BIOTECH 2

Doctors center
2024/ 2025
ECHNOL
T O
BIO
GY
part 2
for biochemistry diploma
Dr/ N. S
Phone number:01011591239
Nucleic acids :
 There are 2 types OF Nucleic acids DNA and RNA
 Composed from nucleotide subunit
 Each nucleotide subunit is composed of a pentose sugar (deoxyribose), a
nitrogenous base, and a phosphate group.
 There are 2 types of nitrogenous base; purine (A, G) and pyrimidine (C,T, U)
1. DNA:
 Composed, of four bases, A, G, C, and T
 DNA lacks the hydroxyl group at that position, hence the name, "deoxy"
ribonucleic acid. DNA has a hydrogen atom at the 2' position.
 Can be coded (exones) or non coding (introns)
 DNA molecules usually consist of two strands arranged in the famous double
helix, the strands of DNA are antiparallel
 The two strands associate via hydrogen bonds between chemically
complementary nitrogenous bases.
 Because of the specificity of hydrogen bonding, in the context of DNA A
always pairs with T (A=T), and G with C (G≡C). Therefore, if the sequence of
one strand of DNA is known, the sequence of the other strand can be
determined as well. In this way, if one strand of DNA is known to have the
sequence 5’-ATGGCT-3’, the other strand must have the sequence 3’-
TACCGA-5’. (Remember that the strands run antiparallel, so the 5’ end of
one strand must be able to pair with the 3’ end of the other.) These strands
are called complementary.
 DNA is packaged differently in prokaryotes and eukaryotes. A eukaryote
contains a well-defined nucleus, whereas in prokaryotes the chromosome lies
in the cytoplasm in an area called the nucleoid. In eukaryotic cells, DNA and
RNA synthesis occur in a separate compartment from protein synthesis. In
prokaryotic cells, both processes occur together.
 In prokaryotes(‫)خلية واحدة‬, the single circular chromosome (plasmid) is
contained in the cytoplasm in an area called the nucleoid (no nuclei) = 50kbp.
In eukaryotes, all of the cell's chromosomes are stored inside a structure
called the nucleus. Each eukaryotic chromosome is linear, like animals, plants,
fungi .
2. RNA (Ribonucleic acid)
 RNA is a single-stranded nucleic acid molecule and made up of ribonucleotides.

 A ribose nucleotide in the chain of RNA consists of a ribose sugar, phosphate
group, and a base.
 In each ribose sugar, one of the four bases is added: Adenine (A), Guanine (G),
Cytosine (C), and Uracil (U), inked by 3'-5'-phosphodiester bonds.
 These the main three types of RNA are: ‫لكن‬DNA ‫ملوش انواع‬
1. mRNA (messenger RNA) ‫يصنع في اسنباة ايشوغل في اسييوبالزم‬

‫اينيخ من اسمكمل مش اسكبدينج سورانددد‬
2. rRNA (ribosomal RNA) ( ‫) سيوبالزم‬
3. tRNA (transfer RNA) ( ‫) سيوبالزم‬
All are involved in the process of translation, but only mRNA carries the
information that determines the primary structure of proteins.
 Although RNA shares many features with DNA, it has some distinct
differences:
1. In RNA, the sugar linked to the phosphates and nitrogenous bases is ribose,
unlike the 2'-deoxy-ribose found in DNA.
2. The pyrimidine components in RNA differ from those in DNA. While RNA
contains the ribonucleotides of adenine, guanine, and cytosine, it rarely includes
thymine. Instead, RNA contains the ribonucleotide uracil.
3. RNA is typically single-stranded, whereas DNA is double-stranded. However,
with complementary base sequences and antiparallel polarity, a single RNA strand
can fold onto itself like a hairpin, acquiring double-stranded characteristics.
4. Since an RNA molecule is single-stranded and complementary to only one of
the gene's strands, the guanine content does not necessarily equal the cytosine
content, nor does the adenine content necessarily equal the uracil content.
Biotechnology and Recombinant DNA Technology

 Genetic Engineering: Also known as recombinant DNA (rDNA) technology, it
involves combining DNA from different species.
 Applications: Used in medicine for pharmaceuticals and in agriculture for
genetically modified crops.
 Importance:Understanding rDNA technology is crucial for its applications in

producing pharmaceutical drugs and genetically modified crops.
The Central Dogma
 Essential Functions of an Organism:
1. Store Genetic Information: Maintain and preserve genetic data.
2. Pass on Genetic Information: Ensure that genetic data is transmitted to future
generations.
3. Express Genetic Information: Use genetic data in life processes.
 Central Dogma:
- Two-Step Process: Describes how genetic information flows from DNA to RNA to
proteins (transcription and translation)
- Transcription:
- Definition: Synthesis of an RNA copy from a DNA segment.
- Enzyme Involved: RNA polymerase synthesizes RNA.
1. DNA Replication:
Prokaryotic Replication:
 Prokaryotes replicate DNA without a nucleus through binary fission ( asexual).
 Gene Transfer: Genetic material transfer in bacteria occurs via conjugation,
transduction, and transformation.
In all eukaryotic cells,
the first step in sexual reproduction is cellular fusion:
1. Gametes: The two cells involved in the process are called gametes.
2. Zygote Formation: When these gametes fuse, they form a cell called a zygote.
3. Nuclear Fusion: After gametic fusion, the nuclei of the gametes combine, resulting
in a zygote nucleus that contains two full sets of genetic material.
4. Chromosome Doubling: The fusion doubles the number of chromosomes; each
gamete with 'n' chromosomes fuses to form a zygote with '2n' chromosomes.
5. DNA Replication: During cell division, the entire genome (total genetic material in
a cell) is duplicated, a process governed by DNA replication.
Despite the fundamental role of DNA polymerases in this process, many aspects of it
are complex and not fully understood.
Enzymes Involved in DNA Replication
1. Helicase: Unwinds the DNA double helix to form a replication fork.
2. Single-Strand Binding (SSB) Protein: Binds to separated DNA strands to keep
them apart and prevent them from re-annealing. ‫سيمنعها من التحاد‬
3. RNA Primase : Adds a short RNA primer to the DNA template strands to provide
a starting point for replication.
4. DNA Polymerase III :Reads the DNA template from the 3’ end to the ’5end and
adds new nucleotides from 5’ to the 3’ end of the new DNA strand. Enzyme that
synthesizes new DNA strands using a single-stranded template.
5. DNA Polymerase I: Removes RNA primers and replaces them with DNA
nucleotides.
6. DNA Ligase: Joins Okazaki fragments on the lagging strand, creating a
continuous DNA strand.
DNA Replication Process

1. Replication Origin (ofi): Specific site on the chromosome where replication
begins, creating a replication bubble.
2. Enzyme Activity: DNA helicase unwinds the double helix, forming a replication
fork. Single-stranded binding proteins prevent the strands from re-annealing.
3. Strand Separation: The double helix unwinds with the help of proteins like DNA
helicase and topoisomerase, using ATP for energy.
4. Primer RNA: Synthesized by RNA polymerase to provide a starting point for
DNA synthesis.
5. DNA Polymerization: DNA polymerase III adds new nucleotides to the primer,
forming the new DNA strand.
6. Primer Removal: DNA polymerase I removes RNA primers and fills in the gaps
with DNA.
7. Strand Joining: DNA ligase joins the short DNA segments to create a continuous
strand.
1. Primase Activity:
- Primase Function: Synthesizes short RNA primers on the single-stranded DNA.
- Special Enzyme: Primase, unlike typical RNA polymerases, initiates chain
elongation.
2. Primer Recognition:
- Specific Sequences: Primases recognize specific DNA sequences to add RNA
primers.
- Primer Removal: RNA primers are later removed by ribonuclease, and DNA
polymerase I fills the gaps with DNA.
3. Leading Strand:
- Continuous Synthesis: The leading strand runs 5' to 3' and is replicated
continuously.
4. Lagging Strand:
- Discontinuous Synthesis: The lagging strand runs 3' to 5' and is replicated in short
segments called (1000:2000) Okazaki fragments.
5. Okazaki Fragments:
- Formation: Short DNA sections attached to RNA primers are created.
- Joining: DNA ligase joins these fragments to form a continuous strand.
 Eukaryotic vs. Prokaryotic Replication

The synthesis of DNA in eukaryotes shares similarities with the process in
prokaryotes, but there are significant differences and complications:
1- Chromosome Structure: Eukaryotic DNA is organized in multiple linear
chromosomes, which are much longer than those in prokaryotes.
2- Replication Rate: The rate of movement of DNA polymerase in eukaryotes is
slower compared to prokaryotes.
3- Compensatory Mechanisms: To accommodate this, eukaryotic cells contain over
20,000 molecules of DNA polymerase, allowing the formation of a large number of
replication forks (more than2000)
- Okazaki Fragments: In eukaryotes, smaller Okazaki fragments are formed, ranging
from 40 to 300 bases.
- Efficiency: Despite the slower polymerase movement, the presence of multiple
replication forks and smaller Okazaki fragments enables a faster rate of DNA
replication compared to that in prokaryotes, such as Escherichia coli.
1) Messenger RNA (mRNA)
1. Heterogeneity and Stability:
- mRNA is the most diverse class in terms of size and stability.
2. Function:
- Acts as a messenger, carrying genetic information from a gene to the protein
synthesis machinery to form specific proteins.
3. 5’Cap:
- The 5' end of mRNA is capped with a 7-methylguanosine triphosphate. This cap is
linked to a 2'-O-methyl ribonucleoside at the 5' hydroxyl through three phosphates.
4. Internal Modifications:
- mRNA molecules often contain internally modified nucleotides like 6-
methyladenylates and other 2'-O-methylated ribonucleotides.
5. Cap Function:
- The cap aids in mRNA recognition by the translating machinery and stabilizes the
mRNA by preventing degradation by 5' exonucleases.
6. Translation Initiation:
- Protein synthesis begins downstream of the 5' capped end of the mRNA.
7. '3 Poly-A Tail:
- The 3' end of most mRNA molecules has a polyadenylate (poly-A) tail ranging
from 20 to 250 nucleotides in length.
-Function:
- Although its exact function is not fully understood, the poly-A tail helps maintain
the mRNA's stability by protecting it from degradation by 3' exonucleases.
2) Transfer RNA (tRNA)
1. Length and Processing:
- tRNA molecules vary in length from 74 to 95 nucleotides.
- They are generated by nuclear processing of precursor molecules.
2. Function:
- tRNA serves as an adapter for translating the nucleotide sequence of mRNA into
specific amino acids.
3. Diversity:
- Each cell contains at least 20 species of tRNA, with at least one (and often
several) corresponding to each of the 20 amino acids required for protein synthesis.
- Although specific tRNAs differ in their nucleotide sequences, they share many
common features.
4. Structure:
- All tRNA molecules contain four main arms:
- Acceptor Arm: Terminates in nucleotides CCA, where the appropriate amino
acid attaches to the 3'-OH group of the A moiety.
- D, TΨC, and Extra Arms: Help define the specific tRNA.
5. Stability:
- tRNAs are quite stable in prokaryotes but less stable in eukaryotes.
- This is the opposite of mRNAs, which are unstable in prokaryotes but
generally stable in eukaryotes.
6. Secondary Structure:
- The primary structure of tRNA allows extensive folding and intramolecular
complementarity, generating a cloverleaf-like secondary structure.
- Typical aminoacyl tRNA with the amino acid (aa) attached to the 3'-CCA
terminal.
- The anticodon, TΨC, and dihydrouracil (D) arms are indicated as positions
of intramolecular hydrogen bonding between these base pairs.
Transcription
(nucleus)
Translation
(cytoplasm)

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Doctors center

for biochemistry diploma

 RNA is a single-stranded nucleic acid molecule and made up of ribonucleotides.

1. mRNA (messenger RNA) ‫يصنع في اسنباة ايشوغل في اسييوبالزم‬

Biotechnology and Recombinant DNA Technology

 Importance:Understanding rDNA technology is crucial for its applications in

DNA Replication Process

 Eukaryotic vs. Prokaryotic Replication

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