Bonds, Water, & the Henderson-Haselbalch equation Flashcards
What are the four primary biomolecules that make up all living organisms?
- Nucleic acids
- Proteins
- Lipids
- Carbohydrates (Sugars)
What are the primary biomolecules of living systems composed of?
The biomolecules of living systems are primarily composed of polymers of smaller compounds.
Nucleic acids - Sugar (Ribose or deoxyribose), PO4, and a nitrogoneous base
Proteins - Amino acids
Lipids - Fatty acids and glycerols
Carbohydrates - Simple sugars (monosaccharides)
What are the interactions between biomolecules based on?
The formation of and breaking of chemical bonds.
Describe covalent bonds.
- Covalent bonds are the strongest bonds in nature and involve the sharing of a pair electrons between adjacent atoms.
- The formation and breaking of covalent bonds requires a significant amount of energy.
- Because covalent bonds are not readily broken, they are not typically found in biological systems.
What kinds of bonds are used in biological systems?
- Non-covalent bonds are found in biological systems. These are weaker than covalent bonds and are readily reversible.
- Although non-covalent bonds are weaker than covalent bonds, they are numerous in biological systems and they are usually found in large numbers in biomolecules. Their accumulated strength allows biomolecules to assume their many conformations.
How do the four major non-covalent bonds differ?
The non-covalent bonds differ in respect to their length, strength, specificity, and response to water.
What are electrostatic interactions?
Electrostatic interactions occur between two atoms that have opposite electrical charges (Interactions between cations & anions). Electrostatic interactions can be either attractive or repulsive, depending on the charges of the interacting species. Electrostatic interactions can be very strong, and fall off slowly with distance (1/r); the distance between atoms helps to determine the energy of the attraction.
What is a hydrogen bond?
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A hydrogen bond is the electromagnetic attractive interaction between polar molecules in which hydrogen (H) is bound to a electronegative atom, such as nitrogen (N), oxygen (O) or fluorine (F).
Strong hydrogen bonds of 20-40 kcal/mol are generally formed between charged donors and acceptors. Weak hydrogen bonds of 1-5 kcal/mol are formed with carbon as the proton donor.
What are van der Waals interactions?
Van der Waals forces include attractions and repulsions between atoms, molecules, and surfaces, as well as other intermolecular forces. They differ from covalent and ionic bonding in that they are caused by the fluctuating polarizations (charges) of nearby particles
What are dipole-dipole interactions?
Dipole-dipole forces are attractive forces between the positive end of one polar molecule and the negative end of another polar molecule. Dipole-dipole forces have strengths that range from 5 kJ to 20 kJ per mole. They are much weaker than ionic or covalent bonds and have a significant effect only when the molecules involved are close together (touching or almost touching).
What is a dipole induced dipole reaction?
Induced dipole forces result when an ion or a dipole induces a dipole in an atom or a molecule with no dipole. These are weak forces.
What are hydrophobic interactions?
- The interactions between water and nonpolar molecules are called hydrophobic interactions.
- The interactions between nonpolar molecules and water molecules are not favorable due to the inability of nonpolar molecules to form hydrogen bonding or electrostatic interactions. When nonpolar molecules are introduced to water, the water molecules will initially surround the nonpolar molecules, forming a “cage” around the molecules. However, the tendency of nonpolar molecules to associate with one another will draw the nonpolar molecules together, forming a nonpolar aggregate.
- Based on the 2nd law of thermodynamics, the total entropy of the system plus its surrounding must always be increasing. Therefore, it is favorable for the nonpolar molecules to associate without the interference of water. The water molecules that initially “caged” the nonpolar molecules are released from the nonpolar molecules’ surfaces, creating an increase in entropy in the surrounding.
Why is water important to biological systems?
The importance of water comes from its molecular structure. Because it is a polar covalent molecule, it has a slight positive and slight negative charge on opposite ends. First, notice the location of the slight positive and negative ends. Second, observe that water is a bent molecule, not linear or straight.
Because water is a bent, partially polar molecule, it possesses the following biologically important characteristics of what is formed by the joining of many water molecule:
- Polarity
- Hydrogen bonding
- Cohesion
- Surface tension
What does polarity mean? How is polarity useful in relating water’s functions to biological systems?
Polarity means that a molecule has both positively and negatively charged ends. In the context of water, its polarity is what is responsible for dissolving polar molecules, such as sugars and ionic compounds such as salt.
What does hydrogen bonding in water allow it to do?
When water molecules align with each other, a weak bond is established between the negatively charged oxygen atom of one water molecule and the positively charged hydrogen atoms of a neighboring water molecule. Hydrogen bonds give water molecules the characteristics of: cohesion and surface tension.
What is the pKa scale for acidity and bascicity of a compound? How does it relate to pH?
The lower the pKa of a substance, the more acidic (stronger acid) it will be. The higher the pKa of a substance, the more basic (stronger base) it will be.
