Ch 4: 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.

Revision

Democritus
ancient greek thinker believed that matter could be divided into smaller and smaller perticles until a basic particle was reached. He was the first to suggest the existence of atoms

atoms
the smallest particle of an element that retains both the chemical and physical properties of that element

John Dalton
performed experiments to arrive at his Atomic Theory

John Dalton’s Atomic theory

1. All matter is composed of extremely small particles called atoms
2. Atoms of the same element are identical. Atoms of different elements are different
3. Atoms cannot be subdivided, created, or destroyed.
4. Atoms of different elements can combine in simple, whole-number ratios to form compounds
5. in chemical reactions, atoms are combined, separated or rearanged

Law of multiple proportions
Atoms of different elements can combine in simple, whole-number ratios to form compounds

Why isn’t all of Dalton’s theory true?
Atoms can be broken down and atoms of the same element are not identical because isotopes of that element exist

Atoms are made up of
protons, neutrons, and electrons

actual mass of protons and neutrons
1.67×10^-24 grams

Chemists use _ comparisons of the masses of atoms
relative

the unit of comparison is the
atomic mass unit (amu)

Atomic mass unit
defined as 1/12 the mass of a carbon atom that contains six protons and six neutrons

For all practicle purposes the mass of a single proton or neutron is
1 amu

symbol of electron
e-

relative electrical charge of electron
1-

Approximate relative mass (amu) of electron
1/1840

Actual mass of electron
9.11×10^-28

symbol of proton
p+

Relative electricalcharge of proton
1+

approximate relative mass of proton
1

actual mass of proton
1.67×10^-24 grams

symbol for neutron
n^0

relative electrical charge for neutron
0

approximate relative mass for nuetron
1

actual mass
1.67×10^-24 grams

John Dalton’s model of the atom
atom was invisible and the smallest particle that could exist

Approximately 50 years after John Dalton’s death, the idea of the invisible atom was shattered after the discovery of
protons, neutrons and electrons

Joseph J. Thomson discovered…
the electron

Joseph J. Thomson proposed a model of the atom referred to as the…
“plum pudding model”

plum pudding model
has negatively charged electrons (raisins) embedded into a lump of positively charged protons (the dough)

The discovery of the electron led to two hypotheses:
-since atoms are neutral, they must contain something positively charged
-since electrons weigh so little, atoms must contain something that accounts for the mass

Robert Milikan
figured out the mass of the electron during his Oil Drop Experiment

Ernest Rutherford
discovered the nucleus of an atom in his “Gold Foil Experiment”

gold foil experiment
Rutherford aimed a beam of alpha particles at a piece of gold foil surrounded by a flouresent screen. most of the particles passed through the foil. a few particles were deflected.

Rutherford concluded that
most of the alpha particles pass through the gold foil because the mass and positive charge is concentrated in a small region of the atom. He called this region the NUCLEUS. particles that pass near or approach thenucleus are deflected

Niels Bohr
-proposed a model of the atom where electrons orbit around the nucleus
-the electrons in a particular orbital have fixed energy and do not lose energy and fall into the nucleus

Bohr’s model was referred to as the
“Planetary model”

The rungs of a ladder are analogous to the energy levels in an atom.
The higher the energy level occupied by the electron, the more energetic it usually is from the nucleus

amount of energy lost or gained by every electron is
not always the same

unlike the rungs of a ladder…
the energy levels in an atom are not equally spaced

quantum of energy
the amount of energy required to move an electron from its present energy level to the next higher one

Erwin Schrodinger
used the new quantum theory to write and solve a mathmatical equation describing the location and energy of an electron in a hydrogen atom

quantum mechanical model
-proposed by Erwin Schrodinger, it is a modern description of electrons in atoms
-does not define the exact path of an electron but is concerned with the likelihood of finding an electron in a certain region of space sround the nucleus

today we use the
Quantum Mechanical model

Atomic number
number of protons in the nucleus of an atom

Mass number
number of protons + number of neutrons

since an atom is neutral…
number of protons = number of electrons

number of protons determines…
what the atom is

Atoms of the same element will always have the same number of and _
protons, electrons

atoms of the same element can have a different number of _, and therefore, a different _
neutrons; mass number

Isotopes
atoms of the same element that have different numbers of neutrons and a different mass number

to distinguish atoms, we use…
chemical symbols

1
H
1
top 1: mass number
bottom 1: atomic number
H: element symbol

hyphen notation
name of the element-mass number

determine number of protons
bottom left number

determine number of electrons
same as protons

determine number of neutrons
mass number-atomic number (top-bottom)

alpha
consists of the nuclei that have been emitted from a radioactive source

alpha particles
contain 2 protons and 2 neutrons

Because of their large mass and charge, alpha particles
do not travel very far and are not very penetrating.

Alpha particles are easily stopped by
a sheet of paper or dead skin cells on the surface of your skin

Alpha particles are dangerous when injested because…
they can penetrate soft tissue

Beta
consists of fast moving electrons formed by the decomposition of a neutron

Beta particles are than alpha particles and have _____
much smaller; 1/2 as much charge

Beta particles are
more penetrating than alpha particles

Beta particles can be stopped by
aluminum foil or thin pieces of wood

Gamma
consists of electromagnetic energy

Gamma particles are very _ and can only be stopped by….
penetrating; several feet of concrete or several inches of lead

nuclear stability– the stability of a nucleus depends on…
its proton to neutron ratio

For elements of low atomic number, below about 20, this ratio is . This means the nuclei have equal numbers of __
one; protons and neutrons

Above atomic number 20, the stable nuclei have more _ than _
neutrons; protons

band of stability
contains all stable nuclei

neutron/proton ratio=1.0
stable ratio for lighter isotopes

neutron/proton ratio=1.5
stable ratio for heavier isotopes

Region A
unstable nuclei undergo beta decay

Region B
unstable nuclei convert a proton to a neutron

Region c
unstable nuclei undergo beta decay

Half-life
the time it takes for half of the nuclei in a radioactive sample to decay

Stability is indicated by its half-life. the longer the half-life…
the more stable the radioisotope

Chemical Reaction
-atoms separate or combine without any changes to the nucleus
-only electrons are involved
-new compounds are formed

Nuclear Reation
-nucleus changes in composition
-new elements are formed by 2 processes: Fusion and Fission

Fusion
two nuclei combine to form a new nucleus

Fusion occurs on the with ___ combining to form __
sun; 2 hydrogens; helium

Fission
nucleus decays, releasing radiation

electron purpose
determines the chemical properties of a substance

proton purpose
determines the identity of the substance

neutron purpose
provides nuclear stability, they are “glue”

Elements 1-20 have atoms that are stable when…
the number of protons and neutrons is approximately equal

Elements above 20 need…
increasingly more neutrons than protons to be stable

Elements above 83…
can’t be stable and are radioactive

the strong nuclear force
the force that holds the nucleus together and does not allow the protons to fly apart due to repulsion