Download DIFFERENT LEVELS OF PROTEIN STRUCTURE PRIMARY

DIFFERENT LEVELS OF PROTEIN STRUCTURE
PRIMARY STRUCTURE
The primary structure of a protein is its unique sequence of amino acids, placed in the
correct order by ribosomes under the coded instructions of DNA.
e.g. Section of a polypeptide chain.
peptide bond
lys
ile
phe
cys
lys
asp
Even a minor alteration to the primary structure of a protein can have devastating
consequences. For instance, a single amino acid substitution in the β chain of haemoglobin
causes sickle cell disease, when valine replaces glutamic acid at a certain point in the chain.
SECONDARY STRUCTURE
Once a polypeptide has formed, its chain of amino acids can fold or turn upon itself as a
result of hydrogen bonding, i.e. The coils and folds are the result of hydrogen bonding at
regular intervals along the polypeptide chain.
One common secondary structure is the alpha (α) helix which results from tight polypeptide
coils held together by hydrogen bonding between every fourth amino acid. Another common
secondary structure is the beta (ß) pleated sheet, in which two regions of the polypeptide
chain lie parallel to each other. Hydrogen bonds between parallel parts of the backbone hold
the structure together.
An example of alpha helices is alpha–keratin in wool. It is coiled so it can stretch and reform
the coiled fibre. Fibrin beta pleated sheets in silk and spider webs provide strength so the
protein can span a large distance.
α helix
ß pleated sheet
(Curtis H & NS Barnes, 1994)
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 37
TERTIARY STRUCTURE
A protein’s tertiary structure refers to the way a polypeptide folds and coils to form a complex
molecular shape (conformation). It’s the way in which alpha helices, beta pleated sheets
and random coils fold with respect to each other. Irregular bends from bonding between
side chains (R groups) of amino acids in the polypeptide chain create the tertiary structure of
a protein.
For example, as a polypeptide folds into its functional shape, amino acids with hydrophobic
(non polar) side chains are usually found in clusters in the middle of the protein, away from
water. Hydrophilic side chains of other amino acids are also attracted to each other, but
more commonly on the outside of the protein molecule, close to water. These interactions
result in the folding, twisting and coiling of the final protein shape.
Distant amino acids (in the primary structure) may in fact be close together due to the
tertiary structure.
(Campbell NA et al, 1999)
The shape of a protein may be further reinforced by strong covalent bonds known as
disulfide bridges which occur between adjacent cysteine amino acids. The sulphur atom of a
cysteine amino acid bonds to the sulphur atom of a second cysteine in the amino acid chain.
Along with hydrophobic interactions, hydrogen, ionic and disulfide bonds all contribute to the
tertiary structure of a protein. The tertiary structure really determines the function of the
particular protein.
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 38
QUATERNARY STRUCTURE
Many proteins consist of more than one polypeptide chain (e.g. haemoglobin contains two α
and two ß polypeptide chains). The quaternary structure is the overall protein structure that
results from the combined shape of all linked polypeptide chains.
Haemoglobin is composed of four polypeptide chains:
two alpha chains and two beta chains.
Shadowed collagen fibres from the neck tendon of a bird
seen under the electron microscope. The banding pattern
is characteristic of collagen.
Collagen is a fibrous protein composed of three polypeptide
chains which supercoil to create a molecule of great strength.
(Campbell NA & JB Reece, 2002)
The forces that create the quaternary structure of proteins are the same as those which
create the polypeptide’s tertiary structure.
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 39
GLOBULAR AND FIBROUS PROTEINS
Proteins can be divided into two main classes: globular and fibrous.
GLOBULAR PROTEINS
Globular proteins comprise “globe-like” proteins that are more or
less soluble in aqueous solutions. The spherical structure is
induced by the protein's tertiary structure.
The molecule's non polar (hydrophobic) amino acids are bounded
towards the molecule's interior whereas polar (hydrophilic) amino
acids are bound outwards, allowing dipole-dipole interactions with
the solvent, creating the molecule's solubility.
e.g. Every membrane protein contains a variety of amino acids, some with hydrophobic
side chains and others with hydrophilic chains. The amino acids with hydrophobic
chains tend to be found across the centre of the protein molecule (in the hydrophobic
interior of the membrane) while amino acids with hydrophilic chains tend to be
located on the ends of the protein on the hydrophilic surfaces of the membrane.
Hence hydrophilic portions of the protein are either exposed to the watery
environment of the cytosol on the inside of the membrane or the extracellular fluid on
the membrane’s exterior.
(Evans B et al, 1999)
Unlike fibrous proteins which only perform structural roles, globular proteins can act as:
•
Enzymes
•
Messenger molecules, e.g. hormones such as insulin
•
Membrane channel and carrier proteins
•
Regulatory proteins
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 40
Fibrous Proteins
Fibrous proteins form structural proteins which confer stiffness and
rigidity to biological components, and are insoluble in aqueous
solutions, e.g.
•
Actin and tubulin polymerise to form long, stiff fibres that
comprise the cytoskeleton of cells.
•
Collagen and elastin are critical components of connective
tissue such as cartilage.
•
Keratin is found in hard or filamentous structures such as hair, nails, feathers, hooves,
and some arthropod exoskeletons in association with chitin.
•
Myosin, kinesin and dynein, which are capable of generating mechanical forces. These
proteins are crucial for cellular motility of single-celled organisms and the sperm of
many sexually reproducing multicellular organisms. They also generate the forces
exerted by contracting muscles.
FUNCTIONS OF PROTEINS
Type of Protein
Example
Structural
Collagen and elastin provide a framework in animal connective tissues,
such as tendons and ligaments. the main protein of cocoons, webs,
silk, cytoskeleton, fingernails.
Storage
Casein, the protein of milk, is a major source of amino acids for baby
mammals.
Transport
Haemoglobin transports oxygen from the lungs to other body tissues in
vertebrates. Protein carrier to carry molecule across cell membrane.
Hormonal
Insulin and glucagon regulate blood sugar levels.
Receptor
Thyroxin receptors bind to thyroxin to trigger an increase in metabolic
rate of the cell.
Contractile
Contractile proteins are responsible for the motion of cilia and flagella.
Defensive
Antibodies combat bacteria, viruses etc.
Enzymes
Amylases break down carbohydrates in food.
Neurotransmitters Endorphins reduce pain or stress by binding to nerve cell receptors.
e.g. acetylcholine.
Regulatory
Turn genes on or off, controlling cell differentiation and activity.
Hormones, enzymes.
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 41
NUCLEIC ACIDS (POLYNUCLEOTIDES)
Nucleic acids (e.g. DNA and RNA) store information that determines how organisms
develop and function. Nucleotides are the monomers of the nucleic acid polymer. Nucleic
acids are organic molecules containing carbon, hydrogen, oxygen, nitrogen (in the base)
and phosphorus (in the phosphate group), i.e. CHONP.
Nucleic acids carry instructions for making proteins by determining the amino acid sequence
of the protein produced at the ribosome.
•
A nucleotide consists of a pentose (5-carbon) sugar, a nitrogenous base and a
phosphate group (negatively charged). Label the following nucleotide:
C
A
B
•
Nucleotides can link together by condensation reactions to form either RNA or DNA.
•
Each polynucleotide has a backbone consisting of phosphates and sugars. One of four
possible nitrogen-containing bases is attached to the sugar molecule.
DNA = DEOXYRIBONUCLEIC ACID
DNA is the largest naturally-occurring molecule, containing the genetic instructions for all
living organisms, i.e. its code is universal. Using genetic technology, DNA from one
organism can be incorporated into the chromosome of any other organism and remain fully
functional.
E.g. transgenic pigs, cotton, mice, tomatoes, etc.
DNA determines all the characteristics of all living organisms, from hair colour, to sex, to the
actual type of species under investigation.
•
DNA is a nucleic acid, containing nucleotide subunits.
Nucleotide = deoxyribose sugar + phosphate group + nitrogenous base (adenine,
thymine, guanine or cytosine)
C
A
B
…. label this DNA nucleotide
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 42
The nitrogenous bases are adenine (A), thymine (T), guanine (G), and cytosine (C).
•
The larger bases (adenine and guanine) are known as purines, while the smaller
bases (thymine and cytosine) are called pyrimidine bases.
lewallpaper.com
•
The size of the bases helps to determine which bases will pair. There is not enough
room for two purines to pair and too much room for two pyrimidines to pair.
•
The sequence of base pairs along the DNA molecule is not the same in all DNA
molecules or for all organisms. This is largely the reason for the wide variation, both
between and within, species.
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 43
THE DOUBLE HELIX
A DNA molecule consists of two nucleotide strands. The bases on each separate strand pair
together in forming a DNA molecule. Only two base pairing combinations are possible.
Adenine (A) binds with thymine (T) and guanine (G) binds with cytosine (C).
Using this knowledge, complete the table below:
Nucleotide Base Content
Organism
% Guanine
Yeast
% Thymine
19
Bull sperm
29.5
Herpes virus
36
This feature is known as complementary base pairing. Hence, the two DNA strands are
said to be antiparallel.
•
The base pairs are held together
by weak hydrogen bonds (two
between A and T; three between G
and C).
•
If the order of bases on one strand
of DNA is: A A T G T C G
Then the sequence of bases on the
other strand is: T T A C A G C
•
A phosphate group hangs from the
5’ end (fifth carbon of a
deoxyribose) of a DNA strand,
while a hydroxyl group hangs from
the 3’ end (third carbon of a
deoxyribose).
(Campbell NA et al, 1999)
•
The DNA molecule forms a double helix shape as a result of the base pairing.
While the two strands are held together by hydrogen bonds between the bases,
stronger covalent bonds exist between sugars and phosphates, and between sugars
and bases.
•
In DNA and RNA, the phosphodiester bond is the
linkage between the 3' carbon of one sugar and the
5' carbon of the next sugar (i.e. between
deoxyribose sugars in DNA and ribose sugars in
RNA). It is a group of strong covalent bonds
between the phosphorus atom in a phosphate
group and two other molecules over two oxygen
molecules.
3’ end
5’ end
fig.cox.miami.edu
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 44
Label the DNA molecules:
A
B
C
One nucleotide strand is known as the template or sense strand (it contains the genes) and
the other is known as the antisense strand.
•
The sequence of base pairs along the DNA molecule varies between the DNA
molecules of different organisms. The only organisms with identical DNA are clones.
e.g. Identical twins.
•
Try this one:
Template Strand:
GTT GAA GCC GTC ATG CCT GAG
Complementary Strand:
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 45
LOCATION OF EUKARYOTIC AND PROKARYOTIC DNA
In eukaryotic cells, DNA is found within the nucleus, mitochondria and chloroplasts.
In prokaryotic cells (e.g. bacteria) DNA is found in a single circular chromosome, and
most bacteria also possess small circular rings of double stranded DNA called plasmids.
A
B
A plasmid can be used to carry genes from
one organism to another.
Note: The plasmids are really much smaller
than depicted in the diagram above.
The circular chromosome of an E. coli bacterium
is revealed after the cell bursts via osmotic shock
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 46
GENES
A gene is a sequence of DNA nucleotides that codes for a particular protein/polypeptide.
RNA = RIBONUCLEIC ACID
Ribonucleic acid (RNA) is a single stranded nucleic acid that is synthesised from a DNA
template strand in a process known as transcription. RNA is made up of nucleotides that
are similar to those of DNA, however, some differences exist:
An RNA nucleotide contains:
•
ribose sugar +
phosphate group +
nitrogenous base: Adenine (A), uracil (U), cytosine (C) or guanine (G).
A
C
B
…. label this RNA nucleotide
•
RNA is synthesised from a DNA template in the process of transcription.
•
Three forms of RNA exist:
Messenger RNA (mRNA) which carries the DNA code to the ribosome for the
purpose of making the desired protein/polypeptide.
Transfer RNA (tRNA) which provides amino acids for the growing polypeptide.
Ribosomal RNA (rRNA) which makes up most of a ribosome.
Remembering that uracil takes the place of thymine in RNA (i.e. uracil also pairs with
adenine), complete the base sequence for the following section of RNA being transcribed
from the DNA molecule:
DNA VS RNA SUMMARY
DNA
RNA
No. of Nucleotide Strands
Sugar
Bases
Functional Location
© The School For Excellence 2016
The Essentials – Unit 3 Biology – Book 1
Page 47