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Chapter 2: Chemistry
2.1 Matter, Elements, Atoms, Atomic Structure, Ions, and Isotopes
Matter
Life is made up of matter.
Matter occupies space and has mass.
All matter is composed of elements, substances that cannot be broken down or changed chemically into other substances.
Each element is made of atoms.
There are a total of 118 of them; each is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties.
Atom
The smallest unit of an element that has the properties of that element.
Matter is composed of these.
Protons and neutrons are found in the nucleus, while electrons are found in the space around them.
Protons have a positive charge (+).
Neutrons have a neutral charge (no charge).
Electrons have a negative charge (-).
Atoms are electrically neutral
number of protons = number of electrons (balance each other out)
Atoms vs. Ions
Atoms can vary in the number of neutrons or electrons.
Isotopes are atoms of the same element that have different numbers of neutrons.
Isotopes have important uses.
An ion is an atom with a charge.
The Periodic Table of Elements
The periodic table provides information about the properties of elements.
The elements are arranged in a way that shows how the electrons in each element are organized and provide details about how atoms will react with each other to form molecules.
Atomic Mass vs. Atomic Number
Atomic Mass = Number of protons and number of neutrons
Atomic number = # of Protons; defines atom
2.2 The Octet Rule, Chemical Bonding and Properties of Water
The Octet rule
A general rule that allows us to predict how atoms will form chemical bonds to make molecules
When atoms have 8 electrons in their highest energy level, they are said to have an octet.
Works well for Carbon, Nitrogen, Oxygen, Fluorine, Sodium, and Magnesium
Example: Hydrogen and Chlorine
Both hydrogen and chlorine are nonmetals, which means they share electrons and form a covalent bond.
Chlorine has 7 valence electrons in its highest energy level (outer shell); To obtain an octet, it needs an additional electron.
Hydrogen has one valence electron (exception to the Octet Rule) and only needs two valence electrons to have a full outer shell.
A covalent bond is formed when the hydrogen comes together with the chlorine and forms a chemical bond by sharing valence electrons; Hydrogen ends up with 2 valence electrons while chlorine ends up with eight.
The octet rule is different for ionic compounds.
Example: Sodium and Chlorine
Sodium is a metal while chlorine is a non-metal, making it an ionic compound (metal + non-metal).
Ionic compounds don’t share valence electrons, they transfer them.
The sodium is going to lose its valence electron to the chlorine, causing it to lose its outer shell.
Since sodium loses an electron, it becomes positive. Chlorine becomes negative since it gains an electron.
*Atoms bond to minimize energy and become more stable.
Chemical Bonds
All bonds represent an emergent property of atoms.
If an atom doesn’t have a filled valence shell of electrons, it can either share electrons with another atom or transfer them.
It either gains enough electrons to fill its outermost shell, or shed enough to empty its outermost shell, leaving a complete valence shell underneath at the next lower energy level.
The interactions between atoms that take place as a result are called chemical bonds.
One thing that determines what kind of bond an atom will have is its electronegativity (the degree to which an atom attracts electrons and holds onto them.
If two atoms come together and they have similar electronegativities, they will share an electron between the two of them, especially when atoms are identical.
Nonpolar Covalent Bond
This bond is created when atoms with the same electronegativity share their electrons.
Example: Two oxygen atoms (O2)
Oxygen has 6 valence electrons on its outermost shell.
Neither one has a complete valence shell of electrons, so they share two electrons and form a double bond.
Polar Covalent Bond
This bond is created when atoms with differences in electronegativity share their electrons.
The electrons will spend a greater amount of time next to the atom with a higher electronegativity
Example: Water molecule (Hydrogen and Oxygen)
Oxygen has a higher electronegativity than hydrogen, so electrons will spend a greater part of their time closer to the oxygen atom rather than to the hydrogen atom.
This results in a water molecule having a partial negative charge around the oxygen atom, and a partial positive charge around the hydrogen atoms.
Ions
If the electronegativities of atoms are different enough, one atom will donate one or more electrons to the more electronegative atom, resulting in two charged species called ions.
The atom that donates one or more electrons is called a cation, becoming positively (+) charged.
The atom that takes on electrons is called an anion, becoming negatively (-) charged.
Ionic Bond
As a result of becoming oppositely charged, cations and anions are attracted to each other through electrostatic attraction, forming an ionic bond.
In water, ionic bonds quickly dissociate.
Ionic bonds are considered weaker than most covalent bonds.
Weak vs. Strong Bonds
It is very important that we have the capability to make bonds of varying strengths.
When building structures, you want to have very strong bonds.
There are other cases where it makes more sense to have weak bonds, such as for reversible interactions.
Example: When signaling molecules (such as hormones or neurotransmitters) bind to a receptor, you want them to have a weak bond so the signaling molecule won’t get stuck there and block the receptor.
We want it to bind reversibly– to bind, send the signal, and then fall off.
Hydrogen Bond
The next weaker bond after the ionic bond.
Example: Water
There are hydrogen bonds that hold different water molecules together, which makes water so cohesive
Why does water form drops that bunch up instead of lying flat?
The hydrogen bond is the very weak attraction between one hydrogen atom that is already covalently bonded to something else (so it has a partial positive charge) and something else partially negative charge (usually an oxygen, nitrogen, or fluorine atom that is bonded to something else.)
In the case of the water, you have the hydrogen from one water molecule attracted to the oxygen in a different water molecule.
Rather than a solid line joining the two atoms (such as in covalent bonds) it’s a dotted line, reminding us that this is a very weak interaction.
Van Der Waals Interactions
Weak attractions or interactions between molecules.
They occur between polar, covalently bound, atoms in different molecules.
These weak attractions are caused by temporary partial charges formed when electrons move around a nucleus; this is important in biological systems.
Properties of Water
Polarity:
The hydrogen and oxygen atoms within water molecules form polar covalent bonds; the shared electrons spend more time around the oxygen atom compared to the hydrogen atom.
There is no overall charge to a water molecule, but there is a slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom.
The slightly positive hydrogen atoms repel each other.
Each water molecule attracts other water molecules due to its positive and negative charges.
Water also attracts other polar molecules (such as sugars) and forms hydrogen bonds.
When a substance readily forms hydrogen bonds with water, it can dissolve in water and is referred to as hydrophilic (“water-loving”).
When a substance (such as oils and fats) does not readily form hydrogen bonds with water, this nonpolar compound is hydrophobic (“water-fearing”) and will not dissolve in water.
Stabilizes Temperature
The hydrogen bonds in water allow it to absorb and release heat energy more slowly than many other substances.
Water absorbs a good amount of energy before its temperature rises
Increased energy disrupts the hydrogen bonds between water molecules.
Since these bonds are created and disrupted quickly, water absorbs an increase in energy and temperature changes only minimally.
Water moderates temperature changes within organisms and in their environments.
Since hydrogen bonds become unstable when energy input continues, it results in the release of individual water molecules at the surface of the liquid (such as a body of water, the leaves of a plant, or the skin of an organism) in a process called evaporation.
Example: Evaporation of sweat, which is 90 percent water, allows for cooling of an organism, because breaking hydrogen bonds requires an input of energy and takes heat away from the body.
As molecular motion decreases and temperatures drop, less energy is present to break the hydrogen bonds between water molecules.
These bonds remain intact and begin to form rigid, lattice-like structures known as ice.
Example: Ice is less dense than liquid water, which allows protection to marine life from freezing in lakes, ponds, and oceans.
Excellent Solvent
Since water is polar, ionic compounds and polar molecules can readily dissolve in it; this makes water a solvent (a substance capable of dissolving another substance).
The charged particles will form hydrogen bonds with a surrounding layer of water molecules, known as a sphere of hydration that keeps the particles separated in water.
Example: When table salt is mixed in water, spheres of hydration form around the ions.
Cohesive
Before water overflows in a glass, it forms a dome-like shape above the rim of the glass, which is caused by cohesion.
In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together at the liquid-air (gas) interface, although there is no more room in the glass.
Cohesion gives rise to surface tension, the capacity of a substance to withstand rupture when placed under tension or stress.
Example: A small piece of paper is able to float on top of a water droplet since cohesion and surface tension keep the water molecules intact and the item floating on top.
These cohesive forces are also related to the water’s property of adhesion, or the attraction between water molecules and other molecules.
Example: Water is able to “climb” up a straw placed in a glass of water since the water molecules are attracted to the straw and adhere to it.
Both cohesion and adhesion are important for sustaining life since they allow for water to be able to flow up from the roots to the tops of plants and feed them.
2.3 pH, Acids, and Bases
Acids, bases, salts, and pH level are inorganic substances that break up or dissociate in solution, or water, to form charged particles or ions.
Acids
Any substance that when added to an aqueous solution, or water, will release a hydrogen ion or increase the concentration of hydrogen ions.
How strong an acid is depends on how many hydrogen ions are produced.
Example: Hydrochloric acid (HCl), which is a hydrogen atom bonded to a chlorine atom, will dissociate or break down into negative chlorine ions and positive hydrogen ions when added to a solution or water.
Hydrochloric acid is considered a strong acid since it completely dissociates in water.
Bases
These are essentially the opposites of acids, in that they shift the hydrogen ion-hydroxide ion balance in favor of the negative hydroxide ion.
They increase the concentration of hydroxide ions when added to a solution.
This can be done by increasing the number of OH- (hydroxide) ions, or decreasing numbers of H+ and H3O+ (hydrogen and hydronium) ions.
Example: Sodium hydroxide (NaOH) will break down or dissociate into positive Na ions and negative OH ions; this makes it a strong base.
Bases can also be strong or weak depending on how well they break apart.
pH Level
This is an abbreviation for the phrase “power of hydrogen”.
The pH scale measures the concentration of hydrogen ions of a solution, or it measures how acidic or basic a substance is.
As the amount of positive hydrogen ions increases, the pH goes down, causing the solution to become more acidic.
As the amount of positive hydrogen ions decreases, the pH goes up, causing the solution to become more basic.
On a pH scale, a pH of 7 means the solution is neutral (number of positive hydrogen ions = number of negative hydroxide ions).
A pH of less than 7 means the solution is more acidic (more hydrogen ions than hydroxide ions).
A pH of greater than 7 means the solution is more basic (more hydroxide ions than hydrogen ions).
Example: On the scale, hydrochloric acid (produced in the stomach) is at the most acidic end having a pH of zero.
Salts
A chemical compound formed from the reaction of an acid with a base.
Example: Hydrochloric acid (HCl) can interact with sodium hydroxide, a base, and form sodium chloride (NaCl) and water (H2O).
Salts break apart or dissociate in a solution of water to form positive and negative ions, making them important for certain body functions.
Some salts that are important in the body are sodium chloride (NaCl) and potassium chloride (KCl).
These salts are often most effective as charged ions or atoms in solution.
2.4 Molecules of Life (Carbohydrates)
Carbohydrates
Simple sugars and polysaccharides.
Their function in cells is to provide a ready source of energy which is released when bonds are broken.
The monomer of a carbohydrate is called a monosaccharide.
Disaccharides
These form when two monosaccharides undergo a dehydration synthesis reaction (an H2O molecule is lost to form a bond).
The covalent bond that holds the two monosaccharides is a glycosidic bond.
Polysaccharides
A long chain of monosaccharides linked by covalent bonds.
The chain may be branched or unbranched, and it may contain different types of monosaccharides.
They may be very large molecules.
Example: Starch, glycogen, cellulose, and chitin are all polysaccharides.
Plants store sugars as starch, while animals store sugars as glycogen.
Cellulose is the structural component of plant cell walls, and chitin is found in fungi cell walls.
2.5 Molecules of Life (Proteins)
Proteins
These produce many essential compounds like hormones and enzymes in the body.
The basic unit of a protein is called an amino acid.
Two amino acids are held together by peptide bonds.
Proteins are sensitive to factors, such as pH and temperatures, and can easily become denatured (deformed).
Protein Structure
The shape of a protein is critical to its function.
There are four levels of protein structure:
Primary: The unique sequence and number of amino acids in a polypeptide chain.
Secondary: Is of two main types, alpha helix and beta pleated sheets; Hydrogen bonding of the peptide backbone causes the amino acids to fold into a repeating pattern.
Tertiary: This is the unique three-dimensional structure of a polypeptide; caused by chemical interactions between various amino acids and regions of the polypeptide.
Quaternary: This protein structure consists of more than one amino acid chain.
When proteins don’t fold properly, it can lead to serious health problems and diseases.
Denaturation
When proteins get exposed to temperature, pH, or chemicals.
The protein structure may change and lose its shape.
Denaturation is often reversible since the primary structure is preserved if the denaturing agent is removed, which allows the protein to resume its function.
Example: When you fry or boil an egg, the protein within the egg white denatures and goes from transparent to white color when cooked.
2.6 Molecules of Life (Lipids)
Lipids
Lipids are hydrophobic and energy-rich.
This class of organic molecules includes triglycerides (fats) and sterols.
Triglyceride is a fat molecule consisting of a glycerol and 3 FA tails.
Important source of store energy.
Lipids are also the building blocks of many hormones and are an important constituent of the plasma membrane.
Lipids include fats, oils, waxes, phospholipids, and steroids.
Saturated Fatty Acids
Solid at room temperature
Animal in origin (ex. Butter, lard)
Have a single bond between their carbon atoms
Unsaturated Fatty Acids
Liquid at room temperature
Plant origin (ex. Olive oil, grapeseed oil)
Have a double bond between their carbon atoms
Phospholipids
A fat molecule that has two fatty acid tails, a glycerol molecule and a phosphate.
Our cell membranes are made up of phospholipids.
A phospholipid has both hydrophobic and hydrophilic regions.
Important: our cell membranes/plasma membranes are composed of phospholipid bilayer, lipids, proteins, and carbohydrates.
Steroids
Steroids have a ring structure.
Although they do not resemble other lipids, they are grouped with them because they are also hydrophobic.
All steroids have four, linked carbon rings (ex. cholesterol).
2.7 Molecules of Life (Nucleic Acids)
Nucleic Acids
These molecules contain genetic information.
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
Monomers of a nucleic acid consist of a 5’ carbon sugar, a nitrogen base and a phosphate.
Two Types of Nitrogen Bases
Purines: Adenine and guanine
Consist of two carbon-nitrogen rings.
Pyrimidines: cytosine, thymine, and uracil
Consist of one carbon-nitrogen ring.
Deoxyribonucleic acid (DNA)
Double helix, with a sugar phosphate backbone and hydrogen bonds between the bases that hold the two strands together.
Sugar is deoxy-ribose.
Genetic material of all organisms.
The nitrogen bases are adenine, thymine, guanine, and cytosine.
Adenine always bonds with thymine, while guanine always bonds with cytosine.
DNA is located in the nucleus.
Ribonucleic Acid (RNA)
Single stranded molecule that codes for protein.
Sugar is ribose.
Genetic material in some viruses.
The nitrogen bases are adenine, cytosine, guanine, and uracil; uracil replaces thymine.