Protein Structure

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.

Primary Structure: The unique sequence of amino acids that makes

up a protein or polypeptide chain.

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 enzymes to break down those hormones.
This stops their effects from being permanent and allows them to be
controlled.

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.

Secondary Structure: The way in which the primary structure of a

polypeptide chain folds.

Tertiary Structure

The final 3D structure of a protein is its Tertiary Structure, which

pertains to the shaping of the secondary structure. This may involve
coiling or pleating, often with straight chains of amino acids in between.

Tertiary Structure: The final 3D structure of a protein, entailing the

shaping of a secondary structure.

Tertiary structure is held together by four different bonds and

interactions:
o

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, noncovalent 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:

o

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.

Quaternary Structure: The structure formed when two or more

polypeptide chains join together, sometimes with an inorganic
component, to form a protein.

Haemoglobin and Collagen

Haemoglobin is a water soluble globular protein which is composed of

two polypeptide chains, two 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 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 Fibres.

Collagen has many functions:

o

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:

o

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 helices while much of the Collagen molecule is made up of
left handed helix structures

Magnification

Living things are composed of Cells. Cells are very small (ususally
between 1 and 100 m) and can only be seen by magnification with a
microscope. A distinction is made between Magnification and
Resolution: Magnification is how large the image is compared to real
life, whereas Resolution is the amount of information that can be seen in
the image - defined as the smallest distance below which two
discrete objects will be seen as one.

To work out the size of an object viewed with a microscope, a

Graticule is used. It is a small transparent ruler that becomes
superimposed over the image. As the same sample may look to be
different sizes under different magnifications, the Graticule must be
calibrated.

Actual Size, Image Size and Magnification are related by the formula:

Image Size = Actual Size Magnification

The Light Microscope

Light Microscopes, or Optical Microscopes, as they are more

correctly termed, use light and several lenses in order to magnify a
sample. Light from the Condenser Lens, and then through the
Specimen where certain wavelengths are filtered to produce an image.
The light then passes through the Objective Lens, which focuses it and
can be changed in order to alter the magnification. Finally, the light
passes through the Eyepiece Lens, which can also be changed to alter
the magnification, and into the eye.

The maximum magnification of light microscopes is usually 1500,

and their maximum resolution is 200nm, due to the wavelength of
light. An advantage of the light microscope is that it can be used to view
a variety of samples, including whole living organisms or sections of
larger plants and animals. It is also relatively inexpensive.

There are two types of light microscope. Compound Microscopes

contain several lenses and magnify a sample several hundred times.
Dissecting Microscopes on the other hand have a low final
magnification but are useful when a large working distance between the
objectives and the stage is required (e.g. during dissection). They have
two eyepieces to produce a 3D stereoscopic view.

Many specimens require preperation before being viewed by a light

microscope, as some may not be coloured or might distort when cut.
Samples are Stained with coloured stains that bind to certain chemicals
or cell structures. For example, Acetic Orcein stains DNA dark red.
Samples may also be Sectioned - embedded in wax; this helps with
preserving structure while cutting.

The Electron Microscope

Light microscopes are great and all, but sometimes their (relatively)
low magnification and resolution are insatisfactory for viewing very small
things, like Organelles within cells. In these circumstances, and Electron
Microscope may be used. Electorns have a much lower wavelength

than light (100000 times shorter in fact, at 0.004nm) which means that
they can be used to produce an image with resolution as great as 0.1nm.
Electron Microscopes can have magnifications of 500000.

There are different types of Electron Microscope. A Transmission

Electron Microscope (TEM) produces a 2D image of a thin sample,
and has a maximum resolution of 500000.

A Scanning Electron Microscope (SEM) produces a 3D image of a

sample by 'bouncing' electons off and dectecting them at multiple
detectors. It has a maximum magnification of about 100000.

The preparation of a sample for electron microscopy is a complex

process. It may involve
o

Chemical Fixation: Stabilising an organism/sample's mobile

macrostructure
Cryofixation: Freezing the sample very rapidly to preserve its

o
state
o
o

Embedding: Embedding in resin, ready to be sectioned

Sectioning: Cutting the sample into thin strips that are

semitransparent to electrons, for example with a diamond knife

Staining: Using heavy metals to scatter electrons and produce

contrast

Freeze Fracturing: Freezing the sample rapidly, and then

fracturing it, for example, when viewing cell membranes

Dehydration: Removing the water form a specimen, for

example, by replacing it with ethanol

Mounting: Placing the sample on a copper grid

It is advantageous to use an Electron Microscope in many situations
because they offer a much higher resolution that Light Microscopes,
so they can be used to image very small objects in detail, and also

because of the 3D images that SEMs offer. However, samples must

be placed in a vacuum as electrons are deflected by particles in the
air, they are very expensive to buy and maintain, and preparing the
samples requires a lot of skill to do.

Organelle Structure and

Function

Organisms are composed of cells, and these cells have specific

structures within in them that allow them to carry out their functions.
These structures are called Organelles. The fine detail of the cell (which
may be revealed by an electron microscope) is called the cell's

ultrastructure. Organelles perform different functions within a cell, and

this is called the Division of Labour.

Membrane Bound Organelles

The Nucleus is the largest organelle in a cell. It contains a dense

structure called the Nucleolus and is surrounded by the Nuclear
Envelope, a structure composed of two membranes, seperated by fluid,
which contain a number of nuclear pores that can allow relatively large
molecules through. The nucleus contains nearly all of the cell's genetic
material. The Nucleolus creates Ribonucleic Acid and Ribosomes,
which then travel out of the nucleus, through the nuclear pores, to the
cytoplasm where they are involced in Protein Synthesis.

The Endoplasmic Reticulum (ER) is found near the Nucleas and is

made up of a number of flattened sacs called Cisternae, which are
continuous with the Nuclear Envelope. The Rough Endoplasmic
Reticulum is called so because it has a lot of Ribosomes on its outer
surface. The Smooth Endoplasmic Reticulum however, does not have
Ribosomes. The Rough transports proteins that are synthesised in
the Ribosomes, and the Smooth synthesises Lipids.

The Golgi Apparatus is a stack of membrane bound flattened

sacs, and are responsible for the modification of proteins received
from the ER. These proteins are then transported in vesicles around the
cell.

Lysosomes are membrane bound spherical sacs which contain

digestive enzymes used to break down materials, such as non-self
microorganisms engulfed by Phagocytes.

Mitochondria are round double membrane bound organelles

responsible for Aerobic Respiration. Their inner membrane is folded
inside to form Cristae, which are folded in the Matrix - the central part
of a Mitochondrion. During Aerobic Respiration, ATP is produced in the
Mitochondria.

Found only in plants and some protoctists, Chloroplasts are

responsible for Photosynthesis. Chloroplasts contain two fluid
separated membranes and the inner membrane is folded into a
network of flattened sacs called Thylakoids that are stacked into
Grana (one Granum, two Grana). The Thylakoids contain Chlorophyll in
which the process of Photosynthesis occurs.

Vesicles are membrane bound sacs that are used to store or

transport substances around the cell. Lysosomes are actually Vesicles.

Vacuoles are essentially larger Vesicles, and they are formed by the
joining together of many Vesicles. They are membrane bound
organelles that have no specific shape and contain water with a
number of different compounds within it. Their function varies
greatly depending on the type of cell they are part of. In plant cells
they are important in maintaining Turgor Pressure.

Non Membrane Bound Organelles

Ribosomes are small spherical organelles, composed of two

subunits, which can be found on the Rough Endoplasmic Reticulum
(and also in the cytoplasm and in mitochondria, and other places).
Ribosomes translate genetic information in the form of mRNA into
proteins.

Centrioles are microtubules found next to the nucleus of animal

cells and some protoctists. They move Chromosomes around by
forming fibres called Spindle, during cell division.
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