Organic/BioChemistry

Inorganic vs.

Organic

Inorganic chemistry:

• compound which usually does not contain carbon AND hydrogen–Ex. O3, NaCl, H2O, CO2

Inorganic Chemistry:

• Compounds that do not need to contain:–Carbon: C AND–Hydrogen: H

Biochemical Compounds

A.K.A Organic chemistry:

• compounds usually found in Living or once living organisms

• contains both Carbon and Hydrogen• other elements found in living things

are: C, H, O, N, Phosphorous• Carbon = “element of LIFE”

Carbon: The element of LIFE

Biochemical Compounds

Types of Organic Compounds

found in all living things include:

1. Carbohydrates

2. Lipids

3. ProteiNs

4. Nucleic Acids

KNOW THESE!!!

Organic Chemistry:

• Organic Compounds (Carbs, lipids, Nucleic Acids, and Proteins) are chemically bonded together or broken down by:

– Dehydration Synthesis:

– Hydrolysis:

Dehydration Synthesis:

• process of joining (bonding) molecules to form large molecules called: MACROMOLECULES

• macromolecules are formed by REMOVING WATER!!– Hence the name dehydration…

as in dehydrate

Hydrolysis:

• process of breaking down macromolecules into smaller molecules called MONOMERS

• smaller molecules are formed by ADDING WATER!

PROCESSSTARTS WITH ...

ENDS WITH ...

Ex.

dehydration synthesis

small molecules (monomers)

large molecules &

water(macro-

molecules) 

growth

hydrolysiswater &

macromolecules

small molecules 

(monomers)digestion

• dehydration synthesis and hydrolysis

Macromolecules

• Smaller organic molecules join together to form larger molecules– macromolecules

• 4 major classes of macromolecules:– carbohydrates– lipids– proteins– nucleic acids

H2O

HO

HO H

H HHO

Polymers

• Long molecules built by linking repeating building blocks in a chain – monomers

• building blocks• repeated small units

– covalent bonds

Dehydration synthesisDehydration synthesis

H2O

HO

HO H

H HHO

How to build a polymer• Synthesis

– joins monomers by “taking” H2O out• one monomer donates OH–

• other monomer donates H+

• together these form H2O

– requires energy & enzymes

enzymeDehydration synthesisDehydration synthesis

Condensation reactionCondensation reaction

H2O

HO H

HO H HO H

How to break down a polymer• Digestion

– use H2O to breakdown polymers • reverse of dehydration synthesis

• cleave off one monomer at a time

• H2O is split into H+ and OH–

– H+ & OH– attach to ends

– requires enzymes– releases energy

HydrolysisHydrolysis

DigestionDigestion

enzyme

CarbonCarbonCompoundsCompounds

includeinclude

that consist ofthat consist of

which containwhich contain

Carbon Compounds - Concept MapCarbon Compounds - Concept Map

Building blocks of all lifeBuilding blocks of all life

CarbohydratesCarbohydrates LipidsLipids Nucleic acidsNucleic acids ProteinsProteins

Sugars andSugars and starchesstarches

Fats andFats and oilsoils NucleotidesNucleotides Amino AcidsAmino Acids

Carbon,Carbon,hydrogen,hydrogen,

oxygenoxygen

Carbon,Carbon,hydrogen,hydrogen,

oxygenoxygen

Carbon,hydrogen,Carbon,hydrogen,oxygen, nitrogen,oxygen, nitrogen,

phosphorusphosphorus

Carbon,Carbon,hydrogen,oxygen, hydrogen,oxygen,

nitrogen,nitrogen,

MacromoleculesMacromolecules

Building BlocksBuilding Blocks

ElementsElements

Macromolecules ID lab

Organic Compounds Cont…Carbohydrates:

• Made of the elements Carbon, Hydrogen & Oxygen

• Usually the Carbon, Hydrogen and Oxygen have a 1:2:1 ratio

• Used in organisms for quick energy

Carbohydrate:

a. Monosaccharide:

–simple sugar (1- ring)

– “ose” ending = sugar

–ex. Fructose, glucose:

Carbohydrate- Monosaccharide:

Carbohydrates:

b. Disaccharide• 2 simple sugars are

chemically bonded together

• ex. Sucrose, lactose

Carbohydrate- Disaccharide:

Carbohydrates:

C. Polysaccharide:• many sugars chemically bonded

together

• form long chains = polymers

• are macromolecules (lg molecules)

• ex. Starches, Chitin, and cellulose (found in fruits and veggies)

Carbohydrate- Polysaccharide

1 23

4

Elements PresentUsed by

organisms for ...

Building Blocks

(Monomers)

Related Terms & Info

carbon hydrogen oxygen

C:H:O = 1:2:1

always!

Quick energy

monosaccharide (simple sugars)

ex: glucose

Disaccharide: 2 connected

monosaccharide

(ex: maltose)

Polysaccharide3 or more connected

monosaccharide

(ex: starch, glycogen, chitin,

cellulose)

Organic Compounds cont.Lipids:

• Fats, cholesterol, waxes, oils• Lipids + H2O3 fatty acids +glycerol

• H to O ratio is much greater than 2:1

• Do not EMULSIFY - break apart in H2O

• Used as Stored energy in organisms

3 Fatty Acids and a Glycerol:

1

2

3

G

L

Y

C

E

R

O

L

Lipids

• 2 classifications of fats:1.Saturated fats

2.Unsaturated fats (which includes polyunsaturated fats)

Lipids:• Saturated fats:

• solid at room temperature

• linked to cardiovascular disease

• have many H-C bonds

Lipids:Unsaturated fats:• not solids at room temp

• not associated with cardiovascular disease

• have 1 or more double C-C bonds

• polyunsaturated fats have more than 1 double or triple C-C bond

Elements Present

Used by Organisms for

...Related Terms & Info

Carbon Hydrogen Oxygen ONLY ! There is

no specific

H:O ratio.

Stored Energy Structure 

(important part of cell

membranes)

saturated fat = C-C bonds are all single bonds

unsaturated fat = contain at least one double or triple C-

C bond

Building Blocks

of Lipids

3 Fatty Acids

1 glycerol

STOP!!! CK POINT

Topic: “chemistry of life”:

1. What elements are found in carbohydrates and lipids?

2. Explain 2 differences between carbohydrates and lipids.

3. Describe the function for each?4. How are monomers bonded together?

Broken apart?

Organic Compounds: NUCLEIC ACIDS: DNA & RNA

We will save the nitty, gritty details of DNA & RNA for later in the year (Genetics).  But for now, you should know there functions & basic structure, and how DNA compares to RNA.

DNA & RNA

DNA & RNA are polymers (many units) --- long chains of smaller repeating units. 

The repeating unit (monomers) in nucleic acids is called a nucleotide.

nucleotide remember this !

nucleotide 1. A phosphate

group

2. The carbohydrate… (see the “ring”?)

3. A nitrogen base:Adenine

Thymine

Guanine

Cytosine

What elements make up a nucleotide?

Repeating Units of Nucleotides

Nucleotide

Nucleotide

How many nucleotides are in the nucleic acid above?

Nucleic Acid: DNA

Nucleic Acid: RNA

Nucleic Acids:  DNA RNAFULL NAME Deoxyribonucleic

acidRibonucleic acid

 BASIC STRUCTURE 2 long twisting strands of

nucleotides in the form of a "double helix"

1 single strand of nucleotides

NUCLEOTIDE SUGAR

Deoxyribose Ribose

NITROGENOUS BASES

guanine (G) cytosine (C) adenine (A) thymine (T)

guanine (G) cytosine (C) adenine (A)

uracil (U)

LOCATION IN A CELL

nucleus  (the

chromosomes)

nucleus, in the cytoplasm, & at the ribosomes

FUNCTION the hereditary material 

of a cell, directs & controls cell

activities

involved in protein synthesis

Organic Compounds: ProteiNs'

• Contain the elements: Carbon, Hydrogen, Oxygen and Nitrogen

• take the shape of coils, helixes and globules

• ex. Collagen, hormones, muscle tissue, enzymes, Hemoglobin

Structure of

ProteiNs:

ProteiNs:

Made up of basic building blocks MONOMERS called:

AMINO ACIDS!!!!

Amino Acids:

• are the structural units (monomers) of protein

• bond together to form proteins

• The bond between amino acids are called

Peptide bonds

Amino Acids:

• The order/sequence and size of amino acid determines the protein made

• 2 amino acids bonded together = dipeptide

• amino acids form long chains called a polypeptide chains

Elements PresentUsed by

organisms for ...

Related Terms & Info

carbon hydrogen oxygen &NITROGEN

(sometimes Sulfur)

 

muscles enzymes

antibodies hormones Pigments

Hemoglobin

peptide bond = the bond that holds amino

acids together in protein molecules

dipeptide = 2 connected amino acids

polypeptide = 3 or more connected

amino acids  

monomersof Proteins: AMINO ACIDS!!!

STOP!!! CK POINT

Topic: “NA and ProteiNs”:

1. What are 2 types of Nucleic Acids?2. What is the “monomer” of a nucleic

acid?3. Describe the primary functions of

nucleic acids.4. Identify elements found in ProteiNs.5. What is the monomer for ProteiNs?

Group Activity:• Group leaders to get a marker• As a group, and when instructed, you

will go to a poster in a designated area in the room

• When the timer begins WRITE 1 ACCURATE FACT

• Wait until instructed, move to the next poster.

• As you move to each poster, read each statement then add an additional fact

Enzymes:

• Are forms of protein!!!!!!!!!!!!!

• Usually end in “ASE”

• Are not changed during a chemical rxn (a substance affects a reaction w/o being changed is called a CATALYST)

Enzymes:• Are organic catalysts :

–Control the rate of rxn within cells

–Catalysts allow rxns to occur at a faster rate

• Are used over and over

• For each chem. rxn, there is a specific enzyme to initiate the rxn

HOW ENZYMES WORK:• Substrate-

– the substance the enzyme acts upon

• Enzyme Active-– the region on the enzyme

• Substrate and Enzyme active site are specific to each other.

• The substrate fits the enzyme active site like a puzzle called: enzyme-substrate complex

HOW ENZYMES WORK:

• When the enzyme and substrate come together:

• The enzyme:

–may cause 2 molecules to join together

–may cause bonds to break

Enzyme-Substrate Complex

Enzyme-Substrate Complex

Factors Affecting Enzyme Action:

1. Concentration and surface area

2. Temperature

3. pH

4. Co-enzymes

Factors Affecting Enzyme Action:

• Concentration – determine rxn rates. Sometimes adding more concentration has little or no effect

Temperature– slowly raising the temp.

increases rate. However, at higher temps.,

the enzyme can breakdown called

Denaturation

• temp and enzymes

• pH level – specific to the enzyme stomach acidic, intestines slightly basic

• Presence of coenzymes (vitamins) allows an enzyme to perform

Carbon Compounds4 groups of carbon compounds found in living things are

carbohydrates, lipids, nucleic acids, and protein.

Living things use carbohydrates as their main source of energy. Plants and some animals also use carbohydrates for structural purposes.

Lipids can be used to store energy. Some lipids are important parts of cell membranes and waterproofing.

Nucleic acids store and transmit hereditary, or genetic, information.

Proteins:• control the rate of reactions and regulate cell processes. • build tissues such as bone and muscle. Others transport

materials or help to fight disease.

Chemical Reactions and Enzymes

Chemical rxns always involve the breaking of bonds in reactants and the formation of new bonds in products.

Cells use enzymes to speed up chemical reactions that take place in cells.

2009-2010

Enzymes:

“Helper” Protein molecules

Flow of energy through life• Life is built on chemical reactions

Chemical reactions of life• Processes of life

– building molecules• synthesis

– breaking down molecules• digestion

+

+

Nothing works without enzymes!• How important are enzymes?

– all chemical reactions in living organisms require enzymes to work• building molecules

– synthesis enzymes

• breaking down molecules– digestive enzymes

– enzymes speed up reactions• “catalysts”

+

+

enzyme

enzymeWe can’t live without enzymes!

Examples synthesis

digestion

+

+

enzyme

enzyme

Enzymes are proteins• Each enzyme is the specific helper to

a specific reaction– each enzyme needs to be the right shape for

the job– enzymes are named for the reaction

they help• sucrase breaks down sucrose• proteases breakdown proteins• lipases breakdown lipids• DNA polymerase builds DNA

Oh, I get it!They end in -ase

Enzymes aren’t used up• Enzymes are not changed by the reaction

– used only temporarily– re-used again for the same reaction with other

molecules– very little enzyme needed to help in many

reactions

enzyme

substrate product

active site

It’s shape that matters!

• Lock & Key model– shape of protein

allows enzyme & substrate to fit

– specific enzyme for each specific reaction

1

2

3

Enzyme vocabulary• Enzyme

– helper protein molecule

• Substrate– molecule that enzymes work on

• Products– what the enzyme helps produce from the

reaction

• Active site– part of enzyme

that substrate molecule fits into

What affects enzyme action

• Correct protein structure– correct order of amino acids– why? enzyme has to be right shape

• Temperature– why? enzyme has to be right shape

• pH (acids & bases)– why? enzyme has to be right shape

Order of amino acids• Wrong order = wrong shape = can’t do its job!

DNA

DNA

chain ofamino acids

chain ofamino acids

foldedprotein

foldedprotein

right shape!

wrong shape!

Temperature• Effect on rates of enzyme activity

– Optimum temperature• greatest number of collisions between

enzyme & substrate• human enzymes

– 35°- 40°C (body temp = 37°C)

– Raise temperature (boiling)• denature protein = unfold = lose shape

– Lower temperature T°• molecules move slower • fewer collisions between enzyme &

substrate

37°

Temperature

temperature

reac

tio

n r

ate

What’s happening here?!

humanenzymes

pH • Effect on rates of enzyme activity

– changes in pH changes protein shape

– most human enzymes = pH 6-8• depends on where in body

• pepsin (stomach) = pH 3

• trypsin (small intestines) = pH 8

7

pH

pH

reac

tio

n r

ate

20 1 3 4 5 6 8 9 10

stomachpepsin

intestinestrypsin

What’s happening here?!

11 12 13 14

2009-2010

For enzymes…What matters?

SHAPE!