Unit 2.1 Intro to Chem for Biologists

Define matter

Anything that has mass and takes up space

What is ‘matter’ made up of?

Atoms

What are atoms made up of? What are their 3 names?

Made up of subatomic particles; Neutrons, protons, and electrons

Define Neutron, where its location, and its charge

A subatomic particle; found in the nucleus of the atom; neutrally charge

Define proton, its location, and its charge

A subatomic particle; found in the nucleus of the atom; positively charged

Define electron, its location, and its charge

A subatomic particle; found orbiting around the nucleus of an atom; negatively charged

Define ion

An atom that carries a positive or negative electric charge as a result of having lost or gained 1 or more electrons

Do atoms have a charge? Why or why not?

Atoms do not have a net electric charge. They are electrically neutral because their number of protons (+) is equal to the number of electrons (-) so they cancel each other out

What are 2 similarities between atoms and ions?

They both have protons and neutrons inside their nucleus and have electrons outside orbiting the nucleus

What is the main difference between atoms and ions?

Atoms have no overall charge while ions are electrically charged

What do ions want to achieve by either gaining or losing electrons?

Stability through an octet configuration

What is an anion and what makes it so?

A negatively charged ion that has more electrons (-) than protons (+)

What is a cation and what makes it so?

A positively charged ion that has more protons (+) than electrons (-)

Lithium has an atomic number of 3. Draw its Bohr Diagram

Chlorine has an atomic number of 17. Draw its Lewis diagram

What is different about how Lewis Diagrams are drawn compared to Bohr Diagrams?

Lewis diagrams only show the valence electrons

How do we find the number of neutrons for an element?

Atomic mass - atomic number

What is a good simile for electrons?

Electrons move in orbits around the nucleus like planets revolving around the sun

What is the proper name for electrons orbits?

Electron shells

Can electrons exist between orbits?

No

Can electrons move up or down from one orbit to another?

Yes

Is there a maximum number of electrons that can exist on different shells? What is that number?

Yes. First shell only holds 2. Subsequent shells can hold 8

When are electrons most stable? What does this mean for them?

Most stable at lower energy when they are closer to the nucleus. Means electrons are always trying to occupy the lowest orbits they can find

How do electrons fill their shells? (direction)

Start from the nucleus and work outwards

In the short written form of Bohr diagrams, how would you write it for Carbon?

C)e2^-)4e^-

Define valence electron

The number of electrons in the outermost (last) shell

What is important about valence electrons between atoms?

Electrons in the outer shell will determine how the element will react with other atoms to form chemical bonds in biological molecules

What happens when 8 valence electrons are achieved?

The atom becomes optimally stable and inert- meaning it does not want to take part in chemical reactions

When looking at a Lewis diagram, what is easy to see and why is this useful?

Can see only the valence electrons and thus make it easier to see how they might reaction with other atoms

What are the 10 chemical families on the periodic table?

Alkali metals, alkali earth metals, transition metals, post-transition metals, metalloids, reactive nonmetals, halogens, noble gases, lanthanides, and actinides

Which family are the most chemically stable elements? Why?

Noble gases; these elements naturally possess their max number of valence electrons. They are extremely non-reactive and tend not to form compounds

What is the octet rule? Why is it great for atoms?

Having 8 electrons in the outer shell; atoms bond to achieve the same configuration as noble gases and become chemically stable. Atoms bond to gain/lose/share electrons in their outer shell so they will end up with 8 valence electrons

What is the main thing to remember about ions versus atoms?

An ion is an atom in which the total number of electrons (-) is not equal to the total number of protons (+)

What is the quick definition of anion?

An atom that has gained electrons (-) to become stable and is now negatively charged

What is the quick definition of cation?

An atom that has last lost electrons (-) and is now positively charged

What is chemical bonding and why is it important?

When atoms join up with other atoms; only way life is possible

What are the 2 categories of chemical bonding?

Intramolecular bonds and intermolecular bonds

Where do intramolecular bonds occur?

Bonds within molecules. Atoms bond resulting in a compound called a molecule. Intramolecular bonds occur within the molecule

What are the 3 types of intramolecular bonds?

• Ionic bonds

• Covalent bonds

• Polar covalent bonds

Define ionic bonds

Bonds that form when one atom transfers electrons to another atom resulting in both atoms ending up with a stable electron arrangement in their outer shell

Between which two families do ionic bonds usually form between?

Metals and non-metals

What kind of charges “attract” each other to form ionic bonds?

Opposite charges, + and -

Draw the Lewis diagram after Potassium and Fluorine form an ionic bond

What is a covalent bond?

When two or more non-metals share one or more pairs of electrons so that both end up with a stable electron arrangement in their outer orbit

Draw the Lewis Diagram for a covalent bond between two Hydrogen atoms

Define polar covalent bond

Formed when there is an unequal sharing of valence electrons between atoms in the pair with one pulling harder on the electrons than the other. Results in different ends of the molecule having different electric charges.

Polar covalent bonds result in “two poles”. What does this mean?

The molecule is said to be a dipole meaning one end is slightly positive and the other end is slightly negative (the atoms that pull the hardest on the negative electrons will become the more negative pole)

Define electronegativity

Atoms differ in their ability to attract electrons in a chemical bond and this measure is called electronegativity

What molecule is an example of a polar covalent bond?

Water! Oxygen has a higher electronegativity value so it pulls harder on the electrons than Hydrogen does. Brings electrons closer to the Oxygen nucleus thus making the Oxygen end slightly more negative and the Hydrogen regions slightly more positive

What are intermolecular bonds?

Chemical bonds between molecules

Which is stronger- intramolecular bonds or intermolecular bonds?

Intramolecular bonds are stronger

How do intermolecular bonds relate to “state”?

These bonds between molecules determine the physical state of molecular substances; the bonds are broken when a substance undergoes a change of state (e.g. solid to liquid, liquid to gas)

What are the 3 types of intermolecular bonds and what is their name?

• London forces

• Dipole-dipole forces

• Hydrogen bonding; called Van der Waals forces

What describes London Forces? What is the strength of this bond?

• Hold non-polar molecules together

• Weakest strength

What describes dipole-dipole forces? What is the strength of this bond?

• Hold polar molecules together

• Medium strength

What 1 thing describes hydrogen bonding of intermolecular bonding? What is the strength of this bond?

• Formed between the electropositive hydrogen dipole and an electronegative dipole of either oxygen, chlorine, OR fluorine

• Strongest strength

What is an example of a London force in intermolecular bonds?

CH₄. Methane

What is an example of dipole-dipole foces in intermolecular bonds?

HCl. Hydrochloric acid

What is an example of hydrogen bonding in intermolecular bonds?

Pure distilled water

What are 3 important things to remember about water?

It is a universal solvent because of its ability to dissolve many ionic and polar compounds, it has a boiling point of 100^oC, and a freezing point of 0^oC

What are the 4 types of biochemical reactions?

• Hydrolysis

• Condensation/dehydration synthesis

• Oxidation & reduction

• Neutralization

What is hydrolysis?

Using water to help break down molecules

In a written chemical equation, what goes on what side?

Reactants are on the left and products are on the right

What is a condensation/dehydration synthesis reaction?

Reaction that occurs when two molecules combine to form one molecule. Opposite of hydrolysis. Water is removed in the synthesis of the new molecule (water is a product not a reactant)

What is a oxidation & reduction reaction? What is the common name for it?

Process of losing electrons is called oxidation; process of gaining electrons is called reduction. An electron transfer between two substances always involves a reduction of one and an oxidation of the other. Also called a “redox reaction”

What is a mnemonic device for remembering oxidation and reduction?

OIL RIG. Oxidation is less, reduction is gain

What is an example of a redox reaction?

Cellular respiration! Glucose + Oxygen → CO₂ + water + energy. Transfer of electrons from glucose helps the cell to make high-energy molecules (ATP) which is used to do work!

What is a neutralization reaction? Where is this always happening?

Reaction of an acid and a base to produce water and salt. Happens when an acid and a base with equal concentrations and equal volumes react. Happening continuously within your cells!

Define ionization

Disassociation of a molecule into ions. E.g. H₂O → OH^- + H⁺

What is pure water?

Water that has been treated to remove impurities like minerals, bacteria, chemicals, and other contaminants. Result is almost 100% H₂O molecules

What is an acid?

When dissolved in water, it increases the concentration of hydrogen ions (H+)

What are 4 properties of an acidic solution?

Sour taste, conducts electricity, turns litmus paper red, and a pH below 7

What is a base?

When dissolved in water, increases the concentration of hydroxide ions (OH^-)

What are the 4 properties of a basic solution?

Bitter taste, slippery feel, turns litmus paper blue, and a pH above 7

Is pure water acidic or basic?

Neither, it’s neutral; contains and equal number of H⁺ and OH^- ions

What is a pH scale?

Method of expressing hydrogen ion concentration. [H⁺] in mol/L. Measured logarithmically so each increment is a tenfold different. Scale of 0-14. Pure water is a 7 because it’s neutral

Describe acids and bases and their strength

Can be classified as either strong or weak depending on the degree to which they ionize when dissolved in water. Strong ones ionize completely; weak ones only partially ionize

For weak acids and bases, in an equation what does a double arrow mean?

Means the reactions are reversible.

What is an equilibrium concentration?

A state when the rate or forward reaction in a chemical reaction becomes equal to the rate of backward reaction. There is no change in the products and reactants and it seems that the reaction has stopped

Are most organic acids and bases strong or weak?

Weak

In a neutralization reaction, where does the water comes from? Where does the salt come from?

Water comes from the H⁺ and OH^- ions in the solution; salt comes from the metal cation and non-metal anions in the solution

What would happen if a strong acid and a strong base with equal concentrations and volumes were mixed? What would be the products? What would be the pH?

• H⁺ ions in the acid and OH^- ions in the base would ionize/dissociate and react completely with each other

• Products would be salt and water.

• pH would be neutral at 7

Neutralization reactions do what? Why is this crucial?

Regulate the pH of the internal environment; determines the speed and direction of many critical biological reactions

What are acid-base buffers?

Solutions that are able to maintain nearly constant pH levels in spite of fluctuating environmental conditions.

How do acid-base buffers work?

By taking up excess H⁺ and OH^- ions thus neutralizing excess acid or base

In the human body, what are 3 examples of acid-base buffers?

Proteins, amino acids, and carbonic acid

Where is the carbonic acid-bicarbonate buffer and what is its function?

Located in blood and extracellular fluid. Maintain and optimal 7.4 pH. If changes by even 0.2-0.4 pH it can be fatal. Contains acid and base so it can neutralize conditions that are either too acidic or too basic. Formed by the reaction of CO₂ with H₂O to form carbonic acid which then ionizes to form bicarbonate and a hydrogen ion. *Reversible

Covalent bonds form between atoms of-

Non-metals

Explain the polar covalent nature of water molecules

The oxygen in the molecule is more electronegative than the hydrogen so a dipole is formed with an area that is more negative (near the oxygen) and an area that is more positive (near the hydrogen atom)

Protein + H₂O →

Amino acid + amino acid

Amino acid + amino acid →

Protein + H₂O

Oxidation is the loss of electrons and the gain of-

Oxygen

Reduction is the gain of electrons and the loss of-

Oxygen

Pure water contains H₂O molecules as well as tiny numbers of-

H⁺ and OH^- ions

The H⁺ and OH^- ions in water are produced through the natural process of-

Ionization

These ions in the water create the properties of-

An acid and a base

When an equal acid and an equal base react together, what 2 things happen?

1. A neutralization reaction occurs

2. Water and salt are produced

The carbonic acid-bicarbonate buffer contains both-

An acid and a base

How is the carbonic acid-bicarbonate buffer formed?

• Reaction of CO₂ with H₂O to form carbonic acid

• Ionizes to form bicarbonate and an H⁺ ion