Cell Chemistry and Macromolecules

Vocabulary flashcards covering cell chemistry, types of chemical bonds, macromolecules (carbohydrates, lipids, nucleic acids, proteins), and metabolic principles based on Lecture 2 notes.

Unity of Biochemistry

The concept that organisms are quite uniform at the molecular level; Jacques Monod (1954) stated that "Anything found to be true in E.Coli must also be true in Elephants."

Atoms

The basic unit of matter consisting of protons and neutrons in a nucleus and electrons in outer shells; the number of outer shell electrons determines chemical properties.

Molecules

Two or more atoms in a definite arrangement held together by chemical bonds; biomolecules are centered around Carbon, which can bind up to 4 other atoms.

Covalent Bonds

Links formed when atoms share electrons to fill their outermost shells and achieve stability; common in Carbon ($C$), Hydrogen ($H$), Nitrogen ($N$), and Oxygen ($O$).

Polar Covalent Bonds

A type of bond involving unequal sharing of electrons resulting in an asymmetric charge distribution, where one atom has a partial negative charge and the other a partial positive charge.

Electronegative atom

The atom in a polar covalent bond that possesses the greater attractive force for electrons.

Non-polar Covalent Bonds

Bonds characterized by the equal sharing of electrons and a lack of electronegative atoms, such as in molecules made entirely of $C$ and $H$.

Ionic Bond

A non-covalent interaction resulting from electrical attraction between opposing charges, involving the transfer of electrons from one atom to another.

Hydrogen Bond

A weak non-covalent bond resulting from electrical attraction where an electropositive hydrogen atom is partially shared by two electronegative atoms.

Van der Waals Forces

Weak, nonspecific interactions between two atoms in close proximity caused by temporary charges called dipoles, which form because electrons are constantly in motion.

Hydrophobic Interactions

An interaction where uncharged non-polar molecules form clumps or aggregates to minimize exposure to polar molecules like water.

Macromolecules

Large polymers made of building blocks known as monomers; examples include proteins ($15\%$ of bacterial cell volume), RNA ($6\%$), and DNA ($1\%$).

Condensation

The process by which polymers are formed by joining monomers, during which water is removed.

Hydrolysis

The process by which polymers are broken down into monomers by the addition of water.

Carbohydrates

Molecules with the general formula $(CH_2O)_n$; they function in cell metabolism and can exist as trioses, tetroses, pentoses, or hexoses.

Ketose

A sugar where the carbonyl group is in an internal position, forming a ketone.

Aldose

A sugar where the carbonyl group is at one end of the molecule, forming an aldehyde.

Isomers

Molecules that have the same chemical formula (e.g., $C_6H_{12}O_6$ for glucose, galactose, and mannose) but differ in the spatial arrangement of atoms.

Disaccharides

Two monosaccharides covalently bonded together, used for energy storage; examples include sucrose, maltose, and lactose.

Polysaccharides

Long chains of sugars that serve structural or storage functions; examples include chitin, cellulose, starch, and glycogen.

Glycogen and Starch

Carbohydrate polymers containing $\alpha(1,4)$ linkages, resulting in branched chains (glycogen) or coils (starch).

Cellulose

A carbohydrate polymer containing $\beta(1,4)$ linkages, resulting in long branches.

Lipids

A large group of non-polar molecules composed mainly of $C$, $H$, and $O$ that dissolve in organic solvents but not in water.

Fats (Triacylglycerol)

Lipids composed of glycerol linked to three fatty acid chains by ester bonds.

Saturated Fatty Acids

Fatty acid chains that contain no double bonds between carbon atoms.

Unsaturated Fatty Acids

Fatty acid chains that contain one or more double bonds.

Steroids

Complex four-hydrocarbon ring structures; examples include cholesterol, an animal plasma membrane component and hormone building block.

Phospholipids

Amphipathic molecules composed of glycerol, two fatty acids, and a phosphate group; they are the major component of cell membranes.

Nucleic Acids

Polymers of nucleotides (DNA and RNA) used for storing genetic information.

Nucleotides

The building blocks of nucleic acids, consisting of a five-carbon sugar, a nitrogenous base, and a phosphate group.

Phosphodiester bond

The sugar-phosphate linkage that joins nucleotides, specifically attaching the $3'$ hydroxyl of one to the $5'$ phosphate of the next.

Amino Acids

The building blocks of proteins, consisting of an $\alpha$-carbon, an amino group ($NH_2$), a carboxyl group ($COOH$), and a variable $R$ group (side chain).

Peptide bonds

Covalent bonds that attach the carboxyl group of one amino acid to the amino group of another to form polypeptide chains.

Disulfide bonds

Covalent bonds formed between cysteine amino acids under oxidizing conditions.

Enzymes

Protein catalysts that accelerate chemical reactions in the cell by reducing activation energy barriers without being changed by the reaction.

Second law of thermodynamics

A principle stating that the state of a system cannot be reversed without increasing the entropy (disorder) of the surroundings.

$\Delta G$ (Free energy change)

The amount of energy available to do work in a system; used to determine if a reaction is energetically favorable.

Exergonic reaction

A reaction that involves the release of energy, where reactants have more energy than products.

Endergonic reaction

A reaction that requires energy absorption, where products have more energy than reactants.

Reaction coupling

The use of an energetically favorable reaction to drive an energetically unfavorable one, resulting in a total free energy change of less than zero.

Activated carrier molecules

Molecules like ATP that store energy in easily convertibles forms (such as chemical groups or high-energy electrons) to power unfavorable reactions.

ATP (Adenosine Triphosphate)

A primary carrier molecule in cells; energy stored in its phosphoanhydride bonds is used for macromolecule synthesis and joining molecules.