Comprehensive University Biology Study Guide: Biology Study Guide (Bio)logy Study Guide

Biological Macromolecules and Chemical Foundations

Carbohydrates are a fundamental class of macromolecules made of Carbon ($C$), Phosphorus ($P$), and Oxygen ($O$) according to the provided material. They adhere to a specific elemental ratio of $1:2:1$. The basic building blocks, or monomers, are known as Monosaccharides, with examples including Glucose, Frutose, and general Sugar. Disaccharides consist of two monosaccharides joined together by a Glycosidic linkage; a prominent example of a disaccharide is Sucrose. Polysaccharides functions are categorized into structural and storage roles. Structural polysaccharides include cellulose, which is found in plants, and Chitin, which is found in Fungi and bugs. Storage polysaccharides include Starch in plants and Glycogen in animals, both of which serve as a means of sugar storage.

Protein Structure and Levels of Bonding

Proteins are composed of Carbon ($C$), Hydrogen ($H$), Oxygen ($O$), and Sulfer. The monomers of proteins are Amino acids, which are joined by Peptide bonds. These are covalent bonds characterized by the sharing of electrons. Protein structure is organized into specific levels. The Primary structure consists of a peptide of amino acids forming a string-like structure. The Secondary structure involves Hydrogen bonds between the backbone of the amino acids, resulting in structures like the alpha helix. The Tertiary structure is the 3D structure held together by Hydrogen, covalent, and Ionic bonds. Regarding digestibility, animals like Ruminants can break Alpha bonds, while humans cannot break Beta bonds, which relates to why certain organisms can digest specific structural carbohydrates like cellulose while others cannot.

Nucleic Acids and Genetic Material

Nuceic Acids are made of Carbon ($C$), Hydrogen ($H$), Oxygen ($O$), Nitrogen ($N$), and phosphorus. The monomer is the nucelotide, and the individual units are held together by a Phosphodiester linkage. There are two primary types of nucleic acids: DNA and RNA. DNA uses the bases Adenine ($A$), Thymine ($T$), Cytosine ($C$), and Guanine ($G$), follows the pairing rules $A-T$ and $G-C$, contains the sugar Deoxyribose, and is double-stranded. RNA uses the bases Adenine ($A$), Uracil ($U$), Cytosine ($C$), and Guanine ($G$), contains the sugar ribose, and is single-stranded.

Lipids, Fats, and Membranes

Lipids are composed of Carbon ($C$), Hydrogen ($H$), Oxygen ($O$), and Phosphorus ($P$). Unlike other macromolecules, lipids are not considered monomers and are nonpolar. Fats are composed of one Glycerol molecule and three fatty acids. Saturated fats contain only single bonds and have Carbon saturated by Hydrogen. Unsaturated fats contain one or more double bonds ($1 \le$ double bond), meaning not all Carbon atoms are saturated by Hydrogen. Phospholipids are a specialized type of lipid with a hydrophilic head (containing Phosphate and Glycerol) and a hydrophobic tail. Steroids also fall under the category of lipids.

Water Chemistry and Properties

Water molecules are held together by polar covalent bonds between Oxygen ($O$) and Hydrogen ($H$). Hydrogen bonds occur between adjacent water molecules. Cohesion refers to water molecules sticking together, while Adhesion involves water sticking to other polar substances. Together, these properties facilitate Capillary actions, such as water traveling up the Xylem in plants. Water also exhibits Surface tension due to the "surface" of hydrogen bonds. It has a High specific heat, requiring a large amount of energy to change temperature. Chemical processes involving water include Hydrolysis, where water is added to create a break between components, and Dehydration, where water is removed to form a bond. The $pH$ scale measures acidity and basicity, where a value greater than $7$ is basic and less than $7$ is acidic. The formula is $pH = -\log[H]$, representing an inverse relationship.

Cellular Organelles and Their Functions

The Nucleus is a double-membrane structure with pores that stores DNA. Ribosomes, composed of RNA and protein, are responsible for ribosome assembly and protein synthesis; they consist of big and small subunits and can be free or bound. The Rough ER is a membrane with ribosomes that provides mechanical support, compartmentalization, intercellular transport, and protein synthesis. The Smooth ER lacks ribosomes and is responsible for detoxifying, lipid synthesis, and storing calcium. The Golgi body is a folded membrane that folds and packages proteins. Mitochota (Mitochondria) feature a double membrane that is folded, where the Krebs cycle occurs to gather fuel. Chloroplasts also have a double outer membrane and are the site of photosynthesis and the Calvin cycle. Lysosomes are membrane-enclosed structures that recycle material and can trigger Apotosis (cell suicide). Vacuoles are membrane-bound sacs that store and release macromolecules and waste, while also managing turgor pressure and osmoregulation.

Membrane Transport and Cell Dynamics

The Plasma membrane is a phospholipid bilayer containing cholesterol molecules and membrane proteins (Integral and Peripheral), as well as carbohydrate groups of glycoproteins and glycolipids. In terms of efficiency, a small cell is better because a smaller size results in a higher Surface Area: Volume ratio. Transport through the membrane includes Simple diffusion (passive, moving down concentration gradient for small, nonpolar molecules), Facilitated diffusion (passive, moving down gradient for small, charged molecules using a protein), and Active transport (requires energy/ATP, moves against concentration gradient using a transport protein). Bulk transport includes Endocytosis for bulky items (phagocytosis for food and pinocytosis for drink) and Exocytosis for exporting items. Osmosis is the movement of water from low solute concentration (high free water) to high solute concentration (low free water). In a Hypertonic solution, the cell loses water and leaks; in a Hypotonic solution, the cell gains water; in an Isotonic solution, movement is equal. Animals cells lysis (pop) in hypotonic solutions and shrivel in hypertonic ones, while plants prefer hypotonic solutions.

Bioenergetics and Enzyme Activity

Gibbs Free Energy is the energy available to do work. Energy cannot be created or destroyed. Endergonic reactions are not spontaneous (like pushing a ball uphill), require work, and absorb energy (e.g., $ADP + P = ATP$). Exergonic reactions are spontaneous (like a ball going down a hill), release energy, and occur as $ATP \rightarrow ADP + P$. Enzymes are protein catalysts that speed up reactions by reducing the reaction rate/activation energy. They are not consumed and can be reused. They function by having a substrate connect to an active site. Denaturation occurs when heat or $pH$ unwinds the enzyme, stopping or slowing it, while cold temperatures also slow them down. Inhibitors can be Competitive (bind to and steal the active site) or Non-competitive (bind to the allosteric site to change the enzyme's shape).

Cellular Respiration and Fermentation

Cellular Respiration starts with sugar and occurs in the Mito Chandria. Glycolysis happens in the Cytoplasm, starting with glucose and producing $2$ pyruvate, $2$ NADH, and $2$ ATP. The Krebs Cycle occurs in the Mitochondria, using Acetyl CoA to produce $2$ $CO_2$, $3$ NADH, $1$ ATP, and $1$ $FADH_2$. Oxidative phosphorylation occurs on the mitochondrial cristae and includes the Electron Transport Chain (ETC) and Chemiosmosis. The ETC pumps protons ($H^+$) into the intermembrane space to generate a proton gradient and only accepts Oxygen as the final electron acceptor. Chemiosmosis involves ATP synthase synthesizing ATP. Fermentation allows for the reuse of glycolysis components; in humans, it produces lactic acid, while in plants, it produces alcohol and $CO_2$ with no additional ATP after the initial $2$ ATP from glycolysis.

Photosynthesis: Light Reactions and the Calvin Cycle

Photosynthesis occurs in the Chloroplast. Light reactions take place in the Thylakoid membrane, starting with $H_2O$ and photons to produce ATP and NADPH. Linear electron flow uses PS II and PS I to synthesize ATP and NADPH, while Cyclic electron flow uses only PS I to synthesize ATP. The Calvin Cycle occurs in the Stroma and relies on the enzyme RuBisCO. It consists of three stages: Stage 1 is Carbon fixation (using $3$ $CO_2$), Stage 2 is Reduction (using $6$ ATP and $6$ NADPH to produce G3P), and Stage 3 is Regeneration of ribulose (using $3$ ATP). It takes $2$ G3P molecules to make $1$ Glucose.

Cell Communication and Signaling

Cell signaling can be unicellular (e.g., bacteria moving toward food as a positive response). Signaling involves a lygane (ligand), which acts as a key for a receptor (the lock). Reception occurs when the lygane binds to the receptor, causing a shape change. Transduction is the signal passing from one protein to another, often via a Phosphoroluk (phosphorylation) cascade where one protein activates a Cynase (kinase) to kick-start amplification. Response occurs via membrane receptors like G-Protein link receptors (where a lygane binds, activating a protein that swaps GDP with GTP to activate enzymes) or Ion channels (where a lygane binds to open a gate for ions).

Feedback Loops and the Cell Cycle

Feedback mechanisms include Positive feedback, which creates a snowball effect to amplify a response (e.g., contractions and hormone production), and Negative feedback, which stabilizes a system to bring it back to normal (e.g., AC or Insulin). The Cell Cycle is divided into Interphase ($90\%$ of the time) and the M Phase. Interphase includes $G_1$ (protein synthesis/growth), S (DNA/chromosome synthesis), and $G_2$ (more growth). Checkpoints are regulated by Cyclin and CDK (the engine); if checkpoints are ignored, uncontrolled cell division occurs, resulting in CANCER. A cell may enter the $G_0$ resting state if it is not ready. Mitosis consists of Prophase (nucleus disappears), Metaphase (Charonsomes line up in the middle), Anaphase (chromosomes are ripped apart), and Telophase (two nuclei form). Cytokinesis is the final division of the cell, where animal membranes pinch and plants form a new membrane/cell plate.