Quiz 1 Flashcards
Life as we know it is primarily composed of what six elements? List in order of decreasing electronegativity.
O - 3.5
N - 3.0
S - 2.5
C - 2.5
P - 2.2
H - 2.1
List some elements that are commonly present in cells as ions
Ca, K, Cl, Na, Mg
What is unique about carbon and supports its role in biological organisms?
Only carbon can form four highly stable covalent bonds and form covalently linked chains of multiple C-C bonds.
What element forms the skeleton of organic molecules, and list examples of structure
Carbon forms C-C bonds which provide the “skeleton” of biomolecules, in the form of linear chains, branched chains and cyclic structures.
What is the role of functional groups in biomolecules?
Functional groups confer specific chemical properties upon the molecule
Heteronuclear linkage
Linkages consisting of two or more different atoms.
What is a polymer and provided examples
polymer: structure composed of covalently attached repeating chemical units. Examples are amino acids (proteins), nucleotides (nucleic acids), monosaccharides (carbohydrates)
What are the four major classes of biomolecules, and can they all be considered polymers?
Proteins, carbohydrates/polysaccharides, lipids, nucleic acids. All of these are polymers except lipids, which are aggregates.
In what form are monosaccharides found in aqueous solution?
Primarily as cyclic structures, with a hemiacetyl (glucose) or hemiketal (fructose) carbon
Hemiacetal
Hemiacetals are compounds that are derived from aldehydes. The Greek word hèmi means half. These compounds are formed by formal addition of an alcohol to the carbonyl group. In Glucose, an intramolecular OH group reacts with the carbonyl group forming a cyclic hemiacetal.
Hemiketal
Hemiketals are compounds that are derived from ketones. The Greek word hèmi means half. These compounds are formed by formal addition of an alcohol to the carbonyl group. In Fructose, an intramolecular OH group reacts with the carbonyl group forming a cyclic hemiketal.
Polysaccharide
Polysaccharidea are made up of many covalently linked monosaccharide units.
Describe the composition of lipids
Lipids are composed of a polar head group (hydrophilic) and a non-polar tail region (hydrophobic).
Give three types of lipids
fatty acids, triglycerides, phospholipids
Are lipids polymers? Does this mean they are or are not considered macromolecules?
Lipds are not polymers and therefore are not considered macromolecules.
Describe the result of mixing lipids with water
Lipids aggregate when mixed with water (polar), maximizing contact of polar head groups with water.
Compare and contrast micelle lipids with bilayer lipids. Which type are prevalent in membranes?
Bilayer lipids are the basic structural element of biological membranes
List the four main types of noncovalent interactions among biomolecules in aqueous solvent, and if applicable, their strength in kJ/mole from strongest to weakest
Ionic interactions (attraction and replsion) ~75 kJ/mole
Hydrogen bonds (between neutral groups or peptide bonds) ~ 25 kJ/mole
van der Waals interactions ~ 4 kJ/mole
Hydrophobic interactions
What are two types of hydrogen bonds, where do they appear, and their strengths?
Peptide bonds are found between amino acids and contribute to secondary structre. Neurtal bonds are found in many places, including water.
What are two types of ionic interactions, and their strengths?
What is the average strength of a covalent bond? How does this compare to a noncovalent interaction? Explain the role of noncovalent interactions on conformation.
Non-covalent interactions are weak (4 - 75 kJ/mole) compared to covalent interactions (~ 400 kJ/mole).
The cumulative effect of the many weak interactions possible for a large biopolymer (macromolecule) often leads to a stable (native) structure, where the weak binding interactions are maximized.
van der Waals interactions
Weak attraction of the electron cloud (negative charge) of an atom to the nucleus of a neighboring atom (positive charge). van der Waals radii are larger than covalent bond length.
Describe the effect of van der Waals forces acting on two atoms at varying distances
van der Waals forces grow stronger with nearer proximity until being overcome by repulsion of the two similarly charged electron clouds.
Define hydrogen bond distance, and described its relative length compared to standard van der Waals forces.
Hydrogen bond distance is defined as the distance between the donor and acceptor atoms, NOT the hydrogen and acceptor atom. Hydrogen bond lengths are shorter than calculated van der Waals interactions.
Hydrogen bonds are the result of what intramolecular forces?
A hydrogen bond is a combination of electrostatic and van der Waals forces.
Describe the basic role of the three atoms that exist in any given hydrogen bond
Forms between an electronegative atom with a slight negative charge (called the acceptor atom) and a hydrogen with a slight positive charge, by virtue of the hydrogen being covalently bonded to an electronegative atom (called the donor atom).
Can a positively charged nitrogen atom that is bound to a hydrogen atom act as a donor atom in a hydrogen bond?
Yes.
What geometric confirmation confers highest stability in a hydrogen bond?
Hydrogen bonds are strongest when the three atoms involved lie in a straight line. In biomolecules, many times atom positions are constrained, precluding optimal geometry and resulting in weaker hydrogen bonds
Why might a hydrogen bond not be as stable as possible in a biomolecule?
Hydrogen bonds are strongest when the three atoms involved lie in a straight line. In biomolecules, many times atom positions are constrained, precluding optimal geometry and resulting in weaker hydrogen bonds
Hydration
Water molecules cluster around ions and polar groups stabilizing (dissolving) them. This is known as hydration.
How does water affect biomolecules.
Water interacts with biological molecules via hydrogen bonding and electrostatic interations; it also participates in biochemical reactions. The polar character of water makes it an excellent solvent for polar and ionic substances.
pH = ?
pH = log (1/ [H+] ) = log ( 1 ) - log ( [H+] ) = -log ( [H+] )
What is the primary difference between weak and strong acids and bases? Where does this leave biomolecules?
Weak acids and bases do not fully dissociate or protonate in water; biomolecules are weak acids
1 molar (M) indicates what units?
moles / L
[Xx] represents what unit of measurement?
M or moles / L
Define pKa using intuitive techniques
Ka = [H+][A-}/[HA}
pKa = -log (Ka) = -log [H+][A-]/[HA]
When [A-] = [HA], then pKa = -log[H+] = pH
pKa
pKa is the solution pH at which the molar concentrations of the undissociated acid and its conjugate base are equal.
Biological buffers
Consistent pH is maintained by biological buffers, which are a mixture of weak acids and their conjugate bases.
What is the role of biological buffers and how do they work?
Cells and organisms must maintain specific pH, which is usually near pH 7, keeping biomolecules in an optimal ionic state. Consistent pH is maintained by biological buffers, which are a mixture of weak acids and their conjugate bases. Buffers resist pH changes when the solution pH is close to the pKa for the conjugate acid-base pair
Describe the general rule of thumb for a weak acid or weak base in a biological system
+/- 1 pKa unit; then the acid (base) is 10% or 90% ionized/un-ionized
+/- 0.5 pKa unit; then the acid (base) is 25% or 75% ionized/un-ionized
+/- 0.3 pKa unit; then the acid (base) is 33% or 67% ionized/un-ionized
= to the pKa; then the acid (base) is 50% ionized/un-ionized
Describe the role of a charged side chains in differing pHs
The side-chain of acidic amino acids can give up a proton (H+) to become negatively charged.
• The side-chain of basic amino acids can take up an extra proton to become positively charged. Histidine is only weakly basic at neutral pH (pH 7), as only some of the side-chains have taken up a proton (about 10%)
List amino acids with positively charged side chains. Are these considered acidic or basic amino acids?
Basic
List amino acids with negatively charged side chains. Are these considered acidic or basic amino acids?
Acidic
