Chapter 1 - Atoms & Molecules

Part I: Elements & Atoms: The Building Blocks of Matter

Matter

  • Of a physical substance; that which occupies space & has mass



Elements & Compounds


Elements

  • A pure substance that cannot be created /broken down by ordinary chem means

Compounds

  • Is a substance consisting of 2/+ elements combined in a fixed ratio

    • Has a characteristics diff from those of its elements [emerging properties]

Molecule

  • 2/+ atoms covalently bonded together can form a molecule

All matter in the natural world consists of 1/+ fundamental substances [elements] that are distinct from all other matter [cannot be created/broken down by ordinary chem means]. While the body can assemble many of the chem compounds needed for life from basic elements, it cannot create elements, they must come from the environment.

All the elements in the body are derived [obtained] from the consumption of foods & oxygen one breathes.

Do Not Memorize %

In nature, elements rarely occur alone, instead, they tend to form a molecule.




Common Elements in Humans & Their Function

  • The 4 most common in the body are: Carbon [C], Oxygen [O], Hydrogen [H], & Nitrogen [N]


Carbon [C]

  • It forms the backbone of all molecules: carbohydrates, lipids, proteins & nucleic acids


Oxygen [O]

  • Human carry billions of O molecules, transported via red blood cells

  • O is also apart of water and in all macromolecules: carbohydrates, lipids, proteins & nucleic acids


Hydrogen [H]

  • It is present in water and all macromolecules: carbohydrates, lipids, proteins & nucleic 


Nitrogen [N]

  • Is excreted as a byproduct of the body through the food one eats


Inorganic & Organic Compounds

Inorganic Compound

  • A substance that does not contain both carbon & hydrogen

    • Many inorganic compounds contain H atoms [H2O & HCl]

    • Few inorganic compounds contain C atoms [CO2]

Organic Compounds

  • A substance that contains C-H bonds

    • Many organic compounds can be synthesised via covalent bonds within organisms

    • They can be assembled into very large molecules w/ complex structures which makes them useful to living cells in various ways

      • E.g. structural components of cells/functional components that allow chem reactions to proceed


Atoms & Subatomic Particles


Atom

  • The smallest unit of an element that retains the unique properties of that element

    • E.g. an atom of H is a unit of H [the smallest amt of H that can exist]

1.  Atomic Structures & Energy


Subatomic Particles

  • Particles that are smaller than an atom & make up all matter, 3 important types are:

    • Protons, neurons, & electrons

    • The protons & neutrons gives mass to the atom, the # of protons = to the # of e-s

There are different ways of illustrate the atom’s structure:

  1. Bohr model [planetary model] 

    1. Is helpful in visualising atomic structure but is flawed as e-s do not travel in fixed orbitals

  2. Electron cloud 

    1. Is a more accurate depiction as it illustrate where area around an atom’s nucleus e-s are most likely to be found

Opposite charges attract ∴ the + charged nucleus keeps e-s from straying far

The # of protons & e-s are = within a neutral atom ∴ the atom’s overall charge is neutral



2.  Atomic Number & Mass Number


Atomic #

  • # of protons in the nucleus of an atom

Atomic Mass

  • Sum of the # of protons & neutrons in the nucleus of an atom

The Periodic Table of the Elements

  • An arrangement of the elements in a table according to their atomic #; elements having similar properties b/c of their e- arrangements compose columns in the table, while elements having the same # of valence shells compose rows in the table

An C atom is unique to C, but a proton of C is not, all protons are the same, whether it comes from different elements are not. The same is true for neutrons & e-s. The # of protons makes each element distinct. All C atoms, whether in a liver/coal, contain 6 protons. The atomic # = the # of protons in the nucleus of the atom, ids the element. B/c an atom tends to have = # of protons & e-s the atomic # usually ids the # of e-s as well.

In an elements most common form, many also contain = # of neutrons & protons.

  • E.g. Basic C has 6 neutrons & protons for a total of 12 subatomic particles


3.  The Behaviour of Electrons


Electron Shell

  • Area of space a given distance from an atom’s nucleus in while e-s are grouped

Valence Shell

  • Outermost e- shell of an atom


In the human body, atoms do not exist as independent entities

  • They constantly react w/ other atoms to form & break down more complex substances

e-s do not follow the Bohr model they do tend to stay within certain regions of space [e- shell]

  • The atoms of elements found in the body have 1-5 e- shells [use 2n2 to calc max e- at shelln]

    • All e- shells apart from the first may also be considered “complete” w/ 8 e-s thus making it inert

      • Max e- capacity is the same for all elements

    • A main factor that dictates the propensity of an atom to participate in chem reactions is the # of e-s in an atom’s valence shell

      • Atoms can gain, give up, or share e-s to gain an Octet

      • More e-s in valence = less reactive, fulfil Octet = inert



Part II: Chemical Bonds


Ions & Ionic Bonds


Ions

  • Atoms/molecules w/ a net electrical charge due to the loss/gain of more e-s 

    • F- is found in bones is an anions [-] due to the gaining of e-(s)

    • K+ is vital in all body cell is a cation [+] due to the loss of e-(s)

Ionic Bonds

  • Chem bonds that form when oppositely charged ions are attracted to each other

    • Substances formed through ionic bonding are always referred to compounds

Electrocardiogram [EKG/ECG]

  • In biological fluids most individual atoms exist as ions, these dissolved ions produce electrical charges within the body, thus can be observed as waves on an EKG

    • This electrical activity which derives from the interactions of the charged ions is also known as electrolytes


Covalent Bonds & Polarity


Covalent Bond

  • Chem bond that occurs when 2 atoms share e-s pair, thus stabilizing each other

    • I.e. the e-s move back & forth between the elements

    • B/c of the close sharing of pairs of e-s [1 e- from each], most covalent bonds are not broken in H2O

  • Chem energy present in the covalent bonds in many organic molecules can be transferred to other molecules, in the form of new bonds.

    • E.g. some energy contained in the bonds of a glucose molecule can be harvested & used by living cells to attach a phosphate group to a molecule of adenosine diphosphate adenosine triphosphate [ATP]

    • E.g. the compound for glucose is a vital body fuel, which consist of the same 3 elements

      • Carbon, hydrogen, and oxygen

        • C based molecule that contain H thus it is an organic compound

1. Nonpolar Covalent Bonds

A nonpolar covalent bond is a type of bond that occurs when 2 atoms share e-s equally. The distribution of e-s is symmetrical, resulting in no significant +/- charge regions w/in the molecule.

The # of e- pairs shared between atoms can vary:

  • Single Bond: 1 pair of e-s shared

  • Double Bond: 2 pairs of e-s shared

  • Triple Bond: 3 pairs of e-s shared

2. Polar Covalent Bonds

A polar covalent bond is a type of chem bond that occurs when 2 atoms w/ different electronegativities share e-s unequally. Resulting in the atom w/ higher electronegativity to have a partially - charge, while the other partially + creating a dipole.

H2O molecule: b/c O atoms have more protons, the - charged e-s present in H2O are more strongly attracted to the O nucleus. Each H atom’s single e- ∴ migrates towards the O atom creating the dipole.


Hydrogen & Dipole-ion Bonds 

Hydrogen Bond

  • Formed when a slightly + H atom already bonded to 1 electronegative atom [E.g. O in H2O] is attracted to another electronegative atom from another molecule

    • Hydrogen bonds always include a H atom that is already part of a polar molecule

    • Most common e.g. is H2O [2 rain drops merge into larger bead/creek spills into river]

      • Hydrogen bonding occurs b/c the -O atom in 1 H2O molecule is attracted to the +H atoms of the 2 other H2O molecules

Dipole-ion Bond

Water molecules readily dissolve charged molecules like NaCl due to dipole-ion interactions. In these interactions, the polar water molecule (with a slightly positive hydrogen end and a slightly negative oxygen end) is attracted to the oppositely charged ions. The positive end of the water molecule is drawn to the negatively charged chloride ions (Cl-), while the negative end is attracted to the positively charged sodium ions (Na+). This attraction overcomes the ionic bond holding the NaCl together, allowing the ions to dissolve.

Conversely, water molecules repel nonpolar molecules like oils, causing them to form distinct droplets. This is demonstrated by the inability of oil to dissolve in water.


Physical Properties of Water

Hydrogen bonding in water significantly impacts its physical properties.

  • Density: Unlike most substances, ice (solid water) is less dense than liquid water, allowing it to float.

  • Boiling Point: Water's boiling point (100°C) is much higher than predicted based on chemical trends, due to the energy required to overcome hydrogen bonds.

  • Specific Heat Capacity: Water has a high specific heat, meaning it requires a large amount of energy to change temperature, crucial for regulating temperatures in living organisms and the environment.