Biological molecules

The FOUR Classes of Large Biomolecules

• All living things are made up of four classes of

large biological molecules:
• Carbohydrates
• Lipids
• Protein
• Nucleic Acids

• Macromolecules are large molecules composed

of thousands of covalently bonded atoms

• Molecular structure and function are inseparable

 The FOUR Classes of Large Biomolecules

• Macromolecules are polymers, built

from monomers
„ A polymer is a long molecule consisting of many
similar building blocks
„ These small building-block molecules are called
monomers
„ Three of the four classes of life’s organic
molecules are polymers
– Carbohydrates
– Proteins
– Nucleic acids
The synthesis and breakdown of polymers
• A dehydration reaction occurs when two monomers
bond together through the loss of a water molecule
• Polymers are disassembled to monomers by hydrolysis,
a reaction that is essentially the reverse of the
dehydration reaction
Dehydration Synthesis
Hydrolysis: Breakdown of polymers
 The Diversity of Polymers

• Each cell has thousands of different macromolecules.

• Macromolecules vary among cells of an organism,

vary more within a species, and vary even more
between species.

• An immense variety of polymers can be built from a

small set of monomers.
 Carbohydrates: serve as Fuel
and Building Material

• Carbohydrates include sugars and the polymers

of sugars

• The simplest carbohydrates are monosaccharides,

or single sugars

• Carbohydrate macromolecules are

polysaccharides, polymers composed of many
sugar building blocks
 Breaks down into microscopic
molecules

Loaf of bread Bread crumbs Polysaccharide

Monosaccharide Disaccharide
 Sugars: Monosaccharides

• Monosaccharides have molecular Glucose

formulas that are usually multiples
of CH2O

• Glucose (C6H12O6) is the most

common monosaccharide

• Monosaccharides are classified by

Main “fuel” for
‟ The location of the carbonyl group
bacteria, plants
‟ The number of carbons in the and animal cells
carbon skeleton
13
 Sugars: Disaccharides
• A disaccharide is formed when a dehydration
reaction joins two monosaccharides

• This covalent bond is called a glycosidic linkage

 Functions of Disaccharides

 Sucrose, for example, is table sugar, and it

is the most common disaccharide that
humans eat.
 Lactose is found in breast milk and provides
nutrition for infants.
 Maltose is a sweetener that is often found in
chocolates and other candies.
 Since it is an energy storage source, many
plants such as sugar cane are high in
sucrose.
Disaccharide

16
 Polysaccharides

• Polysaccharides, the polymers of sugars, have storage

and structural roles
• The structure and function of a polysaccharide are
determined by its sugar monomers and the positions of
glycosidic linkages
 Types of Polysaccharides: Storage

• Starch, a storage
polysaccharide of
plants, consists
entirely of glucose
monomers
• Plants store surplus
starch as granules
within chloroplasts
and other plastids
• The simplest form of
starch is amylose
 Types of Polysaccharides: Storage

• Glycogen is a storage
polysaccharide in
animals
• Humans and other
vertebrates store
glycogen mainly in
liver and muscle cells
Types of Polysaccharides: Structural

• The polysaccharide cellulose is a major

component of the tough wall of plant cells
• Like starch, cellulose is a polymer of glucose, but
the glycosidic linkages differ
• The difference is based on two ring forms for
glucose: alpha () and beta ()
Such Elegance!
 Polysaccharide
Random Acts of Biology
• Cellulose in human food passes through the
digestive tract as insoluble fiber
• Some microbes use enzymes to digest cellulose
• Many herbivores, from cows to termites, have
symbiotic relationships with these microbes

• Chitin, another structural polysaccharide, is found

in the exoskeleton of arthropods (crunch!)

• Chitin also provides structural support for the cell

walls of many fungi
Use of Cellulose
Source of Chitin
Use of Chitin

25
Amino acid and Protein
Proteins are polymers of amino acids.
 Facts of Protein
• Proteins are major components of all cellular
systems
• Proteins consist of one or more linear polymers
called polypeptides
• Proteins are linear and never branched
• Different AA’s are linked together via PEPTIDE
bonds
• The individual amino acids within a protein are
known as RESIDUES
• The smallest known P’ is just nine residues long -
oxytocin
• The largest is over 25,000 residues - the structural
protein Titin
 Titin
Oxytocin is a peptide hormone Titin also known as connectin, is
and neuropeptide. It is normally a protein. Titin is a giant protein,
produced in the hypothalamus greater than 1 µm in length, that
and released by the posterior functions as a spring which is
pituitary. It plays a role in social responsible for the passive elasticity
bonding, reproduction, childbirth, of muscle.
and the period after childbirth.
This is an amino acid. It is
the monomer for a
protein. It contains C, H,
O and N. It has 3 groups:
an amino group, an R-
group, and a carboxyl
group. The R-group is
considered a variant
group because it
changes.
20 amino acids structure
 Breaks down into microscopic
molecules

Polypeptide

Meat

Amino Acid
Monomer: amino acid
Polymer: polypeptide
 Proteins
 Elements: C-H-O-N
 Monomer (Building Block):
amino acids (20 different ones!)
 Polymer: proteins (tons)
 Examples of proteins:
hemoglobin in red blood cells,
albumin in eggs, enzymes that
control reactions in the body,
and antibodies
 Found in: fish, eggs, meat
Non-covalent bonds within and between Peptide chains
are as important in their overall conformation and
function

1) Ionic bonds
2) Hydrogen bonds
3) Van der Waals forces
The side groups of the linear unfolded polypeptide are
intermingled. Only when correctly folded do we see the
wonder of Nature!
The 3D folding of a P’ is governed solely by the sequence
of the AA’s. Under some physiological conditions & in vitro
many P’s can reversibly unfold and refold
Haemoglobin - is the iron-containing oxygen-transport
metalloprotein in the red blood cells of the blood in vertebrates
and other animals

Here we see
the use of two
different
polypeptides
made by
different genes
Virus Coat Protein
Function of Proteins
• Provides us with building
blocks for life!
• Also regulate most functions
in a cell.
• Glycoproteins (antigens)
• Combines w/DNA to form
chromosomes
• Turns genes on and off
• Antibodies (fights disease)
Function of Proteins
 Provides structure & strength
(fibers)
 Transports molecules in & out
cells
 Hemoglobin (transports O2)
 Enzymes (speeds up reactions)-
has ‟ase suffix..Amylase
 Acts as hormones (insulin)-
many proteins have suffix of -in
 Prions
 Prions are misfolded proteins with the ability to transmit
their misfolded shape onto normal variants of the same
protein.
 They characterize several fatal and transmissible
neurodegenerative diseases in humans and many other
animals.
 Prions cause diseases, but they aren't viruses or bacteria
or fungi or parasites.
 Abnormal aggregates of proteins called amyloids,
accumulate in infected tissue and are associated with
tissue damage and cell death in Alzheimer's
disease and Parkinson's disease.
Prions
04_08_Prion diseases.jpg
Lipids and Fats
 Lipids are Hydrophobic
Lipids are a diverse group of hydrophobic
molecules
• Lipids are the one class of large biological
molecules that do not form polymers
• The unifying feature of lipids is having little or no
affinity for water (water fearing)
• Lipids are hydrophobic because they consist
mostly of hydrocarbons, which form nonpolar
covalent bonds
• The most biologically important lipids are fats,
phospholipids, and steroids
 Fats: Start with a Simple Little
Glycerol Molecule

• Fats are constructed from two

types of smaller molecules:
glycerol and fatty acids
• Glycerol is a three-carbon alcohol
with a hydroxyl group attached to
each carbon
• A fatty acid consists of a carboxyl
group attached to a long carbon
skeleton
Dehydration Reaction 1: Add a Fatty Acid

• Next, add a “fatty acid” through a dehydration

synthesis reaction
• What makes it an acid? The C double bond O,
single bond OH!
 Dehydration Reaction 2!!

• Next, add a SECOND “fatty acid” through a

dehydration synthesis reaction
 Dehydration Reaction THREE!!!

• The joining
of the C of
the fatty acid
to the O of
the hydroxyl
group of the
glycerol is
called an
ester
linkage.
 Saturated or Unsaturated?
• Fats made from
saturated fatty acids
are called saturated
fats, and are solid at
room temperature
• Most animal fats are
saturated (lard)
• Saturated fatty acids
have the maximum
number of hydrogen
atoms possible and no
double bonds
 Saturated or Unsaturated?
• Fats made from
unsaturated fatty acids are
called unsaturated fats or
oils, and are liquid at room
temperature
• Plant fats and fish fats are
usually unsaturated
• Unsaturated fatty acids
have one or more double
bonds
 Saturated or Unsaturated?
• A diet rich in saturated
fats may contribute to
cardiovascular disease
through plaque deposits

• Hydrogenation is the
process of converting
unsaturated fats to
saturated fats by adding
hydrogen
 What’s a Trans fat?

• Hydrogenating vegetable oils also creates

unsaturated fats with trans double bonds
• These trans fats may contribute more than
saturated fats to cardiovascular disease
 Saturated or Unsaturated?

• Certain unsaturated fatty acids are not synthesized

in the human body
• These must be supplied in the diet
• These essential fatty acids include the omega-3 (ω-
3) fatty acids, required for normal growth, and
thought to provide protection against cardiovascular
disease
 Fats: Major function is storage!

• The major function of

fats is energy storage
• Humans and other
mammals store their
fat in adipose cells
• Adipose tissue also
cushions vital organs
and insulates the
body
 Phospholipids
• When phospholipids are added to water, they self-
assemble into a bilayer, with the hydrophobic tails
pointing toward the interior
• The structure of phospholipids results in a bilayer
arrangement found in cell membranes
• Phospholipids are the major component of all cell
membranes
Carbohydrate
Phospholipid
bilayer

Nonpolar
Hydrophobic
Polar
Hydrophilic
 A Single Phospholipid Molecule

Choline
Hydrophilic head

Phosphate

Glycerol
Hydrophobic tails

Fatty acids

Hydrophilic
head

Hydrophobic
tails

(a) Structural formula (b) Space-filling model (c) Phospholipid symbol

 Soaps

Hydrophobic part: nonpolar

Hydrophilic part: polar (remains in contact with environment)

O
- +
3 RCO N a

l Sodium soaps
n)
 Soaps
When soap is mixed with dirt (grease, oil, and …), soap
micelles “dissolve” these nonpolar, water-insoluble
molecules.
 Steroids
• Steroids are lipids characterized by a carbon
skeleton consisting of four fused rings
• Cholesterol, an important steroid, is a component
in animal cell membranes
• Although cholesterol is essential in animals, high
levels in the blood may contribute to
cardiovascular disease
 Sex Hormones
Progestins (Female Sex Hormones):

The progestin progesterone is called the “pregnancy

hormone”; it is responsible for the preparation of the uterus for
implantation of a fertilized egg.
 Sex Hormones
Androgens (Male Sex Hormones):

Testosterone and Androsterone are androgens made in the

testes.
They control the development of secondary sex
characteristics in males.
 Sex Hormones
- Synthetic androgen analogues, called anabolic steroids,
promote muscle growth.
- They have the same effect as testosterone, but are more
stable, so they are not metabolized as quickly.

- They have come to be used by athletes and body builders,

but are not permitted in competitive sports.
- Prolonged use of anabolic steroids can cause physical and
psychological problems.
Nucleic Acids: Information
Molecules
 The biochemical activity of a cell depends on
production of a large number of proteins, each
with a specific sequence.
 The information necessary to produce the correct
proteins is passed through generations of
organisms, even though the protein molecules
themselves are not.
 Nucleic acids carry information inside cells, just as
disks contain the information in a computer

65
 Two main varieties of nucleic acids are
 deoxyribonucleic acid (DNA)
 ribonucleic acid (RNA)

 DNA encodes the genetic information used to

assemble proteins
 Cells use a type of RNA called messenger RNA
(mRNA) to direct the synthesis of proteins .
 mRNA consists of transcribed single-stranded
copies of portions of the DNA.
 These transcripts serve as blueprints specifying
the amino acid sequences of proteins.
Nucleic acids are nucleotide polymers
 Nucleic acids are long polymers of repeating
subunits called nucleotides.
 Each nucleotide consists of three components:
 A pentose, or five-carbon sugar (ribose in RNA and
deoxyribose in DNA);
 a phosphate (-PO4 ) group
 an organic nitrogenous (nitrogen-containing) base
 Nitrogen Bases
• The nitrogen bases in nucleotides consist of two general types:
- purines: adenine (A) and guanine (G)
- pyrimidines: cytosine (C), thymine (T) and Uracil (U)
 Pentose Sugars
• There are two related pentose sugars:
- RNA contains ribose
- DNA contains deoxyribose
• The sugars have their carbon atoms numbered with
primes to distinguish them from the nitrogen bases
 Nucleosides and Nucleotides
 A nucleoside consists of a nitrogen base linked by a glycosidic
bond to C1’ of a ribose or deoxyribose
 Nucleosides are named by changing the nitrogen base ending to
-osine for purines and –idine for pyrimidines
 A nucleotide is a nucleoside that forms a phosphate ester with
the C5’ OH group of ribose or deoxyribose
 Nucleotides are named using the name of the nucleoside
followed by 5’-monophosphate
Names of Nucleosides and
Nucleotides
 Primary Structure of Nucleic Acids
 The primary structure of a nucleic acid is the nucleotide sequence
 The nucleotides in nucleic acids are joined by phosphodiester bonds
 The 3’-OH group of the sugar in one nucleotide forms an ester bond
to the phosphate group on the 5’-carbon of the sugar of the next
nucleotide
 Reading Primary Structure

 A nucleic acid polymer has a free 5’-

phosphate group at one end and a
free 3’-OH group at the other end
 The sequence is read from the free
5’-end using the letters of the bases
 This example reads
5’—A—C—G—T—3’
75
 Secondary Structure: DNA Double Helix

• In DNA there are two strands of nucleotides that wind together

in a double helix
- the strands run in opposite directions
- the bases are arranged in step-like pairs
- the base pairs are held together by hydrogen bonding
• The pairing of the bases from the two strands is very specific
• The complimentary base pairs are A-T and G-C
- two hydrogen bonds form between A and T
- three hydrogen bonds form between G and C
• Each pair consists of a purine and a pyrimidine, so they are the
same width, keeping the two strands at equal distances from
each other
Eukaryotic Nuclear DNA organization

• Nucleosome: DNA
associated with histone
protein
• Chromatin: collection of
nucleosome and linker
DNA
• Chromosome: condensed
chromatin
– Ends of chromosomes
are called telomeres
(very repetitive
sequences)
Nobody can pack as
nature has packed:
DNA Condensation

If you were to take one

molecule of DNA from a
human cell and stretch it
out to its full length, it
would be approximately
two meters long. So it is
truly incredible that such an
enormously long molecule
can be compressed into
the microscopic space of
the nucleus of a cell.

Unpacking of DNA as a fraction of time (femto seconds)

and space (1014 cells) is a far far bigger challenge
Next Lecture:
Central Dogma of Molecular Biology