Chapter 2

Radioactive Isotope Uses in Biology

(1) Radioactive Tracers: diagnostic tools in medicine, incorporated into biologically active molecules traced to track atoms during metabolism (the chemical processes of an organism) -Certain kidney disorders are diagnosed by injecting small doses of radioactively labeled substances into the blood, analyzed in urine -Used in combination w/ imaging instruments (PET scanners) that can monitor growth & metabolism of cancers in the body -Positron Emission Tomography Scan (PET Scan): a clinical application for a radioisotope -Picture depict elevated levels of radioactively labeled glucose, which is used in our body for metabolism -This deviation can be used as an indicator of suspected cancerous tissue since the rate of which our body uses glucose for metabolism in cancer cells is different -Doses of most isotopes used in medical diagnosis are relatively safe, but radiation from decaying isotopes also poses a hazard by damaging cellular molecules (depending on type and amount of radiation) -Exposure to radiation needs to be carefully controlled and regulated -P32: a radioactive isotope of phosphorus containing 15p & 17n, handled by PPE in order to ensure safe levels of exposure (more than average, but with proper handling and care will not cause undue harm) (2) Radiometric Dating: the measure of radioactive decay in fossils to date them by the ratio of different isotopes and calculate how many half-lives have passed since the organism was fossilized (Carbon-14 is standard for radiometric dating: comparison of C-14 to C-12 in the organism to C-14 to C-12 in the atmosphere) -Fossils provide a large body of evidence for evolution, but while the layering of fossil beds establishes that deeper fossils are older than more shallow ones, actual age (years) cannot be determined by position alone -C-14 only works for fossils about 75,000 years old, anything over has too little C-14 -Parent isotope decays into its daughter isotope at a fixed rate (half-life: time it takes 50% of the parent isotope to decay) -Half-life values range from seconds to days to billions of years -Uranium-238 has a half life of 4.5 billion years, used to determine that moon rocks are approximately that old, similar to Earth's age

Each element consists of a certain type of atom that is different from the atoms of any other element

-Atom: the smallest unit of matter that still retains the properties of an element, composed of subatomic particles -We symbolize atoms with the same abbreviation used for the element that is made up of those atoms (ej. C stands for carbon the element and a carbon atom)

Atoms of the various elements differ in their number of subatomic particles

-Atomic Number: the number of protons that are found in an atoms nuclei -All atoms of a particular elements have the same atomic number, and have the same chemical properties -Written as a subscript (below) to the left of the symbol for the element -Unless otherwise noted, an atom is neutral in its electrical charge, thus protons must be balanced by an equal number of electrons -Atomic number tells us the number of protons and electrons -Mass Number: total number of protons and neutron in an atom's nucleus -Written superscript (above) to the left of the symbol for the element -We determine the number of neutrons by subtracting the atomic number from the mass number -The simplest atom is hydrogen, which has no neutrons

Ionic Bond

-Cations and anions attract each other -The transfer of electrons is not a bond, but allows for a bond's formation because it results in two ions of opposite charge

Environment affects the strength of ionic bonds

-Ionic bonds are not as strong as covalent bonds, certain forces can disrupt these interaction and cause the crystal structure to dissociate, resulting in mixtures that contain free sodium or chlorine ions (what happens when salt is pleased in aqueous solution) -In a dry crystal structure the bonds are so strong that it takes a hammer and chisel to break through enough of them to crack the crystal -In water, the ionic bonds are much weaker because each ion is partially shielded by its interaction with water molecules -Most drugs are manufactured as salts because they are quite stable when dry, but can dissociate easily in water

Element

-A pure substance that cannot be broken down to other substances by chemical reactions (today chemists recognize 92 elements occurring in nature) -An element contains only one kind of atom, composed in a unique organization of atoms

Compound

-A substance consisting of 2 or more different elements combined in a fixed ratio -Table salt is sodium chloride (NaCl), sodium and chloride in a 1:1 ratio) -Pure sodium is metal, pure chlorine is poisonous gas, but edible when combined as sodium chloride -A compound has characteristics different from those of its elements

Matter

-All organisms are composed of matter, which is anything that takes up space and has mass, and exists in many forms (solids, liquids, gases) -A living organism can harness the power of chemicals (e.j. wood ants eject formic acid from their venom glands, likely directing towards predator) -Matter is made up of elements

Neutron and protons are almost identical in mass (each about 1.7x10^-24 grams)

-Dalton: unit of measurement named after British scientist John Dalton who helped develop atomic theory around 1800 -The dalton is the same as the atomic mass unit (amu) -Neutrons and protons have masses close to 1 dalton -The mass of an electron is only about 1/2000 that of a neutrons of protons, thus we ignore them in computing total mass of an atom

Essential Elements

-Elements that an organism needs to live a healthy life & reproduce -Of the 92 natural elements, 20-25% are natural elements -Essential Elements are similar among organisms, but there is some variation -Four elements (oxygen (O), carbon (C), hydrogen (H), and nitrogen (N) make up approximately 96.3% of living organisms - Other elements (calcium (Ca), phosphorus (P), potassium (K), sulfur (S), etc.) make up the remaining 3.7%

An atom's electron vary in the amount of energy they possess

-Energy: the capacity to cause change (by doing work) -Potential Energy: energy that matter possess because of its location/structure -Matter has a natural tendency to move towards the lowest possible state of potential energy (PE) -Electrons have potential energy due to their distance from the nucleus -Further from nucleus, the greater an electron's potential energy

Some naturally occurring elements are toxic to organisms

-In humans, arsenic has been linked to numerous diseases and can be lethal -In some areas, arsenic can make its ways into groundwater (southern Asia) -Some species have become adapted to environments containing toxic elements -Serpentine contains elevated levels of chromium, nickel, and cobalt -A small number of plant species have endured natural selection to adapt to serpentine, researchers are studying whether these plants could be used to absorb toxic metals in contaminated areas for safe disposal

A molecule has a characteristic size and shape, which are key to its function in the living cell

-Most molecules with more than 2 atoms have complicated shapes, determining by the position of the atoms' orbitals -When an atom forms covalent bonds, the orbitals in its valence shell undergo rearrangement (the tetrahedral shape of a carbon atom bonded with 4 other atoms is often the repeating motif within complex shapes)

Subatomic Particles

-Neutrons: particles that are electrically neutral -Protons: positively electrically charged particles -Protons and Neutrons are packed together in a dense core (atomic nucleus) at the center of the atom, held together by forces based on proximity. Protons give the nucleus a positive charge -Electrons: negatively electrically charged particles that are rapidly moving in a "cloud" of negative charge around the nucleus -The opposite attraction keeps electrons in vicinity of the nucleus -In most cases, the amount of protons and electrons balance each other out, thus being electrically neutral

Each electron shell contains electrons at a particular energy level, distributed among a specific number of orbitals of distinctive shapes and orientations

-Orbitals are components of electron shells: the first shell only has one spherical orbital (1s), but the second shell has 4: 1 large spherical orbital (2s), 3 dumbbell shaped orbitals (2p). -No more than 2 electrons can occupy a single orbital -Electrons in each of the 4 orbitals in the second shell have nearly the same energy level, but they move in different volumes of space

Emergent Properties

-Properties that arise from through interactions among smaller parts that alone do not exhibit such properties -Sodium and chlorine as pure metal and poisonous gas individually, but is edible when combined as sodium chloride

Trace Elements

-Required by an organism in only minute quantities -Some trace elements are needed by all forms of life (Iron (Fe)) -Other trace elements are required only by certain species -Iodine (I) is an essential ingredient of a hormone produced in the thyroid gland for vertebrates -Daily intake of .15mg of iodine is adequate for most normal activity of the human thyroid, but an iodine deficiency causes a goiter (abnormal size of the thyroid gland)

Atoms are mostly empty space

-The size of an atom's nucleus (protons and neutrons) is significantly smaller than the entire atom -Electrons are the only subatomic particles directly involved in chemical reactions -Behaviors of an electron within an atom determines how the combine or interact with other atoms

Although most of the strongest chemical bonds in organisms are covalent bonds, many large biological molecules are held in their functional form by weak interactions

-When 2 molecules in the cell make contact, they may adhere temporarily by weak interactions -The reversibility of weak interactions can be an advantage as two molecules can come together, affect one another in some way, then separate -Ionic bonds in water, Hydrogen bonds and Van der Waals interactions are weak interactions crucial to life

Each atom that can share valence electrons has a bonding capacity corresponding to the number of covalent bonds the atom can form

-When the bonds form, they give the atom a full complement of electrons in the valence shell -The bonding capacity is called the atom's valence, and is usually equal to the number of unpaired electrons required to complete the valence shell

Electron Orbital

3-dimensional space where an electron is found 90% of the time. -Concentric-circle diagrams do not give a real picture of an atom -In reality, we can never know the exact location of an atom, but describe the space in which electrons spend most of their time

CONCEPT 2.2

An element's properties depend on the structure of its atoms

Radioactive Isotope

An isotope in which the nucleus decays spontaneously, giving off particle and energy. -When this decay leads to a change in the number of protons, this transformers the atom to an atom of a different element

CONCEPT 2.4

Chemical reactions make and break chemical bonds

Ionic Compounds/Salts

Compounds formed by ionic bonds. -Salts are often found in nature as crystals of various sizes and shapes -Each salt crystal is an aggregate of vast numbers of cations and anions bonded by their electrical attraction and arranged in a 3-dimensional lattice -Unlike a covalent compound (consists of molecules having a definite size and number of atoms), an ionic compound does not consist of molecules -The formula for an ionic compound indicates the ratio of elements in a crystal of the salt -Not all salts have equal numbers of cations and anions -The term ion also applies to entire molecules that are electrically charged

Molecular Formula

Consists of the chemical symbols for the constituent elements followed by numeric subscripts describing the number of atoms of each element present in the molecule

Isotopes

Different atomic forms of the same element that can have more neutrons present in the nucleus than other atoms of the same element (thus a greater mass). -The addition of these neutrons changes the atomic mass number -In nature, an element can occur as a mixture of its isotopes -Many elements do not have distinct names for their isotope forms, but deviations with respect to their atomic mass (e.j. carbon) -Must have the same number of protons (protons determine the element) -Although isotopes have slightly different masses, they behave identically in chemical reactions -For an element with more than one naturally occurring isotope, the atomic mass is an average of those isotopes, weighted by their abundance

Van der Waals Interaction

Due to uneven distribution of electrons which can result in accumulation by chance in one part of a molecule, these are individually weak interactions (non-directional) that occur only when atoms are very close together. -For Van der Waals interaction, these are snapshots in time where there can be uneven distribution of those electrons, a temporary fluctuation in charge -These are interactions between molecules that are close to one another in proximity and will be based on non-polar molecules (electronegativities are the same and opposites attract) -The weakest of all of the discussed interactions, it can disappear if the atoms move too far apart from one another -When many such interactions occur simultaneously, they can be powerful -Allows gecko lizards to climb up walls though the balance between max surface contact with the wall and stiffness of the foot. -The Van der Waals Interactions between foot molecules and wall's surface are so numerous despite their individual weakness, together they support its weight -Discovery has led to development artificial adhesive called Geckskin

Hydrogen Bond

When a hydrogen atom is covalently bonded to an electronegative atom, the hydrogen atom has a partial positive charge that allows it to be attracted to a different electronegative atom nearby. -Expressed as dotted line -In living cells, the electronegative partners are usually oxygen or nitrogen -Although this bond is weak, they can have an additive force. When you have a lot of hydrogen bonding, that can be strong and essential to the immersion properties of water

Polar Covalent Bond

When an atom is bonded to a more electronegative atom, the electrons of the bond are not shared equally. -It is still considered electrically neutral -Regions of partial negative charge (δ- ; delta minus) and partial positive charge ((δ+ ; delta positive) arise from this division of time electrons spend between atoms

Ions

When two atoms are so unequal in their attraction for valence electrons that the more electronegative atom strips an electron completely away from its partner. -This helps to satisfy both atoms since it reduces one atom to a complete lower shell while completing the valence shell of the other atom, but are both no longer electrically balanced -Cation: a positively charged ion because of the loss of an electron (oxidized) -Anion: a negatively charged ion because of the gain of an electron (reduced)

Structural Formula

Where a line represents a single bond (1 pair of electrons) (ej. H-H)

Space-Filling Module

a model of a molecule showing the relative sizes of the atoms and their relative orientations -comes closest to representing the actual shape of the molecule

The chemical behavior of an atom is determined mostly on the number of electrons in its outermost shell (valence shell)

In an atom, the lowest state of potential energy is in the first shell -In an atom with more than 2 electrons, additional electrons must occupy higher shells because the first shell is full -The second shell holds a max of 8 electrons -Valence Electrons: electrons in outermost shell (valence shell) -Atoms with the same number of electrons in their valence shells exhibit similar chemical behaviors -Inert: an atom with a complete valence shell is nonreactive to other atoms (helium, neon and argon are the only 3 elements that have full valence shells) -All other atoms are chemically reactive because they have incomplete valence shells and a desire to reach stability, driving their chemical behavior (octet rule)

Molecule shape is crucial

It determines how biological molecules recognize and respond to one another with specificity. -Size and shape is key to function as there is a relationship between form and function -Biological molecules often bind temporarily through weak interactions, but only if their shapes are complementary -Endorphins (discovered in 1975) are single molecules made by the pituitary gland that bind to receptors, relieving pain. Opiates have shapes similar to endorphins and mimic them by binding to endorphin receptors in the brain. This can elicit a pathway that can have a downstream response which can impart feelings of euphoria -We can then harness our knowledge of molecular shape, geometry, stability, desire to fill valence shells, in order to design or construct chemicals synthetic in nature or modified from those already existing.

CONCEPT 2.1

Matter consists of chemical elements in pure form and in combinations called compounds

Pure Elements

Molecules containing only one element. -Compounds are combinations of 2 or more different elements

Matter is conserved in a chemical reaction

Reactions cannot create or destroy atoms but can only rearrange (redistribute) the electrons among them. -All chemical reactions involve some type of shifting of atoms, from one molecule to another, from an ionic compound, and can result without any change to number or identity of atoms -Photosynthesis is an important examples of this as this process is the foundation of almost all ecosystems for food and oxygen -Input of energy here is sunlight, but we end up with the same number and types of atoms that we had when we started

The cumulative effects of weak interactions is to ____.

Reinforce the 3-dimensional shape of the molecule

Electronegativity

The attraction/affinity of a particular atom for the electrons of a covalent bond. -The more electronegative an atom is, the more strongly it pulls shared electrons toward itself -Electronegativity will increase on the periodic table as we progress from left to right across rows, and decrease down a column -The upper right corner will have the highest electronegativity -Oxygen is one of the most electronegative elements

CONCEPT 2.3

The formation and function of molecules depend on chemical bonding between atoms

Factors Affecting the Rate of Reaction

The greater the concentration of the reactants molecules, the more frequently the will collide with one another and have an opportunity to react and from products. -As products accumulate, collision resulting in the reverse reaction become more frequent -Eventually, the forward and reverse reactions occur at the same rate, and the relative concentrations of products and reactants stop changing -Ej. environmental conditions (temperature), amount of reactants available driving a reaction forwards or backwards, or if there is a substance in use to increase the rate of the reactions/product formation

Chemical Reaction

The making and breaking of chemical bonds, leading to changes in the composition of matter. -In a written equation for a chemical reaction, an arrow indicated the conversion of the starting materials (reactants) to the resulting materials (products) -Coefficients indicate the number of molecules involved -There may be multiple steps that allow us to transition from reactant to final product

Chemical Equilibrium

The point at which the reactions offset one another exactly. -This is a dynamic equilibrium; reactions are still ongoing in both directions, but with no net effect on the concentrations of reactants and products -Equilibrium does not mean that the reactants and products are equal in concentration, but that their concentrations have stabilized at a particular ratio -In some chemical reactions, the equilibrium point may lie so far that the reactions go essentially to completion; virtually all the reactants are converted to products

Covalent Bond

The sharing of a pair of valence electrons by 2 atoms, maintaining neutrality so there is no net charge (expressed as solid line) -Each atom is associated with the shared electrons in order to complete their valence shells -Molecule: two or more atoms held together by a stable association by energy -Single Covalent Bond: sharing of one pair of valence electrons (e.j. H2 bond) -Double Covalent Bond: sharing of two pairs of valence electrons (ej. O2 bond); stronger -The strength of a covalent bond depends on the number of shared electrons -Double bonds will need more energy to break compared to a single bond -Triple Covalent Bond: the strongest formation of a covalent bond, sharing three pairs of valence electrons (e.j. Formation of nitrogen gas)

Atoms either share or transfer their valence electrons usually resulting in the atoms staying close together, held by attractions called chemical bonds

The strongest kinds of chemical bonds are covalent bonds and ionic bonds in dry ionic compounds (ionic bonds in aqueous solutions are weak) -Formation and function of molecules depends on chemical bonding between atoms, and we have a sense of which elements will be more reactive than others based on how complete their valence shell is -Depending on this, that will play a role in what type of chemical bond it will participate in -The degree of electron sharing can vary between atoms and can also impart particular behavior

Atomic Mass

The total mass of an atom (in daltons), close to its mass number. -NOT weight, that is what gravity exerts on the substance -Almost all of an atom's mass is concentrated in its nucleus (electron mass is negligible)

An electron's energy level is correlated with its average distance from the nucleus

They can be found in different electron shells, each with a characteristic average distance and energy level. -If an electron is at the same distance as another electron, they are both found in the same energy level -The first shell is the closest to the nucleus, electrons here have the lowest potential energy; the second shell is further and electrons have more PE. -An electron can move from one shell to another only by absorbing/losing energy equal to the difference of potential energy between its position in the old shell and in the new shell (then moves further from the nucleus) -Light energy can excite an electron to a higher energy level (first step taken by plants for photosynthesis) -When electrons lose energy, they fall back to a shell closer to the nucleus -The lost energy is usually released to the environment as heat

Lewis Dot Structure

electron sharing depicted in an electron distribution diagram, surrounded by dots that represent valence electrons (ej. H : H)

Non-Polar Covalent Bond

in a covalent bond between two atoms of the same element (pure elements), the electrons are shared equally because both have the same electronegativity

All chemical reactions are theoretically reversible

the products of the forward reactions become the reactants for the reverse reaction (depicted as 2 opposite-headed arrows)