lecture 2.pptxmolecular biooooologyyyyyyy

Plant Molecular Biology
(B208)
Prepared by
:
Dr. Basma Mohamed Hendam
Lecturer of plant Cytology and Genetics, Faculty of Science, Mansoura
University
Lecture 2
:

• DNA Structure: The Double Helix
• Watson and Crick model
• DNA Structure as Related to Function
• RNA structure and its types
Lecture Outline

DNA Structure, Functions and
Properties

DNA: The Genetic Material
• DNA was first extracted from nuclei in 1870
• named ‘nuclein’ after their source.
• Chemical analysis
– determined that DNA was a weak acid rich in phosphorous.
• Its name provides a lot of information about DNA:
– deoxyribose nucleic acid:
– it contains a sugar moiety (deoxyribose),
– it is weakly acidic,
– and is found in the nucleus.
• Because of its:
– nuclear localization
– subsequent identification as a component of chromosomes
– it was implicated as a carrier of genetic information

Primary Structure of Nucleic Acids
Nucleic acids were discovered as “nuclein” by a Swiss physician and biologist
Miescher in the year 1869, and their name was created by Altmann (1889). For
the synthesis of nucleic acids nucleosides are used, which are made of a
nitrogenous base and pentose (five carbon atoms sugar), connected by a N-
glycosidic bond to the first carbon being a nitrogenous base. In DNA the
saccharide is deoxyribose (2-deoxy-βD-ribose), while in RNA it is ribose (β-D-
ribose). They differ from each other because ribose contains on its second carbon
an –OH group while deoxyribose only has a –H group.

lecture 2.pptxmolecular biooooologyyyyyyy

The Watson-Crick Model: DNA is a double helix
• In the Watson–Crick structure, DNA
consists of two long chains of subunits,
each twisted around the other to form a
double stranded helix.
• The double helix is right handed, which
means that as one looks along the barrel,
each chain follows a clockwise path as it
progresses.
• The two strands are antiparallel.
• The dark spheres outline the “backbone”
of each individual strand, and they coil in
a clockwise direction.

• The building blocks of the DNA
molecule are called nucleotides.
• A nucleotide is a monomer of a
nucleic acid polymer and is made of
a nitrogenous base, pentose and
phosphate (the rest of H3PO4). The
individual nucleotides in a nucleic
acid differ only by their nitrogenous
base.
 Chemical structure of nucleotides:
• nitrogenous base
•Deoxyribose Sugar
•Phosphate
• The nucleotides are linked
together into a chain by covalent
bonds (a strong chemical bond
involving electron sharing).
• This chain is referred to as a DNA
strand.

• In DNA, each base is chemically linked to one molecule of the sugar
deoxyribose, forming a compound called a nucleoside.
• When a phosphate group is also attached to the sugar, the nucleoside
becomes a nucleotide (Figure 2.4). Thus a nucleotide is a nucleoside
plus a phosphate.

Base
The chemical structures of the bases are shown in Figure 2.3. Note that
two of the bases have a double-ring structure; these are called purines.
The other two bases have a single-ring structure; these are called
pyrimidines.

• The subunits of each strand are nucleotides, each of which contains
any one of four chemical constituents called bases attached to a
phosphorylated molecule of the 5-carbon sugar deoxyribose.
• The four bases in DNA are
• Adenine (A) • Guanine (G)
• Thymine (T) • Cytosine (C)
• The pairing between A and T and between G and C is said to be
complementary; the complement of A is T, and the complement of G is
C. The complementary pairing means that each base along one strand of
the DNA is matched with a base in the opposite position on the other
strand. The complementary pairing is also called Watson–Crick
pairing.
• The arrangement of the nitrogen bases determines the genetic message.
At each position, there are 4 possibilities,
– therefore for a 100 base pair long molecule of DNA,– there are 4100
variations possible.

• Polynucleotide Chains: In terms of biochemistry, a DNA strand is
a polymer—a large molecule built from repeating units. The units
in DNA are composed of 2'-deoxyribose (a five-carbon sugar),
phosphoric acid, and the four nitrogen- containing bases denoted
A, T, G, and C.
• Each DNA strand has a polarity, or directionality, like a chain of
circus elephants linked trunk to tail. In this analogy, each
elephant corresponds to one nucleotide along the DNA strand.
• The polarity is determined by the direction in which the
nucleotides are pointing. The “trunk” end of the strand is called
the 3' end of the strand, and the “tail” end is called the 5' end. In
double-stranded DNA, the paired strands are oriented in opposite
directions, the 5‘ end of one strand aligned with the 3' end of the
other.

• In nucleic acids, such as DNA and RNA, the nucleotides are joined to
form a polynucleotide chain, in which the phosphate attached to the 5'
carbon of one sugar is linked to the hydroxyl group attached to the 3'
carbon of the next sugar in line (Figure 2.5).
• The chemical bonds by which the sugar components of adjacent
nucleotides are linked through the phosphate groups are called
phosphodiester bonds.
• The 5'–3'–5'–3' orientation of these linkages continues throughout the
chain, which typically consists of millions of nucleotides. Note that the
terminal groups of each polynucleotide chain are a 5'-phosphate (5'-P)
group at one end and a 3'-hydroxyl (3'-OH) group at the other.
• The asymmetry of the ends of a DNA strand implies that each strand
has a polarity determined by which end bears the 5' phosphate and
which end bears the 3' hydroxyl.

• Each backbone in a double helix
consists of deoxyribose sugars
alternating with phosphate groups
that link the 3' carbon atom of one
sugar to the 5' carbon of the next in
line.
• The two polynucleotide strands of
the double helix have opposite
polarity in the sense that the 5' end
of one strand is paired with the 3'
end of the other strand.
• Strands with such an arrangement
are said to be antiparallel.
Antiparallel Strands

• The strands feature complementary
base pairing, in which each base is
paired to a complementary base in
the other strand by hydrogen bonds.
• The DNA double helix is held together
mainly by- Hydrogen bonds.
• Hydrogen bond a chemical non
covalent bond in which a hydrogen
atom of one molecule is attracted to
an electronegative atom, especially a
nitrogen, oxygen, usually of another
molecule.
• (A hydrogen bond is a weak bond in
which two participating atoms share
a hydrogen atom between them.)

Chargaff’s Rules
• Erwin Chargaff developed a chemical technique to measure the amount
of each base present in DNA.
• The molar concentration of any base be represented by the symbol for
the base in square brackets; for example, [A] denotes the molar
concentration of adenine.
• Chargaff used his technique to measure the [A], [T], [G], and [C]
content of the DNA from a variety of sources.
 These relationships are now called Chargaff’s rules:
• The amount of adenine equals that of thymine: [A] = [T].
• The amount of guanine equals that of cytosine: [G] = [C].
• The amount of the purine bases equals that of the pyrimidine bases:
[A] + [G] =[T] + [C].
• A+T does not have to equal G+C

DNA Structural forms
• DNA is a dynamic molecule, constantly in motion. In some regions,
the strands can separate briefly and then come together again in the
same conformation or in a different one.
• Three DNA Forms : A- form, B- form and Z – form
• The right-handed double helix is the standard B form, but
depending on conditions, DNA can actually form more than 20
slightly different variants of a right-handed helix, and some regions
can even form helices in which the strands twist to the left (called
the Z form of DNA).

• In the standard structure, which is called the B
form of DNA, each chain makes one complete
turn every 34 Å.
• The helix is right-handed, which means that as
one looks down the barrel, each chain follows a
clockwise path as it progresses.
• The bases are spaced at 3.4 Å, so there are ten
bases per helical turn in each strand and ten base
pairs per turn of the double helix.
• The two grooves spiraling along outside of the
double helix are not symmetrical; one groove,
called the major groove, is larger than the other,
which is called the minor groove.
34

• In the B form of DNA, the paired bases are planar, parallel
to one another, and perpendicular to the long axis of the
double helix. This feature of double-stranded DNA is
known as base stacking.
• The upper and lower faces of each nitrogenous base are
relatively flat and nonpolar (uncharged). These surfaces
are said to be hydrophobic because they bind poorly to
water molecules, which are very polar.
• Owing to their repulsion of water molecules, the paired
nitrogenous bases tend to stack on top of one another in
such a way as to exclude the maximum amount of water
from the interior of the double helix.
• Hence a double stranded DNA molecule has a hydrophobic
core composed of stacked bases, and it is the energy of
base stacking that provides double-stranded DNA with
much of its chemical stability.

DNA Structure as Related to Function
In the structure of the DNA molecule, we can see how three essential
requirements of a genetic material are met:
1. Any genetic material must be able to be replicated accurately, so that
the information it contains will be precisely replicated and inherited
by daughter cells. The basis for exact duplication of a DNA molecule is the
pairing of A with T and of G with C in the two polynucleotide chains. Unwinding
and separation of the chains, with each free chain being copied, results in the
formation of two identical double helices.
2. A genetic material must also have the capacity to carry all of the
information needed to direct the organization and metabolic activities
of the cell. The product of most genes is a protein. In DNA, this is done by means
of a genetic code in which groups of three bases specify amino acids. Because the
four bases in a DNA molecule can be arranged in any sequence, and because the
sequence can vary from one part of the molecule to another and from organism to
organism.

3. A genetic material must also be capable of undergoing occasional
mutations in which the information it carries is altered. Furthermore, so
that mutations will be heritable, the mutant molecules must be capable of being
replicated as faithfully as the parental molecule. Watson and Crick suggested that
heritable mutations might be possible in DNA by rare mispairing of the bases, with
the result that an incorrect nucleotide becomes incorporated into a replicating DNA
strand.

31
RNA Structure, Types and
Functions

32
• RNA structure is unique in having both an informational content
present in its sequence of bases and a complex, folded three-
dimensional structure that endows some RNA molecules with catalytic
activities. Many scientists believe that in the earliest forms of life, RNA
served both for genetic information and catalysis.
• The structure of RNA is similar to, but not identical with, that of DNA.
There is a difference in the sugar (RNA contains the sugar ribose
instead of deoxyribose), RNA is usually single-stranded (not a duplex),
and RNA contains the base uracil (U) instead of thymine (T), which is
present in DNA.
Double-stranded RNA:
• Double-stranded RNA (dsRNA) is RNA with two complementary
strands, similar to the DNA found in all cells. dsRNA forms the genetic
material of some viruses (double-stranded RNA viruses).
RNA (Ribonucleic acid )

34
 Actually, three types of RNA take part in the synthesis of
proteins:

36
• A molecule of messenger RNA (mRNA), which carries the genetic
information from DNA and is used as a template for polypeptide
synthesis. In most mRNA molecules, there is a high proportion of
nucleotides that actually code for amino acids.
• For example, the mRNA for PAH is 2400 nucleotides in length and
codes for a polypeptide of 452 amino acids; in this case, more than 50
percent of the length of the mRNA codes for amino acids.
• mRNA carries information about a protein sequence to the ribosomes,
the protein synthesis factories in the cell.
• It is coded so that every three nucleotides (a codon) correspond to one
amino acid.
1
.
Messenger RNA (mRNA)

38
• The mRNA is then exported from the nucleus to the cytoplasm, where
it is bound to ribosomes and translated into its corresponding protein
form with the help of tRNA.
• In eukaryotic cells, once precursor mRNA (pre-mRNA) has been
transcribed from DNA, it is processed to mature mRNA. This removes
its introns—non-coding sections of the pre-mRNA.
• In prokaryotic cells, which do not have nucleus and cytoplasm
compartments, mRNA can bind to ribosomes while it is being
transcribed from DNA.

• Messenger RNA (mRNA) is created by transcription from structural genes (in human
cells there are more then 20 500).
• The result of transcription of a structural gene in the nucleus of an eukaryotic cell, is a
precursor RNA (pre-mRNA), which is called also heterogeneous nuclear RNA
(hnRNA). This primary transcript must be modified (maturated), in order to become
a mature mRNA.
• Matured mRNA is a linear single-strand RNA chain, which has on its 5' end a guanine
nucleotide bonded by an atypical 5' - 5' triphosphate bond, the so called “cap”.
• These structure is not only the protection of the mRNA against the destructive action
of RNases and site, where the regulation proteins bind to it, and „protect“ the mRNA
during its passage to the cytoplasm.
• The cap is recognized by sc. preinitiation complex, which allows the mRNA to connect
to the small subunit of the ribosome, as essential proposal to initialization of
translation (formation of active ribosome).
• On the 3' end of the mRNA is present long poly-A chain, containing about 100-250
nucleotides with adenyl, that not only protects the molecule from this end, but has a
significant effect on the number of times, an mRNA can be used for translation.

41
RNA Processing in Eukaryotes
• In eukaryotes, the new mRNA is not yet ready for translation. At this
stage, it is called pre-mRNA, and it must go through more processing
before it leaves the nucleus as mature mRNA. The processing may include
splicing, editing, and polyadenylation.
• In eukaryotes, mRNA consists of alternating exon/intron segments
exons are the coding parts; introns are spliced out before translation.
Splicing
• A gene is a continuous stretch of genomic DNA from which one (or
more) type (s) of protein(s) can be synthesized. Genes contain coding
regions (exons) separated by non-coding regions (intron).
• Introns are removed from pre-mRNA through a process called splicing,
resulting in mRNA.
• Alternative splicing: Different combinations of introns and exons may
be used to synthesize different proteins from a single gene and is
regulated by activators and repressors.

42
• Splicing removes introns from mRNA. Introns are regions that do
not code for the protein. The remaining mRNA consists only of regions
called exons that do code for the protein. The ribonucleoproteins in
the diagram are small proteins in the nucleus that contain RNA and
are needed for the splicing process.
• Editing changes some of the nucleotides in mRNA. For example, a
human protein called APOB, which helps transport lipids in the blood,
has two different forms because of editing. One form is smaller than
the other because editing adds an earlier stop signal in mRNA.
• Polyadenylation adds a “tail” to the mRNA. The tail consists of a
string of As (adenine bases). It signals the end of mRNA. It is also
involved in exporting mRNA from the nucleus, and it protects mRNA
from enzymes that might break it down.

46
• Several types of ribosomal RNA (rRNA), which are major constituents
of the cellular particles called ribosomes on which polypeptide
synthesis takes place.
• Ribosomal RNA (rRNA) is the catalytic component of the ribosomes.
• Eukaryotic ribosomes contain four different rRNA molecules: 18S,
5.8S, 28S and 5S rRNA. Comprises the 70S ribosome in bacteria and
the 80S in Eukaryotes.
• rRNA molecules are synthesized in the nucleolus. In the cytoplasm,
ribosomal RNA and protein combine to form a nucleoprotein called a
ribosome.
• The ribosome binds mRNA and carries out protein synthesis. Several
ribosomes may be attached to a single mRNA at any time.
• rRNA is extremely abundant and makes up 80% of the 10 mg/ml RNA
found in a typical eukaryotic cytoplasm.
2. Ribosomal RNA (rRNA)

48
• A set of transfer RNA (tRNA) molecules, each of which carries a
particular amino acid as well as a three-base recognition region that
base-pairs with a group of three adjacent bases in the mRNA.
• As each tRNA participates in translation, its amino acid becomes the
terminal subunit added to the length of the growing polypeptide chain.
The tRNA that carries methionine is denoted tRNAMet, that which carries
serine is denoted tRNASer, and so forth.
• Transfer RNA (tRNA) is a small RNA chain of about 80 nucleotides that
transfers a specific amino acid to a growing polypeptide chain at the
ribosomal site of protein synthesis during translation.
• It has sites for amino acid attachment and an anticodon region for codon
recognition that site binds to a specific sequence on the messenger RNA
chain through hydrogen bonding.
3. Transfer RNA (tRNA)

• Because the genetic code is degenerated (particular amino acid could be coded by
more variants of triplets), there may exist more than one tRNA – for the same amino
acid. The structure of the tRNA (in 2D) is similar to a quatrefoil.
• The selfpairing of certain complementary sequences of nitrogen bases which are
distant from each other, form double stranded segments, while the unpaired areas
form loops (arms). Inside unpaired parts of loops are located minority bases.
• On the 3' ends of the strand are the CCA sequences and on the terminal nucleotide
with adenine connects the transported amino acid.
• On the 5' end of tRNA is usually a nucleotide with guanine. In the tRNA molecule two
main parts are recognized.
• The first part is the so-called anticodon loop (the middle loop), which contains the
anticodon and perform tRNA function during decoding of the genetic information
written in the structure of mRNA.
• The second major part of the tRNA is the acceptor arm, on whose 3' end a
predestined amino acid is bound. Bases of the anticodon are complementary to the
codon inside the mRNA, to which they are paired antiparallely.

We read the anticodon sequence of bases from the 3' end of the tRNA molecule to 5'
end. The anticodon enables the binding of a specific tRNA to an exactly defined
spot on the mRNA, through the codon-anticodon bond, for example:
Codon in the mRNA: 5' – GUA - 3'
Anticodon in the tRNA: 3' – CAU - 5'

51
• tRNA primary structure: The linear sequence (primary structure) of
tRNAs is 60–95 nt long, most commonly 76. There are many modified
nucleosides present, notably, thymidine, pseudouridine, dihydrouridine
and inosine.
• tRNA Secondary structure: The cloverleaf structure is a common
secondary structural representation of tRNA molecules which shows the
base pairing of various regions to form four stems (arms) and three
loops. The 5- and 3-ends are largely base-paired to form the amino acid
acceptor stem which has no loop. Working anticlockwise, there is the D-
arm, the anticodon arm and the T-arm. Most of the invariant and semi-
variant residues occur in the loops not the stems.
• tRNA tertiary structure: Nine hydrogen bonds form between the bases
(mainly the invariant ones) in the single-stranded loops and fold the
secondary structure into an L-shaped tertiary structure, with the
anticodon and amino acid acceptor stems at opposite ends of the

Next Lecture:
Central Dogma & Protein
synthesis

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