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General Biology > 2: The Chemical Foundation of Life > Flashcards

2: The Chemical Foundation of Life Flashcards

Atoms, Isotopes, Ions, and Molecules - The Building Blocks, Water, Carbon

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1
Q

What is an anion?

A

A negative ion that is formed by an atom gaining one or more electrons.

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2
Q

What is an atom?

A

The smallest unit of matter that retains all of the chemical properties of an element.

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3
Q

What is the atomic mass of an atom?

A

The calculated mean of the mass number for an element’s isotopes.

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4
Q

What is the atomic number of an atom?

A

The total number of protons in an atom.

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5
Q

What is a balanced chemical equation?

A

A statement of a chemical reaction with the number of each type of atom equalized for both the products and reactants.

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6
Q

What is a cation?

A

A positive ion that is formed by an atom losing one or more electrons.

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7
Q

What is a chemical bond?

A

An interaction between two or more of the same or different atoms that results in the formation of molecules.

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8
Q

What is a chemical reaction?

A

A process leading to the rearrangement of atoms in molecules.

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9
Q

What is chemical reactivity?

A

The ability to combine and to chemically bond with each other.

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10
Q

What is a compound?

A

A substance composed of molecules consisting of atoms of at least two different elements.

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11
Q

What is a covalent bond?

A

A type of strong bond formed between two of the same or different elements; forms when electrons are shared between atoms.

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12
Q

What is an electrolyte?

A

An ion necessary for nerve impulse conduction, muscle contractions and water balance.

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13
Q

What is an electron?

A

A negatively charged subatomic particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a negative charge of -1 unit.

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14
Q

What is an electron configuration?

A

The arrangement of electrons in an atom’s electron shell (for example, 1s22s22p6).

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15
Q

What is an electron orbital?

A

How electrons are spatially distributed surrounding the nucleus; the area where an electron is most likely to be found.

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16
Q

What is electron transfer?

A

The movement of electrons from one element to another; important in the creation of ionic bonds.

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17
Q

What is electronegativity?

A

The ability of some elements to attract electrons (often of hydrogen atoms), acquiring partial negative charges in molecules and creating partial positive charges on the hydrogen atoms.

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18
Q

What is an element?

A

One of 118 unique substances that cannot be broken down into smaller substances; each element has unique properties and a specified number of protons.

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19
Q

What is equilibrium?

A

A steady state of relative reactant and product concentration in reversible chemical reactions in a closed system.

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20
Q

What is a hydrogen bond?

A

A weak bond between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules.

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21
Q

What is an inert gas?

A

An element with filled outer electron shell that is unreactive with other atoms. AKA noble gas.

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22
Q

What is an ion?

A

An atom or chemical group that does not contain equal numbers of protons and electrons.

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23
Q

What is an ionic bond?

A

A chemical bond that forms between ions with opposite charges (cations and anions).

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24
Q

What is an irreversible chemical reaction?

A

A chemical reaction where reactants proceed unidirectionally to form products.

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25
Q

What is an isotope?

A

One or more forms of an element that have different numbers of neutrons.

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26
Q

What is the law of mass action?

A

A chemical law stating that the rate of a reaction is proportional to the concentration of the reacting substances.

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27
Q

What is the mass number of an atom?

A

The total number of protons and neutrons in an atom.

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28
Q

What is matter?

A

Anything that has mass and occupies space.

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29
Q

What is a molecule?

A

Two or more atoms chemically bonded together.

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30
Q

What is a neutron?

A

An uncharged particle that resides in the nucleus of an atom; has a mass of one amu.

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31
Q

What is a nonpolar covalent bond?

A

A type of covalent bond that forms between atoms when electrons are shared equally between them.

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32
Q

What is a nucleus?

A

The core of an atom; contains protons and neutrons.

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33
Q

What is the octet rule?

A

The rule that atoms are most stable when they hold eight electrons in their outermost shell.

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34
Q

What is an orbital?

A

The region surrounding the nucleus; contains electrons.

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35
Q

What is the periodic table?

A

The organizational chart of elements indicating the atomic number and atomic mass of each element; provides key information about the properties of the elements.

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36
Q

What is a polar covalent bond?

A

A type of covalent bond that forms as a result of unequal sharing of electrons, resulting in the creation of slightly positive and slightly negative charged regions of the molecule.

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37
Q

What is a product?

A

A molecule found on the right side of a chemical equation.

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38
Q

What is a proton?

A

A positively charged particle that resides in the nucleus of an atom; has a mass of one amu and a charge of +1.

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39
Q

What is a radioisotope?

A

An isotope that emits radiation composed of subatomic particles to form more stable elements.

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40
Q

What is a reactant?

A

A molecule found on the left side of a chemical equation.

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41
Q

What is a reversible chemical reaction?

A

A chemical reaction that functions bi-directionally, where products may turn into reactants if their concentration is great enough.

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42
Q

What is a valence shell?

A

The outermost shell of an atom.

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43
Q

What is a van der Waals interaction?

A

A very weak interaction between molecules due to temporary charges attracting atoms that are very close together.

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44
Q

How many elements are found in nature?

A

Of the 118 known elements, only 92 occur naturally. The others are synthesized in laboratories and are naturally unstable.

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45
Q

Which elements are common to all living organisms?

A

Oxygen (O) (65%), carbon (C) (18%), hydrogen (H) (10%), and nitrogen (N) (3%).

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46
Q

What is the mass of one atomic mass unit?

A

About 1.67 x 10-24 grams.

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47
Q

What is another term for atomic mass unit (amu)?

A

Dalton.

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48
Q

What is the mass of an electron?

A

About 9.11 x 10-28 grams, or about 1/1800 of an amu.

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49
Q

How is carbon-14 created?

A

C14 is a naturally occurring radioisotope that is created in the atmosphere from N14 by the addition of a neutron and the loss of a proton because of cosmic rays. This is a continuous process, so C14 is always being created.

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50
Q

How much C14 is found in organisms?

A

In living organisms, the relative amount of C14 to C12 is equal to the concentration in the atmosphere. When the organism dies, the ratio between C14 and C12 declines as C14 decays gradually to N14 by a process called beta decay—the emission of electrons or positrons.

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51
Q

What is the half-life of a radioisotope?

A

The time it takes for half of the original concentration of an isotope to decay back to its more stable form.

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52
Q

What is the half-life of C14?

A

Approximately 5730 years.

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53
Q

What is the limit to carbon-dating?

A

About 50,000 years.

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54
Q

What are the half-lives of other radioisotopes?

A

K40 has a half-life of 1.25 billion years, and U235 has a half-life of about 700 million years.

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55
Q

Who created the periodic table?

A

Russian chemist Dmitri Mendeleev (1834—1907) in 1869.

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56
Q

What is the Bohr model?

A

An early model of the atom that was developed in 1913 by Danish scientist Niels Bohr (1885—1962), which depicts the atom as a central nucleus containing protons and neutrons with ring-shaped electron orbitals surrounding the nucleus at increasing distances marked with the symbol “n” (1n, 2n, 3n, etc.)

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57
Q

What are some limitations of the Bohr model?

A

Although useful to explain the reactivity and chemical bonding of certain elements, the Bohr model of the atom does not accurately reflect how electrons are spatially distributed surrounding the nucleus, which are found in electron orbitals.

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58
Q

How can the location of an electron be determined?

A

Electronic orbitals result from the fact that electrons behave not just like particles, but also like waves. Mathematical equations from quantum mechanics known as wave functions can predict within a certain level of probability where an electron may be at any given time. The area where an electron is most likely to be found is called its orbital. It is impossible to calculate exactly where an electron is located.

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59
Q

How are electron shells organized?

A

Within each electron shell are subshells, and each subshell has a specified number of orbitals containing electrons. Subshells are designated by the letters s, p, d, and f.

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60
Q

What does the s subshell look like?

A

The s subshell is spherical in shape and has one orbital.

61
Q

What does the p subshell look like?

A

The p subshell has three dumbbell-shaped orbitals.

62
Q

What do the d and f subshells look like?

A

The d and f subshells have more complex shapes and contain five and seven orbitals, respectively.

63
Q

How is the 1n principal shell organized?

A

The principal shell 1n has a single s subshell and can hold two electrons.

64
Q

How is the 2n principal shell organized?

A

The principal shell 2n has one s and one p subshell, and can hold a total of eight electrons.

65
Q

How is the 3n principal shell organized?

A

The principal shell 3n has s, p, and d subshells and can hold 18 electrons.

66
Q

How is the 4n principal shell organized?

A

The principal 4n shell has s, p, d, and f orbitals and can hold 32 electrons.

67
Q

What is an example of a reversible chemical reaction?

A

In human blood, excess hydrogen ions (H+) bind to bicarbonate ions (HCO3−) forming an equilibrium state with carbonic acid (H2CO3). If carbonic acid were added to this system, some of it would be converted to bicarbonate and hydrogen ions.

HCO3− + H+ ↔ H2CO3

68
Q

How often is equilibrium achieved in biological systems?

A

Rarely, because the concentrations of the reactants or products or both are constantly changing, often with the product of one reaction being the reactant for another.

69
Q

How are anionic elements designated?

A

Anions are designated by their elemental name being altered to end in “-ide”, for example chloride and sulfide.

70
Q

How many covalent bonds may be formed between two atoms?

A

Single, double, and triple bonds may be formed, with the larger number of bonds being stronger.

71
Q

How many covalent bonds does molecular nitrogen (N2) have?

A

The two nitrogen atoms are triple-bonded to each other.

72
Q

What is an example of a polar covalent bond?

A

Water (H2O)

73
Q

What are some examples of nonpolar covalent bonds?

A

Molecular oxygen (O2) and methane (CH4) (C and H do not have the same electronegativity but are similar).

74
Q

What does a pharmaceutical chemist do?

A

Pharmaceutical chemists are responsible for the development of new drugs and trying to determine the mode of action of both old and new drugs. They are involved in every step of the drug development process.

75
Q

How are new drugs developed?

A

Drugs can be found in the natural environment or can be synthesized in the laboratory. In many cases, potential drugs found in nature are changed chemically in the laboratory to make them safer and more effective, and sometimes synthetic versions of drugs substitute for the version found in nature.

76
Q

What happens after the initial discovery or synthesis of a drug?

A

Chemists develops the drug, perhaps chemically altering it, testing it to see if the drug is toxic, and then designs methods for efficient large-scale production. Then, the process of getting the drug approved for human use begins.

77
Q

How are drugs approved for human use?

A

In the United States, drug approval is handled by the Food and Drug Administration (FDA) and involves a series of large-scale experiments using human subjects to make sure the drug is not harmful and effectively treats the condition it aims to treat. This process often takes several years and requires the participation of physicians and scientists, in addition to chemists, to complete the testing and gain approval.

78
Q

What are some examples of drugs discovered in living organisms?

A

Paclitaxel (Taxol), an anti-cancer drug used to treat breast cancer, discovered in the bark of the pacific yew tree. Another example is aspirin, originally isolated from willow tree bark.

79
Q

What is an example of traditional medicine informing modern medicine?

A

The use of willow bark to make medicine has been known for thousands of years, dating back to ancient Egypt. It was not until the late 1800s that the aspirin molecule, known as acetylsalicylic acid, was purified and marketed for human use.

80
Q

What is an example of a drug that had unforeseen consequences that lead to other applications?

A

The drug minoxidil (Rogaine) was originally developed to treat high blood pressure, but it was found that individuals taking the drug would grow new hair, and so was eventually marketed to men and women with baldness to restore lost hair.

81
Q

What is an acid?

A

A molecule that donates hydrogen ions and increases the concentration of hydrogen ions in a solution.

82
Q

What is adhesion?

A

Attraction between water molecules and other molecules.

83
Q

What is a base?

A

A molecule that donates hydroxide ions or otherwise binds excess hydrogen ions and decreases the concentration of hydrogen ions in a solution.

84
Q

What is a buffer?

A

A substance that prevents a change in pH by absorbing or releasing hydrogen or hydroxide ions.

85
Q

What is a calorie?

A

The amount of heat required to change the temperature of one gram of water by one degree Celsius.

86
Q

What is capillary action?

A

Behavior that occurs because water molecules are attracted to charges on the inner surfaces of narrow tubular structures such as glass tubes, drawing the water molecules to the sides of the tubes.

87
Q

What is cohesion?

A

Intermolecular forces between water molecules caused by the polar nature of water; responsible for surface tension.

88
Q

What is dissociation?

A

Release of an ion from a molecule such that the original molecule now consists of an ion and the charged remains of the original, such as when water dissociates into H+ and OH−.

89
Q

What is evaporation?

A

Separation of individual molecules from the surface of a body of water, leaves of a plant, or the skin of an organism.

90
Q

What is the heat of vaporization of water?

A

A high amount of energy required for liquid water to turn into water vapor.

91
Q

What does it mean to be hydrophilic?

A

Describes ions or polar molecules that interact well with other polar molecules such as water.

92
Q

What does it mean to be hydrophobic?

A

Describes uncharged non-polar molecules that do not interact well with polar molecules such as water.

93
Q

What is litmus or pH paper?

A

Filter paper that has been treated with a natural water-soluble dye that changes its color as the pH of the environment changes so it can be used as a pH indicator.

94
Q

What is the pH scale?

A

A scale ranging from zero to 14 that is inversely proportional to the concentration of hydrogen ions in a solution.

95
Q

What is a solvent?

A

A substance capable of dissolving another substance.

96
Q

What is specific heat capacity?

A

The amount of heat one gram of substance must absorb or lose to change its temperature by one degree Celsius.

97
Q

What is a sphere of hydration?

A

When polar water molecules surround charged or polar molecules thus keeping them dissolved and in solution.

98
Q

What is surface tension?

A

Tension at the surface of a body of liquid that prevents the molecules from separating; created by the attractive cohesive forces between the molecules of the liquid.

99
Q

What is a substituted hydrocarbon?

A

A hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons.

100
Q

What are the special properties of water?

A

The polarity of the water molecule and its hydrogen bonding allow for special properties including its high heat capacity and heat of vaporization, its ability to dissolve polar molecules, its cohesive and adhesive properties, and its dissociation into ions that leads to the generation of pH.

101
Q

What happens when water is boiled?

A

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 (steam or water vapor).

102
Q

What happens when water is frozen?

A

The water molecules form a crystalline structure maintained by hydrogen bonding (there is not enough energy to break the hydrogen bonds) that makes ice less dense than liquid water, which is a phenomenon not seen in the solidification of other liquids.

103
Q

Why is frozen water less dense than liquid water?

A

It is due to the way hydrogen bonds are oriented as it freezes: the water molecules are pushed farther apart compared to liquid water. With most other liquids, solidification when the temperature drops includes the lowering of kinetic energy between molecules, allowing them to pack even more tightly than in liquid form and giving the solid a greater density than the liquid.

104
Q

What is the main benefit of the lower density of frozen water to living organisms?

A

It causes the ice to float, which forms an insulating barrier that protects the animals and plant life in the water from freezing.

105
Q

What is the downside of the lower density of frozen water to living organisms?

A

The ice crystals that form upon freezing rupture the delicate membranes essential for the function of living cells, irreversibly damaging them. Cells can only survive freezing if the water in them is temporarily replaced by another liquid like glycerol.

106
Q

Why does land cool faster than the sea?

A

The specific heat capacity of water is about five times more than that of sand.

107
Q

How is the heat capacity of water used by living organisms?

A

It allows warm-blooded animals to more evenly disperse heat in their bodies.

108
Q

How much heat energy is required to vaporize water?

A

586 calories

109
Q

How is the heat of vaporization of water used by living organisms?

A

As water evaporates, energy is taken up by the process, cooling the environment where the evaporation is taking place. In many living organisms, the evaporation of sweat, which is 90% water, allows the organism to cool so that homeostasis of body temperature can be maintained.

110
Q

Why is cohesion and adhesion of water important for living organisms?

A

They are used to transport water from the roots to the leaves in plants. These forces create a “pull” on the water column. This pull results from the tendency of water molecules being evaporated on the surface of the plant to stay connected to water molecules below them, and so they are pulled along. Plants use this natural phenomenon to help transport water from their roots to their leaves.

111
Q

What happens when water molecules ionize into hydrogen (H+) and hydroxide (OH−) ions?

A

The hydroxide ions are kept in solution by their hydrogen bonding with other water molecules, and the hydrogen ions immediately form hydronium ions (H3O+) with water molecules.

112
Q

What is a mole?

A

6.02 x 1023 particles of a substance

113
Q

What is the concentration of hydrogen ions that dissociate from pure water?

A

1 x 10-7 moles H+ ions per liter of water

114
Q

How is pH calculated?

A

pH is calculated as the negative of the base 10 logarithm of the concentration of hydrogen ions dissociating from pure water. The log10 of 1 x 10-7 is -7.0, and the negative of this number (indicated by the “p” of “pH”) yields a pH of 7.0, which is known as neutral pH.

115
Q

What is an example of a strong and weak acid?

A

Hydrochloric acid (HCl) completely dissociates into hydrogen and chloride ions and is highly acidic, whereas the acids in tomato juice or vinegar do not completely dissociate and are considered weak acids.

116
Q

What is an example of a strong and weak base?

A

Sodium hydroxide (NaOH) and many household cleaners are highly alkaline, whereas seawater is a weak basic solution which has a pH near 8.0, close enough to neutral pH that marine organisms adapted to this saline environment are able to thrive in it.

117
Q

What is the pH inside the human body?

A

The pH inside cells is about 6.8 and the pH in the blood is about 7.4. The environment in the stomach, however, is highly acidic, with a pH of 1 to 2.

118
Q

How do body cells survive in the stomach?

A

They cannot survive and are constantly dying. New stomach cells are constantly produced to replace dead ones, which are digested by the stomach acids. It is estimated that the lining of the human stomach is completely replaced every seven to ten days.

119
Q

What are some examples of liquids at different pH levels?

A
  1. gastric acid
  2. lemon juice
  3. orange juice
  4. tomato juice
  5. black coffee
  6. urine
  7. distilled water
  8. sea water
  9. baking soda
  10. milk of magnesia
  11. ammonia solution
  12. soapy water
  13. bleach
120
Q

How do living organisms manage the ingestion of acidic and basic substances?

A

They use buffers to regulate a constant blood pH. The buffer maintaining the pH of human blood involves carbonic acid (H2CO3), bicarbonate ion (HCO3—), and carbon dioxide (CO2). When bicarbonate ions combine with free hydrogen ions and become carbonic acid, hydrogen ions are removed, moderating pH changes. Similarly, excess carbonic acid can be converted to carbon dioxide gas and exhaled through the lungs. This prevents too many free hydrogen ions from building up in the blood and dangerously reducing the blood’s pH. Likewise, if too much OH— is introduced into the system, carbonic acid will combine with it to create bicarbonate, lowering the pH.

121
Q

How do antacids work?

A

Used to combat excess stomach acid, many of these over-the-counter medications work in the same way as blood buffers, usually with at least one ion capable of absorbing hydrogen and moderating pH, bringing relief to those that suffer “heartburn” after eating.

122
Q

What is an aliphatic hydrocarbon?

A

A hydrocarbon consisting of a linear chain of carbon atoms.

123
Q

What is an aromatic hydrocarbon?

A

A hydrocarbon consisting of closed rings of carbon atoms.

124
Q

What are enantiomers?

A

Molecules that share overall structure and bonding patterns, but differ in how the atoms are three dimensionally placed such that they are mirror images of each other.

125
Q

What is a functional group?

A

A group of atoms that provides or imparts a specific function to a carbon skeleton.

126
Q

What is a geometric isomer?

A

An isomer with similar bonding patterns differing in the placement of atoms alongside a double covalent bond.

127
Q

What is a hydrocarbon?

A

A molecule that consists only of carbon and hydrogen.

128
Q

What are isomers?

A

Molecules that differ from one another even though they share the same chemical formula.

129
Q

What is an organic molecule?

A

Any molecule containing carbon (except carbon dioxide).

130
Q

What are structural isomers?

A

Molecules that share a chemical formula but differ in the placement of their chemical bonds.

131
Q

What is a substituted hydrocarbon?

A

A hydrocarbon chain or ring containing an atom of another element in place of one of the backbone carbons.

132
Q

What is the simplest hydrocarbon?

A

Methane (CH4)

133
Q

What is the geometry of methane?

A

The geometry of the methane molecule, where the atoms reside in three dimensions, is determined by the shape of its electron orbitals. The carbons and four hydrogen atoms form a shape known as a tetrahedron, with four triangular faces, and so is described as having tetrahedral geometry.

134
Q

What is the geometry of hydrocarbons?

A

Hydrocarbons may exist as linear carbon chains, carbon rings, or combinations of both. Furthermore, individual carbon-to-carbon bonds may be single, double, or triple covalent bonds, and each type of bond affects the geometry of the molecule in a specific way.

135
Q

Which suffixes are used to indicate carbon bond count?

A

The suffixes “-ane”, “-ene”, and “-yne” refer to the presence of single, double, or triple carbon-carbon bonds, respectively.

136
Q

How do the number of carbon-carbon bonds affect the geometry of a molecule?

A

Single bonds allow rotation along the axis of the bond, whereas double bonds lead to a planar configuration, and triple bonds to a linear one.

137
Q

Where can the benzene ring be found?

A

Some amino acids and cholesterol and its derivatives, including the hormones estrogen and testosterone. The benzene ring is also found in the herbicide 2,4-D. Benzene is a natural component of crude oil and has been classified as a carcinogen.

138
Q

What is an example of a hydrocarbon with both aliphatic and aromatic portions?

A

Beta-carotene

139
Q

What is an example of structural isomers and their uses?

A

Butane and isobutene (C4H10). Butane is suited for use as a fuel for cigarette lighters and torches, whereas isobutene is suited for use as a refrigerant and a propellant in spray cans.

140
Q

What is an example of geometric isomers?

A

In butene (C4H8), the two methyl groups (CH3) can be on either side of the double covalent bond central to the molecule. When the carbons are bound on the same side of the double bond, this is known as the cis configuration. If they are on opposite sides of the double bond, it is known as the trans configuration. In the trans configuration, the carbons form a more or less linear structure, whereas the carbons in the cis configuration make a bend (change in direction) of the carbon backbone.

141
Q

What is the difference between saturated and unsaturated fats?

A

Triglycerides without double bonds are called saturated fats, and those with at least one double bond are called unsaturated fats. Saturated fats are a solid at room temperature and usually of animal origin.

142
Q

What is the difference between cis and trans unsaturated fats?

A

When some of the bonds are in the cis configuration, the resulting bend in the carbon backbone of the chain prevents the triglyceride molecules from packing tightly, so they remain liquid (oil) at room temperature, whereas triglycerides with trans double bonds (“trans fats”) have relatively linear fatty acids that are able to pack tightly together at room temperature and form solid fats.

143
Q

Why is trans fat consumption discouraged?

A

In the human diet, trans fats are linked to an increased risk of cardiovascular disease.

144
Q

What are some examples of L- and D- forms of enantiomers?

A

In nature, only the L-forms of amino acids are used to make proteins. Some D forms of amino acids are seen in the cell walls of bacteria, but never in their proteins. Similarly, the D-form of glucose is the main product of photosynthesis and the L-form of the molecule is rarely seen in nature.

145
Q

What are some important functional groups in biological macromolecules?

A

Hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl.

146
Q

How are functional groups classified according to their relationship to water?

A

Functional groups are usually classified as hydrophobic or hydrophilic depending on their charge or polarity characteristics.

147
Q

What is an example of a hydrophobic functional group?

A

The non-polar methane molecule.

148
Q

What is an example of a hydrophilic functional group?

A

The carboxyl group found in amino acids, some amino acid side chains, and the fatty acids that form triglycerides and phospholipids. This carboxyl group ionizes to release hydrogen ions (H+) from the COOH group resulting in the negatively charged COO— group, which contributes to the hydrophilic nature of whatever molecule it is found on. Carbonyl also has a partially negatively charged oxygen atom that may form hydrogen bonds with water molecules, making the molecule more hydrophilic.

149
Q

What are some ways in which hydrogen bonds are important in functional groups?

A

Hydrogen bonds between functional groups (within the same molecule or between different molecules) are important to the function of many macromolecules and help them to fold properly into and maintain the appropriate shape for functioning. Hydrogen bonds are also involved in various recognition processes, such as DNA complementary base pairing and the binding of an enzyme to its substrate.

General Biology (47 decks)

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