Building blocks of matter and biomolecules - Vocabulary

Matter, Elements, and Atoms

• Matter is anything that has mass and takes up space.
• Elements are the basic building blocks of matter that cannot be broken down by chemical means.
• Atoms are the smallest units of an element that retain the element's physical and chemical properties. These bond together to form molecules.
• Subatomic particles:
  • Protons are positively charged.
  • Neutrons are neutral.
  • Electrons are negatively charged and orbit around the nucleus.
  • The nucleus contains protons and neutrons; electrons orbit the nucleus.
• In an uncharged (neutral) atom, the number of protons equals the number of electrons.
• The chemical symbol for the element sodium is Na.
• The atomic number is the number of protons.
• By adding up the protons, neutrons, and the average number of neutrons, we get the mass number.
  • Protons + Neutrons = Mass number (A = Z + N)
• There are 92 elements that occur naturally.
• Isotopes are atoms that have the same atomic number (Z) but a different atomic mass (A) because the number of neutrons (N) differs.
• Radioisotopes are useful in dating old objects, imaging body organs and tissues through X-rays, and killing cancer cells.
• Radiation can be harmful by damaging cells and DNA and/or causing cancer.
• Important equations and concepts:
  • Mass number: A = Z + N where Z = number of protons, N = number of neutrons.
  • For a neutral atom, Z = ext{number of protons} = ext{number of electrons}.

Subatomic Particles and Atomic Structure

• Protons: positively charged
• Neutrons: neutral (uncharged)
• Electrons: negatively charged; orbit the nucleus
• Nucleus: protons and neutrons collectively
• Atoms bond to form molecules; structure determines element’s properties

Bonding and Molecules

• Molecules are made of atoms bonded together and can be composed of the same atom or different atoms.
• Ionic bonds:
  • Atoms donate or take on electrons to form ions.
  • Result in a stable outer electron shell.
  • Bond occurs between charged particles (ions).
• Covalent bonds:
  • Atoms share electrons.
  • Result in a stable outer shell.
• Water has several key properties related to bonding:
  • Water is a universal solvent for polar molecules.
  • Water exhibits cohesion (attraction between like molecules) and adhesion (attraction to other substances).
  • Water has high surface tension and high heat capacity/heating properties.
  • Water's hydrogen bonds contribute to these properties and to the behavior of water in biological systems.
  • Solid water (ice) is less dense than liquid water, enabling life to exist in aquatic environments.

Properties of Water and Hydrogen Bonding

• Water properties:
  • Universal solvent for polar molecules.
  • Cohesion and adhesion support the movement of water in plants and organisms.
  • High heat capacity helps regulate temperatures in large bodies of water and within organisms.
  • High heat of evaporation contributes to cooling mechanisms.
  • Ice is less dense than liquid water:
    ho{ ext{ice}} < ho{ ext{water}}.
• Bonds holding water molecules together:
  • Hydrogen bonds occur between a hydrogen atom covalently bonded to one electronegative atom (e.g., O) and another electronegative atom (e.g., O) nearby.
  • These bonds are relatively weak and can be broken and reformed easily.
• pH basics:
  • pH stands for the potential of Hydrogen (H⁺).
  • pH scale: 0 to 14; 7 is neutral; below 7 is acidic; above 7 is basic.
  • pH can be measured using pH paper.
  • The concentration of hydrogen ions changes by a factor of 10 for each whole-number change in pH.
  • Acids dissociate and release hydrogen ions (H⁺).
  • Bases take up hydrogen ions (H⁺) or release hydroxide ions (OH⁻).
  • Relationship formula: ext{pH} = -\log_{10}[H^{+}]

Dehydration and Hydrolysis (Organic Molecules)

• Dehydration reaction: removal of water to link subunits into larger molecules.
• Hydrolysis reaction: addition of water to break larger molecules into subunits.
• Digestive system example: after lunch, hydrolysis breaks down food into smaller subunits.

Carbohydrates

• Monosaccharides are the subunits of carbohydrates.
• C, H, and O are present in a 2:1 ratio, typically summarized as ext{H:O} = 2:1.
• Primary function: short- and long-term energy storage.
• Occur in simple and complex forms (e.g., sugars and starches).

Lipids

• Lipids are molecules that do not dissolve in water (hydrophobic).
• Functions: energy storage, components of cell membranes, and signaling (steroids).
• Major types include fats and oils, phospholipids, and steroids.
• Differences between fats and oils:
  • Fats: usually of animal origin; solid at room temperature; long-term energy storage; insulation from heat loss; cushioning for organs.
  • Oils: usually of plant origin; liquid at room temperature.
• Summary: fats are generally animal-derived and solid; oils are plant-derived and liquid.

Proteins

• Proteins are made of subunits called amino acids.
• Functions include: hormones, enzymes, antibodies, transport, and structural roles.
• Proteins can denature, meaning a change in shape that causes loss of function.
• Four levels of protein organization:
  • Primary: linear sequence of amino acids joined by peptide bonds.
  • Secondary: localized folding into pleated sheets and helices.
  • Tertiary: three-dimensional shape of the entire protein in space.
  • Quaternary: association of more than one polypeptide.
• All proteins have primary, secondary, and often tertiary structure; only some have quaternary structure.

Nucleic Acids

• Nucleic acids are made of nucleotide subunits.
• Primary function: to make proteins (via transcription/translation processes).
• Includes two main types: RNA and DNA.
• Bases found in nucleotides:
  • Adenine (A) and Guanine (G) are double-ringed purines.
  • Cytosine (C), Thymine (T), and Uracil (U) are single-ringed pyrimidines.
• In DNA, A pairs with T and G pairs with C.

DNA vs RNA: Structural Differences (as summarized in transcript)

• The transcript includes a "Summary of DNA and RNA structural differences" but does not provide detailed differences.
• Key note: DNA and RNA are both nucleic acids with different roles, bases, and structures (details not fully enumerated in the provided transcript).

Connections and Implications

• fundamental units of matter (atoms) combine through various bonds (ionic and covalent) to form molecules and macromolecules (carbohydrates, lipids, proteins, nucleic acids).
• Water's unique properties support life by enabling solvent actions, temperature regulation, and stable environments for biochemical reactions.
• Understanding pH, acid-base chemistry, and hydrolysis/dehydration reactions is essential for grasping metabolism, digestion, and cellular processes.
• The organization of proteins (primary to quaternary) underpins their diverse functions in biology.
• Nucleic acids encode information necessary to synthesize proteins, linking genetics to metabolism and physiology.

Key Formulas and Notation Recap

• Mass number: A = Z + N
• Neutral atom condition: Z = ext{number of protons} = ext{number of electrons}
• pH relationship: ext{pH} = -\log_{10}[H^{+}]
• Water density relation (ice vs liquid): \rho{ ext{ice}} < \rho{ ext{water}}
• Carbohydrate ratio: \text{H:O} = 2:1
• General bond concepts:
  • Ionic bonds: electrons donated/accepted to form ions
  • Covalent bonds: electrons shared to form stable outer shells