Chemical Basis of Life

What are the definitions of chemistry, matter and mass?

• Chemistry — the science of the structure and interactions of matter

• Matter — anything that takes up space and has mass (touchable)

  • All forms of matter are composed of chemical elements

• Mass — amount of matter in a substance

How is the physical weight of an object determined?

The weight of an object is determined by the pull of gravity on its mass

Can a chemical element be broken down into simpler substances?

No, elements cannot be broken down

What defines a chemical compound?

A combination of 2 or more different elements

• It exhibits differing characteristics from its individual elements

How many different chemical elements are found within the body?

27 different elements

Which 4 essential elements make up 96% of living matter?

• Carbon (C)

• Hydrogen (H)

• Oxygen (O)

• Nitrogen (N)

What 3 major elements help make up the remaining 4% of living matter?

• Calcium (Ca)

• Phosphorus (P)

• Potassium (K)

What is the general definition and enzymatic role of trace elements?

Elements found in low amounts but are still essential to life

• Many act as cofactors for enzymes — allow enzymes to drive functional reactions

What are 5 essential trace elements in the body?

• Iron (Fe)

• Magnesium (Mg)

• Iodine (I)

• Copper (Cu)

• Zinc (Zn)

What is the physiological requirement for iron (Fe)?

Functions as the primary binding site for oxygen inside red blood cells (RBCs)

What is the physiological requirement for iodine (I)?

Required for the production and structural formation of thyroid hormone

What is the definition of an atom?

The smallest unit of matter that retain the properties and characteristics of an element

What components make up the nucleus and orbitals of an atom?

• Nucleus contains:

  • Protons (positive charge)

  • Neutrons (no charge)

• Orbitals contain:

  • Electrons (negative charge)

What does the atomic number represent?

The total number of protons located in the nucleus of an atom

What does the mass number represent, and what can alter it?

The total number of protons and neutrons combined (in the nucleus)

• It changes with isotopes due to the addition or loss of neutrons

What does atomic mass represent?

The average mass of all naturally occurring isotopes of that atom

What defines a radioactive isotope?

An atom with the same number of protons but a different number of neutrons

• Spontaneously gives off particles or energy

What are the capacity rules for the first 2 electron shells to achieve molecular stability?

Molecules are stable when these valence shells are completely full

• First shell (inner) — 2e-

• Second shell (+) — 8e-

How are ions created, and what are the charge properties of anions vs. cations?

Formed by electron transfer between atoms — an atom that has lost or gained an electron

• Anion — negative charge (-) from gaining electrons

  • e.g. Cl^- — more likely to accept e- and become negative

• Cation — positive charge (+) from losing electrons

  • e.g. Na⁺, K⁺, Ca²⁺ — more likely to donate e- and become positive

Anions and cations attract each other

What physical structure is characteristic of solid ionic compounds?

Typically form crystal-like structures

• e.g. salts

What physiological role do electrolytes play, and what are 5 examples?

Electrolytes drive critical electrical signaling in nerve and muscle physiology

• Sodium (Na⁺)

• Potassium (K⁺)

• Calcium (Ca²⁺)

• Hydrogen (H⁺)

• Chloride (Cl^-)

How are molecules formed?

Through the sharing of electrons between 2 or more atoms

• e.g. O₂, H₂

What defines a compound in terms of its breakdown capability?

A substance that can be chemically broken down into 2 or more different elements

• e.g. NaCl

What valence factor determines the likelihood that an atom will form a chemical bond?

The number of electrons in the valence shell

What is a covalent bond, and how strong is it compared to other bonds?

Occurs when atoms share their valence electrons

• It is the strongest bond type

• Can form single, double, triple bonds

What defines an inorganic compound, and what is a body example?

Simple molecules that do not contain carbon atoms

• Water is the most important inorganic compound

What elements do organic compounds always contain (2 + 1 sometimes), and what bond type do they use?

Organic compounds always contain carbon (C) and hydrogen (H); sometimes contain oxygen (O)

• Always form covalent bonds

What are 4 chemical characteristics of carbon in organic molecules?

• Has 4 valence electrons — forms 4 covalent bonds

• Compounds do not dissolve easily in water

• Serves as a good source of energy

• Forms a wide range of molecular shapes

What is a carbon skeleton?

The carbon chains that form the structural basis of most organic molecules — vary in length and shape

What defines a hydrocarbon?

A molecule containing only carbon and hydrogen

What is an isomer?

A molecule with the same molecular formula as another — possessing different structures and properties

What is a functional group of an organic molecule?

The chemically reactive group of atoms that give the molecule its distinctive chemical properties

What are the formulas for 6 important functional groups of organic compounds?

• Hydroxyl: R − OH

• Carbonyl: R − C = O

• Carboxyl: R − O = C − OH

• Amino: R − NH₂

• Sulfhydryl: R − SH

• Phosphate: R − PO₄^2- (composed of P, O, and OH groups)

What is a free radical, and how does it cause cell injury?

An unstable atom with an unpaired electron

• Steals an electron from another molecule (oxidation)

• Destabilizes that target molecule, leading to cell injury and disease

  • e.g. waste products from metabolism, UV light, nicotine, alcohol, fried foods

What are the 2 core tenets of the free radical theory of aging?

• Free radicals build up and damage cell membranes

• This cumulative damage leaads to disease and triggers apoptosis (intentional cell death/suicide)

How do antioxidants combat free radical damage and aging?

They can safely donate electrons to free radicals without destabilizing themselves — remove the radical threat

• e.g. Vitamin E, Vitamin C, Beta-carotene (found in berries, carrots)

What causes a polar covalent bond to form, and what electrical imbalances does it create?

Electrons are shared unequally because a highly electronegative atom pulls the electrons closer to itself

• This creates partial charges — one side is slightly positive, the other side is slightly negative

What is a hydrogen bond, and which 3 elements must be present for it to occur?

An attraction between a partially positive hydrogen atom and a strongly electronegative atom

• Occurs only with oxygen (O), nitrogen (N), fluorine (F)

What is a dipole bond?

Occurs when the partial positive charge of an atom on one molecule attracts the partial negative charge of a lone pair of electrons on another molecule

What is the definition of reactants and products in a chemical reaction?

• Reactants — starting substances

• Products — ending substances

What chemical rule dictates the direction of a reversible reaction in the body?

• If more reactants — the reaction moves forward to make products

• If more products — the reaction reverses to make reactants

What is the definition of energy, and what are potential and kinetic energy?

Energy is the capacity to do work

• Potential energy — stored energy

• Kinetic energy — the energy of movement

What is chemical energy?

A form of potential energy stored within chemical bonds

What is the law of conservation of energy?

Energy and mass can neither be created nor destroyed during a chemical reaction

What defines an exergonic reaction

A reaction that gives off energy — results in a net release of free energy

• Happens spontaneously

What defines an endergonic reaction?

A reaction that takes in energy — absorbs free energy from its surroundings

• Non-spontaneous

What is activation energy?

The minimum amount of energy needed to start a chemical reaction

What is the function of a catalyst?

It lowers the activation energy — makes chemical reactions more likely to occur

What are enzymes?

Protein catalysts that are required for most bodily reactions

What occurs during a hydrolysis reaction?

Water is added to break one or more chemical bonds within a compound

What is a synthesis (anabolic) reaction?

The formation of a larger molecule from smaller components

• e.g. building glycogen

What is a decomposition (catabolic) reaction?

The breakdown of a molecule into smaller fragments

• e.g. glucose metabolism

What is an exchange chemical reaction?

A reaction where part of a reactant swaps over to become part of a product

What defines an oxidation-reduction (redox) reaction?

A reaction that occurs with the removal or addition of electrons

What do anabolism and catabolism do with energy?

• Anabolism — consumes energy to build complex molecules

• Catabolism — releases energy by breaking down complex molecules

What is the difference between oxidation and reduction?

• Oxidation — the loss of electrons

• Reduction — the gain of electrons

Reducing agents cause reduction in another substance; the reducing agent itself gets oxidized (and vice versa)

How do reducing agents and oxidizing agents interact?

• A reducing agent causes another substance to gain electrons — the reducing agent itself gets oxidized

• An oxdizing agent causes another substance to lose electrons — the oxidizing agent itself gets reduced

What 3 types of cellular work are powered by ATP?

• Mechanical work — movement

• Transport work — moving ions / particles

• Chemical work — driving reactions

What chemical mechanism occurs during ATP hydrolysis?

An exergonic reaction that uses water to split a phosphate bond — releases the stored energy from ATP

• Can be coupled with other reactions that require energy

What metabolic pathway drives the regeneration of ATP from ADP and phosphate?

A catabolic pathway

What are some characteristics of a living cell?

• Thousands of reactions occurring

• Can convert energy in many ways (e.g. bioluminescence)