Chapter 3
Special Topics in Organic Chemistry
Special Topics in Organic Chemistry
Course code: ( 4024583-2 )
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Lecture 3
Chapter 3
Special topics in Organic chemistry
Special Topics in Organic Chemistry
Course code: ( 4024583-2 )
Nucleic acid
Definition:
The genetic material within the living cell, which ensures transmission of genetic characteristics during cell division or reproduction. Those materials are the DNA and the RNA.
• All living cells contain both DNA and RNA (except some cells such as mature red blood cells), while viruses contain either DNA or RNA, but usually not both.
• Nucleic acids were found in the nucleus, where they derived their name (Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm).
Composition:
• Biological macromolecule, composed of units called nucleotides, also associated with nuclear proteins.
• Nucleotides linked together by phosphodiester bond to form nucleic acids.
Classification:
1 - Deoxyribonucleic acid DNA.
2 - Ribonucleic acid RNA.
3 Dr. Hanadi Katouah
Nucleic acid
Biological importance:
• Found in all living cells, where the function is in encoding, transmitting and expressing genetic information.
• The nucleic acid sequence, the order, or the specific sequence of the nucleotides within a DNA or RNA molecule are the mechanism for storing and transmitting genetic information via protein synthesis. Any disturbance in this mechanism will lead to the presence or absence of the genetic information and perhaps appearance of diseases.
Medical and industrial importance:
Used in the biotechnology, medical research and pharmaceutical industry.
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Nucleic Acids
• Nucleic acids are molecules that store information for cellular growth and reproduction
• There are two types of nucleic acids:
- deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
• These are polymers consisting of long chains of monomers called nucleotides, also associated with nuclear proteins.
• A nucleotide consists of a nitrogenous base, a pentose sugar
and a phosphate group:
Nitrogen Bases
• The nitrogen bases in nucleotides consist of two general types:
- purines: adenine (A) and guanine (G)
- pyrimidines: cytosine (C), thymine (T) and Uracil (U)
Pentose Sugars
• There are two related pentose sugars:
- RNA contains ribose
- DNA contains deoxyribose
• The sugars have their carbon atoms numbered with primes
to distinguish them from the nitrogen bases
Nucleosides and Nucleotides
• A nucleoside consists of a nitrogen base linked by a glycosidic bond to C1’ of a ribose or deoxyribose
• Nucleosides are named by changing the the nitrogen base ending to -osine for purines and –idine for pyrimidines
• A nucleotide is a nucleoside that forms a phosphate ester with the C5’ OH group of ribose or deoxyribose
• Nucleotides are named using the name of the nucleoside
followed by 5’-monophosphate
Names of Nucleosides and Nucleotides
AMP, ADP and ATP
• Additional phosphate groups can be added to the nucleoside 5’-monophosphates to form diphosphates and triphosphates
• ATP is the major energy source for cellular activity
Primary Structure of Nucleic Acids
• The primary structure of a nucleic acid is the nucleotide sequence
• The nucleotides in nucleic acids are joined by phosphodiester bonds
• The 3’-OH group of the sugar in one nucleotide forms an ester bond
to the phosphate group on the 5’-carbon of the sugar of the next
nucleotide
Polynucleotides
Nucleotides linked together in the form of non-branched units by the phosphodiester bond, this bond is between the carbon atom No. 3 in the sugar and the phosphate group associated with the carbon atom No. 5 in the followed sugar.
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Example of DNA Primary Structure
• In DNA, A, C, G, and T are linked by 3’-5’ ester bonds
between deoxyribose and phosphate
Example of RNA Primary Structure
• In RNA, A, C, G, and U are linked by 3’-5’ ester bonds
between ribose and phosphate
Reading Primary Structure
• A nucleic acid polymer has a free 5’- phosphate group at one end and a free 3’-OH group at the other end
• The sequence is read from the free 5’-end using the letters of the bases
• This example reads
5’—A—C—G—T—3’
Secondary Structure: DNA Double Helix
• In DNA there are two strands of nucleotides that wind together in a double helix
- the strands run in opposite directions
- the bases are are arranged in step-like pairs
- the base pairs are held together by hydrogen bonding
• The pairing of the bases from the two strands is very specific
• The complimentary base pairs are A-T and G-C - two hydrogen bonds form between A and T - three hydrogen bonds form between G and C
• Each pair consists of a purine and a pyrimidine, so they are
the same width, keeping the two strands at equal distances
from each other
Base Pairing in the DNA Double Helix
DNA
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Deoxyribonucleic acid (DNA) is a nucleic acid containing the genetic information used in the development and functioning of the living organisms.
•
The DNA segments carrying this genetic information are called genes.
The sequence of the genes forms the genetic code. The genetic code specifies the sequence of the amino acids within the proteins.
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The DNA is consists of simple units called nucleotides. These nucleotides are consist of deoxyribose sugar, phosphate and all the nitrogenous bases except uracil. These nucleotides are joined by phosphodiester bonds.
•
DNA is composed of two long polymers of nucleotides and form a double helix or a twisted ladder structure. These two strands run in opposite directions to each other and therefore, anti-parallel.
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These two strands are held together by hydrogen bonds. This bond is between the complementary bases, which are known as base pairs (the nitrogenous bases in one strand and the nitrogenous bases in the other strand). Adenine pairs with thymine by a double hydrogen bond.
Cytosine pairs with guanine by a triple hydrogen bond.
•
In the DNA the backbone of the ladder represents the deoxyribose sugar and the phosphate in each strand. The steps of the ladder will represent the nitrogenous bases and the hydrogen bonds, which link them together.
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DNA
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DNA : A T & G C
==2== 3
RNA
• Ribonucleic acid (RNA) is a nucleic acid, which convertes genetic information from genes into the amino acid sequences of proteins.
• RNA were composed of single polymer of nucleotides.
• RNA is consists of ribose sugar, phosphate and all the nitrogenous bases except thymine. Adenine pairs with uracil. Cytosine pairs with guanine.
The three forms of RNA are:
1) Messenger RNA (mRNA): found in the nucleus and acts to carry genetic
sequence information between DNA and ribosomes to be transported out of the nucleus for directing protein synthesis. It is the least in presence between the three types of RNA. As a result, it is switched temporarily until the gene is translated into proteins and then breaks down after that.
2) Transfer RNA (tRNA): found in the cytoplasm and serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA.
3) Ribosomal RNA (rRNA): is a major component of the ribosome, and catalyzes peptide bond formation through linking the amino acids in sequence after
decoding the m-RNA.
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RNA
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RNA : A U & G C
Nuclear proteins
1) Ribosomes: are proteins associated with ribosomal RNA and play an important role in the process of manufacturing proteins.
2) Chromatins and Histones: are proteins found in the DNA of eukaryotic cells. Chromatin exists in the form of a long strip called nucleosome, after wrapping around basic proteins called histones.
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General information DNA replication
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DNA replication forms two identical DNA double helices
Within cells DNA is organized into long structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
