Topic 2: Biochemistry

Molecules to metabolism
Topic Two : Biochemistry

• Atoms are the smallest forms of matter that
retain the chemical characteristics of a given
element
• Atoms have a nucleus , which:
Contains protons (p+
)
May contain neutrons (n0
)
Clouds of electrons (e-
) surround the nucleus
2.1 U.1 Molecular biology explains living processes in terms of the chemical substances
involved.
Atoms

CHON
• A mnemonic acronym for the four most common elements in
living organisms: carbon, hydrogen, oxygen, and nitrogen.
• 99.1% of a human body is made of CHON
2.1 U.1 Molecular biology explains living processes in terms of the chemical
substances involved.

Carbon contains 4 bonds sites making
it the backbone for all organic compounds
Carbon contains 4 bond sites (which can from strongest of all bonds,
covalent) which is why it is the backbone for all organic compound

Bonding
• Atoms stick together by linkages we call bonds.
• All biological reactions involve some sort of reorganization of
bonds.
• Bond reorganization (breakage or building of bonds) results in
the uptake or release of energy.
• Bond energy is the energy needed to break a given bond.
Types of Bonds
1. Ionic Bonds
 In ionic bonds, electrons are donated by one atom
to another
 An electronegative atom steals an electron from
another atom to fill its valence shell
 That is, one or more electrons LEAVE one atomic
center to ‘live’ with another
Molecules

2. Covalent Bonds
• In covalent bonds, two electrons are shared per bond
• More than one bond can occur between two atoms

2.1 U.2 Carbon atoms can form four covalent bonds allowing a diversity of
stable compounds to exist.
• Carbon atoms contain four
electrons in their outer shell
allowing them to form four
covalent bonds with potential four
other different atoms, e.g. methane
(CH4).
• Covalent bonds are the strongest
type of bond between atoms. Stable
molecules can be formed.
• The result of these properties is an
almost infinite number of different
possible molecules involving carbon.
• Organic compounds are formed only
when the compound contains Carbon
and Hydrogen.
Organic Molecules

• Biochemistry a study of biological processes from the structures
of the molecules and how they interact with each other
• There are many molecules important to living organisms
including water, carbohydrates, lipids, proteins and nucleic acids
• Molecular biologists break down biochemical processes into
their component parts (reductionism)
• When they look at the sum of all these reactions as a whole,
they can study the emergent properties of that system

2.1 A.1 Urea as an example of a compound that is produced by living organisms but can
also be artificially synthesized.
Nature of Science: Falsification of
theories—the artificial synthesis of urea
helped to falsify vitalism.
Wöhler accidentally synthesized urea in 1828,
while attempting to prepare ammonium
cyanate. In a letter to a colleague he says “I can
no longer, so to speak, hold my chemical water
and must tell you that I can make urea without
needing a kidney, whether of man or dog". This is
supposed to undermine vitalism as organic
chemicals were previously thought to be
synthesized only by organisms.

2.1 U.3 Life is based on carbon compounds including carbohydrates, lipids, proteins and
nucleic acids.
Four Groups of Organic Molecules
1. Carbohydrates
• Sugars
• Monomers are commonly ring
shaped molecules
• Carbohydrates can be used for
structure and energy in living
things
Monomers: Individual units of organic molecules

2. Lipids (Fats, Oils, Waxes and steroids)
• Made up of fatty acids and glycerol
• insoluble in water
• Play many important roles in your body, from providing
energy to producing hormones.
2.1 S.2 Identification of biochemicals such as sugars, lipids or amino acids from molecular
diagrams.
Fatty Acid

3. Amino acids
• The building blocks of
proteins.
• AA + AA + AA … = protein
• Every amino acid has:
– Terminal Hydrogen
– Carboxyl Group
– Amino group
– Variable group (R group)
nucleic acids.

nucleic acids.
4. Nucleic acids
• Contain carbon, hydrogen,
oxygen, nitrogen and
phosphorus
• Chains of sub-units called
nucleotides
• Nucleotides consist of base,
sugar and phosphate groups
covalently bonded together
• If the sugar is ribose then the
nucleic acid formed is RNA if the
sugar is deoxyribose then DNA is
formed.
• DNA and RNA are the used to
make new cells or make
proteins in existing cells
Simplified Nucleotide

2.1 S.1 Drawing molecular diagrams of glucose, ribose, a saturated fatty acid
and a generalized amino acid.
Try drawing by hand the
following molecules:
• Glucose
• Ribose
• A generalized saturated
fatty acid and glycerol
• A generalized amino acid
• Nucleotide

2.1 S.2 Identification of biochemicals such as sugars, lipids or amino acids from
molecular diagrams.

2.1 S.2 Identification of biochemicals such as sugars, lipids or amino
acids from molecular diagrams.

Living things are constantly acquiring material to maintain themselves. Some of
these things are converted into them, but membranes breakdown, enzymes wear
out and DNA gets oxidized. So these things get discarded. The material that is
consumed by that living thing must be converted into a usable forms. That is what
metabolism is all about
Metabolism is divided into two components;
 Anabolism (Synthesis large molecules from smaller ones)
 Catabolism (Breaking down of large molecules into their component
parts)
2.1 U.5 Anabolism is the synthesis of complex molecules from simpler molecules
including the formation of macromolecules from monomers by condensation reactions.
http://fc02.deviantart.net/fs70/f/2013/014/1/
9/bodybuilder_159_by_stonepiler-d5rhr6l.jpg
Maltase is a condensation
two molecules of glucose
into maltose forming a bond.
Lactase is an enzyme that
hydrolyses Lactose into Glucose
and Galactose breaking the bond

Anabolic Reactions require energy
as you are building large molecules from
small ones (takes energy to build things)
• Some anabolic processes
are protein synthesis, DNA synthesis
and replication, photosynthesis, and
building complex products
carbohydrates, such as cellulose,
starch and glycogen
• If you can’t remember which one
is which, think anabolic steroids
are used to build muscles in
athletes and body builders and
catapults are used to break down
walls in wars
2.1 U.5 Anabolism is the synthesis of complex molecules from simpler molecules
including the formation of macromolecules from monomers by condensation reactions.
http://fc02.deviantart.net/fs70/f/2013/014/1/
9/bodybuilder_159_by_stonepiler-d5rhr6l.jpg

2.1 U.6 Catabolism is the breakdown of complex molecules into simpler molecules
including the hydrolysis of macromolecules into monomers.
• Catabolism are reactions
that break down larger
molecules into smaller ones
or their component parts
• Catabolic reactions releases
energy (sometimes captured
in the form of ATP)
• Some examples of catabolic
reactions are digestion of
food, cellular respiration, and
are processes. Think of
"catapults" used to break
down enemy walls during
wars
• Oxidation reactions

Water
Essential idea: Water is the medium of life.

• A water molecule consists of
an oxygen atom covalently
bound to two hydrogen atoms
• Since O is more
electronegative than H,
an unequal sharing of
electrons occurs
• This creates a polar
covalent bond, with H
having a partial positive
charge and O having a
partial negative charge
• The partial + charge is
attracted to the partial –
charge creating an
intermolecular attraction
between the water molecules
called a “Hydrogen bond.”
2.2 U.1 Water molecules are polar and hydrogen bonds form between them.

Water is a kinetic energy/ heat energy sponge
• Liquid Water can absorb a lot of heat energy without changing
temperature. Water’s high specific heat minimizes temperature
fluctuations to within limits that permit life
– Heat is absorbed when hydrogen bonds break
– Heat is released when hydrogen bonds form
2.2 A.2 Use of water as a coolant in sweat.

Water is a kinetic energy/ heat energy sponge
– Heat of Fusion heat energy that can be released before something
will start melting/ becoming a liquid.
*Note that heat is released but the temperature does not
change
– Heat of Vaporization heat energy that can be absorbed before
something starts to boil and become a gas.
*Note that heat is absorbed but the temperature does not
change
Heat of
vaporization
**When you sweat, water turns from a liquid to a gas
taking with it a large amount of heat

Heat of Vaporization
Water 2257 joules Methane 760 joules
2.2 A.1 Comparison of the thermal properties of water with those of methane.
Water resists changing from a liquid to a gas. It take almost three times the amount of
heat energy to change water from a liquid to a gas, as compared to methane. A
water a substance that creates a stable environment for living things

2.2 A.1 Comparison of the thermal properties of water with those of methane.
Methane
• waste product of anaerobic
respiration in certain
prokaryotes living in
anaerobic conditions
• Methane can be used as a
fuel
• If present in the atmosphere
it contributes to the
greenhouse effect.
Methane Water
Formula CH4 H2O
Molecular mass 16 18
Bonding Single covalent
Polarity nonpolar polar
Density (g cm-3) 0.46 1
Specific Heat Capacity
(J g-1 oc-1)
2.2 4.2
Latent heat of
vaporization (J g-1)
760 2257
Melting point (oC) -182 0
Boiling point (oC) -160 100
Key chemical
property that
causes the major
differences seen
in the physical
properties.
Methanogenic prokaryotes
• can be found in swamps,
wetlands, the guts of
animals (including cattle
and sheep)
• can also be found in waste
dumps

Evaporative Cooling
Heat of vaporization
• Evaporation is transformation of a
substance from liquid to gas
• As a liquid evaporates, its remaining
surface cools, a process called
evaporative cooling
• Evaporative cooling of water helps
stabilize temperatures in organisms
and bodies of water
• A body temperature of above 40°C is
likely to be fatal due to the damage
done to enzymes in critical
biochemical pathways
• When you sweat, water turns from a
liquid to a gas taking with it a large
amount of heat
2.2 A.2 Use of water as a coolant in sweat.

2.2 U.2 Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and
solvent properties of water.
Cohesive Properties
• Water is a polar molecule, with a negative oxygen end and a positive hydrogen
end.
• Hydrogen bonds that exist between water molecules create a high level
of attraction linking water molecules together. This attraction between two
of the same molecules is called cohesion.
• These cohesive forces allow water to move up vascular tissue in plants
against gravity. It also creates surface tension on water that allows some organisms
to walk on water.
http://www.kellyisola.com/tag/transformation-2/

Adhesive Properties
• Not only does water bind
strongly to itself, it also
forms H-bonds with other
polar molecules. This is
called adhesion.
• This is an important property
in transpiration as well,
as water adheres to the
cellulose in the walls of the
xylem vessels
• As water is evaporated from
the stomata, the adhesion can
help the water move up
through the xylem
Capillary Action

Thermal Property
• Water has a high specific heat capacity (amount of energy needed
to raise temperature of a substance by a certain temperature
level). Basically, water can absorb a lot of heat and give off a lot of
heat without drastically changing the temperature of water.
• This is very important as a cooling mechanism for humans. As we
sweat, the water droplets absorb heat from our skin causing the water to
evaporate and our bodies to cool down.

2.2 A.3 Modes of transport of glucose, amino acids, cholesterol, fats, oxygen and
sodium chloride in blood in relation to their solubility in water.
Blood
Blood transports many different substances to
different parts of the body using a variety of
methods
• Water is critical both as a solvent in which
many of the body's solutes dissolve
• In addition, due to its polarity water is
a great solvent of other polar
molecules and ions. This is vital
because it allows water to act as
a transport medium (blood and cytoplasm)
of important molecules in biological
organisms.
Plasma 55%
• 91% Water
• 7% Blood Proteins
• 2% Nutrients (amino acids, sugars,
lipids)
• Hormones and ions
Cellular Components 45%
• White Blood cells
• Red Blood Cells

Solvent Properties
• Water is known as the “universal solvent” because of its ability to dissolve many substances
because of its polarity.
• Water is able to dissolve other polar molecules such as many carbohydrates, proteins
and DNA; and positively and negatively charged ions such as Na+.
• This is essential because it allows water to act as a transport medium (blood and
cytoplasm) of important molecules in biological organisms

2.2 U.3 Substances can be hydrophilic or hydrophobic.
Hydrophilic (water loving)
• All substances that dissolve in water are hydrophilic, including polar
molecules such as glucose, and particles with positive or negative
charges such as sodium and chloride ions.
• Substances that water adheres to, cellulose for example, are also hydrophilic.
The diagram of
glucose showing
the positive
charges
attracting water
molecules

Hydrophobic (Water hating)
• Molecules are hydrophobic if they do not have negative or positive charges
and are nonpolar and are insoluble in water
• All lipids are hydrophobic, including fats and oils
• Hydrophobic molecules dissolve in other solvents such as propanone
2.2 U.3 Substances can be hydrophilic or hydrophobic.
A water and oil mixture separating over time due
to the hydrophobic properties of oil molecules

Glucose
• Glucose has 5 hydroxyl groups
(OH) connected to it. Due to
the electronegative difference
between oxygen and hydrogen
this functional group is slightly
polar
• The polarity of glucose
makes it soluble molecule in
water, making it possible to
be transported in the blood
plasma
• Blood plasma consists mainly
of water (95%) plus dissolved
substances which it transports.

Amino acids
• R group in the twenty different amino acids can vary and be polar, non-
polar or charged.
• R group determines the degree of solubility
• Soluble amino acids can be carried by the blood plasma

2. Fats
• Large, non-polar molecules, insoluble in
water
• They are carried in blood inside
lipoprotein complexes
1. Cholesterol
• hydrophobic, apart and a small
hydrophilic region at one end, not
enough to make cholesterol dissolve in
water.
• They are carried in blood in lipoprotein
complexes
Lipoprotein complex
• Outer layer consists of single layer of
phospholipid molecules hydrophilic
phosphate heads of the phospholipids
face outwards and are in contact with
water.
• The hydrophobic tails face inwards and
are in contact with the cholesterol and fat
molecules
• Proteins are also embedded in the
phospholipid layer

Oxygen
• Non-polar molecule but, due
to the small size of oxygen
it is soluble in water, but
only just
• As temperature of water
increases the solubility of
oxygen decreases
• At body temperature (37 °C)
very little oxygen can be
carried by the plasma, too little
to support aerobic respiration
• hemoglobin in red blood
cells carry the majority of
oxygen

Ionic compound
• freely soluble in water
• As an example NaCl
(Sodium Chloride)
dissolving to form
sodium ions (Na+) and
chloride ions (Cl-)
• carried in the blood
plasma due to the
polar nature of
water
Slightly negative
oxygen surrounds
the positive Sodium
Slightly positive
hydrogens
surrounds the
negative Chloride

Rules of molecules
1. Numbering the carbon locates in the molecule. Below are four different examples
of C6H12O6
molecular diagrams.

Example of numbering
Properties of Deoxyribose
• Deoxyribose differs as shown
in the diagram, and forms the
backbone of DNA
• DNA is made of repeating
units of nucleotides.
Nucleotides have two other
parts, a base attached to the
1 carbon and a phosphate
group attached to the 3
carbon and the 5 of another
nucleotide.
molecular diagrams.

Rules of linking molecules
1. Numbering the carbons located in
the molecule.
2. Where and what are the functional groups in a molecule.
Example: below three different C6H12O6 molecules. Where the hydroxyl group (OH) is
determines bonding, structure and function
molecular diagrams.

1. Numbering the carbons
locations in the molecule.
2. Where are the functional
groups. Example: below three
different C6H12O6 molecules.
Example: Branching or
straight chain of
polysaccharides
molecular diagrams.

1. Numbering the carbons
located in the molecule.
2. Where are the functional
groups. Example: below
three different C6H12O6
molecules.
Example: Branching or
straight chain of
polysaccharides
molecular diagrams.

Carbohydrates and lipids
Essential idea: Compounds of carbon, hydrogen and oxygen are used
to supply and store energy.

Carbohydrates
Are organic compounds made of
carbon, hydrogen and oxygen.
Sometimes classed sugars. Most
sugars names end with there ose.
As an example glucose.
Carbohydrates.
1. Monosaccharide Single units
called monomers.
2. Disaccharides 2 monomers
joined.
3. Polysaccharides long chains of
repeating units
2.3 U.1 Monosaccharide monomers are linked together by condensation reactions to
form disaccharides and polysaccharide polymers.
http://www.cookrepublic.com/images/blog/archive/almondrose_bread4.jpg

1. Monosaccharides
• Also called simple sugar, are the simplest form of sugar and
the most basic units of carbohydrates.
• The general formula is CnH2nOn.
• They cannot be further hydrolyzed to simpler chemical
compounds. They are usually colorless, water-soluble,
and crystalline solids.
• Some monosaccharides have a sweet taste.

B. beta Glucose the structure to the
right
•C6H12O6
•Carbon 5 is connected to Carbon 1
•Each Carbon has an -OH group
•Each Carbon has an -H (C6 has 2)
A. alpha Glucose the structure to the
right
•C6H12O6
•Carbon 5 is connected to Carbon 1
•Each Carbon has an -OH group
•Each Carbon has an -H (C6 has 2)

C. Ribose the structure to the right
• C5H10O5
• A single-ring pentose sugar
• Each Carbon has a -H group (C5 has 2)
• It is the backbone of RNA and with a
missing oxygen on carbon 5 part of DNA
• It soluble
D. Galactose the structure to the right
• C6H12O6
• Galactose is less sweet than glucose
• It is found in dairy products, in sugar beets
and gums.
• When combined with glucose, through a
dehydration reaction, the result is the
disaccharide lactose found in most milks.

E. Fructose
• A 5 carbon (pentose) sugar
• It is one of the three dietary
monosaccharides, along with
glucose and galactose, that
are absorbed directly into
blood during digestion
• Commonly found in fruits and
honey
• It is the sweetest naturally
occurring carbohydrate

2. Disaccharides
• Contain two monosaccharides or monomers linked together to make
a polymer.
• A bond is formed by removing a hydroxyl group (OH) from one
monosaccharide and a hydrogen atom for the other with the help of
an enzyme.
• These molecules form a glycosidic bond through the process of
condensation (Dehydration synthesis).
2.3 U.1 Monosaccharide monomers are linked together by condensation reactions to form
disaccharides and polysaccharide polymers.

A. Maltose
• (C12H22O11)
• Made up of two Glucose monosaccharides
• Maltose links together to make up the polymer starch, found in
plants.
• The production of maltose is an important part of the brewing
process of beers.
was α glucose
was α glucose
https://ugandapeopleandculture.files.wordpress.com/2013/03/sweet-potato-in-basket-lo-r.jpg

B. Lactose
• (C12H22O11)
• The two subunits that make up lactose are glucose and galactose, our friends from a
couple of slides ago.
• commonly found in milk
• The enzyme that splits lactose into glucose and galactose is called lactase, and it is
located on the surface of the cells lining the small intestine.
• Lactose intolerance is a common medical condition that results in abdominal pain
caused by reduced or absent activity of enzyme lactase.

C. Sucrose
• (C12H22O11) is also known as table sugar, is extracted, and refined, from either
sugar cane plants or sugar beet plants.
• The two monosaccharides (glucose and fructose) that linked together.

3. Polysaccharides
• Macromolecules that are
polymers of a few hundred or
thousand monosaccharide.
Important in:
 Energy Storage
 Structural support
Examples
Starch (energy)
Glycogen
(energy)
Cellulose
(structure)
2.3 U.1 Monosaccharide monomers are linked together by condensation
reactions to form disaccharides and polysaccharide polymers.

A. Cellulose
• Cellulose molecules are unbranched
chains of β-glucose linking 1-4 carbon
atom on the next β-glucose.
• Hydrogen bonds link between the
separate chains. This holds them together
to form one molecule, Cellulose.
• The glucose subunits in the chain are
oriented alternately upwards and
downwards, bonding on the 1-4 carbons.
• The consequence of this is that the
cellulose molecule is a straight chain,
rather than curved.
• They have very high tensile strength (the
basis of cell walls).
2.3 A.1 Structure and function of cellulose and starch in plants and
glycogen in humans.
Hydrogen Bonding

B. Starch (Amylose)
glycogen in humans.
• Found only in plants as a energy storage
molecule.
• Amylose is harder to digest and less is
soluble then Amylopectin.
• It is linking together α-glucose molecules
that have 1-4 carbon linkages creating NO
bending or branching
• The consequence of this 1-4 bonding is that
the starch molecule is linear (helical)

glycogen in humans.
C. Starch (Amylopectin)
• Found only in plants as a storage
molecule.
• Starch is insoluble.
• It is linking together α-glucose
molecules that have 1-4 and 1-6
carbon linkages creating bending and
branching (about one every 20
subunits)
• The consequence of this is that the
starch molecule is curved, rather than
straight

D. Glycogen (C6H10O5)n
• Glycogen is made by animals and
also some fungi.
• It is stored in the liver and some
muscles in humans.
• It is linking together α-glucose
molecules that have 1-4 and 1-6
carbon linkages creating bending
and branching (about one every
10 subunits). When compared to
Amylopectin there is much more
branching.
glycogen in humans.

Cellulose Starch Glycogen
Amylose Amylopectin
Source Plant Plant Plant Animal
Subunit 𝛽 − 𝐺𝑙𝑢𝑐𝑜𝑠𝑒 𝛼 − 𝐺𝑙𝑢𝑐𝑜𝑠𝑒 𝛼 − 𝐺𝑙𝑢𝑐𝑜𝑠𝑒 𝛼 − 𝐺𝑙𝑢𝑐𝑜𝑠𝑒
Bonds 1-4 1-4 1-4 and 1-6 1-4 and 1-6
Branches No No Yes per 20 sub
units
Yes
per 10 sub
units
Polysaccharides of Glucose
glycogen in humans.

Monosaccharides
glucose Energy molecule used in
aerobic respiration
galactose Nutritive sweetener in foods
fructose Fruit sugar
Ribose
Disaccharides
maltose Malt sugar found in barley,
consists of 2 glucose
molecules
lactose Sugar found in milk
sucrose Transport sugar found in
plants because of its
solubility
Polysaccharides
starch (amylose) Storage carbohydrate in
plants (more linear shape)
glycogen Storage carbohydrate in
animals
cellulose Main component in plant cell
walls
starch (amylopectin) Storage carbohydrate in
plants (more globular shape)

2.3 S.1 Use of molecular visualization software to compare cellulose,
starch and glycogen.
The easiest way to use jmol is to use the ready-made models from on the biotopics website
• Click on the models or the logo below to access them
• Play with the models, move them, zoom in and out
• Test yourself by answering the questions below:
1. Select the the glucose molecule and identify the colors used to represent carbon,
hydrogen and oxygen atoms
2. Using the models identify and describe the differences between glucose, sucrose
and fructose (hint: descriptions will be clearest if you refer to the numbered carbon
atoms.
3. Look at the amylose model and zoom out from it. Describe the overall shape of the
molecule.
4. Zoom in on the amylose molecule. Each glucose sub-unit is bonded to how many other
sub-units? Which carbons atoms used to form the glycosidic bonds? Are there any
exceptions to these rules?
5. Select the amylopectin model and zoom in on the branch point. This glucose sub-unit is
bonded how many others and which carbon atoms are used for bonded compared with
the un-branched amylose molecule?
6. Using a similar approach to that above investigate the structure of glycogen and find the
similarities and differences between it and both amylose and amylopectin.

2. Lipids
• Diverse group of molecules that are non-polar.
• Constructed from a glycerol attached to 3 fatty acid chains.
• Glycerol is a 3-C alcohol.
• Fatty acids are hydrocarbons with a carboxyl group at one end and a methyl
group at the other end..
• Hydrocarbon tail is extremely hydrophobic. They can contain multiple double
bonds (polyunsaturated), one double bond (monounsaturated) or no double
bonds (saturated).
• Building a lipid molecule is an anabolic/condensation reaction
molecular diagrams.

2.3 U.2 Fatty acids can be saturated, monounsaturated or polyunsaturated.
• Mono and Poly Unsaturated fatty acids are naturally curved and
have one or more double bond to a carbon in the fatty acid chain.
• Saturated fatty acids are straight and the carbon atom has all its
bond sites filled with other atoms (no double bonds).
Double Bonds

Trans fats Artificially produced by hydrogenating vegetable oils Once a
Cis fatty acid has been hydrogenated (reaction with H2) it behaves like a
saturated fat and becomes a straight chain.
Nature of Science: Evaluating claims—health claims made about lipids in diets need to
be assessed.
• The reaction cause the fatty acid to have a higher melt temperature (30–
40 °C); and extend the shelf-life of food. At one time
• Thought to be healthier for you, because it was not produced by animals.
• Inexpensive (During war time rationing. It also allowed a much
Longer shelf life of fats and oils).
• Trans-fats are kosher & suitable for vegetarians.
Found in margarines, hydrogenated vegetable oils and fast foods
It was not until very recently that trans fats they were found to be a risk factor in
many illnesses.

• Saturated fat acids contain
no double bonds and are
straight chains.
• Cis fatty acids contain a
double bond in the fatty acid
chain and are curved.
– usually from plant sources
– Less risk of CHD
• Trans fatty acid are
unsaturated, contain a double
bond straight.
– Vast majority of trans fatty
acid are artificially produced
– Very high CDH risk, they
mimic saturate
2.3 U.3 Unsaturated fatty acids can be cis or trans isomers.
CDH- Coronary Heart Disease

Cis-isomers Trans-isomers
Very common in nature Rare in nature – usually artificially produced to
produce solid fats, e.g. margarine from vegetable oils.
the hydrogen atoms are on the same side of the two
carbon atoms
the hydrogen atoms are on the same side of the two
carbon atoms
The double bond causes a bend in the fatty
acid chain
The double bond does not causes a bend
in the fatty acid chain
Therefore cis-isomers are only loosely packed Trans-isomers can be closely packed
Triglycerides formed from cis-isomers have low melting
points – they usually liquid at room temperature
Triglycerides formed from trans-isomers have high
melting points – they usually solid at room
temperature

Saturated, monounsaturated or polyunsaturated?
Q1 Oleic Acid
Q2 Caproic Acid
Q3 α-Linolenic Acid

Saturated, monounsaturated or polyunsaturated?
Q1 Oleic Acid 1 double bond therefore monounsaturated
Q2 Caproic Acid no double bonds therefore saturated
Q3 α-Linolenic Acid 3 double bonds therefore polyunsaturated
n.b. the term saturated refers to
whether more hydrogen can be
added to the fatty acid. A double
bond can be replaced if two
hydrogen atoms are added. If there
are no double bonds a fatty acid is
said to be saturated as no more
hydrogen atoms can be added.
https://commons.wikimedia.org/wiki/Fatty_acids#Polyunsaturated_fatty_acids_2

Q1 trans or cis isomers?
???
???

Q1 trans or cis isomers?

Q2 trans or cis isomer of α-Linolenic Acid?

Q2 trans or cis isomer of α-Linolenic Acid?
All 3 double bonds are cis, each one causes a bend in
the fatty acid chain.

• Glucose in the bloodstream is used to yield ATP (To carry out metabolic
activities) or converted to glycogen or fat
• Glycogen is the medium-term energy storage molecule in animals. It is
stored in the liver and muscles. The energy stored in glycogen is more
readily available than the energy stored in fat.
2.3 A.3 Lipids are more suitable for long-term energy storage in humans than carbohydrates.
Carbohydrates vs Fats

Reasons for using lipids for long-
term energy storage:
• Amount 16% of out body is
made up of fat while only
about 1% is made up of
carbohydrates.
• The amount of energy
released in cell respiration
per gram of lipids is double
that for carbohydrates (and
protein)
• Lipids add 1/6 as much to
body mass as
carbohydrates: fats are
stored as pure droplets
whereas when 1g glycogen
is stored it is associated with
2g of water. This is especially
critical for active animals as
energy stores have to be
carried.
After traveling an average of 50 miles from the ocean
to a hatching ground, penguins and mate While the
mother returns to the sea for food, the father sits on
the egg for around 64 days until it hatches. Once the
baby penguin emerges, the father keeps it warm and
even feeds it nutrients secreted from his own
esophagus without eating on its own. It relies on large
fat storages to get through this time

Functions of lipids
• Energy storage
• Insulation
• Protection (of internal organs)
• Buoyancy
• Component of cell membranes
• Electrical insulation by myelin
sheath
• Hormones (SIGNALING)
• Cell receptors

High Density Lipoproteins
(HDL): “Good Cholesterol”
Transport triglycerides out of
the blood into cell that then
are used. This reduce the risk
of Coronary Heart Disease
Low Density Lipoproteins
(LDL): “Bad Cholesterol”:
Transport triglyceride and
does not excrete them from
the blood vessels. As there
numbers increasing risk of
Coronary Heart Disease
increases.
be assessed.
Remember from slide 46: Cholesterol
and fats are carried in the plasma (due to its
non polar nature) surround by Lipoproteins.

Why are Trans fats bad?
The Shape of trans fats make them bad for your cardiovascular system.
–Unsaturated trans fats are linear and thus they lay flat against your arteries making
is more difficult for them to flow with your passing blood.
–These linear, unsaturated, trans fatty acids combine with cholesterol and form a
substance called plaque and can be deposited along the walls of your arteries
blocking or slowing blood flow. It this happens in the coronary arteries you can have
a heart attack.
be assessed.

The omega-number tells us the location of the first double bond from the methyl group
There are suggested health benefits linked to the intake of cis-omega-3 fatty
acids (from oily fish). It has been suggested that they reduce the likelihood of
blood to clot, and therefore reduce the risk of heart attacks and strokes.
Where population studies of people who eat large amounts of omega-3 in
their diet (such as fishing communities), the results suggest a health benefit from
there diet.
That there is a correlations, randomized controlled trials have not found
significant links. health benefits linked to the intake ofcis-omega-3 fatty acids
(from fish).
This is an Omega-3 fatty acid
be assessed.

Example: Omega-3 and Omega-6 Fatty Acids
The name omega 3 and omega 6 comes from which
carbon has the double bond in the fatty acid chain.
be assessed.

be assessed.
Fatty Acids Sources & Examples Possible Effects Evidence
Omega-3 Fish, nuts & Veg. oils Reduced blood
pressure and
triglycerides
Good clinical
evidence
Trans Fats Partially hydrogenated
veg. oils and margarines,
deep fried food
convenience foods
Reduces helpful
cholesterol (HDL) and
risks inc. in BP, CHD,
heart attacks and
stroke
Strong clinical &
epidemiological
evidence
Saturated Fats Meat, seafood, full-
cream, cheese, palm oil,
coconut oil
Inc. LDL & can lead to
atherosclerosis, CHD,
stroke & heart attacks
Strong clinical &
epidemiological
evidence (correlation
What kind of evidence can we look for?
• Population studies (cohort studies) can show correlation, but not attribute cause.
• Random, controlled trials (clinical studies) can attribute correlation and maybe
cause.
• Remember there is variation within all populations and genetic factors may also
play a role.

Key questions to consider
for the strengths are:
• Is there a (negative or
positive) correlation
between intake of the lipid
being investigated and
rate of the disease?
• Has this difference been
assessed statistically?
• How widely spread is the
data? This can be
assessed by the spread of
data points.
Evidence for health claims comes from research. Some of this research is more scientifically
valid than others. Evaluation = Make an appraisal by weighing up the strengths and
limitations
Key questions to consider for the
limitations are:
• Was the measure of the health a
valid one?
• How large was the sample size?
• Does the sample reflect the
population as a whole or just a
particular group?
• Was the data gathered from human
or animal trials?
• Were all the important control
variables, e.g. level of activity,
effectively controlled?
• Were the levels and frequency of the
lipids (or substance studied) intake
realistic?
be assessed.

be assessed.
• A positive correlation has been found between
saturated fatty acid intake and rates of CHD in
many studies.
• Correlation ≠ causation. Another factor, e.g.
dietary fiber could be responsible.
• There are populations that do not fit the
correlation such as the Maasai of Kenya. They
have a diet that is rich in meat, fat, blood and
milk. They therefore have a high consumption of
saturated fats, yet CHD is almost unknown
among the Maasai.
• Diets rich in olive oil, which contains cis-
monounsaturated fatty acids, are traditionally
eaten in countries around the Mediterranean. The
populations of these countries typically have low
rates of CHD and it has been claimed that this is
due to the intake of cis-monounsaturated fatty
acids.
• Genetic factors in these populations could be
responsible.
• Other aspects of the diet could explain the CHD
rates.
• There is also a positive correlation between
amounts of trans-fat consumed and rates of CHD.

2.3 S.2 Determination of body mass index by calculation or use of a nomogram.
Body Mass Index (BMI) is used as a
screening tool to identify possible
weight problems, however, BMI is not
a diagnostic tool. To determine if
excess weight is a health risk further
assessments are needed such as:
• skinfold thickness measurements
• evaluations of diet
• physical activity
• and family history
The table below can be used to assess
an adult’s status
BMI Status
Below 18.5 Underweight
18.5 – 24.9 Normal
25.0 – 29.9 Overweight
30.0 and Above Obese
In some parts of the world food
supplies are insufficient or are
unevenly distributed and many
people as a result are underweight.
In other parts of the world a likelier
cause of being underweight is
anorexia nervosa. This is a
psychological condition that
involves voluntary starvation and
loss of body mass.
Obesity is an increasing problem
in some countries. Obesity
increases the risk of conditions
such as coronary heart disease and
type II diabetes. It reduces life
expectancy significantly and is
increasing the overall costs of
health care in countries where
rates of obesity are rising.

Charts such as the one to the right can
also be used to assess BMI.
BMI is calculated the same way for both
adults and children. The calculation is
based on the following formula:
BMI = mass in kilograms
(height in meters)2
n.b. units for BMI are kg m-2
Example:
Mass = 68 kg, Height = 165 cm (1.65
m)
BMI = 68 ÷ (1.65)2 = 24.98 kg m-2
In this example the adult would be
(borderline) overweight - see the
table on the previous slide

An alternative to calculating the
BMI is a nomogram. Simply use a
ruler to draw a line from the body
mass (weight) to the height of a
person. Where it intersects the
W/H2 line the person’s BMI can be
determined. Now use the table to
assess their BMI status.
http://helid.digicollection.org/documents/h0211e/p434.gif
BMI Status
18.5 – 24.9 Normal
30.0 and
Above
Obese

1. A man has a mass of 75 kg and a
height of 1.45 meters.
a. Calculate his body mass index.
(1)
b. Deduce the body mass status of
this man using the table. (1)
c. Outline the relationship
between height and BMI for a
fixed body mass. (1)

1. A man has a mass of 75 kg and a
height of 1.45 meters.
a. Calculate his body mass index.
(1)
b. Deduce the body mass status of
this man using the table. (1)
c. Outline the relationship
between height and BMI for a
fixed body mass. (1)
BMI = mass in kilograms ÷ (height in meters)2
= 75 kg ÷ (1.45 m)2
= 75 kg ÷ 2.10 m2
= 35.7 kg m-2
35.7 kg m-2 is above 30.0 (see table below)
therefore the person would be classified obese.
BMI Status
18.5 – 24.9 Normal
30.0 and Above Obese
The taller a person the smaller the
BMI;
(negative correlation, but not a
linear relationship)

2. A woman has a height of 150 cm and
a BMI of 40.
a. Calculate the minimum amount
of body mass she must lose to
reach normal body mass status.
Show all of your working. (3)
b. Suggest two ways in which the
woman could reduce her body
mass. (2)

4. A woman has a height of 150 cm and
a BMI of 40.
a. Calculate the minimum amount
of body mass she must lose to
reach normal body mass status.
Show all of your working. (3)
b. Suggest two ways in which the
woman could reduce her body
mass. (2)
BMI = mass in kilograms ÷ (height in meters)2
therefore
mass in kilograms = BMI ÷ (height in meters)2
Actual body mass = BMI ÷ (height in meters)2
= 40 kg m-2 x (1.50 m)2
= 90 kg
Normal BMI is a maximum of 24.9 kg m-2
Normal body mass = 24.9 kg m-2 x (1.5 m)2
= 56 kg
To reach normal status the woman needs to lose
90 kg – 56 kg = 34 kg
Reduce her nutritional intake /
diet / reduce the intake of lipids;
Exercise / increase activity levels;

2.4 Proteins
Essential idea: Proteins have a very wide range of functions in living organisms.
Titin: above, is the largest sequence protein known

• Twenty different amino acids are
used by the ribosomes to create
polypeptides needed by our
bodies.
• These amino acids contain contain
a basic structure, an amine (NH2)
group, a carboxyl (-COOH) group
which combine to form the
peptide bond, a hydrogen atom
and a “R” group
• The different “R” groups are what
makes the amino acids different
and allow the proteins to form a
wide array of structures and
functions
• Some are charged or polar, hence
they are hydrophilic
• Some are not charged and are
non-polar, hence they are
hydrophobic
2.4 U.2 There are 20 different amino acids in polypeptides synthesized on ribosomes.

Amino Acids with different R groups
• 20 amino acids are encoded by
the universal genetic code.
• Essential amino acids cannot
be made by the body. As a
result, they must come from
food. 9 essential amino
acids one example is valine
4 groups of amino acids based
on there R group
1. Hydrophobic amino acids
R-group is non-polar. Example:
Valine
2. Hydrophilic amino acids
R-group is polar, hydrophilic but
uncharged. Example: Serine
3. Acidic amino acids
R-group is acidic or negatively
charged. Example Glutamic acid
4. Basic amino acids
R-group is basic or positively
charged. Example Lysine

Ribosomes (to the left) are the molecules
within cells that facilitate the formation of
peptide bonds and are where in the cell
proteins are synthesized
peptide bond

2.4 U.3 Amino acids can be linked together in any sequence giving a huge range of
possible polypeptides.

If a polypeptide contains just 7 amino acids there can be 207
= 1,280,000,000 possible polypeptides generated.
Given that polypeptides can contain up to 30,000 amino acids (e.g.
Titin) the different possible combinations of polypeptides are
effectively infinite.
2.4 U.3 Amino acids can be linked together in any sequence giving a huge range of
possible polypeptides.

2.4 U.4 The amino acid sequence of polypeptides is coded for by genes.

There are four levels of protein structure. Which level a protein
conforms to is determined by it’s amino acid sequence and the
internal bonding that occurs based on the amino acids R group.
2.4 U.6 The amino acid sequence determines the three-dimensional conformation of a protein.
2.4 U.5 A protein may consist of a single polypeptide or more than one polypeptide linked together.

1. Primary structure:
•The order/ number of amino
acids in a polypeptide chain.
•Just one type of bond a covalent
peptide bond between each amino
acid
•Linear shape (no internal
bonding)
Changes in the R group can
result in interactions within
the strands:
• Hydrogen bonds
• Ionic bonds
• Covalent bonds. (disulphide
bridge)
• Hydrophobic regions
• Interactions between
multiple amino acids
strands

2. Secondary Structure:
Add a second type of bond (hydrogen bonding) making them Fibrous
Proteins, in addition to the covalent bond in primary structure. This causes the
structure of the polypeptide to fold and coil in two ways:
• Alpha Helix
• Beta pleated sheets

3. Tertiary Structures
Tertiary structure is the three-
dimensional conformation of a
polypeptide in two additional
ways
1. Additional bonding
(ionic bonding or disulfide
bridges along with
hydrogen and covalent
bonding)
2. Intermolecular forces
(bonding) Hydrogen
bonding or hydrophobic
interactions

4. Quaternary structure
In addition to all the bond
types of a tertiary structure
quaternary structures have
two or more polypeptides
strands that aggregate
together
Example: Hemoglobin

Proteins are commonly described as either
being fibrous or globular in nature.
1. Fibrous Proteins
• Insoluble in Water
• Structural (support/strength)
Example
Collagen (tissue
strengthening)
Keratin (hair/nails)
Elastin (skin)
2. Globular Proteins
• Can be soluble in water
• Functional actively involved in a cell’s
metabolism (enzymes and antibodies)
Examples
Amylase (digestion of
starch)
Insulin (blood sugar
regulation)
Hemoglobin (carry O2)
Immunoglobulin
(antibodies)
2.4 U.6 The amino acid sequence determines the three-dimensional conformation of a
protein.

Catalase Reaction
http://potatocatalasea2joshiobrien.weebly.com/uploads/1/3/8/1/13818604/1037140_orig.jpg
Sliding filament
http://figures.boundless.com/19642/full/figure-38-04-04.jpe

2.4 U.7 Living organisms synthesize many different proteins with a wide range of
functions.
Function Description Key examples
Catalysis
There are thousands of different enzymes to catalyze specific
chemical reactions within the cell or outside it.
Rubisco
Muscle contraction
Actin and myosin together cause the muscle contractions used
in locomotion and transport around the body.
Actin and myosin
Cytoskeletons
Tubulin is the subunit of microtubules that give animals cells
their shape and pull on chromosomes during mitosis.
Tubulin
Tensile
strengthening
collagen
Blood clotting
Plasma proteins act as clotting factors that cause blood to turn
from a liquid to a solid in wounds.
Fibrin
Transport of
nutrients and
gases
Proteins in blood help transport oxygen, carbon dioxide, iron
and lipids.
Serum albumin
Nothing can compare with the versatility of proteins.
Their functionality and usage in organisms is unrivalled.

Function Description Key examples
Cell adhesion
Membrane proteins cause adjacent animal cells to stick to each
other within tissues.
Integrins
Membrane
transport
Membrane proteins are used for facilitated diffusion and active
transport, and also for electron transport during cell respiration
and photosynthesis.
CoQ10
Hormones
Some such as insulin, FSH and LH are proteins, but hormones are
chemically very diverse.
Insulin
Receptors
Binding sites in membranes and cytoplasm for hormones,
neurotransmitters, tastes and smells, and also receptors for light in
the eye and in plants.
Rhodopsin
Packing of DNA
Histones are associated with DNA in eukaryotes and help
chromosomes to condense during mitosis.
Histones
Immunity
This is the most diverse group of proteins, as cells can make huge
numbers of different antibodies.
Immunoglobulins
Biotechnologically has allowed us to use proteins in industry examples are:
• enzymes for removing stains in clothing detergent
• monoclonal antibodies for pregnancy tests
• insulin for treating diabetics
• Disease treatments
Genetically modified organisms are often used as to produce proteins. This however is still a
technically difficult and expensive process.
2.4 U.7 Living organisms synthesize many different proteins with a wide range of
functions.

Examples of Proteins
1. Rubisco
• Full name ribulose bisphosphate carboxylase
• Enzyme - catalyzes the reaction that fixes carbon dioxide from the atmosphere
into carbon compounds during photosynthesis.
• Found in high concentrations in leaves and algal cells
2.4 A.1 Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as
examples of the range of protein functions.

2. Insulin
• A hormone secreted by β cells in the pancreas. These proteins signal cells to
absorb glucose and help reduce the glucose concentration of the blood.
• Affected cells have proteins on their surface to which insulin can bind to. This
causes a channel to open for glucose.
• Effected cells transport glucose carried by the blood to the liver.

3. Actin or Myosin
• A muscle contraction consists of a series of repeated events.
• First, calcium triggers a change in the shape of troponin and reveals
the myosin-binding sites of actin beneath tropomyosin.
• Then, the myosin heads bind to actin and cause the actin filaments to slide

4.Rhodopsin
• A pigment that absorbs light
• Membrane protein of rod cells of the retina (light sensitive region at the back of the eye)
• Even very low light intensities can be detected.
Rhodopsin in a rod appears red and
purple in the diagram below
for monochromatic vision in the dark

5.Collagen
• A number of different forms. All are rope-like proteins made of three polypeptides wound
together.
• About a quarter of all protein in the human body is collagen
• Gives strength to tendons, ligaments, skin and blood vessel walls.
• Forms part of teeth and bones, helps to prevent cracks and fractures to bones and teeth

6. Spider Silk
• The protein in dragline silk is fibroin. The exact composition of the proteins depends on
factors including species and diet.
• Fibroin consists of approximately 42% glycine and 25% alanine as the major amino acids
• Dragline silk is stronger than steel and tougher than Kevlar

Proteome
• All of the different proteins of an individual are produced by a
genome (all the different nitrogen bases in DNA).
• Proteomes vary in different cells (different cells make different proteins) and
at different times within the same cell (cell activity varies)
• Proteomes vary between different individuals because of not only cell activity
but slight variations in amino acid sequences
• Within species there are strong similarities between proteomes
2.4 U.8 Every individual has a unique proteome.

2.6 Structure of DNA and RNA
Essential idea: The structure of DNA allows efficient storage of
genetic information.

2.6 U.1 The nucleic acids DNA and RNA are polymers of nucleotides.
A nucleotide: a single unit of a nucleic acid
There are two types of nucleic acid: DNA and RNA.
Nucleic acids are very large
molecules that are constructed by
linking together nucleotides to
form a polymer.

covalent bond
covalent bond
A nucleotide: a single unit of a nucleic acid
• five carbon atoms = a pentose sugar
• If the sugar is Deoxyribose the polymer
is Deoxyribose Nucleic Acid (DNA)
• If the sugar Ribose the polymer is
Ribose Nucleic Acid (RNA)
• acidic
• negatively charged
• contains nitrogen
• has one or two rings
in it’s structure

Nitrogenous Bases
• Double ring PURINES
Adenine (A)
Guanine (G)
• Single ring PYRIMIDINES
Thymine (T)
Cytosine (C) T or C
A or G
7.1 U.2 DNA structure suggested a mechanism for DNA replication

Base-Pairings
• Purines only pair with Pyrimidines
• Three hydrogen bonds required to bond
Guanine & Cytosine
CG
3 H-bonds
7.1 U.2 DNA structure suggested a mechanism for DNA replication

• Nucleotides a linked into a
single by condensation
reaction
• Bonds are formed between
the phosphate of one
nucleotide and the pentose
sugar of the next.
• The phosphate group
(attached to the 5'-C of the
sugar) joins with the
hydroxyl (OH) group
attached to the 3'-C of the
sugar
• Successive condensation
reactions between
nucleotides results in the
formation of a long single
strand

2.6 U.3 DNA is a double helix made of two antiparallel strands of nucleotides linked by
hydrogen bonding between complementary base pairs.
• DNA is double stranded and shaped
like a ladder, with the sides of the
ladder made out of repeating
phosphate and deoxyribose sugar
molecules covalently bonded
together. The two strands are
antiparallel to each other due to
base pairing.
• The rungs of the ladder contain two
nitrogenous bases (one from each
strand) that are bonded together by
hydrogen bonds.
• The nitrogenous bases match up
according the Chargaff’s Rules in
which adenine always bonds to
thymine, and guanine always bonds
with cytosine. These bonds are
hydrogen bonds.

2.6 S.1 Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using
circles, pentagons and rectangles to represent phosphates, pentoses and bases.
Use this simple, but very
effective You Tube video
to learn how to draw the
nucleotides making up a
short section of a DNA
molecule.
To make sure you have
learn this skill you need
to practice it repeatedly.
http://youtu.be/kTH13oI8BSI

RNA DNA
Bases
Adenine (A)
Guanine (G)
Uracil (U)
Cytosine (C)
Adenine (A)
Guanine (G)
Thymine (T)
Cytosine (C)
Sugar
Ribose Deoxyribose
Number of strands
Single stranded, and often,
but not always, linear in
shape
Two anti-parallel,
complementary strands
form a double helix
2.6 U.2 DNA differs from RNA in the number of strands present, the base composition
and the type of pentose.
http://commons.wikimedia.org/wiki/File:RiboseAndDeoxy.gif

2.6 A.1 Crick and Watson’s elucidation of the structure of DNA using model making.
While others worked using an experimental
basis Watson and Crick used ball-and-stick
models to test their ideas on the possible
structure of DNA. Building models allowed
them to visualize (pre-computer) the
molecule and to quickly see how well it
fitted the available evidence.
It was not all easy going however. Their first
model, a triple helix, was rejected for
several reasons:
• The ratio of Adenine to Thymine was not
1:1 (as discovered by Chargaff)
• It required too much magnesium
(identified by Franklin)
From their setbacks they realized:
• DNA must be a double helix.
• The relationship between the bases and
base pairing
• The strands must be anti-parallel to allow
base pairing to happenWatson and Crick’s
Model

Because of the visual nature of their work the second and the correct model
quickly suggested:
• Possible mechanisms for replication
• Information was encoded in triplets of bases
Watson and Crick gained Nobel prizes for their discovery. It should be
remembered that their success was based on the evidence they gained from the
work of others. In particular the work of Rosalind Franklin and Maurice Wilkins,
who were using X-ray diffraction was critical to their success.
2.6 A.1 Crick and Watson’s elucidation of the structure of DNA using model making.

Bibliography / Acknowledgments
Jason de Nys

Topic 2: Biochemistry

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