BIOD 101 mix study guide: Matter is anything that takes up space

Matter is anything that takes up space, by having a volume, and has mass. Matter can exist in a solid, liquid, gaseous (vapor), or plasma state. All matter is made up of certain basic substances called elements. Elements can be further classified as being either essential or trace elements. Essential elements are required for human life Trace elements are required only in small quantities. Elements cannot be broken down to simpler substances and there are only ninety-two naturally occurring elements. Although all organisms are made up of elements, the majority of the composition (~98%) is comprised of only six elements: carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. Molecules are formed when elements combine with one another. If the types of atoms in a molecule are different from each other, a compound is formed. Perhaps the best-known compound is water—the combination of two hydrogen atoms with a single atom of oxygen. Ionic Bonds Ions are atoms (or molecules) with a net electrical charge that can be negative or positive based on the gain or loss of electrons, respectively. Thus, an atom that gains electrons becomes negatively charged as its number of electrons is now greater than its number of protons. Similarly, an atom that loses electrons becomes positively charged as its number of electrons is now less that its number of protons. Cations are positively charged ions. Anions are negatively charged ions. As molecules are formed, electrons are transferred from one atom to another, resulting in the formation of cations or anions. Ions thus play a large role in the formation of stable interactions between atoms (or molecules) due to the fact that opposite charges attract. As such, ionic bonds are generated based on the attraction between oppositely charged particles. Covalent Bonds A covalent bond occurs when electrons are shared by two atoms to complete the valence shells of both. In general, covalent bonds exist between two non-metals. For example, a covalent bond can be formed between two hydrogen atoms or a hydrogen atom and another atom. Hydrogen Bonds Polar molecules also interact easily with other polar molecules. For this reason, ionic substances and other polar covalent molecules dissolve well in water, which, as stated above, is also polar. The partial positive charges on the hydrogen atoms in a water molecule cause the hydrogen atoms to be attracted to oxygen atoms of other water molecules. This attraction forms a relatively weak bond called a hydrogen bond, which is often represented by a dotted line because it is easily broken. Any molecule containing O-H or N-H bonds can form hydrogen bonds, which cause these molecules to be quite soluble in water. The hydrogen bonds, while weak individually, are fairly strong in mass. For this reason, water molecules are tightly bonded to one another and other molecules. Hydrogen bonds also cause water to have a relatively high boiling point and freezing point. Organic Chemistry and Biochemistry of Life Biomacromolecules are found in living organisms and are comprised of four main types of organic compounds: (1) carbohydrates, (2) lipids, (3) proteins and (4) nucleic acids. The term biomacromolecule reflects its form and function as it can be broken down into smaller segments of bio (life), macro (large) and molecule (group of atoms bonded together, often centered around carbon). Each biomacromolecule is made up of many attached units of smaller molecules called monomers (monomeaning “one”). The biomacromolecules are said to be polymers (poly- meaning “many”) since they contain many monomers. The four types of biomacromolecules found in living organisms are listed :1.Carbohydrate 2. Lipid 3. DNA and RNA (Nucleic Acids) 4. Protein Carbohydrates Carbohydrates, commonly referred to as sugars, are the primary source of fuel for organisms and have the same three elements in their main structure: carbon, hydrogen, and oxygen (C, H, and O, respectively). The hydrogen to oxygen ratio in a carbohydrate will always be 2:1, as previously shown in the formula for water, H2O. Glucose, for example, is C6H12O6 and has twice as many hydrogens as oxygens. Take care not to confuse hydrocarbons with carbohydrates; they are not the same thing. Hydrocarbons have only a H and C, while carbohydrates have H, C, and O. Note: To remember the composition of carbohydrates, focus on the word "hydrate" as referring to water. Also, most sugars end with the suffix “ose”. If you see something in writing, and you aren’t sure what it is, look at the suffix; “ose” is a strong clue it’s some kind of carbohydrate. Monosaccharides are simple sugar (saccharide) carbohydrates made up of a single monomer (mono). Examples of monosaccharides include glucose (the sugar in our blood stream), fructose (a sugar found in fruit), and ribose and deoxyribose (the sugars found in DNA and RNA). • When showing the structural formulas, all the atoms are rarely shown due to how crowded the structural diagram would become. As shown in Figure 1.1, many of the carbon and hydrogen atoms have been left off the rings. In such cases, the ‘points’ along the ring are assumed to be a carbon unless otherwise indicated. The exception occurs relative to the functional groups as they influence the general properties of the molecule, often making carbohydrates polar. A functional group can be many different things such as a single hydrogen, or a chain of carbohydrates. They can be thought of as the “flavoring” and are the very things that give monosaccharides (and later we will see amino acids) their unique chemical characteristics. As such, the functional groups are most often shown. Table 1.3 displays a list of biologically important chemical functional groups. Polysaccharides are complex sugars made of many (poly) monosaccharides linked together and are named according to the number of sugars. For example, Trioses have the formula C3H6O3 ; pentoses have the formula C5H10O5 ; and hexoses C6H12O6 . Examples of polysaccharides include glycogen and starch Structurally, other carbohydrates may be comprised of more than one ring structure. For instance, starch and glycogen contain many monomer units of glucose joined together. As shown in Figure 1.2, the “n” refers to the number of monomers in a chain. Both starch and glycogen are formed by the joining together of differing amounts of glucose via a dehydration reaction. Dehydration reactions are called so because, intuitively, a water molecule is lost from the reactant side of the chemical equation. Conversely, starch and glycogen are broken down through hydrolysis into individual glucose molecules that can be used by the organism for energy. Hydrolysis involves the separation of water molecules to break bonds in the reacting molecule. As such, starch is the primary form utilized by plants to store glucose while humans and animals use glycogen which is found within liver and muscle cells. Lipids Lipids are unique among the biomacromolecules because most of them are insoluble in water. Additionally, lipids are not monomers but are assembled from smaller molecules that are chemically linked together. Examples include fats, oils, steroids, and phospholipids. Lipids are insoluble in water because they are made mostly of non-polar hydrocarbon chains. The hydrocarbon is simply a chain of carbon atoms with hydrogen atoms attached. Similar to carbohydrates, lipids contain the elements carbon, hydrogen and oxygen, but the hydrogen and oxygen are not in a 2:1 ratio. Phosphorus and nitrogen may also compose some lipids. Note: As water is polar, it will only dissolve other polar or ionically bonded substances. As lipids are non-polar, this is why they are insoluble in water but can be dissolved with nonpolar solvents such as alcohol.