AAMC 1 - Bio/Biochem

Question 1

What role does clathrin play in the cell?

Answer 1

Clathrin functions in formation of vesicles for intracellular trafficking

Question 2

What is a nuclear localization signal?

Answer 2

The nuclear localization signal is a sequence that tags the protein for it to be transported into the nucleus.

Question 3

Are introns present in mature mRNA?

Answer 3

No.

Introns are absent in mature mRNA

Question 4

What must be present on the mature mRNA of transmembrane proteins for them to be correctly expressed? What does this accomplish?

Answer 4

Transmembrane proteins require specific modifications that occur in the rough endoplasmic reticulum. The mRNAs for these proteins contain a specific signal sequence that directs them to dock onto the ribosomes on the RER. Ribosomes transfer the proteins into the lumen of the RER where they undergo structural modifications. These modified proteins will be incorporated into membranes or secreted from the cell. That signal sequence is a necessary, specific sequence found in the mRNA of proteins that allows for docking onto the RER.

Question 5

What is chemiosmosis and what is unique about it’s relationship with NAD+/NADH compared to the rest of cellular respiration?

Answer 5

Chemiosmosis is the utilization of a proton motive force during oxidative phosphorylation. Chemiosmosis is the only step of cellular respiration where NAD⁺ is neither reduced to form NADH, nor is NADH oxidized to form NAD⁺.

Question 6

If a man with a mutant copy of Ace2 (x-linked) has a child with a woman that is heterozygous for the mutant Ace2 allele, what is the probability that the child will be a female and homozygous for the mutant Ace2 allele?

Answer 6

25%

Question 7

What is the total number of fused rings present in a steroid?

A. 1

B. 2

C. 4

D. 6

Answer 7

C. 4

A steroid is composed of a 6-6-6-5 fused ring assembly, which is a total of 4 fused rings.

Question 8

How many rings are found in a monoterpene?

Answer 8

A single ring can be found in a monoterpene

Question 9

How many rings does an indole contain?

Answer 9

An indole has two fused rings

Question 10

When concentrated urine is being produced, in which of the following regions of the kidney will the glomerular filtrate reach its highest concentration?

A. Proximal convoluted tubule

B. Distal convoluted tubule

C. Cortical portion of the collecting duct

D. Medullary portion of the collecting duct

Answer 10

D. Medullary portion of the collecting duct

The collecting duct is the final structure in which water reabsorption occurs, which concentrates filtrate. The medullary portion of the collecting duct is the last portion of the tubules where reabsorption can occur. In the portion of the tubule that follows, there will be no more reabsorption. Thus, the medullary portion of the collecting duct contains the most concentrated glomerular filtrate that will correspond to the urine.

Question 11

In which direction does the Na⁺K⁺ ATPase transport ions across the cell membrane upon ATP hydrolysis?

A. Na⁺ is transported out of the cell; K⁺ is transported into the cell.

B. Na⁺ is transported into the cell; K⁺ is transported out of the cell.

C. Both Na⁺ and K⁺ are transported into the cell.

D. Both Na⁺ and K⁺ are transported out of the cell.

Answer 11

A. Na⁺ is transported out of the cell; K⁺ is transported into the cell.

Question 12

___________ regulate the expression of other genes by binding to DNA

Answer 12

Transcription factors regulate the expression of other genes by binding to DNA

Question 13

Considering the structure of STN, what is the most likely mechanism for its entry into the cell?

A. Active transport

B. Receptor mediated endocytosis

C. Diffusion directly through the membrane

D. Passage through an ion channel

Answer 13

C. Diffusion directly through the membrane

The structure of STN shows that it is a hydrophobic molecule. These types of molecules pass through the membrane by simple diffusion.

Question 14

A protein is known to be found in cholesterol rich regions of the plasma membrane. What is another name for these cholesterol rich areas?

Answer 14

In a lipid raft

A lipid raft is an area in the membrane where there is a high concentration of cholesterol, and a different composition of carbohydrates, proteins and other lipids compared to the rest of the membrane.

Question 15

True or False:

Enzymes alter the rate of chemical reactions by all of the following:

Co-localization of substrates, altering local pH, and altering substrate structure.

Answer 15

True.

Enzymes do NOT, however, alter the primary structure of a protein.

Question 16

Can an animal virus infect a bacteria?

Answer 16

No.

Animal viruses can only infect animal cells, not bacteria

Question 17

In general, telomeres are NOT important to bacterial cells because most bacterial chromosomes:

A. do not replicate.

B. are circular.

C. replicate quickly and efficiently.

D. are composed of single-stranded DNA.

Answer 17

B. are circular

Telomeres help protect DNA during replication and prevents its degradation. Bacterial DNA is circular, so there is not the same need for telomeres to act as capping ends.

Question 18

Which of the following best describes the bond that would form between the following two nucleotides if they were located adjacent to each other as shown in a single strand of DNA?

A. A bond between the phosphate of the thymine and the phosphate of the adenine

B. A bond between an oxygen in the thymine base and a nitrogen in the adenine base

C. A bond between the phosphate of the thymine and the sugar of the adenine

D. A bond between the phosphate of the adenine and the sugar of the thymine

Answer 18

D. A bond between the phosphate of the adenine and the sugar of the thymine

Nucleotides are linked to one another by phosphodiester bonds between the sugar base of one nucleotide (thymine) and the phosphate group of the adjacent nucleotide (adenine) in a way that the 5′ end bears a phosphate, and the 3′ end a hydroxyl group.

Question 19

Someone is overproducing cortisol. What effect will this have on white blood cell count?

Answer 19

Glucocorticoids, like cortisol, suppress immune function, which is mediated by white blood cells. Therefore, the activity of white blood cells will decrease, not increase, in response to excess glucocorticoid exposure.

Question 20

If a patient with Addison’s disease is given too high a replacement dose of glucocorticoids (cortisol), the effect over time will be an increase in:

A. muscle mass.

B. muscle weakness.

C. red blood cell count.

D. heart rate.

Answer 20

B. muscle weakness.

High levels of circulating glucocorticoids will increase protein degradation in various tissues, muscles included. A direct consequence of protein degradation in muscles is muscle weakness.

Question 21

Exercise promotes the insulin-independent uptake of glucose in working skeletal muscles. Given this, regular exercise would most likely reduce blood glucose levels in patients with which type(s) of diabetes?

A. Type 1 only

B. Type 2 only

C. Both Type 1 and Type 2

D. Neither Type 1 nor Type 2

Answer 21

C. Both Type 1 and Type 2

Question 22

Are proteins cleaved in ribosomes after being translated?

Answer 22

No.

Ribosomes function to translate proteins but they do NOT cleave them.

Question 23

What is the role of the endomembrane system, and what structures does it include?

Answer 23

The endomembrane system is the set of membrane-bound organelles that are involved mainly in the modification and transportation of proteins.

This includes the nuclear envelope, Golgi apparatus, endoplasmic reticulum, vesicles and lysosomes.

Question 24

During the production of insulin, the translated polypeptide is cleaved into the mature form and secreted from the cell. The cleavage most likely takes place in which of the following locations?

A. Nucleus

B. Ribosomes

C. Endomembrane system

D. Cytoplasm

Answer 24

C. Endomembrane system

The endomembrane system is the portion of the cells that is in charge of modifying proteins that will be secreted. Thus, it is most likely that insulin cleavage will occur in the endomembrane system.

The endomembrane system is the set of membrane-bound organelles that are involved mainly in the modification and transportation of proteins.

This includes the nuclear envelope, Golgi apparatus, endoplasmic reticulum, vesicles and lysosomes.

Question 25

Does the brain use less glucose than other parts of the body?

Answer 25

No.

The brain is the MAIN consumer of glucose in the body. It often metabolizes glucose more than any other tissue in the body.

Question 26

Despite the effects of diabetes, the brains of diabetic patients still receive adequate nourishment. This is most likely because the brain uses:

A. less glucose than do other body tissues.

B. insulin-independent transporters for the uptake of glucose.

C. fatty acids for energy instead of glucose.

D. insulin-dependent transporters for the uptake of glucose.

Answer 26

B. insulin-independent transporters for the uptake of glucose.

The brain cells contain glucose transporters that are insulin independent.

Question 27

Can the brain use fatty acids as a fuel source?

Answer 27

No.

Brain cells are unable to use fatty acids for energy.

Question 28

________ is secreted by the stomach in response to signals of an impending meal. Sight, sound, taste, and especially smell all act as signals for its release. It increases appetite and also stimulates secretion of orexin.

Answer 28

Ghrelin is secreted by the stomach in response to signals of an impending meal. Sight, sound, taste, and especially smell all act as signals for its release. It increases appetite and also stimulates secretion of orexin.

Question 29

In addition to Ghrelin, _______ further increases appetite, and is also involved in alertness and the sleep–wake cycle. Increased Ghrelin and Hypoglycemia are triggers for orexin release.

Answer 29

In addition to Ghrelin, orexin further increases appetite, and is also involved in alertness and the sleep–wake cycle. Increased Ghrelin and Hypoglycemia are triggers for orexin release.

Question 30

_______ is a hormone secreted by fat cells that decreases appetite by suppressing orexin production.

Answer 30

Leptin is a hormone secreted by fat cells that decreases appetite by suppressing orexin production.

Question 31

You walk into your favorite restaurant. Although you were not hungry before entering, you smell the food and see others eating. Suddenly, you experience hunger. What physiological change is occuring to make this happen?

Answer 31

Your body is increasing its release of Ghrelin, a hormone secreted by the stomach when preparing for a meal. This is triggered by sight, smell, and taste. It increases appetite and stimulates secretion of orexin, another hormone that increases appetite.

Question 32

Why would an increases rate of lipolysis and beta-oxidation increase appetite?

Answer 32

Lipolysis is the breakdown, or destruction, of fat cells for energy. Fat cells produce leptin, a hormone that decreases appetite by suppressing orexin.

If fat cells are being destroyed, leptin release is decreasing and appetite will increase.

Question 33

Knowing the effects of diabetes mellitus, which of the following is LEAST likely to be a symptom of diabetes mellitus?

A. Loss of appetite

B. Sweet-tasting urine

C. Unexplained weight loss

D. Feelings of fatigue

Answer 33

A. Loss of appetite

Diabetes would result in an increase of lipolysis and beta-oxidation, destroying fat cells for energy. Fat cells produce leptin, a hormone that decreases appetite by inhibiting orexin.

If fat cells are destroyed, so is their effect of decreasing appetite.

Question 34

Adding heat to a closed biological system will do all of the following EXCEPT:

• *A.** increase the internal energy of the system.
• *B.** increase the average of the vibrational, rotational, and translational energies.
• *C.** cause the system to do work to maintain a fixed internal energy.
• *D.** increase the enthalpy of the system.

Answer 34

C. cause the system to do work to maintain a fixed internal energy.

In a closed biological system, enthalpy, heat, and internal energy are all directly related because there is no change in pressure or volume. Because pressure and volume are fixed, work cannot be done, thus (C) is correct.

Question 35

“Which of the following side effects would be anticipated in someone taking leptin to promote weight loss?

• *A.** Drowsiness
• *B.** Increased appetite
• *C.** Irritability
• *D.** Fever

Answer 35

A. Drowsiness

Leptin acts to decrease appetite by inhibiting the production of orexin. Orexin is also associated with alertness, so decreasing the level of orexin in the body is expected to cause drowsiness. Even without this information, the answer should be apparent because the body tends to maintain an energy balance. If consumption decreases, energy expenditures are expected to decrease as well.

Question 36

True or false:

The side chains of all acidic and basic amino acids exhibit both acidic and basic properties.

Answer 36

This statement is true.

The environmental pH determines whether an acidic or basic side chain acts as an acid or base. For example: glutamic acid is an acidic amino acid. Although its side chain is deprotonated at physiological pH, and therefore is considered acidic, it acts as a base under low pH conditions.

Question 37

True or false: The pKa value of an acid is defined as the pH at which 100% of the acid has been converted to its conjugate base.

Answer 37

False.

An acid’s pKa value is the pH at which the concentrations of the acid and its conjugate base are equal. In other words, it’s the pH in which 50% of the acid molecules in solution have been deprotonated and converted into the conjugate base.

Question 38

At a pH greater than its pKa value, the predominant charge on an amine group will be __

Answer 38

zero.

When pH > pKa, the conjugate base of the positively charged amine group is the predominant form. Therefore, the majority of amine groups in solution will be electrically neutral.

Question 39

True or false:

The isoelectric point is defined as the pH at which all of an amino acid’s ionizable functional groups have been deprotonated.

Answer 39

This statement is false.

The isoelectric point is the pH at which the amino acid has a net charge of zero, which occurs long before all ionizable groups have been deprotonated. Once an amino acid has been fully deprotonated, it will have a net charge of -1 or -2.

Question 40

The pKa values of phenylalanine are provided below.

pKa₁ = 1.83

pKa₂ = 9.13

What is the net charge of phenylalanine at pH 11?

Answer 40

-1

At pH values above its second pKa, the predominant form of phenylalanine has a net -1 charge, since its carboxylic acid group carries a -1 charge and its amine group is largely neutral.

Question 41

A titration curve for a nonpolar amino acid is shown below.

At which of the labeled points are the concentrations of the amino acid and its conjugate base approximately equal?

Answer 41

2 and 4

Point 2 occurs roughly halfway across the first plateau region on the curve, and therefore represents this amino acid’s first pKa value. When the pH is equal to the pKa, there is an equal concentration of acid and its conjugate base.

Point 4 is the second pKa value for this amino acid. At this point, there are equal concentrations of the amine group and its conjugate base.

Question 42

Histidine is depicted below. The pKa values of all ionizable groups are indicated with arrows.

What is the net charge of histidine at pH 4?

Answer 42

+1

At pH 4, histidine’s carboxylic acid has been deprotonated, leaving it with a -1 charge. Since its alpha-amino and side-chain amine group both remain largely protonated and positively charged, the molecule has a net charge of +1.

Question 43

This titration curve most likely corresponds to:

choose between: val, leu, lys, asp, ala

Answer 43

Asp

Aspartate is a triprotic acidic amino acid. Its first two pKa values are rather low because they correspond to the deprotonation of its two extremely acidic carboxylic acid groups. After the second pKa, the curve increases dramatically until it reaches a pH value that is basic enough to deprotonate aspartate’s amine group.

Question 44

The titration of arginine with strong base is depicted in the figure below.

At what pH value does arginine exist as a zwitterion?

Answer 44

11

A pH of 11.0 corresponds to arginine’s isoelectric point (pI). Here, arginine’s carboxylic acid group and one of its two amine groups have been deprotonated, giving each molecule one -1 charge and one +1 charge. These charges cancel out and give the molecule a net charge of zero, making it a zwitterion.

Question 45

pKa is best defined as the pH at which:

Answer 45

The concentrations of acid and conjugate base are equal

At an acidic functional group’s pKa, 50% of the acid form of the group will be deprotonated and 50% will remain protonated. Therefore, the solution will contain equal concentrations of the acid form of the functional group and its conjugate base.

Question 46

A titration curve for glycine is shown below.

What is the pI of glycine?

Answer 46

6

Glycine’s isoelectric point (pI) occurs at the first equivalence point in its titration, which is the central vertical section of the curve. At this point, glycine’s carboxylic acid group is deprotonated and negative, but its amine group remains protonated and positive. Because these positive and negative charges cancel out, leaving glycine with a net charge of zero, it is a zwitterion and therefore this pH is also its pI.

Question 47

At its second half-equivalence point (pH ~ 9.5), what is the overall net charge of a leucine molecule?

Answer 47

between -1 and 0

At pH 9.5, leucine’s carboxylic acid group is fully deprotonated, while its amino group is protonated on half of the molecules and deprotonated on the remainder. Thus, on average, leucine is slightly negatively charged overall.

Question 48

True or false:

The isoelectric point of a polyprotic acid is always located at the first equivalence point along its titration curve.

Answer 48

False.

An amino acid’s isoelectric point (pI) corresponds to the pH at which the amino acid contains both positive and negative charges that cancel out to make the overall molecule electrically neutral. Coincidentally, the pI does occur at the first equivalence point for nonpolar and acidic amino acids. However, basic amino acids are isoelectric at the second equivalence point on the curve.

Question 49

A novel peptide is designed with the amino acid sequence provided below.

Gly-Ala-Lys-His-Val-Tyr-Glu-Ala-Ala-Gly

Extremely acidic environmental conditions have been shown to disrupt a key intermolecular interaction. What is the net charge of this peptide at pH 1.5?

Answer 49

+3

At pH 1.5, all acidic and basic functional groups are protonated. Carboxylic acid groups are electrically neutral at this pH and amine groups carry a positive charge. Note that this means the C-terminus is neutral and the N-terminus contributes a +1 charge. The peptide also contains two basic amino acid (Lys and His) whose side chains will each contribute an additional +1 charge. Therefore, the next charge of this peptide at pH 1.5 is +3.

Question 50

Suppose that 60 mL of 0.1 M NaOH is required to completely neutralize the amine group of glycine in an analyte solution. What quantity (in mmol) of glycine is present in the analyte?

Answer 50

3 mmol

Dimensional analysis is an easy way to perform this calculation. Start by converting all values into scientific notation:

60 mL NaOH = 6 x 10^-2 L NaOH

0.1 M NaOH = 1 x 10^-1 mol NaOH / L NaOH.

We can simply multiply the volume of NaOH by the molarity to obtain the number of moles added. But because we’re talking about glycine’s amine group, we’re actually dealing with the second equivalence point.

At the second equivalence point, 2 moles of NaOH have been added for every 1 mole of glycine present in the analyte. This is because one OH^- was required to neutralize the COOH group and a second OH^- was needed to neutralize the amine. We need to modify our calculation to account for this.

The final setup is:

(6 x 10^-2 L NaOH) x (10^-1 mol NaOH / L NaOH) x (1 mol glycine / 2 mol NaOH) = 3 x 10^-3mol = 3.0 mmol glycine.

Question 51

What biomolecule is SDS-PAGE most often used to study?

Answer 51

Proteins

SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) is most commonly used to separate proteins by mass. The SDS detergent gives the proteins a uniform and negative charge so that all proteins will migrate towards the positively-charged anode.

Question 52

Of the bands labeled, which of the following bands in an SDS-PAGE gel represents the protein with the smallest molecular weight?

Answer 52

D

Smaller proteins run faster through the gel. The smallest proteins will be farthest from the cathode (the negative end). As molecules with the smallest molecular weight migrate the furthest in SDS-PAGE, band D has the smallest molecular weight of the labeled bands.

Question 53

True or False:

DNA microarrays can only analyze fewer genes at a time than a southern blot.

Answer 53

False.

DNA microarrays are laboratory tools that simultaneously analyze the gene expression of thousands of genes. Southern blots detect certain DNA sequences in a sample and can only detect a limited gene number, due to their space constraints.

Question 54

Compare and contrast the use of DNA microarrays and southern blots

Answer 54

DNA microarrays are laboratory tools that simultaneously analyze the gene expression of thousands of genes.

Southern blots detect certain DNA sequences in a sample and can only detect a limited gene number, due to their space constraints.

Question 55

In the image depicting PCR below, what are the molecules drawn in pink called?

Answer 55

Primers

These molecules are primers, a primer is short single-stranded DNA molecules. The PCR stage depicted is the primer annealing stage, where the reaction mixture is cooled to 55-65 °C to allow the primers to anneal to the template strands.

Question 56

A DNA sequence has been analyzed using the Sanger sequencing technique. You have prepared the sequencing gel as shown in the figure below.

Assuming the gel was loaded at the top, what is the sequence of the synthesized DNA?

Answer 56

3’-GGAATAGCTGAGATCACTAAGAAAGGCA-5’

In Sanger sequencing, all four dNTPs (which elongate the chain) and ddNTPs (which terminate the chain) are added to a single tube where DNA replication occurs.

During primer extension, a large number of chains of various lengths are produced. As new strands are synthesized from 5’ to 3’, the 3’ end of the complementary DNA chain will be nearest to the well, while the 5’ end will be farthest.

Question 57

Fill in the blanks: In gel electrophoresis, the anode has a _________ charge and the cathode has a _________ charge. This is an example of a(n) __________ cell.

Answer 57

Fill in the blanks: In gel electrophoresis, the anode has a positive charge and the cathode has a negative charge. This is an example of an electrolytic cell.

In an electrophoresis apparatus, in the anode, a positive charge is applied at one end of the gel, and in the cathode, a negative charge is applied to the other end of the gel, This generates an electric field and is an electrolytic cell, not a galvanic cell.

The applied current forces molecules to move in the intended direction, usually towards the anode.

Question 58

Of the bands labeled, which of the following bands in an SDS-PAGE gel represents the protein with the largest molecular weight?

Answer 58

A

As the molecules with the smallest molecular weight migrate the furthest from the cathode (negative end) in SDS-PAGE, the protein with the largest molecular weight will be the band closest to the top of the gel. Of the bands labeled, A is closest to the top.

Question 59

Name the 3 steps of PCR along with their average temperatures

Answer 59

PCR consists of repeated cyclical steps:

1. The reaction heats to 95°C to denature the two strands of genetic material.
2. The reaction mixture cools to 55-65°C so primers then anneal to the template strands.
3. The temperature increases again to about 72°C to initiate DNA synthesis, catalyzed by Taq polymerase, which elongates the DNA molecule.

Question 60

A DNA sequence has been analyzed using the Sanger sequencing technique. You have prepared the sequencing gel as shown in the figure below.

Assuming the gel was loaded at the top, what is the sequence of the template DNA?

Answer 60

5’-CCTTATCGACTCTAGTGATTCTTTCCGT-3’

In Sanger sequencing, all four ddNTPs are added to a single tube where DNA replication occurs.dNTPs elongate the DNA chain, while ddNTPs terminate replication.

During primer extension, chains of various lengths are produced, all complementary to the template DNA. Since new strands are synthesized from 5’ to 3’, the 3’ end of the complementary DNA chain will be nearest to the well, while the 5’ end will be farthest.