Better living through chemistry

Atoms that makeup living things

• Organisms are made of cells.
• Cells are made of molecules.
•  Molecules are made of atoms.
• Atoms are made of subatomic particles

The six elements that make up 99% of all living matter are carbon, hydrogen, nitrogen, phosphorous, oxygen, and sulfur. A tissue is a group of similar cells that perform a specific function in an organism. An organ is made of tissues synchronized together for a particular role. When two or more organs combine to perform a particular function, they are described as an organ system.

Exploring subatomic particles

• Atoms are made of smaller particles called subatomic particles
• This includes: protons, neutrons, and electrons
• Protons-contain a positive electric charge, a mass number and found at the center of the atom
• Neutron- doesn’t have a charge and has a mass number
• Electrons-contain a negative electric charge and doesn’t have a mass number

The five assumptions of the atomic theory of matter: All matter is composed of small particles called atoms. All atoms of a specific type are similar. The identity of a substance is determined by the relative arrangement and number of atoms present. Atoms are rearranged to give new substances, which results in a chemical change. Lastly, only whole atoms can participate in a chemical change.

The total number of protons in the nucleus of an atom is called the atomic number, while the mass number represents the sum of neutrons and protons in an atom. If two atoms have the same number of protons and electrons but are different in terms of the number of neutrons, they are described as isotopes.

Comparing isotopes

• Proton number in an atom never changes
• Neutron number can vary between different atoms
• Isotopes contain same proton and electron number but different neutron number
• To show neutron number in an isotope, the mass number is included
• Mass number- proton number plus neutron number

Isotopes can be categorized into either stable or unstable isotopes. The stable isotopes have the same number of protons and electrons but are different in the number of neutrons. Such isotopes are used by researchers to diagnose diseases. Unstable isotopes have more neutrons than protons and will decay over time turning into another isotope or element.

How atoms are attracted to each other

• Two or more atoms combine to form molecules
• Chemical bonds are the forces that facilitate the formation of molecules from atoms
• Bonds are formed from taking, giving and sharing electrons between atoms

Atoms of the same element may bond together to form a molecule or crystalline solid. If atoms of different molecules bind, they instead form a compound.

The three types of chemical bonding that occur in atoms are ionic which involves losing and gaining electrons between two atoms, a covalent bond involves the sharing of electrons between atoms, and a hydrogen bond is formed between two different parts of the same molecule.

A polar bond occurs when the electrons are shared equally, while non-polar bond occurs when electrons are shared unequally. When an atom loses one or more electrons, it becomes a position ion which is called a cation. When an atom gains one or more electrons, it becomes an anion.

Valence electrons

• Valence electrons are the electrons that  can be shared or donated to other electrons during the process of bond formation
• Are located in particular orbitals in the outer energy levels of atoms
• Valence electrons of an element can be determined from the periodic table
• Atoms must have a full number of the valence electron in the outermost energy level to be stable
• Atoms follow the octet rule, the rule of eight which allows it to have full valence electron set

A valence electron is found in the highest energy level of an atom and is involved in chemical bonding. If two atoms share one pair of electrons, a single bond is formed, and if two pairs of electrons are shared between two atoms, a double bond is formed.

The tendency of an electron to attract the outermost electrons on another atom to itself is described as electronegativity.

Properties of ions include; Hard and brittle, extremely soluble in water, high vaporization, nonconductive when in solid-state, etc. The properties of metals include: conduct electricity in a solid, gaseous, and liquid state, are highly malleable, ductile, and have a high melting point.

Electronegativity

• Electronegativity is the tendency of an atom to attract certain electrons
• An atom with a strong electron pull is highly electronegative
• Importance of electronegativity in cellular processes include:
• Affects atoms bonding behavior
• Important in reactions between molecules

A covalent bond will be formed when two elements have almost equal electronegativity and those which have a large difference in their electronegativity form an ionic bond.

The closer you get to the nucleus, the greater the electronegative power to attract electrons while those atoms which have a large atom whose outermost electrons are farther away from the nucleus have a smaller electronegative power.

Oxidation and reduction

• Oxidation-process in which an atom gives up an electron
• Reduction- a process in which an atom receives an electron during a reaction

Oxidation involves loss of electrons, loss of hydrogen atoms, gain of an oxygen atom and increase in the oxidation number. On the other hand, oxidation is when an element gains electrons, loses oxygen atoms, gains hydrogen atoms, and has a decrease in oxidation number.

The oxidizing agent is a substance that readily accepts electrons and is reduced at the end of a reaction. A reducing agent, on the other hand, donates electrons and is oxidized as a result.

Ionic bonds

This includes the forces of attraction between positively and negatively charged atoms which are called ions. Ionic bonds usually occur between a cation (metal atom) and an anion (non-metal).

Covalent bonds

• Can be formed between atoms of the same electronegativity
• Covalent bonds are generated from shared electron pairs

The distance between two atoms that are bonded together considering the minimum potential energy is called the bond length. Bond energy is the amount of energy that would be needed to break two bonded atoms.

Hydrogen bonds

• Consists of weak attractions that are  formed between ends of molecules that are polar
• Molecules with a positive charge on their end attract a negatively charged end of another molecule
• Hydrogen is useful in holding DNA strands together to form double helix DNA

Hydrophobic interactions

• Interactions caused by the interaction between nonpolar  molecules

Hydrogen bond in water molecules gives it the following properties: A high heat capacity, a high heat of vaporization, a high cohesion surface tension, and acting as a solvent of numerous types of polar substances.

Polar molecules are described as hydrophilic (water-loving) and can easily dissolve in water while non-polar molecules form hydrophobic interactions (water-hating) and which do not dissolve in water.

The ocean inside your cell

Water is vital for proper cell function in the following ways

• Water is a good solvent- dissolves ion and polar molecules
• Water helps in the movement of things across the plasma membrane
• Water facilitates hydrophobic interactions
• Water helps in maintaining the structures of molecules that are important in cells

Water forms an impart part of the body which enables almost all organ systems to perform their functions effectively.

In the lungs, water acts as a solvent because oxygen is present in water which dissolves in the blood easily to travel to the rest of the body parts.

In the blood, water acts as a solvent for electrolytes and nutrients that are essential for cell metabolism.

In chemical reactions, water participates as either a reactant or product for example in hydrolysis reactions.

The high heat capacity of water is important to the body: The body is made mainly of water and hence can take a lot of heat to significantly change the temperatures of the body. The presence of water molecules, therefore, prevents body temperature fluctuations with slight changes in environmental heat.

Water serves as an excellent lubricant in the body: Water is a major component of saliva, mucous, and other fluids that lubricate various parts and organs of the body. The various organs that slide against each other require lubrication to prevent tear and damage to the tissue.

Measuring Ph

• PH involves the concentration of hydrogen ions in solution
• The pH can be measured using a pH scale

There are three pH levels of solutions

• Acidic solution- a solution with a pH lower than 7.0
• Basic solution – a solution with a pH greater than 7
• Neutral solution- a solution with a pH of 7

The various mechanisms by which the body balances pH

Protein buffers balance pH by donating or accepting ions with the hydroxyl groups. The respiratory system regulates pH by raising or lowering the rate of breathing to alter the concentration of carbon dioxide and oxygen in the blood.

The urinary system regulates pH by excreting Hydrogen ions from the blood or reabsorbing it back into the blood. The bicarbonate buffer system regulates body pH by using a substrate-dependent system, incorporating both the urinary and respiratory systems.

When the concentration of hydrogen ions is above normal, the condition is called acidosis and if the concentration is below normal levels, this is called alkalosis.

 Building and breaking polymers

• Macromolecules- are big molecules which include; proteins, carbohydrates, lipids, and nucleic acids
• Polymer- a long molecule with many repeating units
• Monomer- is the building unit of a polymer
• Monomers combine to form long polymers
• A nucleic acid polymer is formed from repeating units of nucleotides which are the monomers

The process of building a polymer using energy and releasing water molecules is called dehydration synthesis or condensation reaction. The process of breaking down a polymer into its monomers is called hydrolysis and it releases energy but requires water.

Concept/Term	Description/Answer
Atoms	The smallest particles of an element that retain the chemical and physical properties of that element.
Organisms	Living things made of cells.
Cells	Basic units of life, made of molecules.
Molecules	Combinations of atoms, make up cells.
Subatomic particles	Smaller particles that make up atoms: protons, neutrons, and electrons.
Elements	Substances made up of only one type of atom.
Carbon, Hydrogen, Nitrogen, Phosphorus, Oxygen, Sulfur	The six elements that make up 99% of all living matter.
Tissue	Group of similar cells performing a specific function.
Organ	Made up of tissues working together for a specific role.
Organ system	Combination of two or more organs working together for a particular function.
Isotopes	Atoms of the same element with different numbers of neutrons.
Stable isotopes	Isotopes with the same number of protons and electrons but different neutron numbers.
Unstable isotopes	Isotopes with more neutrons than protons, which decay over time.
Ionic bond	Bond formed by losing and gaining electrons between two atoms.
Covalent bond	Bond formed by sharing electrons between atoms.
Hydrogen bond	Weak attraction between different parts of the same molecule.
Valence electrons	Electrons involved in chemical bonding, located in the outer energy levels of atoms.
Octet rule	Atoms tend to gain, lose, or share electrons to have a full valence electron set.
Electronegativity	Atom’s tendency to attract outermost electrons from another atom.
Oxidation	Process of losing electrons during a chemical reaction.
Reduction	Process of gaining electrons during a chemical reaction.
Oxidizing agent	Substance that readily accepts electrons and is reduced in a reaction.
Reducing agent	Substance that donates electrons and is oxidized in a reaction.
Macromolecules	Large molecules including proteins, carbohydrates, lipids, and nucleic acids.
Polymer	Long molecule made up of many repeating units (monomers).
Monomer	Building unit of a polymer.
Dehydration synthesis	Process of building a polymer by removing water molecules.
Hydrolysis	Process of breaking down a polymer into monomers by adding water.
Atomic theory of matter	Assumptions: all matter is composed of atoms, atoms of a specific type are similar, identity of a substance is determined by the arrangement and number of atoms, atoms are rearranged in chemical changes, only whole atoms participate in chemical changes.
Nucleus	Central part of an atom containing protons and neutrons.
Electron	Subatomic particle with a negative charge, found outside the nucleus.
Proton	Subatomic particle with a positive charge, found in the nucleus.
Neutron	Subatomic particle with no charge, found in the nucleus.
Atomic number	Total number of protons in an atom’s nucleus.
Mass number	Sum of protons and neutrons in an atom’s nucleus.
pH	Measure of hydrogen ion concentration in a solution.
Acidic solution	Solution with a pH lower than 7.0.
Basic solution	Solution with a pH greater than 7.0.
Neutral solution	Solution with a pH of 7.0.
Protein buffers	Substances that help maintain pH by accepting or donating ions.
Respiratory system	Regulates pH by adjusting carbon dioxide and oxygen levels in the blood.