Proteins and Nucleic Acids Flashcards Preview

MCAT Biochemistry > Proteins and Nucleic Acids > Flashcards

Flashcards in Proteins and Nucleic Acids Deck (76)
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1
Q

Relatively short chains of amino acids joined together by peptide bonds are termed:

A

peptides.

Peptides are chains of amino acids that are shorter than proteins.

2
Q

The molecule EK (one glutamic acid residue bonded to one lysine residue) is a peptide. More specifically, it is a:

A

dipeptide.

Dipeptides are peptides that consist of only two amino acid residues. As such, they are the shortest peptides possible.

3
Q

How many amino acid residues are present in a tetrapeptide?

A

A tetrapeptide is a peptide that contains four amino acid residues.

For instance, the molecule CysAlaGlyLys is a tetrapeptide.

4
Q

Oligopeptides are molecules that contain between ________ and ________ amino acids.

A

Oligopeptides are molecules that contain between two and 20 amino acids.

In other words, “oligopeptide” is a blanket term for relatively short peptides.

5
Q

While a peptide containing 17 amino acids is termed an oligopeptide, a peptide containing 64 amino acids is an example of a:

A

polypeptide.

For the sake of the MCAT, you can think of polypeptides as linear peptide chains that are longer than oligopeptides (in other words, that contain more than 20 amino acid residues).

6
Q

What is the difference between a polypeptide and a protein?

A

Proteins can consist of one or more polypeptides.

In other words, a polypeptide is always defined as a single linear chain of amino acids. Some proteins are polypeptides, but other proteins are composed of multiple polypeptides attached in a more complex structure.

7
Q

True or false:

The peptide abbreviated HKA is an oligopeptide.

A

True

From the presence of three letters in HKA, we know that HKA contains three amino acid residues. Thus, HKA is both a tripeptide (a peptide containing three residues) and an oligopeptide (a peptide containing two to around 20 residues).

8
Q

Define:

primary structure

A

The primary structure of a protein refers to the linear sequence(s) of amino acids in its polypeptide chain(s).

For example, the primary structure of a protein could be written as AVYPFELK… (and so on).

9
Q

The primary structure of a protein is held together by which kind of bond?

A

Peptide bonds (which are also amide linkages)

Since primary structure refers to a linear amino acid sequence, it is held together solely by peptide bonds, which are covalent amide linkages between amino acid residues.

10
Q

The amino acid residues in a protein are held together by bonds between ________ and ________ atoms.

A

The amino acid residues in a protein are held together by bonds between carbon and nitrogen atoms.

Specifically, a peptide bond connects the carbonyl carbon of one amino acid to the amino nitrogen of another. This forms an amide functional group.

11
Q

Define:

secondary structure

A

Secondary structure refers to the organized, local, relatively simple folding patterns that characterize a protein.

By far the most common patterns of secondary structure that appear on the MCAT are alpha-helices and beta-pleated sheets.

12
Q

Name the two key types of secondary structure.

A

Alpha-helices and beta-sheets (or beta-pleated sheets)

13
Q

The secondary structure of a protein is held together by which kind(s) of bond/interaction?

A

Hydrogen bonds

Secondary structure is largely rigid and predictable. In keeping with that fact, all secondary structure is held together by hydrogen bonds alone, specifically H-bonds between the carbonyl oxygen of one residue and the amino hydrogen of another.

14
Q

True or false:

Alpha helices, a form of secondary structure, largely lack proline.

A

True

Due to its unique shape, proline tends to introduce “kinks” (bends) or breaks in the rigid structure of an alpha helix. Additionally, proline’s structure renders it unable to donate the hydrogen bond needed to stabilize the helix. As a result, proline is found in alpha helices relatively rarely compared to other amino acids.

15
Q

In a beta-pleated sheet, where is proline most likely to be found?

A

Proline is most likely to be found at the edges (or turns).

Just as it does in alpha helices, proline introduces “kinks” or bends in the structure of a beta sheet. For this reason, it is predominantly found in the areas where the sheet is supposed to be bent (that is, the turns between strands).

16
Q

Define:

tertiary structure

A

Tertiary structure refers to the higher-level, complex folding that produces the three-dimensional structure of a protein subunit.

Unlike secondary structure, which falls into a small number of predictable patterns, tertiary structure can vary enormously.

17
Q

The main driving force for protein folding into tertiary structure is what kind of interaction?

A

Hydrophobic interaction

Hydrophobic interactions, or the entropy-driven tendency for nonpolar parts of a protein to cluster together away from the aqueous environment, drive protein folding. (However, multiple other types of interaction have some involvement in tertiary structure.)

18
Q

Name three types of interactions that are involved in tertiary structure.

A

Many types of interactions are involved in protein tertiary structure, including:

  • hydrophobic interactions
  • ionic interactions/salt bridges
  • disulfide bonds
  • hydrogen bonds
19
Q

Define:

quaternary structure

A

Quaternary structure refers to the interactions that hold together the subunits of a multi-subunit protein.

For instance, if the two monomers in a dimer are held together largely by ionic interactions, those interactions comprise the protein’s quaternary structure.

20
Q

True or false:

All proteins contain primary, secondary, tertiary, and quaternary structure.

A

False

While all proteins have primary, secondary, and tertiary structure, only proteins that consist of more than one subunit have quaternary structure.

21
Q

Name three types of interactions that are involved in quaternary structure.

A

Interestingly, quaternary structure involves the same interactions as tertiary structure! These include:

  • hydrophobic interactions
  • ionic interactions/salt bridges
  • disulfide bonds
  • hydrogen bonds
22
Q

In its folded state, the protein hemoglobin contains which levels of protein structure?

Choose from primary, secondary, tertiary, and quaternary structure, and name all levels that apply.

A

All levels (primary, secondary, tertiary, and quaternary structure)

All proteins in their normal folded states have primary, secondary, and tertiary structure. As a multi-subunit protein, hemoglobin also has quaternary structure. For the MCAT, you should have some familiarity with the structure of hemoglobin, which is a tetramer (four-subunit protein).

23
Q

In its folded state, the protein myoglobin contains which levels of protein structure?

Choose from primary, secondary, tertiary, and quaternary structure, and name all levels that apply.

A

Primary, secondary, and tertiary structure

In other words, myoglobin contains all levels of protein structure except quaternary structure, which only applies to multi-subunit proteins. For the MCAT, you should know that myoglobin—unlike hemoglobin—has only one subunit.

24
Q

Name all levels of protein structure to which disulfide bonds contribute.

A

Disulfide bonds are involved in tertiary and quaternary structure.

Disulfide bonds are covalent bonds between sulfur atoms of cysteine residues. Interestingly, these are the only covalent bonds (as opposed to non-covalent interactions) involved in higher-level protein folding.

25
Q

Two cysteine residues that are connected in a disulfide bond can be described using what term?

A

Cystine

Note that this word is just “cysteine” without the “e”! It refers to a cysteine dimer—in other words, two cysteine residues connected by a double bond.

26
Q

Ionic interactions contribute to which level (or levels) of protein structure?

A

Tertiary and quaternary structure

Ionic interactions, or attractions between positive and negative side chains, contribute to tertiary and quaternary structure. (You should know that, in contrast, primary structure is held together only by covalent peptide bonds, while secondary structure is held together only by hydrogen bonds.)

27
Q

An ionic interaction might involve an attraction between glutamate and which of the following amino acids?

  • Aspartate
  • Isoleucine
  • Arginine
A

Arginine

Ionic interactions exist between positively-charged and negatively-charged side chains. Glutamate is negatively-charged, so it would be attracted to arginine’s positively-charged side chain.

(The side chain of aspartate is negative, while that of isoleucine is uncharged.)

28
Q

At physiological pH, a protein is held together largely by ionic interactions between glutamate and arginine residues. At extremely low pH (pH < 1), what would be expected to occur to these interactions?

A

They would be disrupted because glutamate would lose its negative charge.

Ionic interactions are attractive forces between positive and negative charges. At extremely low pH, glutamate’s carboxylic acid side chain is protonated and neutral, disrupting these interactions.

29
Q

Which level (or levels) of protein structure directly involves interactions between the side chains of amino acid residues?

A

Tertiary and quaternary structure

Interestingly, only tertiary and quaternary structure involve side-chain interactions! Primary structure consists of covalent bonds that form the peptide backbone, and secondary structure consists of interactions between backbone (not side-chain) atoms.

30
Q

Define:

a native protein

A

A native protein is a protein in its normal, folded state.

For instance, native hemoglobin refers to the folded, fully functional hemoglobin protein.

31
Q

The arrangement of solvent molecules around a protein or other solute is termed the:

A

solvation layer or solvation shell.

The arrangement of the solvation layer is highly dependent on entropy and plays a critical role in protein folding.

32
Q

When considering only the protein (not its surroundings), which possesses more entropy: an unfolded protein or a native (folded) protein?

A

An unfolded protein

While entropy is a complex concept, for the sake of MCAT biochemistry, it can be conceptualized simply as “disorder.” An unfolded protein has much more flexibility (and thus, more disorder/randomness in its structure) than a tightly folded protein.

33
Q

All else being equal, a decrease in entropy corresponds to a [positive/negative] change in Gibbs free energy.

Choose one term from the box above to accurately complete the sentence.

A

All else being equal, a decrease in entropy corresponds to a positive change in Gibbs free energy.

The formula for the change in Gibbs free energy is ΔG = ΔH − TΔS. Therefore, given the negative sign in this equation, a negative ΔS corresponds to a positive ΔG. The more positive the ΔG, the less spontaneous the reaction.

34
Q

Given that protein folding constitutes a decrease in the entropy of the protein, why do proteins fold spontaneously?

A

Because protein folding increases the entropy of the solvent

From the perspective of the protein alone, folding decreases entropy and therefore would be expected to be thermodynamically unfavorable. However, protein folding also increases the entropy of the solvent. If this occurs to a greater degree than the loss of entropy by the protein, then the overall process will be thermodynamically favorable.

(Note that, while both entropy and enthalpy contribute to thermodynamic favorability, enthalpy is typically not discussed in the context of protein folding.)

35
Q

Which of the following amino acids has a side chain that cannot hydrogen bond with surrounding solvent molecules?

  • Methionine
  • Threonine
  • Lysine
A

Methionine

Methionine is a nonpolar amino acid. Nonpolar amino acids have side chains that cannot hydrogen bond with surrounding solvent molecules.

In contrast, threonine (which is polar uncharged, with an -OH-containing side chain) and lysine (which is basic and has an amino side chain) can both H-bond with the solvent.

36
Q

A protein with external-facing residues that can hydrogen bond with solvent molecules constitutes a [more/less] thermodynamically stable system than a protein with external-facing residues that cannot hydrogen bond.

Choose one term from the box above to accurately complete the sentence.

A

A protein with external-facing residues that can hydrogen bond with solvent molecules constitutes a more thermodynamically stable system than a protein with external-facing residues that cannot hydrogen bond.

The more that a protein can hydrogen bond with surrounding solvent molecules, the less organized the solvation layer will be. Less organization corresponds to greater entropy, which constitutes a more thermodynamically stable system.

37
Q

In a folded globular protein, polar and charged residues tend to be located where?

A

On the exterior of the protein

This ensures that polar side chains, which can hydrogen bond with surrounding solvent molecules, are actually facing the solvent, while nonpolar, hydrophobic residues are not solvent-facing.

38
Q

In a folded globular protein, nonpolar residues tend to be located where?

A

Buried in the protein’s interior

This minimizes contact between nonpolar (hydrophobic) side chains and the hydrophilic solvent molecules.

39
Q

The tendency for nonpolar molecules or parts of molecules to cluster away from a polar solvent is termed:

A

the hydrophobic effect.

The hydrophobic effect, which stems from entropy, is a major driving force behind protein tertiary structure.

40
Q

In a membrane-embedded protein, would asparagine or leucine be more likely to face the extracellular fluid?

A

Asparagine

In proteins, more polar residues tend to be located on the protein exterior (facing the solvent, which in this case is the extracellular fluid). Asparagine is more polar than leucine.

41
Q

On the exterior of a globular protein, a mutation replaces a serine residue with valine. How will this impact the entropy of folding of the protein?

A

The entropic penalty of protein folding will increase.

In other words, protein folding will constitute a greater decrease in entropy, meaning that folding is more unfavorable. This occurs because serine, a polar residue that “prefers” to face the exterior solvent, is being replaced with the nonpolar residue valine.

42
Q

Which part(s) of a transmembrane protein are likely to contain predominantly polar residues?

A

The extracellular and intracellular faces

A transmembrane protein contains three parts: the extracellular face, the intracellular face, and the membrane-spanning portion, which is adjacent to the nonpolar lipid bilayer. Polar residues predominate in the two solvent-facing portions.

43
Q

A large protein trimer is gradually heated until it is considered fully denatured. Which level(s) of protein structure is/are still present?

A

Primary structure only

Since the primary structure of a protein is held together by covalent bonds (specifically peptide bonds), it is much stronger than the other levels, which are held together largely by intermolecular forces. As such, full denaturation involves disrupting all levels of protein structure except primary structure.

44
Q

Most proteins that serve enzymatic functions in the human body have an optimal temperature of what value?

A

37 ºC

This is human body temperature. As one might predict, proteins in the human body tend to function best at this temperature.

45
Q

True or false:

All enzymes in the body have approximately the same optimal pH.

A

False

While all enzymes (and proteins) have an optimal pH, that value is not the same across all enzymes/proteins. For instance, parts of the digestive system are highly acidic, so enzymes that function there tend to have a relatively acidic optimal pH.

46
Q

What is the approximate optimal pH of pepsin?

A

Approximately 1.5-2.0

Pepsin is an enzyme that acts in the stomach, which is highly acidic. As such, pepsin’s optimal pH is much lower than physiological pH. Understanding that this optimal pH is somewhere in the range of 1.5 to 2 is sufficient for the MCAT.

47
Q

Which of the interactions that contribute to protein tertiary and quaternary structure are most dependent on the pH of the surroundings?

A

Ionic interactions

Ionic interactions rely on attractive forces between positively- and negatively-charged amino acid side chains. Since side chain charge varies with pH, ionic interactions are highly pH-dependent.

48
Q

What type of bonds or non-covalent interactions are disrupted by reducing agents?

A

Reducing agents disrupt disulfide bonds.

As such, exposure to reducing agents is generally required in order to fully denature a protein’s tertiary (and sometimes quaternary) structure.

49
Q

From an organic chemistry perspective, reducing agents increase the number of bonds to ________ or decrease the number of bonds to _________.

A

From an organic chemistry perspective, reducing agents increase the number of bonds to hydrogen or decrease the number of bonds to oxygen.

In the case of the reduction of disulfide bonds, reducing agents increase the number of bonds to hydrogen; as such, the disulfide bond (S-S) is broken into two separate -SH groups.

50
Q

Assuming the reaction progresses in the forward direction, does the diagram below depict reduction or oxidation?

A

Oxidation

This diagram shows the formation of a disulfide linkage, which involves the loss of bonds between sulfur and hydrogen. As such, this is oxidation. (The breakage of a disulfide linkage exemplifies reduction.)

51
Q

The reagent beta-mercaptoethanol serves to break disulfide bonds in [secondary/tertiary] structure by [reducing/oxidizing] them.

Choose one term from each box above to accurately complete the sentence.

A

The reagent beta-mercaptoethanol serves to break disulfide bonds in tertiary structure by reducing them.

Beta-mercaptoethanol is a common reducing agent. Even if you didn’t know this, you should understand that disulfide bonds are part of tertiary (not secondary) structure and that they are broken by reduction (not oxidation).

52
Q

Compounds known as detergents disrupt which type of bonds or interactions?

A

Hydrophobic interactions

Detergents are amphipathic compounds; in other words, their molecules contain both polar and nonpolar regions. Detergents disrupt hydrophobic interactions by coating the protein in detergent molecules, which are attracted to the polar protein exterior.

53
Q

True or false:

Sodium dodecyl sulfate (SDS) is a detergent. Its sulfate head is polar, while its carbon chain (the “dodecyl” in its name) is nonpolar.

A

True

As a detergent, SDS is amphipathic, meaning that it contains a polar and a nonpolar region. The front of this card accurately characterizes its structure.

54
Q

The two ends of a protein are termed the ________-terminus and the ________-terminus.

A

The two ends of a protein are termed the N-terminus and the C-terminus.

The N-terminus is the end with a free amino group, while the C-terminus contains a free carboxylic acid group.

55
Q

In which direction are proteins conventionally written?

A

Proteins are written from N-terminus to C-terminus.

For some reason, Clara (the author of this card) remembers this by simply recalling that it’s in reverse alphabetical order, but you could alternatively come up with a simple mnemonic for “NC” that works for you.

56
Q

The tetrapeptide PAGY, which has been investigated for its antioxidant properties, has which amino acid at its C-terminus?

Please answer with the full name of the amino acid.

A

Tyrosine

Proteins are conventionally written from N-terminus to C-terminus, meaning that the final amino acid in this tetrapeptide (Y) is the residue at the C-terminus. Y is the one-letter abbreviation for tyrosine.

57
Q

When a protein is translated from a template strand of mRNA, new amino acids are added to which end of the growing chain?

A

The C-terminus

Proteins are synthesized in the same direction in which they are written: from N-terminus to C-terminus. This means that new amino acids are progressively added to the C-terminus of the growing peptide chain.

58
Q

Peptide bonds form via a nucleophilic attack. In such a reaction, what acts as the nucleophile?

A

The nitrogen atom of the amino group

Here, organic chemistry overlaps with biochemistry! Nucleophiles are species that attack areas of relative positive charge. Thus, nucleophiles tend to possess either a negative charge or one or more lone pairs. The amino group of an attacking amino acid contains a lone pair on its nitrogen atom, which serves as the nucleophile for peptide bond formation.

59
Q

Define:

globular proteins

A

Globular proteins are largely round (spherical), water-soluble, functional proteins.

These proteins often serve as enzymes or transporters in the cytoplasm or the blood.

60
Q

Define:

fibrous proteins

A

Fibrous proteins are elongated, often hydrophobic, structural proteins.

Examples include proteins in connective tissue and the structural proteins that make up our hair, nails, and skin.

61
Q

Albumin is a water-soluble plasma protein found in the blood. Is albumin a fibrous or globular protein?

A

Albumin is a globular protein.

As a water-soluble, functional (not structural) protein that travels through the bloodstream, albumin is a globular protein. In contrast, fibrous proteins are generally fixed in place and play structural roles.

62
Q

Keratin is a highly water-insoluble protein found in nails, hair, calluses, and skin in humans. Is keratin a fibrous or globular protein?

A

Keratin is a fibrous protein.

As a structural protein, keratin is fibrous. Additionally, we are told that keratin is water-insoluble (hydrophobic), which is another common characteristic of fibrous proteins.

63
Q

In the sugar ribose, which carbons are attached to -OH groups?

A

The 2′ and 3′ carbons

When presented with a nucleotide’s structure on the MCAT, it can help to look at these carbons to discern whether you are being presented with RNA or DNA (as DNA lacks the 2′ -OH group).

64
Q

The sugar deoxyribose contains how many carbon atoms?

A

Five

Both deoxyribose and ribose are pentoses, meaning that they contain five carbon atoms.

65
Q

True or false:

In addition to being pentoses (five-carbon sugars), both ribose and deoxyribose typically exist as furanoses (five-membered ring structures).

A

True

It is important to be able to distinguish between the terms used to classify sugars! The terms “pentose/hexose” refer to the number of carbon atoms in a structure, while the terms “furanose/pyranose” refer to the number of atoms (of any kind) in a ring. Ribose and deoxyribose are both pentoses and furanoses.

66
Q

Sanger sequencing, a technique used for sequencing DNA, utilizes dideoxynucleotide triphosphates (ddNTPs) in its reactions. In a ddNTP, which carbon(s) is/are attached to -OH groups?

A

No carbon atoms are attached to -OH groups.

If you aren’t familiar with Sanger sequencing, you can use nomenclature to arrive at the correct answer. The word “dideoxynucleotide” indicates that these molecules are missing an -OH group in addition to what is present on a deoxynucleotide, or DNA nucleotide (which contains only a 3′ -OH group). Therefore, ddNTPs contain neither a 2′ nor a 3′ -OH.

67
Q

In the DNA backbone, the [3′/5′] carbon of the sugar of one nucleotide is connected to the [3′/5′] phosphate of the adjacent nucleotide.

Choose one term from each box above to accurately complete the sentence.

A

In the DNA backbone, the 3′ carbon of the sugar of one nucleotide is connected to the 5′ phosphate of the adjacent nucleotide.

You can answer this question by recalling that the nucleotides in DNA have phosphate groups at the 5′ carbons of their sugars (which can be remembered using the similar “f” sounds in “five-prime phosphate”).

68
Q

Name at least two atoms that are present in adenine, guanine, cytosine, uracil, and thymine.

A

Nitrogen, carbon, and hydrogen are present in all of these bases.

The “nitrogen” part here should be easy, as these are nitrogenous bases. Carbon and hydrogen compose much of the rest of these cyclic structures.

While most of these bases contain oxygen, it is not an answer here because it is not found in adenine.

69
Q

The fact that one DNA strand is read from its 5′ to its 3′ end while its complementary strand is read from 3′ to 5′ means that the strands of a DNA molecule can be described as:

A

antiparallel.

In other words, the two strands of a molecule of double-stranded DNA are oriented in opposite directions.

70
Q

Name the three forms of DNA that can exist with regard to the structure of the double helix.

A

B-DNA, Z-DNA, and A-DNA

These forms differ from each other with regard to the “handedness” (left or right) of the molecule and the exact distances involved, such as the distance between turns of the helix.

71
Q

Under normal physiological conditions, the most prevalent form of DNA is:

Choose from B-DNA, Z-DNA, and A-DNA.

A

B-DNA.

B-DNA is far more common than either Z-DNA or A-DNA and is therefore the DNA structure that you should be most familiar with. B-DNA is a right-handed double helix that contains around 10 bases per turn of the helix and that has clear major (larger) and minor (smaller) grooves in its structure.

72
Q

At physiological pH, which of the following amino acids would be expected to be attracted to DNA?

  • Lysine
  • Glutamic acid
  • Alanine
A

Lysine

It is very important to understand that, due to its backbone phosphate groups, DNA tends to be negatively charged. Therefore, it is attracted to positive species. Of the amino acids provided, lysine is the only one that is positive at physiological pH.

73
Q

Name the metal ion, an alkaline earth metal, that commonly acts as a cofactor for DNA-involved reactions.

A

Mg2+

While the overall mechanisms at play here can be complicated, you can simply think of Mg2+ as a highly positive ion that can stabilize the highly negative charge on DNA’s phosphate groups, which might otherwise repel certain reactants.

74
Q

Which has a lower molecular weight: guanine or uracil?

A

Uracil

Guanine is a purine (double-ring structure), while uracil is a pyrimidine (single-ring structure). Purines are significantly larger and heavier than pyrimidines.

75
Q

True or false:

The DNA backbone is held together by intramolecular forces, while complementary DNA strands are held together by intermolecular forces.

A

True

The sugar-phosphate DNA backbone is held together by covalent bonds, which exemplify intramolecular forces. Complementary strands are connected via the much weaker intermolecular force of hydrogen bonding.

76
Q

Which would require a greater temperature increase to denature: a bond between guanine and cytosine or a bond between adenine and thymine?

A

A bond between guanine and cytosine

Guanine and cytosine are held together by three hydrogen bonds, while adenine and thymine are attached by only two. This makes GC-rich DNA sequences more difficult to denature (with heat or any other denaturant).