Chapter 2: Chemical Components of Cells

Vocabulary-style flashcards covering the chemical components of cells, including bonding, water properties, macromolecules, and noncovalent forces.

Atom

The smallest particle of an element.

Chemical bonds

Interactions that hold atoms together, produced because the laws of physics favor a completely filled outer shell of electrons.

Protons

Positively charged particles located in the atom; their total count determines the atomic number of an element.

Atomic number

The number of protons in an atom which determines the specific element.

Unbonded atom state

A state where the outer electron shell is usually not completely filled and the atom must have equal numbers of electrons and protons to maintain charge neutrality.

Electron sequence

The order in which shells are filled from the inner shell to the outer shell.

Shell 1 capacity

The innermost electron shell which can hold up to $2$ electrons.

Shell 2 capacity

An electron shell which can hold up to $8$ electrons.

Ionic bond

A chemical bond formed by the transfer of an electron from one atom to another, resulting in oppositely charged ions.

Covalent bond

A chemical bond formed by the sharing of electrons between atoms.

Ion

An atom that has lost or gained electrons, becoming positively or negatively charged.

Positive ion

An atom that has lost electrons.

Negative ion

An atom that has gained electrons.

Ionic bond electron quantity

Typically formed when atoms gain or lose just $1-2$ electrons.

Salt crystal

A structure produced by the proximity of positively and negatively charged ions where electrical neutrality is maintained.

Salt dissolution

The process where ionic bonds are disrupted by polar water molecules, allowing the crystal to be dissolved.

Nonpolar covalent bond

A covalent bond involving the equal sharing of electrons between atoms.

Polar covalent bond

A covalent bond involving the unequal sharing of electrons, producing partial charges.

Double bond

The sharing of more than one pair of electrons between two atoms; it is more rigid than a single bond.

Rotational constraint

Atoms shared via double bonds cannot rotate relative to each other and are held in a plane.

Oxygen in $H_2O$

An atom that attracts electrons more strongly than hydrogen, contributing to a polar covalent bond.

Hydrogen bond

A weak noncovalent electrical attraction between a hydrogen in a polar covalent bond and another oxygen or nitrogen atom.

Water boiling point

Relatively high due to the hydrogen bonds formed between molecules.

Surface tension

A unique property of water that is exceptionally high because of hydrogen bonds.

Hydrophilic

"Water-loving" substances, such as ionic or polar molecules, that dissolve in water.

Hydrophobic

"Water-fearing" substances, such as nonpolar molecules, that do not dissolve in water.

Carboxyl group ionization

The polar nature of the $O-H$ bond allows hydrogen to ionize, which can produce a weak acid.

Weak acid

A chemical group that can release a proton and thereby lower the pH of a solution.

Amino group ($NH_2$)

A weak base that tends to acquire protons from water to become $-NH_3^+$.

Weak base

A chemical group that acquires protons from water, thereby increasing the pH.

Pure water pH

Maintaining a value of $7$ because of equal concentrations of both hydroxide and hydronium ions.

Pure water ion concentration

Equal concentration of $10^{-7}M$ for both $H^+$ and $OH^-$.

pH definition

$$-log ([H^+])$$

99% of biological atoms

The percentage comprised by Oxygen, Nitrogen, Carbon, and Hydrogen.

Carbon bonding capacity

Typically forms four bonds, allowing it to create long polymers.

Tetrahedral conformation

The specific spatial arrangement of the four bonds formed by carbon.

Polymers

Macromolecules built from monomers.

Condensation reaction

A chemical reaction that forms covalent bonds between monomers while expelling a water molecule.

Hydrolysis reaction

A reaction used for the destruction of polymers.

Monosaccharides

Simple sugars that serve as the building blocks for polysaccharides.

Polysaccharides

Complex carbohydrates built from monosaccharides; can have branched structures.

Isomers (Sugars)

Molecules with the same formula that have different structures based on the orientation of $OH$ groups.

Carbohydrates formula

$$(CH_2O)_n$$

Polysaccharide functions

Energy source, mechanical support, and cell surface tags.

Cell surface tags

Glycolipids and glycoproteins that allow for the recognition of cells.

Lipids

A diverse class of molecules wholly or partly insoluble in water, built from fatty acids and glycerol.

Fatty acids

Building blocks of lipids consisting of a hydrophilic weak acid group and a hydrophobic chain of $C-C$ and $C-H$ bonds.

Amphipathic

A molecule possessing dual hydrophilic and hydrophobic properties.

Triacylglycerols

Hydrophobic droplets stored in fatty tissue to provide energy as needed.

Fats

Triacylglycerols containing mostly saturated fatty acids.

Oils

Triacylglycerols containing mostly unsaturated fatty acids.

Biological membranes

Formed from lipids where one $OH$ group of glycerol is bonded to a charged head group instead of a fatty acid.

Phospholipid

An amphipathic molecule that produces the lipid bilayer of a cell membrane.

Lipid bilayer

A self-organizing structure where hydrophilic head groups face water and hydrophobic tails pack in the middle.

Membrane fluidity

Influenced by fatty acid tails; unsaturated tails pack together less tightly and form more fluid membranes.

Proteins

Biological polymers made of amino acids.

Amino acid side chains

Also known as R groups, there are $20$ different types which can be charged, polar, or nonpolar.

Polypeptides

Chains of amino acids linked together by peptide bonds.

Peptide bond

A specific covalent bond formed by a condensation reaction between amino acids.

N-terminus

The amino end of a polypeptide chain.

C-terminus

The carboxyl end of a polypeptide chain.

Protein synthesis direction

Synthesis proceeds from the N-terminus toward the C-terminus.

Nucleotides

Subunits of DNA and RNA, also serving as energy carriers.

Ribonucleotide components

Consists of a nitrogen-containing base, a $5$-carbon ribose sugar, and one or more phosphates.

Deoxyribonucleotide

The DNA subunit which contains an $-H$ rather than an $-OH$ at the $2'$ position of the sugar.

Nitrogenous bases

One of four types: adenine, guanine, cytosine, and uracil (or thymine in DNA).

Nucleoside

A compound consisting of a ribose sugar and a nitrogenous base.

Adenosine triphosphate (ATP)

The principal energy carrier in the cell.

Phosphoanhydride bond

The high-energy bond in ATP that releases energy when broken by water.

ATP energy source

Input of energy from sunlight or food.

ADP

Adenosine diphosphate, created when ATP releases a phosphate group through hydrolysis.

Inorganic phosphate ($P_i$)

The phosphate group released during the conversion of ATP to ADP.

Phosphodiester bond

Formed in condensation reactions joining the $3'$ end of one nucleotide to the $5'$ end of the next.

Genetic code

The sequence of bases in DNA/RNA that dictates the synthesis of polypeptides.

Transcription

The synthesis of a complementary strand of RNA from a DNA template.

Replication

The synthesis of a complementary strand of DNA from a DNA template.

Nucleotide base rings

Bases can consist of either one or two rings.

Centrifugation

A technique used to measure the size of biological polymers and macromolecules.

Sucrose gradient

A medium used in centrifugation where molecules sediment based on size.

Sedimentation rate

The speed at which molecules move through a gradient; larger molecules sediment faster.

Noncovalent interactions

Bonds and forces (electrostatic, hydrogen, van der Waals) that specify precise shapes and interactions of macromolecules.

Molecular folding

The process where carbons rotate about bonds to maximize noncovalent bonds, creating a stable form.

Macromolecular complexes

Structures formed through complementary fits and noncovalent forces.

Electrostatic attraction

A noncovalent force creating dynamic interactions based on electrical charges.

Hand in glove fits

The concept that the importance of shape is critical for the function of macromolecules.

Hydrogen bond sandwich

Occurs when a hydrogen atom is placed between two electron-attracting atoms, usually oxygen or nitrogen.

Maximum H-bond strength

Achieved when the three atoms involved in the bond are in a straight line.

Van der Waals attractions

Weak interactions due to fluctuating electrical charges between any two atoms at very short distances.

Van der Waals repulsion

A strong force that occurs if two atoms are too close together.

Van der Waals radius

The characteristic "size" of an atom, allowing it to be treated as a sphere with a fixed radius.

Contact distance

The sum of the van der Waals radii of two noncovalently bonded atoms.

Covalent vs Van der Waals distance

In a covalent bond, atomic nuclei are much closer together than the sum of their van der Waals radii.

Hydrophobic forces

Repulsion from water that forces nonpolar groups together to minimize disruption of the water network.

Water network

A lattice formed by hydrogen bonds between water molecules.

Hydrophobic bonds

An informal term for the attraction between hydrophobic groups caused by water repulsion.

Single covalent bond distance (C-C)

$$0.15\,nm$$

Double covalent bond distance (C=C)

$$0.13\,nm$$

Non-bonded carbon nuclei distance

$$0.4\,nm$$

G and C interaction

Two nitrogenous bases hydrogen-bonded together in a DNA double helix.

H radius (van der Waals)

$$0.12\,nm$$