Molecular Bonds and Forces - Biochemistry
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Which of the following types of bonding or interactions does not usually characterize the interactions which occur between an enzyme's active site and its substrate?
Which of the following types of bonding or interactions does not usually characterize the interactions which occur between an enzyme's active site and its substrate?
Covalent bonding is too strong to allow for the enzyme to subsequently release the substrate or product (depending on if the initial substrate or eventual product does the covalent bonding). Thus, it permanently inhibits the enzyme active site and prevents it from continuing its activity. All of the other interactions are much weaker and allow the enzyme to release the product. They are all ways in which active sites interact with their substrates.
Covalent bonding is too strong to allow for the enzyme to subsequently release the substrate or product (depending on if the initial substrate or eventual product does the covalent bonding). Thus, it permanently inhibits the enzyme active site and prevents it from continuing its activity. All of the other interactions are much weaker and allow the enzyme to release the product. They are all ways in which active sites interact with their substrates.
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Which of the following most correctly describes hydrogen bonding?
Which of the following most correctly describes hydrogen bonding?
Hydrogen bonding occurs when a molecule contains a hydrogen atom bonded to fluorine, oxygen, or nitrogen. This hydrogen becomes partially positive in charge, while the attached atom becomes partially negative. This is due to unequal electronegativity causing increased electron density for the more electronegative atom, and therefore a more negative charge. The partially positive charge then forms an electrostatic attraction to another partially negative atom nearby.
Hydrogen bonding occurs when a molecule contains a hydrogen atom bonded to fluorine, oxygen, or nitrogen. This hydrogen becomes partially positive in charge, while the attached atom becomes partially negative. This is due to unequal electronegativity causing increased electron density for the more electronegative atom, and therefore a more negative charge. The partially positive charge then forms an electrostatic attraction to another partially negative atom nearby.
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In the DNA double-helix structure, what kind of bonds connect the complementary bases together?
In the DNA double-helix structure, what kind of bonds connect the complementary bases together?
In the double-helix structure of DNA, there are 2 hydrogen bonds between adenine and thymine, and 3 hydrogen bonds between cytosine and guanine. Phosphodiester bonds are covalent bonds between the 5-C sugar and phosphate group of nucleotides (and are much stronger than the hydrogen bonds between complementary bases).
In the double-helix structure of DNA, there are 2 hydrogen bonds between adenine and thymine, and 3 hydrogen bonds between cytosine and guanine. Phosphodiester bonds are covalent bonds between the 5-C sugar and phosphate group of nucleotides (and are much stronger than the hydrogen bonds between complementary bases).
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In a solution of water, which of the following amino acids do you expect to be on the outside of a protein in its native state?
In a solution of water, which of the following amino acids do you expect to be on the outside of a protein in its native state?
In a solution of water, the outside of a folded protein is going to be in direct contact with water. Therefore, polar or ionic attractions are most favored on the outside of a protein in a solution of water since these can form attractions. The only amino acid listed that can form either polar or ionic attractions is glutamic acid.
In a solution of water, the outside of a folded protein is going to be in direct contact with water. Therefore, polar or ionic attractions are most favored on the outside of a protein in a solution of water since these can form attractions. The only amino acid listed that can form either polar or ionic attractions is glutamic acid.
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What is not true about hydrogen bonds?
What is not true about hydrogen bonds?
Hydrogen bonds are found in primary structure of protein, as well as between the bases in DNA structure. Hydrogen bonds are only found between hydrogens attached to oxygen, nitrogen, or fluorine. They increase the attraction between water molecules, therefore are harder to break in large numbers, causing an increase in boiling point.
Hydrogen bonds are found in primary structure of protein, as well as between the bases in DNA structure. Hydrogen bonds are only found between hydrogens attached to oxygen, nitrogen, or fluorine. They increase the attraction between water molecules, therefore are harder to break in large numbers, causing an increase in boiling point.
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A researcher adds three molecules together and notices no reactions. Upon further analysis, he notices that molecule A and molecule B form strong intermolecular bonds whereas molecule C doesn’t form any bonds between A and B. Which of the following might be true regarding these three molecules?
I. Molecule A might have nitrogen
II. Molecule B might have fluorine
III. Molecule C might have nitrogen
A researcher adds three molecules together and notices no reactions. Upon further analysis, he notices that molecule A and molecule B form strong intermolecular bonds whereas molecule C doesn’t form any bonds between A and B. Which of the following might be true regarding these three molecules?
I. Molecule A might have nitrogen
II. Molecule B might have fluorine
III. Molecule C might have nitrogen
An example of strong intermolecular bond is a hydrogen bond. A hydrogen bond occurs between a hydrogen atom on a molecule and an either nitrogen, oxygen, or fluorine atom on an adjacent molecule. The question states that there are bonds between molecule A and molecule B. We can assume that these are hydrogen bonds. This means that molecule A can have hydrogen atom and/or nitrogen, oxygen, or fluorine atoms. Similarly, molecule B can also have hydrogen atom and/or nitrogen, oxygen, or fluorine atoms.
Molecule C doesn’t form hydrogen bonds with either of the other two molecules. This means it cannot have hydrogen and/or nitrogen, oxygen, or fluorine atoms. This is because if molecule C had any of these atoms then it would interact with at least one of the other molecules and form hydrogen bonds (because molecule A and molecule B have these other atoms).
An example of strong intermolecular bond is a hydrogen bond. A hydrogen bond occurs between a hydrogen atom on a molecule and an either nitrogen, oxygen, or fluorine atom on an adjacent molecule. The question states that there are bonds between molecule A and molecule B. We can assume that these are hydrogen bonds. This means that molecule A can have hydrogen atom and/or nitrogen, oxygen, or fluorine atoms. Similarly, molecule B can also have hydrogen atom and/or nitrogen, oxygen, or fluorine atoms.
Molecule C doesn’t form hydrogen bonds with either of the other two molecules. This means it cannot have hydrogen and/or nitrogen, oxygen, or fluorine atoms. This is because if molecule C had any of these atoms then it would interact with at least one of the other molecules and form hydrogen bonds (because molecule A and molecule B have these other atoms).
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Classically, covalent bonds are considered __________ bonds and hydrogen bonds are __________.
Classically, covalent bonds are considered __________ bonds and hydrogen bonds are __________.
Covalent bonds occur between atoms within (or intra) molecules. This means that covalent bonds are intramolecular bonds. Hydrogen bonds, on the other hand, occur between hydrogen atoms of one molecule and either a nitrogen, an oxygen, or a fluorine atom in another molecule. Since hydrogen bonds occur between molecules, they are classified as intermolecular bonds. There are some situations in which hydrogen bonds may be formed intramolecularly, but these are special cases.
Covalent bonds occur between atoms within (or intra) molecules. This means that covalent bonds are intramolecular bonds. Hydrogen bonds, on the other hand, occur between hydrogen atoms of one molecule and either a nitrogen, an oxygen, or a fluorine atom in another molecule. Since hydrogen bonds occur between molecules, they are classified as intermolecular bonds. There are some situations in which hydrogen bonds may be formed intramolecularly, but these are special cases.
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A student notes that a molecule forms hydrogen bonds that involve chlorine atoms. What can you conclude about this observation?
A student notes that a molecule forms hydrogen bonds that involve chlorine atoms. What can you conclude about this observation?
Hydrogen bonds occur between a hydrogen atom in one molecule and either nitrogen, oxygen, or fluorine atom in another molecule. It only involves nitrogen, oxygen, or fluorine atoms because these atoms have high electronegativity. Since they have very high electronegativity, these three atoms can easily attract the electron found in the hydrogen atom and form hydrogen bonds. Chlorine doesn’t have high enough electronegativity to form hydrogen bonds.
An atom's state of matter does not determine whether an atom can form hydrogen bonds. Fluorine, just like chlorine, is a halogen and it can form hydrogen bonds.
Hydrogen bonds occur between a hydrogen atom in one molecule and either nitrogen, oxygen, or fluorine atom in another molecule. It only involves nitrogen, oxygen, or fluorine atoms because these atoms have high electronegativity. Since they have very high electronegativity, these three atoms can easily attract the electron found in the hydrogen atom and form hydrogen bonds. Chlorine doesn’t have high enough electronegativity to form hydrogen bonds.
An atom's state of matter does not determine whether an atom can form hydrogen bonds. Fluorine, just like chlorine, is a halogen and it can form hydrogen bonds.
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Which of the following is not true about hydrogen bonds?
Which of the following is not true about hydrogen bonds?
Hydrogen bonds can occur between two molecules (intermolecular) and within parts of a single molecule (intramolecular). They are weaker than covalent bonds but are stronger than a Van der Waals interaction, and this strength is determined by a number of factors including bond angle.
Hydrogen bonds can occur between two molecules (intermolecular) and within parts of a single molecule (intramolecular). They are weaker than covalent bonds but are stronger than a Van der Waals interaction, and this strength is determined by a number of factors including bond angle.
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Hydrogen bonds mostly occur between hydrogen and which other atoms?
Hydrogen bonds mostly occur between hydrogen and which other atoms?
For a hydrogen bond to occur, the atom to which the hydrogen is bonded has to have a high relative Pauling electronegativity. Only oxygen, nitrogen, and fluorine, in the upper right corner of the periodic table, have these electronegativities. Neon, argon, and xenon are, of course, inert noble gases, although xenon is sometimes assigned a high electronegativity. This is due, however, to rare bonding events -- certainly not regular hydrogen bonding. Sodium, magnesium and aluminum often form positively charged ions, so they would not tend to attract a hydrogen nucleus.
For a hydrogen bond to occur, the atom to which the hydrogen is bonded has to have a high relative Pauling electronegativity. Only oxygen, nitrogen, and fluorine, in the upper right corner of the periodic table, have these electronegativities. Neon, argon, and xenon are, of course, inert noble gases, although xenon is sometimes assigned a high electronegativity. This is due, however, to rare bonding events -- certainly not regular hydrogen bonding. Sodium, magnesium and aluminum often form positively charged ions, so they would not tend to attract a hydrogen nucleus.
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What is the maximum number of hydrogen bonds that one water molecule can form?
What is the maximum number of hydrogen bonds that one water molecule can form?
Hydrogen can form hydrogen bonds with nitrogen, oxygen, and fluorine. A water molecule consists of an oxygen atom bonded to two hydrogen atoms. Each hydrogen atom can form a hydrogen bond with a nitrogen, fluorine, or oxygen atom. Also, the oxygen, which has two lone pairs of electrons, can form two hydrogen bonds with hydrogen atoms. This sums to four hydrogen bonds per water molecule.
Hydrogen can form hydrogen bonds with nitrogen, oxygen, and fluorine. A water molecule consists of an oxygen atom bonded to two hydrogen atoms. Each hydrogen atom can form a hydrogen bond with a nitrogen, fluorine, or oxygen atom. Also, the oxygen, which has two lone pairs of electrons, can form two hydrogen bonds with hydrogen atoms. This sums to four hydrogen bonds per water molecule.
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Which molecule will not form hydrogen bonds?
Which molecule will not form hydrogen bonds?
Only nitrogen, oxygen, and fluorine can form hydrogen bonds since these three elements are very electronegative. Thus, their partial negative charge (and the presence of a lone pair of electrons) attracts a partially positive hydrogen atom. Carbon, on the other hand, is not very electronegative and thus cannot form hydrogen bonds.
Only nitrogen, oxygen, and fluorine can form hydrogen bonds since these three elements are very electronegative. Thus, their partial negative charge (and the presence of a lone pair of electrons) attracts a partially positive hydrogen atom. Carbon, on the other hand, is not very electronegative and thus cannot form hydrogen bonds.
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A: adenine
U: uracil
C: cytosine
G: guanine
T: thymine
Which of the following pairs of DNA bases would require the most energy to break?
A: adenine
U: uracil
C: cytosine
G: guanine
T: thymine
Which of the following pairs of DNA bases would require the most energy to break?
Uracil is not a base in DNA, so A-U can be ruled out as an answer. Moreover, C-G and A-T are the correct base pairs, so the other combinations can be ruled out as well. C-G requires more energy to break because there are three hydrogen bonds between these bases, while A-T has only two hydrogen bonds holding them together.
Uracil is not a base in DNA, so A-U can be ruled out as an answer. Moreover, C-G and A-T are the correct base pairs, so the other combinations can be ruled out as well. C-G requires more energy to break because there are three hydrogen bonds between these bases, while A-T has only two hydrogen bonds holding them together.
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How does the strength of hydrogen bonds compare with the strength of ionic bonds?
How does the strength of hydrogen bonds compare with the strength of ionic bonds?
Bond strengths are measured in kilojoules/mole. Hydrogen bonds can have a strength of 
. Ionic bonds can have a strength of 
. This makes hydrogen bonds much weaker than ionic bonds.
Bond strengths are measured in kilojoules/mole. Hydrogen bonds can have a strength of
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What is a chiral center?
What is a chiral center?
The substituents of a chiral center are arranged in a specific manner that cannot be superimposed on its mirror image. An example is a carbon atom with four unique substituent groups.
The substituents of a chiral center are arranged in a specific manner that cannot be superimposed on its mirror image. An example is a carbon atom with four unique substituent groups.
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Why is water conducive to hydrogen bond formation?
Why is water conducive to hydrogen bond formation?
Oxygen is more electronegative than hydrogen. This results in the electrons to spend more time with the oxygen atom making it negatively chared and the hydrogen atoms to be positively charged. The charged water molecule is then able to form hydrogen bonds with polar molecules.
Oxygen is more electronegative than hydrogen. This results in the electrons to spend more time with the oxygen atom making it negatively chared and the hydrogen atoms to be positively charged. The charged water molecule is then able to form hydrogen bonds with polar molecules.
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Which of the following explains why nonpolar molecules such as lipids spontaneously aggregate in water?
Which of the following explains why nonpolar molecules such as lipids spontaneously aggregate in water?
In aqueous solutions, lipid molecules are surrounded by a lattice-like ring of water molecules known as a clathrate shell. This locks up previously free water molecules in this state, which is not entropically favored. Though it is unavoidable that some water molecules will have to be robbed of some of their freedom of motion by forming at least one clathrate shell, the ideal scenario thermodynamically is the one in which the fewest water molecules are stuck in the shell as possible. As a result, lipid bubbles in aqueous solutions tend to go from many to one, as this results in the clathrate shell with the fewest number of water molecules. In the process, many smaller clathrate shells are broken, and many water molecules are freed, thus increasing the entropy of the system.
In aqueous solutions, lipid molecules are surrounded by a lattice-like ring of water molecules known as a clathrate shell. This locks up previously free water molecules in this state, which is not entropically favored. Though it is unavoidable that some water molecules will have to be robbed of some of their freedom of motion by forming at least one clathrate shell, the ideal scenario thermodynamically is the one in which the fewest water molecules are stuck in the shell as possible. As a result, lipid bubbles in aqueous solutions tend to go from many to one, as this results in the clathrate shell with the fewest number of water molecules. In the process, many smaller clathrate shells are broken, and many water molecules are freed, thus increasing the entropy of the system.
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Which amino acid would you expect to find in the core of a protein that is in a solution of water?
Which amino acid would you expect to find in the core of a protein that is in a solution of water?
Proteins will behave similarly to phospholipids in water; the polar groups will form favorable interactions on the surface with water, while the hydrophobic groups will be in the core and away from the water molecules. Usually, amino acids with non-polar residues will be found in the core of proteins. Tryptophan has a nonpolar side chain, and will thus be found in the core of a protein that is in a aqueous environment.
Proteins will behave similarly to phospholipids in water; the polar groups will form favorable interactions on the surface with water, while the hydrophobic groups will be in the core and away from the water molecules. Usually, amino acids with non-polar residues will be found in the core of proteins. Tryptophan has a nonpolar side chain, and will thus be found in the core of a protein that is in a aqueous environment.
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Which of the following is false about hydrophobic effects?
Which of the following is false about hydrophobic effects?
Hydrophobic effects require water to occur. The reason that hydrophobic groups tend to group together is that by doing so, the network of water molecules around them stays intact. There are no other special forces at play between hydrophobic groups. It is precisely the non-polar nature of hydrophobic groups that gives them their character; water molecules are polar. Cell membranes have a phospholipid bilayer with internal hydrophobic regions (the lipid tails), holding together the membrane.
Hydrophobic effects require water to occur. The reason that hydrophobic groups tend to group together is that by doing so, the network of water molecules around them stays intact. There are no other special forces at play between hydrophobic groups. It is precisely the non-polar nature of hydrophobic groups that gives them their character; water molecules are polar. Cell membranes have a phospholipid bilayer with internal hydrophobic regions (the lipid tails), holding together the membrane.
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How do hydrogen bonds compare in strength to covalent bonds, ionic bonds, and London dispersion forces?
How do hydrogen bonds compare in strength to covalent bonds, ionic bonds, and London dispersion forces?
Hydrogen bonds are the strongest of the intermolecular forces. However, that strength is little in comparison the strength of intramolecular forces, such as ionic and covalent bonds. The strongest of the listed forces is covalent bonds, followed by ionic bonds, hydrogen bonds, and then finally London dispersion forces.
Hydrogen bonds are important in biochemistry because of the incredible effect that they have on life due to their relative strength. But remember, this strength is not nearly as as strong as the covalent and ionic bonds, which actually hold atoms within the same molecule together.
Note, hydrogen bonds can be either an intermolecular or an intramolecular force. A hydrogen bond is considered intramolecular if it is occurring between different molecules, and intermolecular if it is occurring within the same molecule.
Hydrogen bonds are the strongest of the intermolecular forces. However, that strength is little in comparison the strength of intramolecular forces, such as ionic and covalent bonds. The strongest of the listed forces is covalent bonds, followed by ionic bonds, hydrogen bonds, and then finally London dispersion forces.
Hydrogen bonds are important in biochemistry because of the incredible effect that they have on life due to their relative strength. But remember, this strength is not nearly as as strong as the covalent and ionic bonds, which actually hold atoms within the same molecule together.
Note, hydrogen bonds can be either an intermolecular or an intramolecular force. A hydrogen bond is considered intramolecular if it is occurring between different molecules, and intermolecular if it is occurring within the same molecule.
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