Atoms and Molecules

Chapter 2: The Chemical Context of Life

• Biology encompasses the study of life, and organisms and their environments adhere to the fundamental principles of physics and chemistry.
• Ants utilize formic acid as protection against predators and microbial parasites.

Matter and Elements

• Organisms consist of matter, which occupies space and has mass.
• Matter is composed of elements, substances that cannot be broken down chemically.
• A compound contains two or more elements in a fixed ratio, exhibiting unique properties from its constituent elements.
• 20-25% of the 92 natural elements are essential for life.
• Carbon, hydrogen, oxygen, and nitrogen constitute 96% of living material.
• Calcium, phosphorus, potassium, and sulfur make up most of the remaining 4%.
• Trace elements are needed in very small quantities.

Atomic Structure

• Each element is made up of unique atoms.
• Atoms are the smallest units retaining an element's properties and are composed of subatomic particles.
• Relevant subatomic particles include:
  • Neutrons: no charge
  • Protons: positive charge
  • Electrons: negative charge
• Neutrons and protons form the atomic nucleus.
• Electrons create a negative charge "cloud" around the nucleus.
• Neutron and proton mass are nearly identical, measured in daltons.
• The atomic number is the quantity of protons in an element's nucleus.
• The mass number totals protons and neutrons in the nucleus.
• Atomic mass, approximating the mass number, signifies the atom's total mass.
• Isotopes of an element share proton count but vary in neutron count.
• Radioactive isotopes decay naturally, emitting particles and energy.

Radioactive Isotopes

• Radioactive isotopes are used as diagnostic tools in medicine
• Radioactive tracers can track atoms through metabolism or be combined with imaging instruments.
• In radiometric dating, scientists measure isotope ratios to estimate fossil or rock age by half-lives.
• Half-life ranges from mere seconds to billions of years.

Electron Energy Levels

• Energy, defined as the capacity to cause changes.
• Potential energy is the energy matter possesses due to its location or structure.
• Electrons differ in potential energy levels, with each electron's potential energy state termed its energy level or electron shell.

Electron Distribution

• An atom's chemistry hinges on the distribution of its electrons across electron shells

Valence Shells

• Valence electrons reside in the outermost or valence shell.
• Valence electrons predominantly dictate an atom's chemical traits.
• Elements featuring a full valence shell are chemically inert, or nonreactive.
• Orbitals represent the three-dimensional space where electrons are found 90% of the time.
• Each electron shell contains specific orbital counts.

Chemical Bonds

• Atoms featuring incomplete valence shells engage in electron transferring, creating chemical bonds.
• Such interaction binds atoms close together, held through chemical bonds.
• A covalent bond occurs when a pair of valence electrons are shared by two atoms.
• Shared electrons are figured as a part of each atoms' valence shell.
• A molecule consists of two or more atoms held by covalent bonds.
• A single covalent bond represents a single shared valence electron pair, while a double covalent bond involves two pairs.

Formulas

• A structural formula uses notation to represent bonding and atoms

Bonding Capacity

• Bonding capacity refers to an atom's valence
• Covalent bonds can join like or unlike elements
• The compound consists of two or more elements combined
• Atoms exert attraction on electrons to differing extents.
• Electronegativity measures an atoms attraction to bonding electrons within a covalent context.
• More electronegative atoms pull shared electrons more strongly.
• In a nonpolar covalent bond, atoms evenly share electrons.
• A polar covalent bond occurs when electron sharing is unequal due to electronegativity differences.
• Partial positive or negative charge results from unequal electron sharing.

Ionic Bonds

• Ionic bonds occur when atoms strip electrons away from bonding partners.
• Transfer of electrons between atoms produces opposite charges.
• A charged atom, or molecule, is called an ion.
• An anion refers to a negatively charged ion and a cation refers to a positively charged ion.
• An ionic bond is an attraction between such differently charged ions
• Ionic compounds, also called salts, are made by ionic bonding and frequently organized as crystals.

Weak Bonds

• Covalent bonds constitute the strongest within organisms.
• Many biological molecules are held in their functional form by weak bonds
• The reversibility is an advantage to these weak bonds.
• Hydrogen bonding emerges when a hydrogen atom already covalently bound to a highly electronegative atom turns attractive to another.
• Oxygen and nitrogen frequently play the electronegative partners' roles in cells.
• Van der Waals interactions arise between molecules closely positioned through chance electron accumulation.

Molecular Shape

• Molecular size/shape are essential in determining the function.
• A molecule's shape depends on its atoms' orbitals.
• Hybridization of s/p orbitals in covalent bonds creates certain shapes.
• The way molecules identify and behave with each other depends on the molecular shape .
• Opiates (morphine) and naturally-occuring endorphins are examples of molecular shape at work, due to how similar shapes bind to receptors in the brain.

Chemical Reactions

• Chemical reactions involve the production and breaking of bonds that start with reactants and end in products.
• Photosynthesis combines carbon dioxide and water to create glucose and oxygen.
• In chemical equations 6 CO2 + 6 H2O yields C6H12O6 + 6 O2.
• All chemical reactions are reversible, and that products revert to reactants
• Chemical equilibrium marks forward/reverse reactions at the same rate such that concentrations stabilize.

Chapter 3: Water and Life

• Water allows Life to exist on Earth
• Water is the only common substance that exists in the natural environment in all three physical states of matter
• Water allows the existence of life because of its unique emergent properties

Water’s Polarity

• The electrons of the polar covalent bonds in water molecules, spend much more time near the oxygen atom.
• Polarity permits the bonding of water molecules with each other in hydrogen bonds.
• Water is a polar molecule due to a distribution of overall charge

Four Properties of Water

• Water's 4 properties that allow life are:
  • Cohesive behavior
  • Temperature moderation
  • Expansion upon freezing
  • Versatile solvent

Cohesion

• Water molecules stick together due to hydrogen bonds; this phenomenon is called cohesion.
• Cohesion facilitates water transport against gravity within plants.
• Adhesion is when there is an appeal involving different kinds of matter i.e water and cell walls
• Surface tension is the degree of struggle of breaking a liquid surface
• Water holds an extremely high surface tension due to hydrogen bonding

Temperature Moderation

• Water gains heat from warmer air and it releases stored heat to cooler surroundings
• Water absorbs/releases a substantial quantity of heat, showing only slim temperature variations.
• Kinetic energy denotes energy from motion with atoms/molecules.
• Thermal energy represents the quantity of kinetic energy

Temperature, Heat, and Calories

• Temperature represents kinetic energy in a body of matter
• Heat refers to thermal energy in transit between bodies of matter
• A calorie measures the amount of temperature required to raise 1 g of water by 1°C.
• 1 kcal = 1,000 cal and is the "Calories" in food packages.

Joule Conversion

• One joule, representing a metric heat unit, provides 1 J =0.239 cal and 1 cal = 4.184 Joules

• Heat needed is termed substance's specific amount to change its temperature by 1°C.

• Specifc heat amount is 1 cal/(g• °C)

• Temperature is stable due to water's high specific amount.

• High amounts result from bonding where they are broken, with hydrogen holding temperature minimal.

• Transformation liquid to gas (or evaporation / vaporization) involves a surface cooling and keeps body temperatures controlled.

Floating Ice

• Ice being less dense than water leads it to float and this has significant impact.
• In bodies of water, any ice always floats along the water as a result of a formation of hydrogen bonds.
• At 4°C Water touches it maximal thickness.

Global Warming

• Climate warming around the globe is worrying scientists because it has a profound effect on arctic environments.
• Shrinking ice glaciers and Arctic ice creates hardship for icy animal habitatis

Water As a Solvent

• Homogenous mix of a liquid is a completely solvable liquid with substances.
• The dissolving agent in a solvable environment is called a solvable and the substance dissolved is the soluble.
• An aqueous solution describes a liquid with water utilized as a solvent.
• Due versatility, water is a potent solvent.
• An ionic is dissolved in water and creates a sphere around itself.

Hydrophillic/Hydrophobic Substances

• Substance with good affinity for water is water
• Water not being fond is hydrophobic
• Oil does not water cause only bond relatively and major source in cells..
• In equal pure water, both + and - + charge equals +
• Solutes known to be bases and acidics will modify the charged amounts
• Acid versus base describes the ratio of + in ph balance

pH Balance

• Solutions rated less that 7 with + more solutions and rated 7+ have more OH
• Biological liquids commonly range between just slightly.
• Internal bodily charge close to neutral is at 7 to sustain a healthy state
• Changes to concentration may heavily affect the chemistry in cells.
• Solutions combine with certain OH and H+ elements to reduce drastic shifts

Acidification

• Fuel quality suffers burnoff in carbon waters around bodies
• Resulting CO2 converts seas acidic. H combines calcification to produce bicarbonate corals and delicate balance.

Chapter 4: Carbon and the Molecular Diversity of Life

• Living organisms consist of carbon-based compounds.
• Carbon is unparalleled for its ability to form various large and varied molecules
• Protiens, DNA and carbohydrates are all carbon compounds.

Organic Chemistry

• Organic Chemistry studies componds holding carbon that come from origin.

Stanley Miller Experiment

• Miller's experiment revealed abiotic synthesis of organic compounds.
• Experiments suggests abiotic synthesis by volvanoes could provide organic compounds.

Building Blocks

• Percents C, H, O, N, S and P in organisms are similiar.
• Variety of carbon molecules comes from bond make an exhaustive variety of molecules.

Four Atoms

Explore electron shells, energy levels, and the periodic table. Learn about electron distribution, chemical behavior, and carbon's unique bonding ability. Understand abiotic synthesis and organic compound formation.