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Terms in this set (49)
Describe the various types of isomers that account for the diversity of biomolecules
- Position Isomerism (aldehyde and ketone group positions in sugars)
- Geometric Isomerism (cis and trans configurations of various bonds in biomolecules)
- Stereo Isomerism (L- and D- configurations of biomolecules)
Name the major classes of biological macromolecules and its chemical unit that make up each
- Nucleotides: DNA/RNA
- Amino acids: Proteins
- Monosaccharides: Polysaccharides
What is conformation?
Conformations are the 3-D arrangements achieved by rotation around bonds forming a macromolecular chain.
What is native structure?
The native structure of a macromolecule is the conformation which has the maximum stability & lowest energy.
What is denaturation?
Denaturation is the process of a macromolecule unfolding from its native conformation to a random coil; this usually requires energy.
What is spontaneous folding?
Spontaneous folding or "self-assembly" is the process of macromolecular folding from a random coil to its native conformation; this releases energy.
What are three functions of amino acids?
- Intermediates in metabolism
- Protein building blocks
- Precursors of nucleotides, vitamins, hormones, etc
Name the four general classes of amino acids found in proteins and give an example of each.
- Non Polar (ala, val, leu, ile, pro, gly, phe, trp, met)
- Polar uncharged (ser, thr, cys, asn, gln, tyr)
- Acidic (glu, asp)
- Basic (arg, lys, his)
Which amino acids contain a positively charged side chain at physiological pH (7.2)?
Basic amino acids have positively charged side chains at physiological pH (arg, lys & his)
Which amino acids contain a negatively charged side chain?
Acidic amino acids have negatively charged side chains at physiological pH (glu & asp)
Which amino acids contain an alcohol group?
Ser and thr have alcohol groups on their side chains
Which amino acids contain an amide group?
Gln and asn have amide groups on their side chains
(Lysine has an amino group, and Arginine has two primary amines and one secondary amine on their side chains)
Which amino acids contain a sulfur atom?
Met and cys have sulfur atoms in their side chains
What sets of non-polar amino acids are homologous?
Polar uncharged amino acids are homologous?
Polar charged amino acids are homologous?
Describe the difference between conformers and isomers
- Isomers have the same chemical formula but different arrangement of atoms in space
- Confomers have the same chemical formula but differ at the rotation around bonds
How many chiral carbons do most amino acids found in proteins contain?
Usually only the alpha carbon is chiral, but glycine has no chiral carbons
Which amino acids found in proteins contain an additional chiral carbon?
Threonine and isoleucine both have two chiral centers.
How do the chemical properties of an L- and its corresponding D- amino acid differ?
Since most amino acids have one chiral carbon, L and D forms are mirror images of one another and thus have identical chemical properties.
How do L- & D- amino acids biological properties differ? Explain.
Only L amino acids however, have biological relevance in proteins.
How do the biological properties differ?
Answer the same question for L-threonine and L-allo-threonine, which differ only by the configuration around the side chain chiral carbon.
In the case of amino acids with 2 chiral carbons such as threonine, there are four possible isomers, two of which are mirror images (enantiomers) and two of which are not (diasteriomers). L and D threonine are mirror images and exhibit the same chemical properties, as do L-allo and D-allo threonine. L and L-allo however, are non-mirror images and have different chemical properties. of the four isomers, only L-threonine is of biological relevance in proteins
What is special about proline?
The side chain of proline has two bonds with the backbone, one with the alpha carbon and one with the nitrogen.
What effect will proline have when incorporated into a polypeptide?
Proline has limited rotation due to the two bonds and therefore is known as a helix breaker since it cannot be part of an alpha helix.
Using your chemical insight and your knowledge of the amino acid side chains, suggest pairs of amino acid side chains that might participate in hydrogen bonds
All nonpolar amino acids can participate in hydrophobic interactions. These include trp, phe, leu, ile, ala, val, gly, pro, and met (even though this is listed as polar uncharged it is often found in hydrophobic environments and considered in this category).
Using your chemical insight and your knowledge of the amino acid side chains, suggest pairs of amino acid side chains that might participate in electrostatic interactions
Charged electrostatic possibilities are: asp, glu, lys, arg, and his. The positively charged side chains (arg, lys, his) can form electrostatic interactions with the negatively charged side chains (asp, glu).
Using your chemical insight and your knowledge of the amino acid side chains, suggest pairs of amino acid side chains that might participate in hydrophobic interactions.
Hydrogen bond possibilities are all the amino acids that can participate in charged electrostatic interactions, as well as all side chains that have a hydrogen that can participate in a hydrogen bond (ser, thr, asn, gln, cys, tyr and trp) or an acceptor nitrogen or oxygen (all just mentioned except trp). These amino acids can also participate in dipole-dipole electrostatic interactions.
Discuss the potential contributions to hydrophobic and Van der Waals interactions, and ionic and hydrogen bonds for the side chains of Asp in a protein.
Asp: The ionizable carboxyl can participate in ionic and hydrogen bonds. Hydrophobic and van der Waals interactions are negligible.
Discuss the potential contributions to hydrophobic and Van der Waals interactions, and ionic and hydrogen bonds for the side chains of Leu in a protein.
Leu: The leucine side chain does not participate in hydrogen bonds or ionic bonds, but it will participate in hydrophobic and van der Waals interactions.
Discuss the potential contributions to hydrophobic and Van der Waals interactions, and ionic and hydrogen bonds for the side chains of Tyr in a protein.
Tyr: The phenolic hydroxyl of tyrosine, with a relatively high pKa, will participate in ionic bonds only at high pH but can both donate and accept hydrogen bonds. Uncharged tyrosine is capable of hydrophobic interactions. The relatively large size of the tyrosine side chain will permit substantial van der Waals interactions.
Discuss the potential contributions to hydrophobic and Van der Waals interactions, and ionic and hydrogen bonds for the side chains of His in a protein.
His: The imidazole side chain of histidine can act as both an acceptor and donor of hydrogen bonds and, when protonated, can participate in ionic bonds. Van der Waals interactions are expected, but hydrophobic interactions are less likely in most cases.
What is the isoelectric point of an amino acid or a protein?
Isoelectric point: pH at which an amino acid or peptide has no net charge.
What is the dominant ionic form of an amino acid at its pI and what is the charge of this form?
The dominant ionic form at pI is the zwitterion, which has both positively and negatively charged groups.
How does the pH of a solution affect the solubility of an amino acid
pH affects the solubility of an amino acid because the charge of different atoms on amino acids change with pH, based on the pKa of each group that is capable of gaining or losing protons. These changes in charge can lead to increased attractive or repulsive interactions, which affect solubility.
Which of the following are acids: zwitterionic glycine, glycine with a net +1 charge, glycine with a net -1 charge?
Acids are proton donors. +1 charge glycine has an extra hydrogen on the carboxyl group, so it is an acid. The glycine zwitterion has a net neutral charge but CAN donate a hydrogen from the amine group, so it is also an acid. -1 charge glycine has no extra hydrogens, so it is not an acid.
+1 charged glycine = +H3N-CH2-COOH (Very low pH) zwitterionic glycine = +H3N-CH2-COO- (Physiological pH)
-1 charged glycine = H2N-CH2-COO- (High pH)
A peptide has one amino group with a pKa = 12 and eleven carboxylic acid groups, all with a pKa of 3. What is the isoelectric point (pI) of this peptide?
We want the pI or the pH with no net charge. Since we have potentially 1 positive charge and 11 negative charges we have to find the pH at which the positive is balanced by each COOH group contributing 1/11th of a negative charge, or a ratio for each COO-: COOH group of 1:10. This must be below pH 3.0, the pK of all the COOH groups.
Using the Henderson-Hasselbalch equation pH = 3.0 + log(1/10) = 3 - 1 = 2.
How many different conformations are possible for a macromolecule made up of 6 chemical units, each that can exist in two different conformations (e.g., by 180 degree bond rotation)?
From lecture, with four possible combinations it was 24 so with 6 possible combinations, it's 26, or 64. However, half the combinations will just be upside down versions of each other, so only 32 will be unique.
In principle, how many total conformations are possible if the units can rotate through any bond angle?
If every angle of rotation is taken into account, then the total conformations are infinite because if you change one component by one degree you have a different combination and on and on and on
What is the most stable form of a macromolecule called?
The most stable form is called the native form.
What does denaturation of a macromolecule mean?
Denaturation is the unfolding of the native form of a compound to its elongated form.
If a particular polypeptide that is very compact in 0.01 M NaCl expands considerably in 0.5 M NaCl, what forces are probably important in determining its overall size and shape?
An increase in the NaCl concentration will increase the number of sodium and chloride ions in solution. Remember that these are charged ions that participate in electrostatic interactions. This would allow charged molecules in solution instead of other molecules within the polypeptide. So if the polypeptide unfolds its probably held together by electrostatic interactions
What kinds of interactions or bonds are responsible for primary structure?
Covalent bonds between amino acids.
What kinds of interactions or bonds are responsible for secondary structure?
H bond interaction between backbone atoms α-helix and β-pleated sheet.
What kinds of interactions or bonds are responsible for tertiary structure?
Tertiary Structure: 3D structure, long range interaction between secondary structures. Hydrophobic interactions, hydrogen bonding, electrostatic interaction, and covalent (disulfide) bond formation.
What kinds of interactions or bonds are responsible for quaternary structure?
Quaternary Structure: same forces that work in tertiary structure.
(In your lecture notes it says that disulfide bonds are part of primary rather than tertiary structure. The primary structure is the completely unfolded form of the polypeptide therefore although the bonds are described in the primary structure the bonds are not actually formed until the protein folds into the tertiary structure.)
What is an amphipathic helix?
An amphipathic helix is an alpha helix that has one side that is hydrophobic and one side that is hydrophilic when you look down the helix.
How would an amphipathic helix orient its tertiary structure?
It would orient itself so that only the hydrophilic side would be exposed the water and it would bury the hydrophobic side.
Two polypeptides A and B, have similar tertiary structures, but A normally exists as a monomer, whereas B exists as a tetramer, B4. What differences might be expected in the amino acid composition of A versus B?
The surface of A would be hydrophilic since it would be exposed on all sides to water (unless it is a membrane protein). Polypeptide A would have polar amino acids exposed at its surface. The surface of B would be hydrophobic in patches where it would make contact with other B peptides. Polypeptide B would have non-polar amino acids in the patches where it contacts the other B peptides and polar amino acids where it contacts water.
Given two globular proteins (approximately spherical in shape), one that is very large (MW ~ 500,000) and one that is small (MW ~15,000), which would you predict would have a higher ratio of hydrophobic to polar or charged amino acids? Explain.
The 500,000 protein would have a higher ratio of hydrophobic amino acids because it would be a bigger protein and therefore have more buried hydrophobic side chains. Think about surface to volume ratio.
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