AP Biology:

Unit 1.1: Structure of Water and Hydrogen Bonding

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• Water - H2O. The hydrogens have partial positive charges and the oxygen has a partial negative charge.

• Water is polar (ends have opposite partial charges or unequal distribution of charges).

• Polar substances like polar. Non-polars (neutral charge) like non-polars. They are hydrophilic (charged/polar substances that interact with/attract water). Non-polars do not attract polar substances. They are hydrophobic (nonpolar substances that repel water) Ex: Water and oil do not get along because oil is nonpolar and water is polar.

• Covalent bonds - Mutual sharing of one or more pairs of electrons between two atoms. It forms when the difference between the electronegativities of two atoms is too small for an electron transfer to occur to form ions. In nonpolar covalent bonds, the electrons are shared equally. In polar covalent bonds, the electrons are not shared equally because one atom is bonded to a more electronegative atom. Water is held together by covalent bonds. 

• Ionic bonds - Results in ions. They occur when there is a large electronegativity difference between two atoms, such as sodium and chlorine. The transfer of one electron will fill the valence electron shell of both atoms.

• Hydrogen bonds - A chemical intermolecular bond that occurs when a hydrogen atom bonds to a highly electronegative (like to keep the electrons around themselves instead of partners) atom (oxygen, nitrogen, fluorine). This creates a dipole in the molecule. These bonds are weaker than covalent, but they’re relatively strong. Each water molecule can form hydrogen bonds with 4 other water molecules.

• Hydrogen bonds between water molecules give water the properties of adhesion, cohesion, surface tension, specific heat, and evaporative cooling.

• Cohesion - the attraction of water molecules. Present because of hydrogen bonds. Ex: Droplets of water.

• Adhesion - When one substance is attracted to another. Ex: Water on a window. Meniscus.

• Capillary action - The movement of a liquid through or along another material against an opposing force, such as gravity (upwards action). This is due to cohesion and adhesion. Ex: Cohesion due to hydrogen bonding contributes to the transport of water and nutrients against gravity in plants and adhesion allows the water molecules to stick to the xylem tissues of a plant. Transpiration is the loss of water from a plant in the form of vapour.

• Surface tension - Difficulty to break the surface of water because of cohesive forces. The tendency of a liquid’s surface to resist rupture when placed under tension or stress. Water molecules at the surface (at the water-air interface) will form hydrogen bonds with their neighbours, just like water molecules deeper within the liquid. However, because they are exposed to air on one side, they will have fewer neighbouring water molecules to bond with and will form stronger bonds with the neighbours they do have.  Ex: Water strider insects rely on surface tension to be able to walk on the surfaces of bodies of water. It also causes spherical objects.

• Specific heat - The amount of heat energy it takes to raise or lower the temperature of one gram of a substance by one degree celsius. Water has a high specific heat, so it can absorb or release a large amount of heat with only a slight change in its own temperature so large bodies of water take a while to evaporate. In liquid water, hydrogen bonds are constantly being formed and broken as the water molecules slide past each other. The breaking of these bonds is caused by the energy of motion (kinetic energy) of the water molecules due to the heat contained in the system. When the heat is raised (for instance, as water is boiled), the higher kinetic energy of the water molecules causes the hydrogen bonds to break completely and allows water molecules to escape into the air as gas. We observe this gas as water vapour or steam. On the other hand, when the temperature drops and water freezes, water molecules form a crystal structure maintained by hydrogen bonding (as there is too little heat energy left to break the hydrogen bonds). This structure makes ice less dense than liquid water.

• Evaporative cooling - Water has a high heat of vaporisation, so water can absorb a lot of heat and leave the surface cooler. Ex: Sweat turning to vapour cools down the body. 

• High solvency - Water is a good solvent for many molecules because of its polarity. When an ionic or polar compound enters water, it is surrounded by water molecules. The relatively small size of water molecules typically allows many water molecules to surround one molecule of solute. The partially negative dipoles of the water are attracted to positively charged components of the solute, and vice versa for the positive dipoles. Ex: Water dissolves salt (NaCl).

• Acids and bases - Reactions are also influenced by whether the solution in which they occur is acidic, basic, or neutral. A solution is acidic if it contains a lot of hydrogen ions (H+). If you dissolve an acid in water, it will release a lot of hydrogen ions. Bases do not release hydrogen ions when added to water. They release a lot of hydroxide ions (OH–). The acidity or alkalinity of a solution can be measured using a pH scale. The pH scale is numbered from 1 to 14. The midpoint, 7, is considered neutral pH. pH > 7 is basic and pH < 7 is acidic.

Unit 1.2: Elements of Life

• Matter - Anything that occupies space and mass. Everything is made up of matter.

• Atoms - Smallest unit of an element that retains the properties of the element. Smallest unit of mass.

• Protons - Positively charged elementary particle that is a fundamental constituent of all atomic nuclei.

• Atomic # - The number of protons in the nucleus of an atom of an element. Ex: Carbon’s atomic # is 6. 

• Atomic mass # - Sum of the protons and neutrons in the nucleus of an atom of an element.

• Neutrons - Elementary particles having no charge.

• Nucleus - The centre of the atom containing protons and neutrons. 

• Electrons - Negatively charged particles that are a fundamental constituent of matter. Cloud of electrons orbit around the nucleus. 

• Dalton/Atomic Mass Unit (amu) - Measure of molecular weight/mass. A single neutron or proton has a weight close to 1 amu. Electrons are much smaller in mass and do not contribute much to an element’s overall atomic mass. 

• Elements - A substance that cannot be broken down to another substance by a chemical reaction. 118 known elements with 25 of them being essential to life. Ones you have to remember for AP Bio; Oxygen (O), Carbon ( C), Hydrogen (H), Nitrogen (N), Calcium (Ca), Phosphorus (P), Potassium (K), Sulphur (S), Sodium (Na), Chlorine (Cl), and Magnesium (Mg). 

• Compounds - Substances that can be broken down further by chemical reactions because they are made of two or more elements that are in a fixed ratio to each other. 

• Isotope - A form of an element in which the atom has the same number of protons, but a different number of neutrons. Stable isotopes do not have a tendency to lose particles. In radioactive isotopes, the nucleus decays spontaneously giving off particles and energy. When the decay leads to a change in the number of protons, the atom transforms to another element.

• Energy - The capacity for work. The ability to change. 

• Potential Energy - Energy that matter possesses because of its location or structure. Matter has a natural tendency to move to the lowest state of potential energy. The most distant electrons are from the nucleus, the greater their potential energy. An electron’s potential energy is called an electron shell. When they absorb energy, they move up an energy level away from the nucleus. When they release energy, they move closer to the nucleus.

• Valence electron - Electrons in the outermost shell. The chemical behaviour of an atom depends mostly on the number of valence electrons. Atoms with the same number of valence electrons exhibit similar behaviour. 

• Chemical bonds - An attractive force that holds together the atoms, ions, or groups of atoms in a molecule or compound. Covalent bonds, ionic bonds, hydrogen bonds, and Van der Waals are all chemical bonds.

• Molecule - 2 or more atoms held together by covalent bonds.

• Structural Formula - Notation that shows the arrangement of atoms in a molecule. Ex:  H-N-H is the structural formula for ammonia.

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                           H

• Molecular formula - Expression that defines the number of atoms for each element in one molecule. Ex: NH3 is the molecular formula for ammonia.

• Ions - An atom that does not contain equal numbers of protons and electrons. Cations are positively charged. Anions are negatively charged. 

• Van der Waals interactions - A weak force of attraction between electrically neutral molecules that collide with or pass very close to each other. 

• Organic molecule - Complex molecule that is primarily made of carbon atoms bonded with other elements and/or carbon atoms.

• Carbon has the ability to form covalent bonds to as many as 4 other atoms due to its # and configuration of electrons. Carbon has 6 electrons, 2 of them fill the inner shell and 4 of them are left in the valence shell. To achieve stability, carbon must find four more electrons to fill its outer shell, giving a total of eight and satisfying the octet rule. It is the building block of every major macromolecule (lipids, proteins, nucleic acids, and carbohydrates). 

• Octet rule - Atoms will lose, gain or share electrons to achieve an electron configuration of eight valence electrons.

• Hydrocarbons - Organic molecules consisting entirely of carbon and hydrogen. They are good fuels because their covalent bonds store a large amount of energy which is released when the molecules are burned. Ex: Propane, butane, and methane.

• Large biological molecules are generally composed of a carbon skeleton (made up of carbon and hydrogen atoms) and some other atoms, including oxygen, nitrogen, or sulphur.

• Functional groups - Groups of atoms that occur within molecules and confer specific chemical properties to those molecules.

• Important functional groups (all are hydrophilic minus methyl which is nonpolar and hydrophobic) - Sulfhydryl, phosphate groups, amino groups, carboxyl groups, carbonyl groups, methyl, and hydroxyl groups. 

• Nitrogen is a building block in proteins, enzymes, amino acids, and nucleic acids. Nitrogen is a key element in the nitrogen cycle, which plays a crucial role in the balance of nutrients in ecosystems. While nitrogen is primarily in the atmosphere as a gas, plants and some microorganisms can convert atmospheric nitrogen into a usable form for other organisms through nitrogen fixation, which is essential for the overall functioning of ecosystems.

• Phosphorus is a key component of nucleic acids, certain proteins, and lipids. Beyond its role in DNA and RNA, which are essential components of the genetic material in all living organisms, phosphorus is also involved in biological processes like energy production. It also plays a crucial role in the balance of nutrients in ecosystems.

Unit 1.3: Introduction to Biological Molecules

• Monomer - Building blocks of macromolecules. When many monomers are bonded to each other, they’re called polymers.

• Dehydration synthesis - Large biological molecules often assemble via dehydration synthesis reactions, in which one monomer forms a covalent bond to another monomer (or growing chain of monomers), releasing a water molecule in the process. You can remember what happens by the name of the reaction: dehydration, for the loss of the water molecule, and synthesis, for the formation of a new bond.

• In the dehydration synthesis reaction above, two molecules of the sugar glucose (monomers) combine to form a single molecule of the sugar maltose. One of the glucose molecules loses an H, the other loses an OH group, and a water molecule is released as a new covalent bond forms between the two glucose molecules.

• Carbohydrates, nucleic acids, and proteins can all contain multiple different types of monomers, and their composition and sequence is important to their function. For instance, there are four types of nucleotide monomers in your DNA, as well as twenty types of amino acid monomers commonly found in the proteins of your body. Even a single type of monomer may form different polymers with different properties. For example, starch, glycogen, and cellulose are all carbohydrates made up of glucose monomers, but they have different bonding and branching patterns.

• Hydrolysis - Polymers are broken down into monomers by hydrolysis reactions. In a hydrolysis reaction, a bond is broken by the addition of a water molecule. During a hydrolysis reaction, a molecule composed of multiple subunits is split in two: one of the new molecules gains a hydrogen atom, while the other gains a hydroxyl (-OH) group, both of which are donated by water. Imagine the diagram above happening in reverse order. 

• Dehydration synthesis reactions build molecules up and generally require energy, while hydrolysis reactions break molecules down and generally release energy. 

• In the body, enzymes catalyse, or speed up, both the dehydration synthesis and hydrolysis reactions. Enzymes involved in breaking bonds are often given names that end with -ase. For example: Lactase breaks up lactose. 

Unit 1.4 + 1.5 + 1.6: Properties of Biological Molecules/Structure and Function of Biological Molecules/Nucleic Acids

Carbohydrates - Ratio of roughly one carbon atom to one water molecule. Formula is: Cx(H2O)y Carbohydrate chains come in different lengths and biologically important carbohydrates belong to 3 categories; monosaccharides, disaccharides, and polysaccharides. Bonds between carbohydrates are called glycosidic bonds (link between a carbon atom and an oxygen atom). 

Monosaccharides - Simple sugars such as glucose and fructose. Monosaccharides have a formula of (CH2O)n and they typically contain 3-7 carbon atoms. Glucose, galactose, and fructose have a formula of C6H12O6, but they are isomers (molecules with the same molecular formula, but differing in molecular structures which results in different properties and functions) of each other. Many 5-6 carbon atoms can exist as a linear chain or in a ring-shape form. Energy source for cells. End in ose. 

Disaccharides - Form when two monosaccharides join together via a dehydration reaction, also known as a condensation reaction or dehydration synthesis. Common disaccharides include lactose, maltose, and sucrose. 

Polysaccharides - Made up of many repeated units of monosaccharides. They can consist of branched or unbranched chains of monosaccharides. Examples include starch, cellulose, and glycogen. Glycogen and starch are sugar storage molecules. Glycogen stores sugar in animals and starch stores sugar in plants. Cellulose, on the other hand, is made up of β-glucose and is a major part of the cell walls in plants. Its function is to lend structural support. Chitin, a polymer of β-glucose molecules, serves as a structural molecule in the walls of fungus and in the exoskeletons of arthropods.

Proteins - Proteins are made of 20 different monomer amino acids joined by peptide bonds which are covalent bonds. The structure of the amino acids have specified chemical and physical properties that determine their function so a slight change in structure at the primary stage can lead to the change in both a protein's structure and function. When two amino acids are joined together by dehydration synthesis, it is called a dipeptide. Polymers of amino acids are polypeptides and are formed when many amino acids join through dehydration synthesis. The folding of one or more polypeptides forms a protein. Some amino acids are polar and others are nonpolar; in addition, some are acidic and others basic. This directly impacts the protein in many ways because it affects the protein's shape and therefore its function. Each amino acid consists of an amino group, carboxyl group and R group (with chemical properties of hydrophobic, hydrophilic, and ionic).

Proteins have four important parts around a central carbon: An amino group (–NH2), a carboxyl group (–COOH), a hydrogen, and an R-group.

Amino acids differ only in the R-group, which is also called the side chain.

There are 4 types of structures for proteins. 

Primary structure of proteins is a linear sequence of amino acids. N-terminal to C-terminal. 

In the secondary structure of protein, the polypeptide begins to twist. It has a-Helix coil structures and zigzag B-sheets. 

When the secondary structure reshapes the polypeptide, amino acids that were far away in the primary structure arrangement can now also interact with each other. This is called the tertiary structure.

When different polypeptide chains sometimes interact with each other, they form a quaternary structure. Haemoglobin is a molecule in the blood that helps distribute oxygen to the tissues in the body. It is formed when four separate polypeptide chains interact with each other.

2^o, 3^o, 4^o structure can be denatured (broken down) by changes in temperature and pH because of the weaker nature of the non-covalent interactions they are built upon. When a protein gets denatured, its structure changes, which leads to a functional change. 

Lipids - Do not form polymers. They are nonpolar and hydrophobic. Important for storage and great for insulation in animals. They are also used for structure and signalling molecules. There are 3 main types of lipids: Triglycerides, phospholipids, and steroids.

Saturated and Unsaturated Fatty Acids - Fatty Acids are long chains of carbon attached to a carboxyl group and can be saturated or unsaturated. There are no double bonds between carbon atoms in saturated fatty acids. They contain a maximum number of hydrogen atoms. They are solid at room temperature. Ex: Butter. Unsaturated Fatty Acids have one or more double and/or triple bonds between carbon atoms and are liquids at room temperature. Ex: Vegetable oils. When 3 fatty acids are joined together and attached to a glycerol molecule, they’re called triglycerides. A fatty acid chain is covered in hydrogen. One end of the chain has a carboxyl group.

Phospholipids - 1 glycerol, 2 fatty acids, and 1 phosphate group. A major component of the cell membrane, called the phospholipid bilayer. The head is hydrophilic (attracts water) and contains the glycerol and phosphate group. The tail is hydrophobic (avoids water) and contains two fatty acids, one is unsaturated and the other is saturated). Phospholipids are amphipathic (both hydrophobic and hydrophilic). 

Steroids - Every steroid has 4 linked carbon rings and many have short tails. Cholesterol is a type of steroid with a short tail, as well as a hydroxyl functional group attached to it. This steroid is an important component of animal cell membranes. Any steroid with a hydroxyl functional group is also classified as an alcohol, thus why they are called sterols.

Nucleic Acids - Made up of nucleotides, they make up our DNA and RNA. Nucleotides consist of a five-carbon sugar, a phosphate, and a nitrogen base (adenine, thymine, guanine, cytosine, uracil). Linear sequences of nucleotides. Ends are defined by the 3’ hydroxyl end and 5’ phosphates end of the sugar in the nucleotide. During DNA and RNA synthesis, nucleotides are added to the 3’ end of the growing strand, forming covalent bonds between nucleotides. DNA is structured as an antiparallel double helix. Each strand runs in opposite 5’ to 3’ orientations. Adenine nucleotides pair with thymine nucleotides via two hydrogen bonds. Cytosine nucleotides pair with guanine nucleotides by three hydrogen bonds. DNA contains deoxyribose and RNA contains ribose. Uracil replaces thymine in RNA. DNA is usually double stranded; RNA is usually single stranded.

Unit 2: Cell Structure and Function

• This is a diagram of a plant cell.

• This is a diagram of an animal cell.

• A cell is life’s basic unit of structure and function.

• As cells increase in volume, the surface area-to-volume ratio decreases, and the exchange of materials becomes less efficient. The surface area-to-volume ratio concept can also be applied to organisms.

• Eukaryotic cells have a multitude of organelles. Fungi, protists, plants, and animals are examples of eukaryotes. 

• Prokaryotes are a lot smaller than a eukaryotic cell and simpler. Bacteria and archaea are examples of prokaryotes. The genetic material in a prokaryote is one continuous, circular DNA molecule that is found free in the cell in the nucleoid.

• Most prokaryotes have a cell wall composed of peptidoglycans that surrounds a lipid layer called the plasma membrane. Prokaryotes also have small ribosomes. Some bacteria may also have one or more flagella. They have a plasma membrane. 

• Plasma Membrane/Cell Membrane - The outer envelope of the cell. It is semipermeable and regulates the movement of substances into and out of the cell. It is made up mostly of proteins and phospholipids. Made up of a phospholipid bilayer. It has two lipid layers. The heads are hydrophobic and the tails are hydrophilic. It is selectively permeable (some substances are allowed in while others aren’t). 

• It is also known as the fluid-mosaic model. 

• Peripheral Proteins - Hang out on the outside of the membrane. Are loosely attached to other proteins or the membrane through hydrogen bonds. They serve multiple roles including transportation, communication, support, and as enzymes.

• The peripheral membrane proteins allow for reactions and movements to happen in the space of the surface of the cell. An example is the ETC where peripheral proteins move electrons around the surface of the level, generating energy for the cell. There are also instances when molecules will attach themselves to the peripheral membrane proteins so that they can be transferred across the cell membrane (typically hydrophobic molecules).

• The extracellular matrix sends messages out. The peripheral membrane proteins receive those messages and then communicate them to the integral proteins of the cell. The integral proteins receive the message and then send them to another peripheral protein, which goes inside the cell, causing a reaction.

• The peripheral membrane proteins function to conduct and help maintain the cytoskeleton of the cell, as well as containing the extracellular matrix of the tissue. Some tubules and filaments make up the cytoskeleton and extracellular matrix. They ought to have a point of attachment to the cell membrane. The peripheral membrane proteins serve as that point of attachment. Peripheral membrane proteins also help with the final step of releasing proteins, which are produced by the cell to the outside of itself. They anchor the cell membrane to the cytoskeleton.

• The most common way for peripheral membrane proteins to act as enzymes is to act on a substance that is on or near the surface of the cell. They may function by breaking down the substance or combining it with other substances to create a new one that the cell, specifically the cell membrane, needs. 

• Integral Protein/Integrins - Integrated completely into the membrane structure, and their hydrophobic membrane-spanning regions interact with the hydrophobic region of the phospholipid bilayer. They have a range of important functions. Such functions include channelling or transporting molecules across the membrane. Other integral proteins act as cell receptors. Transmembrane proteins span the entire plasma membrane. 

• Channel proteins form channels that selectively allow the passage of certain ions or molecules. 

• Nucleus - Usually the largest organelle in the cell. The nucleus not only directs what goes on in the cell, but is also responsible for the cell’s ability to reproduce. It’s the home of the hereditary information—DNA—which is organised into large structures called chromosomes. The most visible structure within the nucleus is the nucleolus, which is where rRNA is made and ribosomes are assembled.The nucleus as a whole is enclosed in a nuclear envelope, which is a double membrane that holds the content of the nucleus in place.

• Endoplasmic Reticulum - The endoplasmic reticulum is tasked with transporting materials within the cell. There is the smooth ER and the rough ER. The smooth ER is tasked with removing toxins and carrying out metabolic processes such as making lipids, phospholipids, and steroids. The rough ER is covered in ribosomes.  It manufactures proteins and membrane parts. The ribosomes attached to the rough ER surface are vital to its protein synthesis function. The rough ER also modifies proteins after translation and prepares them for their respective functions. These modifications include processing and sorting secreted proteins. The ER in plant cells has additional functions that you do not find in animal cells. It plays a central role in cell-to-cell communication in specialised cells. 

• Golgi Apparatus - After the ribosomes on the rough ER have completed synthesising proteins, the Golgi complex modify, process, and sort the products. The organelle has two distinct sides to it, one which receives materials, and the other which ships products out. There are 2 sides on the Golgi apparatus, cis and trans face. Vesicles enter the Golgi apparatus via the cis face and depart via the trans face.

• Mitochondria - Responsible for converting energy from organic molecules into useful energy for the cell. The most common energy molecule in the cell is adenosine triphosphate (ATP). It consists of an inner portion and an outer portion. The inner mitochondrial membrane forms folds known as cristae and separates the innermost area (the matrix) from the inter-membrane space. The outer membrane separates the inner-membrane space from the cytoplasm.The mitochondrion is encapsulated in two of its membranes, has ribosomes and DNA to synthesise proteins. The outer mitochondrial membrane is smooth and permeable to small solutes, but can easily block macromolecules. The inner membrane contains enzymes essential for cellular respiration.

• Lysosome - They have sacs that carry digestive enzymes, which they use to break down old, worn-out organelles, debris, or large ingested particles. Lysosomes are made when vesicles containing specific enzymes from the trans Golgi fuse with vesicles made during endocytosis. Lysosomes are also essential during programmed cell death called apoptosis. The recycling activities of the lysosome are referred to as autophagy, which means eating oneself. They’re rarely found in plant cells because the central vacuole already performs the functions of the lysosome. 

• Vacuoles - They’re fluid-filled sacs that store water, food, wastes, salts, or pigments. Vacuoles serve multiple functions in plant cells. There are several types of vacuoles, mostly responsible for storage. Food vacuoles are created through phagocytosis and carry out intracellular digestion. Contractile vacuoles are found in freshwater protozoans; their main function is to remove excess water from the cell by taking up water from the cell and contracting to pump the water out. There are other types of vacuoles tasked with storage of waste and toxins. In most plant cells, you will encounter a central vacuole. The central vacuole forms as a result of smaller vacuoles from the Golgi and ER accumulating in the cell and joining to form the larger central vacuole. The functions of the central vacuole include storage of organic compounds or inorganic ions and sequestration of harmful cell by-products. The CV is found only in plant cells/

• Chloroplasts - Chloroplasts are only found in plant cells and photosynthesizing bacteria such as cyanobacteria. They also have outer and inner membranes. The chloroplast consists of two main regions, the stroma and the thylakoid space (the space between the thylakoid membranes). The stroma is the fluid-filled space between the outer and inner membranes. In the thylakoid space, there is a stack of inner membranes called the thylakoid membranes where photosynthetic pigments such as chlorophyll are found. Centre of photosynthesis.

• Ribosomes - They are sites of protein synthesis. Their job is to manufacture all the proteins required by the cell or secreted by the cell. Ribosomes are round structures composed of two subunits, the large subunit and the small subunit. The structure is composed of ribosomal RNA (rRNA) and proteins. Ribosomes can be either free floating in the cell or attached to another structure called the endoplasmic reticulum (ER). 

• Cytoplasm - Everything contained within the cell, except the nucleus. The cytosol is the fluid part of the cytoplasm that contains water, salts, and other chemicals, and is jelly-like in its consistency. The organelles are suspended in the cytosol. 

• Cytoskeleton - The cytoskeleton is a network of fibres that stretch throughout the cytoplasm and provides an intricate framework for support and movement. The cytoskeleton also associates with specialised proteins involved in movement such as muscle contractions. Microtubules are made up of the protein tubulin, participate in cellular division and movement. Microfilaments are important for movement. These thin, rodlike structures are composed of the protein actin. Actin monomers are joined together and broken apart as needed to allow microfilaments to grow and shrink.

• Cell Wall - Made of cellulose. Their main function is to maintain the shape of the cell and protect against mechanical stress. Moreover, the cell wall prevents excess water uptake that might result in the death of the cell. 

• Endosymbiotic theory - Presumption that the mitochondria and chloroplasts were once prokaryotic cells and that the mitochondria today evolved from aerobic bacteria, while the chloroplasts arose from cyanobacteria. 

• Endocytosis - When the particles that want to enter a cell are just too large, the cell uses a portion of the cell membrane to engulf the substance. The cell membrane forms a pocket, pinches in, and eventually forms either a vacuole or a vesicle. There are three types of endocytosis. 

• Pinocytosis - The cell ingests liquids. 

• Phagocytosis - The cell takes in solids. 

• Receptor-mediated endocytosis - Involves cell surface receptors that work in tandem with endocytic pits that are lined with a protein called clathrin. When a particle, or ligand, binds to one of these receptors, the ligand is brought into the cell by the invagination, or “folding in '' of the cell membrane. A vesicle then forms around the incoming ligand and carries it into the cell’s interior.

• Exocytosis - A cell ejects waste products or specific secretion products, such as hormones, by the fusion of a vesicle with the plasma membrane, which then expels the contents into the extracellular space.

• Membrane Permeability - Small, nonpolar molecules (O2, CO2, N2) pass directly between the lipids. Large, nonpolar molecules pass slowly through the lipids. H2O passes through aquaporins (channel proteins specific to water). Large, polar molecules/ions (sodium, glucose)  pass through channel proteins. 

• Passive Transport - Does not require ATP. Moving from high to low (concentration gradient). May utilise membrane proteins to move things in and out of the cell. 

• Diffusion - If there is a high concentration of something in one area, it will move to spread out and diffuse into an area with a lower concentration. The substance moves down a concentration gradient. There are 3 types of diffusion.

• Simple Diffusion - A process in which the substance moves through a semipermeable membrane or in a solution without any help from transport proteins.

• Facilitated Diffusion - Movement of hydrophilic molecules/ions through a semipermeable membrane. Facilitated by transport proteins.

• Osmosis - Diffusion specifically for water molecules through a semipermeable membrane.

• Water Potential - Ψ = Ψs + Ψp, sum of solute potential and pressure potential

• Solute Potential - Ψs = −iCRT where: i = ionisation constant C = molar concentration R = pressure constant T = temperature in Kelvin (°C + 273) The ionisation constant refers to the number of ions when the solute dissolves in water. For example, NaCl splits up into Na+ and Cl- when it dissolves in water, making the ionisation constant 2. On the contrary, sugar, C6H12O6, doesn't split up into any ions when it dissolves in water, so its ionisation constant is 1.

• Active Transport - Movement against natural flow. Low to high. Some proteins in the plasma membrane are powered by ATP. An example of active transport is a special protein called the sodium-potassium pump. It ushers out three sodium ions (Na+) and brings in two potassium ions (K+) across the cell membrane. This pump depends on ATP to get ions across that would otherwise remain in regions of higher concentration. Primary active transport occurs when ATP is directly utilised to transport something. Secondary active transport occurs when something is actively transported using the energy captured from the movement of another substance flowing down its concentration gradient.

• Tonicity - The ability of a solution which surrounds the cell to cause the cell to lose or gain water.

• Osmoregulation - The process of maintaining a salt and water balance across membranes within the body’s fluids.

• Osmolarity - The total concentration of solutes in a solution.

• Hypertonic -  When a solution has a higher solute concentration than that inside the cell, and the solutes cannot cross the membrane. If a cell is placed in a hypotonic solution, the cell will lose water and volume.

• Hypotonic - When a solution has a lower solute concentration than that inside the cell. Water will move to where there is more solute so the cell will receive 

• water and expand.

• Isotonic - Equal solute concentration. No net movement.

• Bulk Flow - One-way movement of fluids brought about by pressure.

• Dialysis - The movement of a solute through a selectively permeable membrane.

Unit 3: Cellular Energetics

• 1st Law of Thermodynamics - Energy can be transferred and/or transformed, but it cannot be created or destroyed.

• 2nd Law of Thermodynamics - In every energy transfer , the potential energy of the final state is less than the potential energy of the initial state.

• Entropy - The measure of randomness/

• Metabolic Pathways - A series of interconnected biochemical reactions that convert a substrate molecule or molecules, step-by-step, through a series of metabolic intermediates, eventually yielding a final product or products.

• Anabolic Pathways - Energy is required. Small molecules are assembled into bigger ones. 

• Catabolic Pathways - Large molecules are broken down into smaller ones. Energy is released. 

• Energy - The capacity to cause change. 

• Free Energy - The energy available in a system to do work. 

• Entropy -  

• Exergonic Reaction - Breaking down into simpler molecules. Fewer bonds and less energy required. Free energy left over to do work.

• Endergonic Reaction - Synthesis of more complex molecules. Level of organisation increases. More bonds are formed. A net input of free energy is required. 

• Energy Coupling - The use of an exergonic reaction to drive an endergonic reaction. 

• Role of ATP - Unstable, short-lived. Only used in the cell that produces it. Stores a safe, usable amount of energy.

• Enzymes - Biological catalysts that speed up reactions which is by lowering the activation energy and helping the transition state to form. They lower the activation energy. They have an activation site and a substrate (molecule that the enzyme synthesises). 

• Enzyme specificity - Each enzyme only catalyse one reaction. The active sites of enzymes can only fit one type of molecule.

• Induced Fit - Enzymes have to change its shape slightly to accommodate the shape of the substrates.

• Denaturation - 

• Factors that can denature enzymes; 

• Competitive Inhibitor - 

• Non-competitive inhibitor - 

• Feedback Inhibition - 

• Photosynthesis Equation -

• Oxidation/Reduction - 

• Photosynthesis - 

• Light Reactions - 

• ETC - 

• Calvin Cycle - 

• Cellular Respiration Equation - 

• Glycolysis - 

• Pyruvate Oxidation - 

• The CItric Acid Cycle - 

• Oxidative Phosphorylation - 

• ETC - 

• Chemiosmosis - 

• Anaerobic Respiration -

• Fermentation - 

• Plant Pigments - 

Unit 8: Ecology

• Ecosystem -  A dynamic interaction between living elements such as plants, animals, and microorganisms and nonliving elements such as air, soil, water, and sunlight. Ecosystems vary in size from small bogs to entire deserts and rainforests.

• Biosphere - The entire part of the Earth where living things exist.

• Community - A group of populations interacting in the same area.

• Population - A group of individuals that belong to the same species and that are interbreeding.

• Trophic Level - Steps in a food chain of an ecosystem.

• Energy enters an ecosystem in the form of sunlight. This energy is used up and lost as heat as it moves through the ecosystem.

• Producers - Autotrophic. Plants + Algae. Convert thermal energy from the sun into chemical energy through photosynthesis. Bottom trophic level. 

• 2nd trophic level - Primary Consumers. Herbivores/omnivores.

• 3rd trophic level - Secondary consumers. Carnivores/omnivores who eat primary consumers.

• 4th trophic level - Tertiary/Quaternary consumers. Carnivore/omnivores that are apex predators. Top of the food chain. Have no predators.

• Decomposer - Bacteria and fungi that break down dead plant and animal matter. They secrete enzymes on the surface of the dead organisms to break the organism down and then absorb the digested, smaller food molecules.

• Scavengers - Feed on dead animals. For example, crows, vultures and hyenas are scavengers.

• Ex. of a food chain: Grass > Grasshopper > Snake > Hawk > Fungi

• As energy passes from trophic level to trophic level, only a fraction of the energy available at one trophic level is transferred to the next trophic level. The amount of energy available to a trophic level depends on the amount of energy stored by the level just below it. Total energy decreases as you move up the trophic levels. 

• The energy in an ecosystem can be measured and recorded in the form of biomass. The term biomass refers to the total mass of all organisms, plants, and animals in an ecosystem. Biomass production is the amount of biomass produced for a given amount of solar energy. The amount of biomass decreases as you move up the pyramid. Biomass of the producers is always greater than that of the consumers. That is because energy lost to heat in respiration is truly lost to the ecosystem and not all biomass consumed can be used by the consumer; some of it is indigestible and passes out as waste. Some of the energy contained in the waste is consumed by decomposers and returns to the ecosystem, but some is lost. In general, only 10 percent of the energy consumed at a particular trophic level is available to the next trophic level; the rest is lost through the processes described above. The mass of organisms at each level is called the "standing crop." A biomass pyramid is a way to graphically represent the living matter present per area unit of different levels.

• Chemosynthesis - The process by which certain microbes create energy by mediating chemical reactions. So the animals that live around hydrothermal vents make their living from the chemicals coming out of the seafloor in the vent fluids! Because they are a local food source, hydrothermal vents typically have high biomass, in stark contrast to the very sparse distribution of animals outside of vent areas where animals are dependent on food dropping down from above.

• Carbon Cycle - The cycle by which carbon moves through Earth’s various systems.

• Nitrogen Cycle - A repeating cycle of processes during which nitrogen moves through both living and nonliving things: the atmosphere, soil, water, plants, animals and bacteria. In order to move through the different parts of the cycle, nitrogen must change forms.

• Primary Production - The amount of light energy converted to chemical energy or food by producers during a given time period. This food is then successively transferred through an ecosystem. Primary production also depends on the angle of the sun (recall that the angle of the sun determines the length of the day). In summer, primary production takes place at a higher rate and in greater abundance. Only a small fraction of the sun's radiation is used for photosynthesis, while most of it is reflected back. Additionally, plants use some of the energy they receive for respiration rather than energy production. 

• Gross Primary Production - The total amount of energy produced, including energy used by plants for respiration. In other words, it is the amount of light energy converted to chemical energy by photosynthesis per unit of time.

• Net Primary Production - The difference between GPP and the energy used by the primary producers for respiration (R). NPP = GPP - R.

• Respiration - The amount of CO2 that an organism loses due to metabolic activities.

• PP is measured in calories per square metre per year.  

• Factors affecting productivity; temperature, rainfall, and light. 

• Biogeochemical cycles: water, carbon, nitrogen, and phosphorus.

• Water Cycle - The water cycle revolves around the hydrosphere, atmosphere, and land. The heat produced on Earth's surface by the sun causes water molecules to evaporate and rise into the atmosphere in the form of water vapour. This heat also causes transpiration, the process in which water lost from plants enters the atmosphere. As water vapour rises up into the atmosphere, it cools down through condensation to form tiny droplets that eventually become clouds. When the droplets become large enough, the water falls to Earth's surface as precipitation in the form of rain, snow, sleet, or hail. Once water returns to Earth's surface, it either flows along the ground into rivers, lakes, and oceans or seeps into the soil to become groundwater. Once again, the water cycle begins.

• Nitrogen Cycle - Nitrogen accounts for 79% of the air we breathe. All living organisms require nitrogen to make amino acids, which in turn are needed to build proteins.Although there is a lot of nitrogen in the atmosphere, most organisms cannot use it directly, so it must first be converted (fixed) into a form that can be used. This conversion is done only by certain bacteria, which are known as nitrifying bacteria. These bacteria help circulate nitrogen in the biosphere through nitrogen fixation and denitrification. The nitrifying bacteria in the roots of legumes and in the soil convert nitrogen into ammonia through nitrogen fixation. Next, other bacteria in the soil convert the ammonia into nitrates and nitrites. Then, plants use the nitrates and nitrites to produce plant proteins and nucleic acids. Finally, animals consume the plants and then use the plant proteins and nucleic acids to make their own proteins and nucleic acids. So nitrogen from the atmosphere transfers to plants and then to animals. Nitrogen is returned to the soil through denitrification. First, decomposers break down plant and animal matter, including proteins and nucleic acids, to nitrates. Then, denitrifying bacteria in the soil convert the nitrates into nitrogen gas. So denitrification releases nitrogen back into the atmosphere, where the nitrogen cycle starts all over again.

• Phosphorus Cycle - Phosphorus compounds don't have a gaseous state and are only found in soil and rock sediment. Over time, rocks weather to release phosphorus into the soil. The phosphorus accumulated in the soil eventually washes away into rivers, streams, and oceans. Marine organisms use this phosphorus, and so it accumulates in their shells and bones. Phosphorus that remains on land cycles between land organisms and the soil. Plants absorb phosphates from the soil or from water and build organic compounds. Insoluble phosphorus compounds, which cannot be taken in by plants, are made soluble by certain microorganisms. Soil bacteria secrete different organic acids, like acetic acid and lactic acid, and convert soil phosphates into a soluble form of phosphorus for plants.  They also decompose phosphate–rich organic compounds into soluble inorganic phosphate through a mineralization process. Factors affecting phosphate–dissolution, or solubilization, are pH, moisture, and aeration. Some bacteria absorb phosphates for metabolism, so when they die, the phosphates are used by plants. When animals eat phosphorus–loaded plants, phosphorus continues through the food chain. Eventually, it returns to the soil through decomposition and excreta of consumers, and so the phosphorus cycle starts over. 

• Greenhouse gases - Carbon dioxide, methane, and other organic compounds are known greenhouse gases. These gases absorb light energy and trap it as heat. 

• Biotic Factors - The biological or living organisms within an ecosystem.

• Abiotic Factors - The physical or nonliving entities within an ecosystem.

• Niche - Its unique set of behaviours and interactions in the habitat. The role it plays. 

• Principle of exclusion - No two species can occupy the same niche in the same habitat at the same time. In an ecosystem, competition occurs when organisms of the same or different species share the same place at the same time and depend on the same resources. As a result, one of two things can happen: either one organism fails to survive or it moves somewhere with less competition and creates its own niche there.

• Density - The number of individuals of a given population within a set area.

• Two types of limiting factors: density-dependent and density-independent. 

• Density-dependent - Every ecosystem has a carrying capacity that is achieved when the population reaches the limit of available resources needed to support that population. In such a situation, the limiting factors include competition, predation, parasitism, and diseases. 

• Density-independent - Limiting factors that affect all populations, regardless of its size, are called density–independent factors. Populations often grow and shrink in response to these factors. Climatic conditions such as weather cycles or natural disasters. Human activities such as poaching animals or damming rivers. 

• Symbiotic relationships are when two or more organisms form close associations with each other.

• Mutualism - Ecological relationship where two or more organisms are mutually benefiting each other.

• Commensalism - It is a symbiotic association between two organisms in which one of them benefits from the other. The other neither benefits nor is harmed by this association.

• Parasitism - It is a symbiotic association in which one organism, called the parasite, benefits from the other, called the host. The parasite may live within or on the host, harming it, but does not benefit from killing it.

• Human Impact on the Environment; deforestations, pollution, industrialization, introducing diseases, greenhouse effect, ozone depletion, poaching, trophy hunting, 

• Ecological succession is the gradual change in a community in which the original community is replaced with a new one. This succession occurs in two ways, primary succession and secondary succession. Primary succession occurs on a surface that previously has not supported any habitat. The surface is not only devoid of vegetation and animals but also lacks soil. The first inhabitants of this surface are the pioneer species. Secondary succession is the series of changes in the community of a particular habitat that has previously been colonised. It helps restore habitats after events such as fire or flooding.

• Human activities have led to a decrease in biodiversity, introduced invasive species, and led some species nearly to extinction.

Unit 6: Gene Expression and Regulation 

DNA Structure & Function 

• DNA

  •  Double Helix Antiparallel Structure 

  • Phosphate and Deoxyribose Backbone 

  • Nitrogen Bases 

Purines - Adenine Guanine (two rings) 

Pyrimidines - Thymine Cytosine (one ring) 

• DNA Replication is Semi - Conservative 

• Steps of DNA Replication: 

  • Helicase untwist double helix 

  • Topoisomerase relieves the supercoiling ahead of helicase

  • Single -Strand binding Proteins (SSBPs) coats DNA strands, holding the two sides of DNA apart

  • RNA polymerase primate creates a 16 nucleotide primer (a temporary structure to keep in place

  • DNA polymerase catalyses the creation of new DNA strand in the 5’ to 3’ end by adding mice;peptides 

    • Leading strand is synthesised continuous

    • Lagging is discontinuous and makes DNA into okazaki fragments

  • RNA H (exonuclease) removes RNA primers (uracil) 

  • DNA polymerase 1 replaces the nucleotides lost by RNA primers 

  • RNA ligase seals and nicks between okazaki fragments 

  • SSBPs fall away and DNA recoils 

• DNA is wrapped around histones 

• Euchromatin - less compacted interphase chromatin accessible for transcription 

• Heretrohromatin - inaccessible for transcription 

• Genetic Engineering uses restriction enzymes to create recombinant DNA 

• A plasmid in bacteria is a small ring of extracellular DNA 

• Gel Electrophoresis - a method of separating DNA fragments 

• Replication fork - region where DNA strands are being unwind 

• SSBps - bind to separated pairs and prevent them from unpairing 

• Mismatched repair - enzymes remove and replace incorrectly paired nucleotides 

• Nucleotide excision repair - segment of DNA containing damaged is cut out by DNA cutting enzyme, nuclease and the resultant gap is filled with nucleotides 

• Telomeres - are nucleotide sequences with no genes but multiple repetitions of one short nucleotide sequence

  • Act as a buffer zone that protects organisms genes 

  • Enzyme telomerase catalyses the lengthening of telomeres in germ cells, restoring original length 

• Nucleoid - dense region of DNA not bounded by membrane 

• DNA is percicily combined with protein complex of DNA and protein called chromatin 

• 30 nm fibre → looped domains → metaphase chromosome 

Gene Expression 

• microRNAs (miRNAs) small, single stranded RNA molecules capable of binding to complementary sequences in mRNA molecules 

  • miRNA either degrades the target mRNA or simply blocks its translation 

• Small Interfering RNAs (siRNAs) - small noncoding RNAs similar in size and function to miRNAs

• RNA Interference (RNAi) - blocking of gene expression by siRNAs. Used to disable specific genes to investigate their function 

• Gene expression - process by which DNA directs the synthesis of proteins 

  • The expression of genes that code includes: transcription and translation 

• Eukaryotes have 3 types of RNA polymerase 

  • Type I and II make rRNA and tRNA 

  • Type II pre-mRNA synthesis 

• Three Steps of Transcription: 

1. Initiation: Transcription factors bind to DNA at enhancer/promoter region. Promoter is the TATA box (10 - 35 bp upstream). RNA pol II bind to TF. 

2. Elongation: RNA pol adds nucleotides to the 3’ end of growing pre mRNA 

3. Termination: Prokaryotes have terminator sequence, so RNA poly falls of DNA. Eukaryotes have a polyadenylation signal sequence of AAUAAA 10 - 35 bases downstream and a protein cuts of RNA transcript 

• Pre-mRNA has introns removed and exons spliced together by snRNPs: 

  • Introns - interfering sequences that don’t get translated to protein. Good for alternative gene splicing and crossing over. 

  • Exons - expressed sequences able to make a variety of proteins 

  • snRNPs - small nuclear ribonucleoproteins recognizes splice sites at the end of introns 

  • Spliceosomes - snRNPs and other proteins correctly arrange exons 

  • Ribozymes - RNA molecules that function as enzymes for splicing 

• tRNA - transfers amino acids to ribosomes by paring its anticodon to mRNAs codons 

• rRNA - ribosomal subunits made in the nucleus and has three sites for tRNA binding 

• Three Steps of Translation: 

1. Initiation - small ribosomal subunit (30s) binds with mRNA and methionine tRNA binds. Large 50s binds to complete ribosome and forms the Translation Initiation Complex 

2. Elongation - elongation factors (A to P to E) 

3. Termination- stop codon binds to releasing factor so hydrolysis of amino acid chain, ribosome dissociates 

• mRNA translation is not monogamous:

  • Polyribosomes - multiple ribosomes simultaneously translating a single mRNA  

• Chaperone Proteins - chemically modifies polypeptide by adding macromolecules and clipping off excess amino acids 

• Mutations: 

  • Point Mutation - one base pair substitution in the genetic material of the cell 

    • Based pair substitution - one base pair change in the DNA, leads to silent, missense (wrong amino acid) or nonsense mutations 

    • Frameshift mutation - insertion/deletion of base changes reading frame 

• Messenger RNA (mRNA) - carries genetic message from the DNA to the protein-synthesising machinery of the cell 

• Codon - triplets of nucleotides 

• Template strand - strand of DNA that gets transcribed 

• Reading frame - the ability to extract the intended message depends on the reading symbols in the correct groups 

• Molecular Components of Transcription: 

  • Promoter - DNA sequence where RNA pol binds and initiates transcription 

  • Terminator - (in bacteria) sequence that ends transcription 

• RNA Modification 

  • RNA processing - modifying pre-mRNA. Both ends of the primary transcript are altered and splicing occurs. 5’ end receives 5’ cap, a modified form of guanine. 3’ end receives poly - A tail, more adenine. 

Regulation of Gene Expression 

• Regulatory Sequences are stretches of DNA that can be used to promote or inhibit protein synthesis

• Regulatory protein are used to assist with the promotion or inhibition of protein synthesis 

• The interaction of regulatory sequences with regulatory proteins controls transcription  

• Transcription Factors are proteins that promote or inhibit transcription of a gene

• Operons are closely linked genes that produce a single mRNA molecule during transcription 

  • They are under control of the same regulatory sequence 

  • An operator is a sequence that either inhibits or promotes transcription by binding with regulatory proteins 

• The lac operon is an example of an inducible system because its usually turned off 

  • When the regulatory protein is bound to the obturator, RNA polymerase cannot bind to regulatory sequence 

• Inducers are molecules that can bind to the regulatory protein and cause it to change change shape

• When an inducer binds to the regulatory protein, the protein changes shape. This causes regulatory protein to release from the operator and frees up RNA polymerase to transcribe the operon’s genes.