AP Bio Midterm PDF

# UNIT 1 ## Functional groups: 1. **Hydroxyl (-OH)** - Characteristic of alcohols like ethanol (C₂H₅OH) - Image: A diagram of a hydroxyl group (CH₃CH₂OH), where an oxygen atom is connected to a hydrogen atom, and the rest is part of a carbon ch...

# UNIT 1 ## Functional groups: 1. **Hydroxyl (-OH)** - Characteristic of alcohols like ethanol (C₂H₅OH) - Image: A diagram of a hydroxyl group (CH₃CH₂OH), where an oxygen atom is connected to a hydrogen atom, and the rest is part of a carbon chain. 2. **Carbonyl (C=O)** - Found at the end or within a carbon chain like Acetone (CH₃COCH₃) - Image: A diagram of a carbonyl group (R'C=OR), showing a carbon double-bonded to oxygen, connected to a hydrogen atom and two "R" groups. 3. **Carboxyl (COOH)** - Polar, weak acidic group in fatty acids and amino acids - Combination of a hydroxyl and a carbonyl group - Characteristic of carboxylic acids like acetic acids (CH₃COOH) - Image: A diagram of a carboxyl group (RCOOH) with the carbon double-bonded to an oxygen, single-bonded to an OH group and the other end connected to an "R" group, which represents a side group. 4. **Amino (NH₂)** - Found in amines and amino acids like Glycine (NH₂CH₂COOH) ## Polymers - **Monomers:** the repeating small units that make up polymers like glucose in starch and amino acids in proteins - **Polymers:** the chain-like macromolecules of similar monomers that are bonded together like starch formed by glucose and proteins formed by amino acids ## Polymer Reactions - **Hydrolysis:** a molecule break into two by adding water, break down polymers into monomers, like digestion of carbohydrates into glucose - Image: A diagram of hydrolysis showing two molecules of glucose connected, with an H₂0 molecule on the arrow, leading to two separate molecules of glucose. - **Dehydration:** two molecules are bonded with the loss of water, monomers forming polymers like formation of proteins from amino acids and synthesis of glucose to other forms of sugar - Image: A diagram of dehydration showing two molecules of glucose connected, with a water molecule on the arrow, leading to one molecule of maltose and a water molecule. # UNIT 2 ## Cell Structure and Function - **Prokaryotic Cells:** - do not have a nucleus and membrane-bound organelles - tend to be smaller with circular DNA like bacteria. - **Eukaryotic Cells:** - have a membrane-bound nucleus and organelles. - Tend to be larger with linear DNA associated with histones like plants and animals. ## Organelles | Organelle | Function | Location | | ------------------------ | -------------------------------------------------------------------------------------------------------- | ------------------------- | | Centrioles | organizes microtubules during cell division | animal cells only | | Lysosomes | with hydrolytic enzymes for digestion | animal cells only | | Chloroplasts | the site of photosynthesis | plant cells only | | Cell wall | provides structural support and protection, and central vacuole (stores water, nutrients, waste, | plant cells only | | | maintains turgor pressure) | | ## Protein Synthesis - **Transcription:** mRNA is synthesized in the nucleus - **Translation:** mRNA is translated into a polypeptide by ribosomes on the rough ER. - **Folding and Modification:** protein folds and is being modified in the ER. - **Packaging:** protein is transported to the Golgi apparatus for further modification and sorting. - **Destination:** protein is packaged into **vesicles** and sent to the cell membrane. ## Cytoskeleton | Cytoskeletal element | Function | | ----------------------- | --------------------------------------------------------------------------------------------------------------------- | | Microtubules | Support, transportation, chromosome separation like cilia, flagella, and spindle fibers | | Microfilaments | Cell shape, movement, division like actin filaments | | Intermediate filaments | Structural support, tension resistance like keratin and nuclear lamina | ## Cell Membrane - **Phospholipid Bilayer:** - The phospholipid head is **polar-hydrophilic**, the tails are **nonpolar-hydrophobic**. - Can be found in the cell membrane in cells, they form a phospholipid bilayer creating a supportive barrier for substances to enter or exit the cell. - **Polysaccharides:** - Are long chains of carbohydrates with monomer monosaccharides. - In animals, polysaccharides are **glycogens** for energy storage. - In plants, polysaccharides are **starch** for energy storage and **cellulose** for structural support. - **Saturated Fatty Acids:** - Don't have double bonds, have straight structure, and they are solid under room temperature. - **Unsaturated Fatty Acids:** - Have double bonds, have slight bent structure with a kink in one of the tails, and they are liquid under room temperature. # UNIT 3 ## Enzymes - **Active site:** the region where the substrate binds. - **Substrate:** the reactant that the enzymes act upon. - **Enzyme-substrate complex:** the temporary molecule that forms when the substrate binds to the enzyme. - **Product:** the result after the reaction happens. - **Allosteric site:** the site for regulation by non-substrate molecules that change the shape of the enzyme to influence substrate fitting. ## Enzyme Reactions - Enzymes “speed up” reactions by lowering the activation energy barrier for the reaction to happen faster and more efficiently. The active site binds to the substrate to stabilize the transition state. Enzymes bring substrates to the right orientation for the reaction. - **Temperature, pH, and substrate concentration** can affect the function of an enzyme. - Optimal temp increases enzyme activity. - Too high temp denatures the enzyme. - Each enzyme has an optimal pH range that if deviated, the shape and function of the enzyme would change. - Increased substrate concentrations increase reaction rate until the saturation point is reached where all active sites are occupied. - **Mutation:** If a mutation occurs on a segment of DNA that codes for an enzyme, the enzyme's amino acid sequence, shape (active site), and function would change. The enzyme may lose its function as it can no longer bind to substrates. - **Competitive Inhibition:** The inhibitor binds to the active sites to prevent substrate binding directly. It is often reversible by increasing substrate concentration. - **Noncompetitive Inhibition:** The inhibitor binds to an allosteric site that changes the enzyme's shape to prevent the substrate binding indirectly. It cannot be reversed by increasing substrate. ## Energy and Metabolism - **ATP:** Energy is stored in the bonds between phosphate groups. Hydrolysis of the terminal phosphate releases energy for cellular processes. ATP is regenerated through phosphorylation. (ADP + Pi = ATP) - **Autotrophs:** are organisms that produce their own food. For example, plants, their energy source is light, and they produce their own food through photosynthesis. - **Heterotrophs:** are organisms that consume other food/organisms with energy like animals eat other animals. ## Photosynthesis - The primary purpose of photosynthesis is to convert solar energy into chemical energy stored in glucose and provide energy for plants. - **NADPH:** is the primary electron carrying molecule in photosynthesis. It carries electrons from photosynthesis to the Calvin cycle to synthesize glucose. - **Photosynthesis** occurs in **chloroplasts**. - **Light-dependent reactions** happen in **thylakoid membranes**. It captures the light energy to produce ATP and NADPH while splitting water to release oxygen. 1. Light excites chlorophyll in photosystem II. 2. Water is splits, releasing CO₂ and providing electrons. 3. Electrons travel down the electron transport chain, ATP is generated through chemiosmosis. 4. Electrons reach photosystem I and are re-energized to form NADPH. - **Light-independent reactions (Calvin cycle)** happen in **stroma**. It uses ATP and NADPH to convert CO₂ into glucose through carbon fixation. 1. CO₂ is fixed to RuBP by Rubisco. 2. ATP and NADPH from light-dependent reactions power the reduction phase to form G3P. 3. RuBP is regenerated so the cycle can continue. ## The Calvin Cycle - The three phases of the Calvin cycle: 1. **Carbon fixation:** Incorporation of carbon dioxide into organic molecules. - Purpose: to attach CO₂ to RuBP, catalyzed by the enzyme Rubisco to form a stable organic compound. 2. **Reduction:** conversion of 3-phospoglycerate (3-PGA) into glyceraldehyde-3-phosphate (G3P) using ATP and NADPH. - Purpose: use ATP and NADPH to produce G3P, a three-carbon sugar that is the precursor to glucose and other carbohydrates. 3. **Regeneration of RuBP:** regeneration of ribulose-1, 5-bisphosphate (RuBP) to allow the cycle to continue. - Purpose: recycle RuBP so the cycle and proceed and happen again so there will be continuous carbon fixation ## Photorespiration - Photorespiration occurs when the enzyme Rubisco binds to O₂ instead of CO₂, which happens under high oxygen concentrations, low carbon dioxide levels and high temperatures. - It reduces the efficiency of photosynthesis by using ATP and produce no sugar because it fails to fix carbon efficiently. - Glucose and oxygen are consumed to produce carbon dioxide, water, and ATP. # UNIT 4 ## Cell Communication - **Direct Contact Communication:** Animal cells use gap junctions like cardiac muscles coordinate contraction by allowing ions to pass directly between cells. Plant cells use plasmodesmata, like the small holes on the cell wall connect adjacent cells. - **Long-Distance Signaling:** Both animals and plants use hormones for long-distance signaling. - In animals, hormones are secreted into the bloodstream and travels to target cells like insulin in the bloodstream and acts on distant cells. It tends to be fasters. - In plants, hormones diffuse as gases or are transplanted through the vascular system. It tends to be slower. - **Paracrine Signaling:** signals are released by one cell and diffuse to nearby target cells like growth factors. - **Synaptic Signaling:** in neurons, the neurotransmitters are released into a synapse to stimulate an adjacent neuron or muscle cell like acetylcholine in neuromuscular junctions. - **Second Messengers:** like cAMP, calcium ions, and IP₃ relay and amplify the signal from the receptor to intracellular targets. It allows the signal to be distributed quickly and efficiently and for the cells to respond to low concentrations of signaling molecules. ## Signal Transduction - **Protein Kinase:** does phosphorylation, which means it adds phosphate groups to proteins. It often activates or regulate protein function. - **Protein Phosphatase:** does dephosphorylation, which means it removes phosphate groups and inactivate or alter their activity. - **Cell Response:** A cell can respond to a signal by activation of gene expression, changes in enzyme activity, reorganization of the cytoskeleton, and initiation of cell division or apoptosis. - **Chemicals:** activate a pathway by binding to receptors or enzymes to start or amplify a signaling cascade, like hormones binding to their receptors to activate transcription factors. - **Chemicals:** inhibit a pathway by blocking receptors or enzymes to prevent a signaling cascade like beta-blockers inhibit adrenaline signaling. - **Receptor protein mutation:** If a receptor protein is mutated, it cannot receive a ligand because the ligand-receptor binding is highly specific. The ligand receptor only binds to a very specific type of ligand and has a very specific shape. The mutation would disrupt signal transduction because the receptor cannot initiate the cascade. ## Homeostasis - **Homeostasis:** maintains a stable internal environment despite external conditions change. This balance ensures that conditions like temperature, pH, and glucose levels remain optimal for cell function. - **Slight fluctuations:** are normal and happen as part of dynamic equilibrium which allow the system to adjust and maintain overall stability. - **Negative Feedback:** is a mechanism that reduces or reverses a deviation from a set point to maintain homeostasis. For example, blood glucose regulation. When high blood glucose happens, insulin is secreted and the glucose will be uptake by cells so the blood glucose level decreases. - **Positive Feedback:** is a mechanism that amplifies a deviation to drive a process to completion. For example, the oxytocin release during childbirth. The stretching of the cervix cause oxytocin release for strong contractions to further stretch the cervix. - **Difference:** Negative feedback stabilizes a system by counteracting deviations from the norm. Positive feedback amplifies the changes to push a process forward until the endpoint. # Cell Cycle - **Sister chromatids:** Identical copies of DNA connected at the centromere. - **Centromere:** The constricted region where sister chromatids are joined. - **Kinetochore:** Protein complex at the centromere where spindle fibers attach during mitosis. - **Homologous chromosomes:** are pairs that have the same length, centromere position, and gene loci. Each comes from one parent and contains alleles for the same traits, though they may vary in specific sequences like maternal and paternal chromosomes in a pair. ## Stages of Cell Cycle 1. **Interphase:** - G1 phase: cell growth and preparation for DNA replication - S phase: DNA synthesis and replication - G2 phase: preparation for mitosis and organelle replication 2. **M phase:** mitosis and cytokinesis - Prophase: Chromatin condenses into chromosomes; spindle fibers form. - Metaphase: Chromosomes align at the metaphase plate. - Anaphase: Sister chromatids are pulled to opposite poles. - Telophase: Nuclear membranes reform; chromosomes decondense. - Cytokinesis: Cytoplasm divides, forming two daughter cells. - **Somatic cells:** are body cells that are diploid (2n) and undergo mitosis for division-like skin, muscle, or nerve cells. - **Gametic cells:** are reproductive cells that are haploid (n) and are produced through meiosis like sperm and egg cells. - **External Cell Regulators:** - Growth factors: proteins that stimulate cell division - Density-dependent inhibition: cells stop dividing when they become too crowded. - Anchorage dependence: cells must attach to another surface to divide. - **Cancer cells:** evade these regulators by: - Producing their own growth signals and factors. - Ignoring signals from neighboring cells and don't stop dividing. - Losing anchorage dependence and enable metastasis. - **Checkpoints during the cell cycle:** - G1 checkpoint ensures the cell is reading for DNA replication, check for size, nutrients, and DNA integrity. - G2 checkpoint ensures DNA replication was successful and repairs damage. - M checkpoint (spindle checkpoint) ensures chromosomes are properly attached to the spindle fibers before proceeding to anaphase. - **Cancer cells evade these checkpoints by:** - Producing mutant proteins that prevent error detection. - Ignoring signals to pause or repair. - Proceeding with division with damage and incomplete replication.