Biology 138 Second Semester Review Flashcards

DNA Structure, Protein Synthesis, and Mutations

• DNA (Deoxyribonucleic Acid) Structure:     * Shape: The DNA molecule is a double helix.     * Nucleotide Components: A nucleotide is the building block of DNA and is composed of a deoxyribose sugar, a nitrogenous base, and a phosphate group.     * Historical Discovery:         * Chargaff: Discovered that the amounts of adenine equal thymine, and cytosine equals guanine (Chargaff's Rules).         * Franklin: Used X-ray diffraction to take photographs of DNA (Photo 51), suggesting a helical structure.         * Watson & Crick: Figured out that the DNA molecule was specifically a double helix structure.     * Structural Components of DNA:         * Pyrimidine Bases: Single-ring nitrogenous bases.         * Purine Bases: Double-ring nitrogenous bases.         * Hydrogen Bonds: Weak bonds that hold the nitrogenous base pairs together in the center of the helix.         * Covalent Bonds: Strong bonds that hold the sugar-phosphate backbone together.         * Sugar-Phosphate Backbone: The outer sides of the DNA ladder, composed of alternating phosphates and deoxyribose sugars.

• Comparison of DNA and RNA:     * DNA: Double-stranded, contains the sugar deoxyribose, and the nitrogenous base Thymine ($T$).     * RNA: Generally a single-stranded helix, contains the sugar ribose, and uses the nitrogenous base Uracil ($U$) instead of Thymine ($T$).     * Nitrogenous Bases found in DNA: Adenine, Thymine, Guanine, and Cytosine.     * Nitrogenous Bases found in RNA: Adenine, Uracil, Guanine, and Cytosine.

• Chargaff’s Rule Application:     * If a DNA strand contains $10\,\%$ Adenine ($A$):         * Thymine ($T$): $10\,\%$         * Cytosine ($C$): $40\,\%$         * Guanine ($G$): $40\,\%$         * Uracil ($U$): $0\,\%$ (Uracil is not present in DNA).

• Key Biological Processes:     * Replication:         * Definition: The process by which the cell makes an exact copy of DNA before it divides.         * Molecules Involved: Helicase (to unzip), DNA Polymerase (to copy and fill), DNA Ligase (to join fragments).         * Location: Nucleus.     * Transcription:         * Definition: The process by which DNA is copied onto RNA.         * Molecules Involved: DNA, RNA Polymerase, mRNA.         * Location: Nucleus.     * Translation:         * Definition: The process by which the DNA code is uncoded from the mRNA and turned into proteins.         * Molecules Involved: mRNA, tRNA, rRNA, ribosomes, and amino acids.         * Location: Cytoplasm (Specifically at the Ribosomes).

• Molecules and Sequences:     * mRNA (messenger RNA): Copies DNA code and transports it from the nucleus to the ribosome.     * tRNA (transfer RNA): Decodes the code brought by mRNA and brings specific amino acids.     * rRNA (ribosomal RNA): Aligns tRNA and mRNA, then creates the actual proteins.     * Example Sequence Transition:         * DNA: TAC CCC GAT CAG GGC TTA ACT         * mRNA: AUG GGG CUA GUC CCG AAU UGA         * Amino Acids: Start-Gly-Leu-Val-Pro-Asn-Stop

• Mutations:     * Definition: A heritable change in the DNA of an organism.     * Causes: Errors during DNA replication or environmental factors (mutagens).     * Types (Illustrated using "THE RED DOG ATE THE CAT"):         * Point Mutation: A change in a single nucleotide base.         * Missense Mutation: A change that results in a different amino acid being coded for (e.g., THE FAT DOG ATE THE CAT).         * Nonsense Mutation: Alters an amino acid codon into a "Stop" codon, prematurely ending the protein (e.g., THE RED DOG STOP).         * Silent Mutation: A base is changed but it still codes for the same amino acid (e.g., THE RED DOG EAT THE CAT).         * Frameshift Mutation: Shifts the reading frame through insertions or deletions, often the most severe.             * Insertion: Adding nucleotide bases (e.g., THE ERE DDO GAT ETH ECA T).             * Deletion: Loss of nucleotide bases (e.g., THR EDD OGA TET HEC AT).

Biotechnology

• Definitions and Concepts:     * Genetic Engineering: Directly manipulating DNA of an organism.     * Recombinant DNA: DNA that is taken from one organism and used/transferred to another organism as if it were their own.     * Restriction Enzymes: Enzymes that only cut DNA at certain specific sequences called recognition sites.     * Recognition Site: Specific sequences (usually palindromes) where restriction enzymes are programmed to cut.     * Transgenic Organism: Organisms that contain recombinant DNA from another species.     * Plasmid: A bacterial vector that carries genetic information from one organism to another.     * Selective Breeding: Breeding organisms together to produce offspring with specific desired traits.

• Restriction Fragments:     * Blunt Ends: DNA is cut in two straight, even halves.     * Sticky Ends: DNA is cut with overhanging single-stranded ends. These are more helpful for recombinant DNA technology because they easily bond with complementary sequences.

• Gel Electrophoresis:     * Process: Separates DNA fragments by size using an electric field.     * Property used: DNA has a negative charge and moves toward the positive cathode.     * Separation: Smaller pieces travel faster and further than longer/heavier ones.     * Application: Used for DNA fingerprinting.

Meiosis

• Chromosome Counts (Diploid $2n$ vs Haploid $n$):     * Humans: Body cell ($2n = 46$), Gamete ($n = 23$). Humans have $23$ homologous pairs.     * Dog: Body cell ($2n = 78$), Gamete ($n = 39$).     * Corn: Body cell ($2n = 20$), Gamete ($n = 10$).     * Note: Chromosome number is not related to the complexity of the organism.

• Meiotic Process:     * Goal: To create gametes (sex cells/germ cells).     * Crossing Over: Occurs during Prophase I; non-sister chromatids exchange DNA segments.     * Genetic Diversity Mechanisms: Crossing over, Independent Assortment, and Random Fertilization.     * Reduction Division: Meiosis I is the reduction division because it reduces the number of chromosomes by half.     * Oogenesis vs Spermatogenesis: Spermatogenesis produces $4$ functional sperm; Oogenesis produces $1$ functional egg and $2$ to $3$ nonfunctional polar bodies.

• Karyotypes:     * Definition: A photomicrograph (picture) of the chromosomes in a dividing cell.     * Information provided: Reveals sex (XX for female, XY for male) and genetic disorders (extra or missing chromosomes).     * Chromosomes: Autosomal chromosomes are standard body chromosomes ($1-22$); sex chromosomes determine gender ($23^{rd}$ pair).

• Zygote: Formed when an egg and sperm fuse together; it represents the first stage of a new organism.

Genetics

• Key Terms:     * Genetics: The study of traits and inheritance.     * Genotype: The specific alleles an organism possesses (e.g., $TT$, $Tt$).     * Phenotype: The visible, physical trait expressed (e.g., tall).     * Heterozygous (Hybrid): One dominant and one recessive allele ($Tt$).     * Homozygous (Purebred): Two of the same alleles ($TT$ or $tt$).     * Alleles: Different forms of a gene.

• Patterns of Inheritance:     * Incomplete Dominance: Neither allele is dominant; the offspring show a blended trait (e.g., Black fur + White fur = Gray fur).     * Codominance: Neither trait is dominant over the other, so both show up simultaneously (e.g., AB blood type).     * Multiple Alleles: The existence of three or more alleles in a population for a single trait (e.g., Blood types A, B, O).     * Sex-Linked: Traits linked to sex chromosomes ($X$ or $Y$), such as hemophilia or colorblindness.

• Genetic Problem Solving:     * Blood Types: A woman (A type) and man (B type) with children of both A and B types must have genotypes $I^Ai$ and $I^Bi$.     * Black/Gray Rabbits: Crossing a Black ($BB$) and Gray ($Bb$) rabbit results in $50\,\%$ Black ($BB$) and $50\,\%$ Gray ($Bb$).     * Dragon Dihybrid Cross: If breeding heterozygous fire-breathing black dragons ($FfHh$) with flameless heterozygous black dragons ($ffHh$), the chance of a flameless green-scale offspring ($ffhh$) is calculated based on recessive probabilities ($\frac{1}{2} \times \frac{1}{4} = \frac{1}{8}$ or $12.5\,\%$\/$6.25\,\%$ check notes).

Evolution

• Evidence for Evolution:     * Homologous Structures: Structures that look the same but differ in function, indicating common ancestry.     * Analogous Structures: Structures that look different but serve the same function (e.g., bird wing vs. butterfly wing).     * Vestigial Structures: Structures used by ancestors but no longer used by the modern organism (e.g., whale pelvis).     * Embryology: Studying animal embryos reveals common evolutionary paths.     * Fossils: Preserved remains; older fossils are found in deeper undisturbed strata.

• Natural and Artificial Selection:     * Natural Selection: Nature selects the individuals best fitted to the environment. Darwin's criteria: 1. Survival of the fittest, 2. Diversity, 3. Adaptation.     * Artificial Selection: Humans choose desired traits in organisms.     * Types of selection: Stabilizing, Directional, and Disruptive.

• Dating and Earth History:     * Carbon-14 Dating: Uses the ratio of carbon-14/carbon-12. Living organisms maintain equilibrium with the atmosphere; after death, $^{14}C$ decays into $^{14}N$.     * Half-Life Calculations:         * Thorium-230 ($t_{1/2} = 75,000$ years): To reach $\frac{1}{8}$ of the original (3 half-lives), it takes $225,000$ years.         * Potassium-40 ($t_{1/2} = 1300\text{ million}$ years): After 4 half-lives, $\frac{1}{16}$ of the sample remains.     * Father of Evolution: Charles Darwin.     * Age of Earth: Approximately $4.54\text{ billion}$ years.     * Early Life: First organisms were anaerobic prokaryotes.

• Hardy-Weinberg Equilibrium:     * Conditions: 1. Large population, 2. Random mating, 3. No mutations, 4. No migration, 5. No natural selection.     * Equations: $p + q = 1$ and $p^2 + 2pq + q^2 = 1$.     * Example: If $2\,\%$ have a recessive trait ($q^2 = 0.02$), then $q \approx 0.14$, $p \approx 0.86$, and the heterozygous percentage ($2pq$) is approximately $24\,\%$.

Body Systems

• Digestive System:     * Pathway: Mouth $\rightarrow$ Esophagus $\rightarrow$ Stomach $\rightarrow$ Small Intestine $\rightarrow$ Colon (Large Intestine) $\rightarrow$ Rectum $\rightarrow$ Anus.     * Mechanical Digestion: Occurs in the Mouth and Stomach.     * Chemical Digestion: Occurs in the Mouth, Stomach, and Small Intestine.     * Accessory Organs: Salivary Glands, Liver, Pancreas, Gallbladder (food does not pass directly through these).     * Peristalsis: Wave-like muscle contractions that propel food through the digestive tract.     * Villi: Projections in the small intestine that maximize absorption of nutrients.     * Enzymes:         * Amylase: Digestion of carbs (Mouth).         * Pepsin/Trypsin: Digestion of proteins (Stomach/Small Intestine).         * Lipase/Bile: Digestion of lipids/fats (Small Intestine).

• Circulatory System:     * Vessels:         * Arteries: Carry oxygenated blood (except pulmonary) away from the heart; thick muscular walls.         * Veins: Carry deoxygenated blood to the heart; thin walls; possess valves to prevent backflow.         * Capillaries: Smallest vessels where diffusion/gas exchange takes place.     * Blood Elements:         * Plasma ($55\,\%$): Fluid containing proteins and nutrients.         * Erythrocytes (Red Blood Cells): Contain hemoglobin to transport $O_2$.         * Leukocytes (White Blood Cells): Phagocytic cells that ingest bad bacteria.         * Platelets: Cell fragments that clot blood after injury.

• Respiratory System:     * Pathway of Air: Nasal Passage/Mouth $\rightarrow$ Pharynx $\rightarrow$ Larynx (with Glottis/Epiglottis) $\rightarrow$ Trachea $\rightarrow$ Bronchi $\rightarrow$ Bronchioles $\rightarrow$ Alveoli.     * Gas Exchange: Occurs in the alveoli via diffusion into capillaries.     * Breathing Mechanism: The diaphragm contracts and flattens during inhalation to draw air in and relaxes during exhalation.

Questions & Discussion

• Question: What property of DNA caused the pieces to move in gel electrophoresis?     * Response: DNA is negatively charged, so it is attracted to the positive cathode.

• Question: Why can't the provided pedigree be sex-linked?     * Response: Because a male has the disorder and the pattern of inheritance shown suggests it is autosomal recessive.

• Question: What did the Miller-Urey experiment demonstrate?     * Response: It demonstrated that organic molecules (amino acids) could form under the conditions of early Earth, even without oxygen.