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atomic structure Flashcards

1
Q

Describe the classic circular orbital description of atoms

A

It depicts electrons circling the nucleus, which is useful for understanding bonding between atoms, but does not accurately represent the location of electrons or the three-dimensional shapes of molecules.

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2
Q

Define the significance of sodium (Na) in the periodic table

A

Sodium is element number 11 in the periodic table, indicated by having 11 electrons

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3
Q

How many electrons can the first three shells of an atom accommodate?

A

The first shell can accommodate 2 electrons, the second shell can hold 8 electrons, and the third shell can hold 18 electrons (8 electrons are all we care about)

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4
Q

Explain the limitations of the classic circular orbital model

A

While it is useful for understanding atomic bonding, it fails to provide a real indication of electron locations and the three-dimensional shapes of molecules.

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5
Q

How does the shell representation of atoms help in understanding their structure?

A

It visually represents the arrangement of electrons in different energy levels, indicating how many electrons each shell can hold

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6
Q

Describe the maximum number of electrons that can be contained in Shell 1

A

Shell 1 can contain up to 2 electrons

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7
Q

Define the term ‘valence shell’ in the context of atomic structure

A

The valence shell is the outer shell of an atom that contains the electrons involved in chemical bonding.

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8
Q

What is the significance of the periodic table in relation to electron configuration?

A

The periodic table indicates how many electrons an element has, their arrangement, and the status of the outer shell.

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9
Q

What characteristic do all elements in Group 1 of the periodic table share?

A

All elements in Group 1 are highly reactive and have a valence shell with a single electron.

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10
Q

Describe the significance of valence electrons in chemical reactivity.

A

Valence electrons in the outer shell dictate chemical reactivity and the formation of compounds. Filling or emptying this outer valence shell is essential for bond formation between atoms.

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11
Q

Define the Lewis dot symbols and their purpose.

A

Lewis dot symbols represent the valence electrons of an atom, with each dot corresponding to one electron. They are useful for visualizing how atoms use their valence shells to form bonds.

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12
Q

What does the periodic table represent in terms of atomic structure?

A

The periodic table organizes elements based on their atomic number, which corresponds to the number of protons and helps in understanding their electron configurations and chemical properties.

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13
Q

What role do outer shell electrons play in bond formation?

A

Outer shell electrons are crucial for bond formation as they determine how atoms interact and combine to form compounds.

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14
Q

Describe the stability of atoms in relation to their valence shell.

A

Atoms are most stable when they have a full valence shell of 8 electrons, or 2 electrons for hydrogen, which has only one inner shell.

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15
Q

Define the Octet Rule in the context of atomic stability

A

The Octet Rule states that atoms are most stable when they have eight electrons in their valence shell, with exceptions such as phosphorus.

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16
Q

Explain the valency of oxygen and sulfur.

A

Both oxygen and sulfur have 6 electrons in their valence shell and require 2 additional electrons to complete it, giving them a valency of 2.

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17
Q

What is the significance of valency in chemical bonding?

A

Valency indicates the number of electrons an atom can gain, lose, or share to achieve a full valence shell, which is crucial for forming bonds and compounds.

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18
Q

Describe covalent bonding

A

Covalent bonding involves atoms sharing electrons to complete their valence shells.

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19
Q

Explain ionic bonding.

A

Ionic bonding occurs when atoms gain or lose electrons to form oppositely charged ions.

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20
Q

How is a single covalent bond defined?

A

A single covalent bond is defined as one shared pair of electrons between two atoms.

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21
Q

What is the valency of oxygen and hydrogen in water?

A

Oxygen has a valency of 2, while hydrogen has a valency of 1.

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22
Q

Identify the characteristics of noble gases.

A

Noble gases have full valence shells, are chemically unreactive, and do not form covalent bonds.

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23
Q

How do atoms achieve full valence shells through bonding?

A

Atoms achieve full valence shells by either sharing electrons in covalent bonds or transferring electrons in ionic bonds.

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24
Q

What is the significance of valence shells in chemical bonding?

A

Valence shells determine how atoms bond with each other, as atoms seek to complete their outer shells.

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25
Q

Provide an example of a compound formed by ionic bonding.

A

Salt (sodium chloride) is an example of a compound formed by ionic bonding.

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26
Q

What type of bonding is present in ammonia?

A

Ammonia exhibits covalent bonding, as nitrogen shares electrons with hydrogen.

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27
Q

Define covalent bonding.

A

Covalent bonding is the sharing of electrons to complete part-filled electron shells.

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28
Q

How is ionic bonding characterized?

A

Ionic bonding is characterized by the transfer of electrons to complete or empty part-filled electron shells.

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29
Q

Explain the relationship between shared pairs and covalent bonds.

A

The number of covalent bonds is equal to the number of shared pairs of electrons.

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30
Q

What is the significance of lone pairs in chemical bonding?

A

Lone pairs are unbonded pairs of electrons that can influence the shape and reactivity of molecules.

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31
Q

Differentiate between single, double, and triple bonds.

A

A single bond consists of one shared pair of electrons, a double bond consists of two shared pairs, and a triple bond consists of three shared pairs.

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32
Q

How does valency relate to covalent bonds?

A

Valency is defined as the number of covalent bonds an atom can form, which corresponds to the number of shared pairs of electrons.

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33
Q

Illustrate the concept of electron sharing in molecular formation

A

Electron sharing occurs when atoms form covalent bonds, allowing them to achieve full outer electron shells.

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34
Q

What is the importance of understanding electron shells in chemistry?

A

Understanding electron shells is crucial for predicting how atoms will interact, bond, and form compounds.

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35
Q

Describe the significance of non-covalent bonding interactions in biological macromolecules.

A

Non-covalent bonding interactions are crucial for the activity, specificity, folding, and stability of biological macromolecules.

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36
Q

How do non-covalent interactions contribute to the stability of a molecule?

A

Non-covalent interactions, as intramolecular forces, help determine and maintain the overall shape and stability of a molecule, providing a framework for functions such as enzyme activity and lipid arrangement in cell membranes.

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37
Q

Explain the role of non-covalent interactions as intermolecular forces.

A

As intermolecular forces, non-covalent interactions are responsible for positioning and holding together multiple copies of the same polypeptide chain in biologically active molecules, such as haemoglobin.

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38
Q

Define polar bonds and their relevance to non-covalent interactions.

A

Polar bonds are groups of atoms with uneven charge distribution, leading to partial positive (δ+) and negative (δ-) charges, which interact through attraction and repulsion, playing a major role in non-covalent interactions.

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39
Q

What are dipoles and how do they relate to non-covalent interactions?

A

Dipoles are molecules or groups of atoms that have both δ+ and δ- charges, either permanently or transiently, and their interactions are significant in the stability and activity of biological macromolecules.

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40
Q

How do differences in electric charge contribute to non-covalent interactions?

A

Non-covalent interactions arise from differences in electric charge, primarily through electrostatic forces, which lead to attractions between opposite charges and repulsions between like charges.

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41
Q

Describe the nature of covalently bonded atoms in relation to electron sharing.

A

Covalently bonded atoms often do not share electrons equally, leading to the formation of polar bonds.

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42
Q

Describe the concept of electronegativity.

A

Electronegativity is a measure of an atom’s ability to attract shared electrons in a bond, and it follows the trends of the periodic table.

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43
Q

How does a large difference in electronegativity affect bonding?

A

A large difference in electronegativity results in the more electronegative atom completely withdrawing shared electrons, leading to ionic bonding.

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44
Q

Provide an example of ionic bonding based on electronegativity differences.

A

An example of ionic bonding is between sodium (Na) with an electronegativity of 0.9 and chlorine (Cl) with an electronegativity of 3.0, resulting in a difference of 2.1.

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45
Q

What type of bonding occurs with similar electronegativities?

A

Similar electronegativities lead to covalent bonding, as seen in the bond between carbon (C) with an electronegativity of 2.5 and hydrogen (H) with 2.1.

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46
Q

Explain the polarization of HCl and its behavior in solution.

A

HCl has an electronegativity difference of 0.9, making it a polar covalent molecule as a gas, but it ionizes completely in solution to form H+ and Cl-.

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47
Q

How do lone electron pairs influence the polarization of bonds?

A

Lone electron pairs, such as those on oxygen in O-H bonds, enhance charge distribution and contribute to the polarization of the bond.

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47
Q

Identify the electronegativities of oxygen and hydrogen and their implications for bonding.

A

Oxygen has an electronegativity of 3.5 and hydrogen 2.1, resulting in a difference of 1.4, which polarizes the O-H bond.

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48
Q

What role do hydrogen bonds play in biological macromolecules?

A

Hydrogen bonds, formed between electronegative atoms like O, N, or F, are central to the structure and function of biological macromolecules.

49
Q

Discuss the significance of water in biological systems.

A

Water (H2O) constitutes 50-70% of the human body and is crucial for various biological processes, including the formation of hydrogen bonds.

50
Q

Define the characteristics of hydrogen bond donors and acceptors.

A

Hydrogen bond donors are typically O, N, or F (strongly electronegative), while acceptors are usually O or N with lone pairs of electrons.

51
Q

Describe the nature of hydrogen bonds.

A

Hydrogen bonds are a special class of dipole-dipole interactions where a hydrogen atom bonded to an electronegative atom (δ+) is attracted to another electronegative atom (δ-) with non-bonded electrons, such as nitrogen or oxygen.

52
Q

How do hydrogen bonds contribute to the structure of proteins and DNA?

A

Hydrogen bonds form regular patterns that contribute to the formation of stable structures in proteins (like α-helices) and DNA (base-pairing), which are essential for their biological functions.

53
Q

Define the strength of a single hydrogen bond compared to other types of bonds.

A

A single hydrogen bond is relatively weak at about 20 kJ/mol, which is much weaker than a covalent bond but stronger than van der Waals interactions.

54
Q

Explain the significance of hydrogen bond distance in structural biology.

A

The typical distance for a strong hydrogen bond is around 2.5 to 3 Å (0.25 to 0.3 nm), which is crucial for understanding molecular interactions in structural biology.

55
Q

What is the role of hydrogen bond donors and acceptors?

A

Hydrogen bond donors are typically hydrogen atoms bonded to electronegative atoms, while acceptors are electronegative atoms with lone pairs that can attract the hydrogen, facilitating the formation of hydrogen bonds.

56
Q

How do hydrogen bonds affect the properties of ice?

A

Hydrogen bonds are additive, meaning that many hydrogen bonds can create a strong structure, such as in ice, which has a lower density than liquid water due to its hydrogen bonding arrangement.

57
Q

Describe hydrophobic forces and their relation to electrostatic interactions.

A

Hydrophobic forces arise from the interactions of polar molecules and are influenced by electrostatic forces, determining whether a molecule is stable in an aqueous environment.

58
Q

Differentiate between hydrophobic and hydrophilic molecules.

A

Hydrophobic molecules are water-hating and tend to be unstable in water, while hydrophilic molecules are water-loving and can interact favorably with water.

59
Q

How does the alignment of hydrogen bond donor and acceptor affect bond strength?

A

Hydrogen bonds are strongest when the donor hydrogen and acceptor atom are aligned in a straight line, maximizing the interaction.

60
Q

What is the importance of hydrogen bonding in biological functions?

A

Hydrogen bonding is often crucial in biological functions as it stabilizes structures and facilitates interactions necessary for the activity of biomolecules.

61
Q

Describe the characteristics of water molecules in terms of polarity.

A

Water molecules are polar, exhibiting δ+ and δ- charges arranged as a dipole.

62
Q

How do polar molecules interact with water?

A

Polar molecules interact with water through the formation of hydrogen bonds (H-bonds).

63
Q

Define hydrophilic molecules.

A

Hydrophilic molecules are those that are polar and can interact with water, making them soluble and stable in solution.

64
Q

What are amphipathic molecules?

A

Amphipathic molecules have both hydrophobic and hydrophilic parts.

65
Q

Explain the solubility of hydrophobic molecules in water.

A

Hydrophobic molecules are non-polar and do not interact with water, making them insoluble and unstable in solution.

66
Q

Identify the types of groups likely found in hydrophilic molecules.

A

Hydrophilic molecules likely contain polar groups such as OH, NH, NH2, NH3, and C=O.

67
Q

What types of groups are typically found in hydrophobic molecules?

A

Hydrophobic molecules typically contain non-polar groups such as CH, CH2, and CH3.

68
Q

Describe van der Waals forces.

A

Van der Waals forces arise from transient dipoles, induced dipoles, and charge-charge interactions, summing to create significant forces between molecules.

69
Q

What is steric repulsion in the context of molecular interactions?

A

Steric repulsion occurs when non-bonded atoms cannot approach each other closely due to the repulsion of their negative electron clouds.

70
Q

How do van der Waals interactions contribute to protein structure?

A

Van der Waals interactions contribute to the closely packed core of proteins, where many parts of the protein are in close non-bonded contact, creating a network of attractive interactions.

71
Q

What role do transient dipoles play in molecular interactions?

A

Transient dipoles arise from electron movements and can induce changes in charge on other molecules, contributing to van der Waals forces.

72
Q

Explain the significance of non-covalent molecular interactions in biological systems.

A

Non-covalent molecular interactions are crucial for the stability and function of biological macromolecules, influencing their structure and interactions.

73
Q

Describe the three main types of non-covalent interactions between molecules.

A

The three main types of non-covalent interactions are hydrogen bonds, van der Waals forces, and hydrophobicity.

74
Q

Define hydrogen bonds in the context of molecular interactions.

A

Hydrogen bonds arise from interactions between permanent dipoles, where one dipole includes a hydrogen atom and the other has a lone pair of electrons or a negative charge.

75
Q

How do van der Waals forces contribute to molecular interactions?

A

Van der Waals forces arise from interactions between transient and/or induced dipoles and between charges.

76
Q

Explain the concept of hydrophobicity in molecular interactions.

A

Hydrophobicity arises from, but does not directly involve, dipole-dipole interactions, often leading to the aggregation of non-polar molecules in aqueous environments.

77
Q

What role do ionic forces play in non-covalent interactions?

A

Ionic forces are considered ‘strong’ weak interactions that occur between ionized groups, such as the interaction between positively charged NH3+ and negatively charged COO- groups.

78
Q

Define a salt bridge in the context of ionic forces.

A

A salt bridge is the interaction between an acidic group (COO-) and a basic group (NH3+) in proteins, representing a significant non-covalent interaction.

79
Q

How do electrostatic forces relate to non-covalent molecular interactions?

A

All dipole-dipole interactions, including hydrogen bonds and ionic forces, arise directly or indirectly from electrostatic forces.

80
Q

What is the significance of acidic and basic amino acids in proteins regarding ionic forces?

A

Acidic and basic amino acids contain ionized groups (COO- and NH3+) that participate in ionic interactions, which are crucial for protein structure and function.

81
Q

Describe the role of functional groups in biomolecules.

A

Functional groups alter the physical and chemical properties of biological molecules, bringing reactivity and often polarity.

82
Q

Explain the significance of the ‘R’ group in functional groups.

A

The ‘R’ group refers to the remainder of the molecule that is attached to the functional group, influencing the molecule’s overall properties.

83
Q

How do functional groups contribute to intermolecular interactions?

A

Many functional groups allow for the formation of intra and inter-molecular interactions, such as hydrogen bonds.

84
Q

Define heterolytic and homolytic reactions.

A

Heterolytic reactions involve the breaking of a bond where one atom takes both electrons, while homolytic reactions involve the equal sharing of electrons between two atoms.

85
Q

What is the importance of free radicals in biological systems?

A

Free radicals play a crucial role in various biological processes, including signaling and the initiation of biochemical reactions.

86
Q

Identify common elements found in functional groups of biomolecules.

A

The majority of functional groups are based on carbon (C), hydrogen (H), oxygen (O), nitrogen (N), and sometimes sulfur (S) and phosphorus (P).

87
Q

How do hydroxyl groups affect molecular properties?

A

Hydroxyl groups act as hydrogen bond donors and acceptors, influencing the solubility and reactivity of compounds.

88
Q

Describe the structural formula of carbonyl groups in aldehydes.

A

The structural formula of aldehydes is represented as RCHO, where R is a hydrocarbon chain.

89
Q

What suffix is used for naming alcohols?

A

Alcohols are named by adding the suffix ‘-ol’ to the name of the corresponding hydrocarbon

90
Q

Explain the difference between aldehydes and ketones in terms of their structure.

A

Aldehydes have the carbonyl group (C=O) at the end of the carbon chain (RCHO), while ketones have it within the chain (RCOR’).

91
Q

What is the structural formula for amines?

A

Amines have the structural formula RNH2, based on ammonia (NH3), and can form primary, secondary, and tertiary amines.

92
Q

How do carboxylic acids behave in terms of hydrogen bonding?

A

Carboxylic acids can act as both hydrogen bond donors (due to the -OH group) and acceptors (due to the C=O group).

93
Q

Explain the difference between primary, secondary, and tertiary amines.

A

Primary amines have one alkyl group attached to the nitrogen, secondary amines have two, and tertiary amines have three. Only primary and secondary amines can participate in hydrogen bonding.

94
Q

Describe the alkyl group and provide examples.

A

Alkyl groups are named from the alkane chain attached to the molecule, with examples including methyl, ethyl, and propyl.

94
Q

Describe the structure and naming of amides.

A

Amides have the general formula RCONH2. They are similar to carboxylic acids but replace the -OH group with -NH2, and are named by replacing ‘-oic acid’ with ‘-amide’ (e.g., ethanamide).

95
Q

What are thiols and their significance in protein structures?

A

Thiols, with the formula RSH, can form disulfide bonds (R-S-S-R), which are important linkages in protein structures.

96
Q

Define thioesters and their relationship to carboxylic acids.

A

Thioesters are derivatives of carboxylic acids with the general formula RCOSR, where the hydroxyl group of the carboxylic acid is replaced by a thiol group.

97
Q

What is an acyl group and how is it formed?

A

An acyl group is formed by the removal of a hydroxyl group from an oxo-acid, with the general formula being an alkyl group with a double-bonded oxygen.

98
Q

What is the general formula for phosphates?

A

Phosphates have the general formula RPO4H2 and can form acyl-phosphate groups when linked with a carboxyl group, making them highly reactive.

99
Q

Explain the concept of aryl groups.

A

Aryl groups are similar to alkyl groups but relate to aromatic compounds, with the simplest example being the phenyl group.

100
Q

What is the purpose of curly arrows in reaction schemes?

A

Curly arrows are used in reaction schemes to indicate the movement of electrons during chemical reactions.

101
Q

How does the difference in electronegativity between carbon and oxygen affect their bond?

A

The difference of 1.0 indicates that the bond is polar, with electron density drawn towards the oxygen, creating a partial negative charge on the oxygen.

101
Q

How does unequal sharing of electrons influence chemical reactions?

A

Unequal sharing of electrons in heterolytic reactions affects the distribution of electrons in the bond, which in turn influences reactivity.

102
Q

Describe the role of electrons in covalent bonds.

A

Covalent bonds are formed from the sharing of valence electrons to complete a full outer shell.

103
Q

What types of reactions are influenced by electronegativity and functional groups?

A

Electronegativity and functional groups influence substitution and addition reactions, which are important in various biochemical processes.

104
Q

How do homolytic and heterolytic bond breaking differ?

A

In homolytic bond breaking, the electron pair splits, with each electron moving to a separate atom, generating free radicals. In heterolytic bond breaking, the electrons remain as a pair, leading to unequal distribution.

105
Q

What character does the carbonyl oxygen possess due to its electronegativity?

A

The carbonyl oxygen has a partial negative charge, making the carbon electrophilic and susceptible to nucleophilic attack.

106
Q

Define electronegativity.

A

Electronegativity is the tendency of an atom to attract electrons.

107
Q

Explain the significance of bond polarity in biochemical reactions.

A

Bond polarity affects reactivity, which is crucial in biochemical reactions such as substitution and addition reactions.

108
Q

Describe acyl substitution reactions.

A

Acyl substitution reactions involve the departure of a leaving group, which is then replaced by a new group.

109
Q

Identify the importance of functional group reactivity in biochemical processes.

A

Functional group reactivity is essential for processes like protein synthesis, DNA replication, and ATP generation.

110
Q

How does the electronegativity of oxygen affect acyl substitution reactions?

A

The higher electronegativity of oxygen makes the bond polar, resulting in the carbon being electrophilic.

111
Q

What is the electronegativity of carbon and oxygen?

A

The electronegativity of carbon is 2.5, while the electronegativity of oxygen is 3.5.

112
Q

Define a leaving group in the context of acyl substitution

A

A leaving group is an atom or group that departs from a molecule during a chemical reaction, allowing for the substitution of a new group.

113
Q

Identify some examples of heteroatoms that can act as leaving groups.

A

Examples of heteroatoms that can act as leaving groups include -OH, -OR, -NH2, and -SR.

114
Q

Explain the role of nucleophiles in acyl substitution reactions.

A

Nucleophiles donate a lone pair of electrons to form a bond with the electrophilic carbon during acyl substitution.

115
Q

What role does ATP play in certain acyl substitution reactions?

A

ATP is required to ‘activate’ carboxyl groups in some reactions, facilitating the substitution process.

116
Q

How does the presence of a lone pair of electrons influence nucleophilicity?

A

The presence of a lone pair of electrons allows nucleophiles to donate electrons, making them reactive in acyl substitution reactions.

117
Q

Describe the structure and naming convention of carboxylic acids.

A

Carboxylic acids have the general formula RCOOH. They are named by adding ‘-oic acid’ to the name of the corresponding alkane (e.g., ethanolic acid).

118
Q

Define esters and their naming convention.

A

Esters have the general formula RCOOR’. Their names reflect the alcohol (alkoxy-derived) and carboxylic acid group, such as ethyl propanoate.

biochem (7 decks)

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