Bio Exam Review - Ana PDF

Unit 1: Biochemistry Review 1. Bonding and Atomic Structure Covalent Bonds - Definition: Covalent bonds are formed when two atoms share one or more pairs of electrons. This type of bond typically occurs between non-metal atoms. - Example: In a water molecule (H₂O), each hydrogen atom shares an ele...

Unit 1: Biochemistry Review 1. Bonding and Atomic Structure Covalent Bonds - Definition: Covalent bonds are formed when two atoms share one or more pairs of electrons. This type of bond typically occurs between non-metal atoms. - Example: In a water molecule (H₂O), each hydrogen atom shares an electron with the oxygen atom, resulting in a stable molecule. This sharing allows both atoms to achieve a full outer electron shell. Ionic Bonds - Definition: Ionic bonds are formed when one atom donates an electron to another atom, resulting in the formation of charged ions. The atom that loses an electron becomes a positively charged ion (cation), while the atom that gains an electron becomes a negatively charged ion (anion). - Example: In sodium chloride (NaCl), sodium (Na) donates one electron to chlorine (Cl). This transfer creates Na⁺ and Cl⁻ ions, which are held together by the electrostatic forces of attraction. Hydrogen Bonds - Definition: Hydrogen bonds are weak attractions that occur between molecules with polar covalent bonds. They form when a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) is attracted to another electronegative atom. - Example: In water (H₂O), the hydrogen atoms are positively charged, while the oxygen atom is negatively charged. This polarity allows water molecules to form hydrogen bonds with each other, which contributes to water’s unique properties, such as its high boiling point and surface tension. 2. Isotopes - Definition: Isotopes are atoms of the same element that have the same number of protons (and thus the same atomic number) but differ in the number of neutrons. This variation in neutrons leads to different atomic masses. - Example: Carbon-12 and Carbon-14 are both isotopes of carbon. Carbon-12 has 6 neutrons, while Carbon-14 has 8 neutrons. Carbon-14 is radioactive and is used in dating organic materials. 3. Polarity - Definition: Polarity refers to the distribution of electrical charge over the atoms in a molecule. Molecules with an uneven distribution of charge are polar, meaning they have a partial positive charge on one side and a partial negative charge on the other. - Example: Water (H₂O) is a polar molecule because the oxygen atom is more electronegative than the hydrogen atoms, resulting in a bent shape. This polarity allows water to dissolve many ionic and polar substances, making it an excellent solvent. 4. Reactions Condensation/Synthesis - Definition: In condensation reactions (also called synthesis reactions), two smaller molecules combine to form a larger molecule, releasing a molecule of water in the process. This reaction is essential in the formation of larger biological molecules. - Example: The formation of a disaccharide like sucrose from glucose and fructose involves a condensation reaction, releasing water. Hydrolysis - Definition: Hydrolysis is a reaction where a larger molecule is broken down into smaller molecules by the addition of water. This process is crucial for digestion and metabolism. - Example: During digestion, polysaccharides like starch are hydrolyzed into monosaccharides like glucose by adding water. 5. Macromolecules Carbohydrates - Function: Carbohydrates serve as a primary source of energy and structural components in cells. - Examples: Simple sugars (monosaccharides) like glucose and complex carbohydrates (polysaccharides) like starch and cellulose. Lipids - Function: Lipids store energy, insulate the body, and form cell membranes. - Examples: Fats, oils, and phospholipids. Proteins - Function: Proteins perform a variety of functions, including acting as enzymes, hormones, and structural components. - Examples: Enzymes like amylase, structural proteins like collagen. Nucleic Acids - Function: Nucleic acids store and transmit genetic information. - Examples: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). 6. Enzymes - Definition: Enzymes are biological catalysts that speed up chemical reactions by lowering the activation energy required for the reaction to occur. - Active Site: Each enzyme has a specific region called the active site where substrates bind. This specificity allows enzymes to facilitate particular reactions efficiently. - Example: The enzyme catalase breaks down hydrogen peroxide into water and oxygen, helping to protect cells from oxidative damage. 7. Transport in Cells - Cell Membrane: The cell membrane is a selectively permeable barrier that controls the entry and exit of substances. It consists of a lipid bilayer with embedded proteins, allowing for communication and transport. 8. Transport Mechanisms Passive Transport - Definition: Passive transport is the movement of molecules across the cell membrane without the use of energy. It occurs along the concentration gradient, from high to low concentration. - Examples: - Diffusion: Movement of small nonpolar molecules (e.g., oxygen) directly through the membrane. - Osmosis: The diffusion of water across a semipermeable membrane. Active Transport - Definition: Active transport requires energy (usually from ATP) to move molecules against their concentration gradient, from low to high concentration. - Example: The sodium-potassium pump actively transports sodium ions out of and potassium ions into cells, maintaining cellular function. 9. Concentration Gradient - Definition: A concentration gradient is the difference in the concentration of a substance across a space. It is a driving force for the movement of substances during passive transport. - Example: In the case of diffusion, particles move from an area of higher concentration to an area of lower concentration until equilibrium is reached. 10. Terms Related to Cell Membrane Transport Diffusion - Definition: The movement of particles from an area of high concentration to an area of low concentration until equilibrium is reached. - Example: The spreading of perfume molecules in a room. Osmosis - Definition: The diffusion of water across a semipermeable membrane. - Example: Water moving into plant roots from the soil. Isotonic - Definition: A solution with an equal concentration of solutes inside and outside the cell, resulting in no net movement of water. - Example: A red blood cell in isotonic saline maintains its shape. Hypertonic - Definition: A solution with a higher concentration of solutes outside the cell, causing water to move out and the cell to shrink. - Example: A red blood cell placed in a hypertonic solution of salt water. Hypotonic - Definition: A solution with a lower concentration of solutes outside the cell, causing water to move in and the cell to swell. - Example: A red blood cell placed in pure water. 11. Lab Tests Biuret Test - Definition: A chemical test used to detect the presence of proteins in a solution. - Result: A purple color indicates the presence of proteins. Benedict's Test - Definition: A test used to detect reducing sugars in a solution. - Result: A color change from blue to green, yellow, or red indicates the presence of reducing sugars. Iodine Test - Definition: A test used to detect starch in a sample. - Result: A blue-black color indicates the presence of starch. 12. Fluid Mosaic Model - Definition: The fluid mosaic model describes the structure of cell membranes as a dynamic and flexible layer made of lipid molecules with proteins embedded throughout. This arrangement allows for the movement of molecules and the function of the membrane. - Importance: The fluidity of the membrane enables cellular processes such as signaling, transport, and cell recognition. Unit 2: Metabolic Processes Review 1. Key Terminology - Metabolism: This refers to the total sum of all chemical reactions that occur within an organism. It can be divided into two main categories: - Anabolism: This process involves building larger, more complex molecules from smaller ones. It requires energy input. - Example: The synthesis of proteins from amino acids. - Catabolism: This is the breakdown of larger molecules into smaller ones, releasing energy in the process. - Example: The breakdown of glucose during cellular respiration. - Potential Energy: This is energy that is stored in an object due to its position or configuration. - Example: Water stored in a dam has potential energy due to its height. - Kinetic Energy: This is the energy of motion. - Example: A moving car has kinetic energy. - Entropy: A measure of disorder or randomness in a system. As entropy increases, the amount of usable energy in the system decreases, making it less organized. - Example: In a closed system, as time passes, energy becomes more dispersed. 2. Cellular Respiration - Overview: Cellular respiration is the process by which organisms convert glucose and oxygen into carbon dioxide, water, and energy in the form of ATP (adenosine triphosphate). Aerobic Cellular Respiration: This process requires oxygen and occurs in several stages: 1. Glycolysis: - Location: Cytoplasm. - Inputs: 1 molecule of glucose, 2 ATP, NAD+. - Outputs: 2 molecules of pyruvate, 4 ATP (net gain of 2 ATP), 2 NADH. - Explanation: Glycolysis is the first step in breaking down glucose to extract energy. 2. Pyruvate Oxidation: - Location: Mitochondria. - Inputs: 2 molecules of pyruvate, NAD+. - Outputs: 2 Acetyl CoA, 2 NADH, 2 CO₂. - Explanation: Pyruvate is converted into Acetyl CoA, which enters the Krebs Cycle. 3. Krebs Cycle (Citric Acid Cycle): - Location: Mitochondrial matrix. - Inputs: 2 Acetyl CoA, NAD+, FAD. - Outputs: 6 NADH, 2 FADH₂, 2 ATP, 4 CO₂. - Explanation: This cycle generates high-energy electron carriers and a small amount of ATP. 4. Electron Transport Chain and Chemiosmosis: - Location: Inner mitochondrial membrane. - Inputs: NADH, FADH₂, O₂. - Outputs: Approximately 28-34 ATP, H₂O. - Explanation: Electrons from NADH and FADH₂ are passed through protein complexes, driving ATP synthesis via chemiosmosis. - Structure of Mitochondria: Mitochondria have a double membrane: - Outer Membrane: Smooth and contains proteins. - Inner Membrane: Folded into cristae, where the electron transport chain occurs. - Intermembrane Space: Space between the membranes. - Mitochondrial Matrix: Contains enzymes for the Krebs Cycle. Anaerobic Respiration: Occurs in the absence of oxygen and includes: - Lactic Acid Fermentation: Converts pyruvate into lactic acid, occurring in muscles during strenuous exercise. - Ethanol Fermentation: Converts pyruvate into ethanol and CO₂, occurring in yeast. 3. Key Terms in Cellular Respiration - Substrate-Level Phosphorylation: This refers to the direct production of ATP from ADP during glycolysis and the Krebs cycle, without the involvement of an electron transport chain. - NAD+/NADH and FAD/FADH₂: These are electron carriers that transport electrons to the electron transport chain, playing crucial roles in energy metabolism. - Electrochemical Gradient: This is the difference in concentration and charge across a membrane, driving ATP synthesis during chemiosmosis. 4. Photosynthesis - Overview: Photosynthesis is the process by which plants, algae, and some bacteria convert light energy into chemical energy, specifically glucose. Structure of Chlorophyll and Chloroplasts: - Chlorophyll: The green pigment found in chloroplasts, essential for capturing light energy. - Chloroplast: Organelles in plant cells where photosynthesis occurs, containing thylakoids (where light reactions occur) and stroma (where the Calvin cycle occurs). Light Reactions: - Photosystem I (P680) and Photosystem II (P700): These are complexes that absorb light and generate ATP and NADPH. - Inputs: Light, water, NADP+, ADP. - Outputs: O₂, NADPH, ATP. - Explanation: Light energy is converted into chemical energy in the form of ATP and NADPH. Calvin Cycle: - Key Processes: - Carbon Fixation: Incorporating CO₂ into organic molecules. - Light Compensation Point: The level of light intensity at which photosynthesis equals respiration. - Inputs: ATP, NADPH, CO₂. - Outputs: Glucose, ADP, NADP+. - Explanation: The Calvin cycle uses energy from ATP and NADPH to convert CO₂ into glucose. 5. Comparing Photosynthesis and Cellular Respiration - Overall Equations: - Photosynthesis: 6CO2+6H2O+light energy→C6H12O6+6O2 ​ - Cellular Respiration: C6H12O6+6O2→6CO2+6H2O+energy (ATP) - Relationship Between Components: - NAD vs. NADP: Both are electron carriers; NAD+ is used in cellular respiration, while NADP+ is used in photosynthesis. This illustrates how energy flows through these two processes, highlighting their interconnected nature. Unit 3: Molecular Genetics Review 1. Key Terminology - Transformation: - Definition: This is the process by which a cell takes up foreign DNA from its environment. - Example: Bacteria can incorporate plasmids (small DNA molecules) from their surroundings, allowing them to acquire new traits, such as antibiotic resistance. - Nucleus: - Definition: The nucleus is a membrane-bound organelle found in eukaryotic cells that houses the cell's DNA. - Function: It controls cellular activities by regulating gene expression. - DNA and RNA: - DNA (Deoxyribonucleic Acid): The molecule that stores genetic information in the form of a sequence of nucleotides. - RNA (Ribonucleic Acid): A nucleic acid involved in protein synthesis and gene regulation. It serves as a messenger carrying instructions from DNA. - Protein Coat: - Definition: The protective outer layer of a virus, typically made of protein subunits. - Function: It helps the virus attach to and enter host cells. 2. Bacteriophage - Definition: A bacteriophage is a type of virus that specifically infects bacteria. - Structure: It consists of genetic material (either DNA or RNA) encased in a protein coat. - Function: Bacteriophages can inject their genetic material into bacterial cells, leading to the production of new virus particles, often resulting in the lysis (destruction) of the host cell. 3. Structure of DNA - Double Helix: - Definition: DNA has a double-helix structure, resembling a twisted ladder, with two strands running in opposite directions. - Antiparallel: - Definition: The two strands of DNA are oriented in opposite directions, one running from 5’ to 3’ and the other from 3’ to 5’. - Importance: This orientation is crucial for DNA replication and function. - Complementary Base Pairing: - Definition: In DNA, adenine (A) pairs with thymine (T), and cytosine (C) pairs with guanine (G). - Importance: This pairing ensures accurate replication and transcription of genetic information. 4. DNA Replication - Key Enzymes and Processes: - DNA Helicase: Unwinds the DNA double helix, creating two single strands for replication. - DNA Gyrase: Relieves the torsional strain that builds up ahead of the replication fork during DNA unwinding. - Anneal: Refers to the process where the separated DNA strands come back together. - Replication Bubble and Fork: - Definition: The replication bubble is a region where DNA has been unwound and replication is occurring, while the replication fork is the point where the two strands are separated. - DNA Polymerase: - Definition: Enzymes that synthesize new DNA strands by adding nucleotides to the growing chain. - Types: Include DNA polymerase I, II, and III, each with specific functions. - Okazaki Fragments: - Definition: Short segments of DNA synthesized on the lagging strand during replication. - Leading Strand: The continuously synthesized strand of DNA in the direction of the replication fork. - Lagging Strand: The strand synthesized in short fragments (Okazaki fragments) away from the replication fork. - RNA Primer: A short RNA sequence that is required to start DNA synthesis. - Primase: The enzyme that synthesizes the RNA primer. - DNA Ligase: The enzyme that joins Okazaki fragments together to form a continuous strand. 5. Protein Synthesis - Central Dogma: The flow of genetic information is described by the central dogma, which states that DNA is transcribed into RNA, which is then translated into proteins. Transcription: - Definition: The process of copying a segment of DNA into messenger RNA (mRNA). - Modifications: Includes adding a 5’ cap and a poly-A tail to the mRNA and splicing out introns (non-coding sequences). Translation: - Definition: The process of synthesizing proteins from mRNA at the ribosome. - Key Components: - RNA: A nucleic acid that plays a role in protein synthesis. - mRNA: Carries the genetic code from DNA to the ribosome. - tRNA: Transfers specific amino acids to the ribosome and has an anticodon that pairs with the corresponding mRNA codon. - Stages: 1. Initiation: The start of protein synthesis at the ribosome. 2. Elongation: The addition of amino acids to the growing polypeptide chain, following the sequence coded by mRNA. 3. Termination: The process ends when a stop codon is reached, releasing the newly synthesized protein. 6. Mutations - Definition: Changes in the DNA sequence that can lead to alterations in protein synthesis. - Types of Mutations: - Point Mutation: A change in a single nucleotide (substitution). - Silent Mutation: A point mutation that does not change the amino acid sequence. - Missense Mutation: A point mutation that changes one amino acid in the protein sequence, potentially altering its function. - Nonsense Mutation: A mutation that creates a premature stop codon, leading to a truncated protein. - Frameshift Mutation: Caused by the insertion or deletion of nucleotides, shifting the reading frame and altering the entire amino acid sequence downstream. 7. Regulation of Gene Expression - Definition: Mechanisms that control when and how much of a gene product (such as protein) is produced in a cell. - Lac/Trp Operon: - Example: In prokaryotes, these operons are classic models of gene regulation. The lac operon is activated in the presence of lactose, while the trp operon is repressed when tryptophan is abundant. 8. Biotechnology - Recombinant DNA: DNA molecules formed by combining DNA from different sources, often used in genetic engineering. - Gel Electrophoresis: A technique used to separate DNA fragments based on size by applying an electric current to a gel. - Plasmids/Cloning: Plasmids are circular DNA molecules used as vectors to clone genes in bacteria, allowing for the amplification of specific DNA sequences. - DNA Sequencing: The process of determining the exact sequence of nucleotides in a DNA molecule. Key Techniques: - Restriction Enzymes: Enzymes that cut DNA at specific recognition sites, essential for DNA manipulation in cloning. - Blunt Ends: Cuts that leave straight ends in the DNA, which can be ligated to other blunt ends but are less efficient than sticky ends. - Sticky Ends: Overhanging ends created by certain restriction enzymes that can easily pair with complementary DNA sequences. - Agarose: A gel used in electrophoresis for separating DNA based on size. - PCR (Polymerase Chain Reaction): A method to amplify a specific DNA segment, making millions of copies for analysis. - Gel Pattern: A visual representation of DNA fragments after electrophoresis, used to analyze size and quantity. Unit 4: Population Dynamics Review 1. Key Terminology - Population Ecology: - Definition: The study of populations, focusing on their sizes, densities, distributions, and dynamics over time. - Importance: Understanding population ecology helps predict how populations respond to environmental changes. - Population: - Definition: A group of individuals of the same species living in a specific area at the same time. - Example: A herd of deer in a forest. - Population Density: - Definition: The number of individuals per unit area. - Calculation: Density=​ Area Number of Individuals ​ - Example: If there are 50 rabbits in a 10-acre area, the population density is 5 rabbits per acre. - Mark-Recapture: - Definition: A method used to estimate population size by capturing individuals, marking them, releasing them, and then recapturing to see how many marked individuals are in the second sample. - Example: If 20 fish are caught and marked, and later 30 fish are caught with 5 marked ones, the population size can be estimated using ratios. - K vs. R Selection: - K-Selected Species: - Definition: Species that invest more time and resources in fewer offspring, leading to stable populations near the carrying capacity. - Example: Elephants, which have long gestation periods and care for their young. - R-Selected Species: - Definition: Species that produce many offspring with little parental investment, leading to fluctuating population sizes. - Example: Frogs, which lay thousands of eggs with little to no care. 2. Changes in Population - Geometric Growth: - Definition: Describes populations that grow in discrete time intervals. - Formula: Nt=N0λt - Where Nt is the population size at time t, N0 is the initial population size, and λ is the finite growth rate. - Example: A population of bacteria that doubles every hour. - Exponential Growth: - Definition: Describes continuous growth that occurs under ideal conditions with unlimited resources. - Formula: Nt=N0ert - Where r is the intrinsic growth rate. - Example: A population of yeast in a nutrient-rich environment. 3. Factors Affecting Population Change - Carrying Capacity: - Definition: The maximum number of individuals that an environment can sustainably support. - Importance: It is influenced by resources such as food, water, and shelter. - Open and Closed Populations: - Open Populations: Allow for immigration and emigration, affecting population size. - Closed Populations: No movement of individuals in or out, so size changes only through birth and death rates. - Density-Dependent Factors: - Definition: Factors that impact population size based on the population's density, such as competition for resources, predation, and disease. - Example: In crowded areas, competition for food may increase mortality rates. - Density-Independent Factors: - Definition: Factors that affect population size regardless of density, such as natural disasters, climate changes, or human activities. - Example: A forest fire that kills individuals regardless of the population density. 4. Relationships - Predator/Prey Relationship: - Definition: The dynamic interaction between predator and prey species that influences each other's population sizes. - Example: The relationship between wolves (predators) and deer (prey) regulates their respective populations. - Symbiosis: - Definition: Interactions between different species, classified into three types: - Parasitism: One species benefits at the expense of another (e.g., ticks on mammals). - Mutualism: Both species benefit from the interaction (e.g., bees and flowering plants). - Commensalism: One species benefits while the other is neither helped nor harmed (e.g., barnacles on whales). 5. Population Dispersion Patterns - Clumped Dispersion: - Definition: Individuals are grouped together, often due to resource availability or social behavior. - Example: Herds of elephants that gather around water sources. - Uniform Dispersion: - Definition: Individuals are evenly spaced due to territoriality or competition. - Example: Some bird species that maintain territories. - Random Dispersion: - Definition: Individuals are distributed randomly, often where resources are plentiful and not limited. - Example: Plants with wind-dispersed seeds that grow in various locations. 6. Research Methods - Quadrat: - Definition: A square frame used to study population density in a specific area by counting individuals within the frame. - Example: Used in ecology to assess plant populations in a grassland. - Transect: - Definition: A method of sampling along a line, allowing researchers to study changes in populations or communities across different habitats. - Example: Measuring species diversity across a gradient from a riverbank to a forest. 7. Defense Mechanisms - Definition: Strategies used by organisms to avoid predation and increase their chances of survival. - Examples: - Camouflage: Blending in with the environment to avoid detection (e.g., stick insects). - Warning Coloration: Bright colors to signal danger or toxicity (e.g., poison dart frogs). - Mimicry: Evolving to resemble another species for protection (e.g., non-venomous snakes mimicking venomous ones). - Physical Defenses: Structures like shells or spines that deter predators (e.g., sea urchins). Unit 5: Homeostasis Review 1. Homeostasis - Definition: Homeostasis is the process by which living organisms regulate their internal environment to maintain stable conditions necessary for survival, despite changes in the external environment. - Example: Humans maintain a constant body temperature around 37°C (98.6°F). If the temperature rises, mechanisms like sweating kick in to cool the body down. Conversely, if the temperature drops, shivering generates heat. 2. Feedback Mechanisms - Negative Feedback: - Definition: This mechanism counteracts changes, returning the system to its original state or set point. It acts like a thermostat, activating responses to reverse changes. - Example: When blood sugar levels rise after eating, the pancreas secretes insulin. Insulin helps cells absorb glucose, lowering blood sugar back to normal levels. - Positive Feedback: - Definition: This mechanism amplifies changes, pushing the system further away from its original state. It is less common but crucial in certain biological processes. - Example: During childbirth, the release of oxytocin increases contractions. As contractions intensify, more oxytocin is released, continuing this cycle until the baby is born. 3. Importance of Temperature Regulation - Role: Temperature regulation is vital for enzyme function and metabolic processes. Enzymes have optimal temperature ranges; deviations can slow reactions or denature enzymes. - Impact of Extreme Temperatures: High temperatures can lead to heat exhaustion or heat stroke, while low temperatures can result in hypothermia. Both conditions can impair bodily functions and lead to severe health issues. 4. Importance of Excreting Waste - Function: Waste excretion is essential for removing metabolic waste and toxins from the body, preventing damage to cells and organs. - Key Processes: The kidneys filter blood, producing urine that contains waste products like urea and excess salts. Efficient waste removal is critical for maintaining homeostasis and fluid balance. 5. Urinary System and Nephron - Overview: The urinary system consists of the kidneys, ureters, bladder, and urethra, working together to filter blood, excrete waste, and regulate fluid balance. - Nephron Structure and Function: - Glomerulus: A network of capillaries where blood filtration begins. It allows water, ions, and small molecules to pass into Bowman's Capsule. - Bowman's Capsule: Surrounds the glomerulus and collects the filtrate (the filtered fluid). - Proximal Convoluted Tubule (PCT): Reabsorbs nutrients (like glucose and amino acids), water, and ions back into the bloodstream, helping maintain fluid and electrolyte balance. - Loop of Henle: Plays a critical role in concentrating urine and reabsorbing water and salts, creating a gradient that aids in urine concentration. - Distal Convoluted Tubule (DCT): Further adjusts the composition of urine by reabsorbing more water and ions based on the body’s needs. - Collecting Duct: Receives urine from multiple nephrons and transports it to the renal pelvis, where it is stored before excretion. 6. Kidney Disease - Overview: Kidney diseases impair the kidneys' ability to filter blood and maintain homeostasis. Common conditions include: - Diabetes Mellitus: Affects insulin production or function, leading to high blood sugar levels. Over time, this can damage blood vessels in the kidneys, resulting in diabetic nephropathy. - Diabetes Insipidus: Characterized by an inability to concentrate urine, leading to frequent urination and extreme thirst due to insufficient production of the hormone ADH (antidiuretic hormone). - Bright’s Disease: Refers to a group of kidney diseases characterized by inflammation. It often leads to protein leakage into the urine, causing swelling and other symptoms. - Kidney Stones: Solid mineral deposits that form in the kidneys and can block urine flow, causing severe pain and potential kidney damage.