Chapter 2: Life's Chemistry and the Importance of Water

Merged flashcards from Chapter 2 of Principles of Life, 3rd Edition.

Atoms

The smallest unit of a chemical element, comprised of a nucleus with protons and neutrons as well as electrons in orbitals

Element

A substance consisting of only one kind of atom that cannot be converted to another substance by ordinary chemical means

Protons

Positively charged particles in an atom that reside in the nucleus

Electrons

Negatively charged particles in an atom that reside in orbital shells around the nucleus

Neutrons

Uncharged particles in an atom that reside in the nucleus; numbers of these can vary with the isotopes of an atom

Nucleus

Where protons and neutrons are gathered in an atom

Electron shells

Where rapidly moving electrons are found, far from the nucleus, such that atoms are mostly empty space

Atomic mass

The mass of the protons plus the mass of the neutrons

Dalton (Da)

The unit of measurement of atomic mass, formerly the atomic mass unit

Atomic number

The number of protons in the nucleus; usually the top number

Periodic table

Where elements are presented in order of atomic number and organized into vertical columns; elements in the same column have the same number of electrons in the outermost shell

Valence shell

The outermost shell of an element; how many electrons reside here in the outermost s and p orbitals determine an element’s chemical properties

Isotopes

Variations of an element with different neutron counts and thus atomic mass

Bohr model

The most common model for atoms proposed by physicist Niels Bohr, where electrons orbiting the nucleus are shown in electron shells differing in distance

Atomic orbital

Where electrons actually move in each shell for a defined area of space, each with one or two electrons each, including:

• Spherical s orbitals

• Dumbbell-shaped p orbitals

• More higher energy shells with distance

Octet rule

States that an atom will lose, gain, or share electrons to achieve 8 electrons in the outermost shell

Noble gases

The elements in the last column of the periodic table with 8 electrons in the outermost shell, being unreactive to other elements

Electronegativity

An atoms’s tendency to attract electrons from another atom; smaller atoms closer to 8 electrons have higher levels of this — like the most abundant atoms H, C, N, and O

Radioactive decay

The loss of atomic particles to become different isotopes of the same element, or even other elements

• Seen with carbon-14 decaying to form nitrogen-14 for greater stability

Chemical bond

An attraction between two atoms

Covalent bond

Strong bonds that result from the sharing of electrons

• Forms when two atoms attain more stable configurations by sharing one or more pairs of electrons

• Represented in structural formulas by lines drawn between the bonded atoms

• Electronegativities cannot be too dissimilar; most common biological molecules have similar electronegativities and form covalent bonds if needed

Orientation

Property of covalent bonds where the length of a covalent bond between a given two elements is the same, and where the angle of each covalent bond with respect to others is also the same

Bond strength

Depends on the atoms involved to determine if a reaction will form

Nonpolar covalent bond

A type of covalent bond that occurs when atoms are shared about equally with the “pull” of each nucleus on the electrons not having a large delta (under a 0.5 difference)

Polar covalent bond

A type of covalent bond where electrons are unequally shared between the two atoms, in a slight charge difference

• Seen in H₂O, with electrons pulled closer to oxygen due to greater electronegativity

Dipole

A separation of opposite electric charges, such as those in a polar covalent bond

Dipole-dipole interactions

Where a compound can be attracted to slightly oppositely charged atoms in other bonds, creating a weak bond

Ionic bond

Strong bonds that result from the transfer of atoms to another configuration

• Occurs between high and low electronegative atoms, creating oppositely-charged ions (greater than 2 difference)

• These tend to form crystal lattices with regular, recurring arrangement of the anions and cations (like in table salt)

• They also often dissolve in water, rendering the strength irrelevant

Ion

An atom that gains or loses one or more electrons

Cation

The positively charged ion that lost one or more electrons

Anion

The negatively charged ion that gained one or more electrons

Molecule

This is formed when two or more atoms join together chemically

Compound

A molecule formed by at least two different elements

Hydrogen bond

A weak bond caused by electrostatic attractions between slightly-positively charged H and slightly-negatively charged O or N atoms

• This is an example of a dipole-dipole interaction

• Many can form within one molecule or between molecules, adding strength and determining molecular shape in some cases

van der Waals interactions

Transient electrostatic attraction between two atoms, each of which is in a nonpolar covalent bond

• Very small dipoles may form here because of minute asymmetries in electron orbit, which can induce a temporary dipole if close enough

Molecular stability

Inversely correlated to a bond’s potential energy to attain more of this

Energy

The capacity to do work, divided into kinetic (movement) and potential (stored) types

First law of thermodynamics

States that energy cannot be created or destroyed, only conserved

Bond strength

Inversely correlated with a bond’s potential energy and stability; higher levels of energy have lower levels of this

Second law of thermodynamics

States that the total amount of usable energy in a system goes down due to the increase of entropy, defined as randomness or lack of concentration

Usable energy

How much energy is available in the system that is not lost to entropy; this goes down with each transfer due to the second law of thermodynamics

Chemical reaction

An interaction between different groups of atoms, divided into reactants (inputs) and products (outputs)

• These conserve energy but result in differences in entropy, properties, and bond energy

Hydrolysis

An exergonic, reversible chemical reaction that releases energy through the use of water; this is naturally more favored

Condensation reaction

An endergonic chemical reaction resulting in the combination of two substances, it results in water as a byproduct and stores free energy in its products

• This requires an input of energy and is less favored

Free energy

A change in the total usable energy between reactions and products, often represented as delta G; this divides exergonic (releasing) and endergonic (absorbing) reactions

Reaction rate

In a chemical reaction, how much of a product is formed over time; this is limited by the required activation energy of the reaction, temperature, and concentration (as these affect collisions)

Equilibrium

The state that occurs when endergonic and exergonic reactions settle into the same reaction rates with no change in relative concentration

Specific heat

The amount of heat needed to raise 1 gram of water by 1 degree Celsius

• This is naturally high in water and enables its existence in many organisms, buffering temperature

Heat of vaporization

The amount of energy needed for vaporization

• This is naturally high in water and enables the cooling of living organisms due to its absorption

Density

The ratio of a substance’s mass to volume

• This is lower in ice compared to water due to greater organization, which enables lakes to freeze top to bottom

Hydrogen bonds

Bonds between hydrogen atoms of different molecules; these can create cohesion (which holds water together for surface tension) and adhesion (which allows water to adhere to another surface)

Solvent

What dissolves a specific substance; these change distributions but do not break molecular structures

• Water is a type of this, forming weak attractions with substances with polarity, thus dividing hydrophilic and hydrophobic reactions

Hydrophilic

The tendency to be attracted to and dissolve in water; this is greater in polar molecules due to the creation of a hydration shell surrounding both ions

• The sum of these forces against a bond’s strength determines dissolution

• Common in biology

Hydrophobic

The tendency to not be attracted to and dissolve in water; this is seen in non-polar substances such as oil which do not form hydration shells

Amphipathic

Substances that are both hydrophilic and hydrophobic

Self-ionization

When H₂O spontaneously ionizes into H₃O⁺ and OH^-

• Occurs in very small amounts

Neutral solution

A solution in which the concentration of H⁺ (hydronium) ions is equal to the concentration of OH^- (hydroxide) ions

Acids

These raise H⁺ concentrations relative to OH^-

• Can be strong or weak depending on substance’s resistance to allowing a free H+

Bases

These produce more OH^- against H⁺ when as a result of dissociation, forming water with some of the H⁺ ions

• Can be strong or weak depending on stability; OH- is just very unstable and easily absorbs an H+

Buffer

A solution that reduces the impact of acids or bases on pH relative to if they were not present at all

• Acids adding H⁺ react with a negative ion in a buffer to form the original reactant, reducing the acid’s impact

• Bases adding OH^- react with the H⁺ in a buffer to form water, reducing basic impact

• Required in living systems, seen in blood to have a constant pH

pH

The negative log of the concentration of H₃O ions

• Neutral substances have concentrations of 10^-7 H₃O M

• Acidic substances have concentrations greater than 10^-7 H₃O M, resulting in a lower number

• Basic substances have concentrations less than 10^-7 H₃O M, resulting in a greater number

Functional groups

Groups of atoms that affect the four macromolecules through their number and location by conferring different properties

Organic chemistry

The study of carbon due to the available bonds that make it highly versatile

Methyl

A nonpolar group important for the modification of proteins and cytosine (C) nucleotide

• Type of alkyl, expressed as CH₃ to a substance

Hydroxyl

A polar group involved in hydrogen bonding and condensation reactions

• Type of alcohol, expressed as OH to a substance

Sulfhydryl

A polar group that can form stabilizing disulfide bridges in proteins

• Type of thiol, expressed as SH to a substance

Aldehyde

A very reactive polar group important in energy releasing reactions

• Expressed as C that is double bonded to O and single bonded to H

Keto

A polar group important in carbohydrates and energy reactions

• Type of ketone, expressed as carbon double bonded to oxygen

Carboxyl

A charged, acidic group that ionizes in living tissues to form COO^- and H⁺, reacting with amino groups to form peptide bonds

• Expressed as C double bonded to H and single bonded to OH

Amino

A charged, basic group that accepts H⁺ in living tissue to form NH₃⁺; and reacts with carboxyl groups to form peptide bonds

• Expressed as N single bonded to two different H atoms

Phosphate

A polar, hydrophilic, and acidic molecule that ionizes in living tissues and enters into condensation reactions

• Strongly exergonic with hydrolysis in water

Structural isomers

Molecules with the same chemical composition but different groupings and joinings, like glucose and fructose both having C₆H₁₂O₆

Stereoisomers

Molecules with the same chemical compositions and groups but differ in their three-dimensional geometry