Atoms and Bonds

Question 1

Describe the fundamental principle of the formation of covalent bonds.

Answer 1

Covalent bonds are formed when pairs of electrons are shared between pairs of atoms. The fundamental principle of this formation is that an atom is most stable when its outermost shell is filled with electrons. The number of bonds an atom is able to form is dependent on the number of atoms in its outermost shell.

Question 2

How much energy is needed to break a single covalent bond?

Answer 2

The amount is quite large–about 80-100 kilocalories per mole of molecules. This means molecules with covalent bonds are usually stable under most conditions.

Question 3

Contrast single covalent bonds with double and triple covalent bonds.

Answer 3

In a single bond, one pair of electrons is shared between two atoms. In a double, that number rises to two pairs, and in a triple, three. Because of this, while the atoms in a molecule with single bonds are free to rotate, those in a double or triple bond are unable to do so.

Question 4

Explain how electronegativity impacts the structure of a molecule.

Answer 4

When a molecule is composed of atoms of the same element, it has no electronegativity, meaning the electrons are shared equally between the atoms. When two unequal atoms are bonded, however, the more positively charged nucleus of one atom exerts a greater attractive force on the outer electrons than the other. This is called the electronegative atom.

Question 5

Among the atoms most commonly present in biological molecules, which two are the most electronegative?

Answer 5

Oxygen and nitrogen.

Question 6

Define polarization.

Answer 6

Polarization of a molecule occurs when one atom exerts more attraction on the shared electrons in the covalent bond than the other. This causes the more electronegative atom to have a negative charge and the other atoms a positive charge.

Question 7

Describe how sodium and chlorine become charged ions.

Answer 7

The single electron in the outer shell of each sodium atom migrates to the outer shell of a chlorine atom. Thus, the sodium atoms have a positive charge (called a cation) and the chlorine atoms have a negative charge (called an anion) and a filled outer shell.

Question 8

Define noncovalent bonds

Answer 8

Noncovalent bonds do not depend on shared electrons; rather, they rely on attractive forces between atoms of the opposite charge. Noncovalent bonds mediate much of the dynamics of the molecules of the cell.

Question 9

How strong are noncovalent bonds?

Answer 9

Noncovalent bonds are easily broken, requiring only about 1-5 kcal/mole to break. However, though they are weak individually, when applied in concert, noncovalent bonds have much more strength (such as the attractive forces in DNA or between different parts of a large protein.

Question 10

Define ionic bond.

Answer 10

An ionic bond (also called a salt bridge) is made when an electrostatic attraction between a positively and negatively charged atom occurs.

Question 11

Why aren’t ionic bonds between free ions of much important in relation to cellular biology?

Answer 11

When free ions are surrounded by water, the forces of the polar water molecules inhibit the ions to the extent that they cannot approach each other sufficiently to bond. Because cells are so water-dense, bonds between free ions are rare.

Question 12

Give an example of a weak ionic bond between oppositely charged groups of large molecules that is of importance.

Answer 12

When negatively charged phosphate atoms in a DNA molecule and associated with positively charged groups on the surface of a protein, ionic bonds can bind them together.

Question 13

How does a hydrogen bond occur?

Answer 13

Hydrogen is not very electronegative. Therefore, when it is bonded to highly electronegative atoms such as N or O, it is left with a slight positive charge. This charge is attracted to the cluster of shared electrons with a slight negative charge. As a result, the bare positive charge can approach the negative charge and form an association.

Question 14

Where do hydrogen bonds most commonly occur?

Answer 14

Hydrogen bonds are most common among polar molecules and are important in determining the properties and structure of water.

Question 15

How strong are hydrogen bonds?

Answer 15

Hydrogen bonds are rather weak (though when added they can provide stability to molecules such as DNA). It requires about 2-5 kcal/mole to break a hydrogen bond. This allows enzymes access to the DNA molecule if necessary.

Question 16

Describe a hydrophobic interaction.

Answer 16

When nonpolar molecules (such as lipids) are forced into a solution of polar molecules (such as water), the molecules are forced into aggregates. This is the reason that nonpolar molecules cluster in the center of proteins, where polar activity is low.

Question 17

Explain how a van der Waals force occurs.

Answer 17

In any given molecule, even if the electrons are shared equally (as in a nonpolar molecule), electrons may be clustered on one side at any given moment. Sometimes when two nonpolar molecules are next to one another and their electrons are positioned just right (this circumstance is called a transitory dipole, they may form a noncovalent bond called a van der Waal force.

Question 18

How strong are van der Waals forces?

Answer 18

It requires about 0.1-0.3 kcal/mole to break.

Question 19

Name the three essential properties of water.

Answer 19

1. Water is a highly asymmetric molecule with the O atom at one end and the two H atoms at the opposite end.
2. Each of the two covalent bonds in the molecule is highly polarized.
3. All three atoms in a water molecule are adept at forming hydrogen bonds.

Question 20

How many hydrogen bonds can one molecule of water form?

Answer 20

Each molecule of water can form hydrogen bonds with four other water molecules.

Question 21

How does hydrogen bonding impact the thermal properties of water?

Answer 21

When water is heated, that energy goes into breaking the hydrogen bonds, not increasing the movement of the molecules. It takes an extensive amount of energy to convert water to steam because of hydrogen bonds.

Question 22

Name the essential functions of water within a cell.

Answer 22

Water acts as a solvent; it acts as the fluid matrix around which the insoluble membrane of the cell is constructed; it is the medium through which the components of the cell move; it is a reactant and product; it forms a shell around ions in the cell; it forms hydrogen bonds with organic molecules with polar groups; it maintains the structure and function of macromolecules and the complexes they form.

Question 23

Describe the dissociation of acetic acid.

Answer 23

Acetic acid breaks down into the acetate ion and a proton/hydrogen ion.

Question 24

Define base.

Answer 24

Any molecule capable of accepting a proton.

Question 25

Define acid.

Answer 25

Any molecule capable of donating a proton.

Question 26

Define conjugate base.

Answer 26

A conjugate base is an acid that has given up a proton and has become a base.

Question 27

Define conjugate acid.

Answer 27

A conjugate acid is a base that has accepted a proton and become an acid.

Question 28

Define amphoteric molecule.

Answer 28

A molecule that can serve as either an acid or a base.

Question 29

How is the acidity of a solution measured?

Answer 29

It is measured by the amount of hydrogen ions and expressed in terms of pH.

Question 30

Describe the relationship between one pH unit and H+ concentration.

Answer 30

An increase in one pH unit corresponds to a tenfold decrease in H+ concentration.

Question 31

Define buffers.

Answer 31

Buffers are compounds that react with free hydrogen or hydroxyl ions to resist changes in pH. Buffer solutions usually contain a weak acid with its conjugate base.

Question 32

Define biochemicals.

Answer 32

Biochemicals are compounds produced by living organisms.

Question 33

What qualities of carbon make it so well suited for the chemistry of life?

Answer 33

Carbon, having four electrons in its outermost shell, is able to bond with four other molecules. Carbon bonds well to other carbon atoms, meaning it can form long chains of carbon molecules. While silicon is too large of an atom to sufficiently attract electrons in its outermost shell, carbon is of the right size to do so.

Question 34

Define functional groups.

Answer 34

Functional groups are particular groupings of atoms that often behave as a unit and give organic molecules their physical properties, chemical reactivity, and solubility in aqueous solutions.

Question 35

Define macromolecules.

Answer 35

These are the large molecules that form the structure and perform the functions of the cell. They may contain anywhere from dozens to millions of carbon atoms.

Question 36

What are the four major categories of macromolecules?

Answer 36

1. Proteins
2. Nucleic acids
3. Polysaccharides
4. Certain lipids

Question 37

How are polymers made?

Answer 37

Polymers are composed of a large number of low-molecular-weight monomers through the process of polymerization.

Question 38

What are the precursors of the macromolecule groups?

Answer 38

Sugars -> polysaccharides; amino acids -> proteins; nucleotides -> nucleic acids; fatty acids -> lipids.

Question 39

Define metabolic pathway.

Answer 39

In the cell, molecules have complex chemical structures and must be synthesized. Each series of chemical reactions is termed a metabolic pathway.

Question 40

Define metabolic intermediates.

Answer 40

The compounds made along the way of the metabolic pathway that do not always have a specific function.

Question 41

Give some examples of molecules of miscellaneous function in the cell.

Answer 41

Vitamins; certain steroid or amino acid hormones; molecules involved in energy storage such as ATP; regulatory molecules such as cyclic AMP; and metabolic waste products such as urea.