Biochemistry and Organic Compounds Review

Comprehensive flashcard set covering foundational chemistry, properties of water, carbon bonding, carbohydrates, lipids, nucleic acids, proteins, and enzyme kinetics.

Element

Matter composed of atoms that all have the same atomic number (number of protons).

Atom

The smallest component of an element that still has properties of the element, consisting of a positively charged nucleus surrounded by a charged cloud of electrons.

Proton

A subatomic particle located in the nucleus with a positive charge of $+1$.

Neutron

A non-charged nuclear particle with the same mass as the proton.

Electron

A negatively charged subatomic particle ($-1$) with a mass less than a proton.

Isotope

Atoms with the same number of protons and electrons, but different numbers of neutrons.

Periodic Table Tile Components (Oxygen)

Information displayed on an element box: Element Name (Oxygen), Atomic Number ($8$, representing protons in the nucleus), Chemical Symbol ($\text{O}$, $1\text{--}2$ letters often from Latin or Greek), and Atomic Mass ($15.9994$, total number of protons, neutrons, and electrons).

Polarity (Water)

An uneven pattern of electrical charge across a molecule, such as in water ($H_2O$) where oxygen has $8$ protons and attracts shared electrons more strongly than hydrogen, which has only $1$ proton.

Hydrogen Bond

A weak chemical bond formed between a hydrogen atom in one molecule and a negatively charged region in another molecule.

Cohesion

The attractive force between particles of the same kind, which produces surface tension, allows insects to walk on water, and enables water to bulge on a glass filled to the brim.

Adhesion

The attractive force between unlike substances, which enables capillary action when water climbs upward in a narrow glass tube against gravity.

Organic Compound

A compound containing carbon atoms that are covalently bonded to other carbon atoms and to other elements such as hydrogen, oxygen, and nitrogen.

Single Covalent Bond

A chemical bond in which two atoms share one pair of electrons.

Double Covalent Bond

A chemical bond in which two atoms share two pairs of electrons.

Triple Covalent Bond

A chemical bond in which two atoms share three pairs of electrons.

Functional Group

A cluster of atoms that influences the properties of the molecules it composes and serves as a structural building block determining compound characteristics.

Hydroxyl Group

A functional group consisting of $-OH$ that gives molecules polar and hydrophilic properties.

Carboxyl Group

A hydrophilic functional group consisting of $-COOH$ found in compounds like fatty acids and amino acids.

Amino Group

A functional group consisting of $-NH_2$ present in amino acids.

Hydrophilic

Literally "water loving"; refers to polar or ionic molecules or functional group ends that interact with or dissolve in water.

Hydrophobic

Literally "water fearing"; refers to non-polar molecules or hydrocarbon ends that do not dissolve in or interact with water.

Dehydration Synthesis (Condensation Reaction)

A chemical reaction joining two monomers into a polymer or macromolecule with the requirement of energy and the release of $1$ water molecule per bond formed.

Hydrolysis

A chemical reaction that splits macromolecules or polymers into smaller monomers through the addition of $1$ water molecule per bond broken.

Carbohydrate

An organic compound composed of Carbon, Hydrogen, and Oxygen in a general formula of $(CH_2O)_n$ that stores energy and typically has a name ending in "-ose".

Monosaccharide

A simple sugar monomer of carbohydrates with a $1:2:1$ ratio of $\text{C}:\text{H}:\text{O}$ and chemical formula $C_6H_{12}O_6$, including glucose, fructose, and galactose.

Isomer

Compounds with the same molecular formula (such as $C_6H_{12}O_6$) but different structural arrangements of their atoms.

Disaccharide

A double sugar composed of two monosaccharides joined by a dehydration synthesis reaction, such as sucrose, lactose, or maltose.

Sucrose

A disaccharide (table sugar) formed by the bonding of glucose and fructose.

Lactose

A disaccharide found in milk composed of glucose and galactose.

Maltose

A disaccharide composed of two glucose molecules joined together.

Glycogen

A storage polysaccharide in animals made of hundreds of glucose molecules in highly branched chains, stored in the liver and muscles to stabilize blood glucose levels.

Starch

A plant polysaccharide that serves as stored glucose.

Cellulose

A structural polysaccharide in plants that forms cell walls, cotton, and wood, providing strength and rigidity; it functions as dietary fiber in humans, who lack the enzyme to digest its linkages.

Lipid

A large, non-polar organic molecule insoluble in water but soluble in non-polar solvents, storing twice as much energy per gram ($1\,g$) as carbohydrates.

Triglyceride Formation

The synthesis of a fat molecule from one glycerol molecule (containing $3$ carbons and $3$ hydroxyl groups) and three fatty acid chains.

Saturated Fatty Acid

A fatty acid with no double covalent bonds between carbon atoms, straight chains that pack closely together, high melting temperatures, and a solid state at room temperature.

Unsaturated Fatty Acid

A fatty acid containing at least one double covalent bond between carbon atoms, producing bends in the chain that prevent tight packing, resulting in lower density, lower melting temperature, and a liquid state at room temperature.

Phospholipid Bilayer

A membrane structure formed in watery environments where polar hydrophilic heads face outward toward water and non-polar hydrophobic fatty acid tails face inward toward each other.

Wax

A structural, highly waterproof lipid composed of a long fatty acid chain linked to an alcohol, serving as protective coatings on plants and as earwax in animals.

Steroid

A lipid characterized by a carbon backbone of four fused rings, exemplified by cholesterol and hormones such as testosterone.

Nucleotide

The monomer of nucleic acids composed of three parts: a 5-carbon sugar, a nitrogen base, and a phosphate group.

DNA (Deoxyribonucleic Acid)

A double-stranded, double-helical nucleic acid containing deoxyribose sugar and the nitrogen bases adenine, thymine, cytosine, and guanine, which stores and transmits genetic information for synthesizing proteins.

Complementary Base Pairing

The hydrogen bonding rule in DNA stating that adenine ($\text{A}$) always pairs with thymine ($\text{T}$) and cytosine ($\text{C}$) always pairs with guanine ($\text{G}$).

Anti-parallel

The opposite directional arrangement of the two strands in a DNA molecule, where one strand runs from the $5'$ end (phosphate group) to the $3'$ end, while the opposite strand runs from $3'$ to $5'$.

RNA (Ribonucleic Acid)

A single-stranded nucleic acid containing ribose sugar and the nitrogen bases adenine, uracil, cytosine, and guanine ($\text{A, U, C, G}$).

Codon

A three-letter base sequence in mRNA transcribed from the anti-sense DNA template strand that codes for exactly one amino acid in a polypeptide chain.

ATP (Adenosine Triphosphate) Reaction Cycle

A reversible cellular energy reaction in which ATP hydrolyzes into ADP and inorganic phosphate ($\text{P}_i$) to release energy, and is regenerated by adding energy to ADP and $\text{P}_i$.

Amino Acid Structure

The monomer of proteins, containing a central carbon atom covalently bonded to a single hydrogen atom ($-H$), a carboxyl group ($-COOH$), an amino group ($-NH_2$), and a variable "R Group" (side chain).

Peptide Bond

A covalent bond joining two amino acids together through a dehydration synthesis reaction between the amino group of one and the carboxyl group of another.

Polypeptide

A polymer of proteins composed of three or more amino acids bonded one at a time via dehydration synthesis reactions.

Enzyme

A reusable catalytic protein ending in "-ase" that speeds up specific chemical reactions without being changed, working best at body temperature.

Lock and Key Model

An analogy describing enzyme specificity where the enzyme represents the lock, the substrate acts as the key, and the active site functions as the keyhole.

Activation Energy

The initial energy required to start a chemical reaction, which is lowered by the catalytic action of an enzyme.

Substrate

The specific reactant molecule that binds to the active site of an enzyme to undergo a chemical reaction.

Active Site

The region on an enzyme that physically fits and binds the reactant molecule during a catalytic reaction.

Dipeptide

A molecule formed by joining two amino acids together through a dehydration synthesis reaction.

R-Group (Side Chain)

The variable portion attached to the central carbon of an amino acid that imparts unique chemical traits, shape, and polarity to each of the $20$ different varieties.

Polyunsaturated Fatty Acid

A lipid molecule containing two or more double covalent bonds between carbon atoms, preventing tight packing and remaining liquid at room temperature.

Cholesterol

A structural steroid featuring four fused carbon rings that stabilizes the lipid bilayer of animal cell membranes and facilitates proper nerve transmission.

Capillary Action

The process by which water climbs upward through narrow tubes or porous materials against gravity due to the combined action of cohesive and adhesive forces.

Density of Ice

The physical property in which water expands upon freezing to form a crystalline lattice, making the solid state less dense and able to float on its liquid form.

Temperature Moderation (Water)

The ability of water to absorb or release relatively large amounts of thermal energy with only small changes in its own temperature.

Glucose

A six-carbon simple sugar with the formula $C_6H_{12}O_6$ that functions as the primary source of metabolic energy for cells.

Fructose

The sweetest naturally occurring monosaccharide ($C_6H_{12}O_6$) found primarily in fruits and honey.

Galactose

A six-carbon monosaccharide isomer found in dairy products that commonly links with another hexose to form milk sugar.

Template (Anti-sense) Strand

The strand of DNA oriented from the $3'$ end to the $5'$ end that provides the base sequence for transcribing a complementary messenger RNA strand.

Nucleus (Atomic)

The dense central region of an atom containing protons and neutrons.

Atomic Number

The number of protons contained within the nucleus of an atom, defining its elemental identity.

Atomic Mass

The total combined mass of the protons, neutrons, and electrons within an atom.

Chemical Symbol

A one- or two-letter abbreviation representing a chemical element, frequently derived from Latin or Greek names.

Octet Rule Electron Capacities

The maximum stable electron counts per energy level in typical representative elements: $2$ in the first shell, $8$ in the second shell, and $8$ in the third shell.

Valence Electrons in Carbon

The $4$ electrons present in carbon's outermost electron shell that allow it to form up to $4$ covalent bonds.

Carbon Backbone Configurations

The structural arrangements formed by covalently linked carbon atoms, specifically straight chains, branched chains, or closed rings.

Hydrocarbon

A non-polar, hydrophobic molecular region composed entirely of covalently bonded carbon and hydrogen atoms.

Surface Tension

The cohesive property at the surface of a liquid that creates a thin, skin-like barrier capable of supporting small objects.

Water as a Polar Solvent

The capacity of water to dissolve ionic compounds like $NaCl$ and polar molecules like sugars by surrounding their charged regions.

Polysaccharide Digestion Pathway

The breakdown of complex dietary carbohydrates into maltose units via hydrolysis, which are subsequently hydrolyzed into individual glucose units.

Blood Glucose Regulation by the Liver

The physiological process of converting excess blood sugar into stored glycogen after meals, and breaking down glycogen into free glucose between meals.

Dietary Fiber

The indigestible plant cell wall component composed of cellulose, which humans cannot break down due to a lack of the required digestive enzyme.

Energy Density of Lipids

The storage capacity of fats, yielding twice as much usable chemical energy per gram as carbohydrates.

Fatty Acid

A lipid building block consisting of a carboxyl group attached to a long hydrocarbon chain typically containing $16\text{ to }18$ carbon atoms.

Glycerol

A three-carbon alcohol molecule bearing $3$ hydroxyl groups that bonds with fatty acids to construct a fat molecule.

Phospholipid Structure

A membrane lipid composed of a glycerol molecule bonded to two hydrophobic fatty acid chains and one polar, hydrophilic phosphate group.

Biological Functions of Waxes

Waterproofing and protective coverings, serving as a barrier on plant exteriors and forming earwax in animals to block foreign microorganisms.

Nucleic Acid Elemental Composition

The specific combination of chemical elements that constitute nucleic acids: Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus ($\text{CHONP}$).

DNA Double Helix Structural Anatomy

The molecular architecture in which alternating deoxyribose sugars and phosphate groups make up the exterior backbone, while complementary nitrogen bases pair within the interior.

5-Prime ($5'$) and 3-Prime ($3'$) Nucleic Acid Ends

The chemical orientation of a nucleotide strand, where one end terminates in a free phosphate group and the opposite end terminates with a free sugar group.

Structural Differences Between DNA and RNA

The distinguishing traits where DNA is double-stranded with deoxyribose sugar and thymine, whereas RNA is single-stranded with ribose sugar and uracil.

High-Energy Phosphate Bonds in ATP

The chemical linkages between the phosphate groups of adenosine triphosphate whose hydrolysis releases immediate cellular energy.

Protein Functions in Living Systems

Essential cellular tasks including enzymatic catalysis, membrane transport, structural support, nutrient storage, muscle contraction, and antibody defense.

Protein Denaturation

The loss of a protein's three-dimensional shape and biological function caused by extreme changes in temperature or solvent environment.

Number of Standard Biological Amino Acids

The set of $20$ distinct building blocks used by living organisms to construct all synthesized polypeptides.

Enzyme Reusability

The property of catalytic proteins remaining chemically unaltered after facilitating a reaction, permitting repeated catalytic cycles.

Enzyme Specificity

The characteristic wherein an individual enzyme catalyzes only one particular reactant, exemplified by lactase binding solely to lactose.