Unit 1 - Chemistry of Life

covalent bond

the sharing of electrons between two atoms

ionic bond

the transfer of electrons (between a cation and an anion)

hydrogen bond

forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

van der waals interactions

attractions between molecules that are close together as a result of charges

what type of bonds form in water molecules?

polar covalent bonds

what type of bonds form between water molecules?

hydrogen bonds

why do water molecules form hydrogen bonds with each other?

because the polar covalent bonding in the water molecules causes the unequal sharing of electrons between the atoms of the molecule, allowing bonds to form between the slightly positive and slightly negative ends of water molecules

cohesion

water molecules sticking to other water molecules with hydrogen bonds

adhesion

the attraction between water and other substances or surfaces

capillary action

water moving against gravity by cohesion and adhesion working together

surface tension

how hard it is to break the surface of a liquid, water has high surface tension due to its hydrogen bonds (cohesion)

moderation of temperature by water

water absorbs heat from warmer air and releases stored heat to cooler air. water can absorb or release large amounts of heat with only a slight change in its own temperature

water’s high specific heat

water resists changing its temperature because of its high specific heat. the high specific heat of water minimizes temperature fluctuations to limits that permit life

evaporative cooling

as a liquid evaporates, its remaining surface cools. evaporative cooling in water helps stabilize temperatures in organisms and in bodies of water

density of ice

ice floats in water because hydrogen bonds in ice are more ordered, making ice less dense. ice creates a blanket on the surface of a body of water, insulating the temperature of the water for the survival of living organisms

solution

a liquid that is a completely homogeneous mixture of substances

solvent

does the dissolving

solute

is being dissolved

aqueous solution

water is the solvent

why is water the universal solvent of life?

due to its polarity

what happens when an ionic compound is dissolved in water?

each ion is surrounded by a sphere of water molecules called a hydration shell

hydrophilic

loves water

hydrophobic

hates water

hydrogen ion (H+)

the ion that loses one of its electrons and is transferred as a proton

hydroxide ion (OH-)

molecule that loses the proton

hydronium ion (H₃O+)

molecule with the extra proton

acid

a substance that increases the H+ of a solution

base

a substance that reduces the H+ of a solution

what happens to strong acids and bases in water?

they completely dissociate

buffers

substances that minimize changes in concentrations of H+ and OH- in a solution

what kinds of molecules is carbon able to form?

large, complex molecules

why can carbon form large, complex molecules?

because it has 4 available bonds

what does ‘organic’ in biology mean?

something contains carbon and hydrogen and comes from a living thing

vitalism

the belief that in a life force outside jurisdiction of physical and chemical laws

Redi

performed the maggot experiment, where he saw that maggots only formed when flies came in contact with the meat; disproving spontaneous generation.

Spallenzani

his experiment showed that it is not an inherent feature of matter that it can be destroyed by an hour of boiling. he realized that spontaneous generation could not happen without air.

Pasteur

boiled meat broth in a flask that prevented falling particles from coming in contact with the broth but allowed air to reach it. certain air particles caused the particles to spoil disproving spontaneous generation

when was vitalism disproved?

when chemists were able to synthesize organic molecules

Stanley Miller

demonstrated the abiotic synthesis of organic compounds

the Miller Urey experiment

Miller simulated Earth’s early atmosphere and oceans to test if organic molecules could be created abiogenically. organic molecules formed.

mechanism

the view that physical and chemical laws govern all natural phenomena

what does the electron configuration of carbon cause?

its compatibility with many different elements

what do carbon chains form?

the skeletons of most organic molecules

hydrocarbons

organic molecules consisting of only carbon and hydrogen

what happens when hydrocarbons undergo reactions?

they release large amounts of energy

isomers

compounds with the same molecular formula but different structures and properties

structural isomers

have different covalent arrangements of their atoms

cis-trans isomers

have the same covalent bonds but differ in spatial arrangements

enantiomers

isomers that are mirror images of each other

what industry are enantiomers important in?

the pharmaceutical industry

what is the form of the carbon skeletons' of estradiol and testosterone?

four fused carbon rings

how do testosterone and estradiol differ?

in the chemical groups attached to the rings of the carbon skeleton

functional groups

the components of organic molecules that are most commonly involved in chemical reactions

what about the functional groups gives each molecule its unique properties?

the number and arrangement of the groups

what are the seven most important functional groups?

• hydroxyl group

• carbonyl group

• carboxyl group

• sulfhydryl group

• phosphate group

• methyl group

• amino group

hydroxyl group (-OH) or (HO-)

• polar due to electronegative oxygen

• forms hydrogen bonds with water

• compound name: alcohol

carbonyl group (>C=O)

• ketoses - sugars with ketone groups

• aldoses - sugars with aldehydes

• compound name: ketone or aldehyde

carboxyl group (-COOH)

• acts as an acid

• compound name: carboxylic acid or organic acid

amino group (-NH₂)

• acts as a base

• compound name: amine

sulfhydryl group (-SH) or (HS-)

• two (-SH) groups can react to form a disulfide bridge that helps stabilize proteins

• compound name: thiol

phosphate group (-OPO₃⁻²)

• contributes negative charge

• when attached, confers on a molecule the ability to react with water, releasing energy

• compound name: organic phosphate

methyl group (-CH₃)

• affects the expression of genes

• affects the shape and function of sex hormones

• compound name: methylated compound

adenosine triphosphate (ATP)

• an important organic phosphate

• consists of an organic molecule (adenosine) attached to a string of three phosphate groups and one adenine

• stores the potential to react with water, a reaction that releases energy to be used by the cell

adenosine diphosphate (ADP)

• consists of an organic molecule (adenosine) attached to a string of two phosphate groups and one adenine

what are the four biological macromolecules?

carbohydrates, lipids, proteins, and nucleic acids

macromolecule

large and complex molecules

monomer

repeating units that serve as building blocks

polymer

a long molecule consisting of many similar monomers

enzymes

specialized molecules that speed up chemical reactions

dehydration synthesis

occurs when two monomers bond together through the loss of water

hydrolysis

occurs when a polymer breaks apart into monomers through the addition of water

carbohydrates

include sugars and the polymers of sugars

monosaccharides

simplest carbohydrates

polysaccharides

polymers composed of many sugar building blocks

what is the ratio of the molecular formulas for monosaccharides?

CH₂O (1:2:1)

what are monosaccharides classified by?

• the location of the carbonyl group as aldose or ketose

• the number of carbons in the carbon skeleton

what is the function of carbohydrates?

to serve as major fuel for cells as raw material for building molecules

disaccharide

formed when a dehydration synthesis reaction joins two monosaccharides

what is kind of covalent bond joins a carbohydrate with another molecule?

a glycosidic bond

starch

• a storage polysaccharide of plants, consist entirely of glucose monomers

• plants store extra starch as granules in chloroplasts and other plastids

cellulose

• a structural polysaccharide

• a major component of the tough cell wall of plant cells

what is the difference of glycosidic linkages between starch and cellulose?

• starch has alpha rings (glucose) and is largely helical

• cellulose has beta rings (glucose) and is straight and unhinged

• enzymes that digest starch by hydrolyzing alpha linkages cannot hydrolyze beta linkages in cellulose

chitin

• a structural polysaccharide found in the exoskeleton of arthropods

• provides structural support for the cell walls of many fungi

do lipids include true polymers?

no because they are not composed of repeating units of monomers

what is the unifying feature of lipids?

they do not mix well with water or they do not mix at all because they consist of mostly hydrocarbons

what are the three most important lipids?

fats, phospholipids, and steroids

what are fats constructed from?

glycerol and fatty acids

glycerol

a three carbon alcohol with a hydroxyl group attached to each carbon

fatty acid

consists of a carboxyl group attached to a long carbon skeleton

why do fats separate from water?

water molecules hydrogen bond to each other and exclude the fats

ester linkage

the bond between the hydrocarbon and the carboxylic ends of a fat

saturated fatty acids

• have the maximum number of hydrogen atoms possible and NO double bonds

• solid at room temp

• most animal fats

unsaturated fatty acids

• have one or more double bonds

• liquid at room temp

• usually plants and fish fats

hydrogenation

the process of converting unsaturated fats to saturated fats by adding hydrogen

what does hydrogenating vegetable oils create?

unsaturated fats with trans double bonds (trans fats)

what is the major function of fats?

to store energy to use when its needed

phospholipid

composed of two fatty acids and a phosphate group attached to glycerol

what happens when phospholipids are added to water?

• they self-assemble into double-layered structures called bilayers

  • this allows them to form the cell membrane

steroids

lipids characterized by a carbon skeleton consisting of four fused rings

cholesterol

a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized