A Level Notes

Biomolecules
 Water has many useful properties, and so it is ubiquitous in life on earth.
The useful properties of water arise from its structure.

 A Water molecule consists of two Hydrogen atoms covalently bonded to

an Oxygen atom. Because oxygen is more electronegative than hydrogen, it
has a greater pull on the shared electrons. This that the oxygen atom
is slightly negative (δ-) (because of the closer electrons), and hydrogen
is slightly positive (δ+). Water is therefore called a Polar Molecule.

 The slightly negative and slightly positive regions of the water molecule are
attracted to charged regions of other molecules, forming Hydrogen
Bonds (which are weak in comparison with other chemical bonds). Water will
form Hydrogen Bonds within itself.
 Water also takes part in some metabolic reactions, for example,
in Hydrolysis and Condensation reactions.

Sugars
 Monosaccharides are the monomers of Carbohydrates. Carbohydrates make
up about 1/10 of the organic matter in a cell, their functions include:
 Energy Source - They provide the energy for respiration
 Energy Storage e.g. Glycogen (animals) and starch (plants)
 Structure e.g. Cellulose
 They contain the elements Carbon, Hydrogen and Oxygen in the proportions
Cn(H2O)n.
 Monosaccharides come in many different forms; three to six carbon atoms.
 Monosaccarides are all soluble in water, sweet tasting and form crystals.
They are grouped according to the number of Carbon atoms, being called triose
(3C), tetrose (4C), pentose (5C) or hexose (6C)sugars. Most common is
hexose sugars.
 When Glucose forms a ring structure, it can do so in two different ways; α
Glucose, and β Glucose. This difference in structure leads to a difference in
properties.

 Monosaccharides can be bonded together to produce a disaccharide (2

sugars), or maybe even a polysaccharide (many), like Starch. Done
through a Condensation Reaction, forming a Glycosidic Bond. This
bond can be broken by Hydrolysis.
 The bond is named after the Carbon atoms that are involved in the bond.
 The bond between two Glucose molecules in Amylose is called a (1→4)
Glycosidic Bond. Carbons 1 and 4 are bonding.

Sugars from Condensation; Polymers

 α Glucose can form long chains with thousands of subunits called

and Amylose molecule (what is amylopectin??). Glucose units are
bonded together by Condensation Reactions forming (1→4)
Glycosidic Bonds.
 Amylose molecules tend to form coiled springs due to the way in which
the glucose units bond, making it compact.
 Large molecules such as amylose differ from glucose in that they are not
water soluble.
 Starch consists of a mixture of Amylose and a branched carbohydrate
chain called Amylopectin. The branches are formed when a one end of a
chain joins with a glucose in another, forming a (1→4) Glycosidic
Bond.
 Glycogen is almost identical to starch but differs in that the chains of
(1→4) linked glucoses are shorter, giving it a more highly branched
 structure. This branching allows for the fast breakdown of the
molecule during respiration.

 β Glucose chains, like the one above, are called Cellulose molecules,

and can contain 10000 glucose units. They are stronger than Amylose
and are only found in plants.

 Cellulose fibers are arranged in a very specific way. Long Cellulose

chains bunch together, held by Hydrogen bonds, to form Microfibrils &
Macrofibrils.

 Macrofibrils have a very high mechanical strength, similar to that of

steel. In plant cell walls, they criss-cross over each, forming a cross-
hatched structure, held by Hydrogen bonds, which is very strong. This
also allows water to move though and along the cell wall. The strength
of the cell walls prevent the cell form bursting, as it would in an
animal cell, when water passes into the cell. The pressure cause by the
water makes the cell Turgid, supporting the plant through Turgor
Pressure.
 Other Carbohydrate Polymers are used by a number of other
organisms to provide support, such as Peptidoglycan, which forms the
basis of bacterial cell walls, and Chitin, which makes up the exoskeleton
of insects.
Lipids
 Made of Carbon, Hydrogen and Oxygen
 Insoluble in water
 Lipids perform many functions:
o Energy Storage
o Making Biological Membranes
o Insulation
o Protection - e.g. protecting plant leaves from drying up
o Buoyancy
 o Acting as hormones
 Made from two molecules: Glycerol and Fatty Acids.
 Fatty acids have an Acid Group.
 Fatty acids are either saturated or unsaturated.

1.Saturated if every possible bond is made with a Hydrogen atom - no

C=C bonds.
2. Unsaturated fatty acids contain C=C bonds.
 Triglycerides are lipids consisting of one glycerol molecule bonded with three
fatty acid molecules.
 The bonds between the molecules are covalent and are called Ester bonds.
They are formed during a condensation reaction.
 Triglycerides are hydrophobic and so insoluble in water.

Phospolipids
 Phospholipids are similar to triglycerides in they consist of a glycerol
‘backbone’ and fatty acid ‘tails’, however, the third fatty acid has been replaced
by a phosphate group ‘head’.

 While the fatty acid ‘tails’ are hydrophobic, means the tails will move away
from the water.

 The phosphate ‘head’ is hydrophilic. This means the phosphate group will
move towards water.

 Phospholipids can contain saturated and unsaturated fatty acids. This allows for
the control of the fluidity of membranes.

Proteins
Proteins are polymers. The monomers of proteins are amino acids.

 All proteins have the same basic structure.

  There are 20 naturally occurring ‘R’ groups, which corresponds to 20 different
amino acids.

 Plants make all the amino acids they

need themselves, Structure of the Amino Acid as long as they can
obtain Nitrate from the soil.

 Animals on the other hand cannot make

amino acids themselves.

 Must take in proteins as part

of their diet. These proteins are
then broken down into
amino acids that can form
other proteins.

 Amino acids are toxic and as they

cannot be stored, they must be excreted
from the body in a process
called deaminati on. In animals, this
occurs in the liver, where amino
acids are converted to urea and
pass out in the urine.

Peptide Bonds
 Amino acids can be joined together, forming Peptide Bonds.
  All amino acids are joined in exactly the same way.
 A Condensation reaction forms between the amino group of one and the acid
group of another. When two amino acids are joined together in this way, a
dipeptide molecule is formed.


Primary Structure

 Proteins are made up of polypeptide chains, which are amino

acids joined together with peptide bonds. The unique sequence of
amino acids that make up a protein or polypeptide chain is called
the Primary Structure.
 Peptide bonds are created by enzyme catalysed condensation
reactions and broken down by enzyme catalysed hydrolysis
reactions. Breaking down proteins is important in many areas of
the body, not merely in digestion. For example, in hormone
regulation, cells that are targeted by hormones contain

Secondary Structure
After synthesis, polypeptide chains are folded or pleated into different
shapes, called their Secondary Structure. Two common examples of
 secondary structures are Alpha Helices and Beta Pleated Sheets.
Secondary structure is held together by many Hydrogen bonds, overall
giving the shape great stability.

Tertiary structure

Tertiary structures are held together by four different bonds and interactions:

 Disulphide Bonds - Where two Cysteine amino acids are found together, a

strong double bond (S=S) is formed between the Sulphur atoms within the
Cysteine monomers.
 Ionic Bonds - If two oppositely charged ‘R’ groups (+ve and -ve) are found
close to each other, and ionic bond forms between them.
 Hydrogen Bonds - Your typical everyday Hydrogen bonds.
 Hydrophobic and Hydrophilic Interactions - Some amino acids may be
hydrophobic while others are hydrophilic. In a water based environment, a
globular protein will orientate itself such that it’s hydrophobic parts are towards
its centre and its hydrophilic parts are towards its edges
 Tertiary structure can be broken by the action of heat. Increasing the kinetic
energy of protein with a tertiary structure makes it vibrate more, and so the
bonds that maintain its shape (which are mainly weak, non-covalent bonds) will
be more likely to break. When a protein loses its shape in this way it is said to
be Denatured. Even when cool the protein will not (or is highly unlikely to)
form its original complex shape.
 Proteins with a 3D structure fall into two main types:
 Globular - These tend to form ball-like structures where hydrophobic
parts are towards the centre and hydrophilic are towards the edges,
which makes them water soluble. They usually have metabolic roles, for
example: enzymes in all organisms, plasma proteins and antibodies in
mammals.
 Fibrous - They proteins form long fibres and mostly consist of repeated
sequences of amino acids which are insoluble in water. They usually
have structural roles, such as: Collagen in bone and cartilage, Keratin
in fingernails and hair.

Quaternary Structure

Some proteins are made up of multiple polypeptide chains, sometimes

with an inorganic component (for example, a haem group in
 haemoglogin) called a Prosthetic Group. These proteins will only be
able to function if all subunits are present.

 Haemoglobin is a water soluble globular protein which is composed of two α

polypeptide chains, two β polypeptide chains and an inorganic prosthetic haem
group. Its function is to carry oxygen around in the blood, and it is facilitated in
doing so by the presence of the haem group which contains
a \text{Fe}^{2+}Fe2+ ion, onto which the oxygen molecules can bind.

 Collagen is a fibrous protein consisting of three polypeptide chains wound

around each other. Each of the three chains is a coil itself. Hydrogen bonds
form between these coils, which are around 1000 amino acids in length, which
gives the structure strength. This is important given collagen’s role, as
structural protein. This strength is increased by the fact that collagen molecules
form further chains with other collagen molecules and form Covalent Cross
Links with each other, which are staggered along the molecules to further
increase stability. Collagen molecules wrapped around each other
form Collagen Fibrils which themselves form Collagen
 Collagen has many functions:
 Form the structure of bones
 Makes up cartilage and connective tissue
 Prevents blood that is being pumped at high pressure from bursting the
walls of arteries
 Is the main component of tendons, which connect skeletal muscles to
bones
 Haemoglobin may be compared with Collagen as such:
 Basic Shape - Haemoglobin is globular while Collagen is fibrous
 Solubility - Haemoglobin is soluble in water while Collagen is insoluble
 Amino Acid Constituents - Haemoglobin contains a wide range of
amino acids while Collagen has 35% of it primary structure made up of
Glycine
 Prosthetic Group - Haemoglobin contains a haem prosthetic group
while Collagen doesn’t possess a prosthetic group

 Tertiary Structure - Much of the Haemoglobin molecule is wound into

α helices while much of the Collagen molecule is made up of left handed
helix structures
Nucleic Acids
 Nucleic Acids (DNA and RNA) are polymers
 Monomers
are Nucleotides. Each
nucleotide is composed of
Structure of a Nucleic Acid
 a Pentose
Sugar (Deoxyribose in
DNA and Ribose in
RNA)
 an Organic Nitrogenous
Base
 a Phosphate Group
 Nucleotides are joined
together by
a Condensation Reaction. The bond between the two monomers is called
a Phosphodiester Bond.
 Many nucleotides joined together; a Sugar-Phosphate ‘backbone’.

 There are five bases (A, C, T, G, U) that can form nucleotides

 There are only really four different nucleotides that code for DNA.

 The organic bases are grouped into Pyrimidines and Purines.

 The Pyrimidines are:
 Thymine
 Uracil
  Cytosine
 The Purines are:
 Adenine
 Guanine

Too much Nucleic Acid, especially in one’s extremities, may develop a condition
known as Gout. In the liver, excess Purines are broken down in Uric Acid, which is
then excreted in the urine. However, if one’s blood contains too much of this Uric
Acid, it may form crystals that are deposited in the joints, which can be particularly
painful.

Nucleotides,

 DNA (Deoxyribonucleic Acid) is composed of two Polynucleotide

Strands (the polymers of nucleotides), which form what looks like a ladder.
The Nitrogenous Bases in DNA store the instructions for making polypeptide
chains, essentially coding for every feature of the entire organism.

 The two polynucleotide strands run ‘antiparallel’ to each other, with

Nitrogenous Bases projecting inwards. The term ‘antiparallel’ means that the
strands run in opposite directions, parallel to one another. The antiparallel
strands twist in a complete DNA structure, forming a Double Helix.

 The strands are held together by Hydrogen Bonds between the Nitrogenous

Bases that are opposite each other. Bases bonded together are termed ‘paired’,
and are very specific as to which Base they will join to. A Purine will only
pair with a Pyrimidine. Not only that, but the Adenine Purine will only pair
with the Thymine Pyrimidine (A-T), and the Guanine Purine will only pair
with the Cytosine Pyrimidine (G-C). These base pairings are
termed Complementary Base Pairings.
 The reason that Purines will only bond with Pyrimidines is that Purines
are larger molecules (composed of a double ring structure), so in order to
ensure that the polynucleotide strands are equally spaced apart, the larger
Bases must pair with the smaller bases. The root for the specific
Complementary Base Pairings is the number of Hydrogen bonding sites
available. Adenine and Thymine have two sites each,
whereas Guanine and Cytosine have three sites each.
Replication (https://www.youtube.com/watch?v=TNKWgcFPHqw)

 DNA must be copied when cells divide. This is called Replication. This

process takes place during Interphase.

 The Double Helix is untwisted and the antiparallel strands are unzipped -

the Hydrogen bonds between the bases are broken. Free floating
Nucleotides join with the exposed Nitrogenous Bases, forming Hydrogen
bonds - this part of the ‘reason’ for Complementary Base Pairing. The new
Nucleotides are bonded together by the enzyme DNA Polymerase, which
form complete strands opposite the original strands. The two new DNA
molecules form Double Helices.

 The new molecules contain one strand of the original an one new strand, and

so this type of replication is called Semi-Conservative Replication.

Protein Synthesis

 RNA (Ribonucleic Acid) is a polynucleotide, similar to DNA, one of whose

roles is protein synthesis. RNA is structurally different from DNA, in that
 It is usually single stranded.
 It contains the Nitrogenous Base Uracil instead of Thymine.
 Its Nucleotides contain Ribose sugar, as opposed to Deoxyribose sugar.
 DNA contains Genes, which code for specific Polypeptide Chains.
RNA reads the instructions (Transcription) and assembles the Polypeptide
Chain (Translation).
 During Transcription, the DNA molecule ‘opens up’, exposing the gene to be
read. Free RNA nucleotides, which are complementary using the base paring
rules C-G and A-U (since Uracil is similar to Thymine) bond to the exposed
bases on the Template Strand.
 The RNA backbone then forms creating an mRNA (messenger RNA) molecule
which is identical to the Coding Stand (opposite to the Template Strand). The
mRNA then ‘peels away’ from the DNA strand.
 The mRNA strand leaves the nucleus through a nuclear pore and attaches to
a Ribosome, which is composed of rRNA (ribosomal RNA). tRNA (Transfer
RNA) carries amino acids. When the tRNA carrying the correct amino acid in
the sequence collides with the Ribosome, the amino acid joins with the
previous amino acid, forming a Peptide Bond.
  This produces a polypeptide chain, whose Primary Structure is dictated by
the sequence of bases in the gene. Primary Structure gives rise
to Secondary and Tertiary Structures.

Core Practical 1

LO: be able to estimate the concentrations of Reducing sugars in solution using the
Benedicts Test, and estimate the concentrations of starch in a similar manner with
Iodine.

Qualitative and Quantitative Tests (https://www.youtube.com/watch?

v=6vau7isV6U4)

A qualitative test is one that determines a relative measure of something. As an

example, the solution is sweeter or the light is brighter.

In quantitative tests there is a measurement that has a value. We are going to look at
semi-quantitative measurements.

Sugar Tests Video (Reducing, Non-reducing and Starch)

https://www.youtube.com/watch?v=d6tHWPW5WLM

Student Check
Circulation & The Cardiac Cycle

LO: Understand the different exchange surfaces

Circulation
§ Very small animals (like flatworms) don’t require a special transport system
because they can get the substances they need and excrete the substances
don’t by diffusion alone.
§ However, for larger animals this is not sufficient. Larger animals require a
variety of different tissues to support them. This means that they have a
bigger size, so substances take longer to diffuse to an from their internal
tissues; also they have a smaller surface-area-to-volume ratio, so substances
can’t diffuse fast enough.
§ In addition, animals that are more active use substances like food and Oxygen
more quickly, and also produce waste products faster, hence there is again an
increased need for a special transport system.
Single and Double Circulatory Systems
 The animal transport system consists of:
 A fluid medium to transport substances (the Blood)
 A pump to push the fluid around the body
 Specialised exchange surfaces
§ Most transport systems also contain tubes (Blood Vessels) to hold the blood.
§ This is the Circulatory System, which is a very efficient transport system.
 There are two types of circulatory system:
 A Single Circulatory System is a simple loop in which blood flows:
Heart > Gills > Body > Heart
 A Double Circulatory System is a double loop in which blood flows:
Heart > Lungs > Heart > Body > Heart
§ Fish have a single circulatory system, while mammals have a double
circulatory system.
§ In a double circulatory system, the loop that goes to the lungs is called the
Pulmonary Circuit, while the loop that goes to the body is called the
Systemic Circuit.

§ The double circulatory system is advantageous for active animals since,

while in the single circulatory system the blood pressure is limited by the
delicate nature of the tiny capillaries in the gills, in the double circulatory
system the blood pressure can be high in the systemic circuit while
remaining low and safe in the pulmonary circuit. This allows animals with a
double circulatory system to be more active, since blood can reach their
respiring tissues faster due to the higher pressure.
 § Fish are not as active as other animals, so their single circulatory system is
sufficient for their needs, while more active animals like mammals need a
double circulatory system.
Disaccharides
Maltose ------ Glucose + Glucose
Lactose --------- Galactose + Glucose
Sucrose ---------- Glucose + Fructose
HW:
Try and find any uses of fats and oils in the world, type of uses do we have for fats? (10)
Provide a short bullet form answer of what functional materials are made from fats.

Movement of Materials in and Out of Cells

Diffusion This was found by a Scotsman!! His name was Robert Brown. He discovered that
things move in a rather random fashion called Brownian Motion. Diffusion is the movement of
materials from an area of high concentration to an area of low concentration. The net movement
of the particles from a region of high to low concentration will eventually create an even
distribution of gases or liquids. This movement from High to Low comes through Brownian
Motion.
Facilitated Diffusion This movement occurs when there is a requirement for an ionophore.
In other words there is a need for a gate or door that the materials have to move through. One
example of this is the hormone ADH (Anti-Diuretic Hormone). Without this in place water
cannot move from the blood and as a result you don’t go tot the bathroom as much.
Osmosis The movement of water is referred to as Osmosis. The movement occurs from
having Water Potential. If we remember our Physics and Potential Energy, energy moves from
an area of High Energy to an area of Low energy.
The same is true of Osmosis and Water Potential. In this case the water moves from an area of
High Water Potential to and area of Low Water Potential. Another way of putting this is that
water moves from an area of less concentrated solution to area of more concentrated.
Active Transport This is the movement of materials from an area of low concentration to an
area of high concentration. In other words, the movement of materials against the concentration
gradient. This process requires energy and carrier proteins in the cell membrane which you will
find out about later in the course.

It is the net movement of substance It describe the process of passive

from a high to low concentration
The kinetic energy of the molecules
results in random motion causing
diffusion.
transport of molecules across the cell
membrane with help of
transmembrane protein. It usually
occur when molecule cant pass
through the plasma because of their
charge

Temperature so when there is high temperature they will move more

Solvent density increase

LO: Know the definitions of the transport systems

Understand the way the transport systems interact with each other e.g. the Active Transport of
materials impacts osmosis

Factors that affect active transport and facilitated diffusion

 Heamolysed: all the
It is the moving of water molecules from a higher water leaves the red
water potential to a lower water potential. blood cells

Turged
R.b.c it is the
too much
normal one
water
It is one of the most going in
Solute: It is the solid important ways where
that dissolve in the plants and animals
solvent.
keep their bodies
Water potential: is conditions stable.
the energy required It only allows water to
per quantity of water be transported to the Plasesed
to transport a Turged: Pleasmolysed:
cell membrane but no
quantity of water. High
Solution : is the water
mixture of solute and concentr
solvent molecules ation