The Scientific Method Study Guide PDF

The Scientific Method Dr. Asamani AD Biology Midterms Study Guide The Scientific Method 1. Observation ​ What it is: The scientific method begins with observation of the natural world or an event that sparks curiosity. It’s the first step of noticing some...

The Scientific Method Dr. Asamani AD Biology Midterms Study Guide The Scientific Method 1. Observation ​ What it is: The scientific method begins with observation of the natural world or an event that sparks curiosity. It’s the first step of noticing something unusual, interesting, or unexplained. This could be anything from seeing a pattern in nature to noticing an unexpected outcome in an experiment. ​ Example: You observe that plants in your garden grow taller when placed near a window with sunlight, while those further away seem to grow slower. 2. Ask a Question ​ What it is: From the observation, you form a question about the phenomenon. The question should be specific and focused on what you want to understand or explain. ​ Example: "Why do plants near the window grow taller than those further away?" 3. Hypothesis ​ What it is: A hypothesis is a testable explanation or prediction about the phenomenon based on your background knowledge or prior research. It’s an educated guess that provides a possible answer to your question. ​ Example: "If plants receive more sunlight, then they will grow taller." 4. Experiment ​ What it is: This is the stage where you test your hypothesis through experimentation. You design a controlled experiment where you manipulate one variable (the independent variable) and measure its effect on another variable (the dependent variable). ​ Example: You set up two groups of plants: one placed near the window (receiving more sunlight) and one placed in a darker part of the room. 5. Procedure ​ What it is: The procedure outlines the specific steps you'll follow in the experiment. This ensures the experiment is carried out in a controlled and reproducible way, with clear instructions on how to manipulate the variables and measure the results.  ​ Example: ○​ Step 1: Place Group A (sunlight) near the window and Group B (no sunlight) in a darker corner. ○​ Step 2: Water both groups equally every day. ○​ Step 3: Measure the height of the plants every 2 days for 3 weeks. 6. Materials ​ What it is: The materials are the items or tools you will need to carry out the experiment. This could include plants, pots, a ruler for measuring height, sunlight, water, and so on. ​ Example: ○​ 2 sets of plants (same species) ○​ Ruler ○​ Watering can ○​ Timer or calendar to track days ○​ Notebook or computer to record results 7. Data ​ What it is: During the experiment, you collect data—this can be quantitative (numerical measurements) or qualitative (observational notes). Data is the evidence that you use to test your hypothesis. ​ Example: You record the height of the plants every two days: ○​ Group A (sunlight): Day 1—5 cm, Day 3—7 cm, Day 5—10 cm, etc. ○​ Group B (no sunlight): Day 1—4 cm, Day 3—5 cm, Day 5—5.5 cm, etc. 8. Analyze ​ What it is: Once you’ve gathered your data, you analyze it to see if there are patterns or relationships that support or contradict your hypothesis. This might involve calculating averages, comparing results, or creating graphs or charts to visualize the data. ​ Example: After three weeks, you notice that plants in Group A (sunlight) have grown significantly taller than those in Group B. You calculate the average growth for each group to see if the difference is statistically significant. 9. Conclusion ​ What it is: The conclusion summarizes the results of the experiment and determines whether the data supports or refutes your hypothesis. It explains the meaning of the results and what they suggest about the question you started with. ​ Example: Based on your analysis, you conclude that the hypothesis is correct: plants exposed to more sunlight grow taller. Group A grew an average of 25 cm, while Group B grew only 8 cm. 10. New Hypothesis/Theory ​ What it is: If the results support your hypothesis, you may form a new hypothesis or expand on the existing one to explore additional questions or refine your understanding. If the hypothesis is rejected, you may need to revise it and design a new experiment. This step is where the scientific process becomes iterative and self-correcting. ​ Example: Based on your conclusion, you may hypothesize, "What if the amount of water or type of soil also affects plant growth, along with sunlight?" You could design a new experiment testing these factors. Alternatively, you could refine your existing hypothesis: "Plants will grow taller with both sunlight and water combined." You could then test this by introducing different water amounts to see if it further impacts growth. Summary of the Steps: 1.​ Observation: Notice something intriguing. 2.​ Ask a Question: Pose a question about the observation. 3.​ Hypothesis: Propose an explanation or prediction. 4.​ Experiment: Design and conduct an experiment to test the hypothesis. 5.​ Procedure: List the steps needed to perform the experiment. 6.​ Materials: Gather everything needed for the experiment. 7.​ Data: Collect and record the results of the experiment. 8.​ Analyze: Look for patterns or trends in the data. 9.​ Conclusion: Summarize the results and decide whether the hypothesis is supported. 10.​New Hypothesis/Theory: Use the findings to refine your understanding or test new hypotheses. The scientific method is a flexible, iterative process, meaning that experiments and hypotheses may evolve as new questions arise or more data becomes available. The Nature of Science Dr. Asamani AD Biology Midterms Study Guide The Nature of Science The nature of science refers to the characteristics and principles that define how science works as a process of gaining knowledge and understanding about the natural world. It's important to recognize that science is progressive and dynamic, and that scientific knowledge is continually evolving. Additionally, scientific advancements are often the result of collaboration among many scientists, even though a few individuals may receive the public recognition for a discovery. 1. Science is Progressive ​ What it means: Science builds upon existing knowledge over time. The process of scientific discovery is cumulative—new theories and concepts often develop from or refine previous understanding. ​ How it works: As new tools, methods, and evidence become available, scientific knowledge deepens, leading to more refined theories or even entirely new ways of understanding phenomena. This is why science doesn’t just “stay the same”; it constantly evolves. ​ Example: The theory of evolution by natural selection, first proposed by Charles Darwin, has been expanded and refined over time with advancements in genetics, paleontology, and molecular biology. What we know about evolution today is far more nuanced and complex than what was understood in Darwin's time. 2. Science is Dynamic ​ What it means: Science is not a static or rigid body of knowledge; it's constantly changing and adapting. New discoveries, technologies, and ideas can challenge existing theories and lead to revisions or even paradigm shifts. ​ How it works: Scientific knowledge is open to change as new evidence is gathered. If a hypothesis or theory is found to be incorrect, scientists update or replace it with a more accurate explanation. This dynamic nature ensures that science remains an accurate and reliable way of understanding the world. ​ Example: The geocentric model (the idea that the Earth is the center of the universe) was replaced by the heliocentric model (that the Earth orbits the Sun) after astronomers like Copernicus, Galileo, and Kepler gathered evidence that contradicted the earlier view. This shift was a major turning point in science. 3. Collaboration in Science  ​ What it means: Science is a collaborative endeavor that often involves many scientists working together, sharing ideas, and building upon each other’s work. Although some discoveries are credited to one or a few scientists, science is almost always the result of cumulative effort. ​ How it works: Research teams often consist of scientists with different specialties, working in different places and with different tools. They share findings, offer critiques, and help refine each other’s work. Scientific progress is rarely achieved in isolation; collaboration is a key component. ​ Example: The discovery of DNA structure is a great example of collaboration. While James Watson and Francis Crick are credited with determining the double helix structure of DNA, they were heavily influenced by the X-ray diffraction images taken by Rosalind Franklin, and their work built on the prior research of many others, including Maurice Wilkins. Watson, Crick, and Franklin all contributed pieces to the puzzle, and their collaboration led to the breakthrough. 4. One or Two Scientists May Get the Credit ​ What it means: While many scientists contribute to a discovery, the public recognition or credit often goes to one or two individuals. This is due to factors like historical context, the prominence of the scientist, or the way discoveries are communicated to the public. ​ How it works: In scientific history, a few people often get the fame for a discovery, even though others may have been instrumental in the research process. Recognition, however, doesn’t diminish the contributions of the many other individuals involved in the work. ​ Example: Isaac Newton is famous for developing the laws of motion and gravity, but these ideas were influenced by earlier work from scientists like Johannes Kepler and Galileo Galilei. Similarly, Albert Einstein is credited with developing the theory of relativity, but his work was also influenced by earlier physicists like Hendrik Lorentz and Henri Poincaré. 5. Science is Empirical and Based on Evidence ​ What it means: Science relies on empirical evidence, which is gathered through observation and experimentation. Scientific conclusions must be based on evidence that is reproducible and testable. ​ How it works: Scientific knowledge comes from repeated experimentation, observation, and testing. Results must be measurable and observed under controlled conditions, ensuring the reliability and validity of findings. ​ Example: In medicine, new treatments or drugs are rigorously tested through clinical trials to ensure they are safe and effective before they are approved for use by the public. 6. Science is Objective and Self-Correcting  ​ What it means: Science strives for objectivity, meaning that researchers aim to minimize personal biases and subjective interpretations. Scientific knowledge is also self-correcting, meaning that when errors or new evidence arise, the scientific community revises or discards previous conclusions. ​ How it works: Peer review, repetition of experiments, and ongoing debate help ensure that scientific conclusions are accurate and reliable. When new data challenges current understanding, scientists investigate it and adjust their theories accordingly. ​ Example: The shift from the idea of an "ether" (a substance once believed to fill empty space and carry light waves) to the understanding that space can be a vacuum was a self-correcting process. Once the Michelson-Morley experiment failed to detect the ether, the scientific community revised its understanding, paving the way for Einstein's theory of relativity. 7. Science Involves Creative Thinking ​ What it means: While science is grounded in evidence and logic, it also involves creativity. Scientists must think creatively to design experiments, interpret results, and form new hypotheses. The ability to think outside the box is crucial for scientific breakthroughs. ​ How it works: Scientists often need to come up with innovative solutions to complex problems, whether it’s developing a new experimental method, creating a new model, or synthesizing existing knowledge in a novel way. ​ Example: The development of the periodic table by Dmitri Mendeleev was a highly creative endeavor, as Mendeleev noticed patterns in the elements and predicted the properties of elements yet to be discovered. Summary of the Nature of Science: 1.​ Science is progressive: Builds upon existing knowledge, continually advancing with new discoveries and technologies. 2.​ Science is dynamic: Constantly evolving in response to new evidence or better understanding, leading to paradigm shifts or refined theories. 3.​ Collaboration is key: Many scientists work together, and discoveries are often the result of a collective effort. 4.​ Recognition is often given to one or a few scientists: Despite many contributors, history tends to credit one or two key individuals for discoveries. 5.​ Empirical and evidence-based: Relies on observable, measurable data from experiments and observations. 6.​ Objective and self-correcting: Aims for unbiased, accurate conclusions, and revises ideas when new evidence arises. 7.​ Creative thinking is essential: Requires innovative solutions and new ways of thinking to solve problems and advance knowledge. The nature of science emphasizes that science is an ongoing, collaborative, and evolving process that seeks to explain and understand the world around us. While individual scientists may get recognition for discoveries, science itself is a collective effort that is shaped by the contributions of many over time. Life Processes and Homeostasis Dr. Asamani AD Biology Midterms Study Guide Life Processes Life functions are the essential processes that living organisms carry out to sustain life and ensure survival. These functions include metabolism, the chemical reactions that convert energy and materials into usable forms for growth and maintenance; growth, the process by which organisms increase in size and complexity; reproduction, which ensures the continuation of species; response to stimuli, allowing organisms to react to changes in their environment; and homeostasis, the regulation of internal conditions to maintain a stable environment despite external changes. Together, these life functions enable organisms to survive, adapt, and evolve over time. Integumentary System ​ Function: Protective barrier against external threats, regulates body temperature, houses sensory receptors. ​ Components: Skin, hair, nails, sweat glands, sebaceous glands. Skeletal System ​ Function: Provides support, protects internal organs, allows movement, stores minerals. ​ Components: Bones, cartilage, ligaments, tendons. Muscular System ​ Function: Enables body movements, maintains posture, generates heat. ​ Components: Smooth muscles, skeletal muscles, cardiac muscle. Nervous System  ​ Function: Controls bodily functions, relays messages between brain and body, facilitates sensory perception, motor control, and cognition. ​ Components: Brain, spinal cord, nerves. Cardiovascular System (Circulatory System) ​ Function: Transports oxygen, nutrients, and waste products; regulates body temperature, pH, and electrolyte balance; assists in immune response. ​ Components: Heart, blood vessels (arteries, veins, capillaries), blood. Lymphatic System ​ Function: Helps defend against infection, assists in immune function, transports lymph. ​ Components: Lymph nodes, lymph vessels, spleen, thymus, tonsils. Respiratory System ​ Function: Facilitates gas exchange (oxygen in, carbon dioxide out). ​ Components: Lungs, trachea, bronchi, bronchioles, diaphragm. Digestive System ​ Function: Breaks down food into nutrients for absorption and excretes waste products. ​ Components: Mouth, esophagus, stomach, small intestine, large intestine, liver, pancreas. Reproductive System ​ Function: Facilitates reproduction by producing gametes and supporting the development of offspring. ​ Components (Female): Ovaries, fallopian tubes, uterus, vagina. ​ Components (Male): Testes, seminal vesicles, prostate gland, penis. Immune System ​ Function: Defends the body against pathogens and foreign substances. ​ Components: White blood cells, lymph nodes, spleen, thymus, antibodies. Endocrine System ​ Function: Produces and secretes hormones that regulate various body functions, including metabolism, growth, and mood. ​ Components: Glands (e.g., pituitary, thyroid, adrenal glands), pancreas. Excretory System (Urinary System) ​ Function: Removes waste products from the body and maintains fluid and electrolyte balance. ​ Components: Kidneys, bladder, ureters, urethra, skin, liver (through bile). Homeostasis refers to the ability of an organism or system to maintain a stable internal environment despite changes in external conditions. It is a vital process that helps organisms regulate factors like temperature, pH, hydration, and nutrient levels to keep them within a range that is optimal for survival. Homeostasis involves a complex interplay of sensors, feedback mechanisms, and effectors that detect deviations from the ideal state and make adjustments to bring conditions back into balance. For example, humans maintain a core body temperature of around 37°C (98.6°F); if the temperature rises or falls too much, the body activates mechanisms like sweating or shivering to regulate it. This dynamic equilibrium is essential for the proper functioning of cells, organs, and overall health. Examples of System Interactions to Maintain Homeostasis: ​ Temperature Regulation: When body temperature rises (e.g., during exercise or in a hot environment), the nervous system triggers responses from the skin (sweating), blood vessels (vasodilation), and the circulatory system (increased blood flow to the skin) to cool the body down. The endocrine system also helps adjust metabolic rate to regulate heat production. ​ Blood Sugar Control: When blood sugar levels rise after eating, the pancreas releases insulin, which helps cells absorb glucose. This action is supported by the circulatory system, which transports the insulin to target tissues. The liver may also store excess  glucose as glycogen. When blood sugar is low, glucagon is released to stimulate the release of glucose from the liver. ​ Fluid and Electrolyte Balance: The kidneys regulate fluid and electrolyte balance by filtering the blood and adjusting urine production. When dehydration occurs, the hypothalamus triggers thirst, and the kidneys conserve water. The nervous system and endocrine system (e.g., antidiuretic hormone, aldosterone) also regulate how much water is reabsorbed by the kidneys. Each of these systems is highly integrated, working together to respond to internal and external changes, allowing the body to maintain the equilibrium necessary for health and survival. Photosynthesis and Cellular Respiration Dr. Asamani AD Biology Midterms Study Guide Photosynthesis and Cellular Respiration Definition:​ Photosynthesis is the process by which plants and some microorganisms convert light energy, water, and carbon dioxide into glucose and oxygen, which are vital for sustaining life on Earth. Key Highlights ​ Self-Sustaining Producers:​ Plants synthesize their own food (glucose) through photosynthesis, making them crucial for ecosystems as primary producers. ​ Two Stages of Photosynthesis:​ The process occurs in two main stages: ○​ Light-Dependent Reactions: Occur in the thylakoid membranes of chloroplasts, where sunlight is captured, and water is split, releasing oxygen. ○​ Light-Independent Reactions (Calvin Cycle): Occur in the stroma, where ATP and NADPH produced in the light-dependent reactions are used to convert CO₂ into glucose. ​ Oxygen Release:​ The splitting of water in the light-dependent reactions not only generates oxygen as a byproduct but also provides electrons necessary for the process. ​ Energy Carriers:​ ATP and NADPH are critical energy carriers that drive the reactions of the Calvin Cycle, facilitating the synthesis of glucose. ​ Ecological Importance:​ Plants contribute significantly to oxygen production and form the foundation of food webs, supporting diverse life forms. ​ Adaptations for Survival:​ Some plants, like cacti, have evolved specialized forms of photosynthesis (CAM photosynthesis) to conserve water in arid environments, showcasing nature's resilience. Photosynthesis Chemical Equation The overall reaction for photosynthesis can be summarized as:​ 6CO₂ + 6H₂O → C₆H₁₂O₆ + 6O₂​ This equation indicates that six molecules of carbon dioxide and six molecules of water are converted, using light energy captured by chlorophyll, into one molecule of glucose and six molecules of oxygen. The Calvin Cycle Definition:​ The Calvin Cycle, the second phase of photosynthesis, operates independently of light but relies on ATP and NADPH from the light-dependent reactions. It consists of three key phases: 1.​ Carbon Fixation:​ CO₂ is fixed into a 6-carbon compound by the enzyme RuBisCO, leading to the formation of two 3-phosphoglycerate (3-PGA) molecules. 2.​ Reduction Phase:​ ATP and NADPH are used to convert 3-PGA into glyceraldehyde-3-phosphate (G3P), a three-carbon sugar. For every three CO₂ molecules that enter the cycle, six G3P molecules are produced, but only one exits to contribute to glucose synthesis. 3.​ Regeneration of RuBP:​ The remaining five G3P molecules are converted back into three molecules of RuBP, using ATP, allowing the cycle to continue and enabling further carbon fixation. Importance:​ The Calvin Cycle is essential for producing glucose, which is crucial for plant growth and energy storage, supporting life on Earth. Key Insights from the Calvin Cycle ​ Role of RuBisCO:​ RuBisCO is a critical enzyme for carbon fixation, emphasizing the importance of enzymatic processes in converting inorganic carbon into organic compounds necessary for life. ​ Energy Flow:​ The Calvin Cycle illustrates the transformation of light energy into chemical energy (ATP and NADPH), showcasing the efficiency of photosynthesis in energy utilization. ​ Versatility of G3P:​ G3P serves as a precursor for various carbohydrates, demonstrating the cycle’s flexibility in supporting different metabolic pathways and energy storage forms. ​ Sustainability of the Cycle:​ The regeneration phase ensures the cycle can continue indefinitely, highlighting the intricate design of metabolic pathways that facilitate continuous energy and carbon processing.  ​ Foundation of Life:​ Photosynthesis is the cornerstone of energy flow in ecosystems, providing organic matter and oxygen that support nearly all life forms. Cellular respiration is the process by which cells break down glucose (or other nutrients) to produce energy in the form of ATP (adenosine triphosphate), which is used to power various cellular activities. It occurs in three main stages: glycolysis, the Krebs cycle (also called the citric acid cycle), and oxidative phosphorylation (which includes the electron transport chain and chemiosmosis). 1.​ Glycolysis: This occurs in the cytoplasm, where one molecule of glucose (a 6-carbon sugar) is broken down into two molecules of pyruvate (a 3-carbon compound), releasing a small amount of energy in the form of ATP and NADH (another energy carrier). 2.​ Krebs Cycle: The pyruvate molecules produced in glycolysis are transported into the mitochondria, where they are further broken down. During this cycle, carbon dioxide (CO₂) is released, and high-energy electrons are transferred to carriers like NADH and FADH₂. 3.​ Oxidative Phosphorylation: This occurs in the inner mitochondrial membrane, where electrons from NADH and FADH₂ are passed through the electron transport chain. This flow of electrons helps create a proton gradient, which powers the enzyme ATP synthase to produce large amounts of ATP. Oxygen acts as the final electron acceptor, combining with electrons and protons to form water (H₂O). Overall, cellular respiration is a critical process for converting the chemical energy stored in food into usable energy for cells. In the presence of oxygen, this process is aerobic respiration and produces much more ATP compared to anaerobic respiration (or fermentation), which occurs without oxygen and results in less energy yield. Lulu the Lioness: A Heroine's Journey Dr. Asamani AD Biology Midterms Study Guide Lulu the Lioness: A Heroine’s Journey Understanding Genotype Analysis and Karyotype Examination in Determining Parentage in Animals In animal biology, determining parentage—the identification of a biological mother and father of offspring—is crucial for various research purposes such as breeding programs, wildlife conservation, population genetics, and understanding inheritance patterns. Genotype analysis and karyotype examination are two powerful techniques used to help establish parentage and refine hypotheses about genetic relationships among animals. Here’s how they work and how you can use the data they provide to determine parentage: 1. Genotype Analysis: Genotype analysis focuses on identifying and comparing specific genes or genetic markers in an animal’s DNA. This method looks at the alleles (variants of a gene) present in the animal’s genome to determine which alleles were inherited from the parents. How Genotype Analysis Works to Determine Parentage: ​ DNA Collection: Scientists collect genetic material from the animal (e.g., blood, hair, tissue, or saliva samples) to analyze its DNA. ​ Marker Identification: Specific genetic markers (such as microsatellites, single nucleotide polymorphisms (SNPs), or other genetic sequences) are identified in both the offspring (e.g., cubs) and potential parents. ​ Allele Matching: Every individual inherits one allele from each parent for each gene. By comparing the alleles in the offspring and potential parents, scientists can determine which parent contributed which allele to the offspring. ○​ If a cub has a specific allele at a given genetic marker that is only found in one of the potential parents, that parent is likely the biological parent. ○​ If both parents share an allele and the offspring inherits that allele from both, they confirm parentage. Example: ​ Suppose a lion cub has a genetic marker for coat color that is only found in one potential mother, and the same marker is absent in the potential father. The mother is  confirmed to be the biological parent because the cub has inherited the coat color allele from her. ​ If the cub shows a combination of alleles that could only come from a specific set of parents (based on what the mother and father carry), the genetic data conclusively supports that pair as the parents. How to Use Genotype Data to Determine Parentage: 1.​ Collect DNA samples from the offspring (cubs) and all potential parents. 2.​ Identify genetic markers in each individual and check which alleles they possess. 3.​ Compare allele patterns between the offspring and potential parents to identify matching alleles and trace the inheritance of these markers. 4.​ Confirm parentage by checking which parent contributed which alleles to the offspring, using the patterns of inheritance. Genotype analysis is highly effective because it can identify parentage with a high degree of accuracy, even in complex or large populations, by looking at multiple genetic markers across the genome. 2. Karyotype Examination: A karyotype examination involves the analysis of the complete set of chromosomes in an animal’s cells, helping to identify the number, shape, and size of chromosomes. A karyotype is essentially a visual map of an organism's chromosomes, which can be used to study chromosomal abnormalities, sex determination, and genetic relationships between individuals. How Karyotype Examination Works to Determine Parentage: ​ Chromosome Collection: Cells are collected from the animal (usually through blood or tissue), and the chromosomes are isolated. ​ Chromosome Staining and Imaging: The chromosomes are stained and then examined under a microscope, often during metaphase (a stage of cell division where chromosomes are most visible). This allows researchers to count chromosomes, identify structural features, and match chromosomes in pairs. ​ Chromosome Pairing: Karyotypes allow scientists to see homologous chromosome pairs (chromosomes inherited from each parent). By examining how chromosomes are inherited, researchers can confirm whether the chromosomal patterns in the offspring match those expected from the parents. Example: ​ In many animals, females have XX chromosomes (two X chromosomes), while males have XY chromosomes (one X and one Y chromosome). By examining the sex  chromosomes in the cubs, scientists can easily identify the biological sex of the offspring and confirm the contributions from both the mother and the father. ​ Chromosome abnormalities (such as extra chromosomes or missing segments) may provide clues as to the parentage or genetic health of the offspring. If both parents contribute abnormal chromosomes, the offspring might also inherit these abnormalities. How to Use Karyotype Data to Determine Parentage: 1.​ Collect cell samples from the cubs and potential parents. 2.​ Examine the chromosomes under a microscope, creating a karyotype for each individual. 3.​ Compare chromosome patterns between the offspring and potential parents, focusing on the number and structure of chromosomes. 4.​ Confirm parentage by checking for matching chromosomal patterns that indicate which parent contributed which chromosomes to the offspring. While karyotype analysis is powerful, it tends to provide less detailed information about specific genetic relationships compared to genotype analysis. However, it can still be useful for confirming broader genetic relationships and checking for chromosomal abnormalities that might affect inheritance. Summary: Using Genotype Analysis and Karyotype Examination Together to Determine Parentage Genotype Analysis and Karyotype Examination complement each other in determining parentage in animals. ​ Genotype analysis helps identify specific genetic markers and alleles inherited from the parents, allowing for precise confirmation of biological relationships. ​ Karyotype examination provides a broader view of the chromosomes, helping confirm the overall chromosomal patterns and sex of the offspring, and can identify potential genetic anomalies. By combining both methods: 1.​ Genotype analysis helps in the detailed identification of parentage based on allele matching. 2.​ Karyotype examination can provide further confirmation of these relationships and identify any chromosomal issues or inconsistencies that might affect the inheritance patterns. These techniques together provide a robust, accurate method for determining parentage and understanding the genetic relationships within animal populations, aiding in breeding programs, conservation efforts, and genetic studies. Genetics Dr. Asamani AD Biology Midterms Study Guide Genetics Genetics Overview: Genetics is the branch of biology that studies heredity and variation in organisms. It explores how traits are passed from parents to offspring through DNA, genes, and chromosomes, and how these traits are expressed through phenotypes. Here’s a detailed breakdown of the key concepts mentioned: 1. DNA (Deoxyribonucleic Acid) DNA is the molecule that carries the genetic instructions for the development, functioning, and reproduction of all living organisms. It is made up of three main parts: 1.​ Sugar (Deoxyribose): A 5-carbon sugar molecule that forms the backbone of the DNA structure. 2.​ Phosphate Group: The phosphate group is attached to the sugar and links nucleotides together in a chain to form the backbone of DNA. 3.​ Nitrogenous Bases: These are the “coding” part of the DNA and come in four types: ○​ Adenine (A) ○​ Thymine (T) ○​ Cytosine (C) ○​ Guanine (G)​ The bases form base pairs (A with T, and C with G) and are critical in the structure and function of DNA. DNA forms a double helix structure, where two strands are coiled together. Each strand is composed of a sugar-phosphate backbone with nitrogenous bases in the center. 2. RNA (Ribonucleic Acid) RNA is a molecule similar to DNA but plays a key role in protein synthesis. While DNA stores the genetic information, RNA helps express that information. It is single-stranded and has ribose sugar instead of deoxyribose.  ​ mRNA (messenger RNA): Carries genetic instructions from the DNA in the nucleus to the ribosome, where proteins are made. ​ tRNA (transfer RNA): Helps decode mRNA by bringing amino acids to the ribosome for protein synthesis. ​ rRNA (ribosomal RNA): Forms part of the structure of the ribosome and aids in protein synthesis. 3. Replication DNA replication is the process by which a cell copies its DNA to prepare for cell division. This ensures that each new cell has an identical copy of the genetic material. Replication occurs in the nucleus and follows these steps: ​ Unwinding: The enzyme helicase unwinds the double helix structure. ​ Complementary Base Pairing: The enzyme DNA polymerase matches each strand with complementary nucleotides (A with T, C with G). ​ Formation of Two Identical DNA Strands: This results in two identical DNA molecules, each with one original strand and one new strand (semi-conservative replication). 4. Transcription Transcription is the process of copying a gene’s DNA sequence into an mRNA molecule. This process occurs in the nucleus. Here’s how it works: ​ Initiation: RNA polymerase binds to a specific region of DNA called the promoter. ​ Elongation: RNA polymerase moves along the DNA, synthesizing an mRNA strand that is complementary to the DNA template strand. ​ Termination: The RNA polymerase reaches a stop signal, and the newly formed mRNA is released. The mRNA then carries the genetic information to the ribosome for translation. 5. Translation Translation is the process by which mRNA is decoded to build a protein. This occurs in the ribosome and involves tRNA and rRNA: ​ mRNA enters the ribosome, where tRNA molecules bring amino acids to the ribosome based on the mRNA sequence.  ​ The mRNA sequence is read in groups of three bases called codons (each codon codes for a specific amino acid). ​ The ribosome links amino acids together to form a polypeptide chain, which folds into a functional protein. 6. Parts of Single and Double-Stranded Chromosomes ​ Single-Stranded Chromosome: A chromosome that consists of one strand of DNA. This is typically seen during DNA replication before the chromosome replicates into two sister chromatids. ​ Double-Stranded Chromosome: After replication, the chromosome is present as two identical sister chromatids connected by a centromere. Each chromatid contains a complete set of DNA. 7. DNA, Chromosome, Genes, and Alleles ​ DNA: The molecule that carries genetic information. ​ Chromosomes: Structures made of DNA that contain many genes. Humans have 46 chromosomes (23 pairs). ​ Genes: Segments of DNA that code for specific proteins or traits. ​ Alleles: Different versions of a gene. For example, a gene for eye color might have different alleles for blue, brown, or green eyes. 8. Karyotype A karyotype is an image or diagram that shows the complete set of chromosomes of an organism, arranged in pairs by size and shape. Karyotypes help in: ​ Identifying chromosomal abnormalities, like extra chromosomes (e.g., Down syndrome, which involves an extra chromosome 21). ​ Determining the sex of an individual (e.g., XX for female, XY for male in humans). 9. The Punnett Square A Punnett Square is a tool used to predict the probability of offspring inheriting particular alleles from their parents. It shows the possible combinations of alleles from each parent. Dominant and Recessive Alleles: ​ Dominant Alleles: Alleles that express their trait even when only one copy is present (e.g., brown eyes "B"). ​ Recessive Alleles: Alleles that only express their trait when two copies are present (e.g., blue eyes "b"). Phenotype and Genotype: ​ Genotype: The genetic makeup of an individual (e.g., BB, Bb, bb). ​ Phenotype: The physical expression of the genotype (e.g., brown eyes, blue eyes). Example Punnett Square: ​ If one parent has genotype Bb (heterozygous for brown eyes) and the other has genotype bb (homozygous recessive for blue eyes), a Punnett square would show that there is a 50% chance of having a child with brown eyes and a 50% chance of having a child with blue eyes. 10. Mutations A mutation is a change in the DNA sequence. Mutations can occur naturally or be caused by environmental factors (like radiation). They can affect an organism in several ways: ​ Silent Mutations: Do not affect the organism’s phenotype because they do not change the protein. ​ Missense Mutations: Lead to a change in one amino acid, which can affect the protein’s function. ​ Nonsense Mutations: Create a premature stop codon, leading to a truncated (incomplete) protein. ​ Frameshift Mutations: Occur when a nucleotide is added or deleted, altering the reading frame and potentially leading to a nonfunctional protein. Mutations can be: ​ Beneficial: They might provide an advantage in survival (e.g., resistance to a disease). ​ Neutral: Have no impact on survival or reproduction. ​ Harmful: Cause diseases or disorders (e.g., sickle cell anemia). Summary Genetics involves understanding how DNA, genes, and chromosomes work to determine traits and how these are passed down from parents to offspring. Key processes like replication, transcription, and translation drive how genetic information is copied, expressed, and used to build proteins. Tools like the Punnett Square help predict inheritance patterns, and understanding mutations helps explain genetic diseases and variation. Together, these concepts form the basis of inheritance and genetic variation in all living organisms. Codon Table Organized by Leading Nucleotide Codons Starting with U (Uracil) Codo Amino Acid n UUU Phenylalanine (Phe) UUC Phenylalanine (Phe) UUA Leucine (Leu) UUG Leucine (Leu) UCU Serine (Ser) UCC Serine (Ser) UCA Serine (Ser) UCG Serine (Ser) UAU Tyrosine (Tyr) UAC Tyrosine (Tyr) UAA Stop codon UAG Stop codon UGA Stop codon UGU Cysteine (Cys) UGC Cysteine (Cys) UGG Tryptophan (Trp) Codons Starting with C (Cytosine) Codo Amino Acid n CUU Leucine (Leu) CUC Leucine (Leu) CUA Leucine (Leu) CUG Leucine (Leu) CCU Proline (Pro) CCC Proline (Pro) CCA Proline (Pro) CCG Proline (Pro) CAU Histidine (His) CAC Histidine (His) CAA Glutamine (Gln) CAG Glutamine (Gln) Codons Starting with A (Adenine) Codo Amino Acid n AUU Isoleucine (Ile) AUC Isoleucine (Ile) AUA Isoleucine (Ile) AUG Methionine (Met) - Start codon ACU Threonine (Thr) ACC Threonine (Thr) ACA Threonine (Thr) ACG Threonine (Thr) AAU Asparagine (Asn) AAC Asparagine (Asn) AAA Lysine (Lys) AAG Lysine (Lys) Codons Starting with G (Guanine) Codo Amino Acid n GUU Valine (Val) GUC Valine (Val) GUA Valine (Val) GUG Valine (Val) GCU Alanine (Ala) GCC Alanine (Ala) GCA Alanine (Ala) GCG Alanine (Ala) GAU Aspartic acid (Asp) GAC Aspartic acid (Asp) GAA Glutamic acid (Glu) GAG Glutamic acid (Glu) GGU Glycine (Gly) GGC Glycine (Gly) GGA Glycine (Gly)  GGG Glycine (Gly) Summary of Codon Table by Leading Nucleotide ​ Codons starting with U (Uracil): Encode for amino acids like Phenylalanine, Leucine, Serine, Tyrosine, Cysteine, and Tryptophan. ​ Codons starting with C (Cytosine): Encode for Leucine, Proline, Histidine, and Glutamine. ​ Codons starting with A (Adenine): Encode for Isoleucine, Methionine (start codon), Threonine, Asparagine, and Lysine. ​ Codons starting with G (Guanine): Encode for Valine, Alanine, Aspartic acid, Glutamic acid, and Glycine. This arrangement allows for easier lookup of codons based on their leading nucleotide, and can be useful in understanding how codons are distributed and how amino acids are synthesized during protein translation. Nucleotide Table The nucleotides are the building blocks of nucleic acids (DNA and RNA). There are four types of nucleotides in DNA and RNA, which differ slightly. DNA Nucleotides: ​ Adenine (A): Pairs with Thymine (T) in DNA. ​ Thymine (T): Pairs with Adenine (A) in DNA. ​ Cytosine (C): Pairs with Guanine (G) in DNA. ​ Guanine (G): Pairs with Cytosine (C) in DNA. DNA bases form pairs through hydrogen bonds: ​ A pairs with T. ​ C pairs with G. RNA Nucleotides: RNA is similar to DNA but replaces Thymine (T) with Uracil (U): ​ Adenine (A): Pairs with Uracil (U) in RNA. ​ Uracil (U): Pairs with Adenine (A) in RNA. ​ Cytosine (C): Pairs with Guanine (G) in RNA.  ​ Guanine (G): Pairs with Cytosine (C) in RNA. In RNA, the base T from DNA is replaced by U (Uracil): ​ A pairs with U in RNA. ​ C pairs with G in both DNA and RNA. ​ G pairs with C in both DNA and RNA. Summary of Key Points: 1.​ Codons: Triplets of nucleotides in mRNA that code for specific amino acids. There are 64 possible codons, with 61 coding for amino acids and 3 signaling the end of translation (stop codons). 2.​ DNA vs. RNA: ○​ DNA contains the bases A, T, C, G, and forms double-stranded molecules. ○​ RNA contains the bases A, U, C, G, and is single-stranded. 3.​ Start and Stop Codons: ○​ The start codon is AUG, which codes for Methionine (Met) and signals the beginning of protein synthesis. ○​ The stop codons (UAA, UAG, UGA) signal the end of translation. Understanding how codons and nucleotides function together helps explain how genetic information is translated into proteins, ultimately determining the traits of an organism. Evolution and Ecology Dr. Asamani AD Biology Midterms Study Guide Evolution and Ecology Evolution & Ecology: The fields of evolution and ecology are deeply interconnected and focus on understanding how organisms change over time and interact with each other and their environments. Here's an explanation of the key concepts in each area: 1. Evolutionary Tree / Common Ancestor An evolutionary tree (also called a phylogenetic tree) is a diagram that shows the evolutionary relationships among species. It illustrates how species are related to one another through common ancestors. ​ Common Ancestor: This is the most recent species from which two or more species have evolved. All life forms share a common ancestor if you trace their lineage far enough back in time. ​ The branches of an evolutionary tree represent different species or groups, and the nodes (points where branches meet) represent common ancestors. ​ The tree helps us understand divergent evolution, where species evolve different traits from a shared ancestor, and convergent evolution, where different species independently evolve similar traits. Example: The common ancestor of all mammals would have given rise to different branches, leading to species such as humans, whales, and bats. 2. Ecological Succession Ecological succession refers to the process by which ecosystems change and develop over time. It is the gradual replacement of one community of species by another in an ecosystem. There are two types of ecological succession: ​ Primary Succession: Occurs in an environment where no previous community existed, such as after a volcanic eruption or glacier retreat. Initially, hardy species like lichens or mosses begin to colonize the area, followed by grasses, shrubs, and eventually trees.  ​ Secondary Succession: Occurs in areas where a community has been disturbed or destroyed (such as after a forest fire or farming). Soil remains, allowing the area to recover more quickly with the establishment of pioneer species, followed by grasses, shrubs, and trees. Ecological succession can take hundreds to thousands of years to reach a climax community, where the ecosystem reaches stability. 3. Biotic vs. Abiotic Factors ​ Biotic Factors: These are the living components of an ecosystem. They include all the organisms such as plants, animals, fungi, bacteria, and other microorganisms that interact in the environment. Biotic factors influence the survival and behavior of organisms.​ ​ Examples:​ ○​ Predation: Lions hunt gazelles. ○​ Competition: Trees compete for sunlight and nutrients. ○​ Symbiosis: Lichens (fungus and algae) living together. ​ Abiotic Factors: These are the non-living components of an ecosystem. They include physical and chemical factors like temperature, sunlight, soil composition, water, and air quality. Abiotic factors influence the types of organisms that can live in a given environment.​ ​ Examples:​ ○​ Temperature: Cold temperatures can limit the types of plants that can grow in a region. ○​ Water: Availability of water influences plant and animal life in a desert. ○​ Soil: Nutrient-rich soil supports diverse plant life. 4. Ecological Niche An ecological niche is the role or function of an organism in its environment, including how it gets its food, where it lives, and how it interacts with other organisms. A niche encompasses everything an organism needs to survive, reproduce, and maintain its species. ​ Habitat: The physical environment where an organism lives. ​ Trophic Level: The organism’s position in the food chain (e.g., herbivore, carnivore, decomposer).  ​ Interactions: How the organism interacts with other species (e.g., predator, prey, mutualism). Two species cannot occupy the same niche indefinitely because they would compete for the same resources, leading to what is known as the competitive exclusion principle. 5. Food Chain vs. Food Web ​ Food Chain: A linear sequence that shows how energy and nutrients move through an ecosystem. It typically starts with a primary producer (like plants or algae), then moves to primary consumers (herbivores), followed by secondary consumers (carnivores), and ends with decomposers (organisms that break down dead material).​ ​ Example:​ ○​ Grass → Grasshopper → Frog → Snake → Eagle. ​ Food Web: A more complex and interconnected representation of the food chains within an ecosystem. It shows that organisms can be part of multiple food chains, meaning they have multiple sources of food and are preyed upon by different species.​ ​ Example:​ ○​ A food web might show how a fox eats both rabbits and birds, while plants are consumed by rabbits and insects. Food Chain vs. Food Web: While a food chain is a simple, direct pathway of energy transfer, a food web provides a more realistic view of ecosystem dynamics, as organisms often have multiple interactions. 6. Prey vs. Predator Predation is an interaction where one organism (the predator) hunts and kills another organism (the prey) for food. ​ Predators are typically carnivores, and they have adaptations for hunting, such as sharp teeth, claws, speed, or camouflage.​ ​ Example: A lion hunting a zebra.​ ​ Prey organisms often develop adaptations to avoid being eaten, such as camouflage, defensive mechanisms (like spines or toxins), or speed.​  ​ Example: A zebra may use its speed to escape a lion, or a rabbit might hide in a burrow to avoid a predator.​ Predator-prey relationships help control population sizes and maintain ecosystem balance. When predator populations decrease, prey populations can increase, and vice versa. 7. Energy Transfer Energy transfer refers to how energy moves through an ecosystem, typically from one organism to another. The flow of energy is best understood through the concept of a trophic pyramid. ​ Producers (usually plants or algae) are at the base of the pyramid, capturing solar energy through photosynthesis. ​ Primary Consumers (herbivores) consume the producers. ​ Secondary Consumers (carnivores) eat the primary consumers. ​ Tertiary Consumers (top predators) are at the top of the food chain. Energy is lost at each level in the form of heat (through metabolism and movement), so only about 10% of the energy is passed to the next trophic level. This is known as the 10% Rule. Example: ​ Grass (producer) → Grasshopper (primary consumer) → Frog (secondary consumer) → Snake (tertiary consumer). At each level, the organisms use energy for metabolism, movement, and reproduction, so the higher up the food chain you go, the less energy is available to organisms at each successive level. Summary of Evolution & Ecology Concepts ​ Evolutionary Tree/Common Ancestor: A diagram showing the evolutionary relationships between species, all of which share a common ancestor. ​ Ecological Succession: The gradual process of change and development in an ecosystem, leading to a stable climax community. ​ Biotic/Abiotic Factors: Biotic factors are the living components of an ecosystem, while abiotic factors are the non-living components like temperature, water, and soil. ​ Ecological Niche: The role an organism plays in its environment, including its habitat, diet, and interactions with other organisms.  ​ Food Chain vs. Food Web: A food chain is a linear pathway of energy transfer, while a food web is a more complex system showing multiple interactions between organisms. ​ Prey vs. Predator: The relationship where one organism (the predator) hunts and kills another organism (the prey) for food. ​ Energy Transfer: The flow of energy through an ecosystem, with energy being lost at each trophic level, leading to a pyramid structure where producers have the most energy and top predators have the least. These concepts are fundamental in understanding how life evolves, interacts, and sustains itself in the natural world. Taxonomy Dr. Asamani AD Biology Midterms Study Guide Taxonomy Classification of Living Things (Taxonomy) Classification is the process of organizing living organisms into groups based on shared characteristics. This system of classification is called taxonomy, and it helps scientists to identify, name, and understand the relationships among various organisms. The main goal of classification is to organize biological diversity in a structured and meaningful way. Hierarchical System of Classification: The classification system follows a hierarchical structure with several levels, ranging from the broadest category (Domain) to the most specific (Species). The traditional system of classification includes seven main levels: 1.​ Domain 2.​ Kingdom 3.​ Phylum (plural: Phyla) 4.​ Class 5.​ Order 6.​ Family 7.​ Genus (plural: Genera) 8.​ Species Each level in the hierarchy contains one or more groups from the level below it. Here's a breakdown of each level: 1. Domain The Domain is the broadest and most inclusive level of classification. There are three domains of life: ​ Bacteria: Single-celled organisms that lack a nucleus (prokaryotic). ​ Archaea: Single-celled organisms that are similar to bacteria but have distinct biochemical and genetic differences (also prokaryotic).  ​ Eukarya: Organisms that have a true nucleus and organelles (eukaryotic), including plants, animals, fungi, and protists. 2. Kingdom A kingdom is the next level of classification. There are traditionally five kingdoms, although some systems recognize additional kingdoms or revise the classification: ​ Animalia (animals): Multicellular, eukaryotic organisms that are typically mobile and consume organic material. ​ Plantae (plants): Multicellular, eukaryotic organisms that produce their own food through photosynthesis. ​ Fungi (fungi): Eukaryotic organisms, including molds, yeasts, and mushrooms, that decompose organic material. ​ Protista (protists): A diverse group of mostly single-celled eukaryotes, including algae, protozoa, and slime molds. ​ Monera (bacteria and archaea): Unicellular, prokaryotic organisms, including bacteria and archaea. 3. Phylum (plural: Phyla) The phylum groups organisms based on significant structural similarities. For example, animals with a backbone belong to the phylum Chordata. Phylum represents a broad category that includes a variety of organisms that share fundamental body plans or features. Examples: ​ Chordata: Includes animals with a notochord (like vertebrates: mammals, birds, fish). ​ Arthropoda: Includes insects, spiders, and crustaceans, characterized by exoskeletons and jointed limbs. 4. Class A class is a more specific category within a phylum. Organisms in a class share more detailed characteristics. Examples: ​ Mammalia: Includes all mammals, which are characterized by having hair or fur and mammary glands that produce milk.  ​ Aves: Birds, characterized by feathers, beaks, and laying hard-shelled eggs. ​ Reptilia: Reptiles, like snakes, lizards, and turtles, which are cold-blooded and have scales. 5. Order An order groups organisms within a class that share even more specific features. Examples: ​ Carnivora: Includes carnivorous mammals like dogs, cats, and bears. ​ Primates: Includes humans, monkeys, and apes. ​ Chiroptera: Bats, characterized by wings and the ability to fly. 6. Family A family is a group of related organisms within an order. Members of the same family have many similar characteristics. Examples: ​ Felidae: The cat family, which includes lions, tigers, leopards, and domestic cats. ​ Canidae: The dog family, including wolves, foxes, and domestic dogs. ​ Hominidae: The great ape family, including humans, chimpanzees, gorillas, and orangutans. 7. Genus (plural: Genera) A genus is a group of species that are closely related and very similar. It is one of the most specific levels in classification. Each species within a genus shares a common ancestor. Examples: ​ Panthera: The genus that includes big cats like lions (Panthera leo) and tigers (Panthera tigris). ​ Homo: The genus that includes humans (Homo sapiens) and closely related species like Neanderthals (Homo neanderthalensis). 8. Species The species is the most specific level of classification. A species is a group of individuals that can interbreed and produce fertile offspring. Species share the most detailed genetic and physical characteristics. Example: ​ Homo sapiens: Modern humans. ​ Panthera leo: Lions. ​ Canis lupus: Wolves. Binomial Nomenclature The system of binomial nomenclature is used to give species a two-part scientific name, which includes: 1.​ Genus: The first part, capitalized (e.g., Homo for humans). 2.​ Species: The second part, not capitalized (e.g., sapiens for humans). This naming system is universal and helps ensure that organisms are universally identified. For example: ​ Homo sapiens (Humans) ​ Panthera leo (Lion) ​ Canis lupus (Wolf) Why Classification is Important 1.​ Organizing Information: Classification helps scientists organize vast amounts of biological information. It provides a systematic way to study organisms and their relationships. 2.​ Understanding Relationships: By grouping organisms into categories, scientists can understand evolutionary relationships and trace the lineage of species. 3.​ Identifying New Species: Taxonomy helps in identifying and naming new species discovered in the wild. 4.​ Conservation Efforts: Knowing how species are related can aid in conservation efforts by highlighting the importance of preserving ecosystems and biodiversity. Modern Taxonomy and Phylogeny In modern taxonomy, the classification system is based not just on physical traits, but also on genetic data, particularly DNA sequences. This is known as phylogenetic classification, where organisms are grouped based on their evolutionary relationships rather than just their appearance. Cladistics is a method used in modern taxonomy that organizes species based on common ancestry and evolutionary traits, often represented in a cladogram, a branching diagram showing the evolutionary relationships among species. Summary of the Classification System: 1.​ Domain: The broadest category. 2.​ Kingdom: Major groups like animals, plants, fungi. 3.​ Phylum: Groups organisms with shared body plans. 4.​ Class: More specific characteristics within a phylum. 5.​ Order: Groups within a class with additional similarities. 6.​ Family: A closely related group of organisms within an order. 7.​ Genus: Groups of closely related species. 8.​ Species: The most specific group, where organisms can interbreed. Classification helps us make sense of the diversity of life, understand the evolutionary history of organisms, and provides a way to identify and study species systematically.