7.1.

:- DNA STRUCTURE:

7.1.1:- Describe the structure of DNA including the anti parallel strands, 3`-5`
linkages and hydrogen bonding between purines and pyrimidines.

The main features of the structure are:

 DNA is double-stranded, so there are two polynucleotide

stands alongside each other.

 The strands are antiparallel, i.e. they run in opposite

directions thus 5' to 3' is parallel to 3' to 5'.
 The two strands are wound round each other to form a
double helix.

 The two strands are joined together by hydrogen bonds

between the bases.

 The bases therefore form base pairs, which are like rungs of
a ladder.

 The base pairs are specific. A only binds to T (and T with A),
and C only binds to G (and G with C).

 These are called complementary base pairs (or sometimes

Watson-Crick base pairs). (A-T and G-C)

This means that whatever the sequence of bases along one

strand, the sequence of bases on the other stand must be
complementary to it.

7.1.2:- Outline the structure of nucleosomes.

The double helix has major and minor groves on its

outer diameter.
 • These groves expose chemical groups that can form hydrogen bonds.
• These chemical groups within DNA are bonded to by proteins.
• DNA is bonded to proteins called HISTONES.
• The diagram to the left is of a nucleosome:
• DNA is wound around and hydrogen bonded to eight histones.
• The combination of DNA and histones is secured by the 'H1 linker' protein.

7.1.3:- State that nucleosomes help to superscript chromosomes and help to

regulate transcription.

Nucleosomes are important in two ways. The

first is nucleosomes help to organize the DNA
so that it can fit into mucus. When they are in
this compact arrangement, the chromosomes
are described to prevent transcription.

Transcription is the process in which the anti

sense strand of the DNA is used as a template
for producing a strand of RNA . In order for
transcription to occur, RNA polymerase needs
to be able to attach to the promoter region of
the 3′ end of the structural gene on the DNA .
It the DNA is organized into nucleosomes. The
promoter region is usually not accessible to RNA polymerase and therefore
transcription will not occur.

When the cell requires transcription to occur enzymes will alter the shape of the
nucleosomes to allow RNA polymerase to attach to the promoter region of the
DNA strand and to start the process of transcription.

7.1.4:- Distinguish between unique or single copy genes and highly repetitive
sequences in nuclear DNA.

Nuclear DNA contain sequences that

regulate genes and sequences that have no
currently known function.
Unique genes are called single copy genes or
codable genes. They make up only about
1.5% of the human genetic material. These
are the genes that carry out genetic
information as outlined in mandolin
genetics.

The remainder of human genetic materials includes repetitive sequences of DNA

that seem to have or known function for the individual. It has been suggested that
they play or role in genetic control process, but the details are not yet understand.
Some repetitive sequences are used in DNA research for example determines
percentage or crime forensics.

7.1.5:- State that eukaryotic genes can contain exons and introns.

While in prokaryotes, genes are unintercepted section of DNA it appears that in

eukaryotic cell coding section of DNA are interruptions with long non-coding
intervening sequences. In other word many genes are discontinuous. The
intervening sequences are called intons while the coding sequences are called
axons (since they are expressed).

7.2:- DNA REPLICATION:

7.2.1:- State that DNA replication occurs in a 5`-3` direction.

Ans: From Book

7.2.2:- Explain the process of DNA replication in prokaryotes, including the role of
enzymes (helicase, DNA polymerase ,RNA primes and DNA ligase) Okazaki
fragments and deoxynucloside triphosphates.
Ans:- DNA replication is a semiconvervative process. It involves
The following steps-

* The DNA is a helix (like a twisted ladder) which needs to be

unwound by the enzyme helicase

* Helicase also breaks the hydrogen bonds between the two strands (between the
base pairs) separating the strands .One of the old strands will be 3′ -5′ while the
other strand will be 5′ -3′

Present in the cell are deoxyribonucleoside triphosphates which are composed of

an organic base a deoxyribose sugar and three phosphate groups .They are
sometimes referred to as dATP, dCTP, dGTP and dTTP.

• Before a new strand of DNA can be formed, it is necessary to start with

an RNA primer. The RNA primer is a few RNA nucleotides which bind
to the old DNA strand .The enzyme RNA primer will bind these RNA
nucleotides together.
• Now that the RNA primer is in place, the deoxyribonucleoside
triphosphates will form hydrogen bond between their organic bases and
the complementary base on the exposed strand of the old DNA, i, e A
with T and C with G.

• In the new strand that is forming in the 5′ -3′ direction the leading strand
DNA polymerase 111 will bind the new nucleotides to the growing
strand by covalent bonds formed via condensation reactions. DNA
polymerase 111 only works in a 5′ -3′ direction.
 • As it attaches to the growing DNA strand, the second and third
phosphates groups are removed from the dioxinribonucleotide
triphosphate changing it into deoxyribonucleotide.

• The another new strand the lagging strand would have to grow in 3′ -5′
direction to keep up. However DNA polymerase III can not work in this
direction. As a result the lagging strand is formed in short regiments of
100-200 nucleotides (called Okazaki fraagenents) in a 5′ -3′ direction
according to the same process .

 RNA primer formed from RNA nucleotides by RNA primer.

 Deoxyribonucleotide tripphosphates from hydrogen bonds with the
exposed organized bases of the old. DNA strand.
 DNA polymerase III working in a 5′ to 3′ direction (i,e. away from the
direction in which the DNA unwinds and unzips) binds the DNA
nucleotides to from an okazaki fragment.
 DNA polymerase I will then remove the RNA prime of the okazaki
fragment and replace the RNA nucleotide with DNA nucleotides.
 DNA legase then catalyses the formation of the bonds attaching the
DNA segments to create one strand.

7.2.3:- State that DNA replication is initiated at many points in eukaryotic

chromosomes.

Ans:- From Book

7.3- TRANSCRIPTION:

7.3.1:- State that transcription is carried out in a 5′ -3′ direction.

Transcription is the enzyme controlled process of synthesizing RNA from a DNA

template. It is carried out in a 5′ to 3′ direction ( of the new RNA strand). This
means that new RNA nucleotides are added to the 3′ end of the growing RNA
strand. The process involves RNA polymerase, mRNA,tRNA and rRNA all need
to be transcribed for protein synthesis to take place.

7.3.2:- Distinguish between the sense and antisense strands of DNA.

The DNA strand which is transcribed is called the anti sense strand e.g .CAT

The strand that is not transcribed is called the sense strand e.g .GTA (this is
transcribed).

7.3.3:- Explain the process of transcription in prokaryotes including the role

of the promoted region ,RNA polymerase ,nucleoside triphosphates and the
terminator.

Transcription in prokaryotes cells involves a promoter region . This is the site for
binding RNA polymerase which will attach the individual nucleotides together to
form a single stands of RNA. At the end of gene a terminator site is found which
will stop the transcription process.

RNA polymerase is similar to DNA polymerase and work in almost the same way;
however it can also function in a 3′ to 5′ direction. RNA nucleotides in the form
of ribo nucleoside triphosphates form by hydrogen bonds with the complementary
nucleotide of the DNA strand.

The only difference between ribonucleoside triphosphate and deoxyribonucleoside

triphosphate is one hydroxyl group ( -OH group) on C2 in the pentose sugar. This
change the deoxyribose into ribose.

7.3.4:- State that eukaryotic RNA needs the removed of introns to form
mature m RNA.

It appears that the entire section of the DNA (intrones and axons) is transcribed
into RNA. Before the RNA leaves the nucleous a cap which is a single altered
nucleotide added to the 5` end (the front) which will protect the mRNA from
degradation by phosphates and nucleases and assist important synthesis. A tail will
increase the stability of the mRNA but is not required for transcription or for
transport to the cytoplasm.

Before the m RNA leaves the nucleous enzymes will very precisely cut the bond
between exon and introns and attach the remaining exon nucleotides to each other
(The intron are taken out) .This process is called splicing. The RNA is now ready
to be transported to the cytoplasm and called mature mRNA.

7.4:- TRANSLATION.

7.4.1:- Explain that each tRNA molecule is recognized by a tRNA activating

enzyme that binds a specific amino acid to the t RNA, using ATP for energy.

At the 3′ end, the amino acid will bind to the tRNA. Each amino acid has its own
tRNA with a unique anticodon.

The amino acid is bound to the tRNA in a two step process catalyzed by its own
tRNA activating enzyme.

1. The amino acid will react with ATP and become activated, the ATP losses
its energy in this process.
2. The activated amino acid will then bind to the acceptor stem of its own
tRNA.

7.4.2:- Outline the structure of ribosome’s including protein and RNA

composition, large and small subunits three tRNA binding sites and mRNA
binding sites.

All ribosome’s are made of protein and ribosomal RNA(rRNA). The nucleolus
contains (many copies )of the information on how to make rRNA. Ribosome’s
consists of two subunits- a small and a large unit. The smaller subunit is made of
two molecules of r RNA and some proteins, including the enzyme peptides transfer
which links together the amino acids. Brought in by tRNA. The smaller subunit has
the binding site for mRNA, the larger subunit has the binding e sites (known as A
P sites) for tRNA.

7.4.3:- State that translation consists of initiation elongation and translocation

and termination.

Translation takes place in a 5′ to 3′ direction of the mRNA and can be divided

into 3 stages
 Initiation
 Elongation
 Termination

The polypeptide sequence is produced starting with the amino acid on the N
terminus and finishing with the amino acid on the C terminus..

7.4.4:- State that translation occurs in a 5`-3` direction.

The start codon which works the beginning point of translation is found at the 5`
end of the mRNA. This means that translation takes place in a 5` to 3` direction
( of the mRNA) .

7.4.5:- Draw and label a diagram

showing the structure of a peptide
bond between two amino acids.

During translation amino

acids are joined
together to form
polypeptides.
 • The specific sequence of amino acids is called the primary
structure.
• Between each amino acid a peptide bond forms to join them
together.
• In this example the amino acids are both Alanine in which
the R group is a single hydrogen.
• The carboxyl acid end on the first amino acid is orientated to
the amino group of the second amino acid.
• The -OH group and -H are removed to form water
(condensation reaction).
• The bond forms between the terminal carbon on the first
amino acid and the nitrogen on the second amino acid.
• The backbone of the molecule has the sequence N-C-C-N-C-
C
• Polypeptides maintain this sequence no matter how long the
chain.
• The R groups project from the backbone.
• As the amino acids are added in translation the polypeptide
folds up into it specific shape.

7.4.6:- Explain the process of translation including ribosome’s, polysomes,

start codons and stop codons.

Before initiation:
1) t RNA + amino acid +ATP tRNA activating enzyme
activated tRNA amino acid complex + AMP.

Initiation:-
2) The start codon on the mRNA is AUG, so the first tRNA must have the anti
-Codon UAC and carry the amino acid mothionine(met).
3) The tRNA will bind to the base of the p site on the small subunit of the
ribosome with the aid of an APTase enzyme.
4) The rRNA of the small subunit will recognize and attach to the ribosomal
binding site on the mRNA. This site is found near the 5` end of the mRNA.
5) The small subunit of the ribosome will slide along the mRNA until the base of
the P site reaches the start codon(AUG).
6) The large subunit containing the binding sites for tRNAs join the complex.

Elongation:

7) With the first tRNA attached to the P side a slight change in the shape of the
ribosome’s occurs, opening up the site next tRNA to bind.
8) The second tRNA will bind to the A site.
9) The amino acid of first tRNA will be released from the tRNA and from a
peptide t RNA (in the A site). The process is catalyzed by peptide translation
which is part of the ribosome.
10) The ribosome now moves three nucleotides (one Codon) along the mRNA
(towards the 3` end)
11) This means that the first tRNA (minus its amino acid met) can now be found
in the E binding site the second tRNA (with the growing polypeptide chain
 attached) is now in the P site and the A site is available for the third tRNA
( with amino acid ) to bind.

Termination:

12) The stop codons on the mRNA are found near the 3` end of the mRNA.
13) When the A site moves over one of the three stop Codon, this is a signal to
stop protein syntheses since there is no tRNA available that has an anticodon
complementary to a stop codon. Instead a protein release factor comes in to
break the bond between the polypeptide chain and the last tRNA ( in the P
position) by hydrolysis.
14) The polypeptide is released from the ribosome.
15) The tRNA are released and the ribosome will dissociate into a large and a
small subunit. All of these elements may be used again.

7.4.7:- State that free ribosome synthesize proteins for use primarily with in
the cell and that bound ribosome’s synthesize proteins primarily for secretion
of the Lysosomes.

Ans:- The distribution of ribosome’s depends on the function of the protein they
make . If the proteins are to be used inside the cell the ribosome’s trend to be found
throughout the cytoplasm. If the protein is to be exported (secretion) or used by
lysosomes, the ribosome’s are generally associated with the Endoplasmic
reticulum. These proteins will then enter the lumen of the RER as they are
produced and from there move to the golgi apparatus where they are packaged into
vesicles.