PRT3402- Agricultural Biochemistry
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UNIT 5
Structure and function of nucleic acids
Introduction to Unit
Deoxyribonucleic acid or DNA is the genetic material in living cells that encode
all the information required for growth, development, structure, reproduction and
functions carried out by the cells. The DNA can replicate very accurately to ensure
that the progeny will receive the same information from the parent cell. Discovery of
DNA as the genetic material and the evidence of double helix structure of DNA are
the major historical turning points in the field of genetics. In this unit the structure of
nucleic acids and the organization of genes, genome and the process of information
flow will be described. Explanations will also be given how genes are expressed and
leads to protein synthesis in the cell. Finally the phenomenon of mutations is also
described.
Learning Outcomes
At the end of this unit the students will be able to:
1. Recognise the basic structure of nucleic acids and how its chemistry
affect its function and the function of genes.
2. Describe how DNA sequences are translated, transcribed and genes
are expressed.
3. Explain the role of RNA (ribonucleic acid) and how it works in tandem
with DNA to produce amino acid sequences and proteins.
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TOPIC 1: STRUCTURE OF PURINES, PYRIMIDINES, DNA AND RNA
Main Points
1.1
Genetic code in cells are carried by nucleic acids which are of two types –
deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The linear segment
of the DNA which is made up of a continuous DNA sequences contain
thousands of genes while the RNA is used to transmit the information to the
cell machinery to be translated and transcribed. Both nucleic acids are closely
related in determining the inheritance of genes from parents to progenies.
1.2
A nucleotide has three components: a phosphate group, a five-carbon sugar
and a nitrogen-containing base.
1.3
The phosphate group and sugars form the backbone of each strand of DNA or
RNA. The bases are joined to the sugars and stick-out sideways. The sugar in
DNA is always a deoxyribose and in RNA it is ribose. Both are pentoses or 5carbon sugars.
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1.4
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Nucleotides are joined by linking the phosphate on the 5’-carbon the
(deoxy)ribose of one nucleotide to the 3’-position of the next nucleotide and
the phosphate group is joined to the sugar on either side by ester linkages,
and
1.5
the
overall
structure
is
a
phosphodiester
linkage.
There are five nitrogenous bases associated with nucleotides. Adenine (A),
guanine (G), cytosine (C) and thymine (T) are the bases for DNA are while
RNA contains A, G and C but T is replaced by uracil (U). In terms of genetic
information, T is equivalent to U. U, T and C are pyrimidines while A and T are
purines.
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1.6
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While nucleotides have a nitrogenous base, phosphate and sugar nucleosides
refer to molecules with only a base and sugar.
1.7
DNA is a double stranded molecule whereas RNA is single-stranded. Besides
that DNA double strands wound around each other in a helical arrangement,
giving rise to the famous double helix structure of DNA. This structure was
first proposed by Francis Crick and James Watson in 1953. DNA forms a right
handed double helix.
1.8
A linear and double stranded arrangement of a DNA helix is shown below. As
seen from the diagram you will notice that there is a base pairing between the
two strands and the pairing is that A always pairs with T (A-T) and G always
pairs with C (G-C). As a result, the number of adenines is always equal to
thymines and similarly the number of cytosines is equal to guanines. The
base pairing is via hydrogen bonding whereby A-T has two hydrogen bonds
and G-C have three hydrogen bonds.
1.9
The structure below also showed that in one chain the linkages are in the
direction of 3'5' while in another complementary chain the linkages are in
the 5'3' direction.
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1.10
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There are other alternative forms of DNA as shown below.
Types of DNA
Characteristics
A
right handed, shorter when little H2O is
available
B
right handed, thinner than A when in
solution
C
right handed, under greater dehydration
D and E
lacking guanine, right handed
Z
left handed, zig-zag appearance
1.11
Some characteristics of DNA include the ability to denature and re-nature
whereby the double strand can separate from each other and using
complementary base-pairing of A-T and C-G allows the formation or synthesis
of two new strands so restoring the double stranded DNA. Denaturation can
occur if the DNA is heated to 100oC and hydrogen bonds will be broken
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separating the two complementary strands. Strands with higher GC content
and low in AT is more resistant to thermal heating. When a heated solution of
totally denatured DNA is slowly cooled, single strands meet their
complementary strand and DNA will re-nature. This is the basis of
hybridization.
1.12
Similar to DNA, there are several different types of RNA as indicated below.
RNA Type
Size
Function
Transfer RNA (tRNA)
Small
Transports amino acids to
site of protein synthesis
-at least one tRNA bonds
to each amino acid
Ribosomal RNA (rRNA)
Several kinds-
Combines with proteins to
Variable in size
form ribosomes, the site of
protein synthesis
Messenger RNA (mRNA)
Variable
Directs amino acid
sequence of proteins
Small nuclear RNA
Small
Process initial mRNA to its
(snRNA)
mature form in eukaryotes
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TOPIC 2 : DNA REPLICATION AND GENE EXPRESSION: TRANSCRIPTION AND
TRANSLATION
Main Points
2.1
In DNA replication, each strand of a DNA double helix could serve as a
template for the synthesis of it’s complementary strand. If the helix were unwound,
replication can take place and this will result in the production of two new but
identical DNA strands. Each replicated DNA molecule would consists of one old and
one new strand. This is known as the semi conservative DNA replication.
2.2
A large number of proteins assembled into complexes that carry out DNA
replication. There are three distinct stages in DNA replication
2.3

Initiation

Elongation

Termination
E. coli has a circular DNA where replication begins at the origin and
proceeds bi-directionally towards the termination point. In prokaryotes, replication
proceeds at 1,000 base pairs per second with 2 replication fork which can be
completed in 38 minutes. Eukaryotes have bigger and larger amount of DNA
and hence requires many origin of replication but can still complete replication of
all DNA in approx 38 minutes.
2.4
The semi-conservative replication begins at unique location and proceeds
in both directions. The synthesis of new strands of DNA occurs at two replication
forks where replisomes are located. When the replication forks meet at the
termination site, the two double stranded DNA molecule separates. Each
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daughter molecule will have one parental strand and one newly synthesized
strand.
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2.5
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E. coli has three types of DNA polymerases:
–
DNA polymerase I repairs DNA and participate in DNA synthesis in the
lagging strand
2.6
–
DNA polymerase II repairs DNA
–
DNA polymerase III is the major DNA replication enzyme.
DNA polymerase reads the chain in the 3’- 5’direction and produces new
chain in the 5’- 3’direction. It has a leading and lagging strand for the new DNA.
In lagging strand the replication is more complex then the leading strand. It
requires RNA primer and form new chain in the reverse direction (Okazaki
fragments). The resulting Okazaki fragments will be joined together using DNA
polymerase I and DNA ligase.
2.7
The replisome contains
–
primosome (helicase activity for unwinding)
–
polymerase
–
Single strand binding proteins (SSB)
–
Topoisomerase II (gyrase) (relieve supercoiling)
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Replication also has proof reading mechanisms (normally there is one error for
every 1000 base pairs).
2.8
DNA translation is the final stage in biological information flow (from DNA to
RNA to proteins) – i.e. replication, transcription and translation. The information in
DNA (sequence of bases) are translated into amino acids sequences and finally as
proteins through the genetic code. The genetic code is a three-nucleotide sequence
which specifies one amino acid known as the codon. Using the alphabet A, T, C and
G of the bases, scientist suggested a combination of three bases giving a total of 64
codes.
2.9
The standard code has several features:
– Universal (unambiguous) – used by all organisms
– Degenerate (one amino acid may have many codons)
– Codons for similar amino acids have similar sequences.
– Only 61 of the 64 codons code for amino acids
– UAA, UAG and UGA are termination codons while AUG code form
methionine as well as the start codon.
2.10
The genetic code for all amino acids using the 3-base sequence is given in
the table below.
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2.11
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Each mRNA carries the codon and for each codon will be an anti-codon
carried by tRNA ribonucleotides triplets. Anti-codon base pair with codon and an
amino acid will be added to the 3’-end of the tRNA will the help of enzyme amino –
acyl synthetase.
2.12
Translation process begins with start codon 5’ AUG 3’ and the end of
translation or protein synthesis is terminated by the ‘stop codons’ - UAA,
UGA.
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UAG
or
PRT3402- Agricultural Biochemistry
2.13
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The diagram above summarizes how DNA sequences are transcribed by
mRNA and translated into protein with the help of tRNA. Finally the sequence of
amino acids will build up as proteins.
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2.14. The location for the entire process of gene expression is somewhat different
between eukaryotes and prokaryotes. Prokaryotes make RNA and protein in
cytoplasm whilst eukaryotes make RNA in the nucleus and protein in the
cytoplasm. These are shown below.
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TOPIC 3 : GENOME STRUCTURE, ORGANIZATION AND FUNCTION
Main Points
3.1
As a genetic material DNA is well-suited for its role. It can encode all
information needed for cell growth, development, structure and reproduction. It is
capable of replicating itself accurately so that progeny cells contain same information
as parent. At the same time it is capable of variation to accommodate the changes
and adaptation evidenced by evolution.
3.2 The gene is the unit for hereditary functional within DNA. Most genes specify
one or more proteins expression involving mRNA as intermediate. The gene
contains information for the structure of protein and for when and where a gene is
active. Information is encoded in the sequence of base pair within the region of DNA
molecule that make up the gene. Other genes do not specify proteins, their products
are non-coding RNA which play various roles in the cell.
3.3 A general and typical structure of a gene is indicated below. The size of a gene
is about 4 kilobase (kb) containing the promoter and transcribed region. The
transcribed region is made-up of exons and introns. Exons are the coding fragments
while introns are the non-coding fragments.
3.4 In eukaryotes, the genome is the complete compliment of DNA. The bulk of
DNA is in nuclear genome (linear) and much smaller in the mitochondrial genome
(which can be circular), respiratory complex and RNA genes). In addition, for
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photosynthetic organism a small portion also found in chloroplast genome (circular,
photosynthetic & RNA genes).
3.5 The nuclear genome is split into a set of linear DNA molecules, each contained
in a chromosome. Chromosome number is variable between organism and the
number appears unrelated to biological features or genome size. The table below
showed some comparison of genome size and number of genes of some biological
samples.
Species
Size of Genome (Mb)
Approximate of genes
Arabidopsis thaliana
125
25,500
Rice (Oryza sativa)
466
45,000 -- 56,000
Human (Homo sapiens)
3200
30,000 – 40,000
Saccharomyces
cerevisiae
12.1
5,800
3.6 Chromosome is a package consisting of DNA & protein. The packaging system
of DNA into chromosome is akin to beads on a string structure and the DNA strand is
wound tightly around the nucleosome. The nucleosome contains 8 histone proteins
and DNA wind twice around nucleosome. The linker histone acts as a clamp.
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3.7
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Gene sequence is present in only one copy per haploid genome. In tobacco
40% of the genome is single copy, however, many are not transcribed. Pseudogenes
are changes occurring in a gene sequence which result in being non-functional.
3.8
Multigene families are groups of genes of identical or similar sequences.
They are a common feature in eukaryotic genomes and - code for products in great
demand. E.g. multiple copies of ribosomal RNA genes, histone genes and seed
storage protein genes are arranged in clusters. Complex multigenes - similar
sequence but sufficiently different for gene products to have distinctive properties.
Members of the family show different patterns of expression. Some are clustered
while others are dispersed throughout the chromosomes.
3.9
In many instances during the process of DNA replication, errors can occur
which gives rise to mutations. Mutations are changes in genetic information which
results in phenotypic variation or disruption of the development of an individual giving
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rise to genetic diversity. Gross mutations occur when the changes involved large
segments of DNA containing several genes.
3.10
The changes may even involve whole chromosomes resulting changes in
chromosome number of an individual. Aneuploidy is where an individual may gain or
loses one or more chromosomes from a normal diploid set. The chromosome
aberrations include: Monosomy (2n – 1), Trisomy (2n + 1, Down syndrome)
Tetrasomy (2n + 2) and Pentasomy (2n + 3). 2n is the normal diploid number.
Aberrations can also include duplications of entire chromosome numbers which are
frequently encountered in plants. The term euploidy describes the mutation due to
exact multiple copies of the haploid chromosome set. Examples of polyploidy include
triploid (3n), tetraploid (4n) and pentaploid (5n). Watermelon is an example of a plant
which exhibit polyploidy.
3.11
Gene mutation can occur in which a single gene is mutated. It can be a
single point mutation in which a single nucleotide can be added or deleted. These
small mutations can give rise to new variation which leads to a new allele or even
phenotype. Some examples of mutations are given below:
Type of mutation
Changes
Base Substitution (Point
Substitution
mutation)
nucleotide for another.
Transition
Substitution
pyrimidine
Examples
of
one
of
by
one GGG change to GAG
another
pyrimidine.
Transversion
Substitution of one purine
AAA changes to AAT
by pyrimidine and viceversa
Insertion
The addition of 1 or more
AGGTTTAGT changes to
nucleotide at any point
AGGGTTTAGT
along the DNA strand
Deletion
Removal of one or more
AGGTTTAGT changes to
nucleotides at any point
AGTTTAGT where the
along the DNA strand.
third base (G) is deleted
Deletion and inversion
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within a gene is called a
frame-shift mutation
Duplication
A segment of DNA present AGGTATAGT changes to
more than once in the
AGGTATTATAGT
gene
Translocation
The movement of segment
of DNA to a nonhomologous chromosome
3.12
Mutations can occur spontaneously during replication and the reasons are
not understood or it can be induced by chemical mutagens such as colchicines, Ethyl
methane sulphonate (EMS) and Methyl nitrosourea (MNU) or physical mutagens
such as UV radiation, X-ray and gamma irradiation. In the field of plant biology,
mutations are induced to obtain plants of superior and desirable characteristics.
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