Biology Notes: Atoms, Molecules, and Carbon-Based Life

2.1 Atoms, Ions, and Molecules

• An atom is the smallest basic unit of matter.
• An element is one type of atom.
• Six elements (carbon (C), oxygen (O), hydrogen (H), nitrogen (N), phosphorus (P), and sulfur (S)) make up 99% of all living things. The elements spell out S-P-O-N-C-H.
• Living things consist of atoms of different elements. For example, Oxygen (O) and Hydrogen (H).

Atomic Structure

• An atom is composed of protons, neutrons, and electrons.
• Proton (p+):
  • Symbol: p+
  • Charge: +1
  • Mass: 1 amu (atomic mass unit)
  • Location: Nucleus
• Neutron (n0):
  • Symbol: n
  • Charge: 0
  • Mass: 1 amu
  • Location: Nucleus
• Electron (e-):
  • Symbol: e-
  • Charge: -1
  • Mass: ~0
  • Location: Energy level (electron cloud)

Periodic Table

• Elements are organized in the periodic table by the number of protons ($p^+$), neutrons ($n^0$), and electrons ($e^-$).
• Rows are called "periods" and represent the number of energy levels.
• Columns are called "groups" and represent the number of valence electrons.
• Each element is represented by its atomic number and atomic mass.

Atomic Number and Atomic Mass

• The atomic number is the number of protons or electrons in an atom.

• The atomic mass is the number of protons plus the number of neutrons.

  Example: For Lithium (Li), which is represented as:

  $_{3}^{7}Li$

  • Number of protons ($p^+$) = 3
  • Number of electrons ($e^-$) = 3
  • Number of neutrons ($n^0$) = 4 (atomic mass – atomic number = $7 - 3 = 4$)

More Practice with the Periodic Table

• Chlorine (Cl), represented as: $_{17}^{35}Cl$

  • Number of protons ($p^+$) = 17
  • Number of electrons ($e^-$) = 17
  • Number of neutrons ($n^0$) = 18

• Iron (Fe), represented as: $_{26}^{56}Fe$

  • Number of protons ($p^+$) = 26
  • Number of electrons ($e^-$) = 26
  • Number of neutrons ($n^0$) = 30

• Silver (Ag), represented as: $_{47}^{108}Ag$

  • Number of protons ($p^+$) = 47
  • Number of electrons ($e^-$) = 47
  • Number of neutrons ($n^0$) = 61

Drawing Atoms

• The number of electrons each energy level can hold:
  • 1st energy level: 2 electrons
  • 2nd energy level: 8 electrons
  • 3rd energy level: up to 18 electrons
• Electrons move around the energy levels (aka “electron shells” or “electron orbitals”) outside the nucleus rapidly to form an electron cloud.

Rules of Electron Placement

• Fill electrons starting from the level closest to the nucleus.
• Electrons prefer to be in pairs, but fill single electrons first before pairing them up.
• Octet rule: An atom in the 2nd energy level tends to have 8 electrons on the outermost energy level.
• When bonds form between two atoms, only the unpaired valence electrons from the two atoms pair up.

Molecules and Compounds

• A molecule is made of two or more elements bonded together (may be the same or different). Examples: $H<em>2O$, $CO</em>2$, $O_2$
• A compound is a large molecule in which elements are chemically bonded in a certain ratio. Example: $C<em>6H</em>{12}O_6$

Ions

• An ion is a charged atom (positive or negative).

• Atoms are more stable as ions when they gain or lose one or more electrons.

  • Group 1 elements tend to lose 1 electron ($e^-$) and form positive ions.
  • Group 7 elements tend to gain 1 electron ($e^-$) and form negative ions.

  Examples:

  • Sodium ion ($Na^+$)
  • Chloride ion ($Cl^-$)

Types of Bonds

• A bond is the force that holds two atoms together.
• Ionic Bond: Forms between oppositely charged ions. Example: NaCl, MgS. Sodium loses an electron to Chlorine in the formation of NaCl.
• Covalent Bond: Forms when atoms share a pair of electrons. Example: $H<em>2O$, $CO</em>2$

2.3 Carbon-Based Molecules

• Carbon-based molecules are the foundation of life. They are called organic molecules or macromolecules (macro- = large).
• Carbons are bonded together to form the “backbone”.
• Four major groups:
  1. Carbohydrates
  2. Lipids
  3. Proteins
  4. Nucleic acids

Monomers and Polymers

• Many macromolecules are made of many small subunits bonded together:
  • Monomers are the individual subunits.
  • Polymers are made of many monomers.

Carbohydrates

• Made of C, H, O in a 1:2:1 ratio (e.g., $C<em>6H</em>{12}O_6$).
• Function: Provide short-term energy.
• Monomers (simple sugar) = monosaccharides (e.g., glucose).
• Polymers (complex sugar):
  • Disaccharides are two monosaccharides linked together (e.g., sucrose).
  • Polysaccharides are made of many monosaccharides (e.g., starches, cellulose, and glycogen).
• Starch is where plants store food.
• Cellulose is what makes up the plant cell wall; it has a straight, rigid structure with glucose monomers forming the polymer. Starch has a branched structure also formed of glucose monomers.

Lipids

• Made of C, H, O.
• Function: Provide long-term energy; make up the cell membrane; used to make hormones.
• Monomers: Carbon chains of fatty acids.
• Polymers: Fats, oils, phospholipids, cholesterol.
• Fats and oils contain fatty acids bonded to glycerol (e.g., triglyceride).
• Fats and oils have different types of fatty acids:
  • Saturated fatty acids (considered "bad" fats)
  • Unsaturated fatty acids (considered "good" fats)
• Phospholipids make up the cell membrane. They are made of a phosphate head and two fatty acid tails.

Nucleic Acids

• Made of C, H, O, N, P.
• Function: Carry and transmit genetic information.
• Monomers: Nucleotides.
• Polymers: DNA and RNA.
• Nucleotides are made of a sugar, phosphate group, and a nitrogen base. They are linked together in a specific order to transmit heredity information.
• DNA (Deoxyribonucleic acid) stores genetic information.
• RNA (Ribonucleic acid) builds proteins.

Proteins

• Made of C, H, O, N, S.
• Function: Structure, regulation, immunity, contraction, transport, catalysis.
• Monomers: Amino acids.
• Polymers: Proteins (e.g., enzyme, transport protein).
• Amino acids differ in side groups, or R groups. Twenty different amino acids are used to build proteins in organisms. Amino acids are linked by peptide bonds.
• Proteins are made of specific sequences of amino acids. The order of the amino acids is determined by the order of the nucleotides in the DNA molecule.
• Properties of amino acids cause proteins to fold up into specific shapes to perform specific functions. SHAPE = FUNCTION!!

2.5 Enzymes

• All chemical reactions in living organisms require enzymes to work.
• Enzymes are proteins that act as catalysts for chemical reactions in living things.
• Catalysts are substances that speed up chemical reactions by decreasing activation energy. Catalysts are not used up in the reaction (recyclable). Example: Digestive enzymes speed up the digestion of food.
• Enzymes are very specific. An enzyme’s structure allows only certain reactants to bind to the enzyme.
  • Substrates = what enzyme acts on.
  • Active site = where substrate and enzyme bind.
• Enzyme-substrate pairs:
  • Amylase breaks down starch.
  • Lactase breaks down lactose.
  • Lipase breaks down lipids.
  • Protease breaks down proteins.
  • DNA polymerase builds DNA.

Lock-and-Key Model

1. Substrates (key) exactly fit the active sites of enzymes (lock).
2. Substrates are brought together (or broken down), and bonds are weakened.
3. A new product is formed and released.
4. Substrates bind to an enzyme at certain places called active sites.
5. The enzyme brings substrates together and weakens their bonds.
6. The catalyzed reaction forms a product that is released from the enzyme.

Factors Affecting Enzyme Activity

• Enzymes function best in a small range of conditions.
• Factors affecting enzyme activities: temperature, pH, enzyme/substrate concentration.
• Enzymes can denature in extreme temperature and pH (shape and function are irreversibly destroyed!!). SHAPE = FUNCTION!! In protein, it’s not the size, it’s the SHAPE that matters!