Other Intermolecular Forces - Biochemistry

A polar molecule has both positive and negative ends. This dipole can interact in many ways with other molecules, both polar and non-polar. If it interacts with a neighboring nonpolar molecule, there is an induced dipole within that neighbor resulting in a dipole-induced dipole force.

Biomolecules contain carbon as their key element, and they mostly contain nonmetallic elements. For example, the human body is about 65% oxygen, 20% carbon, 10% hydrogen, and 3% nitrogen - the remaining major elements that make up the human body are calcium, phosphorous, magnesium, sulfur, potassium, sodium, chlorine, and other trace elements like iron and copper. Ionic bonds are rare in biomolecules, as most biomolecules are bound via covalent bonds. Also, to create a specific biomolecule, many of the bonds must be in specific orientations-specific stereoisomers are important, especially with enzymes.

In , each bond is polar, as oxygen is much more electronegative than carbon. However, these dipole moments are equal in charge and this molecule is linear with carbon in the middle, so the entire molecule is nonpolar.

In water, oxygen is more electronegative than hydrogen; thus, electrons are pulled toward the oxygen atoms more than towards hydrogen atoms. This gives oxygen a partial negative charge and hydrogen a partial positive charge. The entire molecule is polar since water's molecular geometry is bent.

Methane includes a carbon with a hydrogen attached to each of its four bonds. Electrons are distributed relatively equally across each bond since the electronegativities of hydrogen and carbon are comparable, and the entire molecule is tetrahedral. Thus, neither the individual bonds nor the entire molecule are polar.

In , nitrogen is left with a lone pair of electrons after it bonds with three hydrogen atoms. Because of this lone pair, the molecular geometry is trigonal pyramidal and the entire molecule is polar with the nitrogen atom being slightly negative (high electronegativity) and the hydrogen atoms being slightly positive.

While the peptide bond in a polypeptide chain is locked and unable to rotate, the amino nitrogen-alpha carbon bond can rotate. Additionally, the alpha carbon-carboxyl carbon can rotate as well.

However, like in many other molecules, the cis conformation is energetically unfavorable due to steric hindrance. This steric hindrance occurs when the side chains of two residues are right next to each other within the polypeptide. This is unfavorable, and the trans conformation is therefore preferred.

An amphiphile is a molecule that contains both polar and nonpolar groups. Two tailed amphiphiles form bilayer vesicles, whereas one tailed amphiphiles in high concentrations form micelles.

Free floating is surrounded by water molecules which stabilize its positive charge. However, once these water molecules are shed due to movement through the potassium channel, something else must stabilize the positively charged ion. This is accomplished via an amino acid stretch with negatively charged residues. The amino acid stretch responsible for the stabilization is Thr-Val-Gly-Tyr-Gly.

Enantiomers have the same chemical bonds in different configurations that are non-superimposable mirror images of each other. They differ in their configuration at all chiral centers.

van der Walls interactions are weak attractive interactions that occur between any two atoms in close enough proximity for their electron clouds to interact.

A polar molecule has both positive and negative ends. This dipole can interact in many ways with other molecules, both polar and non-polar. If it interacts with a neighboring nonpolar molecule, there is an induced dipole within that neighbor resulting in a dipole-induced dipole force.

Biomolecules contain carbon as their key element, and they mostly contain nonmetallic elements. For example, the human body is about 65% oxygen, 20% carbon, 10% hydrogen, and 3% nitrogen - the remaining major elements that make up the human body are calcium, phosphorous, magnesium, sulfur, potassium, sodium, chlorine, and other trace elements like iron and copper. Ionic bonds are rare in biomolecules, as most biomolecules are bound via covalent bonds. Also, to create a specific biomolecule, many of the bonds must be in specific orientations-specific stereoisomers are important, especially with enzymes.

In , each bond is polar, as oxygen is much more electronegative than carbon. However, these dipole moments are equal in charge and this molecule is linear with carbon in the middle, so the entire molecule is nonpolar.

In water, oxygen is more electronegative than hydrogen; thus, electrons are pulled toward the oxygen atoms more than towards hydrogen atoms. This gives oxygen a partial negative charge and hydrogen a partial positive charge. The entire molecule is polar since water's molecular geometry is bent.

Methane includes a carbon with a hydrogen attached to each of its four bonds. Electrons are distributed relatively equally across each bond since the electronegativities of hydrogen and carbon are comparable, and the entire molecule is tetrahedral. Thus, neither the individual bonds nor the entire molecule are polar.

In , nitrogen is left with a lone pair of electrons after it bonds with three hydrogen atoms. Because of this lone pair, the molecular geometry is trigonal pyramidal and the entire molecule is polar with the nitrogen atom being slightly negative (high electronegativity) and the hydrogen atoms being slightly positive.

While the peptide bond in a polypeptide chain is locked and unable to rotate, the amino nitrogen-alpha carbon bond can rotate. Additionally, the alpha carbon-carboxyl carbon can rotate as well.

However, like in many other molecules, the cis conformation is energetically unfavorable due to steric hindrance. This steric hindrance occurs when the side chains of two residues are right next to each other within the polypeptide. This is unfavorable, and the trans conformation is therefore preferred.

An amphiphile is a molecule that contains both polar and nonpolar groups. Two tailed amphiphiles form bilayer vesicles, whereas one tailed amphiphiles in high concentrations form micelles.

Free floating is surrounded by water molecules which stabilize its positive charge. However, once these water molecules are shed due to movement through the potassium channel, something else must stabilize the positively charged ion. This is accomplished via an amino acid stretch with negatively charged residues. The amino acid stretch responsible for the stabilization is Thr-Val-Gly-Tyr-Gly.

Enantiomers have the same chemical bonds in different configurations that are non-superimposable mirror images of each other. They differ in their configuration at all chiral centers.

van der Walls interactions are weak attractive interactions that occur between any two atoms in close enough proximity for their electron clouds to interact.

A polar molecule has both positive and negative ends. This dipole can interact in many ways with other molecules, both polar and non-polar. If it interacts with a neighboring nonpolar molecule, there is an induced dipole within that neighbor resulting in a dipole-induced dipole force.

Biomolecules contain carbon as their key element, and they mostly contain nonmetallic elements. For example, the human body is about 65% oxygen, 20% carbon, 10% hydrogen, and 3% nitrogen - the remaining major elements that make up the human body are calcium, phosphorous, magnesium, sulfur, potassium, sodium, chlorine, and other trace elements like iron and copper. Ionic bonds are rare in biomolecules, as most biomolecules are bound via covalent bonds. Also, to create a specific biomolecule, many of the bonds must be in specific orientations-specific stereoisomers are important, especially with enzymes.

In , each bond is polar, as oxygen is much more electronegative than carbon. However, these dipole moments are equal in charge and this molecule is linear with carbon in the middle, so the entire molecule is nonpolar.

In water, oxygen is more electronegative than hydrogen; thus, electrons are pulled toward the oxygen atoms more than towards hydrogen atoms. This gives oxygen a partial negative charge and hydrogen a partial positive charge. The entire molecule is polar since water's molecular geometry is bent.

Methane includes a carbon with a hydrogen attached to each of its four bonds. Electrons are distributed relatively equally across each bond since the electronegativities of hydrogen and carbon are comparable, and the entire molecule is tetrahedral. Thus, neither the individual bonds nor the entire molecule are polar.

In , nitrogen is left with a lone pair of electrons after it bonds with three hydrogen atoms. Because of this lone pair, the molecular geometry is trigonal pyramidal and the entire molecule is polar with the nitrogen atom being slightly negative (high electronegativity) and the hydrogen atoms being slightly positive.

While the peptide bond in a polypeptide chain is locked and unable to rotate, the amino nitrogen-alpha carbon bond can rotate. Additionally, the alpha carbon-carboxyl carbon can rotate as well.

However, like in many other molecules, the cis conformation is energetically unfavorable due to steric hindrance. This steric hindrance occurs when the side chains of two residues are right next to each other within the polypeptide. This is unfavorable, and the trans conformation is therefore preferred.