Chapter 2 Biology
When acids are added to a solution, the pH should ________. a. decrease b. increase c. stay the same d. cannot tell without testing
decrease
as volume decreases
density decreases, so it doesnt float
structural isomers
differ in the placement of their covalent bonds: both molecules have four carbons and ten hydrogens (C4H10), but the different arrangement of the atoms within the molecules leads to differences in their chemical properties. For example, due to their different chemical properties, 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.
Isotopes
different forms of an element that have the same number of protons but a different number of neutrons. Some elements—such as carbon, potassium, and uranium—have naturally occurring isotopes.
why does the needle float on water?
due to surface tension, surface area increases, so less pressure, and it rises to the top, also hydrogen bonds are stronger at the top.
Principal shell 2n
has one s and one p subshell, and can hold a total of eight electrons. The p subshell has three dumbbell-shaped orbitals, as illustrated in Figure 2.8
Principal shell 1n
has only a single s orbital, which can hold two electrons.
Which type of bond exemplifies a weak chemical bond? a covalent bond b hydrogen bond c ionic bond d nonpolar covalent bond
hydrogen bond
Which type of bond represents a weak chemical bond? hydrogen bond atomic bond covalent bond nonpolar covalent bond
hydrogen bond
neutron
no charge, but contributes to the mass subtracting the number of protons from the mass number
electrons
(-) charge, very small weighing only 9.11 × 10-28 grams, or about 1/1800 of an atomic mass unit. Hence, they do not contribute much to an element's overall atomic mass.
The four elements common to all living organisms
(O), carbon (C), hydrogen (H), and nitrogen (N)
Protons and neutrons mass
1.67 × 10^-24 grams
If xenon has an atomic number of 54 and a mass number of 108, how many neutrons does it have? a. 54 b. 27 c. 100 d. 108
54
atoms are more energetically stable when they have
8 electrons in their valence shell
Use the periodic table to describe what a Bohr model of Fluorine (F) would look like and explain why the Bohr model is not an accurate representation of the electron orbitals in fluorine.
A Bohr model would have 2 electron rings, and a Bohr model would not show the sub-shell of second ring
cohesion
Before it overflows, the water forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-gas (water-air) interface, although there is no more room in the glass.
Why are hydrogen bonds and van der Waals interactions necessary for cells?
Hydrogen bonds and van der Waals interactions form weak associations between molecules, providing the necessary shape and structure of DNA and proteins to function in the body.
Why can some insects walk on water?
Insects can walk on water because of its high surface tension.
What makes ionic bonds different from covalent bonds
Ionic bond involves the transfer of electrons whereas covalent bond involves the sharing of electrons.
K-41 is one of the naturally occurring isotopes of potassium. Use the periodic table to explain how the structure of K-41 differs from the normal K atom.
K-41 has a total of 2222 neutrons and normal K atom has 2020 neutrons
isomers
Molecules that share the same chemical formula but differ in the placement (structure) of their atoms and/or chemical bonds
substituted hydrocarbons
Molecules with other elements in their carbon backbone
anion
Negative ions are formed by gaining electrons
Water takes up 333 million cubic miles on Earth, yet access to drinking water is a critical issue for many communities around the world. Explain why this is so.
Only 4 percent of the total water on earth is freshwater, out of which 68 percent is found in glaciers.
orbital
The area where an electron is most likely to be found
octet rule
The innermost shell has a maximum of two electrons but the next two electron shells can each have a maximum of eight electrons.
dissociation
When ionic compounds are added to water, the individual ions react with the polar regions of the water molecules and their ionic bonds are disrupted. Dissociation occurs when atoms or groups of atoms break off from molecules and form ions. Consider table salt (NaCl, or sodium chloride): when NaCl crystals are added to water, the molecules of NaCl dissociate into Na+ and Cl- ions, and spheres of hydration form around the ions
most stable elements
inert or noble gases
cohesion
intermolecular forces between water molecules caused by the polar nature of water; responsible for surface tension
acid
is a substance that increases the concentration of hydrogen ions (H+) in a solution, usually by having one of its hydrogen atoms dissociate. The stronger the acid, the more readily it donates H+
s subshell
is spherical in shape and has one orbita
when nacl is mixed with h20
spheres of hydration are formed around the ions
Describe the pH scale and how it relates to living systems. Give an example of how drastic pH changes are prevented in living systems
The pH scale ranges from 0 to 14, where anything below 7 is acidic and above 7 is alkaline. The bicarbonate system in the human body buffers the blood.
organic molecules
any carbon-containing liquid, solid, or gas "backbone," of the macromolecules.
Matter
any substance that occupies space and has mass
Enantiomers
are molecules that share the same chemical structure and chemical bonds but differ in the three-dimensional placement of atoms so that they are mirror images
Hydrocarbons
are organic molecules consisting entirely of carbon and hydrogen, such as methane (CH4) described above. We often use hydrocarbons in our daily lives as fuels—like the propane in a gas grill or the butane in a lighter. The many covalent bonds between the atoms in hydrocarbons store a great amount of energy, which is released when these molecules are burned (oxidized).
Elements
are unique forms of matter with specific chemical and physical properties that cannot be broken down into smaller substances by ordinary chemical reactions. There are 118 elements, but only 92 occur naturally. The remaining elements are synthesized in laboratories and are unstable.
Some of the most abundant elements in living organisms
carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus
not true? a Water is polar. b Water stabilizes temperature. c Water is essential for life. d Water is the most abundant molecule in the Earth's atmosphere.
d
the atmosphere rich in vs little of
rich in nitrogen and oxygen but has little carbon and hydrogen
Potassium has an atomic number of 19. What is its electron configuration?
shells 1, 2, and 3 are full and shell 4 has one electron
The Bohr model
shows the atom as a central nucleus containing protons and neutrons, with the electrons in circular orbitals at specific distances from the nucleus
which of the following is not a functional group that can bond with carbon? a. sodium b. hydroxyl c. phosphate d. carbonyl
sodium
Hydrocarbon chains are formed by
successive bonds between carbon atoms and may be branched or unbranched
proton
(+) charge
atom composed of how many regions
2
hydrophilic
A polar substance that interacts readily with or dissolves in water
capillary action
Adhesion is observed when water "climbs" up the tube placed in a glass of water: notice that the water appears to be higher on the sides of the tube than in the middle. This is because the water molecules are attracted to the charged glass walls of the capillary more than they are to each other and therefore adhere to it Capillary action in a glass tube is caused by the adhesive forces exerted by the internal surface of the glass exceeding the cohesive forces between the water molecules themselves.
covalent bonds
Another way the octet rule can be satisfied is by the sharing of electrons between atoms These bonds are stronger and much more common than ionic bonds in the molecules of living organisms. Covalent bonds are commonly found in carbon-based organic molecules, such as our DNA and proteins. Covalent bonds are also found in inorganic molecules like H2O, CO2, and O2. One, two, or three pairs of electrons may be shared, making single, double, and triple bonds, respectively. The more covalent bonds between two atoms, the stronger their connection. Thus, triple bonds are the strongest.
pH scale
Anything below 7.0 (ranging from 0.0 to 6.9) is acidic anything above 7.0 (from 7.1 to 14.0) is alkaline
Discuss how buffers help prevent drastic swings in pH.
Buffers absorb excess hydrogen and hydroxide ions to prevent increases or decrease in pH. An example is the bicarbonate system in human body
So how can organisms whose bodies require a near-neutral pH ingest acidic and basic substances (a human drinking orange juice, for example) and survive?
Buffers readily absorb excess H+ or OH-, keeping the pH of the body carefully maintained in the narrow range required for survival. Maintaining a constant blood pH is critical to a person's well-being. 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, as shown in Figure 2.20, 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. Without this buffer system, the body's pH would fluctuate enough to put survival in jeopardy.
What property of carbon makes it essential for organic life?
Carbon can form up to four covalent bonds, allowing it to form long chains.
How many neutrons do carbon-12 and carbon-13 have, respectively?
Carbon-12 contains 66 neutrons while carbon-13 contains 77 neutrons.
electrolytes
Certain salts are referred to in physiology Certain salts are referred to in physiology
surface tension
Cohesion allows for the development of this the capacity of a substance to withstand being ruptured when placed under tension or stress.
The unique properties of water are important in biological processes. For the following three properties of water, define the property and give one example of how the property affects living organisms: cohesion adhesion high heat of vaporization
Cohesion is the attraction between the water molecules, which helps create surface tension. Insects can walk on water because of cohesion. Adhesion is the attraction between water molecules and other molecules. Water moving up from the roots of plants to the leaves as a result of capillary action is because of adhesion. Heat of vaporization is the amount of energy required to convert liquid into gas. This property helps humans maintain homeostasis of body temperature by evaporation.
Why are cohesive and adhesive forces important for life?
Cohesive and adhesive forces are important for the transport of 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. Without these properties of water, plants would be unable to receive the water and the dissolved minerals they require
carbon dating
Comparing the ratio of the 14C concentration found in an object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined.
One of the risks for people with diabetes is diabetic ketoacidosis, a build-up of acid in the blood stream. Explain why this is dangerous to humans.
Diabetic ketoacidosis decreases normal pH (7.35-7.45) to a lower value.
evaporation
Even when below its boiling point, water's individual molecules acquire enough energy from other water molecules such that some surface water molecules can escape and vaporize
Water's Polarity
One of water's important properties is that it is composed of polar molecules: the hydrogen and oxygen within water molecules (H2O) form polar covalent bonds. While there is no net charge to a water molecule, the polarity of water creates a slightly positive charge on hydrogen and a slightly negative charge on oxygen, contributing to water's properties of attraction. Water's charges are generated because oxygen is more electronegative than hydrogen, making it more likely that a shared electron would be found near the oxygen nucleus than the hydrogen nucleus, thus generating the partial negative charge near the oxygen. Water also attracts or is attracted to other polar molecules and ions
Why was the discovery of penicillin considered an act of serendipity?
Penicillin was discovered by accident while studying the biology of mold.
Compare and contrast saturated and unsaturated triglycerides.
Saturated triglycerides contain single bonds and are solids at room temperature, while unsaturated triglycerides contain double bonds and are liquids at room temperature
Which of the following statements about organic molecules is true? a Structural isomers share a chemical formula but differ in the placement of their covalent bonds. b Geometric isomers have different chemical formulas but similar bond structures. c Functional groups are any group of atoms that contains carbon. d Organic molecules consist of atoms that provide or impart a specific function to a carbon skeleton.
Structural isomers share a chemical formula but differ in the placement of their covalent bonds.
So how do the cells of the stomach survive in such an acidic environment? How do they homeostatically maintain the near neutral pH inside them?
The answer is that they cannot do it 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.
electron transfer
The movement of electrons from one element to another
atomic number
The number of protons determines an element's atomic number and is used to distinguish one element from another
When the temperature of liquid water is reduced, water freezes and becomes less dense. This is a property not seen in most other liquids. Ice floats on liquid water because it is less dense. What molecular property of water allows for this phenomenon?
When water cools, hydrogen bonds between hydrogen atoms push water molecules further apart.
waters specific heat capacity
a property caused by hydrogen bonding among water molecule Water has the highest specific heat capacity of any liquids. Due to its high heat capacity, water is used by warm blooded animals to more evenly disperse heat in their bodies: it acts in a similar manner to a car's cooling system, transporting heat from warm places to cool places, causing the body to maintain a more even temperature.
solvent
a substance capable of dissolving other polar molecules and ionic compounds.
heat of vaporization
also high for water the amount of energy required to change one gram of a liquid substance to a gas. occurs on the surface of water As liquid water heats up, hydrogen bonding makes it difficult to separate the liquid water molecules from each other, which is required for it to enter its gaseous phase (steam). As a result, water acts as a heat sink or heat reservoir and requires much more heat to boil than does a liquid such as ethanol (grain alcohol), whose hydrogen bonding with other ethanol molecules is weaker than water's hydrogen bonding. Eventually, as water reaches its boiling point of 100° Celsius (212° Fahrenheit), the heat is able to break the hydrogen bonds between the water molecules, and the kinetic energy (motion) between the water molecules allows them to escape from the liquid as a gas.
earths crust
although it contains oxygen and a small amount of hydrogen, has little nitrogen and carbon.
van der waals interactions
are weak attractions or interactions between molecules. Van der Waals attractions can occur between any two or more molecules and are dependent on slight fluctuations of the electron densities, which are not always symmetrical around an atom. For these attractions to happen, the molecules need to be very close to one another. These bonds—along with ionic, covalent, and hydrogen bonds—contribute to the three-dimensional structure of the proteins in our cells that is necessary for their proper function.
ion
atom or chemical group that does not contain equal numbers of protons and electrons
Which of the following statements is true? a. Acids and bases cannot mix together. b. Acids and bases will neutralize each other. c. Acids, but not bases, can change the pH of a solution. d. Acids donate hydroxide ions (OH-); bases donate hydrogen ions (H+).
b
A molecule that binds up excess hydrogen ions in a solution is called a(n) ________. a. acid b. isotope c. base d. donator
base
In a solution, what kind of molecule binds up excess hydrogen ions?
base
why do oil molecules float on top of water?
because nonpolar molecules (water polar) and has a lower density
irreversible
can proceed in one direction until the reactants are all used up. The equations that describe these reactions contain a unidirectional arrow
nucleus
center of atom and contains protons and neutrons
1s
closest orbital to the nucleus
aliphatic hydrocarbons
consist of linear chains of carbon atoms
aromatic hydrocarbons
consists of closed rings of carbon atom
compounds
contain atoms of more than one type of element
Each carbon molecule can bond with as many as________ other atom(s) or molecule(s). a. one b. two c. six d. four
d
Nonpolar covalent bonds
form between two atoms of the same element or between different elements that share electrons equally. For example, molecular oxygen (O2) is nonpolar because the electrons will be equally distributed between the two oxygen atoms. Another example of a nonpolar covalent bond is methane (CH4), also shown in Figure 2.12. Carbon has four electrons in its outermost shell and needs four more to fill it. It gets these four from four hydrogen atoms, each atom providing one, making a stable outer shell of eight electrons. Carbon and hydrogen do not have the same electronegativity but are similar; thus, nonpolar bonds form. The hydrogen atoms each need one electron for their outermost shell, which is filled when it contains two electrons. These elements share the electrons equally among the carbons and the hydrogen atoms, creating a nonpolar covalent molecule.
Ionic bonds
formed between ions with opposite charges. For instance, positively charged sodium ions and negatively charged chloride ions bond together to make crystals of sodium chloride, or table salt, creating a crystalline molecule with zero net charge.
Functional groups
groups of atoms that occur within molecules and confer specific chemical properties to those molecules. They are found along the "carbon backbone" of macromolecules. This carbon backbone is formed by chains and/or rings of carbon atoms with the occasional substitution of an element such as nitrogen or oxygen.
Subshells d and f
have more complex shapes and contain five and seven orbitals, respectively
Geometric isomers
have similar placements of their covalent bonds but differ in how these bonds are made to the surrounding atoms, especially in carbon-to-carbon double bonds. In the simple molecule 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 the cis configuration; if they are on opposite sides of the double bond, it is a 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
Specific heat
he amount of heat one gram of a substance must absorb or lose to change its temperature by one degree Celsius. For water, this amount is one calorie. It therefore takes water a long time to heat and long time to cool. In fact, the specific heat capacity of water is about five times more than that of sand.
outermost region of the atom
holds its electrons in orbit around the nucleus,
electron orbital
how electrons are spatially distributed surrounding the nucleus; the area where an electron is most likely to be found
water forms crystals
hydrogen bonding makes ice less dense than liquid water
bonds weaker than covalent and ionic that occur frequently, and life as we know it would not exist without them
hydrogen bonds and van der waals interactions
Atoms that vary in the number of neutrons found in their nuclei are called ________. a. ions b. neutrons c. neutral atoms d. isotopes
isotopes
radioisotopes
isotopes that emit neutrons, protons, and electrons, and attain a more stable atomic configuration (lower level of potential energy)
pH
measures the concentration of hydrogen ions in a given solution
hydrophobic
non-polar molecules such as oils and fats do not interact well with water, as shown in Figure 2.13 and separate from it rather than dissolve in it, as we see in salad dressings containing oil and vinegar (an acidic water solution).
2 regions of the atom
nucleus and outermost region
mass number
number of protons and the number of neutrons
Chemical reactions
occur when two or more atoms bond together to form molecules or when bonded atoms are broken apart. The substances used in the beginning of a chemical reaction are called the reactants (usually found on the left side of a chemical equation), and the substances found at the end of the reaction are known as the products (usually found on the right side of a chemical equation). An arrow is typically drawn between the reactants and products to indicate the direction of the chemical reaction; this direction is not always a "one-way street." For the creation of the water molecule shown above, the chemical equation would be: 2H + O → H2 O
capillary action
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
The strength of different levels of covalent bonding
one of the main reasons living organisms have a difficult time in acquiring nitrogen for use in constructing their molecules, even though molecular nitrogen, N2, is the most abundant gas in the atmosphere
sphere of hydration
or a hydration shell, as illustrated in Figure 2.15 and serves to keep the particles separated or dispersed in the water.
cation
positive ions that are formed by losing electrons
hydrogen bonds
provide many of the critical, life- sustaining properties of water and also stabilize the structures of proteins and DNA, the building block of cells. When polar covalent bonds containing hydrogen form, the hydrogen in that bond has a slightly positive charge because hydrogen's electron is pulled more strongly toward the other element and away from the hydrogen. Because the hydrogen is slightly positive, it will be attracted to neighboring negative charges. When this happens, a weak interaction occurs between the δ+of the hydrogen from one molecule and the δ- charge on the more electronegative atoms of another molecule, usually oxygen or nitrogen, or within the same molecule. This interaction is called a hydrogen bond. This type of bond is common and occurs regularly between water molecules. Individual hydrogen bonds are weak and easily broken; however, they occur in very large numbers in water and in organic polymers, creating a major force in combination. Hydrogen bonds are also responsible for zipping together the DNA double helix.
base
provides either hydroxide ions (OH-) or other negatively charged ions that combine with hydrogen ions, reducing their concentration in the solution and thereby raising the pH. In cases where the base releases hydroxide ions, these ions bind to free hydrogen ions, generating new water molecules.
Reversible Reactions
re those that can go in either direction. In reversible reactions, reactants are turned into products, but when the concentration of product goes beyond a certain threshold (characteristic of the particular reaction), some of these products will be converted back into reactants; at this point, the designations of products and reactants are reversed. This back and forth continues until a certain relative balance between reactants and products occurs—a state called equilibrium. These situations of reversible reactions are often denoted by a chemical equation with a double headed arrow pointing towards both the reactants and products.
surface tension
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
adhesion
the attraction between water molecules and other molecules. This attraction is sometimes stronger than water's cohesive forces, especially when the water is exposed to charged surfaces such as those found on the inside of thin glass tubes known as capillary tubes.
polar covalent bond
the electrons are unequally shared by the atoms and are attracted more to one nucleus than the other. Because of the unequal distribution of electrons between the atoms of different elements, a slightly positive (δ+) or slightly negative (δ-) charge develops. This partial charge is an important property of water and accounts for many of its characteristics. Water is a polar molecule, with the hydrogen atoms acquiring a partial positive charge and the oxygen a partial negative charge. This occurs because the nucleus of the oxygen atom is more attractive to the electrons of the hydrogen atoms than the hydrogen nucleus is to the oxygen's electrons. Thus oxygen has a higher electronegativity than hydrogen and the shared electrons spend more time in the vicinity of the oxygen nucleus than they do near the nucleus of the hydrogen atoms, giving the atoms of oxygen and hydrogen slightly negative and positive charges, respectively. Another way of stating this is that the probability of finding a shared electron near an oxygen nucleus is more likely than finding it near a hydrogen nucleus. Either way, the atom's relative electronegativity contributes to the development of partial charges whenever one element is significantly more electronegative than the other, and the charges generated by these polar bonds may then be used for the formation of hydrogen bonds based on the attraction of opposite partial charges. (Hydrogen bonds, which are discussed in detail below, are weak bonds between slightly positively charged hydrogen atoms to slightly negatively charged atoms in other molecules.) Since macromolecules often have atoms within them that differ in electronegativity, polar bonds are often present in organic molecules.
Under standard conditions, atoms fill
the inner shells first, often resulting in a variable number of electrons in the outermost shell.
atom
the smallest unit of matter that retains all of the chemical properties of an element. For example, one gold atom has all of the properties of gold in that it is a solid metal at room temperature. A gold coin is simply a very large number of gold atoms molded into the shape of a coin and containing small amounts of other elements known as impurities. Gold atoms cannot be broken down into anything smaller while still retaining the properties of gold.
Molecules
two or more atoms chemically bonded together
atomic mass
which is the calculated mean of the mass number for its naturally occurring isotopes
