Download Structure of Proteins

Higher Biology
Unit 1: DNA and the Genome
2. Gene Expression
Notes
0
Proteins
All proteins are contain the elements:





Carbon (C)
Hydrogen (H)
Oxygen (O)
Nitrogen (N)
And sometimes Sulphur (S)
The subunits of proteins are amino acids. There are 20 different types of amino acids.
Proteins are arranged into four structural levels.
Primary (1o) Structure
 Sequence of amino acid residues in the polypeptide chain.
.
Secondary (2o) Structure
 Two main types of secondary structure.
 helix and sheet arrangements.
 Generated from interactions between the atoms of the amino acid residues in the
polypeptide chain.
1
 In the -sheet arrangement, polypeptide chains are linked together in a side-byside configuration.
 This is again by hydrogen bonding. These bonds are WEAK bonds.
 -sheets can either be PARALLEL (where the adjacent polypeptide strands
extend in the same direction) or ANTIPARALLEL (the strands extend in
opposite directions).
Antiparallel
Parallel
Tertiary (3o) Structure
 More complex than the Secondary structure.
 Describes the way in which the polypeptide folds to give the final protein
structure.
 Determined by HYDROPHOBIC interactions (hate water).
 Contain an additional covalent bond called the DISULPHIDE BOND.
 In the tertiary structure, -helix and -sheet arrangements are found.
2
Quanternary (4o) Structure
 Some proteins are composed of two or more polypeptide SUBUNITS.
 Each subunit has its own specific conformation.
 The organisation of the subunits in a multi-subunit protein is known as the
QUANTERNARY structure of a protein.
 Haemoglobin is an example of this.
 It is composed of four chains of the protein globin.
 It has two - and two -globin subunits, each with its own prosthetic haem group.
3
Haem Group
 Folded proteins can have non-protein groups associated with them.
 Haem is an iron containing group of haemoglobin.
 Proteins may also have carbohydrate, lipid or nucleic acid groups associated with
them.
4
Proteins can be fibrous or globular:
Some proteins may contain non-protein chemicals
The protein haemoglobin contains nonproteins structures containing iron
5
RNA and Protein Synthesis
DNA
RNA
Sugar
Deoxyribonucleic Acid
Sugar
Ribose Acid
Base
ATCG
Bases
AUCG
Strands
Double Stranded
Strands
Single
RNA Nucleotide
6
Transcription
( The synthesis of mRNA strand from a section of DNA)
The following takes place in the nucleus of the cell:
1. DNA double helix ____________
2. Weak ____________ bonds between bases break, separating the two DNA strands
3. Free _______ nucleotides pair with their complementary base pair on the
________ strand. Weak hydrogen bonds form between _________ ___________.
4. RNA polymerase can only add nucleotides to the 3’ end of the growing mRNA
molecule
5. Strong chemical bonds form between the _______ and _________ of
neighbouring nucleotides (bond formation catalysed by RNA polymerase).
6. A strand of messenger RNA has now been made
7. The molecule elongates until a terminator sequence of nucleotides is reached don
the DNA strand.
8. The mRNA strand is called primary transcript of mRNA.
Modification of primary transcript
 In eukaryotes long stretches of DNA exist which do not code for proteins – called
introns.
 Coding regions are called exons
Splicing
 The introns are cut out and removed from the primary transcript of mRNA and the
exons are spliced together to form mRNA with continuous sequences of
nucleotides coding for proteins.
7
8
The mRNA then passes out of the nucleus via a pore in the nuclear membrane into
the cytoplasm
Translation
(The synthesis of protein as a polypeptide chain under the direction of mRNA)
Each triplet of bases on mRNA is called a
codon; each codon codes for an amino acid.
There are 64 triplets.
Transfer RNA (tRNA) is found in the cytoplasm and carries a triplet of bases
called an anticodon
Each anticodon corresponds to a particular
amino acid, carried by the tRNA at its attachment
site
Start and stop codons
The mRNA codon AUG (complementary
to tRNA anticodon UAC) is unusual in
that it codes for methionine (met) and
acts as a start codon.
mRNA codons UAA, UAG and UGA do
not code for amino acids but instead
act as stop codons.
9
The anticodon on the tRNA molecule forms weak hydrogen bonds with the
corresponding codon on the mRNA
The Ribosome
10
Translation stages
1. Ribosome binds to the 5’ end of the mRNA template to that the mRNA’s start
codon (AUG) is in position at binding site P.
2. tRNA molecule picks up its appropriate amino acid (methionine) from the
cytoplasm
3. The tRNA carries the amino acid to the ribosome and becomes attached at site P
by hydrogen bonds between its anticodon (UAC) and the start codon (AUG).
4. The mRNA codon at site A forms hydrogen bonds with the complementary
anticodon on the tRNA molecule carrying its amino acid.
5. When the first two amino acids molecules are next to each other they join with a
peptide bond.
6. As the ribosome moves along one codon he tRNA that was at site P is moved to
site E and discharged from the ribosome to be reused.
7. At the same time the tRNA that was site A is moved to site P.
8. The next tRNA occupies the now vacant site A, and the amino acid the tRNA
caries bonds to the growing polypeptide chain.
9. The process is repeated many times , thus translating the mRNA into a complete
polypeptide chain.
10.When a stop codon is reached the site A on the ribosome releases the polypeptide.
This whole process needs energy from ATP.
11
One gene can code for many proteins, how?
 Particular exons of a gene may be included, or excluded from, the final,
processed mRNA produced from that gene.
 Consequently the proteins translated from alternatively spliced mRNAs will
contain differences in their amino acid sequence and, often, in their biological
functions .
 Alternative splicing allows the human genome to direct the synthesis of many
more proteins than would be expected from its 20,000 protein-coding genes.
It is thought that at least 70% of the approximately 25,000 genes in the human
genome undergo alternative splicing and that, on average, a given gene gives rise
to 4 alternatively spliced variants - encoding a total of 90-100,000 proteins which
differ in their sequence and therefore, in their activities
12