Chemistry as a Foundation for Biology

How do we define elements?

specific number of protons and neutrons

How do you know the number of electrons?

same as protons

Why are electrons important?

means by which atoms interact and bond, creating molecules which biologists care a lot about, critical in thinking about energy

What do elements in a column (group) have in common?

same number of valence electrons

Valence electrons

electrons on the outermost orbital

What do elements in a row (period) have in common?

same number of electron orbitals

Elements of life

carbon, oxygen, hydrogen, nitrogen, phosphorus, sulfur, potassium, calcium, sodium, chlorine, magnesium

Chemical bond

a ‘stable’ attraction between two atoms

How are the number of bonds an atom can form determined?

number of unpaired (valence) electrons in the outermost shell

HONC1234

Hydrogen 1 bond, oxygen 2 bonds, nitrogen 3 bonds, carbon 4 bonds

How is the nature of a bond determined?

relative electronegativities of two atoms

electronegativity

a measure of an elements’ ability to attract electrons

How can you determine electronegativity from the periodic table

going up and to the right is more electronegative

What is the relationship between atomic radius and electronegativity?

the higher the atomic radius, the lower the electronegativity

Why does the inverse relationship between atomic radius and electronegativity exist?

electron orbital is closer to the nucleus in smaller atoms

What type of bonds do atoms that have similar electronegativities form?

equal sharing of electrons

What kind of bonds do atoms with very different electronegativities form?

transfer of electrons

Nonpolar covalent bonds

similar electronegativities, atoms have no charge

Polar covalent bonds

slightly different electronegativities, atoms have a partial charge

Ionic bonds

very different electronegativities, atoms have a full charge because an electron was “stolen”

Why does the addition of a phosphate group have an effect on the structure and function of the molecule?

the oxygens make their end of the molecule more electronegative meaning that it interacts more with polar molecules

Explain the role relative electronegativity plays in bond formation.

relative electronegativity, or the electronegativity that bonded atoms have in relation to each other, plays a large role in bond formation because when two atoms have vastly different electronegativities, they will form an ionic bond, whereas atoms with some difference in electronegativity will form polar covalent bonds, and atoms with very little or no difference will form nonpolar covalent bonds.

What is the guiding “mantra” of biology?

structure \= function

When talking about solutions, what is water referred to as?

universal solvent

Important functional groups

hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, sulfhydryl

Organic molecules

proteins, carbohydrates, nucleic acids, lipids

Solvent

what you dissolve something into

Why does water have partial charges?

polar covalent bonds within them due to differing electronegativity

Hydrogen bonds

partial charges cause attraction between oxygen of one molecule and hydrogen of another, relatively weak in terms of bonding which allows liquid water to change shape

What happens to hydrogen bonds when energy is added to the system?

hydrogen bonds are broken (boiling and turning to gas)

What happens to hydrogen bonds when energy is added to the system?

hydrogen bonds become stronger (ice formation)

Cohesion

water molecules stick together

Adhesion

water molecules sticking to other surfaces

What kinds of molecules does water “like” to stick to?

polar molecules

Surface tension

when cohesion is greater than adhesion

Specific heat

energy needed to raise temperature

What properties of carbon make it a logical backbone for organic molecules?

4 valence electrons allows 4 bonds to occur, tetrahedral shape of bonding, optimal size for electronegativity

If so many molecules have carbon, why are they different?

different structure and other molecules involved

R group

stands in for “something else”

Hydroxyl

polar

Methyl

nonpolar

Carbonyl

polar

Carboxyl

charged, ionizes to release H+, acidic

Amino

charged, accepts H+ to form NH3+, basic

Phosphate

Charged, ionizes to release H+, acidic

Sulfhydryl

polar

What are organic molecules made up of?

part hydrocarbons (hydrogens and carbons) and part functional groups which typically include oxygen, nitrogen, phosphorus, and sulfur

Hydrophilicity

polar molecules and ions dissolve readily in water

Hydrophobicity

nonpolar molecules do not dissolve readily in water

Amphipathic

a molecule that has both polar and nonpolar properties

What is the structure/function relationship of water that allows it to play such a central role in biology?

the structure with oxygen being more electronegative than hydrogen causes polarity allowing it to interact more specifically with charged and partially charged molecules

Why do hydrophilic and hydrophobic mean “loved by water” and “hated by water” rather than “loving water” and “hating water”?

water is the focus of the word and the concept

What do we mean by “dissolve” chemically?

atoms split from their molecular partners

Function of proteins

“workers” of life, 55% of cell mass

Structure of proteins

made of amino acids, shapes driven by functional groups

Function of carbohydrates

energy, structural integrity, 10% of cell mass

Structure of carbohydrates

made of sugars, long chains, hydrophilic

Function of nucleic acids

cell energetics, information flow, 25% of cell mass

Structure of nucleic acids

made of nucleotides, mostly hydrophilic, helical in shape

Function of lipids

cell energetics, structure, signaling, 10% of cell mass

Structure of lipids

made of fatty acids, three types, mostly hydrophobic

3 types of lipids

fats, phospholipids, steroids

Why do oil and water not mix?

oil is nonpolar and water is polar which is why they cannot interact with each other

How does salt melt ice?

the salt interferes with the bonds between the water, causing it to change state from solid to liquid

How does guar gum reduce the abundance of ice crystals in ice cream?

guar gum is hydrophilic so it interrupts the bonds between the water

Structure of amino acids

wide range

Function of amino acids

enzymes, signals, structural

Structure of carbohydrates

regular, repeating structures

Function of carbohydrates

cell walls, energy

Structure of nucleic acids

helical

Function of nucleic acids

information

Structure of lipids

hydrophobic or amphipathic

Function of lipids

membranes, energy, signals

Chemical reactions

changes to the sharing of electrons and the rearrangement of bonds

Catabolic reaction

breaking down molecules into subunits/monomers

Anabolic reaction

building molecules into macromolecules/polymers

How to remember CATabolic reaction

cats knock things off counters which makes them break

Hydrolysis reaction

breaking down molecules requires water addition

Dehydration reactions

building molecules removes water from the organic molecule

Formation of proteins

amino acid + amino acid \= protein + water; anabolic and dehydration

ATP hydrolysis

ATP + H2O \= ADP + Pi; catabolic, hydrolysis

Gibbs Free Energy Equation

Gibbs free energy

energy available for work

Enthalpy

total energy of the system

1st law of thermodynamics

enthalpy

Why do the electrons in the outermost shells have the greatest energy?

requires potential energy to hold the negatively charged electrons away from the positively charged nucleus

For anabolic reactions, is the change in enthalpy positive or negative?

positive

For catabolic reactions, is the change in enthalpy positive or negative?

negative

Entropy

disorder of system

2nd law of thermodynamics

entropy

For an anabolic reaction, is the change in entropy positive or negative?

negative

For a catabolic reaction, is the change in entropy positive or negative?

positive

Endergonic

absorbs of energy

Exergonic

releases of energy

What determines protein shape?

amino acid sequences and the environment

What determines protein function?

protein shape

How do amino acids have diverse chemical identities?

different R groups

Types of proteins

antibodies and complement, contractile and motor, enzymes, hormones, receptors, structural, transport

Amylase

breaks down starch into sugars

Histone deacetylase

determines which genes to express