Organic Molecules

Organic molecules are found in

living things.
 Contain Carbon, Hydrogen, and usually
oxygen
Organic Molecules are
Macromolecules
Macromolecules (polymers) are formed
from smaller building blocks called
monomers.
Polymer Monomer
carbohydrate monosaccharides
protein amino acid
nucleic acid nucleotide
Organic Molecules are
Macromolecules

Monomers combine
to make polymers
 Organic Molecules are Carbon
Compounds
 All of life is built on carbon
 Cells
 ~72% H2O
 ~25% carbon compounds
 carbohydrates
 lipids
 proteins
 nucleic acids
 ~3% salts
 Na, Cl, K…
Organic Molecules are Carbon
Compounds
 Organic chemistry is the study of
carbon compounds
 C atoms are versatile building blocks
 bonding properties
 4 stable covalent bonds

C
H H
H
Hydrocarbons – a component of
organic molecules
Made of carbons and hydrogens. Come in methane
many shapes (Carbon’s versatility) (CH4)
Macromolecules

Building Blocks
of Life
Macromolecules
 Smaller organic molecules join together
to form larger molecules
 macromolecules
 4 major classes of
macromolecules:
 carbohydrates
 lipids

 proteins

 nucleic acids
 Polymers
 Long molecules built by linking repeating
building blocks in a chain
 monomers
 building blocks
 repeated small units
H2O
 covalent bonds
HO H HO H

Dehydration synthesis

HO H
 How to build a polymer
 Synthesis
 joins monomers by “taking” H2O out
 one monomer donates OH–
 other monomer donates H+
 together these form H2O
H 2O
 requires energy & enzymes
HO H HO H
enzyme
Dehydration synthesis
Condensation reaction
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 H2O

 requires enzymes
HO H
 releases energy enzyme
Hydrolysis
Digestion HO H HO H
 CH2OH

H O
H
H
OH H
HO OH

H OH

Carbohydrates
energy
molecules
Carbohydrates
 Carbohydrates are composed of C, H, O
carbo - hydr - ate
CH2O
(CH
(CH2O)
2O)
xx CC6H
6H OO
1212 6 6

 Function:
 energy  energy storage
 raw materials structural materials

 Monomer: sugars
 ex: sugars, starches,sugar
cellulose
sugar sugar sugar sugar s
Sugars
 Most names for sugars end in -ose
 Classified by number of carbons
 6C = hexose (glucose)
 5C = pentose (ribose)

CH2OH CH2OH

H O O H
H
H
OH 6H H 5 HO
HO OH HO H

H OH OH H
Glucose Ribose
 CH2OH

Simple & complex sugars H O

H
H
 Monosaccharides HO
OH H
OH
 simple 1 monomer sugars H OH
 glucose
Glucose
 Disaccharides
 2 monomers
 sucrose

 Polysaccharides
 large polymers
 starch
Building sugars
 Dehydration synthesis
monosaccharides disaccharide

H2O
| | |
glucose glucose maltose
Building sugars
 Dehydration synthesis
monosaccharides disaccharide

H2O
| | |
glucose fructose sucrose
(table sugar)
Polysaccharides
 Polymers of sugars
 costs little energy to build
 easily reversible = release energy

 Function:
 energy storage
 starch (plants)
 glycogen (animals)
 in liver & muscles
 structure
 cellulose (plants)
 chitin (arthropods & fungi)
Linear vs. branched polysaccharides
slow release

starch
(plant)

energy
storage

glycogen
(animal)

fast release
Polysaccharide diversity
 Molecular structure determines function
in starch in cellulose

 isomers of glucose
 structure determines function…
 Digesting starch vs. cellulose

starch
easy to
digest enzyme

cellulose
hard to
digest
Cellulose
 Most abundant organic
compound on Earth
 herbivores have evolved a mechanism to
digest cellulose
 most carnivores have not

 that’s why they

eat meat to get
their energy &
nutrients
 cellulose = undigestible roughage
Any Questions?
Lipids: Fats & Oils

long term energy storage

concentrated energy
Lipids
 Lipids are composed of C, H, O
 long hydrocarbon chains (H-C)
 “Family groups”
 fats
 phospholipids

 steroids

 Do not form polymers

 big molecules made of only 3 subunits
 not a continuing chain
Fats
 Structure:
 glycerol (3C alcohol) + fatty acid
 fatty acid =
long HC “tail” with carboxyl (COOH) group “head”

enzyme
H2O

dehydration synthesis
Building Fats
 Triglycerides
 3 fatty acids linked to glycerol
Dehydration synthesis

H2O

dehydration synthesis

enzyme
H2O

enzyme
H2O

enzyme
HO
Fats store energy
 Long HC chain
 polar or non-polar?
 hydrophilic or hydrophobic?

 Function:
 energy storage
 concentrated
 2x carbohydrates
 cushion organs
 insulates body

 think whale blubber!

Saturated fats
 All C bonded to H
 No C=C double bonds
 long, straight chain
 most animal fats

 solid at room temp.

 contributes to
cardiovascular disease
(atherosclerosis)
= plaque deposits
Unsaturated fats
 C=C double bonds in
the fatty acids
 plant & fish fats
 vegetable oils

 liquid at room temperature

 the kinks made by double

bonded C prevent the
molecules from packing
tightly together

mono-unsaturated?
poly-unsaturated?
 “Trans” fats are a type of isomer
 Fatty acid tails are hydrocarbons.
Unsaturated fats have double bonds
between carbons.

Cis (olive oil)

Trans (partially hydrogenated

vegetable oil)
Form follows function!
Trans fats are straight and solidify at
room temperature.
Saturated vs. unsaturated
saturated unsaturated


 Phospholipids
 Structure:
 glycerol + 2 fatty acids + PO4
 PO4 = negatively charged

Polar Head Attracted to

Hydrophilic Water

Non-polar tail Repelled by

Water
Hydrophobic
Why is this important?
 Phospholipids create a barrier in water
 define outside vs. inside
 they make cell membranes!
Cholesterol
 Important cell component
 animal cell membranes
 precursor of all other steroids

 including vertebrate sex hormones

 high levels in blood may contribute to
cardiovascular disease
Cholesterol
Important component of cell membrane

helps keep
cell membranes

fluid & flexible

Any Questions?
Proteins

Multipurpose
molecules
Proteins
 Most structurally & functionally diverse group
 Function: involved in almost everything
 enzymes (pepsin, DNA polymerase)
 structure (keratin, collagen)
 carriers & transport (hemoglobin, aquaporin)
 cell communication
 signals (insulin & other hormones)
 receptors
 defense (antibodies)
 movement (actin & myosin)
Proteins
 Structure H2O

 monomer = amino acids

 20 different amino acids
 polymer = polypeptide
 protein can be one or more polypeptide
chains folded & bonded together
 large & complex molecules
 complex 3-D shape

hemoglobin

Rubisco growth
hormones
Amino acids
 Structure H O
H | ||
 central carbon
 amino group
—N—
—C— C—OH
 carboxyl group (acid) H |
 R group (side chain)
R
 variable group Oh, I get it!
 different for each amino acid amino = NH2
acid = COOH
 confers unique chemical
properties to each amino acid
 like 20 different letters of an
alphabet
 can make many words (proteins)
Building proteins
 Peptide bonds
 covalent bond between NH2 (amine) of
one amino acid & COOH (carboxyl) of
another
 C–N bond

H2O
dehydration synthesis

peptide
bond
Effect of different R groups:
Nonpolar amino acids
 nonpolar & hydrophobic

Why are these nonpolar & hydrophobic?

Effect of different R groups:
Polar amino acids
 polar or charged & hydrophilic

Why are these polar & hydrophillic?

Protein structure & function
 Function depends on structure
 3-D structure
 twisted, folded, coiled into unique shape

pepsin

hemoglobin

collagen
Primary (1°) structure
 Order of amino acids in chain
 amino acid sequence
determined by gene (DNA)
 slight change in amino acid

sequence can affect protein’s

structure & its function
 just one amino acid change can
make all the difference!

lysozyme: enzyme in
tears & mucus that
kills bacteria
Secondary (2°) structure
 “Local folding”
 folding along short sections of polypeptide
 interactions between

adjacent amino acids

 H bonds
 weak bonds
between R groups
 forms sections of
3-D structure
 -helix
 -pleated sheet
Tertiary (3°) structure
 “Whole molecule folding”
 interactions between distant amino acids
 hydrophobic interactions
 cytoplasm is
water-based
 nonpolar amino
acids cluster away
from water
 H bonds & ionic bonds
 disulfide bridges
 covalent bonds between
sulfurs in sulfhydryls (S–H)
 anchors 3-D shape
 Quaternary (4°) structure
 More than one polypeptide chain bonded
together
 only then does polypeptide become
functional protein
 hydrophobic interactions

collagen = skin & tendons hemoglobin

 Protein structure (review)

R groups
hydrophobic interactions
(H & ionic bonds)

3°
multiple
polypeptides
1° hydrophobic
amino acid interactions
sequence 4°
peptide bonds

determined 2°
by DNA R groups
H bonds
 Just 1
Sickle cell anemia out of 146
amino acids!

I’m But I’m

hydrophilic! hydrophobic!
 Protein denaturation
 Unfolding a protein
 conditions that disrupt H bonds, ionic
bonds
 temperature
 pH
 salinity
 alter 2° & 3° structure
 alter 3-D shape
 destroys functionality
Nucleic Acids
Information
storage
 Nucleic Acids
 Function:
 genetic material
 stores information
 genes
 blueprint for building proteins
 DNA  RNA  proteins
DNA  transfers information
 blueprint for new cells
 blueprint for next generation

proteins
 T
G A
T C
C A
A G
G
A
T
C
Nucleic Acids
 Examples:
 RNA (ribonucleic acid)
 single helix
 DNA (deoxyribonucleic acid)
 double helix
 Structure:
 monomers = nucleotides

DNA RNA
Nucleotides
 3 parts
 nitrogen base (C-N ring) Nitrogen base
 pentose sugar (5C) I’m the
A,T,C,G or U
 ribose in RNA part!
 deoxyribose in DNA
 phosphate (PO4) group
Types of nucleotides Purine = AG
Pure silver!
 2 types of nucleotides
 different nitrogen bases
 purines

 double ring N base

 adenine (A)
 guanine (G)
 pyrimidines
 single ring N base
 cytosine (C)
 thymine (T)
 uracil (U)
Nucleic polymer
 Backbone
 Sugar-phosphate
 N bases hang off the

sugar-phosphate backbone

Dangling bases?
Why is this important?
Pairing of nucleotides
 Nucleotides bond between
DNA strands
 H bonds
 purine :: pyrimidine

 A :: T

 2 H bonds
 G :: C
 3 H bonds

Matching bases?
Why is this important?
DNA molecule
 Double helix
 H bonds between bases
join the 2 strands
 A :: T
 C :: G

H bonds?
Why is this important?
Copying DNA
 Replication
 2 strands of DNA helix are
complementary
 have one, can build other

Matching halves?
Why is this
a good system?
When does a cell copy DNA?
 When in the life of a cell does DNA have
to be copied?
 cell reproduction
 mitosis
 gamete production
 meiosis
DNA replication
“It has not escaped our notice that
the specific pairing we have
postulated immediately suggests a
possible copying mechanism for the
genetic material.”
James Watson
Francis Crick
1953
Watson and Crick … and others…
Maurice Wilkins… and…
Rosalind Franklin (1920-1958)
 CH2OH
Macromolecules H O
H
H
Review OH H
HO OH
 Carbohydrates
H OH
 Empirical formula CH2O
 Functions: Quick energy (sugar), energy

storage in plants (starch), structure

(cellulose in plants, chitin in fungi +
arthropods)
 Monomer = monosaccharide

 Polymer = polysaccharide
Macromolecules
Review
 Lipids
 Made of C, H, and a few O
 Functions: Energy storage in

animals (triglycerides), Cell

membrane structure (phospholipids),
hormones (steroids)
 Fats made of 1 Glycerol, 3 Fatty

acids
 Fatty acids can be saturated (no C-C

double bonds) or unsaturated (C-C

double bonds)
Macromolecules
Review
 Proteins
 Made of C, H, O, N, S, P
 Many diverse functions
 Enzymes
 Membrane channels
 Hormones
 Structure
 Monomer = amino acids
 Polymer = polypeptide
 3-D shape determined by amino acid
sequence. Crucial to protein function
 1°, 2°, 3°, 4° levels of organization
 Macromolecules Review
 Nucleic Acids
 Information storage
 Examples: DNA and RNA

 Complementary base pairing 

genetic code can be copied

 A–T
 C–G
 Purine – Pyrimidine
 Hydrogen bonds hold nitrogenous bases
together
 Monomer = nucleotides
 Sugar, phosphate, nitrogenous base