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Questions and Answers
Which type of interaction is specifically classified as a Van der Waals interaction?
Which type of interaction is specifically classified as a Van der Waals interaction?
What is the dissociation energy range for covalent bonds in kcal/mol?
What is the dissociation energy range for covalent bonds in kcal/mol?
Which type of force typically has the highest dissociation energy?
Which type of force typically has the highest dissociation energy?
Which of the following can be considered a type of Van der Waals interaction?
Which of the following can be considered a type of Van der Waals interaction?
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What is the estimated dissociation energy range of a hydrogen bond in kcal/mol?
What is the estimated dissociation energy range of a hydrogen bond in kcal/mol?
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What is required for two atoms to form a covalent bond?
What is required for two atoms to form a covalent bond?
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How many covalent bonds can a carbon atom make?
How many covalent bonds can a carbon atom make?
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What characterizes an ionic bond?
What characterizes an ionic bond?
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What happens to ionic compounds like NaCl in water?
What happens to ionic compounds like NaCl in water?
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What type of interaction occurs between ions of opposite charge?
What type of interaction occurs between ions of opposite charge?
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What is the result of an intermediate difference in electronegativity between two atoms forming a bond?
What is the result of an intermediate difference in electronegativity between two atoms forming a bond?
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Which of the following describes the nature of charges in biomolecules?
Which of the following describes the nature of charges in biomolecules?
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Why is carbon considered essential for biochemical compounds?
Why is carbon considered essential for biochemical compounds?
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What is the nature of the force that arises from the interaction between an induced dipole and a nearby ion or dipole?
What is the nature of the force that arises from the interaction between an induced dipole and a nearby ion or dipole?
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Which factor is particularly important for the induction of a dipole in non-polar molecules?
Which factor is particularly important for the induction of a dipole in non-polar molecules?
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What type of interaction is described as the weakest attractive force between two non-polar groups?
What type of interaction is described as the weakest attractive force between two non-polar groups?
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At what distance do atoms start to repel each other according to Van der Waals interactions?
At what distance do atoms start to repel each other according to Van der Waals interactions?
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Which of the following statements about induced dipoles is true?
Which of the following statements about induced dipoles is true?
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What property of a carbonyl group influences the methyl group nearby?
What property of a carbonyl group influences the methyl group nearby?
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What does Van der Waals’ work primarily demonstrate?
What does Van der Waals’ work primarily demonstrate?
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What characteristic of proteins enhances the relevance of London dispersion forces despite their weakness?
What characteristic of proteins enhances the relevance of London dispersion forces despite their weakness?
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What property of an atom is described as its tendency to attract electrons?
What property of an atom is described as its tendency to attract electrons?
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Which of the following statements is true regarding noble gases?
Which of the following statements is true regarding noble gases?
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What is the common behavior of atoms with low electronegativity?
What is the common behavior of atoms with low electronegativity?
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Which of the following elements is most likely to gain electrons in a reaction?
Which of the following elements is most likely to gain electrons in a reaction?
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How do elements on the left side of the periodic table typically behave regarding their outer electrons?
How do elements on the left side of the periodic table typically behave regarding their outer electrons?
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What do the noble elements aspire to be like in chemical reactions?
What do the noble elements aspire to be like in chemical reactions?
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Which of the following describes covalent bonds?
Which of the following describes covalent bonds?
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What is the typical characteristic of atoms in the top rows of the periodic table concerning electronegativity?
What is the typical characteristic of atoms in the top rows of the periodic table concerning electronegativity?
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Which characteristic must a molecule have to be considered polar?
Which characteristic must a molecule have to be considered polar?
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Why is carbon dioxide (CO2) not considered a polar molecule?
Why is carbon dioxide (CO2) not considered a polar molecule?
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What defines a hydrogen bond?
What defines a hydrogen bond?
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Which molecular bonds are capable of forming hydrogen bonds?
Which molecular bonds are capable of forming hydrogen bonds?
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What is the strength of hydrogen bonds dependent on?
What is the strength of hydrogen bonds dependent on?
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Which of the following statements about water is correct?
Which of the following statements about water is correct?
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In which scenario would a hydrogen bond be expected to have the highest strength?
In which scenario would a hydrogen bond be expected to have the highest strength?
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What forms intramolecular hydrogen bonds?
What forms intramolecular hydrogen bonds?
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Study Notes
Biochemistry Overview
- The lecture series extends chapter 5 of the textbook.
- The textbook's chapter 5 is considered a basic introduction.
- More detailed content is covered in the lecture series.
- Students should independently study chapter 5 after the lecture.
- Chapter 4 is prerequisite knowledge.
- Chapters 1-3 will be covered later.
Lecture 1: Thermodynamics
- Lecture topics: Energy, entropy, enthalpy, and work.
Lecture 1.2: Interactions
- Topics include: Covalent bond, hydrogen bond, ionic bond, polarity, van der Waals interactions, and hydrophobic effect.
Atoms
- Atoms are composed of a positively charged nucleus surrounded by orbiting electrons.
- Bohr model (outdated) and orbitals are depicted.
Electronegativity
- Some atoms have a strong tendency to attract electrons (high electronegativity).
- Other atoms weakly attract electrons and tend to lose them (low electronegativity).
- Electronegativity correlates with position in the periodic table.
- A periodic table of electronegativity values is shown.
Electronegativity of elements
- Noble elements (inert) are stable.
- Other elements seek to achieve stable noble configurations.
- Elements on the left side of the periodic table generally lose electrons.
- Elements on the right side of the periodic table generally gain electrons.
- Most elements do neither; instead they share electrons
Covalent Bond
- Two atoms share an electron pair.
- This sharing requires atoms with similar electronegativities.
Carbon
- Carbon is a crucial element in biochemistry.
- Most biochemical compounds are built around a carbon backbone.
- Carbon's four valence electrons allow it to form four covalent bonds.
- This capability creates branched or ring-shaped structures with side chains.
C-C bond (Atomic Force Microscopy)
- Atomic Force Microscopy (AFM) can visualize covalent bonds, including between carbon atoms.
- Examples diagrams of covalent bonds are shown
Ionic Bond
- An ionic bond forms when a large difference in electronegativity exists between interacting atoms.
- One electron transfers from one atom to another.
- This results in a positive and a negative ion.
- Ionic compounds in water completely dissociate into their ions.
- Example: NaCl (sodium chloride or table salt)
Example: NaF
- Na donates an electron to F, producing ions (Na+ and F-)
- These ions create a salt crystal structure.
- In water, NaF will dissociate completely into ions
Ionic interactions (salt bridges)
- Oppositely charged ions strongly attract one another.
- Interactions of this type keep salts solid and are widespread in biomolecules.
- Charged atoms and groups are present in DNA, RNA, phospholipids, and proteins.
- Interactions of this type are called "electrostatic" due to permanency of charges.
- Charges can attract (+,-) or repel (++,--) each other
Polarity
- When atoms with intermediate electronegativity differences interact, they form covalent bonds.
- Electrons in the bond are unevenly distributed, creating a polar molecule.
- A partial charge separation occurs in the molecule.
Polarity in molecules
- A polar bond does not guarantee a polar molecule.
- For molecules like Carbon Dioxide (CO2), the polarity of the individual bonds cancel out
- Polarity requires partial charge separation due to asymmetry
Water
- Water is a polar molecule.
- The oxygen atom carries a partial negative charge.
- The hydrogen atoms carry a partial positive charge.
Hydrogen bond
- Partially positive hydrogen atoms in water are attracted to partially negative oxygen atoms in neighboring water molecules.
- Hydrogen bonding creates networks of water molecules.
- H-bonds also form between different molecules containing N-H, O-H, or F-H bonds, because these elements are highly electronegative.
Hydrogen bond (cont.)
- O-H and N-H groups are common in biomolecules
- These groups can form intermolecular H-bonds with other water molecules or other biomolecules.
- Intramolecular H-bonds can occur within a single molecule.
Strength of a hydrogen bond
- Strength depends on the distance and angle between interacting atoms or molecules.
- Short, straight bonds are strongest
- Typical enthalpies of binding depend on specific group to group interactions
Non-hydrogen dipole interactions
- Dipoles (partial charges) exert attractive or repulsive forces on other dipoles depending on orientation
- Dipole interactions are common in molecules like the C=O group.
Induced dipoles
- An ion or dipole can induce a dipole in a neighboring group, even if the neighboring group is usually nonpolar.
- Similarities in electronegativity value prevent strong bonds, such as the C-H bond.
Induced dipoles (cont)
- Atoms or groups that are normally nonpolar become polar due to neighboring dipoles or ions.
- The resulting interactions are called "induced dipoles"
- These induced dipoles create attractive interactions, referred to as "Debye forces" and are weaker than permanent dipoles
Induced dipole (cont)
- Induction of dipoles, in larger molecules with delocalized electrons is readily achieved
- Often seen in ring structures
Two induced dipoles?
- London dispersion forces are the weakest attractive forces between two nonpolar groups .
- These arise from the transient shifting of electrons, which creates temporary dipoles in the neighboring molecules.
Van der Waals interactions
- This Dutch Nobel laureate demonstrated that non-ionic, non-covalent interactions have a distance dependence.
- Atoms repel at very close distances, but attract at intermediary distances.
Van der Waals interactions (cont.)
- van der Waals forces are a collection of weak, distance-dependent attractive forces between atoms and molecules.
- Covalent and ionic bonds are not considered Van der Waals forces,
Strength of Interactions
- A table summarizing bond type, dissociation energies in kcal/mol and kJ/mol.
Hydrophobic effect
- The hydrophobic effect is not an interaction.
- It is the lack of interaction between non-polar molecules and polar molecules (water).
Hydrophobic effect (cont.)
- Polar and nonpolar molecules do not mix; nonpolar molecules are repelled by water.
- The hydrophobic effect occurs due to the greater entropy of bulk water when non-polar molecules are expelled from the water.
- This increased freedom of water molecule movement increases entropy.
Hydrophobic effect (cont.)
- Transferring non-polar molecules from water to a non-polar solvent results in a favorable change in Gibbs Free energy (∆G).
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Description
This quiz focuses on the key concepts of thermodynamics discussed in the Biochemistry lecture series, specifically extending Chapter 5 of the textbook. Students will explore energy, entropy, enthalpy, and various interactions such as covalent and hydrogen bonds. Mastery of these topics builds a foundation for further biochemistry studies.
