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BIOCHEMISTRY

CHEMISTRY OF LIFE

•  Elements: simplest form of a substance - cannot be broken down any further without changing what it is

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 -

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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)

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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)

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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.

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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.

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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 – 6 strong acid •  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

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And now for the BIOCHEMISTYR 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)

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Monosaccharides (simple sugars)

•  Have the formula C6 H12 O6 •  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

What is Missing?

•  Water (H2O) •  Where did it go? •  The formation between two things results in a

loss of water in a process called dehydration synthesis.

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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

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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

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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 + H2O ---> 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

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•  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

Dehydration Synthesis Again

Saturated vs Unsaturated Fats

Saturated fats DO NOT have any double bonds between the carbon molecules in the fatty acid chains. Because of this, the chains can pack tight and these will be solids at room temperature. An example is butter.

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Saturated vs Unsaturated Fats

Unsaturated fats have double bonds between the carbon molecules in the fatty acid chains. Because of this, the chains are loosely packed and these will be liquids at room temperature. An example is olive oil.

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 WHAT DIFFERENTIATES ONE AMINO ACID FROM ANOTHER. THERE ARE 20 AMINO ACIDS. SOME ARE HYDROPHOBIC, HYDROPHILIC AND OTHERS ARE CHARGED

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Proteins form just like lipids and carbs. They are composed of smaller subunits, in this case called amino acids, and form by dehydration synthesis.

Major Protein Functions

•  Growth and repair •  Energy •  Enzymes and hormones •  Buffer -- helps keep body pH constant

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Dipeptide

•  Formed from two amino acid subunits •  Formed by the process of Dehydration Synthesis •  amino acid + amino acid ----- dipeptide + water

Peptide Bond This is a special bond found between the last carbon of one amino acid and the first nitrogen of the next amino acid.

Hydrolysis of a Dipeptide •  Breaking down of a dipeptide into amino acids •  Dipeptide + H2O ---> amino acid + amino acid

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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, aka……DNA and RNA •  Composed of NUCLEOTIDES •  Store & transmit heredity/genetic information •  Nucleotides consist of 3 parts: •  1. 5-Carbon Sugar •  2. Phosphate Group •  3. Nitrogenous Base

Nucleotide

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Nucleotides in DNA

•  Just like amino acids, there are several different nucleotides. They are different in only the nitrogenous base.

•  Adenine •  Thymine •  Cytosine •  Guanine

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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.

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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 •  Begin to be destroyed above 45 degrees C.

(Above this temperature all proteins begin to be destroyed)

•  The protein is said to be DENATURED.

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.

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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.  Upon completion of the reaction, the enzyme and product(s) separate. The enzyme molecule is now available to form additional complexes.

Factors Influencing Rate of Enzyme Action

1.  pH - the optimum (best) in most living things is close to 7 (neutral)

2.  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)

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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.