Biochem Basics Flashcards
Why is specifically ATP is used to store energy in the cell.
Like charges repel, and the three adjacent phosphate groups in ATP contain four tightly bunched-up negative charges. The fact that they repel each other but are confined in a close space means that the triphosphate group stores electric potential energy, which is released when one of those phosphate groups is broken off to form ADP and an inorganic phosphate group.
Place the following in order from least to most polar: Charged molecules, Amines, Carboxylic acids, Alcohols, hydrocarbons, aldehydes/ketones
Hydrocarbons (least polar), Aldehydes/Ketones, Amines, Alcohols, Carboxylic Acids, Charged Molecules
Is the following polar or nonpolar:
This molecule is testosterone. It is technically nonpoalr despite the presence of two polar funtional groups. The nonpolarity of the steroid backbone strcuture outways the polarity of the groups.
CO2 has a dipole moment with the carbon and the oxygen. Is this molecule considered polar or nonpolar and why?
It is technically nonpolar due to the fact that it has 180 molecular geometry. If it were like water which is bent, then it would be polar but the dipole oments sort of cancel eachother ut in the strucutre.
Would the following be able to diffuse across the membrane?
YES! the charges are evenly distributed. It is a nonpolar compound technically.
How does charge/polarity impact the strucutre and function of hormones?
Polarity impacts the mechanism by which a hormone will signal to the cell. Steroid hormones can cross the membrane and exhibit long lasting effects. Peptide hormones cannot cross the memebrane so they tend to act on receptors on the cell and will exhibit quciker short lived effects.
When taking charge and polarity into consideration, what charge should histones have?
Positive. They bind to negative dna
What modifications can be done to histones?
Covalent addition of methyl, phosphate, and acetyl groups
How does acetylation impact the delivery of heroin?
The two -OH groups on morphine are highly polar and engage in hydrogen bonding, thereby impeding (to some extent) the ability of morphine to pass freely through the plasma membrane. In heroin, these groups are acetylated. They become esters (although knowledge of this term is not needed to answer the question), which are considered less polar because they cannot engage in hydrogen bonding. This means that heroin is overall less polar than morphine, and will pass more freely through the plasma membrane. Choices A and C state that compounds must pass through epithelial cells to reach the brain, so we can predict that the rapidity of onset of psychoactive effects will correlate with how quickly they pass through the plasma membrane of these cells. Heroin is predicted to pass through the membrane more rapidly, so its effects are predicted to set in more quickly. (Note that although the answer choices mention the blood-brain barrier, no previous knowledge of this topic is necessary, because the choices provide sufficient information to answer the question.)
B
WHta is histidine’s charge at physiological pH?
Normally it is neutral
WHta is the difference between glutamic acid and glutamate?
Glutamate is the ionic form
Figure 1 Structure of N-(L-α-Aspartyl)-L-phenylalanine, 1-methyl ester (Note: pKa1 = 3.2, pKa2 = 7.7).
The pI of aspartame is approximately…
5.5
The isoelectric point of an amino acid or oligopeptide is when the net charge is zero. Therefore, the pI is the pH where the carboxylate is deprotonated and the amino group is protonated. The pI can be approximated as the average of the pKa values of the carboxylic acid and the ammonium group, which are given in the caption to Figure 1.
pI = (pKa1 + pKa2)/2 = (3.2 + 7.7)/2 = 10.9/2 = 5.5
Figure 1 Structure of N-(L-α-Aspartyl)-L-phenylalanine, 1-methyl ester (Note: pKa1 = 3.2, pKa2 = 7.7).
Prior to its digestion in the small intestine, aspartame must pass through the stomach. What is the net charge of aspartame while in the stomach?
+1
The average pH of gastric juices inside the stomach ranges from 1.5 to 3.5. Even if you did not know this, we should know that the conditions inside the stomach are strongly acidic. Since the pH of the environment is below the stated pKa values of both groups on aspartame, the carboxylate is protonated and not charged, while the amine group is also protonated and will carry a positive charge. The nitrogen in the peptide bond is an extremely poor base, primarily due to the delocalization of the nitrogen lone-pair due to resonance with the carbonyl group. Therefore, the net charge of aspartame in the gastric juices will be +1.
Upon ingestion, aspartame is broken down in the duodenum into its components, aspartic acid, phenylalanine and methanol, with the subsequent formation of toxic metabolites such as formaldehyde and formic acid. Some research indicates that aspartame may lead to the formation of certain cancers as a result of the formation of some of these potentially toxic compounds. A new drug, known as protein AT7 (MW = 5 ⨉ 10^4 amu), has been developed to counter this possibility.
According to the passage, how many amino acid residues are in AT7?
The test makers expect us to know that the average molecular weight of an amino acid residue in a protein is 110 Da. Since a Dalton is equivalent to 1 atomic mass unit (amu), 5 x 104 amu = 50 kDa. If the protein AT7 has a molecular weight = 50 kDa, the approximate number of amino acids in AT7 is:
(5 x 104 Da)(1 residue/110 Da) = 4.5 x 102.
450
Even if you did not know that the average molecular weight of an amino acid is 110 Da, you could quickly estimate it. The –COOH group has a weight of 45 amu (12 amu for the C + [16 × 2] = 32 amu for the O atoms + 1 amu for the H), the alpha carbon weighs 12 amu, and the –NH2 group weighs 16 amu, so the basic amino acid skeleton weighs 73 amu. Adding a rough estimate of ~30 amu for an average side chain would get you to about 100 amu, which is close enough to answer this question correctly.
Looking at the carbonic anhydrase mechanism, what would be an appropriate competetive inhibitor:
A. D2O
B. Cl-
C. H2CO3
D. CO2
The active site of the enzyme is a cation. A small anion is best suited to inhibit the enzyme by binding to the zinc.
Which of the following will have a higher pKb value?
Piperazine because the inductive effects of methyl-piperazine lowers its pkb due to electron donation by the methyl substituent
