BIOCHEMISTRY

CHEMISTRY OF LIFE

• Elements: simplest form of a

substance - cannot be broken down

any further without changing what it is

• Atom: the actual basic unit -

composed of protons, neutrons, and

electrons

THE ATOM

• Just like cells are the basic unit of life, the

ATOM is the basic unit of matter.

• They are very small. If placed side by side

one million would stretch a distance of 1cm.

• The atom is made up of 3 particles.

Particle Charge

PROTON +

NEUTRON NEUTRAL

ELECTRON -

• Electrons are not present within the atom,

instead THEY REVOLVE AROUND THE

NUCELUS OF THE ATOM & FORM THE

ELECTRON CLOUD

• Draw a helium atom. Indicate where the

protons, neutrons and electrons are.

+ +-

-

PROTONSNEUTRONS

ELECTRONS

ATOMIC # = 2 (PROTONS)

ATOMIC MASS = 4

(PROTONS &

NEUTRONS)

ISOTOPES

• atoms of the same element that HAVE A

DIFFERENT NUMBER OF NEUTRONS

• Some isotopes are radioactive. This means

that their nuclei is unstable and will break

down at a CONSTANT RATE over time.

• There are several practical uses for

radioactive isotopes:1. CARBON DATING

2. TRACERS

3. KILL BACTERIA / CANCER CELLS

COMPOUNDS

• a substance formed by the chemical

combination of 2 or more elements in definite

proportions

– Ex: water, salt, glucose, carbon dioxide

• The cell is a COMPLEX CHEMICAL

FACTORY containing some of the same

elements found in the nonliving

environment.

• carbon (C), hydrogen (H), oxygen (O), and

nitrogen (N) are present in the greatest

percentages

TWO TYPES OF COMPOUNDS

• Organic - Contain C, H, and O in some

ratio (usually referred to as chemicals of

life) – Carbohydrates, Proteins, Lipids, Nucleic Acids

• Inorganic - usually "support" life - no

specific ratio of C, H, and O– Water (H2O), Carbon Dioxide (CO2)

CHEMICAL BONDS

• Chemical bonds hold the atoms in a

molecule together.

• There are 2 types of chemical bonds

IONIC and COVALENT

IONIC BONDS

• Occur when 1 or more electrons are

TRANSFERRED from one atom to another.

• When an atom loses an electron it is a

POSITIVE charge.

• When an atom gains an electron it is a

NEGATIVE charge

• These newly charged atoms are now called

IONS

– Example: NaCl (SALT)

COVALENT BONDS

• Occur when electrons are SHARED by atoms.

• These new structures that result from covalent

bonds are called MOLECULES

• ** In general, the more chemical bonds a

molecule has the more energy it contains

SHARING IS CARING!

MIXTURES

• Water is not always pure. It is often found as

part of a mixture.

• A mixture is a material composed of TWO OR

MORE ELEMENTS OR COMPOUNDS THAT

ARE PHYSICALLY MIXED

– Ex: salt & pepper mixed, sugar and sand – can be

easily separated

SOLUTION

Two parts:

• SOLUTE – SUBSTANCE THAT IS BEING

DISSOLVED (SUGAR / SALT)

• SOLVENT - the substance in which the solute

dissolves

• Materials that do not dissolve are known as

SUSPENSIONS.

– Blood is the most common example of a

suspension.

– Cells & other particles remain in suspension.

FORMULA

• The chemical symbols and numbers that

compose a compound ("recipe")

• Structural Formula – Line drawings of the

compound that shows the elements in

proportion and how they are bonded

• Molecular Formula – the ACTUAL

formula for a compound

C2H6O

ACIDS & BASES

• Acids: always (almost) begin with "H" because

of the excess of H+ ions (hydrogen)

– Ex: lemon juice (6), stomach acid (1.5), acid rain

(4.5), normal rain (6)

Facts about Acids

• Acids turn litmus paper BLUE and usually

taste SOUR.

• You eat acids daily (coffee, vinegar, soda,

spicy foods, etc…)

ACIDS & BASES

• Bases: always (almost) end with -OH because

of the excess of hydroxide ions (Oxygen &

Hydrogen)

– EX: oven cleaner, bleach, ammonia, sea water,

blood, pure water

Facts about Bases

• Bases turn litmus BLUE.

• Bases usually feel SLIPPERY to touch and taste

BITTER.

Neutralization Reactions

• When an acid reacts with a base to produce a

salt and water.

pH SCALE

• measures degree of

substance alkalinity or

acidity

• Ranges from 0 to 14

• 0 – 5 strong acid

• 6-7 neutral

• 8-14 strong base

• The goal of the body is to maintain

HOMEOSTASIS (neutrality) – to do this when

pH is concerned, we add weak acids & bases to

prevent sharp changes in pH.

• These are called BUFFERS

And now for the

Biochemistry portion of

things….

CARBOHYDRATES

• Living things use carbohydrates as a key source

of ENERGY!

• Plants use carbohydrates for structure

(CELLULOSE)

– include sugars and complex carbohydrates

(starches)

– contain the elements carbon, hydrogen, and oxygen

(the hydrogen is in a 2:1 ratio to oxygen)

Monosaccharides (simple sugars)

• all have the formula C6 H12 O6

• all have a single ring structure

– (glucose is an example)

Disaccharides (double sugars)

• all have the formula C12 H22 O11

• sucrose (table sugar) is an example

Polysaccharides

• Formed of three or more simple sugar units

• Glycogen - animal starch stored in liver & muscles

• Cellulose - indigestible in humans - forms cell walls

• Starches - used as energy storage

How are complex

carbohydrates formed

and broken down?

Dehydration Synthesis

• Combining simple molecules to form a more

complex one with the removal of water

– ex. monosaccharide + monosaccharide ---->

disaccharide + water

– (C6H12O6 + C6H12O6 ----> C12H22O11 + H2O

• Polysaccharides are formed from repeated

dehydration syntheses of water

– They are the stored extra sugars known as starch

Hydrolysis

• Addition of WATER to a compound to

SPLIT it into smaller subunits

– (also called chemical digestion)

– ex. disaccharide + H2O --->

monosaccharide + monosaccharide

C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6

Lipids (Fats)

• Fats, oils, waxes, steroids

• Chiefly function in energy storage, protection,

and insulation

• Contain carbon, hydrogen, and oxygen but the

H:O is not in a 2:1 ratio

• Tend to be large molecules -- an example of a

neutral lipid is below

• Neutral lipids are formed from the union of one glycerol molecule and 3 fatty acids

• 3 fatty acids + glycerol ----> neutral fat (lipid)

• Fats -- found chiefly in animals

• Oils and waxes -- found chiefly in plants

• Oils are liquid at room temperature, waxes are solids

• Lipids along with proteins are key components of cell membranes

• Steroids are special lipids used to build many reproductive hormones and cholesterol

PROTEINS

• contain the elements carbon, hydrogen, oxygen,

and nitrogen

• composed of MANY amino acid subunits

• It is the arrangement of the amino acid that

forms the primary structure of proteins.

• The basic amino acid form has a carboxyl

group on one end, a methyl group that only

has one hydrogen in the middle, and a amino

group on the other end.

• Attached to the methyl group is a R group.

AN R GROUP IS ANY GROUP

OF ATOMS – THIS CHANGES

THE PROPERTIES OF THE

PROTEIN!

FUNCTIONAL GROUPS

• There are certain groups of atoms that are

frequently attached to the organic molecules we

will be studying, and these are called functional

groups.

• These are things like hydroxyl groups which

form alcohols, carbonyl groups which form

aldehydes or ketones, carboxyl groups which

form carboxylic acids, and amino groups

which form amines.

Major Protein Functions

• Growth and repair

• Energy

• Buffer -- helps keep body pH constant

Dipeptide

• formed from two amino acid subunits

• Formed by the process of Dehydration Synthesis

• amino acid + amino acid ----- dipeptide + water

Hydrolysis of a dipeptide

• Breaking down of a dipeptide into amino acids

• dipeptide + H2O ---> aminoacid + amino acid

Polypeptide (protein)

• composed of three or more amino acids linked

by synthesis reactions

• Examples of proteins include insulin,

hemoglobin, and enzymes.

• ** There are an extremely large number of

different proteins.

• The bases for variability include differences in

the number, kinds and sequences of amino

acids in the proteins

NUCLEIC ACIDS

• in all cells

• composed of NUCLEOTIDES

• store & transmit heredity/genetic information

• Nucleotides consist of 3 parts:

• 1. 5-Carbon Sugar

• 2. Phosphate Group

• 3. Nitrogenous Base

DNA (deoxyribonucleic acid)

• contains the genetic code of instructions that direct a

cell's behavior through the synthesis of proteins

• found in the chromosomes of the nucleus (and a few

other organelles)

RNA (ribonucleic acid)

• directs cellular protein synthesis

• found in ribosomes & nucleoli

CHEMICAL REACTIONS

• a process that changes one set of chemicals into

another set of chemicals

• REACTANTS – elements or compounds that

enter into a chemical reaction

• PRODUCTS – elements or compounds that are

produced in a chemical reaction

• Chemical reactions always involve the breaking of

bonds in reactants and the formation of new

bonds in products.

• In a reaction, energy is either TAKEN IN

(ENDOTHERMIC) or GIVEN OFF

(EXOTHERMIC)

• Can you think of an everyday example of

each type of reaction?

Enzymes and Enzyme Action

• catalyst: inorganic or organic substance which

speeds up the rate of a chemical reaction without

entering the reaction itself

• enzymes: organic catalysts made of protein

• most enzyme names end in -ase

• enzymes lower the energy needed to start a

chemical reaction. (activation energy)

• begin to be destroyed above 45øC. (above this

temperature all proteins begin to be destroyed)

It is thought that, in order for an enzyme to affect the rate of a

reaction, the following events must take place.

1. The enzyme must form a temporary association with the

substance or substances whose reaction rate it affects.

These substances are known as substrates.

2. The association between enzyme and substrate is thought to

form a close physical association between the molecules and

is called the enzyme-substrate complex.

3. While the enzyme-substrate complex is formed, enzyme

action takes place.

4. Upon completion of the reaction, the enzyme and product(s)

separate. The enzyme molecule is now available to form

additional complexes.

How do enzymes work?

• substrate: molecules upon which an enzyme acts

• the enzyme is shaped so that it can only lock up

with a specific substrate molecule

enzyme

substrate -------------> product

"Lock and Key Theory"

• each enzyme is specific for one and ONLY one

substrate (one lock - one key)

• this theory has many weaknesses, but it

explains some basic things about enzyme

function

Factors Influencing Rate of

Enzyme Action

1. pH - the optimum (best) in most living things is

close to 7 (neutral)

• high or low pH levels usually slow enzyme activity

• A few enzymes (such as gastric protease) work

best at a pH of about 2.0

2. Temperature - strongly influences enzyme activity

• optimum temperature for maximum enzyme function is usually about 35-40 C.

• reactions proceed slowly below optimal temperatures

• above 45 C most enzymes are denatured (change in their shape so the enzyme active site no longer fits with the substrate and the enzyme can't function)

3. Concentrations of Enzyme and Substrate

• ** When there is a fixed amount of enzyme and

an excess of substrate molecules -- the rate of

reaction will increase to a point and then level

off.