Atoms, Molecules, and Subatomic Particles

• To understand cells, understanding their parts (atoms and molecules) and their interactions is essential
• Life is sustained by a variety of chemicals and chemical reactions
• Nutrition is about food chemistry
• Drugs and environmental issues involve chemical interactions

Atoms and Subatomic Particles

• Matter is anything that occupies space and has mass
• Matter takes on many different structures when observed at different scales
• Most objects consist of molecules, which are made up of atoms
• Atoms are extremely small
• Atoms are composed of subatomic particles
• Subatomic particles have three main properties: Location, Mass, and Electrical Charge

Location of Subatomic Particles

• Protons and Neutrons reside in the nucleus (center) of the atom
• Electrons are found outside the nucleus in zones called shells

Mass of Subatomic Particles

• Protons and Neutrons each have a mass of 1 atomic mass unit (amu)
• Electrons possess almost no mass and can travel around the nucleus incredibly fast

Electrical Charge of Subatomic Particles

• Describes how particles move when brought near each other, likes repel, opposites attract
• Protons have a positive charge, tending to attract electrons which holds them in a cloud around the nucleus
• Strong nuclear force holds the atom's nucleus together overcoming repulsion between protons, keeping them clustered with neutrons
• Electrons have a negative charge, equal in strength to the positive charge of one proton, and are kept in orbit by kinetic energy
• Neutrons have a neutral charge and don't attract or repel other particles
• The parts of atoms are too small to be seen with a microscope

Elements: Types of Atoms

• Use the atomic number to predict an atom's structure (number of protons and electrons)
• Elements are different types of atoms
• There are 92 naturally occurring elements on Earth
• Major elements in living cells and organisms include carbon (C), hydrogen (H), nitrogen (N), oxygen (O), phosphorus (P), and sulfur (S)
• These elements constitute more than 95% of the mass of a cell
• Carbon is a major component of nearly all biological molecules

Atomic Number

• Each element possesses unique properties
• Defined as the number of protons in the nucleus
• Elements are organized in the periodic table based on their atomic numbers

Isotopes: Forms of an Element

• Isotope can be defined for any given atom, mathematically relate atomic number, atomic mass, and number of neutrons in the nucleus
• Atomic Mass is the sum of an atom's protons and neutrons in the nucleus
• It should not be confused with atomic number, which is only the number of protons
• The average atomic mass of an element is written below the chemical symbol in the periodic table
• Atoms can have fractions of protons or neutrons, causing the atomic mass to not be a whole number
• The atomic mass/weight is an average of different atoms of the same element (like averaging 20 weights)
• Atoms of an element have the same number of protons, but the number of neutrons can be different
• Isotopes are forms/versions/variations of an element with different numbers of neutrons and differ in mass
• Carbon atoms always have 6 protons
• Main carbon isotopes: C-12 (6 protons, 6 neutrons), C-13 (6 protons, 7 neutrons), and C-14 (6 protons, 8 neutrons)
• All atoms of the same element have the same number of protons (ex. If an atom has 6 protons it is a carbon atom)
• Each variation in neutrons makes it an isotope
• Average atomic mass/weight can be found by calculating all isotopes

Heavy Isotopes

• Heavy isotopes have extra neutrons and weigh more than the average for an element
• they are Usually not stable and break apart into smaller isotopes, releasing energy in the process
• Radioactive decay refers to the process of heavy isotopes that break apart

Electron Shells

• Valence shell must be defined to allow one to predict the number of electrons in the valence shell and infer the element's reactivity from atomic numbers 1 to 18
• Break down into lighter isotopes at a constant rate, allowing determination of age of artifacts Emit energy, which can be dangerous but also useful for medical treatments and imaging
• Example: Slightly radioactive isotope of Iodine (I-123) can be given to a person at a low dose and will go to their thyroid
• As the iodine decays, the energy emitted lights up the thyroid and can be detected by a camera to produce an image that can help detect cancer

Valence Electrons

• Reactive part of the atom
• Can move from one atom to another
• Take part in chemical reactions
• In neutral atoms, electrons (negative charge) are in balance with protons (positive charge)
• The atomic number (number of protons) tells you how many electrons are in a neutral atom
• Electrons are concentrated in regions called shells
• The first shell (closest to the nucleus) holds the least energetic electrons and can hold 2 electrons
• Second and third shells can hold up to 8 electrons
• In larger atoms, shells fill up in a more complex manner
• Electrons fill up lower shells before moving to the next higher shell
• Valence shell = The outermost shell in an atom
• Valence electrons are electrons in this shell
• They determine an atom's potential to react or combine (bond) with other atoms
• An element's chemical properties depend mostly on the number of valence electrons
• Atoms are stable (unable to react or change) when they have full outer electron shells (valence shells)
• Helium (He) has 2 electrons
• The first shell can hold 2 electrons and is full, making it stable
• Stable electrons don't react with other atoms to form larger molecules, they stay separate as individual atoms
• All elements along the Helium column of the periodic table have full outer shells and are stable and do not react with other elements
• These are Noble Gases

What are Chemical Bonds

• Biology is driven by reactions between molecules
• Ex: a protein molecule may have over a million atoms
• The atoms are connected to each other by covalent bonds (molecules are atoms held together by chemical bonds)
• Covalent bonds hold large molecules together
• Its parts are intertwined to create a specific shape that enables a specific function
• Ionic bonds hold parts of the protein close together (to maintain the shape) (like strong magnets stuck together)
• Ionic bonds hold relatively large features of molecules steady
• Might create big loops or hold interlocking pieces together
• Has tiny spirals and flat sheets of atoms Held together by hydrogen bonds (like small fridge magnets, loosely attached)
• Weaker than ionic bonds, but play a similar role on a smaller scale
• Attract water molecules to each other

Compare and contrast the different molecule bonds

• Covalent Bond: Strongest, Firmly connects atoms in the same molecule, Electron pairs are shared, creating a strong bond between atoms
• Ionic Bond: Moderate strength, Occurs between ions in a salt crystal or between ions on different parts of large molecules, Attraction between oppositely charged ions, e.g. Na+ and Cl-
• Hydrogen Bond: Weak, short-range, Occurs between different molecules or nearby parts of large molecules, Attraction between partially positive H atoms and areas of molecules with partial negative charges

Ions and Ionic Bonds

• lons will be defined as well as how the number of valence electrons can predict ion formation along with differentiating anions from cations
• The definition and description of ionic bonds
• The number of electrons on an atom can change, and that atom can still be the same element (because the number of neutrons will remain the same)
• Neutral atoms of an element have no overall charge
• There are equal numbers of protons and electrons and they balance each other out
• Atoms with full outer shells are most stable
• Some atoms take on extra electrons or give them up in order to achieve this -- This transforms the neutral atom into an ion
• lon = an atom or molecule that has a positive or negative charge because it has an unequal amount of electrons of protons
• Anions = atoms that have a negative charge because they have more electrons than protons (adding an electron subtracts from the charge --> it makes it more negative)
• On the periodic table, elements to the right (excluding the last column) are more likely to take on extra electrons Ex: chlorine has 7 valence electrons, meaning it's more likely to add an electron to its shell, becoming an anion
• Elements on the left side tend to give up one or more electrons and become cations with a positive net charge (because it gave away some of its negative, and there will be more protons than electrons
• lons are dissolved in water in cells and body fluids, providing key functions
• They move into and out of cells to transmit nerve impulses, trigger muscle contractions, etc

Ionic Bonds

• Ionic bond = moderately strong electrical attraction that holds oppositely charged ions/or molecule parts together
• lonic bonds occur between ions of opposite charges
• When elements with the potential to form ions are brought close together, electrons are transferred to produce oppositely charged ions
• These oppositely charged ions attract each other and form a salt
• Elements in the outer column of the periodic table often react to form salts ex. Sodium and chlorine = table salt
• If charges are unequal there will be fewer of the more strongly charged ions in the crystal, resulting in a net charge of zero for the crystal as a whole
• lonic bonds help to stabilize the shape of large molecules
• Different parts of large molecules can repel like charges or attract opposite charges
• lons float freely and stay separate if surrounded by water
• But oppositely charged ions at close range will be joined together by an ionic bond

Covalent Bonds

• Covalent Bonds Define and describe
• number of bonds an element will form and predict the structure of simple molecules
• The key bonds in biology are covalent bonds In covalent bonds, atoms remain in close contact and share electrons so that their outer shells are filled
• A shared electron is counted "twice" and participates in a larger shell that joins the two atoms
• Covalent bonds are relatively strong and stable connections that hold atoms together and create larger structures known as molecules
• Multiple atoms can combine their outer shells until they all have full outer shells
• Sharing pairs:
• A single pair of shared electrons = covalent bond
• Double bond = Atoms that share two pairs of electrons
• Triple bond = three pairs of electrons
• Combinations of atoms with full shells are more stable than those with partial shells

Molecules

• Interpret drawings (structural and skeletal formulae) of molecules and identify all atoms and covalent bonds in such drawings
• Molecule = two (or more) atoms joined together by a covalent bond
• In diagrams of molecule structure, covalent bonds are often drawn as lines between atoms, each line representing two shared electrons
• A double covalent bond can be drawn as two lines
• When drawing molecules, make sure each atom has a full outer shell
• In diagrams of larger molecules, corners or angles represent carbon atoms
• Missing bonds on the diagram are represented by hydrogen