Molecule Concept, Chemical Bonds, and Biomolecules

Comprehensive vocabulary flashcards covering basic chemistry, atomic models, the periodic table, chemical bonds, intermolecular forces, functional groups, acid-base buffer systems, and stereochemistry from Dr. Göksemin Fatma Şengül's lectures.

Chemistry

The branch of science focused on the properties, composition, and structure of elements and compounds, the transformations they undergo, and their large-scale production methods.

Organic Chemistry

The subdiscipline of chemistry dedicated to the study of the structure, properties, composition, reactions, and preparation of carbon-containing compounds.

Inorganic Chemistry

The branch of chemistry that studies non-carbon-containing chemical substances.

Analytical Chemistry

The field of chemistry focused on obtaining, processing, and communicating information regarding the composition and structure of matter.

Physicochemistry

The branch of chemistry that investigates macroscopic, atomic, subatomic, and particulate phenomena in chemical systems using physical principles such as motion, energy, force, thermodynamics, and quantum mechanics.

Biochemistry

The science studying chemical reactions taking place within living organisms, including their cellular functions, effects, and biological regulation.

Antoine Lavoisier

An 18th-century French chemist regarded as the founder of modern chemistry who discovered that air consists of various gases, elucidated combustion, simplified chemical terminology, and categorized $33$ elements into four groups (gases, metals, nonmetals, and earths).

Matter

Anything that has mass and occupies space, characterized by granular, hollow (void), and mobile structural features.

Mass

A quantitative measure of the amount of matter contained within a physical substance.

Weight

The downward gravitational force acting on an object, mathematically defined as mass multiplied by the acceleration of gravity ($w = mg$).

Plasma

The fourth state of matter, formed at very high temperature and pressure, consisting of a collection of randomly moving ions, electrons, and neutral atoms where charged species interact via long-range Coulomb forces.

Element

A fundamental substance comprised of a single type of atom that cannot be decomposed into simpler substances by chemical reactions.

Compound

A pure substance formed by the chemical combination of two or more elements in a fixed, definite proportion.

Democritus

An ancient philosopher ($460\text{--}370\text{ BC}$) who originated the conceptual description of the atom.

Atomic Number

The fundamental property of an element, denoted as $Z$, representing the number of protons contained within the atomic nucleus.

Mass Number

The total count of protons and neutrons located inside an atom's nucleus, denoted as $A$.

Atomic Mass Unit (AMU)

A standard unit of mass defined as $\frac{1}{12}$ the mass of an unbound neutral carbon atom, corresponding to approximately $1.67 \times 10^{-24}\text{ g}$ or $1.67 \times 10^{-27}\text{ kg}$.

Isotopes

Atoms of the same element containing the same number of protons but differing numbers of neutrons, resulting in different mass numbers.

Valence Electrons

The electrons located in the outermost shell of an atom that participate directly in the formation of chemical bonds.

Core Electrons

The inner electrons of an atom that are tightly bound to the nucleus and do not participate directly in bonding, but influence chemical reactivity.

Octet Rule

The rule stating that atoms tend to gain, lose, or share electrons in order to achieve a stable configuration of eight electrons in their outermost shell.

Radioactivity

The spontaneous emission of high-energy particles or electromagnetic radiation from the nuclei of unstable atoms, first described by Henri Becquerel in $1896$.

Radioactive Emissions

Three distinct radiations identified by Rutherford: alpha ($\boldsymbol{\text{α}}$), beta ($\boldsymbol{\text{β}}$), and gamma ($\boldsymbol{\text{γ}}$), characterized by ionization power ($\boldsymbol{\text{α}} > \boldsymbol{\text{β}} > \boldsymbol{\text{γ}}$) and penetrating power ($\boldsymbol{\text{α}} < \boldsymbol{\text{β}} < \boldsymbol{\text{γ}}$).

Periodic Group

A vertical column of elements in the periodic table sharing similar chemical properties and identical numbers of valence electrons.

Periodic Period

A horizontal row in the periodic table across which atomic radius decreases and electron affinity generally increases from left to right.

Ionic Bond

A chemical linkage formed through the complete transfer of one or more electrons between atoms, resulting in electrostatic attraction between oppositely charged cations and anions.

Covalent Bond

A chemical bond formed by the mutual sharing of electron pairs between atoms, which can occur as single, double, or triple bonds.

Polar Covalent Bond

A type of covalent bond formed between atoms with different electronegativities, causing an unequal sharing of electron pairs that creates partial charges.

Ion-Ion Interaction

An intermolecular electrostatic attraction between positively charged cations and negatively charged anions that stacks into crystalline lattice networks.

Dipole-Dipole Interaction

An attractive intermolecular force that operates between polar molecules containing permanent electrical dipoles.

Ion-Dipole Interaction

An electrostatic attractive force that arises between an ion and the partially oppositely charged end of a neutral polar molecule.

Hydrogen Bond

A specific dipole-dipole attraction formed when a hydrogen atom covalently bound to a highly electronegative atom ($\text{F}$, $\text{O}$, or $\text{N}$) interacts with the lone pair of an adjacent electronegative atom.

London Dispersion Forces

Weak, temporary intermolecular attractions caused by transient, induced dipoles in molecules, increasing in magnitude with higher molecular mass and electron counts.

Catenation

The unique property of carbon atoms to form stable covalent bonds with each other, generating long chains and diverse structural frameworks.

Hydrocarbons

Stable organic compounds consisting entirely of carbon and hydrogen atoms that serve as the foundational backbone for biochemical reactions.

Functional Group

A specific arrangement of atoms or bonds attached to a hydrocarbon skeleton that dictates the distinct chemical reactivity and properties of an organic compound.

Biological Levels of Organization

The hierarchical progression of biological structures: $\text{Atom} \rightarrow \text{Molecule} \rightarrow \text{Macromolecule} \rightarrow \text{Organelle} \rightarrow \text{Cell} \rightarrow \text{Tissue} \rightarrow \text{Organ} \rightarrow \text{System} \rightarrow \text{Organism}$.

Lewis Acid-Base Theory

A chemical theory defining an acid as an electron-pair acceptor and a base as an electron-pair donor.

Henderson-Hasselbalch Equation

The mathematical formula relating buffer $\text{pH}$ to acid dissociation constant ($\text{p}K_a$) and conjugate pair concentrations: $\text{pH} = \text{p}K_a + \log\left(\frac{[\text{Salt}]}{[\text{Acid}]}\right)$.

Buffer System

An aqueous system containing a weak acid and its conjugate base (or a weak base and its conjugate acid) that resists changes in $\text{pH}$ when small amounts of $\text{H}^+$ or $\text{OH}^-$ are added.

Acidosis

A pathological state in which arterial blood $\text{pH}$ drops below the normal physiological reference range of $7.35\text{--}7.45$.

Alkalosis

A pathological state characterized by an elevation of arterial blood $\text{pH}$ above the normal physiological threshold of $7.45$.

Carbonic Anhydrase

A zinc-containing enzyme that accelerates the reversible reaction $\text{CO}_2 + \text{H}_2\text{O} \rightleftharpoons \text{H}_2\text{CO}_3 \rightleftharpoons \text{H}^+ + \text{HCO}_3^-$, regulating acid-base balance and physiological fluid balance.

Phosphate Buffer System

An important physiological buffer system ($\text{HPO}_4^{2-} / \text{H}_2\text{PO}_4^-$) with a $\text{p}K_a$ of $6.86$, operating effectively near physiological blood $\text{pH}$.

Constitutional Isomers

Molecules that have identical molecular formulas but differ in the physical order of atomic connections and structural connectivity.

Chiral Center

An asymmetric carbon atom that is covalently bonded to four distinctly different atoms, chemical groups, or substituents.

Enantiomers

Pairs of stereoisomeric molecules that are non-superimposable mirror images of one another and rotate plane-polarized light in equal but opposite directions.

Diastereomers

Stereoisomers that possess identical constitution but are not non-superimposable mirror images of each other, including cis-trans geometric isomers.

Epimers

A subtype of diastereomers that differ in the absolute stereochemical configuration of a single asymmetric carbon atom (such as glucose and galactose at $\text{C-4}$).

Anomeric Carbon

The hemiacetal or hemiketal carbon atom generated upon cyclization of an open-chain sugar that adopts either an $\boldsymbol{\text{α}}$ configuration (hydroxyl below the ring plane) or a $\boldsymbol{\text{β}}$ configuration (hydroxyl above the ring plane).

Mutarotation

The gradual change in the optical rotation of a solution containing pure $\boldsymbol{\text{α}}$ or $\boldsymbol{\text{β}}$ sugar anomers as they equilibrate through an open-chain form into a dynamic equilibrium mixture ($36\%\;\boldsymbol{\text{α}}\text{-D-glucopyranose}$, $<0.1\%\;\text{open D-glucose}$, $63\%\;\boldsymbol{\text{β}}\text{-D-glucopyranose}$).