Chapter 2-3

Chemistry &

Biochemistry of

Life

Composition of Matter

Matter: anything that occupies

space & has mass

Mass: quantity of matter an object

has; not the same as weight

- All matter made of elements

Sect 1

Elements

-Substances that cannot be broken

down chemically into simpler

substances

- 90% of mass of living things made of

4 elements: C, H, O, N

Atom: simplest particle of an element

that retains properties of that element

-Nucleus contains most mass of an

atom

Proton: positive charge

Neutron: no charge

- # of protons = atomic #

- # of protons + # of neutrons

= mass number

Electrons: negatively

charged particles outside

nucleus

-Have virtually

no mass

Orbital: 3-D region around a nucleus

that indicates the probable location of

an e-

-If # of protons doesn’t = # of e-,

charged atom (ion)

-Sometimes # of protons doesn’t = # of

neutrons, isotopes

-will change atomic mass, but not

identity of element

Compounds

1. A group of atoms in a fixed ratio.

a. Held together by chemical bonds.

b. Represented by formulas:

e.g. - H20, NaCl, C6H12O6 c. Three types of bonds

in biology:

1). Covalent bond - 2

atoms share e- (e.g. -

H2O)

molecule: 2 or more

atoms covalently bonded.

2)Ionic bond - 2 atoms of opposite charge join. The e- are transferred from one (+ ion) to another (- ion).

3) Hydrogen bonds - force of

attraction between a hydrogen molecule w/ a partial positive charge & another atom or molecule w/ a partial or full negative charge

Energy & Matter

Energy: ability to do work

-Chemical E, light E, thermal E, etc

-E is absorbed or released when

chemical bonds are formed or broken

Chemical reaction: 1 or more

substances change to produce 1 or

more different substances

Sect 2

Reactants: substances reacting

together; starting substances in a

chemical rxn

Products: new

compounds/substances formed in

chem. rxn

Metabolism: all chem. rxn’s that

take place in an organism

-E usually has to be

added to reactants to

get a rxn to begin

Activation E: E

needed to start a rxn

Catalyst: chemical substance that

lowers the amount of activation E

necessary

Activation E

Enzyme: protein

or RNA molecule

that catalyzes

chemical rxn’s

w/o being

changed or

destroyed

Oxidation Reduction Reactions

*Oxidation is the loss of electrons.

*Reduction is the gain of electrons.

- Reactions in which e-’s are

transferred; redox reactions

Na + Cl Na+ + Cl-

LEO goes GER

--lose electrons = oxidation

--gain electrons = reduction

- Charge on atoms in H2O is

unequally distributed even though

overall charge is neutral

Sect 3

Water & Solutions

Polarity: describes a molecule

with opposite charges on opposite

ends

O

H H

δ- δ-

δ+ δ+

-polarity allows water to dissolve

polar substances

--accounts for many of

H2O’s properties

Hydrogen bond: force of attraction

between a hydrogen molecule with

a partial or full negative charge

1.Cohesion:

attractive force

that holds

molecules of a

single substance

together (H2O

attracted to H2O)

- gives H2O

surface tension

2. Adhesion: attractive force between

2 particles of different substances

-These forces are strong enough so

H2O clings to other surfaces

3. Capillarity:

attraction between

molecules that

results in the rise of

the surface of a

liquid when in

contact with a solid

- H2O can rise

against gravity up a

narrow tube

4. High Heat Capacity (specific heat):

H2O can absorb or release large

amounts of heat w/ only a slight temp

change

- Breaking H-bonds takes lots of E, & E

is released when they are formed

- Why water takes a long time to boil

-In summer, H2O absorbs heat, releases it

at night

--why is it cold in a desert at night?

- helps keep cells at a constant temp

-When H2O evaporates from surface, takes

heat with it = evaporative cooling (sweating)

5. Ice Floats: ice is less dense than

liquid water

- Due to shape of molecule at 4oC,

large amounts of open space form

when H2O freezes

-allows aquatic organisms to survive on

the bottom of bodies of water

Solutions -Mixture in which one

or more substances

are uniformly

distributed in another

substance

Solute: substance

being dissolved

Solvent: substance in

which solute is

dissolving

2016

Concentration [ ]: amount of

solute dissolved in a fixed

amount of the solution

-the more a solute is

dissolved, the higher the [ ]

Saturated soln: no more

solute can be dissolved

Aqueous soln: H2O is

solvent; where most bodily

rxns occur

This is

sweet tea,

bless your

heart!

Acids & Bases

- Acidity & alkalinity are measures

of amounts of hydronium ions

(H3O+) & hydroxide ions (OH-)

-these form randomly in water due

to collisions of molecules

pH = potential hydrogen

- More H3O+ ions than

OH-; 1-6.9 on pH scale

- H3O+ ions = OH-

ions; 7 on pH scale

- More OH- ions than

H3O+; 7.1-14 on pH

scale

pH scale:

scale for

measuring

the amt of

H3O+ ions &

OH- ions in

soln.

• pH or

litmus paper

Buffers

-Chemical substances

that neutralize small

amounts of either an

acid or a base

--buffering systems

maintain pH values in

healthy bodies

Chapter 3

Biochemistry

Organic compounds:

compounds made primarily of

Carbon atoms

-most matter in living organisms

Inorganic compounds: don’t

contain C (w/ a few exceptions)

Sect 1

Functional Groups

-clusters of atoms that influence the

characteristics of the molecules

they compose & the chemical rxns

they undergo

1.Hydroxyl = -OH

- form alcohols

2.Carboxyl

- form carboxylic acids

O

C OH

3.Amino

- form amines

H

N H

4. Phosphate

O

P

OH

O OH

Large Carbon Molecules

Monomer: small, simple molecule

Polymer: repeated, linked

monomers

Macromolecules: large polymers

*carbohydrates, lipids, proteins, &

nucleic acids

Condensation rxn (dehydration synthesis): - chemical rxn that links monomers together

-H2O formed as a byproduct

-H from 1 monomer & OH from 1 monomer

Hydrolysis rxn:

- H2O is used to

break polymers

into monomers

- reverse of

condensation rxn p. 53

Energy Currency

-Life processes require constant

supply of energy

ATP: adenosine triphosphate

-covalent bonds between

phosphate groups are unstable &

easy to break

- This releases energy used to drive

chemical reactions in organisms

4 Molecules of Life

1.Carbohydrates: Source of energy or

are structural materials in cells

a.Monosaccharide:

- monomer of a carbs simple sugar

- organic compounds made of C, H, & O in ratio of 1:2:1

ie: glucose, fructose, galactose

Sect 2

b. Disaccharide: double sugar

- monosaccharides combine

- Fructose + glucose = sucrose

(table sugar)

c. Polysaccharide: complex

molecule composed of 3 or more

monosaccharides

2 types:

1.Storage:

- animals store glucose as

glycogen in liver or muscle

- plants store glucose as starch

2. Structural

- plants have cellulose (gives

strength & rigidity to plant

cells; makes up 50% of wood)

- arthropods have chitin

2.Proteins: organic compounds made mostly of C, H, O, & N

- Macromolecules made of amino acids

- 20 diff aa’s; differ at their R group (side chains) & give proteins different shapes

- Different shapes = different functions

-aa’s form peptide bonds (covalent

bond formed by condensation rxn)

Polypeptide: long chain of aa’s

-1 or more polypeptide chains make up

proteins

-These long chains bend on

themselves, interact w/ themselves thru

H-bonds to create 3-D shapes

(conformation)

*shape of protein is very important

to its function!!!

Enzymes: RNA or protein

molecules that act as catalysts;

most are proteins

Substrate: reactant being

catalyzed; binds to enzyme at a

specific place called active site

-Has a shape that allows only that substrate to fit

--when substrate binds, there’s a slight change in shape of enzyme

--this lowers EA of rxn by weakening bonds in substrate

-- after rxn, products are released, enzyme is unchanged (can be used again)

Factors that Affect Enzymes

- Enzyme activity is directly related to its shape

- If shape changes (denaturation), so does function

1.Temperature

2.pH

3.Salt concentration

3.Lipids

-large, nonpolar, organic molecules;

don’t dissolve in H2O

- triglycerides, phospholipids, steroids,

waxes, & pigments

- Have large # of carbon-hydrogen

bonds = store lots of energy

Fatty acids:

unbranched carbon

chains that make up

most lipids

Hydrophilic region

(carboxylic acid): will

be attracted to water

Hydrophobic region

(hydrogen carbon

chain): is repelled by

water

a. Triglyceride (fats): composed of

3 molecules of fatty acid joined to 1

molecule of the alcohol glycerol

Saturated fatty acid: each C atom is covalently bonded to 4 other atoms

- Single bonds between carbons

- Each C atom is “full” or saturated

- Solid at room temperature

Unsaturated fatty acid:

C atoms are not

bonded to maximum #

of atoms they can be

-Have double bonds

w/in carbon chain

- Liquid at room

temperature

b. Phospholipids: 2 (not 3) fatty

acids attached to molecule of

glycerol, which has a phosphate

group attached

-make up phospholipid bilayer of

cell membranes due to their ability

to form a barrier between outside &

inside cell

c. Waxes: type of structural lipid

consisting of a long fatty-acid chain

joined to a long alcohol chain; are

waterproof

-form protective coatings on outside

of plants & inside animals

d. Steroids: composed of 4 fused

carbon rings w/ various functional

groups attached

ie: cholesterol as precursor for

testosterone

4.Nucleic Acids: large

& complex organic

molecules that store &

transfer important info

in the cell

Made of nucleotides:

phosphate group, 5-C

sugar & a ring-shaped

nitrogenous base

RNA = ribonucleic acid; stores & transfers

info from DNA for making proteins

-DNA = deoxyribonucleic acid;

determines characteristics of an

organism & directs cell activities