BIO

Definitions 2.1

1) Element – Elements are fundamental substance that contains one kind of atom that is determined by the number of protons (which is equal to the elements atomic number on the periodic table) an atom has. Elements cannot be broken down into simpler substances by chemical reactions.

2) Atom – Atoms consist of 3 subatomic particles: protons, neutrons, and electrons. Protons, have a positive charge, neutrons, have no charge, and both are located in the atom’snucleus at its center. Electrons have a negative charge andorbit around the nucleus in electron shells. Atoms compose all living and nonliving matter and are grouped into elements based on the number of protons an atom has.

a) Protons – Positively charged subatomic particle found in the atom’s nucleus. The number of protons determines which element an atom belongs to and is equal to the element’s atomic number.

i) Atomic number - The atomic number is a number given to each element that is equal to the number of protons an atom has and is unique to each element.

b) Neutrons – Subatomic particles located in an atoms nucleus and have no charge. The number of neutrons determines the elements isotope.

i) Isotopes - are atoms of a particular element that differ in the number of neutrons that their atoms carry.

c) Electrons – Subatomic particle with a negative charge that orbit the atoms nucleus in electron shells. Electrons are the subatomic particles that participate in chemical reactions. More specifically the electrons in the outermost electron shell (the valence shell) determines the atoms chemical behavior.

i) Electron shells – Electron shells are the orbits around an atoms nucleus where the electrons are located. Theelectrons in the outermost electron shell (the valence shell) participate in chemical reactions and will determine an atoms chemical behavior.

(1) Valence shell – The valence shell is the outermost electron shell of an atom. Electrons in this shell will participate in chemical reactions and determine the chemical behavior of the atom.

d) Electronegativity – the attractive force that an atoms nucleus has on electrons. When 2 elements form a chemical bond, the size of the difference between the elements electronegativities will determine whether they form an ionic bond (large difference), a polar covalent bond, or a nonpolar covalent bond (small difference to no difference).

Definitions 2.2

1) Chemical Bond - is an attractive force that links atoms together to form molecules and compounds.

a) Covalent – A chemical bond that forms when two atoms share pairs of electrons.

i) Nonpolar – Nonpolar covalent bonds share pairs of electrons equally. Nonpolar covalent bonds do not carry a charge and are not attracted to water.

ii) Polar – Polar covalent bonds form when the electron pairs are shared unequally between 2 atoms. The unequal sharing causes the molecule to have a partial positive charge (d+) at one end of the bond (because the shared electrons spend less time there) and a partial negative charge (d-) at the other end of the bond (because the shared electrons spend more time there). These polar molecules are attracted to water.

b) Ionic bond – An ionic bond forms between ions of opposite charges (cations and anions).

i) Ion – Ions are charged particle that are formed when an atom gains (anion) or loses (cation) one or more electrons.

(1) Cation – Positively charged ions that form when an atom loses one or more electrons, and the atom now has more protons than electrons.

(2) Anion - Negatively charged ions that form when an atom gains one or more electrons, and the atom now has more electrons than protons.

c) Hydrogen bond – Hydrogen bonds form when a hydrogen is part of a polar covalent bond and have a partial positive charge (d+) which will be attracted to a partial negative charge (d-) on the same or different molecules. Although hydrogen bonds are weak, they can occur in large numbers creating stable molecules or giving water several of it’sunique properties.

d) van der Waals interactions – The movement of electrons around an atom can create small temporary partial charges. van der Waals interactions occur due to the attraction of opposite small temporary partial charges. Although van der Waals interactions are very weak, many of them occurring at the same time can cause a significant amount of force.

2) Molecule - A molecule is formed when two or more atoms form a chemical bond. Atoms can be from the same element (like oxygen gas O₂) or different elements (like water H₂O).

3) Compound - A compound is a molecule formed by at least two different elements (like water H₂O).

Definitions 2.3

1) Energy – The capacity to produce change.

a) Kinetic energy - energy of movement (includes thermal, sound, and electromagnetic energy).

b) Potential energy - stored energy (includes gravitational, elastic, chemical, and nuclear energy).

Definitions 2.4

1) Chemical reaction – a chemical reaction occurs when atoms combine or change their bonding partners.

a) Reactants – The reactants are the atoms and/or molecules before a chemical reaction occurs.

b) Products - The products are the atoms and/or molecules after a chemical reaction occurs.

c) Hydrolysis reaction – Hydrolysis reactions are “water breaking” chemical reactions that include water as a reactant and breaks down complex molecules into simpler molecules. Hydrolysis reactions are an example of an exergonic reaction where energy is released.

d) Condensation reaction – A chemical reaction that has simpler molecules as reactants and makes more complex molecules and water as products. Condensation reactions are an example of an endergonic reaction where the products have more energy (stored potential energy) than the reactants.

e) Activation energy (E_a) – Additional energy required to start a chemical reaction and is required by both exergonic and endergonic reactions.

f) Reaction rate - Measures how fast products are made per unit of time. Reaction rate is influenced by activation energy (E_a) (lower the E_a, the faster the reaction rate), temperature (higher the temperature, faster the reaction rate), and concentration (higher the concentration of reactants, faster the reaction rate).

g) Equilibrium - For reversible reactions, when the reaction rates of the forward and reverse reactions are equal, equilibrium has been reached. At equilibrium the relative concentrations of the reactants and products no longer change.

2) Gibbs free energy - Free energy or Gibbs free energy (DG) of a chemical reaction is the change in the total amount of energy that is available to perform work in a chemical reaction

a) Exergonic – the reaction releases energy resulting in a -DG. The -DG is a result of the reactants having more energy than the products.

b) Endergonic – Requires energy to occur and some the energy is stored in the products resulting in a +DG. The +DG is a result of the products having more energy than the reactants.

Definitions 2.5

1) Specific heat – Specific heat is the amount of heat needed to change the temperature of 1 gram of the substance by 1°C.Water has a high specific heat which shields organisms from        fluctuations in environmental temperature.

2) Heat of vaporization - Water has a high heat of vaporization, which means a lot of heat is required to change water from liquid to gaseous state (evaporation).

3) Cohesion – A property of water where water molecules are attracted to each other which generates surface tension, causes water droplets to round up, and allows plants to bring water from their roots to their leaves.

a) Surface tension – A property of water due to the cohesive nature of water molecules. Surface tension creates a surface barrier to water that allows some organisms, like the water strider insect, to live on the surface of the water without actually going into the water.

4) Adhesion – Adhesion is the attraction of water molecules to different molecules. Along with cohesion, adhesion helps plants bring water from their roots to their leaves.

5) Solvent – A solvent is a substance that dissolves a solute to make a solution. For example, salt (the solute) dissolves in water (the solvent) to make a salt solution. Water is called the universal solvent because it can dissolve many substances.

6) Hydrophilic – Substances that dissolve easily in water. Hydrophilic substances are “water-loving” substances.

a) Hydration shell – When a substance dissolves in water, the water molecules will associate with and surround ions, charged parts of molecules (+ or -), or polar parts ((d+) or (d-)) of polar molecules forming a hydration shell. The partial positive (d+) hydrogen atoms in the water molecule will associate with negative ions and partial negative charges (d-) of a polar molecule (forming hydrogen bonds) and the partial negative (d-) oxygen atom in the water molecule will associate with positive ions and partial positive (d+) charges of a molecule.

7) Hydrophobic – Substances that don’t dissolve easily in water. Hydrophilic substances are “water-hating” substances.

8) Amphipathic - a molecule that has both hydrophilic and hydrophobic regions.

9) pH - is a measure of the acidity or alkalinity of a solution. pH measures the amount of H⁺ (Hydrogen ions) in a solution. The pH scale goes from 0-14 and is an inverse scale meaning that there is more H⁺ at a pH of 0 and the amount of H⁺ decreases as you increase the pH from 0-14. The pH scale is also logarithmic meaning that the difference in H⁺ from a pH of 5 to 3 is not an increase of H⁺ ions of 2, but an increase of 100 (10*10 = 100). A pH of 7 is neutral, a pH below 7 is acidic, and a pH above 7 is basic (or alkaline).

a) Acids – Decrease the pH of a solution by adding (increasing) H⁺ to the solution. Acids have a pH below 7.

b) Bases – Increase the pH of a solution by removing (decreasing) H+ from the solution. Bases have a pH above 7.

c) Buffer – Buffers minimize changes in pH by adding hydrogen ions (H⁺) or hydroxide ions (OH^-) or by removing hydrogen ions (H⁺) or hydroxide ions (OH^-).

Definitions 2.6

1) Functional groups - are small groups of atoms with specific chemical properties. They confer properties to larger molecules (e.g. polarity). One biological molecule may contain many functional groups.

2) Organic chemistry – is the study of carbon. The chemistry of organic molecules is determined largely by the number and location of functional groups.

Questions and Concepts

1. What is an element? What distinguishes one element from another? What determines an elements isotope?

Elements are atoms that are distinguished into group by their number of protons. Elements can have different isotopes that differ in the number of neutrons in the atom’s nucleus.

2. What are the subatomic particles that make up an atom? What are their charges? What role do they have as part of the atom? How would you know if an atom has a neutral charge?

Atoms have 3 subatomic particles. The protons (positively charged) and neutrons (no charge) are found in the atom’s nucleus and the electrons (negatively charged) move around the nucleus in electron shells (electron orbits). The number of protons an atom has tells us what element the atom belongs to while the number of neutrons is used to distinguish between isotopes of different elements. Electrons are the subatomic particle that participates in chemical reactions. An atom will be a neutral atom if the number of positively charged protons is equal to the number of negatively charged electrons.

3. What are electron shells? Describe the role of an atom’s valence shell and an atom’s electronegativity in chemical reactions.

Electrons orbit the atoms nucleus in electron shells. The outermost electron shell is called the valence shell and the electrons in this shell are the ones that participate in chemical reactions. Atoms will gain, lose, or share electrons in their valence shell to fill the valence shell with electrons. The difference between two atoms electronegativities will determine if they gain or lose one or more electrons or if they share pairs of electrons.

4. What is a chemical bond? How are molecules and compounds similar and different?

The attractive force that links atoms together to form molecules and compounds is a chemical bond. Both molecules and compounds are formed by chemical bonds and consist of 2 or more atoms. The difference is that molecules can have 2 or more atoms from the same element (oxygen gas is 2 atoms of oxygen forming the molecule O₂), but compounds must have 2 different elements (water has hydrogen and oxygen atoms forming an H₂O compound). Both O₂ and H₂O are molecules, but only H₂O is a compound.

5. What is a covalent bond? What is the difference between a polar covalent bond and a nonpolar covalent bond?

Covalent bonds are formed when 1 or more pairs of electrons (2 electrons per pair) are shared, with each atom contributing one electron per pair, and can be nonpolar or polar. In nonpolar covalent bonds the electrons are shared evenly between the two atoms. In polar covalent bonds the electrons are shared unevenly causing the molecule to have a partial positive charge (d+) at one end and a partial negative charge (d-) at the other end. The partial negative charge (d-) will be at the end of the more electronegative atom and this is where the shared pairs of electrons will spend more of their time. Whereas the partial positive charge (d+) will be at the end of the less electronegative atom which is where the shared pairs of electrons will spend less of their time.

6. What is an ion? Describe cation and anion and how they form ionic bonds.

Atoms form ions when they gain or lose one or more electrons. Cations are formed when an atom loses one or more electrons and have a positive (+) charge because they have more protons (+) than electrons (-). Anions are formed when an atom gains one or more electrons and have a negative (-) charge because they have less protons (+) than electrons (-). Ionic bonds will form between cations and anions because they have opposite charges will be attracted to each other.

7. What is the difference between an ionic bond and a covalent bond?

Covalent bonds share 1 or more pairs of electrons (2 electrons per pair), whereas ionic bonds do not involve the sharing of electrons. Ionic bonds form when one atom loses one or mor electrons and has a positive (+) charge (cations) and another atom gains one or more electrons (anion) and has a negative (-) charge. The opposite charges between the ions (cation and anion) are attracted to each other and form an ionic bond.

8. How do hydrogen bonds form? How are hydrogen bonds similar to ionic bonds? What are van der Waals interactions? How are hydrogen bonds and van der Waals interactions similar?

Hydrogen bonds form between a partial positive (d+) hydrogen and a partial negative (d-) atom (often oxygen or nitrogen) on the same or different molecule. Hydrogen bonds and ionic bonds are similar in that they are formed by the attractions of different charges, but in hydrogen bonds the charges are partial charges and in ionic bonds the charges are full charges. van der Waals interactions form when there are temporary opposite partial charges that form between the atoms of two molecules. These temporary partial charges occur because electrons are moving and just by chance the electrons may be found is one area, causing the partial negative (d-) charge, and not another area, causing the partial positive (d-) charge. Both hydrogen bonds and van der Waals interactions occur because of the attraction of partial opposite charges, but the van der Waals interactions are temporary and occur due to the chance movement of electrons whereas the hydrogens partial charge come from the hydrogen being part of a polar covalent bond making the partial positive charge and will last if the hydrogen is in that polar covalent bond. Both hydrogen bonds and van der Waals interactions are individually weak bonds but form a strong bond when there are large numbers of them between molecules.

9. Describe the 1^st and 2^nd Laws of thermodynamics in the context of biological chemical reactions.

The 1^st Law of Thermodynamics tells us that the amount of energy before an energy transformation is equal to the energy after the energy transformation, with the 2^ndLaw of Thermodynamic telling us that some of the energy after each energy transformation will be unusable energy.

The molecules and compounds that make up living organisms can store energy (potential energy) and can be broken down to release energy (kinetic energy) for cellular work. When chemical reaction occurs in biological organisms to turn potential energy into kinetic energy, the amount of energy is the same before and after the chemical reaction (1^st law), but some of that energy is now unusable (2^nd law) and must be replenished. Humans replenish usable energy by eating food, whereas plants can use the photosynthesis and energy from the sun.

10. What are the reactants and products of a chemical reaction? Describe exergonic and endergonic reactions. How does the Gibbs free energy change when a chemical reaction is exergonic vs. endergonic?

The atoms and/or molecules at the beginning of the chemical reaction are the reactants of that chemical reaction and the atoms and/or molecules after a chemical reaction has occurred are the products.

The amount of energy in the atoms and/or molecules before a chemical reaction (the reactants) will not be the same as the amount of energy in the atoms and/or molecules after a chemical reaction (products). When the amount of energy in the reactants is greater than the amount of energy in the products the chemical reaction will be an exergonic reaction that releases energy and has a -DG (negative Gibbs free energy). When the amount of energy in the reactants is less than the amount of energy in the products the chemical reaction will be an endergonic reaction that requires energy to form the products (some of the energy will remain in the products) and has a +DG (positive Gibbs free energy). By taking the amount of energy in the products and subtracting the amount of energy in the reactants we can calculate the change in Gibbs free energy and have the correct sign (+ or -) for the DG.

11. Compare and contrast hydrolysis and condensation reactions. Which one would be associated with an endergonic and which one would be associated with anexergonic?

Both hydrolysis and condensation reactions are common in living organisms. Hydrolysis reactions have water as a reactant whereas condensation reactions have water as a product. Hydrolysis reactions break up larger molecules into smaller molecules whereas condensation reactions use smaller molecules to make larger molecules. Hydrolysis reactions are an example of an exergonic reactions while the condensation reaction is an example of an endergonic reaction.

12. Name and describe the properties of water. What is the reason water has these properties?

The properties of water (high specific heat, high heat of vaporization, solid state (ice) floats, cohesion, adhesion, and being a great solvent) are all due to water being a polar molecule and secondly for most of the properties due to the hydrogen bonds between water molecules. Waters high specific heat shields organisms from fluctuations in environmental temperature and its high heat of vaporization provides a cooling effect for organisms (We sweat, but other organisms like kangaroos will like their arms to cool themselves down by evaporation). Water also releases heat slowly allowing the earths oceans to transport heat from the equator to the poles and to moderate costal environments. Ice floats because stable hydrogen bonds form causing water molecules to be evenly space and have mor room between the molecules making ice less dense than liquid water. This means that when water freezes it floats and doesn’t cause lakes and oceans to freeze from the bottom up. Cohesion and adhesion are the properties of water that allow plants to move water up from their roots (bottom of the plant) to their leaves at the top of the plant for use in photosynthesis. Cohesion also allows some organisms to live on the surface of the water, but not in the water (eg. water striders). Water can dissolve many substances and is called the universal solvent since it can dissolve many substances.

13. What determines whether a compound will dissolve in water (meaning that it is hydrophilic)?

Because water is a polar molecule, ions or molecule that have a charge or have a partial charge can be dissolved in water. The partial negative (oxygen) and partial positive (hydrogen) parts of the water molecule will be attracted to opposite charges or partial charges forming a hydration shell around the ion or molecule, thus dissolving the ion or molecule.

14. What does it mean that water is self-ionizing? What is pH measuring? Describe the relationship between the H⁺ and OH^- concentration and the pH value of a solution. Describe an acid and a base. How do acids and bases change the pH of a solution? What is a buffer? How does a buffer help a solution resist changes in pH?

A water molecule (H₂O) can randomly ionize (self-ionize) into a hydrogen ion (H⁺) and a hydroxide ion (OH^-). pH will measure the amount of the hydrogen ions (H⁺) in water. The highest amount of hydrogen ions (H⁺) will be when a solution has a pH of 0 and as the pH increases the amount of hydrogen ions (H⁺) decrease. Another way to think about pH is the relative amounts of the hydrogen ion (H⁺) and a hydroxide ion (OH^-). When they are in equal amounts (H⁺ = OH^-) the pH of the solution is 7 which is the neutral pH. When there are more hydrogen ions (H⁺) than hydroxide ions (OH^-) (H⁺ > OH^-) the pH will be below 7 and be an acidic solution. When there are less hydrogen ions (H⁺) than hydroxide ions (OH^-) (H⁺ < OH^-) the pH will be above 7 and be basic solution.

Acids will have a pH less than 7 and when added to a solution will decrease the pH of the solution because it increases the amount of hydrogen ions (H⁺). Bases will have a pH greater than 7 and when added to a solution will increase the pH of the solution because it decreases the amount of hydrogen ions (H⁺).

Buffers minimize changes in pH by adding hydrogen ions (H⁺) or hydroxide ions (OH^-) or by removing hydrogen ions (H⁺) or hydroxide ions (OH^-)

15. Be able to identify and describe the properties of the selected functional groups from the lecture.

The most important functional groups have a red asterisk next to them and include: hydroxyl groups (OH) that is polar and can be involved in hydrogen bonds and they often participate in condensation reactions. Carboxyl groups (COOH) are part of the amino acid molecule that make up proteins and they will react this the amino group on another amino acid to form a peptide bond. Amino groups (NH₂) are also part of the amino acid molecule that make up proteins and they will react this the carboxyl group on another amino acid to form a peptide bond. Phosphate groups (PO₄^3-)are important to living organisms as part of the energy currency molecule ATP (Adenosine Triphosphate) which is a molecule with 3 phosphate groups. When 1 phosphate group is removed by a hydrolysis reaction the reaction is strongly exergonic.

The less important functional groups have a black asterisk next to them and include: Methyl groups (CH₄) that can bond to DNA molecules and modify an organisms gene expression. Sulfhydryl groups (SH) will help stabilize proteins by forming disulfide bridges, which are covalent bonds between 2 sulfurs of the sulfhydryl group.

The functional groups without an asterisk (Aldehyde and Keto groups) are not needed for what I cover in this class, and you will not be tested on them.

unnecessary