Pearls from AAMC Material/ Khan Academy/ Practice Exams

Question 1

What is a phosphatase?

Answer 1

an enzyme that removes a phosphate group from its substrate

Question 2

We know that anions such as formate and urate (ending in -ate) are….

Answer 2

…anions that can accept protons.

(https://www.khanacademy.org/test-prep/mcat/physical-sciences-practice/physical-sciences-practice-tut/e/biochemistry-changes-that-occur-after-death?_ga=2.94837077.819408990.1653668529-826931683.1648912754)

Question 3

When the pH of the solution is greater than the pKa for a proton, the proton is removed and the compound becomes ____________ at that region.

Answer 3

deprotonated

Question 4

What does fructose-2,6-bisphosphate do?

Answer 4

It stimulates phosphofructokinase (PFK), and inhibits fructose-1,6-bisphosphatase

(Princeton Review practice Exam 1)

Question 5

Peptidoglycans are not found in eukaryotes, only ________.

Answer 5

bacteria

Question 6

All 20 amino acids are primary amines except for ______, which has its N atom in a five-membered ring, making it a secondary amine.

Answer 6

proline

Question 7

Which blotting test is used for detection of a protein?

Answer 7

Western blotting

Question 8

Which test is used for detection of specific RNA sequences?

Answer 8

Northern blot

Question 9

Which test is used for detection of specific DNA sequences?

Answer 9

Southern blot

Question 10

Both column chromatography and thin-layer chromatography separate compounds based on ________, while gas chromatography separates compounds based on ______ ______.

Answer 10

polarity

boiling points

(Khan Academy passage: Separations and purifications)

Question 11

In thin layer chromatography, which uses a polar silica gel for the stationary phase, which substance will elute first?

Answer 11

the non-polar substance will elute first, because it travels with the nonpolar mobile phase

Question 12

In size-exchange chromatography, substances are sorted based on their molecular weight. Which substance elute first? Which elute last?

Answer 12

Larger molecules will elute first
smaller molecules elute last bc they have a longer path to travel.

Question 13

In CATION-Exchange Chromatography, the Stationary Phase (charged beads) is negatively charged; Thus, _______ will be retained in the column.

In ANION-Exchange Chromatography, the Stationary Phase is positively charged. Thus, ______ will be retained in the column.

Remember, this type of analysis is named after the END GOAL, which is to get cations to stick in the column.

Answer 13

CATIONS

ANIONS

Question 14

Where is rRNA synthesized?

Answer 14

in the nucleolus

Question 15

Some RNAs have more than 4 different types of bases. What is an example of this?

Answer 15

tRNA has unique and modified bases apart from the traditional four bases A,U,C, and G (such as inosine, methylinosine, and several others)

Question 16

Which 2 amino acids are known as ALPHA HELIX breakers?

Answer 16

glycine (bc its so flexible)
proline (bc it has a secondary alpha amino group)

(Khan Academy video: Special Cases: Histidine, proline, glycine, cysteine)

Question 17

Which types of protein structure are affected by heat?

Answer 17

Heat can destroy 2°, 3°, and 4° protein structure but leaves 1° structure intact.

(Khan Academy video)

Question 18

An acid, like vinegar disrupts what levels of protein structure?

Answer 18

An acid will disrupt 3° and 4° structure, because it affects ionic bonds.

Question 19

What level of protein structure are enzymes capable of destroying?

Answer 19

Primary structure can be disrupted by enzymes, which would essentially destroy all levels of protein structure.

Question 20

A ______ adds on a phosphate group to a molecule by removing a hydrogen and creating a bond between the oxygen of the hydroxy group and the phosphate of the phosphate group (O-P).

Answer 20

kinase

An amino cannot be phosphorylated by a kinase if it lacks a hydroxyl group.
(unsure if the basic and acidic amino acids can be phosphorylated but I think so; alkyl side chains cannot be phosphorylated)

Question 21

Things to know about SDS-page electrophoresis:

Answer 21

This requires the disruption of the native conformations of the proteins of interest.

It is not carried out under physiological conditions (BME and SDS are not present in living systems).

It uses a voltage gradient to spatially separate electrically charged proteins.

It is carried out in a pH buffered solution to ensure that the proteins being separated maintain the desired electrical charge.

Question 22

SDS is used to ensure that polypeptides have a ________ ______ proportional to the length of the molecule.

Answer 22

negative charge

https://www.khanacademy.org/test-prep/mcat/biological-sciences-practice/x04f6bc56:mcat-bio-biochem-foundation-1-passages/e/the-electrophoretic-separation-of-proteins

Question 23

Prions cause misfolding of proteins which aggregate and cause disease. One well-known mechanism by which this happens is when ______ _-_______ are replaced by β-sheets. The β-sheets have a higher likelihood of binding to one another, and this causes aggregation of proteins.

Answer 23

normal α-helices

(MCAT Self Prep End-of-Lesson cards)

Question 24

β-turns are sharp turns in the amino acid sequence that allow proteins to maintain a compact structure. They are normally located on the _______ of proteins.

Answer 24

SURFACE

(End-of-lesson mastery questions)

Question 25

The secondary structure of keratin is largely composed of α-helices. The majority of these are _____-______ (clockwise) in order to decrease steric hindrance.

Answer 25

right-handed

(End-of-lesson mastery quiz)

Question 26

Vitamin B₃ (niacin) is a precursor for….

Answer 26

….NAD.

Question 27

Vitamin B₅ (pantothenic acid), is a precursor for…

Answer 27

….CoA.

Question 28

Consider the transport of proteins that need to be modified. The usual process to produce these proteins follows these steps: cytoplasm -> endoplasmic reticulum -> Golgi apparatus -> cell membrane. If some molecule aided in RETROGRADE transport from the Golgi apparatus, it would follow the reverse of this path.

Question 29

Do archaea and bacteria have a Golgi apparatus?

Answer 29

No

Question 30

If the concentration of amino acid transport protein is increased, the transport affinity K_t of L-alanine will:

Answer 30

not change!

Transport affinity for substrates (in this case, alanine) is an inherent property of transport proteins, and thus transport affinity is independent of the concentration of transport protein.

[AAMC Free Practice Exam]

Question 31

In standard Michaelis–Menten kinetics, K_t is equal to:

Answer 31

For transporters the transport affinity (K_t) is equivalent to the K_M in Michaelis–Menten kinetics. This means that K_t is the substrate concentration at which the reaction rate is one-half the maximal transport capacity.

[AAMC Free Practice Exam/ Bio/Biochem section, Q 25]

Question 32

The metabolic rate is an internal variable that will help define the capability of an organism to withstand long periods of ________ deprivation. An organism that has a low metabolic rate will be more suitable to withstand long periods of food deprivation than an organism that has a high metabolic rate.

Answer 32

nutrient

[AAMC Free Practice Exam/ Bio/Biochem section]

Question 33

What is the “anatomy” of a fatty acid?

Answer 33

a carboxyl group “head” (CO₂^-) with a hydrocarbon tail

Question 34

The smaller the K_d, the _______ the binding affinity of the ligand for its target.

Answer 34

GREATER

[Q 55 of AAMC Free Practice Exam]

Question 35

The passage indicates that subunit A of STx protein is a polypeptide chain that is cleaved. The cleavage of peptide bonds is catalyzed by a ________.

Answer 35

protease

Question 36

When Leu, a hydrophobic amino acid, is located at a surface-exposed site of proteins, it is in contact with water molecules and, therefore, water molecules must organize themselves into a specific arrangement (called _______ _______) to live with this fact. A substitution of Leu to Thr, which is a polar and hydrophilic amino acid, reduces drastically this entropic penalty because water molecules are now in contact with a hydrophic amino acid.

Answer 36

entropic penalty