CH 1: Chemistry of Life

Matter

anything that takes up space and has mass

made up of elements

• rocks

• metals

• oils

• gases

• organisms

element

substance that cannot be broken down to other substances via chemical reactions

• gold

• copper

• carbon

compound

substance consisting of two or more different elements combined in a fixed ratio

• NaCl

• H2O

has different chemical and physical characteristics from its elements

essential elements

20-25% of natural elements

Organisms need to live a healthy life and reproduce

• Humans need 25

• plants need 17

What are the main 4 elements found in humans?

Hydrogen

Oxygen

Nitrogen

Carbon

trace elements

required by organisms but in small quantities

atom

smallest unit of matter that still retains the properties of an element

What are atoms made out of? Name them?

Subatomic particles

• neutrons

• protons

• electrons

atomic nucleus

center of the atom

protons and neutrons reside there

• protons give atom positive charge

dalton

the unit for atomic mass

atomic number

# of proteins

also tells the number of electrons

mass number

total number of protons + neutrons

atomic mass

total mass of an atom

isotope

the difference in atomic forms

• Some atoms have more neutrons despite being the same element

• proton # remains the same

All have different masses

radioactive isotope

the nucleus decays spontaneously

gives off particles and energy

• leads to a change in proton #

  • transforms into a new element

energy

defined capacity to cause change

potential energy

energy matter possess because of location or structure

• electrons have PE due to their distance from the nucleus

  • negative charge attracted to positive charge of nucleus

electron shells

where electrons are located

PE levels increase the farther the electron moves from the nucleus

electrons can only move shells by absorbing or losing an amount of energy

• gain - moves up

  • lose - falls down

valence electrons

outermost electron shell

• valence shell

An atom with a complete valence shell is unreactive or inert

chemical bonds

the sharing or transfer of valence electrons

occurs with incomplete valence shells

covalent bonds

sharing a pair of valence electrons

strongest bond in ORGANISMS

bonding capacity

atom’s valence

usually equals the number of electrons required to complete the atom’s outermost shell

electronegativity

the attraction of particular atoms for the electrons of a covalent bond

• the more electronegative, the stronger the pull

  • covalent bonds of the same element have equal electronegativity

polar covalent bond

when an atom is bonded to a more electronegative atom

bond is not shared equally

What is one of the most electronegative elements?

Oxygen

ionic bond

two oppositely charged atoms that bond by transferring electrons

• cation

• anion

results in ions

tend to be dissolved in water in organisms

cation

positively charged ion

loses an electron

anion

negatively charged ion

gaining an electron

ion

refers to molecules that are electrically charged

hydrogen bonds

when a hydrogen atom is covalently bonded to an electronegative atom

• hydrogen atom has a partial positive charge

noncovalent attraction

• usually bonds w/ oxygen or nitrogen

van der waals interactions

weak

only occur when atoms and molecules are close together

caused by electrons moving locations (shifts the positive and negative charge of atoms around)

• causes molecules and atoms to stick together

• can occur simultaneously

• helps geckos climb up a wall

why is the shape of a molecule important?

determines how biological molecules recognize and respond to one another with specificity.`

reactants

starting material in a reaction

products

ending material in a reaction

chemical equilibrium

when the reactions offset one another exactly

does not mean the reactants and products are equal in concentration but that their concentrations have stabilized at a particular ratio

Water

H₂O

polar molecule:held by hydrogen bond

• when in liquid form, bond is super weak

• bonds are formed constantly and are constantly breaking

• responsible for many properties of water:

  • cohesion

  • adhesion

  • surface tension

  • high specific heat

  • capillary action

  • universal solvent

cohesion

hydrogen bonds holding the substance together

• droplet

adhesion

clinging of one substance to another

capillary action

liquid flowing through a narrow space without force + against gravity

• uses both adhesion and cohesion

surface tension

A measure of how difficult it is to stretch or break the surface of a liquid

Water has high surface tension

• related to cohesion

kinetic energy

energy of motion

thermal energy

kinetic energy associated with the random movements of atoms or molecules

total kinetic energy

tends to pass from warmer to cooler

is transferred from one body of matter to another via heat

NOT THE SAME AS TEMPERATURE

temperature

average kinetic energy of molecules in a body of matter

calorie (cal)

unit of heat

amount of heat it takes to raise the temperature of 1g of water by 1C

• can be applied to cooling water

kilocalorie is 1000 calories

• quantity of heat required to raise temp of 1kilo of water by 1C

specific heat

defined as the amount of heat that must be absorbed or lost for 1g of that substance to change its temp by 1C

water as a very high specific heat

why is water having high specific heat beneficial?

• large bodies of water can absorb huge amounts of heat from the sun, but only warm up by a few degrees. This will allow the organisms living inside to survive

heat of vaporization

quantity of heat a liquid must absorb for 1g to be converted from liquid to gas

water has a high heat of vaporization for the same reason as specific heat

why is water having high heat of vaporization beneficial?

• helps maintain the Earth’s climate

evaporative cooling

as liquid evaporates, the surface of the liquid that remains behind cools down

why is evaporative cooling beneficial?

• contributes to the stability of temperatures in lakes and ponds

  • prevents water from overheating

Why does ice float on water?

• less dense as a solid than a liquid

• molecules move too slowly to break hydrogen bonds as they solidify

• molecules lock in a crystalline lattice

  • makes the molecules “arm’s-length” apart, which makes the ice less dense than water

why is the density of ice beneficial?

• allows for water to freeze at the top of bodies of water, allowing organism to survive underneath

solution

homogeneous mixture of two or more substances

solvent

dissolving agent of solute

solute

substance that is dissolved

aqueous solution

when solute is dissolved in water

why is water such a great solvent

• polarity of water

  • attracts opposing charges, which splits up molecules faster

• does not have to be ionic to dissolve in water

hydration shell

sphere of water molecules around each dissolved ion

hydrophilic

affinity towards water

usually dissolves if it is not too big

hydrophobic

repels water

does not dissolve

how to calculate molecular mass?

add up all the atomic masses of each atom together

molarity

the number of moles of solute per liter of solution

hydrogen ion

single proton with a positive charge of 1

acid

A substance that increases the hydrogen ion concentration of a solution

remove OH

6-0

base

A substance that reduces the hydrogen ion concentration of a solution

Adds OH

8-14

buffers

minimizes the changes in concentrations of H and OH by moving H from areas of abundance to areas that lack

what is the pH of water?

7

neutral pH

what are the most common elements bonding to carbon

hydrogen

oxygen

nitrogen

what makes up macromolecules

carbon chains

hydrocarbons

chains only made up of carbon and hydrogen

major component of petroleum (fossil fuel)

can undergo reactions and release a large amount of energy

isomers

variation in the shape of organic molecules

compounds that have the same number of atoms of the same element but different structure —> different properties

3 types:

1. structural

2. cis-trans

3. enantiomers

structural isomers

differ in covalent arrangement of atoms

also differ in location of double bond

cis-trans isomer

covalent bonds to same atoms but these atoms differ in spatial arrangements due to inflexibility of double bonds

cis: atoms on the same side

trans: opposite sides

enantiomers

mirror images of each other but differ in shape due to presence of asymmetric carbon (attached to four different atoms or groups of atoms)

left and right hand of molecules

hydroxyl

—OH

alcohol (end in ol)

• ethanol

carbonyl

>C=O

ketone if carbonyl is within carbon skeleton

• acetone

aldehyde if group is at end of skeleton

• propanal

carboxyl

—COOH

carboxylic acid or organic acid

• acetic acid

amino group

—NH₂

Amine

• glycine

sulfhydryl

—SH

thiol

• cysteine

only hydrophobic funcitonal group

phosphate

—OPO₃^2-

organic phosphate

• glycerol phosphate

methyl

—CH₃

methylated compound

• 5-methylcytosine

not reactive

functional groups

chemical groups that affect molecular function

participates in chemical reactions in a characteristic way

ATP

adenosine triphosphate

has a phosphate group

adenosine attached to three phosphate groups

stores energy

macromolecule

carbohydrates

proteins

nucleic acid

aka polymer

polymer

long molecule consisting of similar building blocks linked by covalent bonds

made up of monomers

each polymer is made up of different monomers

condensation reaction

connects monomer to another monomer or polymer

when two molecules are covalently bonded to each other

dehydration reaction

when water molecule is lost, when molecules bond

building

• carbs and proteins are synthesized this way

hydrolysis

break down of polymers

adding water

carbohydrates

sugars

monomer: monosaccharides (simple sugar)

disaccharide (two monomers)

polysaccharide (polymer)

monosaccharide

Glucose is the most common C₆H₁₂O₆

has a carbonyl and multiple hydroxyl groups

disaccharide

two monosaccharides joined by glycosidic linkage

• covalent bond between two monosaccharides by dehydration reaction

sucrose is most common

• glucose + fructose

lactose

maltose

polysaccharides

serve as storage material or building material

polymer of carbohydrates

made up of thousands monosaccharides

storage of polysaccharides

plants store starch (polymer of glucose)

• because glucose is major cell fuel, starch is stored energy

glycogen

polysaccharide stored in animals

stored in liver and muscles