AGR130: Biology in Agriculture - Biological Chemistry Notes

Biological Chemistry

Subject Overview

AGR130 Biology in Agriculture introduces fundamental concepts.

Atoms, Elements, and Compounds

• Atoms: The smallest unit of an element that retains the properties of that element.
• Elements: Can exist as atoms, molecules, or compounds.
  • Example: Hydrogen (H atom or H+ atom), H2 molecule, or as part of H2O.
• Chemical Bonds: Covalent or ionic bonds, which are forms of stored energy.

Why Biologists Care About Chemistry

Biology relies heavily on chemistry, similar to how:

• Sociology is applied psychology.
• Psychology is applied biology.
• Biology is applied chemistry.
• Chemistry is applied physics.

Atoms

The smallest unit making up an element, retaining the properties of the element.

Composition:

• Uncharged neutrons
• Positively charged protons
• Negatively charged electrons

Measurement:

• Subatomic particles are measured in atomic mass units.
• Protons and neutrons each have a mass unit of 1.
• The mass of electrons is negligible.

The Periodic Table

• Element symbol
• Mass number: Total number (equal to total mass) of protons and neutrons in the nucleus.
• Atomic number: Number of protons in the nucleus.
• Isotopes: Atoms of the same element with different numbers of neutrons.

How Atoms Interact to Form Molecules

Ionic Bonds

• An ion is an atom that has lost or gained electron(s).
• Ions form ionic bonds.

Covalent Bonds

• “Sharing electrons”
• Between two atoms of the same element or different elements.
• Can be non-polar or polar.
  • Non-polar: Equal sharing (e.g., O2, N2, H2, CO2).
  • Polar: Unequal sharing (e.g., H2O).

Water

Water is vital due to its properties.

• Small and polar.
• Exhibits hydrogen bonds.
• Cohesive and adhesive properties.

Hydrogen Bonds

• Net negative charge
• Net positive charge

Water - pH

• Some water molecules (H2O) break apart into H+ and OH-.
• pH is neutral when [H+] = [OH-].
• pH 0 – 6 is acidic (H+ > OH-).
• pH 7 is neutral (H+ = OH-).
• pH 8 – 14 is basic (OH- > H+).

Buffers

• A buffer is a molecule that helps maintain a nearly constant pH of a solution.
• Accepts or releases H+ in response to small changes in H+ concentration.
• In excess H+, a buffer combines with H+.
• In excess OH–, a buffer releases H+.

Biological Molecules

Four major classes:

• Carbohydrates
• Proteins
• Lipids
• Nucleic acids

Characteristics:

• Mostly organic (i.e., chains of carbon molecules covalently bonded together).
• Usually have hydrogen bonded as side atoms.
• Specific functionality comes from incorporation of O, N, P, and S.
• Carbon backbone can be linear, branched, or cyclic (and combinations).

Polymers

• Polymers are assembled from smaller building blocks (monomers).
• The smaller units are combined, typically via dehydration synthesis.

Carbohydrates

• Composed of C, H, and O.
• Monomer: saccharide (CH_2O).
  • Common monosaccharides: Glucose (C6H{12}O6), Fructose (C6H{12}O6).
• Polymers: disaccharide, trisaccharide, polysaccharide.

Polysaccharides (CH2O)n

• For energy storage (e.g., starch in plants & glycogen in animals).
• For structure (e.g., cellulose in cell walls).

Chitin

• The major component of the exoskeleton of arthropods and cell walls of fungi.
• Polymer of glucose containing an amino side.

Lipids

Oils, fats, and waxes.

• Composed mainly of carbon and hydrogen.
• Contain only C, H, and O.
• Hydrophobic.
• Possess one or more fatty acid side chains.
• Possess only linear chains of atoms.

Uses:

• Components of cell membranes.
• Energy storage (e.g., fats and oils).
• Waterproofing (e.g., waxes).
• Hormones (e.g., steroids).

Phospholipids

• Critical to the structure and function of cell membranes.
• Two distinctly different ends to the molecule: a polar “head group” & a nonpolar “tail”.
• Interaction of polar and nonpolar ends leads to the essential nature of the plasma membrane.

Steroids

• Lipids containing four fused rings (with various substituents).
• Mainly function as hormones.

Proteins

• Polymers of amino acids joined by peptide bonds.
• Vital role in biochemical reactions (i.e., enzymes).
• Essential role in structures and protective coatings (e.g., keratin).
• Basis of animal movement (e.g., actin and myosin).
• Energy storage.

Dehydration Synthesis:

• Formation of a peptide bond between two amino acids.

Amino Acids

• Twenty amino acids commonly found in organismal proteins.
• Differ by R group (side chain).
• Sequence of amino acids determines structure (and therefore function).
• Interactions between R-groups of distant amino acids can affect overall structure.

Protein Structure

Four levels:

• Primary: The sequence of amino acids.
• Secondary: 3-D arrangement of protein segments (α-helix, β-pleated sheet).
• Tertiary: Overall 3-D structure.
• Quaternary: Arrangement of several large protein subunits.

Nucleic Acids

• Polymers composed of nucleotides.
• Nucleotides have 3 parts:
  • A five-carbon sugar (ribose or deoxyribose).
  • A phosphate group.
  • A nitrogen-containing base.

Primary Function:

• Encoding genetic information to produce proteins (RNA & DNA).
• Genes: the basic units of heredity.
• DNA replicates.
• Nucleotide sequences are usually extremely long.

Nucleic Acids - ATP

ATP (Adenosine Triphosphate) is a nucleic acid.

• Energy “currency.”

Biomolecules

Summary of the four major classes:

• Carbohydrates
• Proteins
• Lipids
• Nucleic acids

Molecule of Life - Examples and Functions

Summary

• Biology is chemistry-based.
• Atoms vs elements vs compounds.
• Water's properties are crucial (especially hydrogen bonds).
• The “molecules of life” are carbohydrates, proteins, lipids, and nucleic acids.
• Carbohydrates for energy storage and structure.
• Lipids for energy storage and membranes.
• Proteins for cell function and tissue structure.
• Nucleic acids for storing information. Biomolecules make up 96% of organism's dry weight. Examples of biomolecules are Glucose, Sucrose, Amino Acid and Fatty acids ([CH2]nCOOH).