CBI.Sum.notes -1-4.pdf

# Atomic structure and bonding This study guide summarizes the fundamental principles of atomic structure and chemical bonding, covering the subatomic particles of atoms, quantum mechanical descriptions of electrons, various types of chemical bonds, and theories explaining their formation. ## 1. Atomic structure ### 1.1 Components of an atom An atom consists of a central nucleus and surrounding electrons [1](#page=1). * **Nucleus:** Contains positively charged protons and neutral neutrons. The nucleus has an overall positive charge determined by the number of protons [1](#page=1). * **Protons:** Positively charged (+1) [1](#page=1). * **Neutrons:** Neutral [1](#page=1). * Protons and neutrons have nearly equal masses [1](#page=1). * **Electrons:** Negatively charged (-1) and have a mass approximately 1/2000th of a proton's mass, contributing minimally to the atomic mass [1](#page=1). ### 1.2 Atomic number and mass number * **Atomic number (Z):** The number of protons in an atom's nucleus. This number determines the element and the number of electrons in a neutral atom [1](#page=1). * **Atomic mass number (A):** The total number of protons and neutrons in the nucleus [1](#page=1). ### 1.3 Atomic mass unit (Da or U) The unified atomic mass unit (Da or U) is defined as 1/12th of the mass of a Carbon-12 atom. It is approximately equal to the mass of a proton or neutron (around $1.66 \times 10^{-27}$ kg) [1](#page=1). * Hydrogen-1 ($^1$H): Approximately 1.008 Da [1](#page=1). * Carbon-12 ($^{12}$C): Exactly 12.00 Da [1](#page=1). * Oxygen-16 ($^{16}$O): Approximately 16.00 Da [1](#page=1). * A typical protein weighs around 30 kDa, which is equivalent to 30,000 Da or $30,000 \times 1.66 \times 10^{-23}$ kg [1](#page=1). ### 1.4 The periodic table * Historically organized by atomic mass, it is now ordered by atomic number (Z) [1](#page=1). * **Groups (Columns):** Elements in the same group have the same number of valence electrons and thus similar chemical properties [1](#page=1). * **Periods (Rows):** Elements in the same period have the same number of electron shells [1](#page=1). ### 1.5 Atomic properties * **Ionization energy:** The energy required to eject an electron from a neutral atom [1](#page=1). * **Electron affinity:** The energy change when an electron is added to a neutral atom [1](#page=1). * **Atomic radius:** The distance from the center of the nucleus to the outermost electron shell [1](#page=1). * **Electronegativity:** The ability of an atom to attract electrons to itself in a chemical bond. It is often estimated as the average of ionization energy and electron affinity. Electronegativity differences help determine bond type [1](#page=1). ### 1.6 Isotopes Isotopes are atoms of the same element (same atomic number) with different numbers of neutrons, resulting in different atomic mass numbers. They exhibit similar chemistry due to having the same number of electrons. The periodic table lists the average atomic mass, which is a weighted average of the isotopic masses [1](#page=1). ### 1.7 Atomic models * **Bohr model:** Describes the hydrogen atom with electrons in specific orbits around the nucleus, but is limited for atoms with more than one electron [1](#page=1). * **Quantum mechanical model:** Treats electrons as having wave-like properties and describes their behavior using the Schrödinger wave equation. Solutions to this equation are wave functions ($\psi$), which, when squared ($\psi^2$), represent the probability density of finding an electron in a particular region around the atom [1](#page=1). * **Atomic orbital:** A region in an atom where there is a 90% probability of finding an electron [1](#page=1). ### 1.8 Quantum numbers Atomic orbitals are described by four quantum numbers that define the properties of an electron within an atom: * **Principal quantum number ($n$):** Determines the size and energy level of the orbital. Larger $n$ values correspond to larger orbitals further from the nucleus with higher energy. $n$ can be any positive integer (1, 2, 3,...) [1](#page=1). * **Orbital (azimuthal) quantum number ($l$):** Determines the shape of the orbital and the subshell. The values of $l$ range from 0 to $n-1$ [1](#page=1). * $l=0$ corresponds to an 's' subshell (spherical orbitals) [1](#page=1). * $l=1$ corresponds to a 'p' subshell (dumbbell-shaped orbitals) [1](#page=1). * $l=2$ corresponds to a 'd' subshell (more complex shapes) [1](#page=1). * $l=3$ corresponds to an 'f' subshell (even more complex shapes) [1](#page=1). * **Magnetic quantum number ($m_l$):** Specifies the orientation of the orbital in space. The values of $m_l$ range from $-l$ to $+l$, including 0 [1](#page=1). * For $l=0$ (s subshell), $m_l=0$ (1 orbital) [1](#page=1). * For $l=1$ (p subshell), $m_l=-1, 0, +1$ (3 orbitals) [1](#page=1). * For $l=2$ (d subshell), $m_l=-2, -1, 0, +1, +2$ (5 orbitals) [1](#page=1). * **Degenerate orbitals:** Orbitals within the same subshell but with different orientations have the same energy (e.g., $p_x$, $p_y$, $p_z$) [1](#page=1). * **Spin quantum number ($m_s$):** Describes the intrinsic angular momentum of an electron, which can be visualized as spin. An electron can have one of two spin states, usually represented as spin up ($+1/2$) or spin down ($-1/2$) [1](#page=1). ### 1.9 Pauli Exclusion Principle and Orbital Occupancy * **Pauli Exclusion Principle:** No two electrons in the same atom can have the same set of four quantum numbers. This means an atomic orbital can hold a maximum of two electrons, and they must have opposite spins [1](#page=1). * **Aufbau Principle:** Electrons fill atomic orbitals of lower energy first before occupying higher energy orbitals [1](#page=1). * **Hund's Rule:** Within a subshell, electrons will individually occupy degenerate orbitals before pairing up in any one orbital. Unpaired electrons in degenerate orbitals will have the same spin [1](#page=1). ## 2. Chemical Bonding ### 2.1 Types of chemical bonds Chemical bonds form when atoms share or transfer electrons to achieve a more stable electron configuration (#page=1, page=2) [1](#page=1) [2](#page=2). * **Ionic Bonds:** Formed by the electrostatic attraction between oppositely charged ions, which are created when atoms with a large electronegativity difference (typically > 2) transfer electrons (#page=1, page=2). The atom that loses electrons becomes a positively charged cation, and the atom that gains electrons becomes a negatively charged anion. Ionic compounds form crystal lattices [1](#page=1) [2](#page=2). * Cations are generally smaller than their parent atoms because they have fewer electrons to repel each other [2](#page=2). * Anions are generally larger than their parent atoms because the increased electron-electron repulsion expands the electron cloud [2](#page=2). * **Covalent Bonds:** Formed by the sharing of electron pairs between atoms, typically non-metals (#page=1, page=2) [1](#page=1) [2](#page=2). * **Bonding pairs:** Shared electrons [2](#page=2). * **Lone pairs:** Unshared electrons [2](#page=2). * When atoms have similar electronegativity, they share electrons more equally, forming nonpolar covalent bonds [2](#page=2). * If there's a difference in electronegativity, the shared electrons are pulled closer to the more electronegative atom, creating a polar covalent bond [2](#page=2). ### 2.2 Molecular Formulae and Representation * **Molecular Formula:** Lists the types and number of atoms in a molecule (e.g., $CO_2$, $C_6H_{12}O_6$) [2](#page=2). * **Empirical Formula:** Shows the simplest whole-number ratio of atoms in a molecule (e.g., for $C_6H_{12}O_6$, it is $CH_2O$) [2](#page=2). * **Structural Formula:** Shows the order of connectivity and arrangement of atoms in a molecule [2](#page=2). * **Skeletal Formula:** A shorthand for organic molecules where lines represent bonds and vertices/ends represent carbon atoms, with implicit hydrogens and heteroatoms shown explicitly [2](#page=2). ### 2.3 Valence Bond Theory and Hybridization Valence Bond Theory explains bonding by the overlap of atomic orbitals [2](#page=2). * **Overlap:** The sharing of electrons occurs in overlapping atomic orbitals. Greater overlap leads to stronger bonds [2](#page=2). * **Hybridization:** Atomic orbitals within an atom can combine to form new hybrid orbitals that are better suited for bonding, with specific shapes and orientations [2](#page=2). * **Sigma ($\sigma$) bonds:** Formed by head-to-head overlap of atomic orbitals along the internuclear axis [2](#page=2). * **Pi ($\pi$) bonds:** Formed by the sideways overlap of parallel p orbitals, occurring above and below the sigma bond axis. Pi bonds are weaker than sigma bonds and restrict rotation around the bond axis [2](#page=2). * **Examples of Hybridization:** * **$sp^3$ hybridization:** One s orbital and three p orbitals combine to form four identical $sp^3$ hybrid orbitals, arranged tetrahedrally. This is seen in methane ($CH_4$) [2](#page=2). * **$sp^2$ hybridization:** One s orbital and two p orbitals combine to form three $sp^2$ hybrid orbitals in a trigonal planar arrangement. The remaining unhybridized p orbital forms a $\pi$ bond. This is seen in molecules with double bonds, like ethene ($C_2H_4$) [2](#page=2). * **$sp$ hybridization:** One s orbital and one p orbital combine to form two $sp$ hybrid orbitals in a linear arrangement. The two remaining unhybridized p orbitals form two $\pi$ bonds. This is seen in molecules with triple bonds, like ethyne ($C_2H_2$) [2](#page=2). ### 2.4 Molecular Orbital Theory (MO Theory) An alternative to Valence Bond Theory, MO Theory combines atomic orbitals to form molecular orbitals that span the entire molecule. It can accurately predict bond lengths and energies but becomes complex for larger molecules [2](#page=2). ### 2.5 Fajans' Rules Fajans' rules predict the degree of ionic or covalent character in a bond based on the polarizing power of the cation and the polarizability of the anion [2](#page=2). * **Covalent character increases when:** * The cation is small and has a high charge [2](#page=2). * The anion is large and has a high charge [2](#page=2). * The cation has a high charge density [2](#page=2). ### 2.6 Bond Length and Strength As bond length increases, bond strength decreases. Bonds with more 's' character in hybridization are generally shorter and stronger than those with more 'p' character [2](#page=2). ## 3. Key Terminology * **Atom:** The smallest particle of an element that retains its chemical identity [3](#page=3). * **Element:** A substance consisting of atoms that all have the same number of protons [3](#page=3). * **Isotope:** Atoms of the same element with different numbers of neutrons [3](#page=3). * **Mole:** A unit representing a specific number of particles, equal to Avogadro's number ($6.022 \times 10^{23}$) [3](#page=3). * **Avogadro's Constant ($N_A$):** $6.022 \times 10^{23}$ $mol^{-1}$ [3](#page=3). * **Molar Mass:** The mass in grams of one mole of a substance, typically expressed in g/mol [3](#page=3). * **Molarity (Molar Concentration):** The amount of solute in moles per liter (or $dm^{-3}$) of solution [3](#page=3). * **Electronegativity:** An atom's intrinsic ability to attract electrons in a bond [3](#page=3). * **Dipole:** A separation of electric charge within a molecule [3](#page=3). * **Dipole Moment:** The magnitude of a dipole [3](#page=3). ## 4. Quantum Numbers and Atomic Orbitals Recap * **Principle quantum number ($n$):** Indicates the energy level and size of the electron shell [1](#page=1). * **Orbital quantum number ($l$):** Determines the shape of the subshell and can range from 0 to $n-1$ [1](#page=1). * For $n=3$, $l$ can be 0, 1, or 2, corresponding to 3s, 3p, and 3d subshells [4](#page=4). * **Magnetic quantum number ($m_l$):** Specifies the orientation of orbitals in space [1](#page=1). * **Spin quantum number ($m_s$):** Describes the intrinsic spin of an electron, which can be spin up or spin down [1](#page=1). ## 5. Bonding Examples * **Sodium Chloride (NaCl) formation:** Sodium (Na) has one valence electron, and Chlorine (Cl) has seven. Chlorine is more electronegative and can pull sodium's valence electron, forming a positive sodium ion ($Na^+$) and a negative chloride ion ($Cl^-$). The electrostatic attraction between these ions forms an ionic bond [4](#page=4). ## 6. Electron Configuration The arrangement of electrons in atomic orbitals follows specific rules. * **Aufbau Principle:** Fill lower energy orbitals first [1](#page=1). * **Hund's Rule:** Fill degenerate orbitals singly before pairing electrons [1](#page=1). * **Pauli Exclusion Principle:** No two electrons in an atom can have the same set of four quantum numbers (#page=1, page=3) [1](#page=1) [3](#page=3). * **Example (Nitrogen, Z=7):** Electron configuration is $1s^2 2s^2 2p^3$. The three electrons in the 2p orbitals occupy separate orbitals with parallel spins according to Hund's rule [4](#page=4). * **Shorthand Notation:** Uses the preceding noble gas to represent core electrons [4](#page=4). * Potassium (K, Z=19): $[Ar 4s^1$ [4](#page=4). * Iodine (I, Z=53): $[Kr 5s^2 4d^{10} 5p^5$ [4](#page=4). --- # Chemical calculations and acid-base chemistry This section covers fundamental chemical calculations and the principles of acid-base chemistry, including the pH scale and buffer systems. ### 2.1 Chemical calculations #### 2.1.1 Moles and Avogadro's Constant * **Mole (mol):** A unit used to measure the amount of a substance, representing a specific number of particles [1](#page=1) [2](#page=2) [3](#page=3). * **Avogadro's Number/Constant ($N_A$ or $L$):** Defined as $6.022 \times 10^{23}$ particles per mole ($mol^{-1}$) [1](#page=1) [2](#page=2) [3](#page=3). **Formula:** Amount (moles) = $\frac{\text{mass (grams)}}{\text{molar mass (g/mol)}}$ [1](#page=1) [2](#page=2) [3](#page=3). #### 2.1.2 Molar Mass * **Molar Mass:** The mass in grams of one mole of a substance. For a compound, it is calculated by summing the relative atomic masses of all its constituent elements [1](#page=1) [2](#page=2) [3](#page=3). * **Dalton (Da) / Unified Atomic Mass Unit (U):** A unit of mass equal to 1/12 the mass of an atom of Carbon-12. It is approximately the mass of a proton or neutron [1](#page=1) [2](#page=2) [3](#page=3). * **Relationship:** 1 gram per mole (g mol$^{-1}$) is equivalent to 1 Dalton (Da) [1](#page=1) [2](#page=2) [3](#page=3). #### 2.1.3 Concentration * **Solution:** A mixture where a solute is dissolved in a solvent [1](#page=1) [2](#page=2) [3](#page=3). * **Concentration:** Can be expressed in three ways: * **Molar Concentration (Molarity):** Amount of solute in moles per unit volume of solution [1](#page=1) [2](#page=2) [3](#page=3). * **Units:** mol dm$^{-3}$ (or M) [1](#page=1) [2](#page=2) [3](#page=3). * **Formula:** Molar Concentration = $\frac{\text{amount of solute (moles)}}{\text{volume of solution (litres or dm}^{-3}\text{)}}$ [1](#page=1) [2](#page=2) [3](#page=3). * A solution with one mole of a substance in one litre is a one molar (1 M) solution [1](#page=1) [2](#page=2) [3](#page=3). * **Mass Concentration:** Mass of solute per unit volume of solution [1](#page=1) [2](#page=2) [3](#page=3). * **Units:** g dm$^{-3}$ [1](#page=1) [2](#page=2) [3](#page=3). * **Formula:** Mass Concentration = $\frac{\text{mass of solute (grams)}}{\text{volume of solution (litres or dm}^{-3}\text{)}}$ [1](#page=1) [2](#page=2) [3](#page=3). * **Volume Concentration:** Volume of solute as a percentage of the total volume of the solution [1](#page=1) [2](#page=2) [3](#page=3). #### 2.1.4 Dilutions * **Dilution:** The process of reducing the concentration of a solute in a solution, usually by adding more solvent [1](#page=1) [2](#page=2) [3](#page=3). * **Formula for single dilution:** $C_1V_1 = C_2V_2$, where $C$ is concentration and $V$ is volume [1](#page=1) [2](#page=2) [3](#page=3). * $V_1$ = volume of stock solution needed [1](#page=1) [2](#page=2) [3](#page=3). * $V_2$ = final desired volume of the diluted solution [1](#page=1) [2](#page=2) [3](#page=3). * **Volume of diluent to add:** $V_2 - V_1$ [1](#page=1) [2](#page=2) [3](#page=3). * **Dilution Factor (DF):** A numerical representation of how many times the original solution has been diluted [1](#page=1) [2](#page=2) [3](#page=3). * DF = $\frac{\text{Stock Concentration}}{\text{Diluted Final Concentration}}$ [1](#page=1) [2](#page=2) [3](#page=3). * DF = $\frac{\text{Final Volume}}{\text{Volume of Stock}}$ [1](#page=1) [2](#page=2) [3](#page=3). * **Serial Dilution:** A rapid method to generate solutions of low concentrations by repeatedly diluting a stock solution [1](#page=1) [2](#page=2) [3](#page=3). > **Tip:** A dilution factor of 1:10 means the original solution has been diluted 10 times. For example, 1 part sample mixed with 9 parts solvent results in a 1:10 dilution ratio and a dilution factor of 10. ### 2.2 Acid-Base Chemistry #### 2.2.1 Acids, Bases, and Water * **Water Dissociation:** Water can dissociate into a hydrogen ion (H$^{+}$) and a hydroxide ion (OH$^{-}$). In reality, protons are not free but associate with water molecules to form hydronium ions (H$_3$O$^{+}$) [1](#page=1) [2](#page=2) [3](#page=3). * $2\text{H}_2\text{O} \rightleftharpoons \text{H}_3\text{O}^+ + \text{OH}^-$ [1](#page=1) [2](#page=2) [3](#page=3). * **Equilibrium Constant ($K_w$):** The ionic product of water is a measure of the dissociation of water [1](#page=1) [2](#page=2) [3](#page=3). * $K_w = [\text{H}^+][\text{OH}^-]$ [1](#page=1) [2](#page=2) [3](#page=3). * At 25°C, $K_w = 1.0 \times 10^{-14} \text{ M}^2$ [1](#page=1) [2](#page=2) [3](#page=3). * **Concentration of H$^{+}$ and OH$^{-}$:** The concentration of hydrogen and hydroxide ions in pure water can be found by taking the square root of $K_w$. * $[\text{H}^+] = [\text{OH}^-] = \sqrt{K_w} = 1.0 \times 10^{-7} \text{ M}$ [1](#page=1) [2](#page=2) [3](#page=3). #### 2.2.2 Brønsted-Lowry Theory * **Acid:** A proton (H$^{+}$) donor [1](#page=1) [2](#page=2) [3](#page=3). * **Base:** A proton (H$^{+}$) acceptor [1](#page=1) [2](#page=2) [3](#page=3). #### 2.2.3 Acidity and pKa * **Acid Dissociation Constant ($K_a$):** A quantitative measure of an acid's strength in solution, representing the equilibrium constant for its dissociation [1](#page=1) [2](#page=2) [3](#page=3). * For a generic acid HA: $\text{HA} \rightleftharpoons \text{H}^+ + \text{A}^-$ [1](#page=1) [2](#page=2) [3](#page=3). * $K_a = \frac{[\text{H}^+][\text{A}^-]}{[\text{HA}]}$ [1](#page=1) [2](#page=2) [3](#page=3). * **pKa:** The negative logarithm (base 10) of the $K_a$ value [1](#page=1) [2](#page=2) [3](#page=3). * $pK_a = -\log_{10}(K_a)$ [1](#page=1) [2](#page=2) [3](#page=3). * **Stronger acids** have higher $K_a$ values and lower (or negative) $pK_a$ values, indicating greater dissociation [1](#page=1) [2](#page=2) [3](#page=3). * **Weaker acids** have lower $K_a$ values and higher $pK_a$ values, indicating less dissociation [1](#page=1) [2](#page=2) [3](#page=3). #### 2.2.4 pH Scale * **pH:** A measure of the acidity or alkalinity of a solution, based on the concentration of hydrogen ions [1](#page=1) [2](#page=2) [3](#page=3). * **pH < 7:** Acidic (higher [H$^{+}$] than [OH$^{-}$]) [1](#page=1) [2](#page=2) [3](#page=3). * **pH = 7:** Neutral (equal [H$^{+}$] and [OH$^{-}$]) [1](#page=1) [2](#page=2) [3](#page=3). * **pH > 7:** Basic/Alkaline (higher [OH$^{-}$] than [H$^{+}$]) [1](#page=1) [2](#page=2) [3](#page=3). * **Logarithmic Scale:** A one-unit change in pH represents a tenfold change in [H$^{+}$] [1](#page=1) [2](#page=2) [3](#page=3). * **Formula:** $\text{pH} = -\log_{10}[\text{H}^+]$ [1](#page=1) [2](#page=2) [3](#page=3). * **Calculating pH of Strong Acids:** The molar concentration of the strong acid is directly used as the [H$^{+}$] concentration, as strong acids fully dissociate [1](#page=1) [2](#page=2) [3](#page=3). * Example: For a 0.1 M HCl solution, $[\text{H}^+] = 0.1$ M, so pH = $-\log_{10}(0.1) = 1$. * **Calculating pH of Weak Acids:** Use the $K_a$ value and assume the concentration of undissociated acid remains relatively constant at equilibrium [1](#page=1) [2](#page=2) [3](#page=3). * **Formula:** $[\text{H}^+] = (\text{K}_a \times [\text{HA}])^{0.5}$ [1](#page=1) [2](#page=2) [3](#page=3). * **pH of Strong Bases:** Calculate the hydroxide ion concentration [OH$^{-}$] from the molarity of the strong base, then use $K_w$ to find [H$^{+}$] and subsequently the pH [1](#page=1) [2](#page=2) [3](#page=3). * **Relationship:** $\text{pH} + \text{pOH} = 14$ [1](#page=1) [2](#page=2) [3](#page=3). * $\text{pOH} = -\log_{10}[\text{OH}^-]$ [1](#page=1) [2](#page=2) [3](#page=3). #### 2.2.5 Buffers and the Henderson-Hasselbalch Equation * **pH Buffer:** An aqueous solution containing a weak acid and its conjugate base, or a weak base and its conjugate acid, that resists changes in pH upon addition of small amounts of acid or base [1](#page=1) [2](#page=2) [3](#page=3). * **Buffering Capacity:** Weak acids and bases buffer most effectively within a pH range of approximately $\pm 1$ unit around their $pK_a$ value [1](#page=1) [2](#page=2) [3](#page=3). * **Preparation:** A buffer solution is typically prepared by mixing a solution of a weak acid with a solution of a salt of that same acid [1](#page=1) [2](#page=2) [3](#page=3). * **Henderson-Hasselbalch Equation:** Used to estimate the pH of a buffer solution [1](#page=1) [2](#page=2) [3](#page=3). * $\text{pH} = pK_a + \log_{10}\left(\frac{[\text{A}^-]}{[\text{HA}]}\right)$ where $[\text{A}^-]$ is the concentration of the conjugate base and $[\text{HA}]$ is the concentration of the weak acid [1](#page=1) [2](#page=2) [3](#page=3). * **Ionization State:** The equation helps determine the ionization state of a functional group based on the pH relative to its $pK_a$ [1](#page=1) [2](#page=2) [3](#page=3). * If $\text{pH} < pK_a$, the group is mostly protonated (acid form) [1](#page=1) [2](#page=2) [3](#page=3). * If $\text{pH} > pK_a$, the group is mostly deprotonated (base form) [1](#page=1) [2](#page=2) [3](#page=3). * If $\text{pH} = pK_a$, the group is 50% ionized [1](#page=1) [2](#page=2) [3](#page=3). --- # Biomolecules: Structure and function Biomolecules are the essential organic molecules that form the basis of life, categorized into four major classes: carbohydrates, lipids, nucleic acids, and proteins, each with unique structures and functions crucial for cellular processes [2](#page=2) [3](#page=3). ### 3.1 Carbohydrates Carbohydrates, commonly known as sugars, are essential for energy storage, fuel, metabolic processes, and structural support. Their general formula is $(CH_2O)_n$ [3](#page=3). #### 3.1.1 Monosaccharides Monosaccharides are the simplest sugars, serving as the building blocks for larger carbohydrates. They are classified into two main subclasses based on the position of their carbonyl group (C=O) [3](#page=3): * **Aldoses**: Contain an aldehyde functional group (R-CH=O) at the end of the carbon chain. Examples include glucose and glyceraldehyde [3](#page=3). * **Ketoses**: Contain a ketone functional group (R-C(=O)-R') within the carbon chain. Examples include fructose and dihydroxyacetone [3](#page=3). Monosaccharides can exist in both open-chain and cyclic forms, with cyclization occurring when a hydroxyl group attacks the carbonyl group, forming a hemiacetal (from aldoses) or hemiketal (from ketoses). This cyclization creates a new stereocenter at the anomeric carbon, leading to two possible configurations: alpha ($\alpha$) and beta ($\beta$) anomers, which differ in the orientation of the hydroxyl group relative to the ring structure. These cyclic forms are often represented using Haworth projections [3](#page=3). #### 3.1.2 Disaccharides Disaccharides are formed when two monosaccharides are linked together by a glycosidic bond through a condensation reaction, releasing water. The nomenclature of disaccharides specifies the monosaccharides involved and the type of glycosidic bond [3](#page=3). * **Glycosidic bond**: Formed between the anomeric carbon of one monosaccharide and a hydroxyl group of another. * **Sucrose**: A disaccharide where both anomeric carbons (C1) of glucose and fructose are involved in an $\alpha$,$\beta$-1,2 glycosidic bond [3](#page=3). * **Lactose**: Composed of glucose and galactose, linked by a $\beta$-1,4 glycosidic bond, with one free anomeric carbon [3](#page=3). #### 3.1.3 Polysaccharides Polysaccharides are long chains of covalently bonded monosaccharides. Their structure and properties are determined by the type of monosaccharide units and the glycosidic linkages [3](#page=3): * **Cellulose**: Formed by $\beta$-D-glucose units linked via $\beta$-1,4 glycosidic bonds, providing structural support in plants [3](#page=3). * **Starch and Glycogen**: Composed of $\alpha$-D-glucose units linked via $\alpha$-1,4 glycosidic bonds. Starch consists of amylose (a linear helix) and amylopectin (branched via $\alpha$-1,6 linkages). Glycogen is more highly branched than amylopectin and serves as an energy store in animals [3](#page=3). Carbohydrates also function in post-translational modifications, such as in the ABO blood groups [3](#page=3). ### 3.2 Lipids Lipids are a diverse group of molecules characterized by their insolubility in water, serving as energy stores, structural components, and signaling molecules [3](#page=3). #### 3.2.1 Fatty Acids Fatty acids are long hydrocarbon chains with a terminal carboxylic acid group. They are classified based on saturation [3](#page=3): * **Saturated fatty acids**: Contain only single bonds between carbon atoms [3](#page=3). * **Unsaturated fatty acids**: Contain one or more double bonds. The stereochemistry of these double bonds (cis or trans, often denoted as Z or E) significantly affects their properties and packing. Cis (Z) configuration introduces a kink in the chain, while trans (E) is straighter [3](#page=3). Fatty acids are further categorized by chain length: short-chain (1-5 carbons), medium-chain (6-12 carbons), long-chain (13-21 carbons), and very long-chain (22+ carbons). Saturation is often indicated by notation like "16:0" for a 16-carbon saturated fatty acid, or "20:2" for a 20-carbon fatty acid with two double bonds. The position of double bonds can be specified from either the methyl end (n-7) or the carboxyl end (C-9) [3](#page=3). #### 3.2.2 Triacylglycerols Triacylglycerols are the primary form of stored energy in animals. They consist of a glycerol molecule esterified to three fatty acids [3](#page=3). #### 3.2.3 Glycerophospholipids Glycerophospholipids are major components of cellular membranes. They have a glycerol backbone esterified to two fatty acid chains and a phosphate group, which is further linked to a head group (e.g., choline, serine, inositol). These molecules are amphipathic, possessing both hydrophobic tails and hydrophilic heads, allowing them to form lipid bilayers, vesicles, and micelles in aqueous environments [3](#page=3). #### 3.2.4 Sphingolipids Sphingolipids are a class of phospholipids that utilize a sphingoid backbone, derived from serine and acetyl-CoA. They can be classified based on their head groups [3](#page=3): * **Sphingomyelins**: Contain a phosphate linked to choline or ethanolamine and are found in myelin sheaths [3](#page=3). * **Cerebrosides**: Have a monosaccharide as a head group and are found in neuron membranes [3](#page=3). * **Gangliosides**: Possess an oligosaccharide head group, including sialic acid units, and are present in the brain [3](#page=3). Sphingolipids are crucial for stabilizing lipid membranes [3](#page=3). #### 3.2.5 Sterol Lipids Sterol lipids, such as cholesterol, are predominantly found in eukaryotes. They feature a rigid, hydrophobic ring system and a polar hydroxyl group, making them amphipathic. Cholesterol is a precursor for steroid hormones and plays a vital role in maintaining membrane fluidity and stability [3](#page=3). #### 3.2.6 Lipid Aggregation Due to their amphipathic nature, lipids spontaneously aggregate in aqueous solutions to minimize contact between their hydrophobic tails and water. This phenomenon, known as the hydrophobic effect, leads to the formation of structures like micelles (from single fatty acids) and lipid bilayers or vesicles (from phospholipids and sphingolipids). The hydrophobic interior of these structures dictates membrane permeability [3](#page=3). * **Melting Temperature ($T_m$)**: The temperature at which a lipid bilayer transitions from a solid to a liquid phase. Saturated fatty acids pack tightly, increasing $T_m$ and membrane rigidity. Unsaturated fatty acids, with their kinks, pack less tightly, decreasing $T_m$ and increasing membrane fluidity [3](#page=3). ### 3.3 Nucleotides Nucleotides are the building blocks of nucleic acids (DNA and RNA) and also play crucial roles in cellular metabolism (e.g., ATP, GTP), second messenger systems (e.g., cAMP), and as enzyme substrates. A nucleotide consists of a ribose sugar, a phosphate group, and a nitrogenous base [3](#page=3). In nucleic acids, nucleotides are linked via phosphodiester bonds between the phosphate group of one nucleotide and the 3' carbon of the sugar of another, forming a sugar-phosphate backbone. DNA typically exists as a double helix, stabilized by hydrogen bonds between complementary base pairs (A-T with two hydrogen bonds, G-C with three hydrogen bonds). The higher number of hydrogen bonds in G-C pairs contributes to a higher melting temperature of DNA. The DNA helix has a diameter of approximately 2 nm, with bases stacked about 0.34 nm apart, and a full turn occurring every 3.4 nm, typically accommodating 10 base pairs [3](#page=3). ### 3.4 Proteins Proteins are polymers of amino acids linked by peptide bonds formed between the carboxyl group of one amino acid and the amino group of another through a condensation reaction. The sequence of amino acids (primary structure) determines the protein's higher-order structures and ultimate function [3](#page=3). * **Primary Structure**: The linear sequence of amino acids [3](#page=3). * **Secondary Structure**: Local folding patterns, such as $\alpha$-helices and $\beta$-sheets, stabilized by hydrogen bonds between backbone atoms [3](#page=3). * **Tertiary Structure**: The overall three-dimensional shape of a single polypeptide chain, stabilized by various non-covalent interactions (hydrogen bonds, ionic interactions, van der Waals forces, hydrophobic interactions) and sometimes covalent disulfide bridges between cysteine residues [3](#page=3). * **Quaternary Structure**: The association of multiple polypeptide subunits to form a functional protein complex [3](#page=3). Protein folding is a complex process often aided by chaperone proteins and driven by the minimization of Gibbs free energy. The structure and function of proteins can be investigated using various bioanalytical techniques, including protein purification via chromatography (size exclusion, ion exchange, affinity) and electrophoresis (SDS-PAGE). Enzymes, which are biological catalysts, are typically proteins whose three-dimensional structure is critical for their function. They speed up reactions by lowering activation energy without being consumed. The kinetics of enzyme-catalyzed reactions are often described by the Michaelis-Menten equation, characterized by parameters like $V_{max}$ (maximum velocity) and $K_m$ (substrate concentration at half $V_{max}$). Enzyme activity is influenced by factors such as pH, temperature, and the presence of inhibitors or cofactors [3](#page=3). --- # Metabolic pathways: Glycolysis, Krebs cycle, and oxidative phosphorylation Metabolic pathways are a series of interconnected biochemical reactions that occur within living organisms to sustain life, primarily focusing on energy production and utilization. ## 4. Metabolic pathways: Glycolysis, Krebs cycle, and oxidative phosphorylation Metabolic pathways are crucial for generating the energy required for cellular functions. This section focuses on three key pathways: glycolysis, the Krebs cycle (also known as the citric acid cycle or TCA cycle), and oxidative phosphorylation. These pathways are central to cellular respiration, the process by which cells convert glucose and other fuel molecules into ATP, the cell's primary energy currency. ### 4.1 Glycolysis Glycolysis is the initial metabolic pathway that breaks down glucose into pyruvate, generating a small amount of ATP and electron carriers (NADH) in the process. This pathway occurs in the cytosol and does not require oxygen, making it an anaerobic process [2](#page=2). #### 4.1.1 Overview of Glycolysis Glycolysis involves a series of ten enzyme-catalyzed reactions that convert one molecule of glucose (a six-carbon sugar) into two molecules of pyruvate (a three-carbon molecule). The overall reaction is [2](#page=2): Glucose + 2 NAD$^+$ + 2 ADP + 2 Pi $\rightarrow$ 2 Pyruvate + 2 NADH + 2 H$^+$ + 2 ATP + 2 H$_2$O [2](#page=2). #### 4.1.2 Stages of Glycolysis Glycolysis can be divided into two main phases: 1. **Investment Phase:** This phase requires an input of energy to prepare glucose for cleavage. * **Reaction 1: Phosphorylation:** Glucose is phosphorylated to glucose-6-phosphate by hexokinase using ATP. This step traps glucose within the cell by making it negatively charged and also prevents it from diffusing out of the cell [2](#page=2). * Reaction: Glucose + ATP $\rightarrow$ Glucose-6-phosphate + ADP [2](#page=2). * **Reaction 2: Isomerization:** Glucose-6-phosphate is converted to fructose-6-phosphate by phosphoglucose isomerase. This step rearranges the molecule to prepare it for symmetrical cleavage [2](#page=2). * Reaction: Glucose-6-phosphate $\rightleftharpoons$ Fructose-6-phosphate [2](#page=2). * **Reaction 3: Phosphorylation:** Fructose-6-phosphate is phosphorylated to fructose-1,6-bisphosphate by phosphofructokinase again using ATP. This is a highly regulated, irreversible step [2](#page=2). * Reaction: Fructose-6-phosphate + ATP $\rightarrow$ Fructose-1,6-bisphosphate + ADP [2](#page=2). 2. **Payoff Phase:** This phase generates ATP and NADH through substrate-level phosphorylation. * **Reaction 4: Cleavage:** Fructose-1,6-bisphosphate is split into two three-carbon molecules: dihydroxyacetone phosphate and glyceraldehyde-3-phosphate by aldolase [2](#page=2). * Reaction: Fructose-1,6-bisphosphate $\rightleftharpoons$ Dihydroxyacetone phosphate + Glyceraldehyde-3-phosphate [2](#page=2). * **Reaction 5: Isomerization:** Dihydroxyacetone phosphate is converted into glyceraldehyde-3-phosphate by triosephosphate isomerase. This ensures both molecules entering the payoff phase are glyceraldehyde-3-phosphate [2](#page=2). * Reaction: Dihydroxyacetone phosphate $\rightleftharpoons$ Glyceraldehyde-3-phosphate [2](#page=2). * **Reactions 6-10:** These reactions convert glyceraldehyde-3-phosphate into pyruvate, producing ATP and NADH. Key reactions include: * Oxidation and phosphorylation of glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate, producing NADH [2](#page=2). * Substrate-level phosphorylation: 1,3-bisphosphoglycerate transfers a phosphate group to ADP, forming ATP, catalyzed by phosphoglycerate kinase [2](#page=2). * Phosphate group rearrangement by phosphoglycerate mutase [2](#page=2). * Dehydration of 2-phosphoglycerate to phosphoenolpyruvate by enolase [2](#page=2). * Final substrate-level phosphorylation: Phosphoenolpyruvate transfers a phosphate to ADP, forming ATP and pyruvate, catalyzed by pyruvate kinase. This is another irreversible step [2](#page=2). #### 4.1.3 Net Products of Glycolysis For each molecule of glucose, glycolysis yields: * 2 molecules of pyruvate [2](#page=2). * 2 molecules of ATP (net production: 4 ATP produced - 2 ATP consumed) [2](#page=2). * 2 molecules of NADH [2](#page=2). ### 4.2 Krebs Cycle (Citric Acid Cycle) The Krebs cycle is a central metabolic pathway that further oxidizes the products of glycolysis, acetyl-CoA, to generate electron carriers (NADH and FADH$_2$) and a small amount of ATP or GTP. It takes place in the mitochondrial matrix [2](#page=2). #### 4.2.1 Overview of the Krebs Cycle Before entering the Krebs cycle, pyruvate is converted to acetyl-CoA through oxidative decarboxylation, a process catalyzed by the pyruvate dehydrogenase complex [2](#page=2). **Pyruvate + NAD$^+$ + CoA $\rightarrow$ Acetyl-CoA + NADH + CO$_2$ + H$^+$** [2](#page=2). The Krebs cycle then begins with acetyl-CoA combining with oxaloacetate to form citrate. Through a series of reactions, citrate is oxidized, releasing carbon dioxide, generating ATP (or GTP), NADH, and FADH$_2$, and regenerating oxaloacetate to continue the cycle [2](#page=2). The overall stoichiometry for one turn of the Krebs cycle (starting from acetyl-CoA) is: Acetyl-CoA + 3 NAD$^+$ + FAD + ADP + Pi + 2 H$_2$O $\rightarrow$ CoA + 3 NADH + 3 H$^+$ + FADH$_2$ + ATP + 2 CO$_2$ [2](#page=2). **Key Steps:** 1. **Citrate Synthesis:** Acetyl-CoA (2 carbons) condenses with oxaloacetate (4 carbons) to form citrate (6 carbons) [2](#page=2). 2. **Isomerization:** Citrate is isomerized to isocitrate [2](#page=2). 3. **Oxidative Decarboxylation:** Isocitrate is oxidized and decarboxylated, producing $\alpha$-ketoglutarate, NADH, and CO$_2$ [2](#page=2). 4. **Oxidative Decarboxylation:** $\alpha$-ketoglutarate is oxidized and decarboxylated to succinyl-CoA, generating NADH and CO$_2$ [2](#page=2). 5. **Substrate-Level Phosphorylation:** The energy released from breaking the thioester bond in succinyl-CoA drives the synthesis of ATP (or GTP) from ADP (or GDP) and Pi, forming succinate [2](#page=2). 6. **Oxidation:** Succinate is oxidized to fumarate, producing FADH$_2$ [2](#page=2). 7. **Hydration:** Fumarate is hydrated to L-malate [2](#page=2). 8. **Oxidation:** L-malate is oxidized to regenerate oxaloacetate, producing NADH [2](#page=2). #### 4.2.1 Electron Carriers The Krebs cycle produces significant amounts of NADH and FADH$_2$, which are crucial for the next stage of energy production. These molecules are reduced electron carriers that will donate electrons to the electron transport chain [2](#page=2). ### 4.3 Oxidative Phosphorylation Oxidative phosphorylation is the primary process for ATP synthesis during aerobic respiration, occurring on the inner mitochondrial membrane. It involves two coupled processes: the electron transport chain (ETC) and chemiosmosis [2](#page=2). #### 4.3.1 Electron Transport Chain (ETC) The ETC is a series of protein complexes embedded in the inner mitochondrial membrane that accept electrons from NADH and FADH$_2$. As electrons move through the chain, they are passed sequentially to electron acceptors with progressively higher reduction potentials [2](#page=2). * **Complexes:** The ETC consists of four main enzyme complexes (Complex I-IV) and mobile electron carriers like ubiquinone (Coenzyme Q) and cytochrome c [2](#page=2). * **Complex I (NADH-Q oxidoreductase):** Oxidizes NADH, transfers electrons to ubiquinone, and pumps protons from the mitochondrial matrix to the intermembrane space [2](#page=2). * **Complex II (Succinate-Q reductase):** Oxidizes FADH$_2$ (which enters the ETC at this complex), transfers electrons to ubiquinone [2](#page=2). * **Complex III (Q-cytochrome c oxidoreductase):** Receives electrons from ubiquinone, transfers them to cytochrome c, and pumps protons across the membrane [2](#page=2). * **Complex IV (Cytochrome c oxidase):** Receives electrons from cytochrome c and transfers them to oxygen, the final electron acceptor, reducing it to water. This complex also pumps protons [2](#page=2). * **Proton Pumping:** The energy released from electron transport is used to pump protons (H$^+$) from the mitochondrial matrix into the intermembrane space, creating an electrochemical gradient known as the proton-motive force [2](#page=2). #### 4.3.2 Chemiosmosis and ATP Synthesis The proton gradient generated by the ETC represents a form of stored potential energy. This energy is harnessed by ATP synthase, a large enzyme complex also embedded in the inner mitochondrial membrane [2](#page=2). * **ATP Synthase:** This enzyme acts as a molecular motor. Protons flow back down their concentration gradient from the intermembrane space into the matrix through a channel in the F$_0$ component of ATP synthase. This flow of protons drives the rotation of a central stalk, which in turn causes conformational changes in the F$_1$ catalytic component [2](#page=2). * **ATP Production:** The conformational changes in the F$_1$ component facilitate the phosphorylation of ADP to ATP, using the energy from the proton flow [2](#page=2). #### 4.3.3 ATP Yield The number of ATP molecules produced per molecule of glucose varies depending on the shuttle system used to transport NADH from glycolysis into the mitochondria. * Each NADH entering the ETC from the mitochondrial matrix yields approximately 2.5 ATP [2](#page=2). * Each FADH$_2$ yields approximately 1.5 ATP [2](#page=2). In total, aerobic respiration can yield a maximum of about 30-32 ATP molecules per molecule of glucose, with the majority produced through oxidative phosphorylation [2](#page=2). ### 4.4 Regulation of Metabolic Pathways These pathways are tightly regulated to meet the cell's energy demands and maintain homeostasis. Regulation often occurs at key irreversible steps, involving allosteric effectors (like ATP, ADP, AMP, citrate, and NADH), covalent modification of enzymes, and hormonal control (e.g., insulin and glucagon). The coordinated regulation of glycolysis and gluconeogenesis ensures that glucose is either produced or consumed appropriately to maintain blood glucose levels [2](#page=2). --- # Enzyme kinetics and regulation Enzyme kinetics and regulation are fundamental to understanding how biological catalysts function and how their activity is controlled within living organisms. ### 5.1 Enzyme kinetics Enzyme kinetics studies the rates of enzyme-catalyzed reactions and the factors that influence them. This field is crucial for understanding drug development, as many drugs target specific enzymes [3](#page=3). #### 5.1.1 Enzyme activity and substrate concentration * The rate of an enzyme-catalyzed reaction is influenced by substrate concentration ([S]) [3](#page=3). * At low substrate concentrations, the reaction rate is directly proportional to the substrate concentration, exhibiting **first-order kinetics** [3](#page=3). * At high substrate concentrations, the enzyme becomes saturated with substrate, and the reaction rate reaches a plateau, becoming independent of further increases in substrate concentration. This is known as **zero-order kinetics** [3](#page=3). * The maximum velocity of a reaction, denoted as $V_{max}$, is reached when the enzyme is saturated with substrate [3](#page=3). #### 5.1.2 Michaelis-Menten kinetics The Michaelis-Menten equation describes the relationship between the initial reaction velocity ($v$) and substrate concentration ([S]) [3](#page=3): $$ v = \frac{V_{max}[S]}{K_m + [S]} $$ * $V_{max}$ represents the maximum reaction velocity, achieved when the enzyme is fully saturated with substrate [3](#page=3). * $K_m$ (Michaelis constant) is the substrate concentration at which the reaction rate is half of $V_{max}$ [3](#page=3). * A low $K_m$ indicates that the enzyme has a high affinity for its substrate, reaching half-maximal velocity at a low substrate concentration [3](#page=3). * A high $K_m$ indicates a low affinity, requiring a higher substrate concentration to reach half-maximal velocity [3](#page=3). * $K_m$ is unique for each enzyme and is independent of enzyme concentration [3](#page=3). #### 5.1.3 Lineweaver-Burk equation (Double reciprocal plot) The Lineweaver-Burk equation is a linearized form of the Michaelis-Menten equation, useful for graphically determining $V_{max}$ and $K_m$. It plots $1/v$ against $1/[S]$ [3](#page=3): $$ \frac{1}{v} = \frac{K_m}{V_{max}} \left( \frac{1}{[S]} \right) + \frac{1}{V_{max}} $$ * The y-intercept of the Lineweaver-Burk plot is $1/V_{max}$. * The x-intercept is $-1/K_m$. * The slope of the line is $K_m/V_{max}$. #### 5.1.4 Turnover number ($k_{cat}$) * $k_{cat}$, also known as the turnover number, represents the maximum number of substrate molecules an enzyme can convert into product per second when the enzyme is working at its maximum speed (saturated with substrate) [3](#page=3). * It is a measure of the catalytic efficiency of an enzyme [3](#page=3). * **Catalytic efficiency** is often expressed as the ratio $k_{cat}/K_m$, providing a measure of how efficiently an enzyme converts substrate to product. A higher $k_{cat}/K_m$ value indicates greater efficiency [3](#page=3). ### 5.2 Factors affecting enzyme activity Several environmental factors can significantly influence the rate of enzyme-catalyzed reactions. #### 5.2.1 Effect of pH * Enzyme activity is highly sensitive to pH [3](#page=3). * Each enzyme has an **optimum pH** at which its activity is maximal [3](#page=3). * Deviations from the optimum pH can alter the ionization state of amino acid residues in the active site or affect the overall enzyme structure, leading to reduced activity [3](#page=3). * Extreme pH values can cause irreversible denaturation of the enzyme [3](#page=3). #### 5.2.2 Effect of temperature * Like pH, temperature has an optimal range for enzyme activity [3](#page=3). * Increasing temperature generally increases reaction rates due to increased kinetic energy of molecules [3](#page=3). * However, beyond the optimum temperature, enzymes become **denatured**. This occurs as excessive heat causes the enzyme molecule to vibrate so rapidly that non-covalent bonds are broken, disrupting its secondary and tertiary structure, rendering it inactive [3](#page=3). ### 5.3 Enzyme regulation Enzyme activity is tightly controlled through various mechanisms to meet cellular needs and respond to environmental changes. #### 5.3.1 Allosteric regulation * **Allosteric regulation** involves molecules binding to an enzyme at a site other than the active site (an **allosteric site**) [3](#page=3). * Binding to an allosteric site can either increase (allosteric activation) or decrease (allosteric inhibition) enzyme activity by causing a conformational change in the enzyme [3](#page=3). * Allosteric inhibitors can decrease enzyme activity by stabilizing a less active conformation or by preventing substrate binding [3](#page=3). * **Allosteric enzymes**, often multi-subunit proteins with quaternary structure, do not typically follow Michaelis-Menten kinetics. Their activity versus substrate concentration plots often show a **sigmoidal shape**, indicating cooperativity [3](#page=3). #### 5.3.2 Reversible covalent modifications * Enzymes involved in signal transduction pathways are frequently regulated by reversible covalent modifications [3](#page=3). * Common modifications include **phosphorylation** (addition of a phosphate group), acetylation, methylation, and carboxylation [3](#page=3). * For example, phosphorylation can induce a conformational change in an enzyme, leading to activation or inactivation, and this modification can be reversed by other enzymes (e.g., phosphatases) [3](#page=3). #### 5.3.3 Enzyme inhibition Enzyme inhibitors are molecules that bind to enzymes and reduce their activity [3](#page=3). * **Reversible inhibitors** form temporary, non-covalent bonds with enzymes and can be further classified: * **Competitive inhibitors:** These molecules bind to the enzyme's active site, competing with the substrate. They increase the apparent $K_m$ but do not affect $V_{max}$, as their effect can be overcome by a sufficiently high substrate concentration [3](#page=3). * **Uncompetitive inhibitors:** These inhibitors bind only to the enzyme-substrate (ES) complex, preventing product release. They reduce both $V_{max}$ and $K_m$ proportionally [3](#page=3). * **Non-competitive inhibitors:** These bind to a site distinct from the active site and reduce enzyme activity by decreasing the effective concentration of active enzyme. They decrease $V_{max}$ but do not alter $K_m$ [3](#page=3). * **Mixed inhibitors:** These can bind to both the enzyme and the ES complex, affecting both $V_{max}$ and $K_m$ in a more complex manner [3](#page=3). * **Irreversible inhibitors** bind covalently to the enzyme, permanently inactivating it [3](#page=3). #### 5.3.4 Cofactors * Many enzymes require **cofactors**, which are non-protein chemical compounds that assist in enzymatic function [3](#page=3). * **Coenzymes** are a type of cofactor that are small, organic molecules, often derived from vitamins, that bind to the active site and participate in the reaction [3](#page=3). #### 5.3.5 Allosteric inhibition vs. other inhibition types * Allosteric inhibitors can produce effects similar to competitive, non-competitive, or uncompetitive inhibition depending on how they affect substrate binding and enzyme conformation [3](#page=3). * A key distinction is that allosteric inhibitors regulate enzyme activity by binding at a site separate from the active site [3](#page=3). --- ## Common mistakes to avoid - Review all topics thoroughly before exams - Pay attention to formulas and key definitions - Practice with examples provided in each section - Don't memorize without understanding the underlying concepts

| Term | Definition | |---|---| | Atom | The smallest unit of an element that retains the chemical properties of that element, consisting of a nucleus (protons and neutrons) and electrons. | | Molecule | An electrically neutral entity composed of two or more atoms chemically bonded together. | | Isotope | Atoms of the same element that have the same number of protons but different numbers of neutrons, resulting in different atomic masses. | | Quantum numbers | A set of numbers used to describe the energy, shape, orientation, and spin of an electron in an atom. The four main quantum numbers are the principal quantum number (n), orbital quantum number (l), magnetic quantum number (m_L), and spin quantum number (m_S). | | Atomic orbital | A region in space around the nucleus of an atom where there is a high probability (typically 90%) of finding an electron. | | Electronegativity | A measure of an atom's ability to attract electrons in a chemical bond. | | Covalent bond | A chemical bond formed by the sharing of electron pairs between atoms. | | Ionic bond | A chemical bond formed by the electrostatic attraction between oppositely charged ions, typically resulting from the transfer of electrons from one atom to another. | | Hybridization | The mixing of atomic orbitals within an atom to form new hybrid orbitals that are better suited for bonding, resulting in different shapes and orientations. | | Sigma bond | A type of covalent bond formed by the direct, head-on overlap of atomic orbitals along the internuclear axis. | | Pi bond | A type of covalent bond formed by the sideways overlap of atomic orbitals, typically p orbitals, above and below the internuclear axis. | | VSEPR theory | Valence Shell Electron Pair Repulsion theory, which predicts the molecular geometry of molecules based on the repulsion between electron pairs in the valence shell of the central atom. | | Mole | A unit of measurement representing a specific number of particles (Avogadro's number, $6.022 \times 10^{23}$) of a substance. | | Molar mass | The mass of one mole of a substance, expressed in grams per mole (g/mol). | | Molarity | A measure of concentration defined as the number of moles of solute per liter (or cubic decimeter) of solution, expressed in mol/L or M. | | Acid | A substance that donates protons (H+) in a solution, according to the Brønsted-Lowry definition. | | Base | A substance that accepts protons (H+) in a solution, according to the Brønsted-Lowry definition. | | pH buffer | An aqueous solution that resists changes in pH upon the addition of small amounts of acid or base, typically containing a weak acid and its conjugate base or a weak base and its conjugate acid. | | Strong acid | An acid that completely dissociates in aqueous solution, releasing all its protons. | | Weak acid | An acid that only partially dissociates in aqueous solution, establishing an equilibrium between the undissociated acid and its ions. | | Isomerism | The phenomenon where two or more compounds have the same molecular formula but different structural or spatial arrangements of atoms, leading to different physical and chemical properties. | | Enantiomers | Stereoisomers that are non-superimposable mirror images of each other, meaning they have the same connectivity but differ in their three-dimensional arrangement and rotate plane-polarized light in opposite directions. | | Diastereomers | Stereoisomers that have different configurations at one or more chiral centers but are not mirror images of each other. | | Anomer | A specific type of epimer that forms at the anomeric carbon of a cyclic saccharide after ring closure. | | Hydrogen bond | A weak intermolecular or intramolecular attraction between a hydrogen atom bonded to a highly electronegative atom (like oxygen, nitrogen, or fluorine) and another electronegative atom with a lone pair of electrons. | | Thermodynamics | The branch of physics concerned with heat and its relation to other forms of energy and work. It studies the transfer and transformation of energy in chemical and physical processes. | | Enthalpy (H) | A thermodynamic property representing the total heat content of a system, defined as the sum of its internal energy and the product of its pressure and volume. | | Exothermic reaction | A reaction that releases energy, usually in the form of heat, into its surroundings, resulting in a decrease in the enthalpy of the system. | | Endothermic reaction | A reaction that absorbs energy, usually in the form of heat, from its surroundings, resulting in an increase in the enthalpy of the system. | | Entropy (S) | A thermodynamic measure of the dispersal or randomness of energy within a system. The second law of thermodynamics states that the total entropy of an isolated system can only increase over time. | | Gibbs free energy (G) | A thermodynamic potential that measures the maximum amount of reversible work that may be performed by a thermodynamic system at a constant temperature and pressure. Its change ($ \Delta G $) determines the spontaneity of a reaction: $ \Delta G < 0 $ is spontaneous, $ \Delta G > 0 $ is non-spontaneous, and $ \Delta G = 0 $ is at equilibrium. | | Catalyst | A substance that increases the rate of a chemical reaction without itself undergoing any permanent chemical change. It functions by providing an alternative reaction pathway with a lower activation energy. | | Nucleophile | A chemical species that donates an electron pair to form a covalent bond. Nucleophiles are typically electron-rich and often carry a negative charge or have a lone pair of electrons. | | Electrophile | A chemical species that accepts an electron pair to form a covalent bond. Electrophiles are typically electron-poor and often carry a positive charge or have an incomplete electron shell. | | Carbohydrates | Organic compounds with the general formula $ (CH_2O)_n $, composed of carbon, hydrogen, and oxygen, serving as primary energy sources and structural components in cells. | | Fatty acids | Long hydrocarbon chains with a carboxyl group ($ -COOH $) at one end, which are fundamental building blocks of lipids. | | Lipids | A diverse group of hydrophobic molecules that includes fats, oils, waxes, steroids, and phospholipids, essential for energy storage, cell membrane structure, and signaling. | | Membranes | Biological structures, primarily composed of phospholipid bilayers, that enclose cells and cellular organelles, regulating the passage of substances and compartmentalizing cellular functions. | | Nucleotides | The monomeric units of nucleic acids (DNA and RNA), consisting of a nitrogenous base, a pentose sugar (ribose or deoxyribose), and one or more phosphate groups. | | Proteins | Macromolecules composed of amino acid subunits linked by peptide bonds, performing a vast array of functions within cells, including enzymatic activity, structural support, and transport. | | Enzyme | A biological catalyst, typically a protein, that accelerates the rate of specific biochemical reactions by lowering the activation energy. | | Michaelis constant ($K_m$) | The substrate concentration at which the reaction rate of an enzyme-catalyzed reaction is half of its maximum velocity ($V_{max}$). It is often used as an indicator of the enzyme's affinity for its substrate. | | Maximum velocity ($V_{max}$) | The maximum rate of an enzyme-catalyzed reaction, achieved when the enzyme is saturated with substrate. | | Turnover number ($k_{cat}$) | The maximum number of substrate molecules that an enzyme molecule can convert into product per unit time, when the enzyme is operating at its maximum rate. | | Glycolysis | The metabolic pathway that converts glucose into pyruvate, producing ATP and NADH in the process. It occurs in the cytoplasm and does not require oxygen. | | Gluconeogenesis | The metabolic pathway that synthesizes glucose from non-carbohydrate precursors, such as lactate, amino acids, and glycerol, primarily occurring in the liver. | | Substrate-level phosphorylation | The direct transfer of a phosphate group from a high-energy substrate molecule to ADP, forming ATP, typically occurring during glycolysis and the Krebs cycle. | | Normoglycaemia | The condition of having a normal blood glucose concentration, typically within the range of 4-8 mM. | | Hypoglycaemia | A condition characterized by abnormally low blood glucose levels. | | Oxidative decarboxylation | A reaction that involves both the removal of carbon dioxide and the oxidation of a molecule, often coupled with the reduction of electron carriers like NAD+. | | Krebs cycle (TCA cycle) | A series of metabolic reactions occurring in the mitochondrial matrix that oxidizes acetyl-CoA, producing ATP, NADH, FADH2, and releasing carbon dioxide. | | Electron transport chain (ETC) | A series of protein complexes embedded in the inner mitochondrial membrane that transfer electrons from NADH and FADH2 to oxygen, coupled with the pumping of protons across the membrane to create a proton gradient. | | Oxidative phosphorylation | The process by which ATP is synthesized using the energy derived from the electron transport chain and the subsequent flow of protons back across the inner mitochondrial membrane through ATP synthase. | | Sterocenter | An atom in a molecule that is bonded to four different atoms or groups, such that switching any two of these groups results in a stereoisomer. | | Stereoisomers | Molecules with the same molecular formula and connectivity but different spatial arrangements of atoms. | | Structural isomers | Molecules with the same molecular formula but different bonding arrangements of atoms. | | Optical isomer | Stereoisomers that are non-superimposable mirror images of each other. | | Racemate | An equimolar mixture of two enantiomers. | | Fischer projection | A two-dimensional representation of a three-dimensional molecule, typically used for sugars and amino acids, where horizontal lines represent bonds projecting out of the plane and vertical lines represent bonds projecting into the plane. | | Anomeric carbon | The carbon atom in a cyclic saccharide that was originally the carbonyl carbon (aldehyde or ketone) in the open-chain form and is now bonded to two oxygen atoms. | | Glycosidic bond | A type of covalent bond that links a carbohydrate molecule to another group, which may be another carbohydrate, a protein, or a lipid. | | Phospholipid | A type of lipid that is a major component of cell membranes, consisting of a hydrophilic head (a phosphate group linked to a variable group) and two hydrophobic fatty acid tails. | | Triacylglycerol | A lipid formed from glycerol esterified with three fatty acids, serving as a major form of energy storage. | | Sphingolipid | A class of lipids that have a backbone of sphingosine, a complex amino alcohol, and are important components of cell membranes, particularly in the nervous system. | | Amphiphilic | Having both hydrophilic (water-attracting) and hydrophobic (water-repelling) properties, characteristic of molecules like phospholipids that form cell membranes. | | Hydrophobic effect | The tendency of nonpolar molecules to aggregate in aqueous solution, driven by the exclusion of water molecules and the increase in entropy of the solvent. | | DNA double helix | The characteristic structure of DNA, consisting of two antiparallel polynucleotide strands wound around a central axis, held together by hydrogen bonds between complementary base pairs. | | Peptide bond | A covalent bond formed between the carboxyl group of one amino acid and the amino group of another, linking amino acids together to form proteins. | | Primary structure of protein | The linear sequence of amino acids in a polypeptide chain. | | Secondary structure of protein | Localized folding of the polypeptide chain into regular structures like alpha-helices and beta-sheets, stabilized by hydrogen bonds between backbone atoms. | | Tertiary structure of protein | The overall three-dimensional shape of a single polypeptide chain, formed by various interactions between amino acid side chains. | | Quaternary structure of protein | The arrangement of multiple polypeptide subunits in a multi-subunit protein complex. | | Bioanalysis | Techniques used to study the structure, function, and interactions of biological molecules. | | Chromatography | A laboratory technique used to separate mixtures of compounds based on their differing distributions between a stationary phase and a mobile phase. | | SDS-PAGE | Sodium dodecyl sulfate-polyacrylamide gel electrophoresis, a technique used to separate proteins based on their molecular weight. | | ATP synthase | An enzyme complex embedded in the inner mitochondrial membrane that uses the energy of a proton gradient to synthesize ATP from ADP and inorganic phosphate. | | Aerobic respiration | The metabolic process that occurs in the presence of oxygen to convert glucose into carbon dioxide and water, generating a large amount of ATP. | | Glycolysis | The metabolic pathway that breaks down glucose into two molecules of pyruvate, producing a net of two ATP molecules and two NADH molecules. | | Gluconeogenesis (GNG) | The synthesis of glucose from non-carbohydrate precursors, such as lactate, amino acids, and glycerol. | | Krebs cycle (TCA cycle) | A series of chemical reactions used to generate energy, in the form of ATP, NADH, and FADH2, by oxidizing acetyl-CoA. | | Oxidative phosphorylation | The process by which ATP is synthesized using the energy released from the transfer of electrons from NADH and FADH2 to oxygen, via the electron transport chain. | | Electron transport chain (ETC) | A series of protein complexes in the inner mitochondrial membrane that facilitate the transfer of electrons and pump protons, creating a gradient that drives ATP synthesis. | | Proton-motive force | The potential energy stored in the proton gradient across a membrane, generated by the electron transport chain, which powers ATP synthesis. | | Warburg effect | The observation that cancer cells often exhibit increased glycolysis even in the presence of oxygen, a phenomenon that supports rapid cell proliferation. | | Endothermic reaction | A reaction that absorbs heat from its surroundings, leading to a decrease in temperature. | | Exothermic reaction | A reaction that releases heat into its surroundings, leading to an increase in temperature. | | Gibbs energy | A thermodynamic potential that measures the maximum amount of non-expansion work that can be extracted from a thermodynamic system. Its change ($ \Delta G $) indicates the spontaneity of a process. | | Catalyst | A substance that increases the rate of a chemical reaction without being consumed in the process. | | Carbohydrates | Organic compounds that serve as a primary source of energy and play structural roles in living organisms, typically with the empirical formula $ (CH_2O)_n $. | | Fatty acids | Long hydrocarbon chains with a terminal carboxyl group, forming the basis of many lipids. | | Lipids | A broad group of naturally occurring molecules including fats, waxes, sterols, fat-soluble vitamins, monoglycerides, diglycerides, triglycerides, and phospholipids, which are characterized by their insolubility in water. | | Membranes | Semipermeable barriers that enclose cells and organelles, primarily composed of a lipid bilayer. | | Nucleotides | The building blocks of nucleic acids (DNA and RNA), consisting of a nitrogenous base, a pentose sugar, and a phosphate group. | | Proteins | Macromolecules made up of amino acid chains, responsible for a vast range of functions in living organisms. | | Enzyme | A biological catalyst that speeds up biochemical reactions by lowering the activation energy. | | $K_m$ | The Michaelis constant, representing the substrate concentration at which the enzyme's activity is half of its maximum. | | $V_{max}$ | The maximum rate of an enzyme-catalyzed reaction when the enzyme is saturated with substrate. | | $k_{cat}$ | The catalytic constant, representing the number of substrate molecules converted to product per enzyme molecule per second. | | Glycolysis | The metabolic pathway that converts glucose into pyruvate, producing ATP and NADH. | | Gluconeogenesis (GNG) | The synthesis of glucose from non-carbohydrate precursors. | | Investment phase (of glycolysis) | The initial steps of glycolysis where ATP is consumed to activate glucose and prepare it for cleavage. | | Payoff phase (of glycolysis) | The latter stages of glycolysis where ATP and NADH are produced through substrate-level phosphorylation and oxidation reactions. | | Substrate-level phosphorylation | The direct transfer of a phosphate group from a high-energy substrate molecule to ADP, forming ATP. | | Normoglycaemia | Normal blood glucose levels. | | Hypoglycaemia | Low blood glucose levels. | | Oxidative decarboxylation | A reaction that removes carbon dioxide and oxidizes a molecule, often coupled with NAD+ reduction. | | Krebs/TCA cycle | A central metabolic pathway that oxidizes acetyl-CoA, generating ATP, NADH, and FADH2. | | Electron transport chain (ETC) | A series of protein complexes in the inner mitochondrial membrane that transfer electrons, ultimately to oxygen, creating a proton gradient. | | Oxidative phosphorylation | The process of ATP synthesis driven by the proton gradient established by the ETC, utilizing ATP synthase. | | Uncouplers | Compounds that disrupt the coupling between the electron transport chain and ATP synthesis by dissipating the proton gradient, leading to increased oxygen consumption without ATP production. | | Warburg effect | The observation that cancer cells preferentially use glycolysis even in the presence of oxygen. | | Endothermic reaction | A reaction that absorbs heat from the surroundings. | | Exothermic reaction | A reaction that releases heat into the surroundings. | | Gibbs energy | A thermodynamic potential that determines the spontaneity of a process. | | Catalyst | A substance that increases the rate of a chemical reaction without being consumed. | | Nucleophile | An electron-pair donor. | | Electrophile | An electron-pair acceptor. | | Carbohydrates | Sugars, starches, and cellulose, important for energy and structure. | | Fatty acids | Long hydrocarbon chains with a carboxyl group, forming lipids. | | Lipids | Hydrophobic molecules essential for cell membranes and energy storage. | | Membranes | Lipid bilayers that enclose cells and organelles. | | Nucleotides | The monomers of nucleic acids (DNA and RNA). | | Proteins | Polymers of amino acids with diverse biological functions. | | Enzyme | A biological catalyst that accelerates reactions. | | $K_m$ | Michaelis constant, indicating substrate concentration at half maximal velocity. | | $V_{max}$ | Maximum reaction velocity of an enzyme. | | $k_{cat}$ | Turnover number, the rate at which an enzyme converts substrate to product. | | Glycolysis | The breakdown of glucose into pyruvate. | | Gluconeogenesis (GNG) | The synthesis of glucose from non-carbohydrate precursors. | | Investment phase (of glycolysis) | The initial energy-consuming steps of glycolysis. | | Payoff phase (of glycolysis) | The ATP and NADH producing steps of glycolysis. | | Substrate level phosphorylation | Direct ATP synthesis from a substrate. | | Normoglycaemia | Normal blood glucose levels. | | Hypoglycaemia | Low blood glucose levels. | | Oxidative decarboxylation | Removal of CO2 and oxidation, e.g., pyruvate to acetyl-CoA. | | Krebs/TCA cycle | A metabolic pathway that oxidizes acetyl-CoA, producing ATP, NADH, and FADH2. | | Electron transport chain (ETC) | A series of protein complexes that transfer electrons, generating a proton gradient. | | Oxidative phosphorylation | ATP synthesis coupled to the ETC and proton gradient. |