Biological Molecules: Elements and States of Matter

• All living things consist of matter.

How matter is organized

• Matter occupies space, and mass is the amount of matter in an object.
• Weight is the force of gravity acting on matter.
• In outer space, weight is close to zero, but mass remains the same.

States of matter

• Solid has definite shape and volume.
• Liquid has a definite volume and changeable shape.
• Gas has a changeable shape and volume.

The organization of matter

• An element is a pure substance that cannot be broken down by chemical or physical techniques.
• All matter (anything with space and mass) comprises elements and their combinations.
• Ninety-two elements occur naturally; others are synthesized in the laboratory.

Elements in biological molecules

• Oxygen (O) makes up 65.0%
• Carbon (C) makes up 18.5%
• Hydrogen (H) makes up 9.5%
• Nitrogen (N) makes up 3.3%
• Calcium (Ca) makes up 1.5%
• Phosphorus (P) makes up 1.0%
• Sulfur (S) makes up 0.3%
• Sodium (Na) makes up 0.2%
• Chlorine (Cl) makes up 0.2%
• Magnesium (Mg) makes up 0.1%
• Trace elements less than 0.01% include Boron (B), Chromium (Cr), Cobalt (Co), Copper (Cu), Fluorine (F), Iodine (I), Iron (Fe), Manganese (Mn), Molybdenum (Mo), Selenium (Se), Silicon (Si), Tin (Sn), Vandium(V) and Zinc (Zn).

Atomic structure

• Each element consists of one type of atom.
• An atom comprises an atomic nucleus surrounded by fast-moving, negatively charged electrons.
• Atomic nuclei contain positively charged protons; the number of protons (atomic number) identifies an element.
• Nuclei of all atoms (except hydrogen) also contain uncharged neutrons.
• Atomic number equals the number of protons.
• Each element has its own number of protons; Carbon has 6, and Oxygen has 8.
• Changing the number of protons changes the element.
• Adding a proton to carbon results in 7, which forms nitrogen.
• Mass equals the number of protons plus the number of neutrons.
• Different masses of the same element are called isotopes, which differ in the number of neutrons.
• Unstable isotopes decay and emit particles until they are stable; these are called radioactive isotopes.
• Human thyroid glands scans, after an injection of iodine-123 into the bloodstream.
• Radioactive iodine concentrates in the thyroid gland.
• Molecules with different component atoms (like carbon dioxide) are compounds
• Chemical and physical properties of compounds are typically distinct from their atoms or elements
• For instance Hydrogen (H) and oxygen (O), the elements found in liquid water (H₂O), are highly flammable.
• Electrons reside within an atom in regions known as energy levels, or shells.
• The maximum number of electrons in a shell is 2n², where 'n' is the shell number (ie 1, 2, 3, etc.).
• The arrangement of electrons in shells constitutes an atom's electronic configuration.
• Example: Sodium has 11 electrons; its electronic configuration of 2, 8, 1.
• Example: Chlorine has 17 electrons; its electronic configuration is 2, 8, 7

Chemical bonds and chemical reactions

• Three critical chemical linkages in biological molecules: ionic, covalent, and hydrogen bonds.
• Chemical reactions happen when atoms/molecules form or break chemical bonds.
• Ionic bonds stem from electrical attractions between atoms that completely gain or lose valence electrons.
• A positively charged ion (lost an electron), like Na+, is a cation.
• A negatively charged ion (gained an electron), like Cl-, is an anion.
• Two atoms share outer electrons in a covalent bond.
• H₂O, CO2, NH3, O2 are held together by covalent bonds
• Polar molecules have slightly positive and negative ends.
• Polar molecules create weak polar bonds with other polar molecules.
• Polar molecules containing hydrogen form hydrogen bonds with other polar molecules.
• Water is a polar molecule.
• Water forms hydrogen bonds with itself and with other polar molecules (hydrophilic)
• It forms a solution that facilitates chemical reactions inside cells.
• Water moderates temperature.
• It is required for photosynthesis.
• Most chemicals are compounds.

Inorganic compounds

• Usually lack carbon and hydrogen and are structurally simple.
• Examples include water, carbon dioxide, oxygen, acids, bases, and salts.

Orgainic compounds

• Contain carbon and hydrogen.
• Always have covalent bonds.
• Water comprises about 2/3 of total body weight.
• Aqueous solutions with +/- ions conduct electrical current, with + and - ions moving toward each other.
• A homogenous mixture of two or more substances is a solution.
• The medium in which other atoms, ions, or molecules are dispersed is the solvent.
• The dispersed substances are the solute.
• When water is the solvent, the solution is an aqueous solution.

Acids and bases

• Acids are proton donors that release H+ (and anions) when dissolved in water, increasing the H+ concentration.
• Example: Hydrochloric acid (HCl) dissociates H+ and Cl- when dissolved in (HCI → H+ + Cl-)
• Bases are proton acceptors that reduce the H+ concentration of a solution; most release a hydroxide ion (OH-) and a cation.
• Example: NaOH releases Na+ + OH-; excess OH- combines with H+ to produce water (OH- + H+ → H₂O)

pH

• The acidity of a solution is determined by the concentration of H+ ions compared to OH- ions.
• Acidity is measured on the pH scale, which ranges from 0 to 14 based on the number of H+ ions in solution.
• Formular for measuring acidity pH = -log10[H+]
• Acids are molecules that release a positive hydrogen ion (H+).
• Bases are molecules that accept a positive hydrogen ion (H+).
• How readily atoms accept/donate hydrogens is reflected by pH.
• Acids have a pH less than 7.
• Bases have a pH greater than 7.
• Water has a pH of seven.
• Basic pH values are from 8-14
• Neutral pH is 7.
• Acidic pH values are from 0-6.
• Body fluids differ in pH, but the range of each is limited and maintained through buffering systems.
• Gastric juice has 1.2 to 3.0 pH.
• Saliva has 6.35 to 6.85 pH.
• Bile has 7.6 to 8.6 pH.
• Blood has 7.35 to 7.45 pH.
• A buffer resists the change in pH.
• Buffers stabilize the pH of a solution by removing or replacing hydrogen ions.

Types of chemical reactions

• Three types of chemical reactions exits
• Decomposition occur AB→ A + B
• Synthesis occur A + B → AB
• Exchange happen AB + CD → AC+BD
• HCL + NaHCO3 → H2CO3 + NaCl
• Decomposition (catabolism) breaks molecules into two or more substances and is typically exergonic.
• All synthesis reactions in the body together comprise anabolism.
• Two or more atoms, ions, or molecules combine to form new & larger molecules, which are usually endergonic.

Explore the composition of living things, focusing on matter, its states (solid, liquid, gas). Discover how elements like oxygen, carbon, and hydrogen form biological molecules and their percentages.