exam 3 bio 200

UNIT 3 INTRODUCTION

• Key Themes:

  • Central Dogma

  • Describes the fundamental flow of genetic information: from DNA to RNA to protein. This means the instructions stored in your DNA are first copied into an RNA message, which then guides the creation of a specific protein. For example, the gene for insulin (on your DNA) is transcribed into an mRNA molecule, which is then translated into the insulin protein that helps regulate blood sugar.

  • Chromosome Theory

  • States that chromosomes are the physical carriers of genes, and their behavior during cell division (especially meiosis) explains Mendel's laws of inheritance. For instance, the reason you inherit one gene for eye color from your mother and one from your father is because each parent contributes a sex cell (gamete) containing one chromosome from each homologous pair.

• Chromosome Condensation in Mitosis:

  • Condensing chromosomes occurs to ensure accurate segregation during cell division. Imagine trying to untangle and evenly distribute two sets of long, messy strings into two piles; it would be much harder than if the strings were tightly wound into compact spools. Chromosome condensation is like spooling the DNA to prevent tangling and ensure each new cell gets a complete set.

  • This process is crucial for maintaining genetic integrity across daughter cells by preventing chromosomes from becoming tangled and ensuring their proper distribution into each new cell.

• Drawing Replicated Homologous Chromosomes:

  • Draw and label:

  • Homologs

    • A pair of chromosomes (one inherited from the mother, one from the father) that carry genes for the same traits at the same locations. For example, if you have a gene for hair color on chromosome 1, both copies of chromosome 1 (the maternal and paternal homolog) will have a gene for hair color at that exact spot.

  • Centromeres

    • The constricted 'waist' of a replicated chromosome, where sister chromatids are joined and where spindle fibers attach during cell division. Think of it as the 'handle' that the cell's machinery grabs onto to pull the chromosomes apart.

  • Sister Chromatids

    • Two identical copies of a single chromosome that are joined together after DNA replication. Before a cell divides, each chromosome copies itself, resulting in two identical 'sisters.' For instance, after replication, a chromosome carrying the allele for 'tallness' will have an identical sister chromatid also carrying the allele for 'tallness.'

• Homologous Chromosomes:

  • Similarities:

  • Same genetic loci (positions of genes) along their length. Both homologs for, say, chromosome 7, will have the gene for cystic fibrosis in the same exact location.

  • Similar in size and banding patterns.

  • Carry genes for the same traits.

  • Differences:

  • May carry different alleles (variants) of genes. For example, one homolog might carry the allele for brown eyes, while the other carries the allele for blue eyes, even though both have the 'eye color' gene at the same locus.

• Karyotype Information:

  • A karyotype display can show:

  • Chromosome number and structure: This includes the total count of chromosomes and any large-scale structural rearrangements (e.g., deletions, duplications, translocations, inversions). For example, a normal human karyotype shows 23 pairs of chromosomes, totaling 46.

  • Detection of chromosomal abnormalities: Such as aneuploidies (e.g., Down syndrome, also known as Trisomy 21, where there is an extra copy of chromosome 21) or structural changes that can lead to genetic disorders. A karyotype can clearly identify this extra chromosome.

• Biological Gender Determination:

  • Determined by sex chromosomes:

  • XY for males: The presence of a Y chromosome (which carries the SRY gene) typically directs the development of male characteristics.

  • XX for females: The absence of a Y chromosome typically leads to the development of female characteristics.

  • Inherited from parents; the father contributes either an X or a Y chromosome, while the mother always contributes an X chromosome. Therefore, the father's contribution determines the biological sex of the offspring. For instance, if the father's sperm carries a Y chromosome, the offspring will be XY (male); if it carries an X chromosome, the offspring will be XX (female).

DNA REPLICATION AND REPAIR

• Limitation of DNA Polymerase III:

  • Cannot initiate synthesis (requires a primer): Imagine trying to build a brick wall without the first brick being placed on a foundation. DNA Polymerase III needs a short RNA 'primer' (like a starter brick) to attach to before it can start adding DNA nucleotides. This primer is laid down by an enzyme called DNA primase.

  • Has limitations on its proofreading abilities: While DNA Polymerase III has a 'backspace' function (3' to 5' exonuclease activity) to correct mistakes as it goes, some errors can still slip through. For example, it might occasionally miss an incorrect base pairing, leading to a point mutation.

• DNA Directionality and Replication:

  • DNA strands have antiparallel orientation (one strand runs 5' to 3', and the complementary strand runs 3' to 5'), affecting replication direction. DNA polymerase can only synthesize new DNA in the 5' to 3' direction. This is like a highway where traffic can only flow in one direction. Because of this, one new strand (the leading strand) can be built continuously, while the other (the lagging strand) must be built in short segments called Okazaki fragments.

• Replication Bubble/Fork:

  • Drawing includes:

  • Indication of leading and lagging strand synthesis: Imagine unwinding a zipper. One side (leading strand) can be copied continuously as the zipper opens. The other side (lagging strand) has to be copied in short bursts, moving backward each time the zipper opens a new section. The two replication forks move in opposite directions from an origin of replication, forming a 'bubble' of unwound DNA.

• Model of DNA Replication:

  • Key components:

  • DNA Helicase: Unwinds the DNA double helix by breaking the hydrogen bonds between complementary base pairs, separating the two strands at the replication fork. Think of it as the 'unzipper' of the DNA double helix.

  • Single-Strand Binding Proteins (SSB): Binds to the separated single DNA strands, preventing them from re-annealing (coming back together) and protecting them from degradation until they can be replicated. These are like 'clips' that hold the zipper open.

  • DNA Primase: Synthesizes short RNA primers required by DNA polymerase to initiate new DNA synthesis on both the leading and lagging strands. This enzyme lays down the 'starter bricks' for DNA polymerase.

  • DNA Polymerase I and III:

    • DNA Polymerase III: The 'main builder' enzyme responsible for synthesizing new DNA strands by adding nucleotides in the 5' to 3' direction, following the template strand. It does most of the heavy lifting in DNA synthesis.

    • DNA Polymerase I: Removes the RNA primers (the 'starter bricks') and replaces them with DNA nucleotides. This is like a 'finisher' enzyme that replaces temporary scaffolding with permanent material.

  • DNA Ligase: Joins the Okazaki fragments on the lagging strand by catalyzing the formation of phosphodiester bonds, sealing the nicks left after primer replacement. This enzyme acts as the 'glue' that seals the gaps between the short DNA segments on the lagging strand.

• Challenges of Linear Eukaryotic Chromosomes:

  • Difficulty in fully replicating the ends (telomeres) during DNA replication: Imagine a shoelace. Each time you copy it, the very tip gets a little shorter because the copying machine can't start right at the absolute end. Eukaryotic chromosomes face a similar problem because DNA polymerase cannot synthesize without a primer, leading to progressive shortening of telomeres with each cell division.

  • Solution: Telomerase enzyme extends telomeres (repetitive nucleotide sequences at chromosome ends) to prevent loss of genetic information. Telomerase is like a special enzyme that adds extra 'plastic tips' back onto the shoelace ends, preventing them from fraying and protecting the important genetic information from being lost.

• Replication Errors:

  1. Detected by proofreading mechanisms: DNA polymerases have a built-in 'spell check' (3' to 5' exonuclease activity) that allows them to remove mismatched nucleotides immediately after their incorporation. If a 'T' is accidentally paired with a 'G' instead of an 'A', the enzyme can remove the 'G' and insert the correct 'A'.

  2. Corrected through mismatch repair and excision repair pathways: If proofreading fails, other repair systems step in. Mismatch repair proteins recognize and correct erroneously paired bases that slipped past proofreading. Excision repair pathways (like nucleotide excision repair or base excision repair) remove damaged bases or segments of DNA that may have been altered by chemical damage or UV radiation. For example, UV light can cause two adjacent thymines to link together (a thymine dimer), which is then removed and replaced by excision repair.

• DNA Damage Repair Importance:

  • Essential for maintaining genetic stability and preventing mutations: Effective repair systems ensure the integrity of the genome, reducing the incidence of diseases like cancer that often arise from unrepaired DNA damage. Without repair, a simple mistake in DNA replication could become permanent and lead to severe consequences for the cell.

• Mutation Importance:

  • Vital for evolution as they introduce genetic variability which can lead to adaptation and natural selection: While often harmful, mutations are the ultimate source of new alleles and genetic diversity, providing the raw material for evolutionary change and the development of new traits. For example, a random mutation might give bacteria resistance to an antibiotic, allowing them to survive and reproduce, leading to a resistant bacterial population. This is highly important for the bacteria, even if it's negative for humans.

CELL DIVISION

• Mitosis Phases:

  • Major events include:

  • Prophase: Chromosomes condense and become visible under a light microscope. The nuclear envelope begins to break down, and the mitotic spindle (composed of microtubules) forms, extending from the centrosomes as they move to opposite poles of the cell. Imagine a classroom where all the books (chromosomes) are scattered and messy; prophase is when they are neatly organized and stacked.

  • Metaphase: Chromosomes align at the cell equator, forming the metaphase plate. Each chromosome's centromere is attached to spindle microtubules from opposite poles, ensuring proper segregation. This is like the books being lined up perfectly in the middle of the room, ready to be divided evenly.

  • Anaphase: Sister chromatids are pulled apart towards opposite poles of the cell, becoming individual chromosomes. This separation is driven by the shortening of kinetochore microtubules. The books are now being pulled to opposite sides of the room, ensuring each new 'classroom' gets a full set.

  • Telophase: The separated chromosomes arrive at the poles and begin to decondense. The nuclear envelope re-forms around each set of separated chromosomes, and the mitotic spindle disassembles. Finally, new nuclear 'walls' form around the two sets of books at opposite ends of the room, preparing for the cell to split.

• Identify Phases:

  • Recognition of phases via visual representation (e.g., microscope images): By observing the arrangement of chromosomes, you can identify the phase. For example, if you see chromosomes randomly scattered but condensing, it's prophase. If they're perfectly lined up in the middle, it's metaphase.

• Cytokinesis Comparison:

  • In animal cells: A cleavage furrow forms (a contractile ring of actin and myosin microfilaments) at the cell's equator, pinching the cell into two daughter cells during cytokinesis. Think of it like tightening a drawstring around the middle of a balloon until it splits into two separate balloons.

  • In plant cells: A cell plate forms. This structure is built from vesicles originating from the Golgi apparatus that fuse at the equatorial plane, creating a new cell wall that divides the daughter cells. This is like building a new internal wall right down the middle of a room to create two new, separate rooms.

• Cell Cycle Checkpoints:

  • G1 Checkpoint: Assesses cellular conditions for DNA synthesis, including cell size, nutrient availability, growth factors, and DNA integrity. It's often referred to as the 'restriction point.' For example, if a cell doesn't have enough nutrients to duplicate its DNA, it will halt at the G1 checkpoint until conditions improve or enter a resting G0 phase.

  • G2 Checkpoint: Verifies successful DNA duplication (replication) before mitosis. It ensures all DNA has been replicated, and any damage has been repaired, preventing the cell from entering M phase with faulty genetic material. If there's unrepaired DNA damage, the cell will pause here. For example, a cell damaged by radiation would stop at G2 to attempt repair or undergo apoptosis.

  • M Checkpoint (Spindle Checkpoint): Ensures all chromosomes are correctly aligned at the metaphase plate and properly attached to the mitotic spindle microtubules before sister chromatids separate. It prevents aneuploidy (abnormal chromosome number). For instance, if one chromosome isn't properly attached to the spindle, the checkpoint will delay anaphase until correct attachment is achieved.

  • Importance: Prevents defective cells from dividing, maintaining cellular integrity, and minimizing the propagation of genetic errors that could lead to diseases like cancer. These checkpoints act as quality control mechanisms, much like a factory inspection line ensuring that only perfect products move to the next stage.

• Mitosis vs Meiosis:

  • Mitosis: Produces 2 identical diploid daughter cells from a single diploid parent cell. It's involved in growth, tissue repair, and asexual reproduction. For example, a skin cell divides by mitosis to produce two identical skin cells to replace old ones.

  • Meiosis: Produces 4 non-identical haploid gametes (sperm or egg cells) from a single diploid germ-line cell. It's essential for sexual reproduction and generates genetic diversity. For instance, a cell in the testes or ovaries undergoes meiosis to produce sperm or eggs, each with a unique combination of genes.

  • Similarities: Both involve phases of division (prophase, metaphase, anaphase, telophase) leading to cytokinesis. Both processes duplicate DNA beforehand.

  • Differences: Meiosis involves two rounds of division (Meiosis I and Meiosis II), chromosome pairing (synapsis), and genetic recombination (crossing over), leading to genetically unique offspring. Mitosis results in genetically identical cells, while meiosis significantly increases genetic variation.

• Synapsis and Crossing Over in Meiosis:

  • Synapsis: Homologous chromosomes physically pair up side-by-side during prophase I of meiosis, forming a structure called a bivalent or tetrad (four chromatids). This precise alignment is facilitated by the synaptonemal complex. Imagine two identical necklaces, each with various beads (genes). Synapsis is when they line up perfectly bead-for-bead.

  • Crossing Over: An exchange of genetic material between non-sister chromatids of homologous chromosomes. This event occurs during synapsis and leads to the recombination of alleles, significantly increasing genetic variability in the resulting gametes. While the two necklaces are lined up, some beads (genetic segments) from one necklace are swapped with corresponding beads from the other. For example, if one chromosome carried alleles for 'tall, brown hair' and its homolog had 'short, blonde hair,' after crossing over, you could get a chromatid with 'tall, blonde hair.'

• Independent Assortment: Random distribution of maternal and paternal chromosomes into gametes during meiosis. This occurs during metaphase I when homologous pairs align independently at the metaphase plate. The orientation of one pair of homologous chromosomes is independent of the orientation of other pairs. For instance, whether the maternal chromosome 1 goes to one pole and the paternal chromosome 2 goes to the same pole, or vice versa, is purely random. This contributes greatly to genetic diversity, allowing for many different combinations of genes in the gametes.

• Reduction Division in Meiosis I:

  • Meiosis I is termed reduction division because it halves the chromosome number from diploid ($2n$) to haploid ($n$). Homologous chromosomes separate, but sister chromatids remain attached. For example, a human diploid cell has 46 chromosomes ($2n=46$). After Meiosis I, the two daughter cells each have 23 chromosomes ($n=23$), but each chromosome still consists of two sister chromatids.

  • Meiosis II resembles mitotic division (equational division) without further reducing chromosome number; sister chromatids separate, resulting in four haploid cells. Each of the 23 chromosomes (with two chromatids) splits, sending one chromatid to each final cell, so the chromosome number remains 23.

GENETICS

• Allele Representation:

  • Alleles are denoted using letter abbreviations (e.g., $A$, $a$). Uppercase letters typically represent dominant alleles, and lowercase letters represent recessive alleles. For example, in pea plants, 'T' might represent the allele for tallness, and 't' for dwarfness.

• Complete Dominance Concept:

  • When one allele (the dominant allele) completely masks the expression of another allele (the recessive allele) in the phenotype of a heterozygote. For instance, if 'T' (tall) is completely dominant over 't' (dwarf) in pea plants, then a plant with genotype $TT$ will be tall, a plant with genotype $tt$ will be dwarf, and a plant with genotype $Tt$ will also be tall; the 't' allele's effect is completely hidden.

• Monohybrid Cross Completion:

  • Determine possible offspring phenotypes and genotypes from a single trait cross using a Punnett square, which predicts the probability of different genetic outcomes. For example, crossing two heterozygous parents for pea plant height ($Tt imes Tt$) would yield offspring genotypes of 1$TT$:2$Tt$:1$tt$ and phenotypes of 3 tall:1 dwarf.

• Steps in Genetics Problem Solving:

  1. Make a key for genotype/phenotype representation: Assign letters to alleles (e.g., $A$ for dominant, $a$ for recessive) and define the phenotype associated with each. For example, 'B = brown eyes, b = blue eyes.'

  2. Identify parental genotypes (if provided): Determine the genetic makeup of the parents involved in the cross. If a brown-eyed person marries a blue-eyed person, and brown is dominant, the brown-eyed parent could be $BB$ or $Bb$, and the blue-eyed parent must be $bb$.

  3. Determine gametes produced by each parent: Based on the Law of Segregation, each gamete receives only one allele for each gene from the parent. For a parent with genotype $Bb$, the gametes would be either 'B' or 'b'.

  4. Diagram allele passage using a Punnett square or pedigree chart: A Punnett square helps visualize all possible combinations of alleles from the parents and predict offspring genotypes and phenotypes for a cross over one or more generations. A pedigree chart tracks traits through multiple generations within a family. For example, a Punnett square for $Bb imes Bb$ would show a 1$BB$:2$Bb$:1$bb$ genotypic ratio for offspring.

  5. Analyze results and provide answers to questions: Calculate genotypic and phenotypic ratios or probabilities based on the constructed diagram. For our $Bb imes Bb$ example, there's a 75% chance of brown eyes ($BB, Bb$) and a 25% chance of blue eyes ($bb$).

• Mendel's Laws:

  • Law of Segregation: Alleles for a heritable character segregate (separate) from each other during gamete formation, so that each gamete receives only one allele for each gene. This means that a parent with genotype $Aa$ will produce gametes that carry either the $A$ allele or the $a$ allele, but never both in the same gamete. This directly relates to the separation of homologous chromosomes during Meiosis I.

  • Law of Independent Assortment: Genes for different traits assort independently of one another during gamete formation, meaning the allele a gamete receives for one gene does not influence the allele received for another gene. For example, the inheritance of alleles for pea plant height (tall vs. dwarf) is independent of the inheritance of alleles for pea color (green vs. yellow). A parent with genotype $TtGg$ (where G=green, g=yellow) will produce gametes in equal proportions of $TG$, $Tg$, $tG$, and $tg$. This occurs because non-homologous chromosomes (carrying different genes) align randomly at the metaphase plate in Meiosis I.

  • Connection to meiosis: These laws are directly explained by the behavior of chromosomes during meiosis. The segregation of alleles corresponds to the separation of homologous chromosomes (and thus the alleles they carry) during anaphase I, and the independent assortment of genes reflects the random orientation of homologous pairs at the metaphase plate in metaphase I.

• Gametes Production:

  • Given genotype (e.g., $Aa$ or $AaBb$), identifying potential gametes is essential for predicting offspring outcomes in genetic crosses. For a genotype $Aa$, the possible gametes are $A$ and $a$. For a genotype $AaBb$, the possible gametes (due to independent assortment) are $AB$, $Ab$, $aB$, and $ab$.

• Pedigree Symbols:

  • Males: Squares, representing biologically male individuals. (e.g., a square in a pedigree chart represents a male family member).

  • Females: Circles, representing biologically female individuals. (e.g., a circle represents a female family member).

  • Relationships: Horizontal lines between shapes represent pairings (marriage or mating) that lead to offspring. Vertical lines descending from a horizontal line connect parents to their children.

  • Siblings: Children from the same parents are connected horizontally from a common parental line.

  • Generations: Often represented by horizontal lines or Roman numeral designations (I, II, III, etc.) to show ancestries and descendants. For example, individuals in generation II are the children of individuals in generation I.

  • Affected individuals: Shaded shapes (filled squares or circles) indicate individuals expressing the genetic condition or trait being studied. For instance, a filled square might represent a male with a genetic disorder like cystic fibrosis.