Biology Notes

  • All cells maintain, increase, and decrease the concentration of substances by developing metabolic pathways. A metabolic pathway is an orderly sequence of reactions with specific enzymes that act at each step along the way.
  • Enzymes are catalytic molecules. That is, they speed up specific reactions without being used up in the reaction. Enzymes are proteins.
  • Enzymes have four special features in common:
1. They do not make processes happen that would not take place ontheir own. They just make the processes take place faster!2. Enzymes are not permanently altered or used up in reactions.3. The same enzyme works for the forward and reverse directions ofa reaction.4. Each enzyme is highly selective about its substrate.
  • Substrates are molecules which a specific enzyme can chemically recognize and to which it can bind. Substrates undergo chemical changes to form new substances called products. Each substrate fits into an area of the enzyme called the active site.
  • It is like a lock-and-key mechanism. Once the enzyme-substrate complex is together, the enzyme holds the substrate in a position where the reaction can occur. Once the reaction is complete, the enzyme unlocks the product and the enzyme is free to facilitate another reaction
  • It takes less energy to boost reactants to the transition state of a lower energy hill. The reaction will proceed more rapidly.
  • Enzymes are critical to life processes. Carbonic anhydrase is an enzyme that speeds up the process by which carbon dioxide leaves cells and enters the bloodstream so it can be removed from the body. The enzyme lipase is produced by the pancreas and functions in the digestion of lipids. RNA polymerase is an enzyme that facilitates the process of transcription. Some diseases, such as Tay-Sachs and phenylketonuria, occur when the body fails to make a critical enzyme.
  • Carbohydrates, lipids, proteins, and nucleic acids are the foundations for the structure and function of every living cell in every organism. They are the building materials of the body and the storehouse for energy for every activity.
  • Carbohydrates: A carbohydrate is a simple sugar or a molecule composed of two or more simple sugars. In general, the ratio of carbon, hydrogen, and oxygen atoms is 1:2:1 in a carbohydrate molecule. There are three classes of carbohydrates: monosaccharides, oligosaccharides, and polysaccharides. Glucose, sucrose, starch, and cellulose are examples of carbohydrates. “Saccharide” means sugar. “Mono” means one.
 Put the two together: one sugar unit. An oligosaccharide is a short chain of two or more covalently bonded sugar units.
  • “Poly” means many. A polysaccharide is a straight or branched chain of sugar units, where you may have hundreds or thousands of the same or different kinds of sugars bonded to one another.
  • Lipids: Lipids are organic compounds that have more carbon-hydrogen (C-H) bonds and fewer oxygen atoms than carbohydrates. They are extremely important for the proper functioning of organisms. Lipids are commonly called fats and oils. They are insoluble in water due to the nonpolarity of the molecules. Cells use lipids for long-term energy storage, insulation and protective coatings. Lipids are the major component of the  membranes surrounding all living organisms. Waxes are long-chain fatty acids attached to an alcohol. An example is cutin in plants. It helps the plants retain water.
  • Proteins: Proteins belong to the most diverse group. They are large, complex polymers essential to all life. They are composed of amino acids made of carbon, hydrogen, oxygen, nitrogen, and sometimes sulfur. Proteins are important in muscle contraction, transporting oxygen in the blood, and the immune system. Proteins, like lipids, are an important component of the membranes that surround cells. Collagen, enzymes, hemoglobin, insulin and antibodies are examples of proteins.
  • Nucleic Acids: Nucleic acids are complex macromolecules that store information in cells in the form of a code. To form nucleic acids, four different kinds of nucleotides are strung together. A nucleotide is a small organic compound that consists of a five-carbon sugar, a  nitrogen  containing base, and a phosphate group. Nucleotides are the structural units of adenosine phosphates, nucleotide coenzymes, and nucleic acids. They make up ATP, NAD+, NADP+, DNA, and RNA.
 EOCT NOTES DOMAIN II  ORGANISMS Energy Is Needed by all Organisms to Carry Out Processes??Energy in a Cell
  • All life on Earth depends on the flow of energy. The number one source of this energy is the Sun. Plants and other photosynthetic organisms are the entry point for this flow of energy. The process of photosynthesis supports almost all life on Earth directly or indirectly. Carbohydrates are a temporary depository of this transferred solar energy, ready to be used by the cells of these photosynthetic organisms or by the cells of organisms, such as animals, fungi, or microbes that consume plant materials. Energy from the sun is stored in nutrient molecules and then released by the metabolism of living cells. In all cells, the processes of life are constantly moving and rearranging atoms, ions, and molecules. All this biological work requires energy.
Understanding ATP
  • ATP, adenosine triphosphate, is a special molecule that stores and releases the energy in its bonds when the cell needs it. Cells work constantly to maintain a vast supply of this energy storage molecule. The energy stored is released when ATP is split into ADP, adenosine diphosphate, plus an inorganic phosphate. Remember that ATP and ADP are nucleotides, which are the building blocks of nucleic acids. When the appropriate enzyme is present, the terminal phosphate group of an ATP molecule can be transferred to a variety of other compounds. This process is known as phosphorylation. The energy released when ATP is split is stored in other energy-intermediate molecules and used to power other biological processes. Most of these processes are endergonic biological reactions in cells.
  • An endergonic reaction is any chemical reaction in which the products have more total energy and more free energy than did the reactants. Endergonic reactions require the input of energy from another source before they can take place. Consider the following reaction: ATP ↔ ADP + P + energy By removing a phosphate group, energy is released for chemical reactions to occur in the cell and ATP becomes ADP. When the cell has an excess of energy, the energy is stored in the bond when the phosphate group is added to the ADP. The double arrow indicates that the reaction occurs in both directions. ATP seems to have become the major energy link between energy-using and energyreleasing reactions. The amount of free energy released when it breaks down is suitable for use in most cellular reactions.
Examples of ways that cells use energy·        Cells use energy to make new molecules, including enzymes, and to build cell organelles and membranes. Cells also use energy to maintain homeostasis. Some cells, such as muscle cells, use energy from ATP in order to move. Nerve cells are able to transmit impulses by using ATP to power the active transport of certain ions. Lightning bugs, certain caterpillars, and many deep-sea organisms produce light from a process known as bioluminescence. The light that is produced is a result of a chemical reaction that is powered by the breakdown of ATP.Trapping Energy - Photosynthesis·        Many of the carbon atoms and oxygen molecules that you breathe once cycled through the tissues of a plant. Plants, algae, and other photosynthetic organisms are important to the maintenance and balance of life on Earth. They convert solar energy to chemical energy in the form of carbohydrates. These organisms must also break down carbohydrates to form ATP. These carbohydrates are usually in the form of simple sugars, mainly glucose.·        Autotrophs trap energy from the sun and use this energy to build carbohydrates in a process known as photosynthesis. This trapped energy is used to convert the inorganic raw materials CO2 and H2O to carbohydrates and O2. The key to this process is the pigment chlorophyll.·        The general equation for photosynthesis is as follows: 6CO2 + 6H2O + energy from sunlight → C6H12O6 + 6O2The Light Reaction in Summary
  • Light reactions take place in the chloroplasts. A lipid bilayer membrane surrounds the chloroplast. Inside the chloroplast is a gel like matrix called the stroma, which contains the ribosomes, DNA, and material for carbohydrate synthesis. The most prominent structures in the chloroplasts are stacks of flattened sacs called grana. Each of these grana contains thylakoids,which are interconnected to each other. It is in the thylakoids that the light reaction takes place. Light hitting chlorophyll causes electrons in the chlorophyll to gain energy and leave the chlorophyll molecule. As these electrons pass down the electron transport chain, they lose energy. This energy is used to make ATP. Water breaks up into hydrogen and oxygen and electrons from water replace the electrons lost by the chlorophyll. Electrons, along with hydrogen ions from water, are added to NADP+ to produce NADPH, which carries the energy to the Calvin cycle.
Two Main Reactions of Photosynthesis:1. Light reactions—These reactions split water molecules, providinghydrogen and an energy source for the Calvin cycle. Oxygen isgiven off.2. Calvin cycle—the series of reactions that form simple sugars usingcarbon dioxide and hydrogen from water.The light reaction is the photo part of photosynthesis.The Calvin cycle is the synthesis part of photosynthesis.The Calvin Cycle in SummaryThe Calvin cycle reaction takes place in the stroma of the chloroplasts. Carbon dioxidecombines with hydrogen to form simple sugars that are used to make other carbohydrates such as complex sugars, starches, and cellulose. An enzyme adds the carbon atom of carbon dioxide to a 5-carbon molecule. The carbon is now fixed in place in an organic molecule. This process is known as carbon fixation. When the carbon combines with the 5-carbon molecule, a 6-carbon molecule forms and immediately splits into two 3-carbon molecules. The two 3-carbon molecules formed are called PGA molecules (phosphoglyceric acid). These molecules are converted into two 3-carbon sugars, PGAL, using the hydrogens of NADPH + H+ and energy from ATP. Some of these sugars leave the cycle and are used to form other complex carbohydrates.Cellular Respiration and ATP Cycle
  • Once plants use light energy to form carbohydrates, other organisms, called consumers, can then use this carbohydrate energy for their own life processes. One way carbohydrate energy is used by organisms is through the process of cellular respiration. This is a multi-step operation. First, glucose is carried to the cell by the bloodstream. In the cytoplasm, the glucose is formed into pyruvic acid by the process of glycolysis. This process uses 2 molecules of ATP, but produces 4 molecules of ATP. The pyruvic acid moves into the mitochondria, where it is broken down into CO and a 2-carbon acetyl group. This acetyl group binds to coenzyme A and then enters the Krebs cycle. In the Krebs cycle, further reactions take place that release CO and high-energy electrons. These electrons are accepted by NAD+ and FAD+, forming NADH and FADH. NADH and FADH then move to the inner membrane of the mitochondrion where they pass through the electron transport chain. Here, electrons are gradually released, producing a total of 32 ATP molecules.
Cellular RespirationKrebs Cycle Electron Transport ChainThe ATP produced in the process of cellular respiration then provides energy for othercellular processes. To release this energy, ATP loses a phosphate group, becoming ADP. This ADP can then gain a phosphate group during cellular respiration to once again store energy as ATP.


    The Binomial Nomenclature System
  • Have you ever been to a zoo and been overwhelmed by the number of different species of animals you saw? Or have you taken a walk in a forest and been amazed by the different plants that you see on the forest floor? What you have seen is a small fraction of what is actually inhabiting our planet with us. In an attempt to make sense of the diversity of life, one tool that scientists use is the classification system.
  • Classification is the grouping of objects based on similarities. Aristotle, who lived from 384 to 322 BC, was the first to use the classification system. He classified living things into two categories: plants and animals. Plants were classified as shrubs, herbs, or trees. Animals were classified according to where they lived. It wasn’t until the 18th century that Carolus Linnaeus, a Swedish botanist, developed a system that is still used today. Linnaeus based his classification on characteristics of organisms that were similar. Take bats, for example. Even though bats fly, Linnaeus grouped bats with mammals because they share similar characteristics; they have hair and produce milk to feed their young. Linnaeus also developed the two word system used to identify species: binomial nomenclature. The first word identifies the genus and is always capitalized. The second word, species, is a descriptive word of that genus and is never capitalized. An example of this would be the following: Quercus alba: is the name for the white oak (alba is Latin for “white”) Quercus rubra: is the name for the red oak (rubra is Latin for “red”)
  • Taxonomy is the branch of biology dealing with the grouping and naming of organisms. The person who studies taxonomy is called a taxonomist. There is a vast array of organisms that we know of, but taxonomists are still identifying organisms. They compare the internal and external structures, analyze the chemical makeup, and compare the evolutionary relationships of species. The taxonomist has a tremendous job. The number of species identified by taxonomists is growing at different rates among different groups of organisms. With the advancing technology of the microscope, many more microorganisms have been discovered. Scientists are also exploring tropical forest canopies and deep ocean areas where they are discovering new species. Knowledge of relationships among species helps the taxonomist identify and group these “new” species into the right class.
The Six KingdomsEubacteriaArchaebacteriaProtistsFungiPlantsAnimals
  • The number of kingdoms in early classification systems varied greatly. In Aristotle’s time, scientists had not yet studied geological time frames. Phylogenetic relationships were not a part of classifying organisms. These early classification systems were based on structural differences that were seen. As scientists discovered evolutionary relationships among species, the classification system changed or was modified to fit these new discoveries. From Aristotle’s two divisions, plants and animals, we now have the six kingdom system.
  • The six kingdoms are comprised of the following: Kingdoms Eubacteria (true bacteria) and Archaebacteria contain prokaryotes, cells without membrane-bound organelles. Prokaryotes are microscopic, and most are unicellular. The Archaebacteria are mainly found in extreme environments like the deep oceans, hot springs, and swamps. Protists are unicellular and multicellular organisms with a variety of characteristics. Protists are eukaryotic organisms that lack complex organ systems and live in moist environments.
  • Fungi are consumers that stay put. They are unicellular or multicellular heterotrophic eukaryotes that absorb nutrients from dead and decaying matter by decomposing dead organisms and wastes in the environment. Plants are multicellular eukaryotes that photosynthesize. Most have cellulose cell walls and tissues that have been organized into organs and organ systems. Animals are multicellular consumers. Animal cells do not have cell walls. Their tissues have been organized into complex organ systems; the nervous system, muscle system and digestive system, as well as others. The organisms are grouped into kingdoms based on genetic and anatomic similarities. At the phylum level, organisms are subdivided again based on evolutionary traits. Organisms are further divided into different classes based upon shared physical characteristics. Within each class, organisms are grouped into orders based on a more specific and limited set of characteristics.
  • This subdividing and grouping has 7 levels in the modern classification system. The most specific level is Species. Members of a species are considered to be the same “kind” of animal and can reproduce with other members of the same species.
Levels ofClassificationKingdomPhylumClassOrderFamilyGenusSpeciesRemember the sentence: King Phillip Came Over For Good Spaghetti