Download Section 4 – Molecules

Unit 1
Cell and Molecular
Biology
Section 4
Molecules
Structure and function of cell
components
Carbohydrates
(ii) Lipids
(iii) Proteins
(iv) Nucleic Acids
(i)
Carbohydrates

Carbohydrates are chemical structures
containing C, H, and O in a ratio of 1:2:1

The general formula is

(CH2O)n
Facts about monosaccharides




Monosaccharides are molecules with the general
formula (CH2O)n.
The main example is glucose.
Monosaccharides such as glucose are all
• of low molecular weight
• sweet
• soluble
• crystalline.
Monosaccharides such as glucose are used as
sources of energy.
Glucose chain structure

Glucose is an example of an
aldose sugar as its terminal group
C1 is an aldehyde (CHO).
Glucose is a reducing sugar due to
the presence of the carbonyl group
CO which can donate electrons.

It is possible for the atoms in a 6carbon sugar to take up different
positions on the carbon chain. This
leads to structural isomers
Optical isomers of glucose
Since molecules
are 3dimensional in
shape optical
isomers can be
formed which are
structurally
identical but are
mirror images of
each other.
D-glucose with OH on
right of C6.
L-glucose with OH on
left of C6.
Ring structure of Glucose

Since glucose
is a relatively
long molecule,
groups within
it can react
and change
the shape of
the molecule
to form a
pyranose ring
structure.
a-D
b-D
Glucose Reacting to form
disaccharides


The monomer glucose reacts by
condensation (or dehydration) to form
disaccharides.
Water is removed in the process.



In the example below two molecules of a-D
glucose react together to form maltose.
The bond holding the glucose molecules
together (highlighted in red) is known as a
glycosidic bond.
Maltose is linked by an a (1-4) glycosidic
bond.
glycosidic bond
If two β-D glucose join the result is cellobiose and the
bond is at an angle (top to bottom)
Structure and function of
polysaccharides




Polysaccharides are complex carbohydrates
made up linked monosaccharide units.
When a polysaccharide is made up of one
type of monosaccharide unit it is called a
homopolysaccharide.
Starch and glycogen are polysaccharides
used for energy storage.
Other polysaccharides such as cellulose and
chitin may be structural in function.
Starch


Starch is a storage compound in plants,
being insoluble in water.
It is a homopolysaccharide made up of two
components: amylose and amylopectin.
Amylose – a straight chain structure
formed by 1,4 glycosidic bonds
between a-D-glucose molecules.
Structure of Amylose Fraction of Starch
CH2OH
CH2OH
H
C
O
H
H
C
O
C
O
H
H
C
1
C
4
O
H
H
C
C
C
C
H
O
H
H
O
H
H
O
O
CH2OH
CH2OH
C
O
H
C
O
H
H
C
O
H
C
O
H
H
C
1
C
4
O
H
H
C
C
C
C
C
OH
H
O
H
H
O
H
O

The amylose chain
forms a helix.

This causes the
blue/black colour
change on reaction
with iodine.
The structure of the
Amylopectin Fraction of Starch

Amylopectin is a branched structure due to
the formation of 1,6 glycosidic bonds.
End of chain 1
CH2OH
H
C
4
C
O
H
C
H
The cross linkages are formed by
dehydration reactions between
carbon 1 of one chain and carbon
6 of a parallel chain
CH2OH
O
H
C
O
H
H
C
C
O
C
O
H
C
H
O
H
H
C
O
H
C1
H
C
H
O
OH
CH2OH
C6H2OH
C
O
H
O
H
C
H
C
O
H
C
1
H
O
H
C
4
C
O
O
H
C
H
C
O
H
H
Start of chain 2
C



Amylopectin causes a
red-violet colour
change on reaction
with iodine.
This change is
usually masked by
the much darker
reaction of amylose to
iodine.
Starch therefore
consists of amylose
helices entangled on
branches of
amylopectin.
Shows branching of amylopectin
Glycogen



Glycogen is a homopolysaccharide made from
repeating a-D-glucose units and is very similar in
structure to amylopectin, i.e. it has a highly
branched structure.
Glycogen is a storage compound in animals;
including humans.
It causes a red-violet colour on addition of iodine
(similar to amylopectin).
Cellulose



Cellulose is the most abundant organic material on
earth.
Most animals however lack the enzyme cellulase
required to break it down to its component
monomers.
Cellulose is made up of long straight chains of bglucose molecules.


The b-glucose molecules are joined by
condensation, i.e. the removal of water,
forming b(1,4) glycosidic linkages.
Note however that every second b-glucose
molecule has to flip over to allow the bond to
form. This produces a “heads-tails-heads”
sequence.

The glucose units are linked into straight
chains each 100-1000 units long.

Weak hydrogen bonds form between
parallel chains binding them into cellulose
microfibrils.

Cellulose microfibrils arrange themselves into
thicker bundles called macrofibrils. (These
are usually referred to as fibres.)

The cellulose fibres are often “glued” together
by other compounds such as hemicelluloses
and calcium pectate to form complex
structures such as plant cell walls.
Other Polysaccharides
Chitin is the main structural component of
the exoskeleton of arthropods (e.g.
spiders, insects and crustaceans) and the
walls of fungi such as yeast.
 Chitin is structurally similar to cellulose
but the monomer is an amino sugar
called glucosamine.
• Glucosaminoglycans are complex
heteropolysaccharides found in the
connective tisues and skin of
vertebrates.

Activity

Read Dart Pg 25-31

Scholar 4.2 carbohydrates

Practice drawing different molecular
structures
Lipids

Lipids have a varied structure but all have the
following properties in common:


The three main groups of lipids are:



Insoluble in water
Soluble in organic solvents
Triglycerides
Phospholipids
Steroids
Lipids are important in cell membrane
structure and also as energy storage
molecules and hormones.
Structure of glycerol

Glycerol is a three carbon alcohol that
contains 3 –OH (hydroxyl) groups
Structure of Fatty Acids

Fatty acids are hydrocarbon chains ending in a
carboxyl group (COOH)
O
HO – C – R


R is an abbreviation for any organic group
About 30 different fatty acids are commonly found in
lipids (they nearly always have an even number of
carbon atoms).

Saturated fatty acids


All available bonds are occupied by
hydrogens
E.g

Palmitic acid CH3(CH2)14COOH
O
OH – C – C – C – C – C – C – C – C – C – C – C – C – C – C – C – CH3

Stearic acid CH3(CH2)16COOH

Unsaturated fatty acids

Some carbon atoms are double bonded with one another,
therefore they are not fully saturated with hydrogen
E.g. Oleic Acid CH3(CH2)7 CH = (CH2)7COOH

Note - this is monounsaturated (1 double bond)


E.g. Linoleic acid
CH3(CH2CH=CH)3(CH2)7COOH

Note – this is polyunsaturated (more than 1
double bond)
Formation of Ester Linkages

Glycerol and fatty acids are joined together
by dehydration (condensation) reactions

The bond linking glycerol and fatty acids is
called an ester bond
O
H
H
C OH
H
C OH
H
C
H
OH
HO – C – R
Ester bond
H
O
H
C
O–C–R
H
C OH
H2O
H
C
H
OH
Triglycerides

Triglycerides consist of a single glycerol
molecule and three fatty acids.
Glycerol


Glycerol (blue) is an alcohol
derivative of glyceraldehyde
and has three hydroxyl groups.
It acts as the backbone of the
structure.
Fatty acids (red) – there are
more than 70 types of fatty
acid but they all have long
hydrocarbon tails and a
terminal carboxyl group
(COOH). The variety of fatty
acids determine the properties
of each triglyceride.
Formation of Triglycerides
Triglycerides form by
condensation (dehydration)
reactions between the
hydroxyl (OH) groups of the
glycerol and the carboxyl
(COOH) group of three fatty
acids.
 Triglycerides are esters
being derived from an
alcohol and a fat.

Structure of triglycerides
Triglycerides in plants


Plants store their energy in
triglycerides with low
melting points which are
liquid at room temperature.
These triglycerides


are referred to as oils
result from reaction between
glycerol and an unsaturated fatty
acid e.g. oleic acid.
Triglycerides in Animals


Animals store their energy
in triglycerides with high
melting points which are
solid at room temperature.
These triglycerides


are referred to as fats.
result from reaction between
glycerol and a saturated fatty acid
e.g. stearic acid.
Triglycerides in cells

Triglycerides are insoluble in water because
they have no charge i.e. they have covalent
bonds. This causes them to form droplets in
the cytoplasm
Functions of triglycerides


Energy storage - triglycerides contain
twice the energy/gram of carbohydrates
or proteins. During aerobic respiration
triglyceride is broken into 2C portions
which are fed into the Krebs cycle.
Source of metabolic water. water is
released on the breakdown of
triglycerides and this property is used
efficiently is by desert mammals.


Insulation – triglycerides are found in
the blubber of whales and other
aquatic animals.
Buoyancy – aquatic animals use
triglycerides to help them float as they
are less dense than water.
Phospholipids

The structure of phospholipids is based on
the structure of triglycerides but the third
hydroxyl group of the glycerol is linked to
phosphoric acid which is often linked to a
large polar group.

The fatty acids which make up
phospholipids have a consistent length
of between 16 and 18 carbons. This
allows them to form neat bilayers.

Phospholipids are said to be
amphipathic, having two very different
sides to their nature.
Hydrophilic portion
Hydrophobic portion


The ‘head’ containing the polar group and the
phosphate group has polar covalent bonds. It is
slightly charged and attracts water, i.e. it is
hydrophilic.
The ‘tail’ containing the long hydrocarbon group
which is non-polar covalent. It is not charged and
repels water, i.e. it is hydrophobic.


The amphipathic nature of
phospholipids is important in the
formation of bilayers such as cell
membranes.
The hydrophilic groups line up on the
outside faces of the membrane. The
hydrophobic portions are arranged
within the membrane.

Phospholipids may have fatty acids
which are saturated or unsaturated.
This affects the properties of the
resulting bilayer/cell membrane:



Most membranes have phospholipids derived
from unsaturated fatty acids.
Unsaturated fatty acids add fluidity to a bilayer
since ‘kinked’ tails do not pack tightly together.
Phospholipids derived from unsaturated
phospholipids allow faster transport of substances
across the bilayer.

Membranes exposed to
the cold have a very high
percentage of
unsaturates e.g. bacteria
grown at low temperature
or the membranes of
reindeer ears –
remember unsaturates
are liquid at much lower
temperatures.


Membranes which are
stiffer such as those
in nerve cells contain
a much higher
percentage of
phospholipids derived
from saturated fatty
acids.
They also contain high
levels of cholesterol
which stiffens
membrane structure
further.
Steroids


Steroids have a common four ring structure.
Each unit within the four-ring structure is
known as an isoprene unit (C5H8).


Different steroids vary in the side chains
attached to the rings.
Notice that cholesterol and testosterone
are almost identical except for the side
groups on C3 and C17.



Steroids are classified as lipids
since they are soluble in organic
compounds but not in water.
They have a very powerful effect
because of this as they can pass
through cell membranes.
Steroids are hormonal in
function and have a wide variety
of functions.
Other examples of steroids are
oestrogen, progesterone,
cortisol, cholesterol and
aldosterone.
Activity

Read and take notes from Dart Pg 32-37

Scholar section 4.3

Use the internet to familiarise yourself with
different ways of presenting the chemical
formulae / structures
Amino acids



Amino acids are the structural building blocks
(monomers) of proteins.
There are twenty different kinds of amino
acids used in proteins.
Proteins are referred to as heteropolymers
due the variety of amino acids involved in
their structure.
Structure of amino acids

Amino acids, like carbohydrates, show
isomerism. Proteins are only made up of
amino acids which are L-isomers.
L-isomer
D-isomer

At neutral pH’s amino acids exist in an ionised
form and have both acidic and basic
properties. This is because the carboxylic
group donates hydrogen ions to the solution
(acidic) whereas the amino group (NH2)
attracts hydrogen ions from the solution.

The repeating sequence of atoms along a
proteins is referred to as the polypeptide
backbone. Attached to this repetitive chain are
the different amino acid side chains
(Rgroups) which are not involved in the peptide
bond but which give each amino acid its unique
property.

Amino acids are grouped according to
whether their side chains are: acidic
 basic
 uncharged
 non
polar
polar
Acidic Amino acids
Aspartic
Acid
Glutamic
Acid
asp
Acidic
Polar
glu
Acidic
Polar
Basic amino acids
Lysine
lys
Basic
Polar
Arginine arg
Basic
Polar
Neutral polar amino acids
Glutamine gln
Neutral
Polar
Tyrosine
Neutral
Polar
tyr
Non-polar amino acids
Isoleucine ile
Neutral
Non-polar
Methionine met
Neutral
Non-polar



The type of side chain is very important as it
affects the solubility of the amino acid.
Hydrophobic features include long non-polar
(uncharged) chains or complex aromatic
rings.
Hydrophilic features include additional
carboxyl groups or amino groups not involved
in peptide bonding which are ionised in
solution.
Structure of proteins

Primary structure


The sequence of amino acids in a given protein is known as its primary
structure.
Secondary structure

Simple proteins with regularly repeating amino acids often form a secondary
structure due to hydrogen bonds between the amino group ( NH) and
carbonyl group ( CO ) of adjacent amino acids.

This additional bonding may twist the long protein chain into a helix known
as an alpha helices

This secondary bonding gives rise to proteins which are structural e.g.

Collagen – 3 alpha helices twisted together
Elastin
Keratin -7 alpha helices twisted together




A second formation resulting from hydrogen bonds
between adjacent peptide bonds is known as β- pleated
sheets
An example of a protein made up of β- pleated sheets is
fibroin found in spiders webs which is extremely strong.
Tertiary structure

The third type of structure found in proteins is called tertiary protein structure.

The tertiary structure is the final specific shape that a protein assumes.

This final shape is determined by a variety of bonding interactions between the
"side chains" on the amino acids. These bonding interactions may be stronger
than the hydrogen bonds between amide groups holding the helical structure.

Bonding interactions between "side chains" may cause a number of folds,
bends, and loops in the protein chain. Different fragments of the same chain
may become bonded together.

There are four types of bonding interactions between "side chains" including:
hydrogen bonding,
salt bridges,
disulfide bonds,
non-polar hydrophobic interactions.





Globular proteins such as enzymes, antibodies, and cell membrane proteins all
show tertiary structure

The hydrophobic interactions of non-polar side chains are believed to contribute
significantly to the stabilizing of the tertiary structures in proteins.

Non groups such as benzene rings repel water and other polar groups and
results in a net attraction of the non-polar groups for each other
Quaternary Structure

The quaternary protein structure involves the clustering of several
individual peptide or protein chains into a final specific shape.

A variety of bonding interactions including hydrogen bonding, salt
bridges, and disulfide bonds hold the various chains into a particular
geometry.

There are two major categories of proteins with quaternary structure fibrous and globular.

Fibrous Proteins:

Fibrous proteins such as the keratins in wool and hair are composed of
coiled alpha helical protein chains with other various coils analogous to
those found in a rope. Other keratins are found in skin, fur, hair, wool,
claws, nails, hooves, horns, scales, beaks, feathers, actin and mysin in
muscle tissues and fibrinogen needed for blood clots.
Globular Proteins

On the other hand, globular proteins may have a combination of
various individual units of various shapes which are mostly
clumped into a shape of a ball. Major examples include insulin,
hemoglobin, and most enzymes.
Nucleotide structures


The building block of a nucleic acid is a
nucleotide.
Nucleotides consist of



A pentose sugar
A nitrogenous base
A phosphate group
Pentose Sugars

Deoxyribose and ribose differ by the group
attachment at the 2’C.
Bases



Purines



There are 5 bases
These can be classified into two types
Double ringed
Adenine and Guanine
Pyrimidines


Single ringed
Cytosine, Thymine and Uracil
Formation of a nucleotide


A condensation reaction occurs between the
OH group on the 5’ C and phosphate group
to form a strong phosphodiester bond.
A condensation reaction occurs between the
base and the 1’ C to form a strong glycosidic
bond
Formation of nucleic acid

A phosphodiester bond also forms between
the 3’ C and the phosphate group of the next
nucleotide to form the sugar phosphate
backbone.
Base Pairing in DNA


A and T join by two weak hydrogen bonds
G and C join by three weak hydrogen bonds
DNA strands

DNA strands
are antiparallel
Enzymes

DNA polymerase



Catalyses the linking together of DNA nucleotides
during replication
DNA polymerase can only add a nucleotide to the
3’ end of the previous nucleotide.
RNA polymerase

Catalyses the linking of RNA nucleotides during
transcription (and in the replication of the lagging
strand during DNA replication)

DNA ligase

Joins short sections of DNA together
DNA replication animation:
http://207.207.4.198/pub/flash/24/menu.swf
Activity







Read DART pg 48 – 53 and take notes
Scholar 4.5
http://www.maxanim.com/genetics/index.htm
 Look at
 Replication fork
 DNA replication
 Meselson-Stahl experiment
Make notes on DNA and RNA structure
Make notes on replication and transcription
Think about how you will remember which bases are purines and
which are pyrimidines
Write a summary of all the different bonds formed between
molecules by dehydration reactions.