Atomic Structure and Electronegativity

Structure of the Atom

Atoms are the fundamental units of matter, composed of a nucleus (containing protons and neutrons) surrounded by electrons.

• Electrons are negatively charged particles that move around the nucleus in regions called electron clouds or orbitals.

• The nucleus contains positively charged protons and neutral neutrons.

• Electrons are often depicted as a cloud of negative charge or as discrete particles orbiting the nucleus.

• The arrangement of electrons determines the atom's chemical properties.

• Example: Helium atom with two electrons shown as a cloud or as two small spheres orbiting the nucleus.

Electronegativity

Electronegativity is a measure of an atom's ability to attract and hold electrons in a chemical bond.

• More protons in the nucleus result in greater electronegativity due to stronger attraction for electrons.

• Smaller atomic radius also leads to greater electronegativity because electrons are closer to the nucleus and more strongly attracted.

• Electronegativity increases across a period (left to right) and decreases down a group (top to bottom) in the periodic table.

• Example: Fluorine is the most electronegative element.

Periodic Trends

The periodic table organizes elements by increasing atomic number and groups elements with similar properties.

• Atomic size decreases across a period and increases down a group.

• Electronegativity values are highest for elements in the upper right (excluding noble gases).

• Example: The second period elements (Li, Be, B, C, N, O, F) show increasing electronegativity and decreasing atomic size from left to right.

Carbon Skeletons and Functional Groups

Carbon Skeleton Variations

Carbon atoms can form diverse structures, which are the backbone of organic molecules.

• Length: Carbon chains can vary in length (e.g., propane vs. butane).

• Branching: Chains may be unbranched or branched (e.g., 2-methylpropane).

• Double bond position: Double bonds can be located at different positions (e.g., 1-butene).

• Rings: Carbon skeletons can form rings (e.g., cyclohexane).

• Example: Isomers are compounds with the same molecular formula but different structures.

Biologically Important Functional Groups

Functional groups are specific groups of atoms within molecules that have characteristic properties and chemical reactivity.

Macromolecules: Polymers and Monomers

Polymers and Monomers

Most biological macromolecules are polymers, made by joining smaller units called monomers.

• Polymer: A long molecule consisting of many similar or identical building blocks (monomers) linked by covalent bonds.

• Monomer: The repeating unit that serves as the building block of a polymer.

• Examples: Polysaccharides (carbohydrates), proteins, and nucleic acids are true polymers; lipids are not true polymers.

Dehydration and Hydrolysis Reactions

Polymers are assembled and disassembled by two main types of reactions:

• Dehydration (condensation) reaction: Joins monomers by removing a water molecule.

• Hydrolysis: Breaks polymers into monomers by adding a water molecule.

• Equation for hydrolysis:

Carbohydrates and Lipids

Carbohydrates

Carbohydrates are sugars and polymers of sugars, serving as energy sources and structural materials.

• General formula: in a ~1:2:1 ratio (e.g., glucose: C6H12O6).

• Short-term energy storage: Glycogen (animals), starch (plants).

• Structural roles: Cellulose (plant cell walls), chitin (exoskeletons of arthropods).

Lipids

Lipids are a diverse group of hydrophobic molecules, including fats, phospholipids, and steroids.

• Not true polymers: Built from fatty acids and glycerol.

• Long-term energy storage: Fats and oils are more energy-dense and lighter than carbohydrates.

• Structural roles: Phospholipids form cell membranes; steroids (e.g., cholesterol) have a 4-ring structure.

Nucleic Acids: DNA and RNA

Structure of DNA

DNA (deoxyribonucleic acid) stores genetic information and has a double helix structure.

• Antiparallel strands: Two strands run in opposite directions (5'→3' and 3'→5').

• Base pairing: Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds; Guanine (G) pairs with Cytosine (C) via 3 hydrogen bonds.

• Complementary: Knowing one strand allows prediction of the other (%A = %T, %G = %C).

• Right-handed helix: The double helix twists clockwise.

• Major and minor grooves: Allow proteins to bind and read DNA sequences.

DNA vs. RNA

Proteins: Structure and Function

Levels of Protein Structure

Proteins are polymers of amino acids and have four levels of structure:

• Primary structure: Sequence of amino acids in a polypeptide chain.

• Secondary structure: Local folding into alpha helices and beta sheets, stabilized by hydrogen bonds.

• Tertiary structure: Three-dimensional shape stabilized by interactions between side chains (R groups).

• Quaternary structure: Association of two or more polypeptide chains (not all proteins have this level).

• Example: Hemoglobin has quaternary structure; myoglobin does not.

Summary Table: Key Biological Macromolecules

Additional info: Some content and explanations have been expanded for clarity and completeness, including definitions, examples, and summary tables.