Download Chapter 12 - Pathways to Biomolecules

Chapter 12 – Pathways to
Biomolecules
Biomolecules
• Biomolecules are molecules such as fats and
oils, carbohydrates, proteins and nucleic acids
that are found in all living things.
• They have an essential role in the supply of
energy to the body, the growth and repair of
organs and tissue, the movement of muscles,
the activity of nervous and hormonal systems
and the elimination of waste.
• Many biomolcules are polymers.
Fats
• Humans can make their own fat internally.
• Though this is not usually necessary as fat is
readily available in the food we eat.
• Fat is a name used to describe a large number
of organic compounds belonging to an even
larger class of biological molecules called
lipids.
• Fats and oils are the best known types of
lipids.
Fats cont…
• Oil in food have very different structures and
properties from hydrocarbon oils.
• Compounds such as waxes and steroids (which
include cholesterol) are also lipids.
• Lipids are based mainly on carbon and hydrogen.
• They also contain small amounts of oxygen and
sometimes some other elements.
• Most lipids are non-polar and insoluble in water.
Fats and Oils
• Have very similar chemical structures.
• They are simply distinguished on the basis of their physical states at
normal temperatures:
– Fats are solids
– Oils are liquids
• Most fats and oils are formed by a condensation reaction between
a single molecule of glycerol and three molecules of fatty acids.
• Fatty acids contain a carboxyl functional group which reacts with
the hydroxyl groups in the glycerol.
• The –COO- groups in fat are ester linkages.
• Three molecules of water are also produced in this reaction.
• Fats and oils formed from this process are called triglycerides.
• Most fats have two or three different fatty acids attached to the
glycerol molecule.
• Triglycerides are large, non-polar molecules and therefore are
insoluble in aqueous.
Types of Fats
• Fats are distinguishable on the basis of the fatty acids
from which they are made:
– Saturated fats are made from fatty acids, such as palmitic
acid, that contain only single carbon-carbon bonds.
Saturated fats are generally unreactive and occur as waxy
solids at room temperature.
– Monounsaturated fats are made from fatty acids, such as
oleic acid, that contain one carbon-carbon double bond.
– Polyunsaturated fats are made from fatty acids, such as
linoleic acid, that contain more than one carbon-carbon
double bond. Polyunsaturated fats have lower melting
temperatures than saturated fats and often occur at
liquids, oils, are room temperature. They are more reactive
than saturated fats.
Types of Fats cont…
• The different physical states of saturated and
polyunsaturated fats are thought to arise because
molecules of saturated fats can pack more closely
together, resulting in stronger dispersion forces
between the molecules.
• The arrangement of the carbon chain sections at
the double bond sites of polyunsaturated fats do
not permit close packing.
• Consequently saturated fats have higher melting
points than unsaturated fats.
What happens to fat in the body?
• Chemical digestion of fat does not start until it reaches the small
intestine.
• There it is mixed with bile, from the gall bladder.
• Bile contains surfactants that convert the fats into an emulsion of
smaller fat globules.
• This increases the surface area, meaning it is able to react more
rapidly.
• Secretions from the pancreas and the walls of the small intestine
contain enzymes that catalyse the hydrolysis of fat into fatty acids
and glycerol; reversing the condensation reaction from which fat
was made.
• Enzymes in the small intestine operate best under alkaline
conditions.
• Once the fatty acids and glycerol have been absorbed into the body,
they are reassembled into triglycerides via condensation reactions.
(see page 180).
Condensation and Polymerisation
• The monomers used to make polymers by a
condensation polymerisation reaction have a
pair of functional groups that are able to react
together, producing a new functional groups
that links monomers and also produces a
small molecule such as water.
• Synthetic polymers such as nylon and
polyester are formed in this way, are are
proteins, DNA, cellulose and starch.
Carbohydrates
• The main structural component of all plants is a
polymer called cellulose.
• Cellulose belongs to a class of compounds called
carbohydrates.
• Green plants in the presence of sunlight, convert
carbon dioxide and water into a number of
substances including the carbohydrate glucose.
• CHOs are a source of energy in our diets.
• CHOs are made from the element C, H and O and
usually have the formula Cx(H2O)y, where x and y are
whole numbers.
Carbohydrates cont…
• CHOs range in size from small molecules, with
Mr’s of between 100 and 200 to very large
polymers with Mr greater than 1 million.
Monosaccharides
• Are the smallest CHOs.
• The are white crystalline solids that highly
soluble in water.
• Most monosaccharides have a sweet taste.
• Monsaccharides together with another group
of CHOs called disaccharides are often called
sugars.
• The most abundant monosaccharide is
glucose.
Monosaccharides cont…
• It has the molecular formula C6H12O6 and the
atoms are arranged in a ring.
• Fructose and Galactose have similar
structures.
• All three of these molecules contain a number
of polar OH groups, enabling them to form
hydrogen bonds with water.
• As a results monosaccharides are highly
soluble in water.
Glucose
• Is the key energy source in most forms of life.
• It is also a major component of the larger
CHOs.
• Glucose and its polymer, starch, are more
rapidly digested than other forms of food.
Fructose & Galactose
• Are not a abundant as glucose.
• Galactose is not found in nature as a free
monosaccharide.
• It occurs frequently as a component of larger
CHOs.
• Fructose is found in many fruit juices and
honey.
• Although fructose is a component of other
large biological molecules, its main role in the
body is an energy source.
Disaccharides
• Is the carbohydrate formed when two
monosaccharides undergo a condensation reaction.
• They too dissolve in water, taste sweet and are called
sugars.
• Maltose is formed when two glucose molecules
react, with the elimination of a water molecule. (a on
next slide)
• Notice how the hydroxyl functional groups react to
form the dissacharide and water.
• The two rings are joined via an oxygen atom.
• This linkage is called a ether (or glycosidic) linkage.
Disaccharides cont…
• Lactose and Sucrose are two other disaccharides.
• Lactose is made from a condensation reaction of
glucose and galactose.
• It is not as sweet as glucose.
• Lactose is synthesised in the mammary glands of
mammals and is the main CHO in milk.
• Sucrose is formed from a condensation reaction of
glucose and fructose.
• It is widely used as a sweetener.
• It is found in the sap of trees and the juices of many
fruits.
Polysaccharides
• Are polymer carbohydrates made by linking
monosaccharides into a chain.
• They are polymers of glucose molecules linked
together in different ways by condensation
reactions.
• They are generally insoluble in water and have
no taste.
• The three most important polysaccharides
are: glycogen, starch and cellulose.
Glycogen
• Is found in animals, where it acts as a glucose
storage molecule.
• As glucose can be oxidised to produce energ
more rapidly than fat, all glucose is
polymerised to glycogen to be stored.
• When there is no more storage space for
glycogen, the glucose is converted into fat.
• As energy is required, the glycogen is
hydrolysed to yield glucose for respiration.
Starch
• The glucose storage molecule in plants; the
plants equivalent of glycogen.
• The starch is stored and used at night to meet
the plant’s ongoing energy requirements
when the glucose production from
photosynthesis has ceased.
Digestion
• During digestion, the polymers must be broken down to
release the glucose monomers.
• The polymers are first hydrolysed.
• This hydrolysis is catalysed by enzymes; every 2nd glucose is
hydrolysed to produce maltose.
• Another enzyme catalyses the hydrolysis of maltose into
glucose, which absorbed into the body.
• These can be regarded as the reverse of condensation
reactions.
Cellulose
• The main structural material in plants.
• It has a Mr ranging from 50,000 to 2.5 million.
• Its chemical structure differs from starch and
glycogen because of the difference the the way the
glucose monomers are joined.
A)Starch
B)Cellulose
Proteins
• Proteins are found in every cell and are fundamental to cell
structure and operation.
• There are thousands of different types of proteins and each
has its own purpose.
Amino Acids
• Proteins are polymers built up from monomer
molecules called amino acids.
• Two of the simpler amino acids are glycine and
alanine.
• Every amino acid has an amine group and a carboxyl
group.
• They have the general formula of H2N-CHZ-COOH
• The major difference between amino acid is the
collection of atoms that make up the side chain,
known as the Z group.
Amino Acids
Amino Acids cont…
• As a consequence of the polar amino and
carboxyl functional groups; amino acids are
soluble in water.
• In solution, the amino group can acts as a
base, and the carboxyl as an acid.
• As a result, the amino acid molecule in a
solution at a particular pH will usually be in
the form of +H3N-CHZ-COO-.
• This sort of molecule is called a zwitterion or
dipolar ion.
Zwitterion
• A proton has been lost from the acidic carboxyl group and the
basic amino group has gained a proton.
• The pH at which an amino acid exists as a zwitterion depends
on the structure of the Z group.
• The dual acidic and basic nature of amino acids means that
several different forms of an amino acid can be in equilibrium
in a solution.
• The predominant form depends on the acidity of the solution.
• In acidic solutions, the +H3N-CHZ-COOH form is most
abundant, whereas H2N-CHZ-COO- form is most abundant in
alkaline solutions.
Amino Acids cont…
• The ability of amino acids to react with both
acids and bases means that they can act as
buffers.
• This means they minimise the effect that the
addition of H+ or OH- ions to a solution would
have on acidity.
Protein Structure
• When a molecule containing a COOH combines with
a molecule containing NH2, a condensation reaction
occurs to form an amide functional group – CONH2-.
• This links the two molecules.
• Water is also formed.
Protein Structure cont…
• Proteins are polymners formed by
condensation reactions between amino acids.
• During these reactions the amino acids join
and form long unbranched chains.
• The amine group of one amino acid reacts
with the carboxyl of another.
• A covalent bond is formed and a molecule of
water is eliminated.
Peptides
• Molecules made from amino acids are often called peptides.
• When two amino acid molecules react together it is called a
dipeptide.
• When three molecules react and tripeptide is formed.
• A polymer made from amino acids is known as a polypeptide.
• Polypeptides built up of more than 50 amino acids are usually
called proteins.
• The group of atoms –CONH- that links the amino acids is an
amide group, referred to as a peptide linkage in proteins.
Structure
• The role that any protein fulfils is dependent
on its shape.
• This is regarded as being made up of a
primary, secondary and tertiary structure.
Primary Structure
• The order of the amino acids is known as the
primary structure.
• The entire shape of a protein is a consequence
of the order in which the AAs are joined.
Secondary Structure
• Parts of the chain can attract each other
creating 3D shapes.
• This coiling, folding or pleating of sections is
described as the protein’s secondary
structure.
Tertiary Structure
• The Z groups in the amino acid units of a protein influence the
overall 3D shape of the molecule.
• The Z groups in some amino acids are relatively large and
their size can cause distortions in the protein structure.
• Further, some of the side groups are capable of forming bonds
with side groups elsewhere on the protein chain.
• As a consequence of such bonds, a variety of protein shapes
exist.
• The overall 3D shape adopted by the protein is called its
tertiary structure.
Enzymes
• Many chemical reactions occur more rapidly
when a catalyst is present.
• The biological catalysts that accelerate the
rate of chemical reactions in living things are a
type of protein called enzymes.
• Enzymes control the manufacture of complex
substances as well as breaking down the
chemicals to provide energy.
Enzymes cont…
• They are usually more efficient than inorganic
catalysts, because they allow reactions to occur
rapidly within the narrow band of temperature in
which life can survive.
• Compared to inorganic catalysts:
– Enzymes produce much faster reactions rates: they can increase the
rate of a reaction by as much as 1010 times.
– Enzymes operate under milder conditions.
– Enzymes are more sensitive: The catalytic activity of many enzymes is
destroyed when they are heated strongly because their delicate
structure breaks down. The enzyme is then described as being
denatured.
– Enzymes are very selective.
Enzymes cont…
• The catalytic activity of an enzyme depends on its
tertiary structure.
• A slight change in its 3D shape can render an enzyme
inoperative.
• The active site of an enzyme is usually a flexible
hollow or cavity within the molecule.
• Some enzymes have small, non-protein parts called
cofactors, such as vitamins or metal atoms
associated with the active site.
• These cofactors are necessary for catalytic effect.
The Lock and Key Process
• A reactant molecule, known as the substrate, is
manoeuvred into the active site.
• Here, at the surface of the enzyme the reaction takes
place.
• The steps are as follows:
1. The reactant (substrate) enters the active site.
2. Bonds formed between the enzyme and substrate
weaken bonds within the substrate, thus lowering the
reaction’s activation energy.
3. The substrate breaks or rearranges into new products
and these products are released.
Enzymes cont…
• Typically reactions occur at a rate of
1000/second on an active site.
• During respiration the enzyme catalyses the
decomposition of 600000 carbonic acid
molecules into carbon dioxide and water each
second.
• In many cases the substrate and enzyme bind
together because part of the substrate and
active site are non polar and so dispersion
forces are significant.
Enzymes cont…
• In other cases, the substrate is held in place by the
attraction between positive and negative charges,
attraction of a metal ion in the enzyme to a negative
dipole in the substrate, or hydrogen bonding
between enzyme and substrate.
• The selectivity of enzymes is one of their most
important features.
• This selectivity arises because the shape and
functional groups in the active site of the enzyme
allow it to bind only with certain substrates. (Thus
the lock and key process).
Lock and Key Bonds
• Some of the bonds that can occur between
the substrate and enzyme include:
– Ion-dipole interactions
– Hydrogen bonds
– Ionic interactions
– Dispersion forces and dipole-dipole interactions
may also be involved as an enzyme-substrate
complex forms.
Denaturation of Enzymes
• The bonds responsible for holding the protein
chains in particular shapes are often weak, so
slight changes can disrupt the attractions
between parts of the chain.
• This causes the chain to unfold and render the
protein ineffective.
• A change the destroys the biological ability of
a protein is called denaturation.
• It may result due to an increased temperature,
a change in pH or the addition of chemicals.
Denaturation of Enzymes cont…
• Enzyme activity is dependent on temperature.
• As temperature increases, the rate of reaction
catalysed by the enzyme increases because of
increased collisions between enzyme and
substrate, until an optimum temperature of
40°C is reached.
• As there is further temperature increase, the
protein is denatured and the reaction rate
rapidly decreases.
Denaturation of Enzymes cont…
• Enzymes operate effectively within a small pH
range.
• Not all enzymes have the same optimum oH.
• The ionisation of amino acids is depended on
pH.
• The bonds that determine the tertiary
structure of the enzyme are altered as change
in pH alter the ionisation of the amino acid
residues in the protein.
Denaturation of Enzymes cont…
• Once a protein has been denatured, the
unfolded chains tend to form randomly
looped structures which come into close
contact.
• The chains become entangled and bond with
each other, often by disulfide bridges, so that
large clumps of protein molecules are formed.
• This process is called coagulation.
Proteins as Markers for Disease
• The body’s natural defences produce proteins
called antibodies in the fight against infection
caused by bacteria or viruses.
• These antibodies are specific to a particular
disease.
• The cells in diseased or damaged body organs
may release specific proteins that are unique
to that organ.
Proteins as Markers for Disease
cont…
• A raised level of these marker proteins in a
patient’s blood or tissue can be used to:
– Identify a disease at early or advanced stages of
development.
– Monitor the progress of the disease.
– Measure the effectiveness of treatment.
– Test for the recurrence of the disease.
Heart Attack
• A heart attack is caused when the blood supply to a
part of the heart muscle is blocked by a clot in one of
the cardiac arteries.
• The cardiac cells are starved of oxygen and nutrients
and are consequently injured or die.
• The cells in the damaged part of the heart muscle
release various cardiac enzymes into the
bloodstream.
• Blood levels of these enzymes increase within a few
hours after a heart attack and drop back to normal
after several days.
Prostate Cancer
• Cancer is an uncontrolled growth of cells.
• It is initially diagnosed by digital examination and by
measuring the level of a protein in the blood.
• Normally a small amount of this protein is present in
the blood.
• Abnormal cancerous or non-cancerous cell growths
block the ducts in the prostate, forcing more of this
protein into the bloodstream.
• The concentration of this protein in the blood is used
as a marker for possible prostate cancer.