Reading...
Play button
Play button
Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
39 Cards in this Set
- Front
- Back
|
Give the names of all the noncovalent interactions you know
|
-Ionic interaction
-dipole interaction including charge-dipole, dipole-dipole, dipole-induced dipole, charge-induced dipole, Hydrogen-bonding, van der Waal’s, and hydrophobic interaction. |
|
|
What determines the strength of an ionic interaction?
|
Size of the charges, distance between the charges, and the dielectric constant of the medium
|
|
|
Is ionic interaction directional?
|
no
|
|
|
Explain why an ionic interaction is much stronger in a nonpolar environment, such as inside a globular protein, than in a polar environment, such as on the surface of a protein in aqueous medium?
|
In a polar environment, polar molecules and other ions compete with the interaction between the charges, thereby reducing the effective charge on the ions and thus reducing the interaction between the two charges. In a noncovalent environment, the two ions interact with the full charge on them and therefore the interaction is stronger than in polar environment.
|
|
|
Give an example of a molecule that has a net permanent dipole.
|
NH3
|
|
|
Give an example of a molecule that has polar bonds but the molecule has no net dipole.
|
CO2
|
|
|
Is charge-dipole interaction directional? Use a specific example to support your conclusion.
|
Yes
C=O Mg2+ vs. Mg2+ C=O The former is favorable and the latter is unfavorable interaction (as the positive charge on the magnesium ion is right next to the positive side of the dipole on CO) |
|
|
What does short-range and long-range interaction mean?
|
The strength of short-range interaction diminishes much faster with the increase of distance between interacting partners than long-range interaction does.
|
|
|
Among the noncovalent interactions that are introduced in class, which one is the longest-range interaction and which one is the shortest range interaction?
|
Longest range: Ionic interaction
Shortest range: Van Der Waals |
|
|
What does a space filling model mean?
|
It is a three dimensional model of a molecule in which each atom is represented by a sphere whose radius is equal to the van der Waal’s radius of the atom.
|
|
|
Give one specific example of a hydrogen bond.
|
N-H ------- O=C-
|
|
|
Explain in detail why benzene is not mixable with water (do not just say benzene is hydrophobic).
|
In benzene, the C-H bond is nonpolar and the whole molecule is nonpolar. Benzene is therefore incapable of forming polar interaction or hydrogen bonding interaction. However, water molecules form both polar interaction and hydrogen bonding. If benzene is exposed to water, water molecules lose the favorable interactions among themselves. They also lose some entropy by becoming more ordered in an effort to maximize the favorable interactions among themselves. Both aspects are energy costly and thus benzene prefer to stay together and away from water to avoid the energy penalty.
|
|
|
Among the acids given below, which is the strongest and which is the weakest acid? H2PO4- (pKa 6.9), TrisHCl (pKa = 8.0), CH3COOH (pKa = 4.74).
|
Strongest: CH3COOH (pKa = 4.74)
Weakest: TrisHCl (pKa = 8.0) |
|
|
If you are to prepare a buffer of pH 7.4, which buffer system will you choose between H2PO4- (pKa 6.9), TrisHCl (pKa = 8.0), CH3COOH (pKa = 4.74)? The given chemical formulas are for the acid form; write also the base form when you give the buffer system (example: CH3COOH/ CH3COO-).
|
Choose a buffer with a pKa that is the closest to the desired pH. In this question, the answer is H2PO4- (pKa 6.9) as the difference is 0.5. TrisHCl (pKa = 8.0) is the next choice as the difference is 0.6.
|
|
|
If you are to prepare buffers with each of the buffer systems [H2PO4- (pKa 6.9), TrisHCl (pKa = 8.0), CH3COOH (pKa = 4.74)], in what pH ranges are each buffer system good for?
|
5.9-7.9; 7-9; 3.74-5.74
|
|
|
If you are to make 1 L 0.1 M H2PO4- / HPO42- (H2PO4- / HPO42- refers to the buffer components, not ratio of the two) buffer at pH 6.9 and you start with the NaH2PO4, how many grams of NaH2PO4 is needed? Do you then add HCl or NaOH to make the final buffer and how many moles of HCl or NaOH do you need to add? MW for NaH2PO4 is 120. H2PO4- (pKa 6.9)
|
When we say “make 1 L of a 0.1M buffer”, the 0.1M refers to the total concentration of the weak acid H2PO4- and its conjugate base HPO42-. Since this question implies that we are making the buffer with only the weak acid component, we need to make sure the concentration of the weak acid (H2PO4- ) is 0.1M. So, 0.1M x 1L = 0.1 mol NaH2PO4 , which is 0.1 molx120g/mol = 12 g NaH2PO4. In order for the buffer to reach the desired pH 6.9, you need the presence of the conjugate base (HPO42- ) and this can be accomplished by adding strong base NaOH to convert some of the H2PO4- into HPO42- . NaOH (or OH-, a strong base) reacts completely with H2PO4- (even though (H2PO4- ) is a weak acid. The amount of NAOH to be added should be equal to the amount of HPO42- to be present at pH 6.9. So, let’s determine the amount of HPO42-. pH=pKa +log [A-]/[HA], pH=6.9 and pKa=6.9, therefore, [A-]/[HA] = 1/1. Since [A-] + [HA] = 0.1 M, [A-] thus is 0.05M, which corresponds to 0.05 mol of HPO42- (1Lx0.05 M= 0.05 mol).
|
|
|
What are the major buffer components in human blood?
|
HCO3-, H2CO3, CO2
|
|
|
What are the major buffer components in the cytoplasm?
|
H2PO4- / HPO42-
|
|
|
When a person hyperventilates, which component of this buffer system changes in concentration? As a result, will pH of the blood increase or decrease? In several cases, does it lead to respiratory acidosis or alkalosis?
|
When a person hyperventilates, CO2 level in the blood drops and therefore leads to lowered acid H2CO3 concentration and thus higher pH (according to Henderson-Hasselbach equation) and thus alkalosis.
|
|
|
What does it mean to say that Lysine and Argine are basic amino acids?
|
? It means they are capable of receive a protein H+ and their solution (just the side chain part) is will have a pH above 7.
|
|
|
What does it mean to say that the R groups of Asp (D) and Glu (E) are acidic?
|
It means that they are capable of donating a H+ and their side chain will have a pH below 7.
|
|
|
Which is the only amino acid that can be a buffer near physiological pH (range 6.9-7.4)?
|
His as the pKa of the side chain of His is 6.0, within the range of (6.9-7.4)+/- 1
|
|
|
The isoelectric point of Glycine is 5.97. What is the net charge at pH 5.97? 4? 6? 8? 12?
In what pH range will glycine be a zwitterion? |
0, 0, 0, 0, -1
Zwitterion between pH of 3.3-8.6 |
|
|
The side chain of Lysine has a pKa of 10.53. In what pH ranges will the side chain be neutral? In what pH range will it be positively charge?
|
When amine is not promoted, it is neutral and so at pH equal or above 11.5 it will be neutral.
It will be positively charged equal or below 9.5. |
|
|
What does the Ramachandran plot show?
|
Allowed phi and psi torsion angles for amino acids in various secondary structures.
|
|
|
If the torsion angles of all amino acids in a protein are defined, is the three-dimensional structure of the polypeptide backbone defined? Why?
|
Yes
|
|
|
Why can Glycine have torsion angle values that are not possible for other amino acids?
|
Its side chain is only a H, very small compared to other side chains and therefore can assume more conformation than all the other amino acids.
|
|
|
Describe an alpha helix including the following specifics:
a. Number of amino acid residues per turn b. Rise per residue and per tern. c. Handedness |
3.6 residues per turn, 1.5 A per amino acid and 5.4 A per turn
In naturally occurring proteins, alpha helices are all right handed |
|
|
Describe and alpha helix including the following specifics:
d. Stabilizing interactions e. Location of side chains f. Hydrogen bonding pattern |
d. Stabilizing interactions: intrachain H-bonding between main chain N-H and main chain C=O; helix dipole with appropriate charges; van der Waal’s interaction within the helix backbone; interactions between different R groups (ionic, H-bonding, hydrophobic, van der Waal’s).
e. Location of side chains: pointing outward from the helix axis f. Hydrogen bonding pattern (show on an extended polypeptide structure) C=O of the nth residue with N-H of the n+4th residue. |
|
|
For a protein that basorbs strongly in the range of 250-300 nm, one expects this protein to have either ________ and/or ________ amino acid residue.
|
phenylalanine and/or triptophan
|
|
|
Under physiological pH, most basic amino acid residues in proteins tend to carry ________ (positive/negative/zero) charges and an example of such an amino acid is _________.
|
positive
lysine or arginine histidine is a basic amino acid, but at physiological pH, it would be neutral |
|
|
The amino acid that is capable of covalently linking different polypeptide chains or different regions of the same polypeptide chain is named________.
|
cysteine
|
|
|
The amino acid residue in proteins that can assume both cis and trans peptide bond configuration is named _______. In most cases, its peptide bond configuration is in the _______ (trans/cis) configuration.
|
proline
trans |
|
|
The amino acid that is capable of assuming the most combinations of torsion angles is named _______.
|
glycine
|
|
|
The reason that the torsion angles for a given peptide bond in an alpha helix are limited to a very narrow range is the following:
|
In real life, there is no ball and stick model. They take up a lot of space so angles are fixed to fit amongst one another. Glycine is the exception of sorts since it is so small.
|
|
|
To make an effective buffer at pH 7.4, the chosen buffer system has to have a pKa in the range of ________. Additionally, in order for the solution to be an effectie buffer, one has to make sure that the following condition is met:
|
6.4-8.4
The concentration of [A-] and [HA] have to be much higher than the external H+ or OH- added. |
|
|
For a 0.1 M buffer with a pKa of 6.9, the maximum buffering capacity is obtained at the following pH:_____. When the conjugate base to acid ration is 1:10, the pH of this buffer is ______. At this ratio, when HCl is added, the pH of the buffer will ________ (not change/slowly increase/slowly decrease/ slowly decrease first then increase), and its buffering capacity will __________ (increase/decrease/not change/increase then decrease/decrease then increase).
|
6.9
5.9 slowly decrease decrease |
|
|
The major noncovalent interaction among benzene (C6H6) molecules is the___________ interaction. THe reason that benzene is hydrophoboic is that_________________.
|
VDW
Benzene has no charge and is symmetric with all Carbons and Hydrogens. |
|
|
Removal of a nonpolar surface from exposure to water is expected to ____________(decrease/increase/have no change) in the entropy of a system.
|
increase
|
