Transcript 1.2 The Chemicals of Life - Father Michael McGivney

1.2 The Chemicals of Life
Hydrocarbons
• Nonpolar and form straight or branched chains
and ring shaped structures.
• Names reflect the number of carbons, the
number and location of any double or triple
bonds and any functional groups.
• Names based on the number of carbons in the
longest carbon chain:
1 carbon......meth
2 carbons....eth
3 carbons....prop
4 carbons....but
5 carbons....pent
6 carbons....hex
7 carbons....hept
8 carbons....oct
9 carbons....non
10 carbons..dec
Organic Chemistry
• The study of carbon compounds
• Most organic compounds are classified as
hydrocarbons.
• Hydrocarbons (hydrogens bonded to
carbons) can be classified as
– Saturated
• Single bonds between carbons
• Do not react with H
– Unsaturated
• Double or triple bonds between carbons
• React with H
Organic Compounds
1. Hydrocarbons
2. Derivatives of halogen acids (water and
ammonia)
3. Carbonyl compounds (C=O)
Naming Organic Compounds
Nomenclature
• The system developed for naming these
compounds is the IUPAC.
• Hydrocarbons are studied and named based
on bond, atom arrangement, and number of
atoms.
1. Alkanes (Paraffins)
CnH2n+2
• Saturated
• Named according to the number of Carbon
atoms
• Names end in ‘-ane’
# of Carbon Atoms Structure
Name
1
CH4
Methane
2
CH3CH3
Ethane
3
CH3CH2CH3
Propane
4
CH3 (CH2) 2CH3
Butane
5
CH3 (CH2)4CH3
Pentane
6
CH3 (CH2) 4CH3
Hexane
7
CH3 (CH2)5CH3
Heptane
8
CH3 (CH2)7CH3
Octane
9
CH3 (CH2) 7CH3
Nonane
10
CH3 (CH2)8CH3
Decane
• Most organic compounds have side chains
or branches known as alkyl’s and the main
chain is the parent.
• When naming alkyl side chains the same
nomenclature seen for the alkanes is used,
but the ‘-ane’ ending becomes a ‘-yl’
ending.
Naming branched alkanes
1. Find the longest continuous carbon chain
(parent), this is not always a straight line.
2. Number the parent chain, starting at the end
closest to the branch.
3. Identify the branch and its numerical position
4. Attach the number and name of the branch to the
name of the parent
5. When more than one branch exists arrange them
in alphabetical order
Ex. CH3CH2CHCH2CH2CH2CH3
CH2CH2CH3
2. Alkenes (Olefins)
•
•
•
•
•
•
•
Unsaturated
Name ends in ‘-ene’ with one double bond
‘-adiene’ with 2 double bonds
‘-atriene’ with 3 double bonds
Ex. CH3CH2CH3
Propane
CH2=CHCH3
Propene
When numbering the carbons in the longest chain,
the first carbon is the one closest to the double
bond.
• Ex. CH3CH=CHCH2CH3
2 pentene
• CH3CH=CHCH=CH2
1,3 pentadiene
3. Alkynes
•
•
•
•
•
•
•
Unsaturated with at least 1 triple bond
Name ends in ‘-yne’ with 1 triple bond
Name ends in ‘-adiyne’ with 2 triple bonds
Name ends in ‘-atriyne’ with 3 triple bonds
Ex. CH3CH2CH3
Propane
CH = CCH3
Propyne
When numbering the carbons, the chain is
numbered to give the lowest number to the
triple bond
CH3CH2C=CH
1-butyne
4. Cyclic Hydrocarbons
• When naming cyclic hydrocarbons the
prefix ‘cyclo-’ is added to the name of the
alkane or alkene.
• Cyclohexane
Cyclohexene
• Benzene is a special form of cycloheane
with 3 double bonds
Benzene
• When side chains are attached to benzene
their names become prefixes to benzene
when benzene is the parent
--CH3
methylbenzene
• When benzene is attached to a chain with
more than 7 carbons it is now called
‘phenyl-’ or if it is attached to a chain with a
functional group.
CH3
CH(CH2)5CH3 2-phenyloactane
Structural Isomers
•
•
•
Isomers = 2 or more different compounds
with the same molecular formula
Structural Isomers = compounds with the
same molecular formula whose atoms
bond in different orders
Ex. Structural isomers for C4H10
a. CH3CH2CH2CH3
b. CH3CHCH3
CH3
butane
Methylpropane
CH3
• CH3CH2CH2-propyl (n-propyl)
n= normal (straight)
iso= isometric
sec = secondary
t = tertiary
or
CH3CH
isopropyl
CH3CH2CH2CH2 –
Butyl (n-butyl)
Isobutyl
t-butyl
Example
• In monosaccharides, the number of isomers
that are possible can be determined by the
number of chiral carbon atoms.
•In a monosaccharide that contains n chiral centers, there are 2n
possible isomers. This idea is illustrated below for a
monosaccharide that contains 2 chiral carbon atoms; 22 = 4
isomers.
Exercise
• How many isomers are there of
• How many chiral carbon atoms are there in
General
Chemistry
Online:
Isomer
Construction
Set
Stereoisomers
•
•
Compounds that have the same structure
but differ in the arrangement of atoms in
space
A example of stereoisomers are geometric
isomers. Geometric isomers only occur in
two types of compounds:
1. Alkenes
2. Cyclic compounds
Geometric Isomers
• Stereoisomers that differ by
having similar compounds
on the same side or opposite
sides of a rigid molecule
(double bond, cyclic
compound)
• When single bonds exist
between carbons, they can
move, spin, rotate and flex
to adjust their conformation.
Carbons attached by double
bonds or attached in a
cyclic compound are unable
to alter their conformation.
• Two like groups on the same side of a rigid
bond are said to be CIS. Like groups on
opposite sides are said to be TRANS.
• These molecules are said to be Chiral
molecules
http://cwx.prenhall.com/petrucci/medialib/media_portfolio/
text_images/083_Chirality.MOV
Exercise 1:
• Which molecules are mirror images of each
other?
Hint: Look at the Chiral carbon atoms
Exercise 2
• Which molecule is a mirror image of this
one:
Functional Groups
• Site of chemical reactivity in a molecule
• Include pi bonds (double or triple bonds) or
an electronegative/electropositive atom
Common Functional Groups
• Carbon with H,O, S and P attachments
• More reactive than the hydrocarbon (C and
H only) of a molecule
• Site of chemical reactions  functional
groups
Functional Groups in Biomolecules
(Table 1, pp. 25, Nelson Biology 12)
Group
Hydroxyl
Carboxyl
Amino
Sulfydryl
Phosphate
Carbonyl
Structure
Formula
Found in
1. Alcohols
• Structure: contains a hydroxyl group (-OH)
bonded to a sp3 hybridized carbon
• Function: used in alcoholic beverages, gasline anti-freeze or as bacteriocidal agent
• Naming: From the parent chain of alkanes
of alkenes, the ‘e’ is replaced with the
ending ‘-ol’
• Example: CH3OH  Methanol
CH2=CHCH2OH  2-propenol
Note: More than one OH group is designated
by di-, tri-, etc…
2. Aldehydes
• Structure: Carbonyl compound that
contains at least one hydrogen attached to a
carbonyl carbon
• Functon: Found in living systems in the
form of sugars and hormones
• Naming: From the parent chain of alkanes
or alkenes, the ‘e’ is replaced with the
ending ‘-al’
• Example:
3. Ketones
• Structure: Carbonyl compound that
contains two alkyl/aryl groups attached to
the carbonyl carbon
• Function: See aldehydes
• Naming: From the parent chain of alkanes
or alkenes, the ‘e’ is replaced with the
ending ‘-one’
• Example:
4. Amines
• Structure: N bonded to 3 other atoms, H, C or
combination of the two
• Function: Found in many proteins and nucleic
acids. Adrenaline stimulates nervous system. Can
be extracted from plants as decongestants
• Naming: The alkyl or aryl group is named then
given the ending ‘-amine’
• Example
5. Amides
• Structure: N bonded to a carbonyl carbon
• Function: in living systems, found in urea
• Naming: from the parent chain of alkanes
or alkenes, the ‘e’ is replaced with the
ending ‘-amide’
• Synthesized from carboxylic acids and
ammonia or amine
6. Thiol
• Structure: Sulfhydryl group (SH)
• Function: amino acids
• Naming: From the parent chain of alkanes
or alkenes, the ‘e’ is replaced with the
ending ‘-thiol’
• ethanethiol
7. Ether
• Structure: O molecule bonded between 2
carbons. Can be open chain or cyclic
(ROR)
• Function: made from reactions involving
alcohols
• Naming: Identify alkyl group to the left of
O and alkyl group to the right and end with
the suffix ‘-ether’
• Methyl ethyl ether
8. Esters
• Structure: C bonded to 2 O atoms, one of
which is bonded to an alkyl group
• Naming: Name alkyl group attached to O.
Then name parent carboxylic acid with
ending changed to ‘-oate’
• Methyl ethanoate
9. Carboxylic Acid
• Structure: contains a carboxylic group
(COOH), made of a carbonyl group and a
hydroxyl group
• Naming: parent alkane is name, ‘e’ is
replaced with ‘-oic acid’
• Methanoic acid
Exercise
• Identify and name the functional groups in
this molecule
Functional
Groups Video
http://www.zerobio.com/videos/functional_circle2.html
Linkage Bonds
•
•
•
Organic macromolecules are composed of
many tiny subunits that are linked together
Carbohydrates, lipids, proteins and nucleic
acids are all assembled in the same way
To link subunits a covalent bond is formed
between two subunits in which:
1. One molecule contains a hydroxyl group
(OH)
2. One molecule contains a hydrogen (H)
• The hydroxyl group combines with the
hydrogen in a process called a dehydration
reaction where water is removed.
• Energy is required to position the two
subunits and to apply enough stress on the
bonds to break them. This process is called
catalysis.
• When macromolecules are broken, water is
added to separate the linkage groups 
hydrolysis reaction.
Macromolecules
Carbohydrates
Lipids
Proteins
Nucleic Acids
Macromolecules
Dehydration Synthesis (Condensation Reaction)
Two subunits link together through the removal of a water
molecule.
Dehydration synthesis is an anabolic reaction that absorbs
energy.
Macromolecules
Hydrolysis Reaction
Two subunits break apart through the addition of a water
molecule.
Hydration synthesis is a catabolic reaction that releases
energy.
Carbohydrates
• Produced through plants and algae through the
process of photosysnthesis
• Carbohydrates are used for energy, building materials
and for cell identification and communication.
• Carbohydrates contain carbon, hydrogen and oxygen
in a 1:2:1 ratio. General formula – (CH2O)n, n
represents the # of C atoms.
• Carbohydrates are classified into 3 groups:
1. Monosaccharides
2. Oligosaccharides
3. Polysaccharides
Monosaccharides
• Simple sugars, ex. glucose, galactose, fructose
• 5 or more carbons – linear in dry state, form ring
structure when dissolved in water.
• α – glucose, 50% chance OH group of C 1 will be
below plane of ring.
• β – glucose, 50% chance OH group of C 1 will be
above plane of ring.
EXERCISE
How many of the structures shown below are
ketoses?
MONOSACCHARIDES
QUIZ: Select the formula that represents a monosaccharide
C4H8O4
C5H10O10
C6H6O12
C6H6O6
Oligosaccharides
• 2 or 3 simple sugars attached by covalent
glycosidic linkages, formed by
condensations (dehydration synthesis)
reactions.
• Ex. Maltose, Sucrose
Polysaccharides
• 100s – 1000s of
monosaccharides held
together by glycosidic
linkages.
• Used for energy
storage and structural
support.
• Starch and Glycogen
– storage
• Cellulose and Chitin –
structure
Condensation and Hydrolysis
Condensation/Hydrolysis
Dehydration
SynthesisHydrolysis
Lipids
• Hydrophobic molecules (“water fearing”)
of C H O that are generally nonpolar
• Used for storing energy, building
membranes and chemical signals.
• Includes fats, phospholipids, steroids (e.g.,
cholesterol and sex hormones) and waxes
(waterproof coating on plants and
animals).
Molecular Structures of Fat
• Triglycerides = glycerol and 3
fatty acids formed by ester
linkage (esterification)
Saturated Fats
• Usually come from animals.
• Solid at room temperature due to
increased van der Waals attractions
• In animals, they are used for longterm energy storage, insulation,
protection and helps dissolve fat
soluble vitamins.
• NO double bonds between carbon
atoms.
Fats
Lipids
Unsaturated Fats
• Usually comes from plant oils.
• Liquid at room temperature.
• One or more double bonds
between carbon atoms.
• Rigid kinks reduce the number
of van der Waals attractions
Lipids
Triglycerides
Esterification of a Triglyceride
• The hydroxyl group of one glycerol reacts with the
carboxyl group of three fatty acids.
• The resulting bond is an ester linkage.
Phospholipids
• Composed of one glycerol, two fatty acids
and a highly polar phosphate group.
• Form cellular membranes (phospholipid
bilayer).
• The phospholipid bilayer is virtually
impermeable to macromolecules,
relatively impermeable to charged ions,
and quite permeable to small, lipid soluble
molecules.
• O2 and CO2 diffuse through with very
little resistance.
• Larger molecules pass through the
membrane using carrier proteins
(facilitated diffusion).
Steroids (Sterols)
• Composed of 4 fused hydrocarbon
rings & functional groups.
• Ex. Cholesterol, testosterone, estrogen,
progesterone.
Waxes
•Long chain fatty acids linked to alcohols or
carbon ring.
•Firm, pliable consistency, used as a
waterproof coating.
Proteins
• Proteins are made of one or
more amino acid polymers that
have been coiled together.
• Of the 20 amino acids that
make up proteins, we must
consume 8, as we can not
make these essential amino
acids on our own: trp, met,
val, thre, phe, leu, ile, lys.
• The bonds that hold amino
acids together are called
peptide bonds.
Amino Acids
• Amphiprotic (posses both acidic, carboxyl,
and basic, amino groups).
• May be polar, nonpolar or charged
depending on the R group
• Sequence determines the final shape
(conformation) of protein.
Proteins
The Four Levels of Protein Folding
• Primary Structure: The sequence of amino acids in a polypeptide
chain, which is determined by the nucleotide sequence of a particular
gene.
• Secondary Structure: The folding and coiling of the polypeptide chain
as it grows into a pleated sheet or helix
• H bond between C=O group and N-H group 4 bonds away forms
a helix.
• When 2 parts of the chain lie parallel forms a pleated sheet
• Tertiary Structure: The polypeptide chain undergoes additional folding
due to side chain interactions.
• Attraction and repulsion between polypeptide and its
environment.
• Stabilized by R group interactions.
• Proline forms natural kink
• Disulfide bridge forms between 2 cysteines and are strong
stabilizers
• Quaternary Structure: Two or more polypeptide chains come together,
such as in collagen and haemoglobin.
• Temperature and pH changes can cause a
protein to unravel (denature). A denatured
protein is unable to carry out its biological
function.
• Chaperone Proteins aid a growing
polypeptide to fold into tertiary structure
• Globular Protein – one or more polypeptide
chains that take on a rounded shape.
Rediscovering
Biology Animation
Archive
Nucleic Acids
• Nucleic acids are found in DNA
(stores hereditary info.), RNA
(ribonucleic acid), ATP and nucleotide
coenzymes (NAD+, NADP+ and FAD)  used in
energy transformations.
• DNA and RNA are nucleotide polymers.
• Nucleotides consist of a nitrogenous base, a fivecarbon sugar and a phosphate group.
• The nitrogenous bases are: adenine (A), guanine
(G), cytosine (C), thymine (T) and uracil (U).
Nucleic Acids
• Cytosine, thymine and uracil are single-ringed
pyramidines, while adenine and guanine are larger
double-ringed purines.
Purines always
bond with a
pyramidine.
• In DNA, A bonds with T with 2 hydrogen bonds, and G
bonds with C with 3 hydrogen bonds.
• The two strands are antiparallel (one strand is upside
down compared to the other).