BIO 4 Final Exam Study Guide PDF

BIO 4 Final Exam Study Guide The following topics will be on the exam. How are scientific hypothesis made and what criteria do they have to meet? A scientific hypothesis is an explanation for an observation, phenomenon, or scientific problem that can be tested through further...

BIO 4 Final Exam Study Guide The following topics will be on the exam. How are scientific hypothesis made and what criteria do they have to meet? A scientific hypothesis is an explanation for an observation, phenomenon, or scientific problem that can be tested through further experimentation and observation. It must be falsifiable, meaning that it can be proven false through experimentation. For example, the hypothesis "all swans are white" is falsifiable because observing a black swan would disprove it. Atomic number, atomic mass number, electrons, protons, and neutrons Atomic Number: The number of protons in an atom's nucleus. This number determines the element to which the atom belongs. Atomic Mass Number: The total number of protons and neutrons in the nucleus of an atom. Electrons: Negatively charged subatomic particles that orbit the nucleus in specific energy levels or electron shells [2, 3]. Protons: Positively charged subatomic particles found in the nucleus of an atom. Neutrons: Neutrally charged subatomic particles found in the nucleus of an atom. Electron energy levels, valence electrons Electron Energy Levels: Electrons occupy specific energy levels around the nucleus. The first shell can hold a maximum of 2 electrons, the second shell 8 electrons. The outermost shell is called the valence shell and electrons in this shell are called valence electrons. Valence Electrons: Electrons in the outermost shell of an atom. These electrons determine an atom's chemical reactivity as they are involved in the formation of chemical bonds. Covalent, ionic, and hydrogen bonds; van der Waals forces Covalent Bonds: Bonds formed when two atoms share a pair of valence 2electrons. This sharing allows both atoms to achieve a more stable electron configuration. Ionic Bonds: Bonds formed due to the electrostatic attraction between oppositely charged ions. These ions are formed when one atom donates one or more valence electrons to another atom. Hydrogen Bonds: Weak bonds formed between a hydrogen atom (covalently bonded to a more electronegative atom, like oxygen) and another electronegative atom (e.g., oxygen or nitrogen). Van der Waals forces: Weak attractions between molecules due to temporary fluctuations in electron distribution, creating temporary dipoles that attract one another. Hydrophobic, hydrophilic, lipophilic Hydrophobic: "Water-fearing" molecules that do not interact well with water, typically nonpolar molecules like fats and oils. Hydrophilic: "Water-loving" molecules that interact readily with water, typically polar molecules or ions. Lipophilic: "Fat-loving" molecules, often synonymous with hydrophobic, meaning they dissolve readily in fats and oils What are the macromolecules made of? Macromolecules are large polymers assembled from smaller repeating monomer subunits. There are four main types: Carbohydrates: Composed of monosaccharides (simple sugars). They serve as energy sources (e.g., glucose) and structural components (e.g., cellulose in plant cell walls). Proteins: Composed of amino acids. They have a wide variety of functions, including catalyzing reactions (enzymes), providing structural support, transporting substances, and regulating cell processes. Nucleic Acids: Composed of nucleotides. DNA and RNA store and transmit genetic information [8, 9]. Lipids: Diverse group of hydrophobic molecules, including fats, phospholipids, and steroids. They serve as energy stores, structural components of cell membranes, and signaling molecules. Storage vs. structural polysaccharides Storage Polysaccharides: Polysaccharides that serve as energy storage molecules. Examples include starch in plants and glycogen in animals. Structural Polysaccharides: Polysaccharides that provide structural support to cells and tissues. Examples include cellulose in plant cell walls and chitin in the exoskeletons of arthropods. Primary, secondary, tertiary, and quaternary protein structure Primary Structure: The unique linear sequence of amino acids in a polypeptide chain. Secondary Structure: Localized folding or coiling of the polypeptide chain, resulting from hydrogen bonds between atoms of the polypeptide backbone. Common secondary structures include alpha helices and beta pleated sheets [10, 11]. Tertiary Structure: Overall 3D shape of a polypeptide, resulting from interactions between the R groups (side chains) of the amino acids. These interactions include hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges. Quaternary Structure: The structure that results from the interaction of multiple polypeptide chains (subunits) to form a functional protein. Endomembrane system The endomembrane system is a network of membranes within a eukaryotic cell that includes the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, vacuoles, and plasma membrane. These components work together to modify, package, and transport proteins and lipids. Diffusion vs. facilitated diffusion vs. osmosis vs. active transport Diffusion: The movement of molecules from an area of high concentration to an area of low concentration. This movement occurs passively, without the input of energy. Facilitated Diffusion: The passive movement of molecules across a membrane with the assistance of transport proteins. These proteins provide channels or carriers that facilitate the movement of specific molecules. Osmosis: The diffusion of water across a selectively permeable membrane from a region of low solute concentration to a region of high solute concentration. Active Transport: The movement of molecules across a membrane against their concentration gradient, requiring the input of energy, typically in the form of ATP. Solvents and solutes and water movement  Solvent: The substance in which a solute dissolves to form a solution. Water is the most common solvent in biological systems. Solute: The substance that dissolves in a solvent to form a solution. Water Movement: Water moves across a selectively permeable membrane from a region of high water concentration (low solute concentration) to a region of low water concentration (high solute concentration). This movement is driven by osmosis. How does thermodynamics relate to respiration and photosynthesis? No particular slides, but group the terms endothermic, positive delta G, anabolic, and nonspontaneous with photosynthesis, and group the terms exothermic, negative delta G, catabolic, and spontaneous with cellular respiration Thermodynamics is the study of energy transformations. The first law of thermodynamics states that energy cannot be created or destroyed but can be transferred or transformed. The second law of thermodynamics states that every energy transfer or transformation increases the entropy of the universe. Cellular Respiration: An exergonic (energy-releasing) process that breaks down glucose and other organic molecules to generate ATP. Cellular respiration is a catabolic process (breaks down complex molecules into simpler ones) with a negative delta G (free energy change), meaning it is spontaneous [16, 17]. Photosynthesis: An endergonic (energy-requiring) process that uses light energy to convert carbon dioxide and water into glucose and oxygen. Photosynthesis is an anabolic process (builds complex molecules from simpler ones) with a positive delta G, meaning it is nonspontaneous. Cellular respiration: who is oxidized and reduced Oxidation: A chemical process involving the loss of electrons. Reduction: A chemical process involving the gain of electrons. Products and location of glycolysis The first stage of cellular respiration, which occurs in the cytoplasm and converts glucose into pyruvate, producing a net gain of 2 ATP and 2 NADH. Products and location of the citric acid cycle (Krebs cycle) Citric Acid Cycle (Krebs Cycle): The second stage of cellular respiration, which occurs in the mitochondrial matrix and completely oxidizes pyruvate to carbon dioxide, generating ATP, NADH, and FADH2. ETC details ETC: A series of electron carrier proteins embedded in the inner mitochondrial membrane. Electrons from NADH and FADH2 are passed down the chain, releasing energy that is used to pump protons across the membrane, creating a proton gradient that drives ATP synthesis. Yeast fermentation Yeast Fermentation: A process that occurs in the absence of oxygen, in which pyruvate is converted into ethanol or lactate. Fermentation regenerates NAD+, allowing glycolysis to continue. Location and products of the light-dependent and light-independent reactions of photosynthesis Light-Dependent Reactions: Reactions that occur in the thylakoid membranes of chloroplasts and capture light energy to generate ATP and NADPH. Light-Independent Reactions (Calvin Cycle): Reactions that occur in the stroma of chloroplasts and use ATP and NADPH to fix carbon dioxide into sugar.  Pigments involved in photosynthesis and light preferences of green plants Pigments: Molecules that absorb light energy. Chlorophyll a is the main photosynthetic pigment, while chlorophyll b and carotenoids are accessory pigments that capture additional light energy. Light Preferences: Green plants absorb light most efficiently in the blue-violet and red regions of the electromagnetic spectrum. Green light is reflected, which is why plants appear green. Haploid vs. diploid Haploid (n): A cell containing only one set of chromosomes. Gametes (sperm and egg) are haploid. Diploid (2n): A cell containing two sets of chromosomes, one set from each parent. Somatic cells (body cells) are diploid [23, 24]. When does replication occur? Replication is the process of copying DNA. It occurs during the S phase of the cell cycle, ensuring that each daughter cell receives a complete set of chromosomes [20, 25]. Mitosis and the cell cycle, meiosis and crossing over Mitosis is a type of cell division that produces two genetically identical daughter cells from a single parent cell. It is responsible for growth, repair, and asexual reproduction in eukaryotes. The cell cycle is the sequence of events that takes place in a cell leading to its division and duplication [26, 27]. Meiosis and Crossing Over Meiosis is a type of cell division that reduces the number of chromosomes by half, producing four haploid daughter cells that are genetically distinct from each other and from the parent cell. This process is essential for sexual reproduction. Crossing over is the exchange of genetic material between homologous chromosomes during prophase I of meiosis, contributing to genetic variation [27 -29]. Cytokinesis in plants and animals Cytokinesis is the division of the cytoplasm that follows mitosis or meiosis, producing two separate daughter cells. Animals: A cleavage furrow forms, pinching the cell in two. Plants: A cell plate forms in the middle of the cell, eventually developing into a new cell wall that separates the daughter cells. Be able to do the various types of genetics problems, i.e., complete dominance, incomplete dominance, codominance, and sex-linked Types of genetics problems include: Complete Dominance: A type of inheritance where the dominant allele completely masks the expression of the recessive allele in heterozygotes. Incomplete Dominance: A type of inheritance where the heterozygote phenotype is intermediate between the two homozygous phenotypes. Codominance: A type of inheritance where both alleles are expressed equally in the heterozygote [30, 31]. Sex-linked: Inheritance patterns of genes located on sex chromosomes (X or Y in humans). These patterns often differ between males and females due to the different chromosome compositions. Replication, transcription, and translation; complementary mRNA to DNA; complementary tRNA to mRNA; E site, P site, and A site The central dogma of molecular biology describes the flow of genetic information within a cell: DNA is transcribed into RNA, and RNA is translated into protein [9, 32, 33]. Replication: The process of copying DNA. Transcription: The process of synthesizing RNA from a DNA template [32, 35]. Translation: The process of synthesizing a polypeptide from an mRNA template [32, 35]. Ribosomes are the sites of protein synthesis in cells. They contain three binding sites for tRNA: E (Exit) Site: Where discharged tRNAs leave the ribosome. P (Peptidyl) Site: Holds the tRNA carrying the growing polypeptide chain. A (Aminoacyl) Site: Holds the tRNA carrying the next amino acid to be added to the chain. Codons and anticodons Codon: A sequence of three nucleotides in mRNA that specifies a particular amino acid during protein synthesis. Anticodon: A sequence of three nucleotides in tRNA that is complementary to a codon in mRNA, ensuring that the correct amino acid is added to the growing polypeptide chain. Characteristics of viruses, lytic cycle, and lysogenic cycle Viruses are infectious particles consisting of genetic material (DNA or RNA) enclosed in a protein coat called a capsid. They are obligate intracellular parasites, meaning they can only replicate inside a host cell. Lytic Cycle: A viral replication cycle that results in the destruction of the host cell. The virus hijacks the host cell's machinery to produce viral proteins and nucleic acids, assembles new viral particles, and then lyses (breaks open) the cell, releasing the new viruses. Lysogenic Cycle: A viral replication cycle in which the viral genome integrates into the host cell's chromosome as a prophage. The viral DNA is replicated along with the host DNA, and new viral particles are not immediately produced. Under certain conditions, the prophage can become active, initiating a lytic cycle. What does ecosystem ecology emphasize? Ecosystem ecology emphasizes energy flow and chemical cycling between organisms and their environment. What does it mean to have “Darwinian fitness”? Darwinian fitness refers to the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals. It is a measure of an organism's reproductive success. K-selected vs. r-selected, density-dependent vs. density-independent K-selected: Species that exhibit traits that maximize their carrying capacity (K) in stable environments. They tend to have few offspring, provide parental care, and have longer lifespans. r-selected: Species that exhibit traits that maximize their intrinsic rate of increase (r) in unstable environments. They tend to have many offspring, provide little parental care, and have shorter lifespans. Density-dependent: Factors that affect population growth in a way that depends on the population's density. Examples include competition for resources, predation, and disease [46, 47]. Density-independent: Factors that affect population growth regardless of population density. Examples include natural disasters and weather events. Ecological footprint slide with various countries Ecological footprint is a measure of human impact on the environment, representing the amount of land and water area required to provide the resources an individual or population consumes and to absorb its waste.  Different types of ecology (population, landscape, community, organismal, ecosystem) Population Ecology: Studies factors that affect population size and how and why it changes over time. Landscape Ecology: Focuses on the exchanges of energy, materials, and organisms across multiple ecosystems within a landscape. Community Ecology: Studies interactions between different species within a community and how these interactions affect community structure and function [48, 50]. Organismal Ecology: Focuses on how an organism's structure, physiology, and behavior meet the challenges of its environment. Ecosystem Ecology: Emphasizes energy flow and chemical cycling between organisms and their Abiotic vs. biotic factors Abiotic Factors: Nonliving components of an ecosystem, such as temperature, water, sunlight, and soil nutrients. Biotic Factors: Living components of an ecosystem, including other organisms, such as plants, animals, fungi, and bacteria. Fundamental vs. realized niches Fundamental Niche: The full range of environmental conditions and resources a species could potentially use and occupy if there were no competition from other species. Realized Niche: The portion of the fundamental niche a species actually occupies in a particular environment, limited by competition and other interactions with other species. Rainshadow A rainshadow is a dry area on the leeward side of a mountain range. As moist air rises over the mountains, it cools and releases precipitation, leaving drier air on the other side. Interspecific interactions Interspecific interactions are relationships between individuals of different species. These interactions include: Competition (-/-): When individuals of different species use a resource that limits the survival and reproduction of both individuals. Predation (+/-): An interaction in which one organism (predator) kills and eats another organism (prey). Herbivory (+/-): An interaction in which an herbivore eats parts of a plant or alga. Parasitism (+/-): One organism (parasite) derives nourishment from another organism (host), which is harmed in the process Mutualism (+/+): A mutually beneficial interaction between two species. Commensalism (+/0): An interaction where one species benefits and the other species is neither harmed nor helped. Mullerian mimicry, Batesian mimicry, aposematic coloration, and cryptic coloration Mullerian mimicry: Two or more unpalatable (toxic or distasteful) species resemble each other, reinforcing their warning signals to predators. Batesian mimicry: A palatable or harmless species mimics an unpalatable species to avoid predation. Aposematic Coloration: Warning coloration used by poisonous or venomous animals to advertise their danger to predators. Cryptic Coloration: Camouflage that allows an animal to blend in with its surroundings.  Random vs. uniform vs. clumped dispersion Random Dispersion: Individuals are spaced unpredictably, with no clear pattern. Uniform Dispersion: Individuals are evenly spaced, typically due to territoriality or competition [47, 54]. Clumped Dispersion: Individuals are grouped together, often due to resource availability or social behavior. Survivorship curves Survivorship curves show the proportion of individuals in a population that survive to different ages. Iteroparity vs. semelparity Iteroparity: Repeated reproduction, producing multiple offspring over a lifetime. Semelparity: "Big-bang" reproduction, producing a single large reproductive event followed by death. Demographic transition A model that describes the transition from high birth and death rates to low birth and death rates as a country develops. Efficiency of energy transfer from one trophic level to the next The efficiency of energy transfer from one trophic level to the next is typically low, around 10%. This means that only a small fraction of the energy stored in one trophic level is available to organisms at the next level. Dominant vs. keystone species Dominant Species: The most abundant species in a community or the species that has the largest biomass. Keystone Species: A species that has a disproportionately large impact on community structure and function relative to its abundance. Primary vs. secondary succession Primary Succession: The colonization of a previously barren habitat, such as a newly formed volcanic island or a glacier-scoured area. Secondary Succession: The recolonization of a disturbed habitat, such as an area cleared by a fire or a forest cleared for agriculture. Percent of genome that codes for exons and introns, etc. only 1.5% of the human genome codes for proteins, rRNAs, or tRNAs Exons: Coding regions of a gene that are expressed and translated into protein. Introns: Noncoding regions of a gene that are transcribed but removed by splicing before translation. 20% og the humsn genome Competitive vs. noncompetitive enzyme inhibition Competitive Inhibition: An inhibitor molecule competes with the substrate for binding to the enzyme's active site. Noncompetitive Inhibition: An inhibitor molecule binds to a site other than the active site, causing a conformational change in the enzyme that reduces its activity. Light preferences for photosynthesis by plants The sources indicate that chlorophyll a is the key light-capturing pigment that participates directly in the light reactions of photosynthesis1. Chlorophyll b and  carotenoids are accessory pigments that broaden the spectrum of light used for photosynthesis12. Different pigments absorb different wavelengths of light. The wavelengths that are absorbed disappear and the wavelengths that are not absorbed are reflected or transmitted3.Chlorophyll a absorbs violet-blue and red light most effectively, while green light is least effective1. This is why most leaves appear green because they reflect and transmit green light3. The action spectrum for photosynthesis, which describes the relative effectiveness of different wavelengths for driving photosynthesis, shows that violet-blue and red light work best for photosynthesis1.Theodor W. Engelmann first demonstrated the action spectrum for photosynthesis in 1883 using a filamentous alga and aerobic bacteria2.The action spectrum is broader than the absorption spectrum of chlorophyll a because accessory pigments, such as chlorophyll b and carotenoids, broaden the spectrum of light used for photosynthesis2. Carotenoids absorb violet and blue-green light and appear yellow or orange because they reflect those colors4. Some carotenoids also function in photoprotection by absorbing excessive light that would otherwise damage chlorophyll or react with oxyge n4 Photorespiration: CAM vs. C4 plants C4 Plants: Plants that have evolved a mechanism to minimize photorespiration (a process that reduces the efficiency of photosynthesis) in hot, dry environments. They use a spatial separation of carbon fixation and the Calvin cycle. CAM Plants: Plants that have evolved a mechanism to minimize water loss in arid environments. They use a temporal separation of carbon fixation (at night) and the Calvin cycle (during the day) [60, 61]. Chemiosmosis The process by which a proton gradient across a membrane is used to drive ATP synthesis. In cellular respiration, the proton gradient is generated by the electron transport chain. In photosynthesis, the proton gradient is generated by the light-dependent reactions. Lac operon; what are the structural parts of it? What regulates it? The lac operon is a group of genes in bacteria that code for enzymes involved in the metabolism of lactose. Structural Parts: Includes a promoter, operator, and genes encoding the lactose- metabolizing enzymes. Regulation: The lac operon is an inducible operon, meaning it is usually turned off but can be turned on in the presence of lactose. Lactose acts as an inducer, binding to the repressor protein and preventing it from binding to the operator, allowing transcription to proceed. Number of chromosomes and number of chromatids after replication - Remember that the chromosome number doesn’t change but the chromatid number doubles Chromosomes: Structures composed of DNA and protein that carry genetic information. In eukaryotes, chromosomes are linear and found in the nucleus. Chromatids: One of two identical copies of a replicated chromosome. Sister chromatids are joined together at the centromere.  The number of chromosomes in a cell does not change after DNA replication, but the number of chromatids doubles. For example, a human cell with 46 chromosomes will have 92 chromatids after DNA replication. Prions vs. viroids Prions: Infectious proteins that can cause neurodegenerative diseases. They are misfolded versions of normal cellular proteins that can induce misfolding in other proteins. Viroids: Small, circular RNA molecules that infect plants. They do not encode proteins but can interfere with plant growth and development.