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CBI.Sum.notes -8-13.pdf
Summary
# Atomic structure and quantum numbers
The behavior and properties of electrons within atoms are precisely described by a set of four quantum numbers, which define the characteristics of atomic orbitals and the electrons they contain [1](#page=1).
### 1.1 Fundamental atomic structure
An atom consists of a central nucleus, containing positively charged protons and neutral neutrons, surrounded by negatively charged electrons [1](#page=1).
* **Nucleus:** Contains protons (positive charge) and neutrons (neutral). The number of protons determines the element's atomic number (Z). Protons and neutrons have similar masses [1](#page=1).
* **Electrons:** Negatively charged particles that orbit the nucleus. Their mass is approximately 1/2000th of a proton's mass and they contribute negligibly to the overall atomic mass [1](#page=1).
* **Atomic Mass Unit (Da or U):** Defined as 1/12th the mass of a carbon-12 atom, it's approximately the mass of a proton or neutron [1](#page=1).
* **Atomic Number (Z):** Equal to the number of protons in the nucleus. It dictates the number of electrons in a neutral atom [1](#page=1).
* **Mass Number (A):** The total number of protons and neutrons in the nucleus [1](#page=1).
* **Isotopes:** Atoms of the same element (same Z, thus same number of protons and electrons) but with different numbers of neutrons, resulting in different mass numbers (A) [1](#page=1).
#### 1.1.1 The Bohr model and quantum mechanical model
* **Bohr Model:** Describes the hydrogen atom with electrons in specific orbits around a central nucleus. It is limited and inaccurate for atoms with more than one electron [1](#page=1).
* **Quantum Mechanical Model:** Recognizes electrons' wave-like properties, described by wave functions derived from the Schrödinger equation. Wave functions represent probability densities, indicating the likelihood of finding an electron in a particular region around the atom [1](#page=1).
### 1.2 Atomic orbitals and quantum numbers
Atomic orbitals are regions where an electron has a 90% probability of being found. These orbitals are defined by four quantum numbers, and no two electrons in an atom can share the same set of all four quantum numbers (Pauli Exclusion Principle) [1](#page=1).
* **1.2.1 Principal quantum number ($n$)**
* Specifies the electron shell and determines the size and energy level of an atomic orbital [1](#page=1).
* Values are positive integers: $n = 1, 2, 3, \dots$ [1](#page=1).
* Larger $n$ values indicate orbitals further from the nucleus, with higher energy and greater size [1](#page=1).
* As $n$ increases, shells can accommodate more subshells [1](#page=1).
* **1.2.2 Orbital quantum number (or azimuthal quantum number, $l$)**
* Specifies the subshell and determines the shape of the orbital [1](#page=1).
* For a given $n$, $l$ can take values from $0$ to $(n-1)$ [1](#page=1).
* Subshells are denoted by letters:
* $l=0 \implies s$ subshell (spherical shape) [1](#page=1).
* $l=1 \implies p$ subshell (dumbbell shape, with lobes on opposite sides of the nucleus) [1](#page=1).
* $l=2 \implies d$ subshell (more complex, lobed shapes) [1](#page=1).
* $l=3 \implies f$ subshell (even more complex shapes) [1](#page=1).
* **1.2.3 Magnetic quantum number ($m_l$)**
* Specifies the number and orientation of atomic orbitals within a subshell [1](#page=1).
* For a given $l$, $m_l$ values range from $-l$ to $+l$, including 0 [1](#page=1).
* The number of possible $m_l$ values for a given $l$ is $(2l+1)$, indicating the number of orbitals in that subshell [1](#page=1).
* For $l=0$ (s subshell), $m_l = 0$ (1 s orbital) [1](#page=1).
* For $l=1$ (p subshell), $m_l = -1, 0, +1$ (3 p orbitals) [1](#page=1).
* For $l=2$ (d subshell), $m_l = -2, -1, 0, +1, +2$ (5 d orbitals) [1](#page=1).
* For $l=3$ (f subshell), $m_l = -3, -2, -1, 0, +1, +2, +3$ (7 f orbitals) [1](#page=1).
* **Degenerate atomic orbitals:** Orbitals within the same subshell but with different orientations have the same energy (e.g., $p_x, p_y, p_z$ orbitals) [1](#page=1).
* **1.2.4 Spin quantum number ($m_s$)**
* Describes the intrinsic angular momentum (spin) of an electron within an orbital [1](#page=1).
* Electrons can have one of two spin values: $+1/2$ or $-1/2$ [1](#page=1).
* Each orbital can hold a maximum of two electrons, provided they have opposite spins (Pauli Exclusion Principle) [1](#page=1).
#### 1.2.4.1 Orbital occupancy principles
* **Aufbau Principle:** Electrons fill orbitals starting with the lowest energy levels first [1](#page=1).
* **Hund's Rule:** Within a subshell, electrons will individually occupy each degenerate orbital before pairing up in any one orbital. Electrons in singly occupied orbitals will have the same spin [1](#page=1).
### 1.3 Example of quantum number relationships
For a given principal quantum number ($n$), the possible values for the orbital quantum number ($l$) range from $0$ to $(n-1)$. For example, if $n=3$, then $l$ can be $0, 1,$ or $2$. Each $l$ value corresponds to a subshell:
* $l=0$: s subshell [1](#page=1).
* $l=1$: p subshell [1](#page=1).
* $l=2$: d subshell [1](#page=1).
Therefore, the third principal shell ($n=3$) contains three subshells: 3s, 3p, and 3d [1](#page=1).
---
# Chemical bonding and molecular geometry
This section explores the fundamental principles governing how atoms connect to form molecules and how the arrangement of these atoms dictates molecular shape.
### 2.1 Types of chemical bonds
Chemical bonds are the forces that hold atoms together in molecules and compounds. The type of bond formed is primarily determined by the difference in electronegativity between the bonded atoms.
#### 2.1.1 Ionic bonds
Ionic bonds form when there is a large difference in electronegativity (typically greater than 2) between atoms, leading to the transfer of electrons from one atom to another [2](#page=2).
* **Formation:** One atom loses electrons to become a positively charged ion (cation), and another atom gains electrons to become a negatively charged ion (anion) [2](#page=2).
* **Characteristics:** Ionic compounds consist of ions held together by strong electrostatic attractions in a crystal lattice structure. Cations are generally smaller than their parent atoms, while anions are larger due to increased electron-electron repulsion [2](#page=2).
* **Example:** Sodium chloride (NaCl) is formed by the ionic bond between sodium (Na) and chlorine (Cl) due to their significant electronegativity difference [6](#page=6).
#### 2.1.2 Covalent bonds
Covalent bonds are formed when atoms share pairs of electrons, typically occurring between non-metal atoms with similar electronegativity values [2](#page=2).
* **Formation:** Atoms share valence electrons to achieve a more stable electron configuration.
* **Bonding pairs:** These are the shared pairs of electrons involved in the covalent bond.
* **Lone pairs:** These are valence electrons that are not shared.
* **Polar covalent bonds:** When atoms with different electronegativities share electrons unequally, the electron pair is drawn closer to the more electronegative atom, creating a polar covalent bond and a partial negative charge on that atom and a partial positive charge on the less electronegative atom [2](#page=2).
* **Example:** Water (H₂O) has polar covalent bonds between oxygen and hydrogen due to oxygen's higher electronegativity. Carbon dioxide (CO₂) has polar covalent bonds, but due to its linear geometry, the molecule itself is nonpolar as the bond dipoles cancel out [2](#page=2).
### 2.2 Atomic orbitals and quantum numbers
Atomic orbitals describe the regions of space around an atom's nucleus where electrons are likely to be found. These orbitals are characterized by four quantum numbers [1](#page=1):
* **Principal quantum number ($n$):** Determines the size and energy level of the orbital. Higher values of $n$ indicate larger orbitals and higher energy [1](#page=1).
* **Orbital (or azimuthal) quantum number ($l$):** Determines the shape of the orbital.
* $l=0$ corresponds to an $s$ orbital (spherical) [1](#page=1).
* $l=1$ corresponds to $p$ orbitals (dumbbell-shaped) [1](#page=1).
* $l=2$ corresponds to $d$ orbitals (more complex shapes) [1](#page=1).
* $l=3$ corresponds to $f$ orbitals (even more complex shapes) [1](#page=1).
* **Magnetic quantum number ($m_l$):** Specifies the orientation of the orbital in space. For a given $l$, $m_l$ can range from $-l$ to $+l$. For example, $p$ orbitals ($l=1$) have three possible orientations ($m_l = -1, 0, +1$), denoted as $p_x$, $p_y$, and $p_z$ [1](#page=1).
* **Spin quantum number ($m_s$):** Describes the intrinsic angular momentum of an electron, which can be either spin up ($+1/2$) or spin down ($-1/2$) [1](#page=1).
#### 2.2.1 Orbital occupancy
The filling of atomic orbitals follows specific principles:
* **Pauli exclusion principle:** No two electrons in an atom can have the same set of four quantum numbers. This means each orbital can hold a maximum of two electrons, which must have opposite spins [1](#page=1).
* **Aufbau principle:** Electrons fill orbitals starting from the lowest energy level upwards [1](#page=1).
* **Hund's rule:** Within a subshell, electrons will individually occupy orbitals with parallel spins before pairing up [1](#page=1).
### 2.3 Molecular geometry and VSEPR theory
Valence Shell Electron Pair Repulsion (VSEPR) theory predicts the three-dimensional geometry of molecules based on the principle that electron pairs (both bonding and lone pairs) around a central atom will arrange themselves to minimize repulsion, thus maximizing the distance between them [2](#page=2).
* **Electron domains:** Each region of electron density (single bond, double bond, triple bond, or lone pair) around the central atom is considered an electron domain.
* **Repulsion order:** The strength of repulsion between electron pairs follows the order: Lone Pair-Lone Pair (LP-LP) > Lone Pair-Bonding Pair (LP-BP) > Bonding Pair-Bonding Pair (BP-BP). This means lone pairs have a greater influence on molecular geometry than bonding pairs [2](#page=2).
**Common molecular geometries based on electron domain arrangement:**
* **Linear:** 2 electron domains, 0 lone pairs (e.g., BeCl₂)
* **Trigonal planar:** 3 electron domains, 0 lone pairs (e.g., BF₃)
* **Tetrahedral:** 4 electron domains, 0 lone pairs (e.g., CH₄) [2](#page=2).
* **Trigonal pyramidal:** 4 electron domains, 1 lone pair (e.g., NH₃). The molecular geometry is pyramidal, derived from a tetrahedral electron geometry [2](#page=2).
* **Bent (or V-shaped):** 4 electron domains, 2 lone pairs (e.g., H₂O). The molecular geometry is bent, derived from a tetrahedral electron geometry [2](#page=2).
### 2.4 Valence Bond Theory and Hybridization
Valence Bond Theory explains chemical bonding by considering the overlap of atomic orbitals [2](#page=2).
* **Sigma ($\sigma$) bonds:** Formed by the end-to-end overlap of atomic orbitals along the internuclear axis [2](#page=2).
* **Pi ($\pi$) bonds:** Formed by the sideways overlap of parallel $p$ or $d$ 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).
#### 2.4.1 Hybridization
Hybridization is the mixing of atomic orbitals within an atom to form new, degenerate hybrid orbitals that are better suited for bonding and explain observed molecular geometries [2](#page=2).
* **sp³ hybridization:** The mixing of one $s$ orbital and three $p$ orbitals to form four identical $sp^3$ hybrid orbitals. This arrangement results in a tetrahedral geometry, as seen in methane (CH₄) [2](#page=2).
* In methane, the central carbon atom undergoes $sp^3$ hybridization, creating four $sp^3$ orbitals, each containing one valence electron. These hybrid orbitals overlap with the $1s$ orbitals of four hydrogen atoms, forming four equivalent C-H sigma bonds [2](#page=2).
* **sp² hybridization:** The mixing of one $s$ orbital and two $p$ orbitals to form three $sp^2$ hybrid orbitals, lying in a plane with $120^\circ$ angles between them, leaving one $p$ orbital unhybridized perpendicular to the plane. This leads to trigonal planar geometries. Double bonds consist of one $\sigma$ bond and one $\pi$ bond [2](#page=2).
* **sp hybridization:** The mixing of one $s$ orbital and one $p$ orbital to form two $sp$ hybrid orbitals, oriented linearly ($180^\circ$ apart), leaving two $p$ orbitals unhybridized. This leads to linear geometries. Triple bonds consist of one $\sigma$ bond and two $\pi$ bonds [2](#page=2).
### 2.5 Molecular Orbital Theory
Molecular Orbital (MO) theory offers an alternative model to Valence Bond Theory by describing molecular orbitals that are formed by the combination of atomic orbitals from all atoms in a molecule. This theory can accurately predict bond lengths and bond energies, though it becomes complex for larger molecules [2](#page=2).
### 2.6 Electronegativity and Bond Polarity
Electronegativity is the measure of an atom's ability to attract electrons towards itself in a chemical bond [1](#page=1).
* **Electronegativity difference:**
* A large difference in electronegativity leads to ionic bonding [2](#page=2).
* A small or zero difference in electronegativity leads to covalent bonding [2](#page=2).
* **Polarity:** The difference in electronegativity between bonded atoms creates a dipole moment, making the bond polar. The overall polarity of a molecule depends on the bond polarities and its geometry. For example, water (H₂O) is polar due to its bent shape and polar O-H bonds [2](#page=2).
### 2.7 Fajans' rules
Fajans' rules predict the degree of covalent character in an ionic bond. An ionic compound gains covalent character when:
1. The cation is small and highly charged, strongly attracting and distorting the electron cloud of the anion (high polarizing power).
2. The anion is large and highly charged, meaning its electron cloud is easily distorted.
3. The cation has a high charge density.
When a cation distorts an anion's electron cloud, electron sharing increases, making the bond partly covalent rather than purely ionic [2](#page=2).
### 2.8 Bond strength and length
Generally, as bond length increases, bond strength decreases. Larger atoms tend to form longer and weaker bonds. Furthermore, bonds with more $s$ character in their hybridization tend to be shorter and stronger than those with more $p$ character [2](#page=2).
---
# Thermodynamics and chemical kinetics
This section explores the fundamental principles of thermodynamics, including the first and second laws, and their application to chemical systems through concepts like enthalpy, entropy, and Gibbs free energy. It also delves into chemical kinetics, examining reaction rates, activation energy, transition states, and the role of catalysts.
### 3.1 Thermodynamics
Thermodynamics is the study of energy, its transformations, and its relationships with matter. It focuses on the relative energies of reactants and products and the exchange of energy between a system and its surroundings. Thermodynamics can predict whether a reaction will proceed spontaneously but does not indicate the rate of the reaction [3](#page=3).
#### 3.1.1 Fundamental Laws of Thermodynamics
* **First Law of Thermodynamics:** Energy cannot be created or destroyed; it can only be transferred or changed in form. The total energy of an isolated system remains constant [3](#page=3).
* **Second Law of Thermodynamics:** The entropy of the entire universe always increases over time. This means that systems tend towards greater dispersal of energy [3](#page=3).
#### 3.1.2 Key Thermodynamic Concepts
* **Potential Energy:** Stored energy within an object or system. Chemical energy is a form of potential energy stored in chemical bonds [3](#page=3).
* **Thermodynamic Temperature:** A measure of the average kinetic energy of particles in a system, expressed in Kelvin (K). Absolute zero (0 K) represents the theoretical lowest possible temperature where particle motion ceases [3](#page=3).
* **Heat:** Energy transferred between a system and its surroundings due to a temperature difference. Heat flows spontaneously from higher to lower temperatures [3](#page=3).
* **Enthalpy (H):** The total energy of a chemical system, encompassing kinetic and chemical energy. The enthalpy change ($\Delta H$) in a system at constant pressure is equal to the heat absorbed or released [3](#page=3).
* **Endothermic Reaction:** A reaction where products have greater chemical potential energy than reactants, requiring energy input ($\Delta H > 0$) [3](#page=3) [6](#page=6).
* **Exothermic Reaction:** A reaction where reactants have greater chemical potential energy than products, releasing energy ($\Delta H < 0$) [3](#page=3) [6](#page=6).
* **Entropy (S):** A thermodynamic measure of energy dispersal or disorder within a system. Entropy change ($\Delta S$) is dependent on temperature. An increase in entropy signifies an increase in the number of ways energy can be distributed [3](#page=3).
* **Gibbs Free Energy (G):** A thermodynamic potential that combines enthalpy and entropy to determine the spontaneity of a reaction under constant temperature and pressure [3](#page=3).
* The change in Gibbs free energy is calculated as: $\Delta G = \Delta H - T\Delta S$ [3](#page=3) [6](#page=6).
* $\Delta G < 0$: Spontaneous (exergonic) reaction, releases free energy [3](#page=3).
* $\Delta G > 0$: Non-spontaneous (endergonic) reaction, absorbs free energy [3](#page=3).
* $\Delta G = 0$: The system is at equilibrium [3](#page=3).
* **Bond Energy:** The average energy required to break one mole of a specific type of bond. It indicates how much energy is needed to break a bond or released when a bond is formed [3](#page=3).
#### 3.1.3 Equilibrium
Chemical equilibrium is reached when the concentrations of reactants and products remain constant over time. The Gibbs free energy change is related to the equilibrium constant ($K$) by the equation: $\Delta G = -RT\ln K$ [3](#page=3).
* **Van't Hoff Equation:** Relates the change in the equilibrium constant of a chemical reaction to the change in temperature: $\ln K = \frac{-\Delta H^\circ}{RT} + \frac{\Delta S^\circ}{R}$ [3](#page=3).
### 3.2 Chemical Kinetics
Chemical kinetics studies the rates of chemical reactions [3](#page=3).
#### 3.2.1 Reaction Rates and Energy Barriers
* **Transition State:** The highest energy point during a reaction, representing an unstable arrangement of atoms where bonds are breaking and forming [3](#page=3).
* **Activated Complex:** The specific arrangement of atoms occurring near the transition state [3](#page=3).
* **Activation Energy ($E_a$):** The minimum energy required for a reaction to proceed. Reactions with higher activation energies proceed more slowly [3](#page=3).
#### 3.2.2 Catalysts
* **Catalyst:** A substance that increases the rate of a chemical reaction without being consumed in the process. Catalysts achieve this by providing an alternative reaction pathway with a lower activation energy. They do not alter the position of equilibrium but help it to be reached faster. Enzymes are biological catalysts that stabilize the transition state, thereby lowering activation energy [3](#page=3) [6](#page=6).
---
# Biomolecules: carbohydrates, lipids, nucleotides, and proteins
Biomolecules are the essential organic compounds that are vital for life, performing a wide range of structural and functional roles within living organisms.
### 4.1 Carbohydrates
Carbohydrates are polyhydroxy aldehydes or ketones, or compounds that can be hydrolyzed to them. They are a primary source of energy and play structural roles in cells. Their general formula is $(CH_2O)_n$ [5](#page=5).
#### 4.1.1 Monosaccharides
Monosaccharides are the simplest sugars and cannot be broken down further by hydrolysis. They are classified based on their functional group [6](#page=6):
* **Aldoses:** Contain an aldehyde group ($R-CH=O$). Examples include glucose and glyceraldehyde [5](#page=5).
* **Ketoses:** Contain a ketone group ($R-C(=O)-R'$). Examples include fructose and dihydroxyacetone [5](#page=5).
Monosaccharides can exist in both open-chain and cyclic forms in aqueous solutions. Cyclization occurs when the carbonyl group reacts with a hydroxyl group within the same molecule, forming a hemiacetal (from an aldose) or hemiketal (from a ketose). This process creates new stereocenters at the anomeric carbon [5](#page=5).
* **Anomers:** The cyclic forms can exist as $\alpha$ and $\beta$ anomers, differing in the configuration of the hydroxyl group at the anomeric carbon. The $\alpha$ anomer has the hydroxyl group on the opposite side of the ring's plane relative to the carbon chain, while the $\beta$ anomer has it on the same side [5](#page=5).
* **Fischer Projection:** A 2D representation of 3D molecules, showing the arrangement of groups around chiral centers. Horizontal lines point towards the viewer, and vertical lines point away [5](#page=5).
* **Haworth Projection:** Used to represent cyclic sugars [5](#page=5).
#### 4.1.2 Disaccharides
Disaccharides are formed when two monosaccharides are linked by a glycosidic bond through a condensation reaction, releasing a molecule of water. The name of the disaccharide indicates the constituent monosaccharides and the type of glycosidic linkage [6](#page=6).
* **Glycosidic Bond:** The covalent bond linking monosaccharides.
* **Sucrose:** $\alpha, \beta$-1,2 glycosidic bond, where both anomeric carbons are involved [6](#page=6).
* **Lactose:** $\beta$-1,4 glycosidic bond, where only one anomeric carbon is involved, allowing for the formation of both $\alpha$ and $\beta$ anomers simultaneously [6](#page=6).
#### 4.1.3 Polysaccharides
Polysaccharides are long chains of monosaccharides linked by glycosidic bonds. Their structure and properties depend on the type of monosaccharide and the glycosidic linkages [6](#page=6).
* **Cellulose:** Formed from $\beta$-D-glucose units linked by $\beta$-1,4 glycosidic bonds. It serves a structural role [6](#page=6).
* **Starch and Glycogen:** Formed from $\alpha$-D-glucose units linked by $\alpha$-1,4 glycosidic bonds. Glycogen is highly branched ($\alpha$-1,6 linkages), while starch contains both linear amylose ($\alpha$-1,4) and branched amylopectin ($\alpha$-1,6). They function as energy storage molecules [6](#page=6).
### 4.2 Lipids
Lipids are a diverse group of molecules that are generally insoluble in water but soluble in organic solvents. They play crucial roles in energy storage, cell membrane structure, and signaling.
#### 4.2.1 Fatty Acids
Fatty acids are long hydrocarbon chains with a terminal carboxylic acid group [6](#page=6).
* **Saturated Fatty Acids:** Contain only single bonds between carbon atoms [6](#page=6).
* **Unsaturated Fatty Acids:** Contain one or more carbon-carbon double bonds. The stereochemistry around these double bonds can be $Z$ (cis) or $E$ (trans). $Z$ configurations introduce kinks in the chain, affecting packing [6](#page=6).
* **Nomenclature:** Described by length and degree of saturation (e.g., 16:0 for palmitic acid, 16 carbons, 0 double bonds). The position of double bonds can be indicated from either end of the chain (e.g., $\omega$-7 or n-7 from the methyl end, or C-9 from the carboxyl end) [6](#page=6).
#### 4.2.2 Triacylglycerols
Triacylglycerols (triglycerides) are formed by the esterification of glycerol with three fatty acids. They are a major form of energy storage in adipose tissue [6](#page=6).
#### 4.2.3 Glycerophospholipids
Glycerophospholipids are a major component of cell membranes. They consist of a glycerol backbone esterified to two fatty acids and a phosphate group, which is often attached to a polar head group (e.g., choline, serine, inositol). These amphiphilic molecules (having both hydrophilic and hydrophobic regions) spontaneously form bilayers in aqueous environments [6](#page=6).
#### 4.2.4 Sphingolipids
Sphingolipids are a class of phospholipids built on a sphingoid backbone, synthesized from serine and acetyl-CoA. Examples include [6](#page=6):
* **Sphingomyelins:** Contain a phosphate group linked to choline or ethanolamine; found in myelin sheaths [6](#page=6).
* **Cerebrosides:** Have a monosaccharide as a head group; found in neuronal membranes [6](#page=6).
* **Gangliosides:** Have an oligosaccharide head group with sialic acid units; present in the brain [6](#page=6).
#### 4.2.5 Sterol Lipids
Sterol lipids, such as cholesterol, are characterized by a four-ring steroid nucleus. They are hydrophobic and rigid, with a polar hydroxyl group contributing to their amphipathic nature. Sterols are crucial for membrane fluidity and stability and serve as precursors for steroid hormones like testosterone and progesterone [6](#page=6).
#### 4.2.6 Lipid Aggregation
Due to their amphipathic nature, lipids tend to aggregate in aqueous solutions to minimize contact between their hydrophobic tails and water. Phospholipids and sphingolipids form lipid bilayers, which are selectively permeable due to their hydrophobic interior. Saturated lipids pack more tightly than unsaturated lipids, leading to higher melting temperatures ($T_m$) and more rigid membranes, while unsaturated lipids decrease $T_m$ and increase membrane fluidity [6](#page=6).
### 4.3 Nucleotides
Nucleotides are the building blocks of nucleic acids (DNA and RNA) and also play vital roles as energy currency (ATP, GTP), signaling molecules (cAMP), and substrates for enzymes. Each nucleotide consists of a ribose sugar, a phosphate group, and a nitrogenous base [6](#page=6).
* **Nucleic Acid Structure:** The sugar-phosphate backbone of DNA and RNA is formed by condensation reactions between the phosphate group of one nucleotide and the 3' hydroxyl group of the sugar of another. DNA typically exists as a double helix, stabilized by hydrogen bonds between complementary base pairs (A-T with 2 H-bonds, G-C with 3 H-bonds). The sequence is read from 5' to 3' [6](#page=6).
### 4.4 Proteins
Proteins are polymers of amino acids linked by peptide bonds. Their structure and function are determined by their amino acid sequence and the way they fold [6](#page=6).
#### 4.4.1 Amino Acid Structure and Peptide Bonds
Amino acids possess a central $\alpha$-carbon atom bonded to an amino group ($-\text{NH}_2$), a carboxyl group ($-\text{COOH}$), a hydrogen atom, and a variable side chain (R-group). Peptide bonds are formed through a condensation reaction between the carboxyl group of one amino acid and the amino group of another, releasing water [6](#page=6).
#### 4.4.2 Protein Structure Levels
Proteins fold into specific three-dimensional structures that are essential for their function. This folding occurs at multiple levels:
* **Primary Structure:** The linear sequence of amino acids in a polypeptide chain [6](#page=6).
* **Secondary Structure:** Localized folding of the polypeptide backbone into $\alpha$-helices and $\beta$-sheets, stabilized by hydrogen bonds between backbone atoms [6](#page=6).
* **Tertiary Structure:** The overall three-dimensional conformation of a single polypeptide chain, stabilized by various non-covalent interactions (hydrogen bonds, ionic interactions, van der Waals forces, hydrophobic interactions) and covalent disulfide bridges between cysteine residues [6](#page=6).
* **Quaternary Structure:** The association of multiple polypeptide subunits to form a functional protein complex [6](#page=6).
#### 4.4.3 Protein Folding
Protein folding is a complex process often guided by chaperones, which assist in achieving the correct conformation and preventing misfolding into kinetically trapped states. The Gibbs free energy drives the folding process towards a stable state [6](#page=6).
---
# Enzymes and metabolic pathways
Enzymes are biological catalysts that accelerate biochemical reactions by lowering the activation energy, facilitating metabolic pathways crucial for life [5](#page=5) [6](#page=6).
### 5.1 Enzyme kinetics
Enzyme kinetics studies the rates of enzyme-catalyzed reactions, providing insights into enzyme mechanisms and the effects of inhibitors [6](#page=6).
#### 5.1.1 Michaelis-Menten equation
The Michaelis-Menten equation describes the relationship between the initial reaction velocity ($v$) and substrate concentration ($[S]$) for an enzyme-catalyzed reaction, assuming a constant enzyme concentration [6](#page=6).
The equation is given by:
$$ v = \frac{V_{max}[S]}{K_m + [S]} $$
where:
* $v$ is the initial reaction velocity [6](#page=6).
* $V_{max}$ is the maximum reaction velocity reached when the enzyme is saturated with substrate [6](#page=6).
* $[S]$ is the substrate concentration [6](#page=6).
* $K_m$ (Michaelis-Menten constant) is the substrate concentration at which the reaction velocity is half of $V_{max}$ [6](#page=6).
#### 5.1.2 $K_m$ and $V_{max}$
* $K_m$ is a measure of the enzyme's affinity for its substrate; a lower $K_m$ indicates a higher affinity, meaning the enzyme reaches half its maximum speed with a lower substrate concentration. $K_m$ is unique for each enzyme and is not related to enzyme concentration [6](#page=6).
* $V_{max}$ represents the maximum rate of the reaction when all enzyme active sites are occupied by substrate. $V_{max}$ is directly proportional to the enzyme concentration [6](#page=6).
#### 5.1.3 $k_{cat}$ (Turnover number)
$k_{cat}$ is the turnover number, representing the number of substrate molecules an enzyme can convert into product per second when operating at maximum velocity (saturated with substrate). It is a measure of the enzyme's catalytic efficiency [6](#page=6).
The catalytic efficiency of an enzyme can be expressed as the ratio $k_{cat}/K_m$ [6](#page=6).
#### 5.1.4 Lineweaver-Burk equation
The Lineweaver-Burk equation is a double reciprocal plot of the Michaelis-Menten equation, plotting $1/v$ against $1/[S]$, which yields a straight line. This linear representation makes it easier to determine $V_{max}$ and $K_m$ values [6](#page=6).
The equation is:
$$ \frac{1}{v} = \frac{K_m}{V_{max}} \frac{1}{[S]} + \frac{1}{V_{max}} $$
### 5.2 Enzyme regulation
Enzymes are regulated to control metabolic pathways and cellular responses [5](#page=5) [6](#page=6).
#### 5.2.1 Enzyme inhibition
Inhibitors bind to enzymes and reduce their activity. They can be reversible (forming non-covalent bonds) or irreversible [6](#page=6).
* **Competitive inhibitors:** Bind to the active site, competing with the substrate. They increase $K_m$ but do not affect $V_{max}$. Their effect can be overcome by increasing substrate concentration [6](#page=6).
* **Uncompetitive inhibitors:** Bind to the enzyme-substrate complex, preventing product release. They decrease both $V_{max}$ and $K_m$ proportionally. Their effect cannot be overcome by increasing substrate concentration [6](#page=6).
* **Non-competitive inhibitors:** Bind to a site other than the active site, affecting catalytic function without preventing substrate binding. They decrease $V_{max}$ but do not affect $K_m$ [6](#page=6).
#### 5.2.2 Allosteric regulation
Allosteric regulation involves the binding of molecules (allosteric effectors) to an allosteric site on the enzyme (distinct from the active site). This binding causes a conformational change that alters the enzyme's activity, either inhibiting or activating it [6](#page=6).
* **Allosteric inhibitors** decrease enzyme activity [6](#page=6).
* Allosteric enzymes, particularly multisubunit proteins, often do not follow Michaelis-Menten kinetics and display a sigmoidal curve when reaction rate is plotted against substrate concentration [6](#page=6).
#### 5.2.3 Reversible covalent modifications
Enzymes can be regulated by the reversible addition or removal of chemical groups, such as phosphorylation (addition of a phosphate group), which can alter enzyme activity by changing its conformation [6](#page=6).
#### 5.2.4 Effect of pH and temperature
Enzymes have an optimal pH and temperature at which their activity is maximal. Deviations from these optima can reduce activity, and extreme conditions (especially high temperatures) can lead to denaturation, irreversibly damaging the enzyme's structure and function [6](#page=6).
### 5.3 Key metabolic pathways
Metabolic pathways are series of enzyme-catalyzed reactions that convert substrates into products, essential for cellular energy production and biosynthesis [5](#page=5) [6](#page=6).
#### 5.3.1 Glycolysis
Glycolysis is a catabolic pathway that breaks down glucose into two molecules of pyruvate, occurring in the cytosol. It yields a net production of 2 ATP and 2 NADH molecules per glucose molecule. It consists of three main phases: the investment phase (requiring ATP), the lysis phase (splitting into two 3-carbon units), and the payoff phase (generating ATP and NADH). Glycolysis does not require oxygen and can proceed under anaerobic conditions, where pyruvate is converted to lactate (in humans) or ethanol (in yeast) through fermentation [6](#page=6).
The overall reaction for glycolysis is:
$$ \text{Glucose} + 2 \, \text{NAD}^+ + 2 \, \text{ADP} + 2 \, \text{P}_i \rightarrow 2 \, \text{Pyruvate} + 2 \, \text{NADH} + 2 \, \text{H}^+ + 2 \, \text{ATP} + 2 \, \text{H}_2\text{O} $$
#### 5.3.2 Gluconeogenesis
Gluconeogenesis is an anabolic pathway that synthesizes glucose from non-carbohydrate precursors, such as pyruvate, lactate, and amino acids. It primarily occurs in the liver and kidney. Gluconeogenesis is essentially the reverse of glycolysis, but three irreversible steps of glycolysis are bypassed by different enzymes with highly negative Gibbs free energy changes, making the reactions exergonic [6](#page=6).
The overall summary of gluconeogenesis is:
$$ 2 \, \text{Pyruvate} + 4 \, \text{ATP} + 2 \, \text{GTP} + 2 \, \text{NADH} + 6 \, \text{H}_2\text{O} \rightarrow \text{Glucose} + 2 \, \text{NAD}^+ + 4 \, \text{ADP} + 2 \, \text{GDP} + 6 \, \text{P}_i + 2 \, \text{H}^+ $$
#### 5.3.3 The Krebs cycle (Citric Acid Cycle)
The Krebs cycle is a series of reactions occurring in the mitochondrial matrix that oxidizes acetyl-CoA, derived from pyruvate, to produce CO2, ATP (or GTP), NADH, and FADH2. It is a central pathway for energy metabolism, linking glycolysis to oxidative phosphorylation [6](#page=6).
The net reaction for one turn of the Krebs cycle (starting with acetyl-CoA) is:
$$ \text{Acetyl-CoA} + 3 \, \text{NAD}^+ + \text{FAD} + \text{ADP} + \text{P}_i + 2 \, \text{H}_2\text{O} \rightarrow \text{CoA} + 3 \, \text{NADH} + \text{FADH}_2 + 3 \, \text{H}^+ + \text{ATP} + 2 \, \text{CO}_2 $$
#### 5.3.4 Oxidative phosphorylation
Oxidative phosphorylation is the process by which ATP is synthesized using the energy released from the electron transport chain (ETC). Electrons from NADH and FADH2 (generated during glycolysis and the Krebs cycle) are passed along a series of protein complexes embedded in the inner mitochondrial membrane. This electron flow pumps protons from the mitochondrial matrix into the intermembrane space, creating a proton gradient (proton-motive force). ATP synthase utilizes this proton gradient to drive the synthesis of ATP from ADP and Pi. Oxygen serves as the terminal electron acceptor, being reduced to water [6](#page=6).
* NADH yields approximately 2.5 ATP molecules [6](#page=6).
* FADH2 yields approximately 1.5 ATP molecules [6](#page=6).
---
## 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
Glossary
| Term | Definition |
|---|---|
| Atom | The smallest particle of an element that retains the chemical properties of that element, consisting of a nucleus (protons and neutrons) and orbiting electrons. |
| Nucleus | The central part of an atom, composed of protons and neutrons, which contains most of the atom's mass and has a positive charge. |
| Proton | A subatomic particle found in the nucleus of an atom, carrying a positive electrical charge. The number of protons defines the atomic number of an element. |
| Neutron | A subatomic particle found in the nucleus of an atom, having no net electrical charge. Neutrons contribute to the atomic mass. |
| Electron | A subatomic particle with a negative electrical charge that orbits the nucleus of an atom. Electrons determine the chemical behavior of an atom. |
| Atomic number (Z) | The number of protons in the nucleus of an atom, which uniquely identifies a chemical element. |
| Atomic mass number (A) | The total number of protons and neutrons in an atomic nucleus. |
| Unified atomic mass unit (U or Da) | A unit of mass used to express the mass of atoms and molecules, defined as 1/12 of the mass of a Carbon-12 atom. |
| Periodic table | A tabular arrangement of the chemical elements, ordered by their atomic number, electron configuration, and recurring chemical properties. |
| Group | A vertical column in the periodic table, containing elements with similar chemical properties due to having the same number of valence electrons. |
| Period | A horizontal row in the periodic table, representing elements with the same number of electron shells. |
| Ionization energy | The minimum energy required to remove an electron from a neutral atom or molecule in its gaseous state. |
| Electron affinity | The energy change that occurs when an electron is added to a neutral atom or molecule in the gaseous state to form a negative ion. |
| Atomic radius | The distance from the center of an atom's nucleus to its outermost electron shell. |
| Electronegativity | A measure of the tendency of an atom to attract a bonding pair of electrons. |
| Isotope | Atoms of the same element that have the same number of protons but different numbers of neutrons, resulting in different atomic masses. |
| Bohr model | An early model of the atom where electrons orbit the nucleus in specific energy levels, similar to planets orbiting the sun. |
| Quantum mechanical model | A model of the atom that describes electrons in terms of wave functions and probability distributions (orbitals) rather than fixed orbits. |
| Atomic orbital | A mathematical function that describes the wave-like behavior of an electron in an atom, defining regions of space where an electron is likely to be found. |
| Quantum numbers | A set of numbers (principal, orbital, magnetic, spin) that describe the properties of electrons in atoms, such as energy level, shape, orientation, and spin. |
| Principal quantum number (n) | Describes the energy level and size of an atomic orbital. Higher values of n indicate higher energy and greater distance from the nucleus. |
| Orbital quantum number (l) | Describes the shape of an atomic orbital. It can take values from 0 to n-1, corresponding to s, p, d, and f subshells. |
| Magnetic quantum number (m_L) | Describes the orientation of an atomic orbital in space. It can take values from -l to +l, including 0. |
| Spin quantum number (m_S) | Describes the intrinsic angular momentum of an electron, often referred to as its "spin." It can have two values, typically +1/2 or -1/2. |
| Pauli exclusion principle | A principle stating that no two electrons in an atom can have the same set of four quantum numbers. This means each orbital can hold a maximum of two electrons, with opposite spins. |
| Aufbau principle | A principle that states that electrons fill atomic orbitals starting from the lowest energy levels and moving to higher ones. |
| Hund's rule | A rule stating that for a given electron configuration, the lowest energy state is the one with the greatest number of unpaired electrons, and these unpaired electrons have the same spin. |
| Molecule | An electrically neutral entity consisting of two or more atoms held together by chemical bonds. |
| Ionic bond | A chemical bond formed by the electrostatic attraction between oppositely charged ions, typically formed between metals and nonmetals with a large electronegativity difference. |
| Cation | A positively charged ion, formed when an atom loses one or more electrons. |
| Anion | A negatively charged ion, formed when an atom gains one or more electrons. |
| Covalent bond | A chemical bond formed by the sharing of pairs of electrons between atoms, typically occurring between nonmetals with similar electronegativities. |
| Polar covalent bond | A covalent bond where the electrons are shared unequally due to a difference in electronegativity between the atoms, resulting in partial positive and negative charges. |
| Molecular formula | A chemical formula that shows the types and numbers of atoms present in a molecule. |
| Empirical formula | The simplest whole-number ratio of atoms in a compound. |
| Structural formula | A formula that shows the arrangement of atoms and bonds within a molecule. |
| Skeletal formula | A shorthand way of drawing organic molecules where carbon atoms are at the vertices and ends of lines, and hydrogen atoms attached to carbon are usually omitted. |
| Valence shell electron pair repulsion (VSEPR) theory | A model used to predict the geometry of molecules based on the repulsion between electron pairs in the valence shell of the central atom. |
| Hybridization | The mixing of atomic orbitals to form new hybrid orbitals with different shapes and energies, which are more suitable for bonding. |
| Sigma bond ($\sigma$ bond) | A covalent bond formed by the direct, end-to-end overlap of atomic orbitals along the internuclear axis. |
| Pi bond ($\pi$ bond) | A covalent bond formed by the sideways overlap of atomic orbitals, typically p orbitals, above and below the internuclear axis. |
| Molecular orbital theory | A theory that describes chemical bonding in terms of molecular orbitals, which are formed by the combination of atomic orbitals. |
| Fajans' rule | Rules that predict the degree of covalent character in an ionic bond, based on factors like the charge and size of the ions. |
| Intermolecular forces | Attractive or repulsive forces that act between molecules, such as London dispersion forces, dipole-dipole interactions, and hydrogen bonds. |
| London dispersion forces | Weak, temporary attractive forces that arise from instantaneous fluctuations in electron distribution in molecules, inducing temporary dipoles. |
| Dipole-dipole interaction | Attractive forces between the positive end of one polar molecule and the negative end of another. |
| Hydrogen bond | A specific type of strong dipole-dipole interaction that occurs when a hydrogen atom bonded to a highly electronegative atom (like O, N, or F) is attracted to a lone pair of electrons on another electronegative atom. |
| Van der Waals forces | A general term for intermolecular forces, including London dispersion forces and dipole-dipole interactions. |
| Thermodynamics | The study of energy and its transformations, particularly the relationships between heat, work, and chemical energy. |
| Enthalpy (H) | A thermodynamic quantity representing the total heat content of a system. The change in enthalpy ($\Delta H$) is the heat absorbed or released at constant pressure. |
| Endothermic reaction | A reaction that absorbs heat from its surroundings, resulting in a positive enthalpy change ($\Delta H > 0$). |
| Exothermic reaction | A reaction that releases heat into its surroundings, resulting in a negative enthalpy change ($\Delta H < 0$). |
| Entropy (S) | A thermodynamic measure of the dispersal of energy or matter within a system. An increase in entropy indicates greater disorder. |
| Gibbs free energy (G) | A thermodynamic potential that measures the maximum amount of non-expansion work that can be extracted from a closed system at constant temperature and pressure. The change in Gibbs free energy ($\Delta G$) indicates the spontaneity of a process. |
| Spontaneous reaction | A reaction that can proceed without continuous external energy input. A spontaneous reaction has a negative change in Gibbs free energy ($\Delta G < 0$). |
| Catalyst | A substance that increases the rate of a chemical reaction without itself being consumed in the process, typically by lowering the activation energy. |
| Chemical kinetics | The study of the rates of chemical reactions and the factors that influence them. |
| Activation energy ($E_a$) | The minimum amount of energy required for a chemical reaction to occur. |
| Transition state | A high-energy, unstable arrangement of atoms that exists momentarily during a chemical reaction, representing the point of highest energy along the reaction pathway. |
| Nucleophile | A chemical species that donates an electron pair to form a chemical bond, typically having a lone pair of electrons or a negative charge. |
| Electrophile | A chemical species that accepts an electron pair to form a chemical bond, typically having a positive charge or an incomplete electron shell. |
| Reaction mechanism | A step-by-step sequence of elementary reactions that describe the overall process of a chemical reaction. |
| SN1 reaction | A unimolecular nucleophilic substitution reaction where the leaving group departs first, forming a carbocation intermediate, which is then attacked by the nucleophile. |
| SN2 reaction | A bimolecular nucleophilic substitution reaction where the nucleophile attacks the substrate at the same time the leaving group departs, occurring in a single step. |
| Redox reaction | A chemical reaction involving the transfer of electrons between species, resulting in a change in their oxidation states. |
| Oxidation | The loss of electrons or an increase in oxidation state. |
| Reduction | The gain of electrons or a decrease in oxidation state. |
| Oxidizing agent | A substance that causes another substance to be oxidized, and is itself reduced. |
| Reducing agent | A substance that causes another substance to be reduced, and is itself oxidized. |
| Biomolecules | Organic molecules that are essential for life, such as carbohydrates, lipids, proteins, and nucleic acids. |
| Carbohydrates | Organic compounds composed of carbon, hydrogen, and oxygen, typically with a hydrogen-to-oxygen atom ratio of 2:1 (as in water), and serving as a primary source of energy and structural components. |
| Monosaccharide | The simplest form of carbohydrate, a single sugar unit that cannot be hydrolyzed into smaller carbohydrates. |
| Disaccharide | A carbohydrate formed by the glycosidic linkage of two monosaccharide units. |
| Polysaccharide | A complex carbohydrate consisting of long chains of monosaccharide units linked by glycosidic bonds. |
| Lipids | A diverse group of hydrophobic molecules that includes fats, oils, waxes, steroids, and phospholipids, primarily involved in energy storage, insulation, and cell membrane structure. |
| Fatty acids | Long hydrocarbon chains with a carboxyl group at one end, forming the building blocks of many lipids. |
| Saturated fatty acid | A fatty acid with no double bonds between carbon atoms in its hydrocarbon chain. |
| Unsaturated fatty acid | A fatty acid containing one or more double bonds between carbon atoms in its hydrocarbon chain. |
| Triacylglycerol | A lipid formed from one molecule of glycerol and three molecules of fatty acids, serving as a major form of energy storage. |
| Phospholipid | A lipid molecule composed of a glycerol backbone, two fatty acid chains, and a phosphate group, which forms the primary structural component of cell membranes. |
| Amphiphilic | Having both hydrophilic (water-attracting) and hydrophobic (water-repelling) properties, characteristic of phospholipids and other molecules that form cell membranes. |
| Sterol lipids | Lipids characterized by a fused four-ring structure, such as cholesterol, which plays roles in membrane fluidity and hormone synthesis. |
| Hydrophobic effect | The tendency of nonpolar molecules to aggregate in aqueous solution, driven by the desire to minimize disruption of water's hydrogen bonding network. |
| Micelle | A spherical aggregation of amphiphilic molecules in aqueous solution, with hydrophobic tails oriented inward and hydrophilic heads outward. |
| Vesicle | A small, fluid-filled sac or bladder, often enclosed by a membrane, formed by lipids in aqueous solution. |
| Lipid bilayer | A two-layered sheet of phospholipid molecules in aqueous solution, forming the basic structure of cell membranes. |
| Nucleotides | The building blocks of nucleic acids (DNA and RNA), composed of a nitrogenous base, a five-carbon sugar, and one or more phosphate groups. |
| Nucleic acids | Polymers of nucleotides that carry genetic information (DNA) or are involved in protein synthesis (RNA). |
| DNA (Deoxyribonucleic acid) | A molecule that carries the genetic instructions for the development, functioning, growth, and reproduction of all known organisms. |
| RNA (Ribonucleic acid) | A nucleic acid that plays a key role in protein synthesis and regulation of gene expression. |
| Amino acids | Organic molecules containing an amino group and a carboxyl group, which serve as the building blocks of proteins. |
| Peptide bond | A covalent bond formed between the carboxyl group of one amino acid and the amino group of another, linking amino acids together in a polypeptide chain. |
| Protein | Large biomolecules consisting of one or more chains of amino acids, performing a vast array of functions within organisms. |
| Primary structure | The linear sequence of amino acids in a protein. |
| Secondary structure | The local folding of a polypeptide chain into regular structures like alpha-helices and beta-sheets, stabilized by hydrogen bonds. |
| Tertiary structure | The overall three-dimensional shape of a single polypeptide chain, determined by interactions between amino acid side chains. |
| Quaternary structure | The arrangement of multiple polypeptide subunits in a protein complex. |
| Enzyme | A biological catalyst, typically a protein, that speeds up specific biochemical reactions by lowering the activation energy. |
| Michaelis-Menten constant (Km) | The substrate concentration at which the reaction rate is half of the maximum velocity ($V_{max}$), indicating the enzyme's affinity for its substrate. |
| $V_{max}$ | The maximum rate of an enzyme-catalyzed reaction, reached when the enzyme is saturated with substrate. |
| $k_{cat}$ | The turnover number, representing the number of substrate molecules converted to product per enzyme molecule per unit time when the enzyme is operating at maximum rate. |
| Glycolysis | A metabolic pathway that breaks down glucose into pyruvate, producing ATP and NADH. It occurs in the cytoplasm and does not require oxygen. |
| Gluconeogenesis (GNG) | The metabolic pathway that synthesizes glucose from non-carbohydrate precursors, primarily occurring in the liver and kidneys. |
| Investment phase (of glycolysis) | The initial steps of glycolysis that consume ATP to activate glucose and prepare it for cleavage. |
| Payoff phase (of glycolysis) | The later steps of glycolysis where ATP and NADH are produced through substrate-level phosphorylation. |
| Substrate-level phosphorylation | The direct transfer of a phosphate group from a high-energy substrate molecule to ADP, forming ATP. |
| Normoglycaemia | The condition of having a normal blood glucose concentration. |
| Hypoglycaemia | The condition of having abnormally low blood glucose levels. |
| Oxidative decarboxylation | A reaction that involves both oxidation and the removal of a carboxyl group as carbon dioxide. |
| Krebs cycle (TCA cycle) | A series of biochemical reactions in the mitochondrial matrix that oxidizes acetyl-CoA, producing ATP, NADH, FADH2, and CO2. |
| Electron transport chain (ETC) | A series of protein complexes embedded in the inner mitochondrial membrane that transfer electrons from NADH and FADH2 to oxygen, generating a proton gradient used for ATP synthesis. |
| Oxidative phosphorylation | The process by which ATP is synthesized using energy derived from the redox reactions of the electron transport chain and the chemiosmotic gradient of protons. |
| ATP synthase | An enzyme complex embedded in the inner mitochondrial membrane that uses the energy of the proton gradient to synthesize ATP from ADP and inorganic phosphate. |
| Proton-motive force | The potential energy stored in the proton gradient across a membrane, consisting of both a chemical gradient (pH difference) and an electrical gradient (charge difference). |
| Endothermic reaction | A reaction that absorbs heat from its surroundings, resulting in a positive enthalpy change. |
| Exothermic reaction | A reaction that releases heat into its surroundings, resulting in a negative enthalpy change. |
| Gibbs energy | A thermodynamic potential that determines the spontaneity of a process. A decrease in Gibbs energy ($\Delta G < 0$) indicates a spontaneous process. |
| Catalyst | A substance that increases the rate of a chemical reaction without being consumed. |
| Nucleophile | An electron-pair donor that is attracted to an electron-deficient atom or center. |
| Electrophile | An electron-pair acceptor that is attracted to an electron-rich atom or center. |
| Membranes | Selectively permeable barriers, typically composed of lipid bilayers, that enclose cells and organelles. |
| Isomerism | The phenomenon where compounds have the same molecular formula but different structural or spatial arrangements of atoms. |
| Structural isomerism | Isomers that have the same molecular formula but different connectivity of atoms. |
| Stereoisomerism | Isomers that have the same molecular formula and connectivity but differ in the three-dimensional arrangement of their atoms. |
| Optical isomerism | A type of stereoisomerism where isomers are non-superimposable mirror images of each other (enantiomers). |
| Enantiomers | Stereoisomers that are mirror images of each other and are non-superimposable. |
| Diastereoisomers | Stereoisomers that are not mirror images of each other, differing in the configuration at one or more stereocenters. |
| Epimers | Diastereoisomers that differ in the configuration at only one stereocenter. |
| Anomer | A specific type of epimer that forms at the anomeric carbon of a cyclic saccharide. |
| Chirality | The property of a molecule or ion having a non-superimposable mirror image. |
| Stereocenter | An atom in a molecule that is bonded to four different groups, making it a center of chirality. |
| Cahn-Ingold-Prelog rules | A system of priority rules used to assign R/S configurations to chiral centers and E/Z configurations to double bonds. |
| Racemate | A mixture of equal amounts of two enantiomers. |
| Geometric isomerism | Stereoisomerism that arises due to restricted rotation around a bond, typically a double bond or in a ring structure. |
| Cis-trans isomerism | A type of geometric isomerism where substituents are on the same side (cis) or opposite sides (trans) of a double bond or ring. |
| E/Z nomenclature | A system used to describe the configuration of geometric isomers based on the priority of substituents according to Cahn-Ingold-Prelog rules. |
| Warburg effect | The observation that cancer cells preferentially rely on glycolysis even in the presence of oxygen, leading to increased lactate production. |
| PET imaging | Positron Emission Tomography, a medical imaging technique that uses radioactive tracers to visualize metabolic activity, often utilizing glucose uptake. |
| PKM2 | Pyruvate kinase M2, an enzyme involved in glycolysis that is often dysregulated in cancer cells. |
| Ketogenesis | The process of producing ketone bodies in the liver, typically during periods of low glucose availability or prolonged fasting. |
| Diabetic ketosis | A metabolic state in uncontrolled diabetes mellitus characterized by high blood glucose levels and the accumulation of ketone bodies, leading to acidosis. |
| Beta-oxidation | The metabolic pathway that breaks down fatty acids into acetyl-CoA in the mitochondria, generating ATP. |
| Adhesion | The tendency of dissimilar particles or surfaces to cling to one another. |
| Cohesion | The tendency of similar or identical particles or surfaces to cling to one another. |
| Thermal denaturation | The process by which heat causes the loss of a protein's secondary, tertiary, and quaternary structure, leading to loss of function. |
| Allosteric regulation | The regulation of an enzyme's activity by the binding of a molecule at a site other than the active site (the allosteric site). |
| Allosteric enzyme | An enzyme whose activity is regulated by allosteric effectors that bind to sites distinct from the active site, often exhibiting cooperativity. |
| Protein purification | The process of isolating a specific protein from a complex mixture, often involving techniques like chromatography and electrophoresis. |
| Chromatography | A laboratory technique used to separate mixtures of compounds based on differences in their physical or chemical properties. |
| Size exclusion chromatography | A type of chromatography that separates molecules based on their size, with larger molecules eluting first. |
| Ion exchange chromatography | A type of chromatography that separates molecules based on their charge, using a stationary phase with charged groups. |
| Affinity chromatography | A type of chromatography that separates molecules based on specific binding interactions between the target molecule and the stationary phase. |
| SDS-PAGE (Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis) | A technique used to separate proteins based primarily on their molecular weight, by denaturing them with SDS and separating them in a gel matrix. |
| Western blot | A technique used to detect specific proteins in a sample using antibodies. |
| Enzyme kinetics | The study of the rates of enzyme-catalyzed reactions, including factors affecting enzyme activity such as substrate concentration, temperature, and pH. |
| Competitive inhibitor | An inhibitor that binds to the active site of an enzyme, competing with the substrate and reducing the reaction rate. |
| Uncompetitive inhibitor | An inhibitor that binds only to the enzyme-substrate complex, reducing both $V_{max}$ and Km. |
| Non-competitive inhibitor | An inhibitor that binds to a site on the enzyme distinct from the active site, reducing $V_{max}$ but not Km. |
| Mixed inhibitor | An inhibitor that can bind to both the free enzyme and the enzyme-substrate complex, affecting both $V_{max}$ and Km. |
| Cofactor | A non-protein chemical compound required for an enzyme's biological activity. |
| Coenzyme | A type of cofactor that is an organic non-protein compound required for the activity of many enzymes. |
| Optimum pH | The pH at which an enzyme exhibits its maximum catalytic activity. |
| Optimum temperature | The temperature at which an enzyme exhibits its maximum catalytic activity. |
| Reversible covalent modification | A type of enzyme regulation where a covalent bond to the enzyme is formed and broken reversibly, often involving phosphorylation or dephosphorylation. |
| Allosteric site | A binding site on an enzyme, separate from the active site, where regulatory molecules (allosteric effectors) can bind to modulate enzyme activity. |
| Sigmoid curve | A characteristic S-shaped curve observed in plots of enzyme activity versus substrate concentration for enzymes exhibiting cooperativity, such as allosteric enzymes. |
| Krebs/TCA Cycle | A series of reactions that take place in the mitochondrial matrix that convert acetyl-CoA to two molecules of CO2, one molecule of ATP, and releases eight electrons that are used to generate three molecules of NADH and one molecule of FADH2. |
| Oxidative phosphorylation | Reaction of the ETC and ATP synthase. Electrons are used to reduce oxygen to water while a proton gradient is established across the inner mitochondrial membrane. This proton gradient is the driving force of the ATP synthase to catalyse the reaction of ADP and Pi to ATP. |
| Proton-motive force | The potential energy stored in the proton gradient across a membrane, consisting of both a chemical gradient (pH difference) and an electrical gradient (charge difference). |
| ATP synthase | An enzyme complex embedded in the inner mitochondrial membrane that uses the energy of the proton gradient to synthesize ATP from ADP and inorganic phosphate. |
| Seahorse instrument | A laboratory instrument used to measure the metabolic status of cells in real-time, including oxygen consumption rate (OCR) and extracellular acidification rate (ECAR). |
| Uncouplers | Compounds that disrupt the coupling between electron transport and ATP synthesis by allowing protons to leak across the inner mitochondrial membrane. |
| Warburg effect | The phenomenon where cancer cells exhibit increased glycolysis and lactate production even in the presence of oxygen. |
| Endothermic reaction | A reaction in which the products have a greater chemical potential energy than the reactants, requiring energy input (heat) to proceed. |
| Exothermic reaction | A reaction in which the reactants have a greater chemical potential energy than the products, releasing energy (heat) when they proceed. |
| Gibbs energy | A thermodynamic potential that defines the spontaneity of a process. The change in Gibbs energy is calculated as $\Delta G = \Delta H - T\Delta S$. |
| Catalyst | A substance that increases the reaction rate without being consumed, typically by lowering the activation energy. |
| Nucleophile | An electron-pair donor that participates in bond formation by donation of an electron pair to an electron acceptor (an electrophile). |
| Electrophile | An electron-pair acceptor that participates in bond formation by accepting an electron pair from an electron donor (a nucleophile). |
| Carbohydrates | Organic compounds with the general formula $(CH_2O)_n$, serving as energy sources and structural components. |
| Fatty acids | Long hydrocarbon chains with a carboxylic acid group at the end; form the building blocks of lipids. |
| Lipids | A diverse group of hydrophobic molecules, including fats, oils, phospholipids, and steroids, important for energy storage, cell membranes, and signaling. |
| Membranes | Lipid bilayers that form the boundary of cells and organelles, controlling the passage of substances. |
| Nucleotides | The monomers of nucleic acids, consisting of a sugar, a phosphate group, and a nitrogenous base. |
| Proteins | Macromolecules composed of amino acid subunits linked by peptide bonds, performing a wide range of cellular functions. |
| Enzyme | Biological catalysts that accelerate chemical reactions by lowering the activation energy. |
| Km | The Michaelis-Menten constant, representing the substrate concentration at which the reaction rate is half of $V_{max}$. |
| Vmax | The maximum rate of an enzyme-catalyzed reaction when the enzyme is saturated with substrate. |
| kcat | The turnover number, indicating the number of substrate molecules converted to product per enzyme molecule per second at saturation. |
| Glycolysis | The metabolic pathway that breaks down glucose into pyruvate, producing ATP and NADH. |
| Gluconeogenesis (GNG) | The synthesis of glucose from non-carbohydrate precursors, primarily occurring in the liver. |
| Investment phase (of glycolysis) | The initial energy-consuming steps of glycolysis. |
| Payoff phase (of glycolysis) | The energy-producing steps of glycolysis. |
| Substrate level phosphorylation | The direct synthesis of ATP from ADP and a high-energy phosphate-containing substrate. |
| Normoglycaemia | Normal blood glucose concentration. |
| Hypoglycaemia | Low blood glucose concentration. |
| Oxidative decarboxylation | A reaction that simultaneously oxidizes a compound and removes carbon dioxide. |
| Krebs/TCA cycle | A cyclic series of reactions in the mitochondrial matrix 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 from NADH and FADH2 to oxygen, coupled to proton pumping. |
| Oxidative phosphorylation | The process of ATP synthesis driven by the electron transport chain and chemiosmosis. |
| Hydrolysis | A chemical reaction in which water is used to break down a compound. |
| Thioester bond | A chemical bond between sulfur and carbon, often found in high-energy compounds like acetyl-CoA. |
| Citrate synthase | An enzyme that catalyzes the first step of the Krebs cycle, the condensation of acetyl-CoA and oxaloacetate to form citrate. |
| Aconitase | An enzyme that catalyzes the isomerization of citrate to isocitrate in the Krebs cycle. |
| Isocitrate dehydrogenase | An enzyme that catalyzes the oxidative decarboxylation of isocitrate to $\alpha$-ketoglutarate in the Krebs cycle. |
| $\alpha$-Ketoglutarate dehydrogenase complex | A multi-enzyme complex that catalyzes the oxidative decarboxylation of $\alpha$-ketoglutarate to succinyl-CoA in the Krebs cycle. |
| Succinyl-CoA synthase | An enzyme that catalyzes the conversion of succinyl-CoA to succinate, producing ATP or GTP via substrate-level phosphorylation. |
| Succinate dehydrogenase | An enzyme that catalyzes the oxidation of succinate to fumarate in the Krebs cycle and is also part of Complex II of the electron transport chain. |
| Fumarase | An enzyme that catalyzes the hydration of fumarate to L-malate in the Krebs cycle. |
| Malate dehydrogenase | An enzyme that catalyzes the oxidation of malate to oxaloacetate in the Krebs cycle, reducing NAD+ to NADH. |
| Beta-oxidation | The catabolic pathway that breaks down fatty acids into acetyl-CoA in the mitochondria. |
| Ketone bodies | Water-soluble molecules produced from fatty acids in the liver during periods of low carbohydrate availability, serving as an alternative fuel source for tissues like the brain. |
| Diabetic ketosis | A serious complication of diabetes characterized by the accumulation of ketone bodies in the blood and urine, leading to acidosis. |
| Gluconeogenesis | The synthesis of glucose from non-carbohydrate precursors. |
| Metabolic regulation | The control of metabolic pathways through various mechanisms, including enzyme activity modulation and gene expression. |
| Pathway flux | The rate at which metabolites move through a metabolic pathway. |
| $\Delta G$ | Change in Gibbs free energy, indicating spontaneity of a reaction. |
| $E_a$ | Activation energy, the minimum energy required for a reaction to occur. |
| Transition state | The unstable, high-energy intermediate state during a chemical reaction. |
| Nucleophile | An electron-rich species that donates electrons to form a bond. |
| Electrophile | An electron-poor species that accepts electrons to form a bond. |
| Carbocation | A positively charged carbon atom. |
| Fischer projection | A two-dimensional representation of a three-dimensional molecule, commonly used for carbohydrates and amino acids. |
| Haworth projection | A way of representing cyclic saccharides in three dimensions, showing the relative positions of substituents. |
| Anomer | Isomers of cyclic saccharides that differ in configuration at the anomeric carbon. |
| $\alpha$-anomer | An anomer where the hydroxyl group at the anomeric carbon is oriented trans to the $-\text{CH}_2\text{OH}$ group. |
| $\beta$-anomer | An anomer where the hydroxyl group at the anomeric carbon is oriented cis to the $-\text{CH}_2\text{OH}$ group. |
| Glycosidic bond | A type of covalent bond that links a carbohydrate molecule to another group, often another carbohydrate or an amino acid. |
| Hydrophobic | Tending to repel water; nonpolar. |
| Hydrophilic | Attracting water; polar. |
| Amphiphilic | Having both hydrophilic and hydrophobic properties. |
| Micelle | A spherical aggregation of amphiphilic molecules in aqueous solution. |
| Vesicle | A small membrane-bound sac. |
| Lipid bilayer | A double layer of lipid molecules, forming the basis of cell membranes. |
| Melting temperature ($T_m$) | The temperature at which a substance transitions from solid to liquid phase. |
| Residue | A repeating unit in a polymer, such as a nucleotide in nucleic acids or an amino acid in proteins. |
| DNA double helix | The characteristic structure of DNA, consisting of two antiparallel strands wound around each other. |
| Peptide bond | The covalent bond that links amino acids in a protein. |
| $\alpha$-helix | A common secondary structure in proteins, a helical arrangement of polypeptide chains stabilized by hydrogen bonds. |
| $\beta$-sheet | A common secondary structure in proteins, a sheet-like arrangement of polypeptide chains stabilized by hydrogen bonds. |
| Protein purification | The process of isolating a specific protein from a mixture. |
| Lysis | The rupture of a cell membrane, often induced by detergents or physical methods, to release cellular contents. |
| Centrifugation | A process that uses centrifugal force to separate components of a mixture based on density. |
| Chromatography | A technique used to separate mixtures of compounds based on differences in their affinity for a stationary and mobile phase. |
| SDS-PAGE | Sodium dodecyl sulfate-polyacrylamide gel electrophoresis, a technique used to separate proteins by size. |
| Enzyme kinetics | The study of the rates of enzyme-catalyzed chemical reactions. |
| Michaelis-Menten equation | An equation that describes the relationship between the initial reaction velocity ($v_0$) and substrate concentration ([S]) for enzyme-catalyzed reactions. |
| $K_{cat}$ | The turnover number, which measures the number of substrate molecules an enzyme can convert into product per unit time. |
| Catalytic efficiency | A measure of an enzyme's effectiveness, often expressed as the ratio $k_{cat}/K_m$. |
| Inhibitor | A molecule that binds to an enzyme and reduces its activity. |
| Competitive inhibitor | An inhibitor that binds to the active site of an enzyme, competing with the substrate. |
| Uncompetitive inhibitor | An inhibitor that binds to the enzyme-substrate complex. |
| Non-competitive inhibitor | An inhibitor that binds to an allosteric site on the enzyme, reducing $V_{max}$ without affecting Km. |
| Mixed inhibitor | An inhibitor that can bind to either the free enzyme or the enzyme-substrate complex. |
| Cofactor | A non-protein chemical compound that is required for the biological activity of many enzymes. |
| Coenzyme | A type of cofactor that is an organic, non-protein molecule that serves as a carrier of small chemical groups. |
| Allosteric regulation | Regulation of enzyme activity by molecules that bind to sites other than the active site. |
| Allosteric site | The site on an enzyme, distinct from the active site, where an allosteric effector binds. |
| Phosphorylation | The addition of a phosphate group to a molecule, often a regulatory mechanism for enzyme activity. |
| 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 that consume ATP. |
| Payoff phase (of glycolysis) | The later steps of glycolysis that produce ATP and NADH. |
| Substrate-level phosphorylation | Direct ATP synthesis by transfer of a phosphate group from a substrate to ADP. |
| Normoglycaemia | Normal blood glucose levels. |
| Hypoglycaemia | Low blood glucose levels. |
| Oxidative decarboxylation | A reaction that simultaneously oxidizes a compound and removes carbon dioxide. |
| Krebs/TCA cycle | A metabolic pathway that oxidizes acetyl-CoA to CO2, generating ATP, NADH, and FADH2. |
| Electron transport chain (ETC) | A series of protein complexes in the inner mitochondrial membrane that transfer electrons and pump protons. |
| Oxidative phosphorylation | ATP synthesis coupled to electron transport and proton flow through ATP synthase. |
| ATP synthase | Enzyme that synthesizes ATP using the energy of a proton gradient. |
| Proton-motive force | The potential energy stored in a proton gradient across a membrane. |
| Seahorse instrument | A device used to measure cellular respiration and glycolysis rates. |
| Uncouplers | Compounds that disrupt the proton gradient across the inner mitochondrial membrane, uncoupling electron transport from ATP synthesis. |
| Warburg effect | The observation that cancer cells preferentially metabolize glucose via glycolysis, even in the presence of oxygen. |
| PKM2 | Pyruvate kinase M2, a key glycolytic enzyme often dysregulated in cancer. |
| PET imaging | Positron Emission Tomography, an imaging technique that uses radiolabeled glucose to visualize metabolic activity. |
| Endothermic reaction | A reaction that absorbs heat from the surroundings ($\Delta H > 0$). |
| Exothermic reaction | A reaction that releases heat to the surroundings ($\Delta H < 0$). |
| Gibbs energy | A thermodynamic potential that determines spontaneity ($\Delta G$). |
| Catalyst | A substance that increases reaction rate without being consumed. |
| Nucleophile | An electron-pair donor. |
| Electrophile | An electron-pair acceptor. |
| Carbohydrates | Sugars, starches, and cellulose; important for structure and energy storage. |
| Fatty acids | Long hydrocarbon chains with a carboxyl group; building blocks of lipids. |
| Lipids | Hydrophobic molecules, including fats, oils, phospholipids, and steroids. |
| Membranes | Lipid bilayers forming cell boundaries and organelle compartments. |
| Nucleotides | Monomers of DNA and RNA, composed of a sugar, phosphate, and nitrogenous base. |
| Proteins | Macromolecules composed of amino acid subunits. |
| Enzyme | Biological catalysts that accelerate reactions. |
| Km | Substrate concentration at half $V_{max}$; indicates enzyme affinity. |
| Vmax | Maximum reaction velocity when the enzyme is saturated. |
| kcat | Turnover number; the rate at which an enzyme converts substrate to product. |
| Glycolysis | Metabolic pathway breaking down glucose to pyruvate. |
| Gluconeogenesis (GNG) | Synthesis of glucose from non-carbohydrate precursors. |
| Investment phase (of glycolysis) | ATP-consuming steps in glycolysis. |
| Payoff phase (of glycolysis) | ATP and NADH-producing steps in glycolysis. |
| Substrate level phosphorylation | Direct ATP synthesis from a substrate. |
| Normoglycaemia | Normal blood glucose levels. |
| Hypoglycaemia | Low blood glucose levels. |
| Oxidative decarboxylation | Reaction that removes CO2 and oxidizes a substrate. |
| Krebs/TCA cycle | Cyclic pathway in mitochondria that oxidizes acetyl-CoA, producing ATP, NADH, and FADH2. |
| Electron transport chain (ETC) | Series of protein complexes in the inner mitochondrial membrane that transfer electrons and pump protons. |
| Oxidative phosphorylation | ATP synthesis coupled to electron transport and proton flow. |
| Pyruvate | The end product of glycolysis, which can be further metabolized aerobically or anaerobically. |
| Acetyl-CoA | A molecule that links glycolysis to the Krebs cycle, formed from pyruvate. |
| NADH | Nicotinamide adenine dinucleotide (reduced form), an electron carrier in metabolic pathways. |
| FADH2 | Flavin adenine dinucleotide (reduced form), an electron carrier in metabolic pathways. |
| Oxidative phosphorylation | ATP synthesis driven by the electron transport chain and chemiosmosis. |
| Proton gradient | A difference in proton concentration and electrical charge across a membrane, used to drive ATP synthesis. |
| ATP synthase | Enzyme that synthesizes ATP using the energy of a proton gradient. |
| Seahorse instrument | A device for measuring cellular metabolic rates. |
| Uncouplers | Compounds that disrupt the proton gradient in mitochondria, uncoupling electron transport from ATP synthesis. |
| Warburg effect | Increased glycolysis in cancer cells even with oxygen present. |
| PKM2 | Pyruvate kinase M2, a key glycolytic enzyme often dysregulated in cancer. |
| PET imaging | Positron Emission Tomography, an imaging technique that uses radiolabeled glucose to visualize metabolic activity. |
| Endothermic reaction | A reaction that absorbs heat ($\Delta H > 0$). |
| Exothermic reaction | A reaction that releases heat ($\Delta H < 0$). |
| Gibbs energy | A thermodynamic potential determining spontaneity ($\Delta G = \Delta H - T\Delta S$). |
| Catalyst | A substance that increases reaction rate without being consumed. |
| Nucleophile | An electron-pair donor. |
| Electrophile | An electron-pair acceptor. |
| Carbohydrates | Sugars, starches, and cellulose; important for structure and energy storage. |
| Fatty acids | Long hydrocarbon chains with a carboxyl group; building blocks of lipids. |
| Lipids | Hydrophobic molecules, including fats, oils, phospholipids, and steroids. |
| Membranes | Lipid bilayers forming cell boundaries and organelle compartments. |
| Nucleotides | Monomers of DNA and RNA, composed of a sugar, phosphate, and nitrogenous base. |
| Proteins | Macromolecules composed of amino acid subunits. |
| Enzyme | Biological catalysts that accelerate reactions. |
| Km | Substrate concentration at half $V_{max}$; indicates enzyme affinity. |
| Vmax | Maximum reaction velocity when the enzyme is saturated. |
| kcat | Turnover number; the rate at which an enzyme converts substrate to product. |
| Glycolysis | Metabolic pathway breaking down glucose to pyruvate. |
| Gluconeogenesis (GNG) | Synthesis of glucose from non-carbohydrate precursors. |
| Investment phase (of glycolysis) | ATP-consuming steps in glycolysis. |
| Payoff phase (of glycolysis) | ATP and NADH-producing steps in glycolysis. |
| Substrate level phosphorylation | Direct ATP synthesis from a substrate. |
| Normoglycaemia | Normal blood glucose concentration. |
| Hypoglycaemia | Low blood glucose concentration. |
| Oxidative decarboxylation | Reaction that removes CO2 and oxidizes a substrate. |
| Krebs/TCA cycle | Cyclic pathway in mitochondria that oxidizes acetyl-CoA, producing ATP, NADH, and FADH2. |
| Electron transport chain (ETC) | Series of protein complexes in the inner mitochondrial membrane that transfer electrons and pump protons. |
| Oxidative phosphorylation | ATP synthesis coupled to electron transport and proton flow. |