4IP Atoms, Molecules, and Water - The Basics of Life

Atoms, Molecules, and Water: The Basics of Life

Lecture Goals:

• Gain an understanding of what atoms are and how they form molecules.
• Learn about the two types of bonds atoms form
• Examine the importance and role of water in biological function
• Examine the four major groups of biological molecules

Course Competencies: 4. Compare and contrast the most stable subatomic particles and describe how they affect the chemical characteristics of matter. (II) 5. Describe the relationship between atoms and molecules and the importance of chemical bonds to atomic stability, molecular structure and chemical characteristics. (II) 6. Describe the relationships between the structure and functions of the four major kinds of organic macromolecules found in living things. (II)

Presentation Links

Day 1 Content

Atoms and Elements

Periodic Table

Molecules and Bonds

Day 2 Content

Properties of Water

pH and buffers

Organic Molecules

Atoms and Elements

• An atom:
• Is a single unit of a single element.

• The basic building blocks of matter.

• An element:
• Is any substance that cannot be broken down into simpler substances by chemical processes (note: nuclear reactions are not chemical reactions).
• Determined by the number of protons in an atom.

Electron

Proton

Neutron

Electron Shell

Parts of an Atom

Nucleus

• The nucleus of an atom is located at the center of an atom. It is composed of two parts:
• Proton:
• Positive charged components.
• The number of protons determines what type of element the atom is.
• The atomic number is the number of protons in that element.

Electron

Proton

Neutron

Electron Shell

Parts of an Atom

Protons and the Periodic Table

Atomic Number: This is the number of protons. Defines what element it is.

Symbol: Every element has a letter symbol. These symbols are used in chemical equations and molecular formulas. For example, CO2 is one carbon atom and two oxygen atoms.

Element name

Carbon

12.0107

Atomic Mass: The average weight of an atom due to protons and neutrons in the nucleus. The number of neutrons vary, so the atomic mass isn't going to be a "whole" number.

Parts of an Atom

Nucleus

• The nucleus of an atom is located at the center of an atom. It is composed of two parts:

• Neutron:
• Neutrally charge components.
• Their presence stabilizes the nucleus, because too many positively charged protons touching will repel each other, making it unstable.
• Neutrons prevent that by giving protons "space" from each other.
• The number of neutrons vary.

Electron

Proton

Neutron

Electron Shell

Parts of an Atom

Electron Shell

• The electron shell is the region surrounding the nucleus that contains electons.
• Electron:
• Negatively charged components.
• These are the components that do the "work" of an atom.
• They form bond and are are a source of energy for chemicals.

Electron

Proton

Neutron

Electron Shell

Check your notes

Check your notes, can you:

• identify the parts of an atom
• determine how many protons and electrons an atom has

00:30

Parts of an Atom

Electron Shell

• Electron shells are different shaped "clouds" where the electrons move and exist.
• We refer to these as orbitals and represent them as rings round the nucleus for easier visualization.
• Each level of shell can hold a different number of electrons.

Parts of an Atom

Electron Shell

• The first shell is the one closest to the nucleus. It holds 2. The second is 8, the third is 18, the fourth is 32... It continues to increase as you go further out.
• For this course know they get bigger, and 8 is the important number most of the time.
• Upper division chemistry courses will go into detail of how orbitals work.

Parts of an Atom

Electron Shell

• Electrons located on the outermost orbital are call valence electrons.

• A full orbital (has 8 valence electrons) is considered a inert atom. They are located on the right-most column on the periodic table.

Parts of an Atom

Electron Shell

• Orbitals that aren't full (lack all 8 electrons) are reactive.

• They interact with other atoms that don't have full orbitals.

• Interacting with other atoms will increase stability by "filling" their outter orbital.

Parts of an Atom

Organization of the Periodic Table

Columns show the number of valence electrons.

Note: Metals in the center of the periodic are complicated with their valence electrons. Chemistry courses will focus on their electron arrangement.

Test your Knowledge

Parts of an Atom

Valence Electrons and Reactivity of Elements

• An atoms number of valence electrons determines how they interact with other electrons.
• Noble gases: inert
• Halogens: "Salt Formers". These are very reactive, especially with the first column of metals. When combined the two form a salt. Tend to "steal" electrons to fill their orbital.
• Metals: Reactivity varies. Some easily "lose" electrons while others easily "share" electrons to complete their orbital.
• The "sharing", "stealing", or "losing" of electrons determines the types of bonds formed.

Check your notes

Check your notes, can you:

• identify the parts of an atom
• determine how many valence electrons an atom has
• determine how many open bond "slots" an atom has

00:30

Atomic Bonds

Types of Molecules

When atoms bond they are called molecules. If they are made of two or more different types of elements they are call compounds. Compounds come in two forms:

• Organic: Any compound that contains carbon and hydrogen

• Inorganic: Any compound that doesn't contain both carbon and hydrogen

Atomic Bonds

Types of Bonds: Ionic Bond

Ionic Bonds: bond between two atoms formed from the electrostatic attraction between oppositely charged ions How that works:This occurs when one atom "takes" the electron from another atom.

• The atom that "took" the electron becomes negatively charged because it has more electrons then protons.
• The atom that "lost" the electron becomes positively charged because it has more protons then electrons.
• They attract to eachother like magnets due to the difference in charge.
• Atoms that have either "taken" or "lost" an electron are call ions.

Atomic Bonds

Types of Bonds: Ionic Bond

Example: Salts Salts are a variety of molecules. Sodium chloride (table salt) is one type of salt. Sodium chloride is made from one sodium atom and one chlorine atom. Notice they are on opposite ends of the periodic table. Sodium readily loses it's one valence electron. This makes sodium stable. Chlorine readily takes an electron, bringing its valence electrons to 8. This makes chlorine stable. The two attract eachother through an ionic bond, making sodium chloride. You can safely eat it because both atoms are stable (sodium no longer catches fire and the chloride is no longer toxic).

Atomic Bonds

Types of Bonds: Covalent Bond

Covalent Bonds: bond between two atoms formed from the sharing of one or more electrons. How that works:This occurs when two nonmetal elements have enough valence electrons where losing and gaining doesn't happen (they aren't close to being stable).

• Two atoms will share their outermost orbital.
• All valence electrons move between both atoms.
• This increases both atoms stability because both outer orbitals behave as though "full".
• If two atoms don't have enough electrons to "fill", additional atoms could bond, forming larger molecules.

Atomic Bonds

Types of Bonds: Covalent Bond

Example: Carbon Dioxide Carbon dioxide is formed from one carbon and two oxygen. Carbon has four open valence electron spots and oxygen has two open valence electron spots. They form a molecule with each oxygen forming two bonds with the carbon. Each oxygen shares two electrons with the carbon, "filling" all of their outer orbitals.

O=C=O

Atomic Bonds

Types of Bonds: Covalent Bond

Atoms are different sizes, so sharing isn't always equal. This is also true for atoms with more electrons in their outer orbital to start (this is called having higher electronegativity). This leads to two types of covalent bonds: nonpolar and polar.

• Nonpolar bonds/molecules
• This is equal sharing of electrons.
• The molecule is neutrally charge because the negatively charged electron is shared equally (doesn't spend more time in one spot or another).
• This is the case when atoms are similar in size and/or electronegativity.
• For instance, carbon-hydrogen bonds

Methane molecule CH4 (Source: wikipedia.org)

Atomic Bonds

Types of Bonds: Covalent Bond

• Polar bonds/molecules
• This is unequal sharing of electrons. One atom (the one with higher electronegativity) has the electron in its orbital more than the other. This is nicknamed an "electron hog".
• This causes a charge within the molecule, where some parts of it are positively charged and parts are negatively charged.
• This happens with molecules that are very different in size and or electronegativity.
• Example: hydrogen and almost every other atom (not carbon)

Water molecule (Source: chemistrytalk.org)

Hydrogen Bonds

• Hydrogen is a very small atom (one proton and one electron).
• When it forms covalent bonds, the other atom will have its electron most of the time.
• This will cause the part of the molecule with hydrogen to become positively charged and the part with the other atom to be negatively charged.
• This is an important "bond" for living things because it is what gives water many of its properties.

Water molecule (Source: chemistrytalk.org)

Check your notes

Check your notes, can you define and identify:

• ionic bonds
• covalent bonds
• hydrogen bonds

00:30

Test your Knowledge

Kahoot! live game will be played during class. Game will become available for replay after class.

Hydrogen Bonds (recall)

• Hydrogen is a very small atom (one proton and one electron).
• When it forms covalent bonds the other atom will have it's electron most of the time.
• This will cause the part of the molecule with hydrogen to become positively charged and the part with the other atom to be negatively charged.
• This is an important "bond" for living things because it is what gives water many of its properties, especially its ability to "stick" to itself, interact with polar (hydrophilic) molecules, and more.

Water molecule (Source: chemistrytalk.org)

Water and Its Properties

Capillary action in plants (Source: Wikimedia Commons)

Meniscus (Source: wikipedia.org)

• Stabilizes temperature
• Cohesive (water sticks to water)
• Adhesive (water sticks to other substances, example: capillary action)
• Requires high energy to change out of liquid state
• Solid state is less dense then liquid state
• Hydrogen bonds with one of the highest electronegative atoms (oxygen)
• Acts as a solvent that dissolves polar and ionic compounds

Water and Its Properties

The Penny Game

• Supplies needed
• A penny per person
• One disposible pippette
• A cup of water
• Instructions
• Every person slowly adds drops of water to the tails side of the penny.
• Keep track of how many drops are added before it overflows. Don't count the overflow drop.

Check your notes

Check your notes, can you:

• explain why water is "sticky"
• define adhesion and cohesion

00:30

Water and Its Properties

Water and pH

• pH can be thought of as "potential of hydrogen"
• Tells us how acidic or basic something is
• Uses a logarithmic scale
• This means each number increment is 10 times more than the previous. Example: pH of 2 is 10 times more acidic than a pH of 3.
• It is a measure of how many H+ (hydrogen ions; essentially protons) are present versus OH- (hydroxide ions)

Water and Its Properties

Water and pH

• H+ concentration VS OH- concentration
• The concentration of the H+ ion can be solved using this equation [H+]= 1.0 *10-pH
• The concentration of the OH- ion can be solved using this equation [OH-]= 1.0 *10-pH+14
• Acids: H+ donors
• Adds to the amount of H+ ions when in a solution
• Acidic solutions below 7 on the pH scale -> more H+ ions
• Bases: H+ acceptors

• Lower the amount of H+ ions when in a solution
• Basic (also called alkaline) solutions are above a 7 on the pH scale (max 14) -> fewer H+, more OH-

Water and Its Properties

Water and pH

• Neutral
• Is a 7 on the pH scale
• Is the pH of pure water
• Even though water is composed of covalent bonds they can also become temporarily ionic bonds because oxygen is so electronegative. That means water is essentially composed of an equal amount of H+ and OH- ions
• This makes water an excellent buffer in many cases
• Buffer: a solution that minimizes pH change, even with dilution

Check your notes

Check your notes, can you:

• define what an acid is
• define what a base is
• explain the role of H+ and OH- in pH

01:30

Other Important Compounds

• Organic Compound
• Contain both carbon and hydrogen
• "Building blocks of life"
• Comes in four main types
• Carbohydrates
• Proteins
• Nucleic Acids
• Lipids

Note: We will be looking at each of these in detail over the next several weeks. The next slides serve as an overview.

Carbohydrates

• Chains of simple sugars, such as
• glucose
• fructose
• Most abundant organic molecules
• Essential for all living things
• Energy access and storage
• Construction of cell walls (plants)
• Immune system response (some animals)

Organic Compounds: Proteins

• Chains of simple amino acids
• 20 different amino acids
• Essential for all living things:
• Hormones
• Homeostatis
• Enzymes
• Body structure
• Cell structure

Nucleic Acids

Thymine

Adenine

Guanine

Cytosine

T G G C A G T A

A C C G T C A T

• Chains of nucleotides
• Nucleotide:
• phosphate group
• sugar
• one of four nucleotide bases
• DNA – deoxyribonucleic acid (genetic material)

Lipids

• Fats and Oils
• Organic compounds that are not water soluble
• Essential for all life:
• Cell membranes (contains the organelles and separates outside from inside a cell)
• Protection from water loss

Organic Compounds and Foods

Try this:

• Select a simple favorite meal
• Look up the components
• What parts are carbohydrates, proteins, nucleic acid, and lipids?

Check your notes

Check your notes, can you describe a:

• carbohydrate
• protein
• lipid
• nucleic acid

01:30

Test your Knowledge

Kahoot! live game will be played during class. Game will become available for replay after class.