BIOCHEMISTRYBIOCHEMISTRY

CHEMISTRY OF LIFECHEMISTRY OF LIFE

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

• AtomAtom: the actual basic unit - : the actual basic unit - composed of protons, neutrons, and composed of protons, neutrons, and electronselectrons

THE ATOMTHE ATOM

• Just like cells are the basic unit of life, the Just like cells are the basic unit of life, the ATOMATOM is the basic unit of matter. is the basic unit of matter.

• They are very small. If placed side by side They are very small. If placed side by side one million would stretch a distance of 1cm. one million would stretch a distance of 1cm.

• The atom is made up of The atom is made up of 33 particles. particles.ParticleParticle ChargeCharge

PROTONPROTON ++

NEUTRONNEUTRON NEUTRALNEUTRAL

ELECTRONELECTRON --

• Electrons are not present within the atom, Electrons are not present within the atom, instead instead THEY REVOLVE AROUND THE THEY REVOLVE AROUND THE NUCELUS OF THE ATOM & FORM THE NUCELUS OF THE ATOM & FORM THE ELECTRON CLOUDELECTRON CLOUD

• Draw a helium atom. Indicate where the Draw a helium atom. Indicate where the protons, neutrons and electrons are. protons, neutrons and electrons are.

+ +-

-

PROTONSNEUTRONS

ELECTRONS

ATOMIC # = 2 (PROTONS)

ATOMIC MASS = 4 (PROTONS & NEUTRONS)

ISOTOPESISOTOPES

• atoms of the same element that atoms of the same element that HAVE A HAVE A DIFFERENT NUMBER OF NEUTRONSDIFFERENT NUMBER OF NEUTRONS

• Some isotopes are radioactive. This means Some isotopes are radioactive. This means that their nuclei is unstable and will break that their nuclei is unstable and will break down at a down at a CONSTANT RATECONSTANT RATE over time. over time.

• There are several practical uses for There are several practical uses for radioactive isotopes:radioactive isotopes:

1.1. CARBON DATINGCARBON DATING2.2. TRACERSTRACERS3.3. KILL BACTERIA / CANCER CELLSKILL BACTERIA / CANCER CELLS

COMPOUNDSCOMPOUNDS

• a substance formed by the chemical a substance formed by the chemical combination of combination of 2 or more elements2 or more elements in definite in definite proportionsproportions– Ex: water, salt, glucose, carbon dioxide Ex: water, salt, glucose, carbon dioxide

• The cell is a The cell is a COMPLEX CHEMICAL COMPLEX CHEMICAL FACTORYFACTORY containing some of the same containing some of the same elements found in the nonliving elements found in the nonliving environment. environment.

• carbon (C), hydrogen (H), oxygen (O), and carbon (C), hydrogen (H), oxygen (O), and nitrogen (N) are present in the greatest nitrogen (N) are present in the greatest percentagespercentages

TWO TYPES OF COMPOUNDSTWO TYPES OF COMPOUNDS

• Organic - Contain C, H, and O in some Organic - Contain C, H, and O in some ratio (usually referred to as chemicals of ratio (usually referred to as chemicals of life) life)

– Carbohydrates, Proteins, Lipids, Nucleic AcidsCarbohydrates, Proteins, Lipids, Nucleic Acids

• Inorganic - usually "support" life - no Inorganic - usually "support" life - no specific ratio of C, H, and Ospecific ratio of C, H, and O

– Water (H2O), Carbon Dioxide (CO2)Water (H2O), Carbon Dioxide (CO2)

CHEMICAL BONDSCHEMICAL BONDS

• Chemical bonds hold the atoms in a Chemical bonds hold the atoms in a molecule together. molecule together.

• There are 2 types of chemical bonds There are 2 types of chemical bonds IONICIONIC and and COVALENTCOVALENT

IONIC BONDSIONIC BONDS

• Occur when 1 or more electrons are Occur when 1 or more electrons are TRANSFERREDTRANSFERRED from one atom to another. from one atom to another.

• When an atom loses an electron it is a When an atom loses an electron it is a POSITIVEPOSITIVE charge. charge.

• When an atom gains an electron it is a When an atom gains an electron it is a NEGATIVENEGATIVE charge charge

• These newly charged atoms are now called These newly charged atoms are now called IONSIONS– Example: NaCl (SALT)Example: NaCl (SALT)

COVALENT BONDSCOVALENT BONDS

• Occur when electrons are Occur when electrons are SHAREDSHARED by atoms. by atoms. • These new structures that result from covalent These new structures that result from covalent

bonds are called bonds are called MOLECULESMOLECULES• ** In general, the more chemical bonds a ** In general, the more chemical bonds a

molecule has the more energy it contains molecule has the more energy it contains

SHARING IS CARING!SHARING IS CARING!

MIXTURESMIXTURES

• Water is not always pure. It is often found as Water is not always pure. It is often found as part of a mixture. part of a mixture.

• A mixture is a material composed of A mixture is a material composed of TWO OR TWO OR MORE ELEMENTS OR COMPOUNDS THAT MORE ELEMENTS OR COMPOUNDS THAT ARE PHYSICALLY MIXEDARE PHYSICALLY MIXED– Ex: salt & pepper mixed, sugar and sand – Ex: salt & pepper mixed, sugar and sand – can be can be

easily separated easily separated

SOLUTIONSOLUTIONTwo parts:Two parts:• SOLUTE – SOLUTE – SUBSTANCE THAT IS BEING SUBSTANCE THAT IS BEING

DISSOLVED (SUGAR / SALT)DISSOLVED (SUGAR / SALT)• SOLVENTSOLVENT - the substance in which the solute - the substance in which the solute

dissolvesdissolves• Materials that do not dissolve are known as Materials that do not dissolve are known as

SUSPENSIONSSUSPENSIONS. . – Blood is the most common example of a Blood is the most common example of a

suspension. suspension. – Cells & other particles remain in suspension.Cells & other particles remain in suspension.

FORMULAFORMULA

• The chemical symbols and numbers that The chemical symbols and numbers that compose a compound ("compose a compound ("reciperecipe")")

• Structural FormulaStructural Formula – Line drawings of the – Line drawings of the compound that shows the elements in compound that shows the elements in proportion and how they are bondedproportion and how they are bonded

• Molecular FormulaMolecular Formula – the ACTUAL – the ACTUAL formula for a compoundformula for a compound

CC22HH66OO

ACIDS & BASESACIDS & BASES• Acids: always (almost) begin with "H" because Acids: always (almost) begin with "H" because

of the excess of H+ ions (hydrogen)of the excess of H+ ions (hydrogen)– Ex: lemon juice (6), stomach acid (1.5), acid rain Ex: lemon juice (6), stomach acid (1.5), acid rain

(4.5), normal rain (6)(4.5), normal rain (6)

Facts about AcidsFacts about Acids• Acids turn litmus paper Acids turn litmus paper BLUEBLUE and usually and usually

taste taste SOURSOUR. . • You eat acids daily (coffee, vinegar, soda, You eat acids daily (coffee, vinegar, soda,

spicy foods, etc…)spicy foods, etc…)

ACIDS & BASESACIDS & BASES• Bases: always (almost) end with -OH because Bases: always (almost) end with -OH because

of the excess of hydroxide ions (Oxygen & of the excess of hydroxide ions (Oxygen & Hydrogen)Hydrogen)– EX: oven cleaner, bleach, ammonia, sea water, EX: oven cleaner, bleach, ammonia, sea water,

blood, pure waterblood, pure water

Facts about BasesFacts about Bases• Bases turn litmus Bases turn litmus BLUEBLUE. . • Bases usually feel Bases usually feel SLIPPERYSLIPPERY to touch and to touch and

taste taste BITTERBITTER. .

Neutralization Reactions Neutralization Reactions

• When an acid reacts with a base to produce a When an acid reacts with a base to produce a salt and water.salt and water.

pH SCALEpH SCALE• measures degree of measures degree of

substance alkalinity or substance alkalinity or acidityacidity

• Ranges from Ranges from 0 to 140 to 14

• 0 – 5 strong acid0 – 5 strong acid• 6-7 neutral6-7 neutral• 8-14 strong base8-14 strong base

• The goal of the body is to maintain The goal of the body is to maintain HOMEOSTASIS (neutrality)HOMEOSTASIS (neutrality) – to do this when – to do this when pH is concerned, we add weak acids & bases to pH is concerned, we add weak acids & bases to prevent sharp changes in pH. prevent sharp changes in pH.

• These are called These are called BUFFERSBUFFERS

And now for the And now for the Biochemistry portion of Biochemistry portion of

things….things….

CARBOHYDRATESCARBOHYDRATES

• Living things use carbohydrates as a key source Living things use carbohydrates as a key source of of ENERGYENERGY! !

• Plants use carbohydrates for structure Plants use carbohydrates for structure ((CELLULOSECELLULOSE) ) – include sugars and complex carbohydrates include sugars and complex carbohydrates

(starches) (starches) – contain the elements carbon, hydrogen, and oxygen contain the elements carbon, hydrogen, and oxygen

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

Monosaccharides (simple sugars) Monosaccharides (simple sugars)

• all have the formula C6 H12 O6 all have the formula C6 H12 O6 • all have a single ring structure all have a single ring structure

– (glucose is an example) (glucose is an example)

Disaccharides (double sugars) Disaccharides (double sugars)

• all have the formula C12 H22 O11 all have the formula C12 H22 O11 • sucrose (table sugar) is an example sucrose (table sugar) is an example

Polysaccharides Polysaccharides

• Formed of three or more simple sugar units Formed of three or more simple sugar units • Glycogen - animal starch stored in liver & muscles Glycogen - animal starch stored in liver & muscles • Cellulose - indigestible in humans - forms cell walls Cellulose - indigestible in humans - forms cell walls • Starches - used as energy storage Starches - used as energy storage

How are complex How are complex carbohydrates formed and carbohydrates formed and

broken down? broken down?

Dehydration Synthesis Dehydration Synthesis

• Combining simple molecules to form a more Combining simple molecules to form a more complex one with the complex one with the removal of waterremoval of water – ex. monosaccharide + monosaccharide ----> ex. monosaccharide + monosaccharide ---->

disaccharide + waterdisaccharide + water– (C6H12O6 + C6H12O6 ----> C12H22O11 + H2O(C6H12O6 + C6H12O6 ----> C12H22O11 + H2O

• Polysaccharides are formed from repeated Polysaccharides are formed from repeated dehydration syntheses of water dehydration syntheses of water – They are the stored extra sugars known as starchThey are the stored extra sugars known as starch

Hydrolysis Hydrolysis

• Addition of Addition of WATERWATER to a compound to to a compound to SPLITSPLIT it into smaller subunits it into smaller subunits – (also called chemical digestion) (also called chemical digestion) – ex. disaccharide + H2O ---> ex. disaccharide + H2O --->

monosaccharide + monosaccharidemonosaccharide + monosaccharide

C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6C12 H22 O11 + H2 O ---> C6 H12 O6 + C6 H12 O6

Lipids (Fats)Lipids (Fats)• Fats, oils, waxes, steroids Fats, oils, waxes, steroids • Chiefly function in Chiefly function in energy storage, protection, energy storage, protection,

and insulation and insulation • Contain carbon, hydrogen, and oxygen but the Contain carbon, hydrogen, and oxygen but the

H:O is not in a 2:1 ratio H:O is not in a 2:1 ratio • Tend to be Tend to be largelarge molecules -- an example of a molecules -- an example of a

neutral lipid is below neutral lipid is below

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

• 3 fatty acids + glycerol ----> neutral fat (lipid) 3 fatty acids + glycerol ----> neutral fat (lipid) • Fats -- found chiefly in Fats -- found chiefly in animalsanimals • Oils and waxes -- found chiefly in Oils and waxes -- found chiefly in plantsplants • Oils are liquid at room temperature, waxes are Oils are liquid at room temperature, waxes are

solids solids • Lipids along with proteins are key components of Lipids along with proteins are key components of

cell membranescell membranes • Steroids are special lipids used to build many Steroids are special lipids used to build many

reproductive hormones and cholesterolreproductive hormones and cholesterol

PROTEINSPROTEINS

• contain the elements carbon, hydrogen, oxygen, contain the elements carbon, hydrogen, oxygen, and nitrogen and nitrogen

• composed of MANY amino acid subunitscomposed of MANY amino acid subunits• It is the arrangement of the amino acid that It is the arrangement of the amino acid that

forms the primary structure of proteins. forms the primary structure of proteins. • The basic amino acid form has a The basic amino acid form has a carboxyl carboxyl

groupgroup on one end, a on one end, a methyl groupmethyl group that only that only has one hydrogen in the middle, and a has one hydrogen in the middle, and a amino amino groupgroup on the other end. on the other end.

• Attached to the methyl group is a Attached to the methyl group is a RR groupgroup. .

AN R GROUP IS ANY GROUP AN R GROUP IS ANY GROUP OF ATOMS – THIS CHANGES OF ATOMS – THIS CHANGES THE PROPERTIES OF THE THE PROPERTIES OF THE PROTEIN!PROTEIN!

FUNCTIONAL GROUPSFUNCTIONAL GROUPS

• There are certain groups of atoms that are There are certain groups of atoms that are frequently attached to the organic molecules we frequently attached to the organic molecules we will be studying, and these are called will be studying, and these are called functional functional groupsgroups. .

• These are things like These are things like hydroxyl groupshydroxyl groups which which form form alcoholsalcohols, , carbonyl groupscarbonyl groups which form which form aldehydesaldehydes or or ketonesketones, , carboxyl groupscarboxyl groups which which form form carboxylic acidscarboxylic acids, and , and amino groupsamino groups which form which form aminesamines. .

Major Protein Functions Major Protein Functions

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

Dipeptide Dipeptide

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

Hydrolysis of a dipeptide Hydrolysis of a dipeptide

• Breaking down of a dipeptide into amino acidsBreaking down of a dipeptide into amino acids• dipeptide + H2O ---> aminoacid + amino aciddipeptide + H2O ---> aminoacid + amino acid

Polypeptide (protein) Polypeptide (protein)

• composed of composed of three or morethree or more amino acids linked amino acids linked by synthesis reactions by synthesis reactions

• Examples of proteins include Examples of proteins include insulin, insulin, hemoglobin, and enzymes. hemoglobin, and enzymes.

• ** There are an extremely large number of ** There are an extremely large number of different proteins. different proteins.

• The bases for variability include differences in The bases for variability include differences in the number, kinds and sequences of amino the number, kinds and sequences of amino acids in the proteins acids in the proteins

NUCLEIC ACIDSNUCLEIC ACIDS

• in all cellsin all cells• composed of composed of NUCLEOTIDESNUCLEOTIDES• store & transmit store & transmit heredity/geneticheredity/genetic information information • Nucleotides consist of 3 parts:Nucleotides consist of 3 parts:• 1. 1. 5-Carbon Sugar5-Carbon Sugar• 2. 2. Phosphate GroupPhosphate Group• 3. 3. Nitrogenous BaseNitrogenous Base

DNA (deoxyribonucleic acid) DNA (deoxyribonucleic acid)

• contains the genetic code of instructions that direct a contains the genetic code of instructions that direct a cell's behavior through the synthesis of proteins cell's behavior through the synthesis of proteins

• found in the chromosomes of the nucleus (and a few found in the chromosomes of the nucleus (and a few other organelles) other organelles)

RNA (ribonucleic acid) RNA (ribonucleic acid) • directs cellular protein synthesis directs cellular protein synthesis • found in ribosomes & nucleoli found in ribosomes & nucleoli

CHEMICAL REACTIONS CHEMICAL REACTIONS

• a process that a process that changeschanges one set of chemicals into one set of chemicals into another set of chemicalsanother set of chemicals

• REACTANTSREACTANTS – elements or compounds that – elements or compounds that enter into a chemical reactionenter into a chemical reaction

• PRODUCTSPRODUCTS – elements or compounds that are – elements or compounds that are produced in a chemical reactionproduced in a chemical reaction

• Chemical reactions always involve the Chemical reactions always involve the breaking of breaking of bonds in reactantsbonds in reactants and the and the formation of new formation of new bonds in products.bonds in products.

• In a reaction, energy is either TAKEN IN In a reaction, energy is either TAKEN IN ((ENDOTHERMICENDOTHERMIC) or GIVEN OFF ) or GIVEN OFF ((EXOTHERMICEXOTHERMIC) )

• Can you think of an everyday example of Can you think of an everyday example of each type of reaction?each type of reaction?

Enzymes and Enzyme Action Enzymes and Enzyme Action • catalystcatalyst: inorganic or organic substance which : inorganic or organic substance which

speeds up the ratespeeds up the rate of a chemical reaction without of a chemical reaction without entering the reaction itself entering the reaction itself

• enzymesenzymes: organic catalysts made of protein : organic catalysts made of protein • most enzyme names end in -ase most enzyme names end in -ase • enzymes lower the energy needed to start a enzymes lower the energy needed to start a

chemical reaction. (chemical reaction. (activation energyactivation energy) ) • begin to be destroyed above 45øC. (above this begin to be destroyed above 45øC. (above this

temperature all proteins begin to be destroyed) temperature all proteins begin to be destroyed)

It is thought that, in order for an enzyme to affect the rate of a It is thought that, in order for an enzyme to affect the rate of a reaction, the following events must take place.reaction, the following events must take place.

1.1. The enzyme must form a The enzyme must form a temporary associationtemporary association with the with the substance or substances whose reaction rate it affects. substance or substances whose reaction rate it affects. These substances are known as These substances are known as substratessubstrates. .

2.2. The association between enzyme and substrate is thought to The association between enzyme and substrate is thought to form a form a close physical associationclose physical association between the molecules and between the molecules and is called the is called the enzyme-substrate complexenzyme-substrate complex. .

3.3. While the enzyme-substrate complex is formed, enzyme While the enzyme-substrate complex is formed, enzyme action takes place. action takes place.

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

How do enzymes work?How do enzymes work?

• substratesubstrate: molecules upon which an enzyme acts : molecules upon which an enzyme acts

• the enzyme is shaped so that it can only lock up the enzyme is shaped so that it can only lock up with a with a specific substratespecific substrate molecule molecule

enzymeenzymesubstrate -------------> productsubstrate -------------> product

"Lock and Key Theory"

• each enzyme is specific for each enzyme is specific for one and ONLY one one and ONLY one substratesubstrate (one lock - one key) (one lock - one key)

• this theory has many weaknesses, but it this theory has many weaknesses, but it explains some basic things about enzyme explains some basic things about enzyme functionfunction

Factors Influencing Rate of Enzyme Factors Influencing Rate of Enzyme Action Action

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

• high or low pH levels usually slow enzyme activityhigh or low pH levels usually slow enzyme activity• A few enzymes (such as gastric protease) work A few enzymes (such as gastric protease) work

best at a pH of about 2.0best at a pH of about 2.0

2. 2. TemperatureTemperature - strongly influences enzyme - strongly influences enzyme activity activity

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

• reactions proceed slowly below optimal reactions proceed slowly below optimal temperatures temperatures

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

3. 3. ConcentrationsConcentrations of Enzyme and Substrate of Enzyme and Substrate • ** When there is a fixed amount of enzyme and ** When there is a fixed amount of enzyme and

an excess of substrate molecules -- the rate of an excess of substrate molecules -- the rate of reaction will increase to a point and then level reaction will increase to a point and then level off. off.