Atoms and Bonds Flashcards
Describe the fundamental principle of the formation of covalent bonds.
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.
How much energy is needed to break a single covalent bond?
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.
Contrast single covalent bonds with double and triple covalent bonds.
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.
Explain how electronegativity impacts the structure of a molecule.
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.
Among the atoms most commonly present in biological molecules, which two are the most electronegative?
Oxygen and nitrogen.
Define polarization.
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.
Describe how sodium and chlorine become charged ions.
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.
Define noncovalent bonds
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.
How strong are noncovalent bonds?
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.
Define ionic bond.
An ionic bond (also called a salt bridge) is made when an electrostatic attraction between a positively and negatively charged atom occurs.
Why aren’t ionic bonds between free ions of much important in relation to cellular biology?
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.
Give an example of a weak ionic bond between oppositely charged groups of large molecules that is of importance.
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.
How does a hydrogen bond occur?
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.
Where do hydrogen bonds most commonly occur?
Hydrogen bonds are most common among polar molecules and are important in determining the properties and structure of water.
How strong are hydrogen bonds?
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.
Describe a hydrophobic interaction.
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.
Explain how a van der Waals force occurs.
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.
How strong are van der Waals forces?
It requires about 0.1-0.3 kcal/mole to break.
Name the three essential properties of water.
- Water is a highly asymmetric molecule with the O atom at one end and the two H atoms at the opposite end.
- Each of the two covalent bonds in the molecule is highly polarized.
- All three atoms in a water molecule are adept at forming hydrogen bonds.
How many hydrogen bonds can one molecule of water form?
Each molecule of water can form hydrogen bonds with four other water molecules.
How does hydrogen bonding impact the thermal properties of water?
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.
Name the essential functions of water within a cell.
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.
Describe the dissociation of acetic acid.
Acetic acid breaks down into the acetate ion and a proton/hydrogen ion.
Define base.
Any molecule capable of accepting a proton.
