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Questions and Answers
Which type of bond is less reactive due to its strength?
Which type of bond is less reactive due to its strength?
What is the bond angle associated with sp hybridised atoms?
What is the bond angle associated with sp hybridised atoms?
What geometric shape do sp3 hybridised atoms adopt?
What geometric shape do sp3 hybridised atoms adopt?
How many pi bonds are formed by sp hybridised atoms?
How many pi bonds are formed by sp hybridised atoms?
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Which of the following atoms can typically be sp2 hybridised?
Which of the following atoms can typically be sp2 hybridised?
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What effect do lone pairs have on bond angles in molecules like water?
What effect do lone pairs have on bond angles in molecules like water?
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What type of hybridisation results in a trigonal geometry?
What type of hybridisation results in a trigonal geometry?
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What restricts rotation about double and triple bonds?
What restricts rotation about double and triple bonds?
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What is the main role of amino acids in biological systems?
What is the main role of amino acids in biological systems?
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Which of the following is a key characteristic that makes a molecule 'drug-like'?
Which of the following is a key characteristic that makes a molecule 'drug-like'?
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What are the basic structural units of nucleic acids?
What are the basic structural units of nucleic acids?
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Which interaction is most critical between drugs and their receptors?
Which interaction is most critical between drugs and their receptors?
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What is the significance of stereochemistry in the context of drug molecules?
What is the significance of stereochemistry in the context of drug molecules?
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Which of these structures is considered as a monosaccharide?
Which of these structures is considered as a monosaccharide?
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Which class of vitamins is primarily important for vision?
Which class of vitamins is primarily important for vision?
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What is a primary function of lipids in the human body?
What is a primary function of lipids in the human body?
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What do skeletal formulae of organic molecules emphasize?
What do skeletal formulae of organic molecules emphasize?
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Which atoms must be explicitly shown in a skeletal formula?
Which atoms must be explicitly shown in a skeletal formula?
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What role do functional groups play in organic molecules?
What role do functional groups play in organic molecules?
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How does the presence of functional groups generally affect a drug molecule's properties?
How does the presence of functional groups generally affect a drug molecule's properties?
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What is one of the primary advantages of using skeletal formulae?
What is one of the primary advantages of using skeletal formulae?
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What composes the hydrocarbon skeleton of a molecule?
What composes the hydrocarbon skeleton of a molecule?
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Why is it important to recognize functional groups in organic molecules?
Why is it important to recognize functional groups in organic molecules?
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In a skeletal formula, what does each line end or vertex typically represent?
In a skeletal formula, what does each line end or vertex typically represent?
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What distinguishes enantiomers from each other?
What distinguishes enantiomers from each other?
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Which of the following best describes a racemic mixture?
Which of the following best describes a racemic mixture?
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What defines a chiral center in a molecule?
What defines a chiral center in a molecule?
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Which type of isomers are diastereoisomers?
Which type of isomers are diastereoisomers?
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What interaction is produced due to the proximity of dipoles?
What interaction is produced due to the proximity of dipoles?
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In which type of bond do most medicinal chemistry bonds generally fall?
In which type of bond do most medicinal chemistry bonds generally fall?
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What causes bond polarity between two atoms in a molecule?
What causes bond polarity between two atoms in a molecule?
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What role do intermolecular interactions play in biological events?
What role do intermolecular interactions play in biological events?
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What role does GABA play in the body?
What role does GABA play in the body?
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Which of the following is an example of a transport protein?
Which of the following is an example of a transport protein?
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Which level of protein structure defines the linear sequence of amino acids?
Which level of protein structure defines the linear sequence of amino acids?
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What is the primary function of structural proteins?
What is the primary function of structural proteins?
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Which of the following proteins plays a role in the immune system?
Which of the following proteins plays a role in the immune system?
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Which statement best describes the function of enzymes?
Which statement best describes the function of enzymes?
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Which option is a derivative of tyrosine that functions as a neurotransmitter?
Which option is a derivative of tyrosine that functions as a neurotransmitter?
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What role do modified amino acids play in proteins that complex with nucleic acids?
What role do modified amino acids play in proteins that complex with nucleic acids?
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What must be obtained through food as essential amino acids?
What must be obtained through food as essential amino acids?
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Why is arginine considered essential for infants and growing children?
Why is arginine considered essential for infants and growing children?
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How are amino acids classified based on the nature of their side chain?
How are amino acids classified based on the nature of their side chain?
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What is the term for compounds that have both positive and negative charges in physiological pH?
What is the term for compounds that have both positive and negative charges in physiological pH?
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At acidic pH, which state is the carboxylic group of an amino acid in?
At acidic pH, which state is the carboxylic group of an amino acid in?
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What characterizes the zwitterion form of an amino acid?
What characterizes the zwitterion form of an amino acid?
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What differentiates polar amino acids from nonpolar amino acids?
What differentiates polar amino acids from nonpolar amino acids?
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Which type of side chain is not a classification for amino acids?
Which type of side chain is not a classification for amino acids?
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Study Notes
Unit 1: Fundamental Chemistry of Drugs and Molecules of Life
- Unit Lead: Dr Richard Wheelhouse
- Unit Facilitators: Dr Sriharsha Kantamneni, Dr Maria Azmanova
- Required References: Study pack, Videos, Web links
- Recommended References: Chemistry in context, Marks' Basic Medical Biochemistry, Introduction to Medicinal Chemistry
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Learning Outcomes:
- Identify important organic functional groups in any molecular structure
- Apply basic rules of chemical nomenclature to drug substances
- Understand how atomic hybridization directs bonding and the shape of atoms and molecules
- Understand the importance of 3D shapes of molecules, including stereochemistry
- Know what makes an organic molecule 'drug-like'
- Identify important interactions between drugs and their receptors
- Describe the basic structure and function of amino acids and proteins, and describe examples which demonstrate their role in biological systems
- Describe the basic structure and function of nucleic acids and explain their widespread importance in biological systems
- Describe the basic structure of monosaccharides and polysaccharides and describe their key functions
- Describe the basic structure of lipids and explain their functional roles in the human body
- Describe the major classes of vitamins and their functional roles, and explain how their deficiencies compromise human health
- Describe the process of drug discovery
- Understand what structure-based design is
Simple Molecules
- Organic Structures: Chemical structures can be represented in different ways (e.g., molecular formula, structural formula, skeletal formula).
- Molecular Models: 3D representations are helpful in understanding chemical reactivity and interactions.
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Functional Groups: Important groups of atoms within molecules which dictate physical and chemical properties.
- Examples: Alcohol, aldehyde, ketone, carboxylic acid, amine, etc.
- Nomenclature: System for naming molecules using prefixes, parent chains, and suffixes, based on the number of carbons and functional groups.
Stereochemistry
- Stereochemistry: Spatial arrangement of atoms in molecules, showing effects on physical and chemical properties.
- Chirality: Molecules that are not superimposable on their mirror images.
- Enantiomers: Chiral molecules that are mirror images of each other.
- Diastereoisomers: Stereoisomers that are not mirror images.
Interactions Between Molecules
- Dipole Interactions: Unequal sharing of electrons leading to partial charges, impacting interactions between molecules.
- Hydrogen Bonding: Strong dipole-dipole interactions where a hydrogen atom is covalently bonded to a highly electronegative atom (e.g., O, N, F) forms a bond with another electronegative atom.
- Hydrophobic Interactions: Non-polar molecules or parts of molecules tend to cluster together in an aqueous environment to minimise contact with water.
- Charge-Charge (Ionic) Interactions: Electrostatic attraction between oppositely charged groups (e.g., salts).
Complex Molecules
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Amino Acids: Building blocks of proteins, containing an amino group, carboxyl group, and a central carbon atom with a variable side chain ('R' group).
- Types: Nonpolar, polar, charged (acidic/basic), aromatic, cyclic.
- Peptide Bonds: Bonds that link amino acids together, forming peptides and proteins (polypeptide chains).
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Protein Structure: Described by four levels:
- Primary: Sequence of amino acids
- Secondary: Local arrangement of amino acids (α-helices, β-sheets)
- Tertiary: Polypeptide's overall 3D folding
- Quaternary: Arrangement of multiple polypeptide chains to form functional units
Nucleic Acids
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Nucleic Acids: (DNA and RNA) composed of nucleotides, storing genetic information required for protein synthesis.
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DNA: Double helix with bases A-T and G-C via hydrogen bonding.
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RNA: Single-stranded molecule involved in transcription and translation processes, carrying genetic information.
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Transcription: DNA information transferred into mRNA.
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Translation: mRNA translated into amino acid sequence which make proteins.
Sugars and Polysaccharides
- Monosaccharides: Simple sugars (e.g., glucose, fructose).
- Polysaccharides: Sugars linked together that function as storage or structural components (e.g., glycogen, starch).
- Glycoproteins/glycolipids: oligosaccharide chains attached to proteins or lipids
Lipids
- Lipids: Hydrophobic molecules (e.g., fats, oils, and cholesterol), major components of cell membranes and energy storage.
- Fats/oils: Composed of fatty acids and glycerol, with both saturated (single bonds) and unsaturated (double bonds) fats.
- Cholesterol: crucial component of cell membranes and important for hormone synthesis.
Enzymes and Inhibitors
- Enzymes: Proteins that catalyse biological reactions by lowering activation energy required.
- Active Sites: Specific region of enzymes where substrates bind for reaction.
- Substrate: The molecule an enzyme acts upon.
- Enzyme/substrate complex: The temporary complex formed when the substrate binds to the enzyme active site, allowing the reaction to occur faster.
- Enzyme function/activity: Can be regulated for faster reaction rates or lowered rates when required.
- Types of enzymes: Six types that catalyse different reactions.
Drug Discovery and Design
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Drugs: Foreign compounds that interact with biological processes to obtain a therapeutic effect.
- Sources: Natural, semi-synthetic, or synthetic.
- Drug Discovery Processes: An iterative process of identifying potential drug molecules and developing them for clinical use through multiple stages including initial experiments through to clinical trials.
- Drug-receptor interaction: Mechanisms and forces involved, including covalent, ionic, hydrogen, and hydrophobic interactions.
- Structure-based drug design: Using computational chemistry to design new drugs based on the structure of protein targets (e.g., enzyme).
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