene clusters (HOXA, HOXB, HOXC, proper development of the body plan in HOXD). Again, the order of the genes within animals. each cluster mirrors their expression pattern Downstream Gene Regulation: Hox genes along the anterior-posterior axis of the don't directly build body structures. Instead, developing embryo. they act as master regulators, controlling the Significance: Colinearity is a fundamental expression of numerous downstream genes. principle of Hox gene regulation and is crucial These downstream genes are responsible for for the proper development of the body plan. the development of specific structures within The conserved nature of this principle across each segment. The color-coded segments on diverse species underscores its evolutionary the fly illustrate how different Hox genes significance. This close relationship between control the development of different body chromosomal organization and spatial gene parts. For example, mutations in specific Hox expression during development is a hallmark genes can lead to transformations of one body of Hox genes' role in body patterning. segment into another. —----------------------------------------------------------- In essence, the image demonstrates that Hox Hox Gene Function: Segment Specification genes act as master switches, orchestrating This image uses Drosophila (fruit fly) the expression of downstream genes to create examples to illustrate the crucial role of Hox the diverse structures of the fruit fly body, genes in establishing segmental identity. reflecting the intricate relationship between Hox Gene Mutations: The two images show gene location, expression, and developmental the head and anterior thorax regions of outcome. Drosophila with and without a mutation in a —----------------------------------------------------------- Hox gene. The normal fly (left) shows the Collinearity: Gene Order = Body Order typical structures of the head and thorax. The Concept of Colinearity in Hox genes: the mutated fly (right) exhibits a transformation of order of genes on the chromosome reflects one segment into another. This transformation their order of expression along the demonstrates the essential role of Hox genes anterior-posterior axis of the body. in specifying the identity of body segments. A Colinearity: The figure demonstrates that the mutation in a Hox gene disrupts the normal physical arrangement of Hox genes on the pattern of gene expression, resulting in chromosome directly corresponds to their abnormal development. The specific Hox gene spatial expression pattern in the developing mutated determines the type of transformation embryo. Genes located at the 3' end of the observed. Mutations in Hox genes can cause cluster are expressed in the anterior (head) the transformation of one segment into region, while genes at the 5' end are another, highlighting their crucial role in expressed in the posterior (tail) region. establishing each segment's unique identity Comparison across species: The image during development. The reference to Griffiths compares the Hox gene organization and et al. 1996 suggests the images are from a expression in Drosophila (fruit fly) and published study showing these effects. humans. Despite the evolutionary distance —----------------------------------------------------------- between these species, the colinearity principle is conserved. This suggests that the fundamental mechanism of Hox gene  Hox Genes and Body Plan Evolution Hox Genes and Body Plan Evolution: The diagram shows a phylogenetic tree depicting the evolutionary relationships among various animal groups. Alongside the tree is a representation of the Hox gene clusters in each group. The color-coding of the Hox genes highlights the expansion and diversification of these genes during evolution. Key Observations: Gene Duplication and Diversification: The image shows that as animals evolved, there was an increase in the number of Hox genes and an increase in the complexity of the Hox gene clusters. This expansion is thought to have played a significant role in the evolution of different body plans. Gene duplication events led to new Hox genes, which subsequently diversified in their expression patterns and functions. Correlation with Body Complexity: Animals with more complex body plans tend to have larger and more complex Hox gene clusters. This correlation suggests that the evolution of new Hox genes provided the genetic basis for the evolution of novel body structures and the overall diversification of animal body plans. Evolutionary Conservation: Although Hox gene clusters have expanded and diversified, there is significant conservation of the genes among different species. This conservation reflects the fundamental role of Hox genes in body plan development. In Summary, the image demonstrates a strong correlation between the evolution of Hox genes and the diversification of animal body forms. The expansion and modification of Hox gene clusters provided the raw material for evolutionary innovation, leading to the remarkable diversity of animal body plans we see today.