Biology Notes Basics of Chem Ch. 2

Matter

• anything that takes up space and has mass

• made of elements

Elements vs. Compound

• a substance that cannot be broken down to other substances by chemical reactions

• compound is a substance that consists of two or more different elements combined in a fixed ratio

Essential elemnts

• elements an organism needs to live a healthy life and reproduce

• humans need about 25, plants need about 17

• Four elements make up 96% of the living matter (O, C, H, N)

• Ca, P, K, S make up about the remaining 4% or so of an organisms mass

Trace elements

• Required by organisms in only minute quantities

• Some like Fe are needed by all forms of life, others only by certain species

Atom

the smallest unit of matter that still retains the properties of an element

• they are so small that it would take a million of them to stretch across a period

Subatomic Particles

• neutrons, protons, and electrons

• Protons and electrons are electrically charged

• Protons give the nucleus a positive charge

• The negatively charged electrons form a cloud around the nucleus

How do we measure subatomic particles

• we use a unit of measurement called the dalton aka atomic mass unity amu

• the neutron and proton are almost identical in mass each about 1.7×10^-24 about 1 dalton

Atomic number vs. Mass number vs. Atomic mass

• AN: number of protons (other wise indicated an atom is neutral)

• AM: the weighted average of the masses of all naturally occurring isotopes of an element, measured in atomic mass units

• MN: the total number of protons and neutrons int he nucleus of an atom

Isotope

• same element different number of neutrons

• a radioactive isotope is one in which the nucleus decays spontaneously, giving off particles and energy (often used as diagnostic tools in medicine as they can be used as tracers to track atoms during metabolism, the chemical processes of an organism)

  • While helpful they can also be hazardous because they damage cellular molecules, the severity of this damage depends on the type and amount of radiation an organism absorbs.

Half-life

• When a “parent” isotope decays into its “daughter” isotope at a fixed rate, expressed as the half-life of the isotope. The time it takes for 50% of the parent isotope to decay

  • Radiometric dating: scientists measure the ratio of different isotopes and calculate how many half lives (in years) have passed since an organism was fossilized or a rock was formed.

Energy

• defined as the capacity to cause change, for instance, by doing work.

• potential energy is the energy that matter possesses because of its location or structure (it takes work to move a given electron farther away from the nucleus, so the more distant an electron is from the nucleus, the greater its PE — it depends on energy level)

Electron shell

• an electron’s energy level is correlated with its average distance from the nucleus, the first shell is closest to the nucleus, and electrons in this shell have the lowest potential energy.

• Electrons in the first shell have the lowest potential energy. Electrons in the second shell have more energy, and electrons in the third shell even more energy

• An electron can move from one shell to another, but only by absorbing or losing an amount of energy equal to the difference in potential energy between its position in the old shell and that in the new shell. When an electron absorbs energy, it moves to a shell farther out from the nucleus.

• Lost energy is usually released to the environment as visible light or ultraviolet radiation

Valence electrons

electrons on the outmost electron shell called the valence shell

• an electron with a full valence shell is non-reactive, that is, it will not interact readily with other atoms (aka inert)

• The three-dimensional space where an electron is found 90% of the time is called an orbital

Orbital

• The three-dimensional space where an electron is found 90% of the time is called an orbital

• You can think of an orbital as a component of an electron shell. The first electron shell has only one spherical s orbital (called 1s), but the second shell has four orbitals: one large spherical s orbital (called 2s) and three dumbbell-shaped p orbitals (called 2p orbitals). (The third shell and other higher electron shells also have s and p orbitals, as well as orbitals of more complex shapes.)

• No more than 2 electrons can occupy a single orbital. The first electron shell can therefore accommodate up to 2 electrons in its s orbital. The lone electron of a hydrogen atom occupies the 1s orbital, as do the 2 electrons of a helium atom. The four orbitals of the second electron shell can hold up to 8 electrons, 2 in each orbital. Electrons in each of the four orbitals in the second shell have nearly the same energy, but they move in different volumes of space.

What are the strongest types of bonds?

• The strongest kinds of chemical bonds are covalent bonds in molecules and ionic bonds in dry ionic compounds. (Ionic bonds in aqueous, or water-based, solutions are weak interactions, as we will see later.)

Covalent Bond

• the sharing of a pair of valence electrons by two atoms

• Two or more atoms held together by covalent bonds constitute a molecule

Electronegativity

• the attraction of a particular atom for the elctrons of a covalent bond

Nonpolar vs. Polar

A nonpolar bond features an equal or nearly equal sharing of electrons between two atoms, while a polar bond involves an unequal sharing of electrons, creating a partial positive and a partial negative charge on the respective atoms

Ionic Bonds

chemical bonds formed by the electrostatic attraction between oppositely charged ions, resulting from the complete transfer of one or more valence electrons from one atom to another

• compounds formed by ionic bonds are called ionic compounds or salts

Weak chemical interactions

• Weaker interactions within and between molecules are also

  indispensable, contributing greatly to the emergent properties of life.

• Many large biological molecules are held in their functional form by weak interactions. In addition, when two molecules in the cell make contact, they may adhere temporarily by weak interactions.

• The reversibility of weak interactions can be an advantage: Two molecules can come together, affect one another in some way, and then separate.

• Ex: ionic bonds, van der waals bonds, hydrogen bonds

• Weak chemical bonds reinforce shapes of large molecules and help molecules adhere to each other

Hydrogen Bonds

Are weak attractions that form between a hydrogen atom covalently bonded to an electronegative atom (like oxygen or nitrogen) and another electronegative atom nearby. They are crucial in biology, stabilizing structures like DNA’s double helix and protein folding.

Usually between N and O in living organisms

Van Der Waals Bonds

Weak, temporary attractions that occur when electrons move around atoms, creating small, momentary charges. When molecules are very close, these slight charges attract, helping stabilize interactions between nonpolar molecules, such as in lipid membranes.

Applications of Radioactive Isotopes

• Dating fossils

• Tracing atoms through metabolic processes

• Diagnosing medical disorders

Molecular Shape and Function

• A molecule’s shape is usually very important to its function

• A molecules shape is determined by the positions of its atoms’ valence orbitals

• In a covalent bond the s & p orbitals may hybridize, creating specific molecular shapes

  • Biological molecules recognize and interact with each other with a specificity based on molecular shape (ex: morphine could be used to replace a natural endorphin because it is around the same size and shape so it fits into the receptor.

Chemical Reaction Technicalities

• Eventually the rate of formation of products is the same as the rate of breakdown of products (formation of reactants), and the systems at chemical equilibrium (no net change in the concentrations of reactants and products)

• Some chemical reactions go to competition; that is, all the reactants are converted to products

• All chemical reactions are reversible