Chapter 2 Biochem

Biology

The scientific study of life and living organisms.

Element

A pure substance that cannot be broken down into other simpler substances through chemical reactions.

Compound

A substance formed by two or more different elements combined in a fixed ratio.

Emergent Properties

Properties exhibited by a compound that are distinct from its individual element constituents.

Covalent Bond

A bond formed when two atoms share a pair of valence electrons.

Ion

A fully charged atom or molecule produced by the loss or gain of electrons.

Hydrogen Bond

A weak bond formed when a hydrogen atom covalently bonded to one electronegative atom is attracted to another electronegative atom.

Van der Waals Interactions

Transient attractions between closely adjacent nonpolar molecules, caused by fluctuations in electron accumulation.

Chemical Reaction

Processes that make or break chemical bonds, altering the chemical composition of matter.

Photosynthesis

A bioenergetic chemical reaction converting solar energy, carbon dioxide, and water into glucose and oxygen.

Essential Elements

Approximately 20% to 25% of naturally occurring elements required by an organism to sustain normal biological function, growth, and reproduction.

Major Essential Elements

Elements that make up 96.3% of human body mass, including Oxygen, Carbon, Hydrogen, and Nitrogen.

Minor Essential Elements

Elements that account for 3.7% of human body mass, including Calcium, Phosphorus, Potassium, Sulfur, Sodium, Chlorine, and Magnesium.

Trace Elements

Elements required by organisms in extremely minute quantities, accounting for less than 0.01% of body mass.

Examples of Trace Elements

Includes Boron, Chromium, Cobalt, Copper, Fluorine, Iodine, Iron, Manganese, Molybdenum, Selenium, Silicon, Tin, Vanadium, and Zinc.

Evolutionary Adaptation to Toxic Elements

Process by which certain species have evolved physiological tolerance to thrive in environments with high levels of toxic elements.

Serpentine Plant Communities

Plant communities that have adapted to soil high in toxic heavy metals and have evolved biochemical pathways to survive.

Atom

The smallest subatomic unit of matter that retains all characteristic chemical properties of an element.

Subatomic Particles

Basic components of an atom, including neutrons, protons, and electrons.

Neutrons

Uncharged particles (0 electrical charge) located inside the atomic nucleus; mass is roughly $1\,\text{dalton}$.

Protons

Positively charged particles (+1 charge) located inside the atomic nucleus; mass is roughly $1\,\text{dalton}$.

Electrons

Negatively charged particles (-1 charge) moving rapidly in a spatial cloud surrounding the central nucleus; mass is negligible (approximately 1/2000 of a proton/neutron).

Atomic Number

The unique count of protons inside an element's nucleus; in a neutral atom, it equals the total number of surrounding electrons.

Mass Number

The combined total count of protons plus neutrons residing in the atomic nucleus.

Calculating Neutrons

Number of Neutrons = Mass Number - Atomic Number.

Isotopes

Distinct structural forms of an element that share identical proton numbers but vary in neutron counts, yielding different mass numbers.

Ionic Bond

The strong electrostatic attraction between oppositely charged cations and anions.

Covalent Bond

Formed when two atoms share a pair of valence electrons.

Valence Electrons

Electrons occupying the outermost valence shell, determining an atom's chemical reactivity.

Nonpolar Covalent Bond

Electrons are shared equally between two atoms with similar electronegativities.

Polar Covalent Bond

Formed when one atom is significantly more electronegative than its partner, causing unequal electron sharing.

Hydrogen Bonds

Weak bonds formed between a hydrogen atom covalently bonded to one electronegative atom and another electronegative atom.

Van der Waals Interactions

Transient attractions between closely adjacent nonpolar molecules, caused by fluctuations in electron accumulation.

Chemical Reaction

Processes that make or break chemical bonds, altering the chemical composition of matter.

Photosynthesis

A bioenergetic chemical reaction converting solar energy, carbon dioxide, and water into glucose and oxygen.

Electron Shells

Specific discrete energy levels where electrons possess potential energy based on their radial distance from the nucleus.

Electron Orbitals

The complex three-dimensional regions of space where an electron is located 90% of the time.

Valence Shell

The outermost electron shell of an atom.

Molecule

A group of two or more atoms bound together by covalent bonds.

Chemical Equilibrium

Achieved when forward and reverse chemical reactions occur at identical rates, stabilizing the concentrations of reactants and products.

Van der Waals Interactions

Transient electrical attractions occurring between closely adjacent nonpolar molecules, caused by random, uneven fluctuations in electron accumulation.

Collective Van der Waals interactions

While individually weak, massed collective Van der Waals interactions provide significant physical force.

Biological Example of Van der Waals Forces

Allows geckos to climb vertical glass walls due to billions of microscopic hair-like setae on their footpads creating aggregated Van der Waals forces with the wall surface.

Orbital Hybridization

A process where an atom's outer $s$ and $p$ orbitals blend into four hybrid teardrop-shaped orbitals, influencing molecular shape.

Molecule shape and function

A molecule's specific shape dictates its recognition and binding capabilities in living cells.

Methane ($\text{CH}_4$) molecular shape

Carbon's four hybrid orbitals bond with four hydrogen atoms to create a regular tetrahedral molecule.

Water ($\text{H}_2\text{O}$) molecular shape

Oxygen's two bonding orbitals and two unbonded electron pairs yield a bent V-shape with a precise bond angle of $104.5^\circ$.

Chemical Reactions

Processes that make or break chemical bonds, altering the chemical composition of matter.

Reactants

The starting chemical substances undergoing reaction.

Products

The final chemical substances produced by the reaction.

Synthesis of Water

A chemical reaction represented by the equation $2\text{H}<em>2 + \text{O}</em>2 \rightarrow 2\text{H}_2\text{O}$.

Photosynthesis

An essential bioenergetic chemical reaction converting solar light energy, carbon dioxide, and water into glucose and oxygen, represented by $6\text{CO}<em>2 + 6\text{H}</em>2\text{O} \rightarrow \text{C}<em>6\text{H}</em>{12}\text{O}<em>6 + 6\text{O}</em>2$.

Chemical Equilibrium

Achieved when forward and reverse chemical reactions occur at identical rates, stabilizing the concentrations of reactants and products.

Reversibility in Chemical Reactions

All chemical reactions are reversible; products of the forward reaction serve as reactants for the reverse process, indicated by double arrows ($\rightleftharpoons$).