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Principle of Biochemistry
5-Nucleotides and Nucleic Acids
        Course code: HFB324
        Credit hours: 3 hours
           Dr Siham Gritly

               Dr Siham Gritly    1
Nucleoside, Nucleotide & Nucleic acid
                                                    p h o s p h a te



                                                        su g a r       base



                      p h o s p h a te              p h o s p h a te

su g a r       base

                          su g a r           base       su g a r       base



                                                    p h o sp h a te

  nucleoside             nucleotides
                                                        sugar          b a se




                                                            nucleic acids

                               Dr Siham Gritly                                  2
DNA, RNA and the nucleobases




           Dr Siham Gritly     3
• Deoxyribonucleotide; monomeric building
  block of DNA; a phosphate group and a
  nitrogenous base both bonded to deoxyribose
• Ribonucleotide; monomeric building block of
  RNA; a phosphate group and a nitrogenous
  base both bonded to ribose sugar
• Duplex; two complementary strands of DNA
• Mutant; genetically altered species or cell

                    Dr Siham Gritly             4
• Nucleoside; nitrogenous base bonded to ribose
  or deoxyribose
• Nucleotide; monomeric building block of
  RNA and DNA; a phosphate group and a
  nitrogenous base both bonded to ribose or
  deoxyribose
• Nucleic Acids are Polynucleotides
• Phosphodiester; two different alcohols
  forming ester linkages with one phosphate ion
                    Dr Siham Gritly           5
• Replication; DNA synthesis
• Template; a section of DNA which is being
  replicated or transcribed; mRNA which is
  being translated
• Transcription; synthesis of RNA from DNA
• Translation; synthesis of proteins from an
  RNA template


                    Dr Siham Gritly            6
Nucleotides and Nucleic Acids
• Introduction;
• Nucleic acids are macromolecules present in
  all living cells in combination with protein
  with high concentration of basic amino acids
  to form nucleoproteins. (protamines and
  histones)

• Nucleic acids compounds carrying information
  -- the genetic molecules (DNA and RNA) .
                     Dr Siham Gritly             7
• The nucleic acids are of two types
• -1-deoxyribonucleic acid DNA
• -2-ribonucleic acid RNA
• DNA is present in the nuclei small amounts
  present in the mitochondria
• RNA is present in the cell cytoplasm (90%)
  about 10% present in the nucleolus


                     Dr Siham Gritly           8
Nucleotides
            Nucleoside phosphates
• Nucleotides are monomers of nucleic acids

• The nucleotides found in cells are derivatives
  of the heterocyclic highly basic, compounds,
  purine and pyrimidine present in DNA and
  RNA (nitrogenous bases)

 Heterocyclic are ring compounds that contain
 both carbon atom and non-carbon atoms --
 mainly nitrogen atom.

                      Dr Siham Gritly              9
Nucleotide Structures of purine and pyrimidine
           Heterocyclic ring compounds


                   Nitrogenous Bases




Single six-sided ring                   Double ring purines
pyrimidinesC4H4N2                       (six- and five-sided)
                                        C5H4N4
                           Dr Siham Gritly                      10
Types of nucleotide bases

• There are five major bases found in cells.
• The derivatives of purine are called adenine
  and guanine (found in both DNA & RNA) ,

• the derivatives of pyrimidine are called
  thymine, cytosine and uracil.
•


                      Dr Siham Gritly            11
The derivatives of purine ; adenine and guanine (found in both
DNA & RNA) 1-Adenine 6-aminopurine, 2-Guanine 2-amino-
6-oxypurine




                           Dr Siham Gritly                  12
the derivatives of pyrimidine are thymine, cytosine and uracil.
Cytosine- 2-oxy-4-aminopyrimidine, Uracil-n2,4-
dioxypyrimidineThymine-2,4-dioxy-, 5-methyl




                            Dr Siham Gritly                       13
• The common abbreviations used for these five
  bases are, A, G, T, C and U.

•   Cytosine & Uracil in RNA
•   Cytosine and thymine in DNA
•   The nucleotide uridine is never found in DNA
•   thymine is almost exclusively found in DNA.
•   Thymine is found in tRNAs but not rRNAs nor
    mRNAs

                       Dr Siham Gritly             14
Nucleotides mainly;
    Pentose sugar+ β-N-glycosidic bond+
             phosphoryl group

• Derivative of purines and pyrimidines are
  nucleotides----contain mainly cyclyized sugar
  Pentose linked to nitrogen hetroatom by β-N-
  glycosidic bond additional to phosphoryl
  group esterified to hydroxy group of the sugar
  (β-D-ribose or β-D-2-deoxyribose)



                     Dr Siham Gritly           15
Nucleotides mainly;
   1-pentose sugar. 2-phosphate groups. 3-a
               nitrogeous base
• 1-5–carbon sugar component
• Ribose
• Deoxyribose




                    Dr Siham Gritly           16
5–carbon sugar component; Ribose and Deoxyribose
                Furanose structures




                     Dr Siham Gritly               17
• 2-Phosphate group Attached to the sugar's
  5' carbon with a phosphodiester bond
• 3-Nitrogen Base component attached to the
  sugar's 1'carbon.




                   Dr Siham Gritly            18
Functions of Nucleotides
• Components of nucleic acids (which are long
  chains of nucleotides)
• ATP (Adonosine TriPhosphate) is central to
  energy metabolism
• GTP (Guanosine TriPhosphate) drives protein
  synthesis
• CTP (Cytidine Triphosphate) drives lipid
  synthesis
• UTP (Uridine Triphosphate) drives carbohydrate
  metabolism

                      Dr Siham Gritly              19
• Energy transport coenzymes (NAD+, NADP+,
  FAD+)
• Chemical intracellular messengers (e.g., Cyclic
  AMP, a cyclic nucleotide that carries messages
  from the cell membrane to molecules within
  the cell, to stimulate essential reactions.
  regulators of cellular metabolism and
  reproduction )

                     Dr Siham Gritly            20
Nucleosides
• Nucleoside consist of purine and pyrimidine
  bases and a sugar β-D-ribose or β-D-2-
  deoxyribose linked through a covalent β-N-
  glycosidic bond
• Therefore Nucleosides are Formed by Joining
  a Nitrogenous Base to a Sugar
• Base is linked via a β-N-glycosidic bond


                    Dr Siham Gritly             21
β-N-glycosidic bond linked nitrogen-9 of the purine
   base or nitrogen-1 of the pyrinidine base with
              carbon1 of pentose sugar




                      Dr Siham Gritly             22
•   The nucleosides of A, G, C,T, U are named
•   Adenine ---Adenosine
•   Guanine ----Guanisine
•   Cytosine ----Cytidine
•   Thymine ----Thymidine
•   Uracil -----Uridine
•   Purine nucleosides end “osine”
•   Pyrinidine ends in “idine”
•   Ribose sugar produced; ribonucleoside
•   2-deoxyribose sugar produced;
    deoxyribonucleosides

                        Dr Siham Gritly         23
• The nucleosides in DNA are called;
  deoxyadenosine,
• deoxyguanosine,
• deoxycytidine, and thymidine,
• the nucleosides in RNA are called;
• adenosine, guanosine, cytidine, and uridine.
• If the base is a purine, then the N-9 (nitrogen) is
  bonded to the C-1' (carbon) of the sugar.
• If the base is a pyrimidine, then the N-1 is
  bonded to the C-1' of the sugar.
                        Dr Siham Gritly                 24
Common nucleosides




      Dr Siham Gritly   25
Glycosidic Bond Configurations




            Dr Siham Gritly      26
The base can exist in 2 distinct orientations about the
N-glycosidic bond. These conformations are identified
  as, syn and anti. It is the anti conformation that
 predominates in naturally occurring nucleotides




     Syn- adenosine                       anti-adenosine

                        Dr Siham Gritly                    27
Nucleotides and nucleosides that are not part of
                 DNA or RNA
       the importance of free nucleotide
• Some nucleotides are not part of DNA or RNA
  but still play important roles in a cell.
• cyclic adenosine monophosphate (cAMP) is an
  intracellular signal: it communicates
  information from one part of the cell to
  another.
• Other nucleotides are coenzymes, which are
  molecules that help enzymes work properly
  (FAD, NAD).

                      Dr Siham Gritly               28
Adenosine triphosphate (ATP)
Adenosine triphosphate (ATP) is a common
and critical energy transfer molecule. The
bonds that hold three phosphate groups to
adenosine store energy. They form when
energy is released and transfer that energy to
other places in a cell.




                           Dr Siham Gritly       29
Adenosine Monophosphates (AMP)




            Dr Siham Gritly      30
Nucleic acid
                polynucletide
• the nucleic acids are polymers of subunits of
  monomers nucleotides.

• Nucleic acid; important substance that all
  cellular organisms use to store their genetic
  information.

• The most common nucleic acids are
  deoxyribonucleic acid and ribonucleic acids
                      Dr Siham Gritly             31
The chemical linkage between nucleotide units in nucleic acids is a
phosphodiester, which connects the 5’-hydroxyl group of one nucleotide to
              the 3’-hydroxyl group of the next nucleotide.

• Phosphodiester bonds are essential to all life, as
  they make up the backbone of each helical strand
  of DNA.
• In DNA and RNA, the phosphodiester bond is the
  linkage between the 3’ carbon atom of one sugar
  molecule and the 5’ catbon atom of another;
• the sugar molecules deoxyribose in DNA
• and ribose in RNA.
• Hydrolysis of phosphodiester bonds can be
  catalyzed by the action of phosphodiesterases

                                Dr Siham Gritly                        32
Sequences of RNA and DNA structures
The chemical linkage between monomer units in
       nucleic acids is a phosphodiester




                   Dr Siham Gritly              33
phosphodiester, connects the 5’-hydroxyl group of one
nucleotide to the 3’-hydroxyl group of the next
nucleotide.




                       Dr Siham Gritly              34
Formation of phosphodiester bonds
Formed by Polymerase and Ligase activities




                 Dr Siham Gritly             35
classes of nucleic acids
1-Deoxyribonucleic acid DNA
• Deoxyribonucleic acid (DNA) is a
nucleic acid containing the genetic
 instructions used in the development
 and functioning of all known living organisms
   (with the exception of RNA viruses).
• The DNA segments carrying this genetic
   information are called genes .
• Genes (specific regions of DNA molecules)
   contain the hereditary information of an
   organism.
                     Dr Siham Gritly             36
• When organisms reproduce The code is read by
  copying stretches of DNA into the related nucleic acid
  RNA in a process called transcription.
• Within cells DNA is organized into long structures
  called chromosomes, (packaged form of the DNA).

• During cell division these chromosomes are duplicated
  in the process of DNA replication, providing each cell
  its own complete set of chromosomes (46).
• Within the chromosomes, chromatin proteins such as
  histones compact and organize DNA.


                         Dr Siham Gritly                   37
DNA structure and function

• DNA structure is the well-known double helix
  formed by Watson-Crick base-pairing of C
  with G and A with T.
• This is known as B-form DNA, and is the
  most favorable and common state of DNA;
• its highly specific and stable base-pairing is
  the basis of reliable genetic information
  storage.

                     Dr Siham Gritly               38
Structure of DNA
naturally occurring DNA molecules are double-
                   stranded




       Watson-Crick model for the structure of DNA
                         Dr Siham Gritly             39
Tertiary Structure of DNA: Supercoils. Each cell
contains about two meters of DNA. DNA is “packaged”
by coiling around a core of proteins known as histones.
The DNA-histone assembly is called a nucleosome.
Histones are rich is lysine and arginine residues




                        Dr Siham Gritly               40
the Watson-Crick model
• James Watson and Francis Crick proposed a
  model for the structure of DNA.

• This model predicted that DNA would exist as
  a helix of two complementary antiparallel
  strands, wound around each other in a
  rightward direction and stabilized by H-
  bonding between bases in adjacent strands.

                    Dr Siham Gritly           41
• They proposed that in any given molecule of
  DNA,;-
• the concentration of adenine (A) is equal to
  thymine (T)
• and the concentration of cytidine (C) is equal
  to guanine (G).
• This means that A will only base-pair with T, and
  C with G. According to this pattern, known as
  Watson-Crick base-pairing, the base-pairs
  composed of G and C contain three H-bonds,
  whereas those of A and T contain two H-bonds.
  This makes G-C base-pairs more stable than A-T
  base-pairs.
                       Dr Siham Gritly                42
Base pairing model




      Dr Siham Gritly   43
Base pairs are stabilized by H-bonding




                Dr Siham Gritly          44
the base-pairs composed of G and C contain three H-
bonds, whereas those of A and T contain two H-bonds.




                      Dr Siham Gritly                  45
Watson-Crick base-pairing of C with G and A
                  with T




                  Dr Siham Gritly             46
Complementarity of strands
 in the DNA double helix


                     -Adenine (A) and thymine (T)
                     always pair together (A–T),
                     -cytosine (C) and guanine (G)
                     always pair together (C–G).

                     In other words, A and T are
                     complementary bases, as are C
                     and G.



          Dr Siham Gritly                       47
Replication of DNA as
                   suggested by
                 Watson and Crick

Replication: process
by which DNA is
copied itself




                       Dr Siham Gritly   48
Two polynucleotide strands, running in opposite directions
(anti-parallel) and coiled around each other in a double helix.
The strands are held together by complementary hydrogen-
bonding between specific pairs of bases




                             Dr Siham Gritly                      49
REPLICTION, TRANSCRIPTION AND TRANSLATION




                 Dr Siham Gritly            50
Function of DNA
• 1-store of genetic information;
• genetic information is the source of
  information for the synthesis of all protein
  molecules. The information is copied or
  transcribed into RNA molecules
• Proteins are then synthesized in the process
  involving the translation of the RNA


                      Dr Siham Gritly            51
• 2-DNA provides the inherited information by
  the daughter cell. DNA provide template for
  the replication of information into daughter
  DNA molecule




                     Dr Siham Gritly             52
2-Ribonucleic acid RNA

• Ribonucleic acid RNA is a long unbranched
  macromolecules consisting of nucleotides
  joined by 3’ to 5’ phosphodiester bonds. It is
  the same as DNA but it possesses different
  characteristic
• RNA differ from DNA in that it is a single
  strand do not contain regions of double helical
  structure

                      Dr Siham Gritly           53
• RNA contain ribose sugar instead of 2-
  deoxyribose that present in DNA
• contain four major bases
• 1-purine bases;-Adenine and Guanine
• 2-pyrimidin bases;- Cytosine and Uracil
• RNA contain Uracil instead of thymine
• RNA pairs Adenine with Uracil and Cytosine
  with Guanine
                    Dr Siham Gritly            54
Structure of RNA
RNA molecules are single-stranded




    RNA contain Uracil instead of thymine
    RNA pairs Adenine with Uracil and
    Cytosine with Guanine
                   Dr Siham Gritly          55
Ribonucleic acid (RNA) functions

• Ribonucleic acid (RNA) functions in
  converting genetic information from genes into
  the amino acid sequences of proteins.
 RNA translates the DNA message to a format
  that can be read by ribosomes, or the cellular
  organelles that assemble proteins (process
  known as translation).
 RNA also plays a role in engage the correct
  amino acids to the protein meeting sites.

                     Dr Siham Gritly           56
types of RNA

• The three universal types of RNA include
• 1-transfer RNA (tRNA), transfer RNA serves as the
  carrier molecule for amino acids to be used in
  protein synthesis, and is responsible for decoding
  the mRNA.
• 2-messenger RNA (mRNA), messenger RNA acts
  to carry genetic sequence information between
  DNA and ribosomes, directing protein synthesis
• 3-ribosomal RNA (rRNA). ribosomal RNA is a
  major component of the ribosome, and catalyzes
  peptide bond formation.
                       Dr Siham Gritly             57
RNA & DNA structures




        Dr Siham Gritly   58
PHOSPHODIESTER BOND LINK NUCLETIDES




              Dr Siham Gritly         59
references
Murry K. Robert, Granner K. daryl, Mayes A.
  peter, Rodwell W. Victor (1999). Harpers
  Biochemistry. Appleton and Lange , twent fifth
  edition
• A. Burtis, Edward R. Ashwood, Norbert W. Tietz
  (2000), Tietz fundamentals of clinical chemistry
• Maton, Anthea; Jean Hopkins, Charles William
  McLaughlin, Susan Johnson, Maryanna Quon
  Warner, David LaHart, Jill D. Wright (1993).
  Human Biology and Health. Englewood
  Cliffs, New Jersey, USA: Prentice Hall. pp. 52–59
                      Dr Siham Gritly             60
references
• Nelson DL, Cox MM (2005). Lehninger's Principles of
  Biochemistry (4th ed.). New York, New York: W. H.
  Freeman and Company.
• Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999)
  Biochemistry. 3rd edition. Benjamin Cummings.
• Naik Pankaja (2010). Biochemistry. 3ed edition, JAYPEE
• Maitland, Jr Jones (1998). Organic Chemistry. W
  W Norton & Co Inc (Np). p. 139. ISBN 0-393-
  97378-6.

                         Dr Siham Gritly               61
Pentose sugar




    Dr Siham Gritly   62
Dr Siham Gritly   63
Dr Siham Gritly   64
Dr Siham Gritly   65

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5 nucleotides and nucleic acids lecture

  • 1. Principle of Biochemistry 5-Nucleotides and Nucleic Acids Course code: HFB324 Credit hours: 3 hours Dr Siham Gritly Dr Siham Gritly 1
  • 2. Nucleoside, Nucleotide & Nucleic acid p h o s p h a te su g a r base p h o s p h a te p h o s p h a te su g a r base su g a r base su g a r base p h o sp h a te nucleoside nucleotides sugar b a se nucleic acids Dr Siham Gritly 2
  • 3. DNA, RNA and the nucleobases Dr Siham Gritly 3
  • 4. • Deoxyribonucleotide; monomeric building block of DNA; a phosphate group and a nitrogenous base both bonded to deoxyribose • Ribonucleotide; monomeric building block of RNA; a phosphate group and a nitrogenous base both bonded to ribose sugar • Duplex; two complementary strands of DNA • Mutant; genetically altered species or cell Dr Siham Gritly 4
  • 5. • Nucleoside; nitrogenous base bonded to ribose or deoxyribose • Nucleotide; monomeric building block of RNA and DNA; a phosphate group and a nitrogenous base both bonded to ribose or deoxyribose • Nucleic Acids are Polynucleotides • Phosphodiester; two different alcohols forming ester linkages with one phosphate ion Dr Siham Gritly 5
  • 6. • Replication; DNA synthesis • Template; a section of DNA which is being replicated or transcribed; mRNA which is being translated • Transcription; synthesis of RNA from DNA • Translation; synthesis of proteins from an RNA template Dr Siham Gritly 6
  • 7. Nucleotides and Nucleic Acids • Introduction; • Nucleic acids are macromolecules present in all living cells in combination with protein with high concentration of basic amino acids to form nucleoproteins. (protamines and histones) • Nucleic acids compounds carrying information -- the genetic molecules (DNA and RNA) . Dr Siham Gritly 7
  • 8. • The nucleic acids are of two types • -1-deoxyribonucleic acid DNA • -2-ribonucleic acid RNA • DNA is present in the nuclei small amounts present in the mitochondria • RNA is present in the cell cytoplasm (90%) about 10% present in the nucleolus Dr Siham Gritly 8
  • 9. Nucleotides Nucleoside phosphates • Nucleotides are monomers of nucleic acids • The nucleotides found in cells are derivatives of the heterocyclic highly basic, compounds, purine and pyrimidine present in DNA and RNA (nitrogenous bases) Heterocyclic are ring compounds that contain both carbon atom and non-carbon atoms -- mainly nitrogen atom. Dr Siham Gritly 9
  • 10. Nucleotide Structures of purine and pyrimidine Heterocyclic ring compounds Nitrogenous Bases Single six-sided ring Double ring purines pyrimidinesC4H4N2 (six- and five-sided) C5H4N4 Dr Siham Gritly 10
  • 11. Types of nucleotide bases • There are five major bases found in cells. • The derivatives of purine are called adenine and guanine (found in both DNA & RNA) , • the derivatives of pyrimidine are called thymine, cytosine and uracil. • Dr Siham Gritly 11
  • 12. The derivatives of purine ; adenine and guanine (found in both DNA & RNA) 1-Adenine 6-aminopurine, 2-Guanine 2-amino- 6-oxypurine Dr Siham Gritly 12
  • 13. the derivatives of pyrimidine are thymine, cytosine and uracil. Cytosine- 2-oxy-4-aminopyrimidine, Uracil-n2,4- dioxypyrimidineThymine-2,4-dioxy-, 5-methyl Dr Siham Gritly 13
  • 14. • The common abbreviations used for these five bases are, A, G, T, C and U. • Cytosine & Uracil in RNA • Cytosine and thymine in DNA • The nucleotide uridine is never found in DNA • thymine is almost exclusively found in DNA. • Thymine is found in tRNAs but not rRNAs nor mRNAs Dr Siham Gritly 14
  • 15. Nucleotides mainly; Pentose sugar+ β-N-glycosidic bond+ phosphoryl group • Derivative of purines and pyrimidines are nucleotides----contain mainly cyclyized sugar Pentose linked to nitrogen hetroatom by β-N- glycosidic bond additional to phosphoryl group esterified to hydroxy group of the sugar (β-D-ribose or β-D-2-deoxyribose) Dr Siham Gritly 15
  • 16. Nucleotides mainly; 1-pentose sugar. 2-phosphate groups. 3-a nitrogeous base • 1-5–carbon sugar component • Ribose • Deoxyribose Dr Siham Gritly 16
  • 17. 5–carbon sugar component; Ribose and Deoxyribose Furanose structures Dr Siham Gritly 17
  • 18. • 2-Phosphate group Attached to the sugar's 5' carbon with a phosphodiester bond • 3-Nitrogen Base component attached to the sugar's 1'carbon. Dr Siham Gritly 18
  • 19. Functions of Nucleotides • Components of nucleic acids (which are long chains of nucleotides) • ATP (Adonosine TriPhosphate) is central to energy metabolism • GTP (Guanosine TriPhosphate) drives protein synthesis • CTP (Cytidine Triphosphate) drives lipid synthesis • UTP (Uridine Triphosphate) drives carbohydrate metabolism Dr Siham Gritly 19
  • 20. • Energy transport coenzymes (NAD+, NADP+, FAD+) • Chemical intracellular messengers (e.g., Cyclic AMP, a cyclic nucleotide that carries messages from the cell membrane to molecules within the cell, to stimulate essential reactions. regulators of cellular metabolism and reproduction ) Dr Siham Gritly 20
  • 21. Nucleosides • Nucleoside consist of purine and pyrimidine bases and a sugar β-D-ribose or β-D-2- deoxyribose linked through a covalent β-N- glycosidic bond • Therefore Nucleosides are Formed by Joining a Nitrogenous Base to a Sugar • Base is linked via a β-N-glycosidic bond Dr Siham Gritly 21
  • 22. β-N-glycosidic bond linked nitrogen-9 of the purine base or nitrogen-1 of the pyrinidine base with carbon1 of pentose sugar Dr Siham Gritly 22
  • 23. The nucleosides of A, G, C,T, U are named • Adenine ---Adenosine • Guanine ----Guanisine • Cytosine ----Cytidine • Thymine ----Thymidine • Uracil -----Uridine • Purine nucleosides end “osine” • Pyrinidine ends in “idine” • Ribose sugar produced; ribonucleoside • 2-deoxyribose sugar produced; deoxyribonucleosides Dr Siham Gritly 23
  • 24. • The nucleosides in DNA are called; deoxyadenosine, • deoxyguanosine, • deoxycytidine, and thymidine, • the nucleosides in RNA are called; • adenosine, guanosine, cytidine, and uridine. • If the base is a purine, then the N-9 (nitrogen) is bonded to the C-1' (carbon) of the sugar. • If the base is a pyrimidine, then the N-1 is bonded to the C-1' of the sugar. Dr Siham Gritly 24
  • 25. Common nucleosides Dr Siham Gritly 25
  • 26. Glycosidic Bond Configurations Dr Siham Gritly 26
  • 27. The base can exist in 2 distinct orientations about the N-glycosidic bond. These conformations are identified as, syn and anti. It is the anti conformation that predominates in naturally occurring nucleotides Syn- adenosine anti-adenosine Dr Siham Gritly 27
  • 28. Nucleotides and nucleosides that are not part of DNA or RNA the importance of free nucleotide • Some nucleotides are not part of DNA or RNA but still play important roles in a cell. • cyclic adenosine monophosphate (cAMP) is an intracellular signal: it communicates information from one part of the cell to another. • Other nucleotides are coenzymes, which are molecules that help enzymes work properly (FAD, NAD). Dr Siham Gritly 28
  • 29. Adenosine triphosphate (ATP) Adenosine triphosphate (ATP) is a common and critical energy transfer molecule. The bonds that hold three phosphate groups to adenosine store energy. They form when energy is released and transfer that energy to other places in a cell. Dr Siham Gritly 29
  • 30. Adenosine Monophosphates (AMP) Dr Siham Gritly 30
  • 31. Nucleic acid polynucletide • the nucleic acids are polymers of subunits of monomers nucleotides. • Nucleic acid; important substance that all cellular organisms use to store their genetic information. • The most common nucleic acids are deoxyribonucleic acid and ribonucleic acids Dr Siham Gritly 31
  • 32. The chemical linkage between nucleotide units in nucleic acids is a phosphodiester, which connects the 5’-hydroxyl group of one nucleotide to the 3’-hydroxyl group of the next nucleotide. • Phosphodiester bonds are essential to all life, as they make up the backbone of each helical strand of DNA. • In DNA and RNA, the phosphodiester bond is the linkage between the 3’ carbon atom of one sugar molecule and the 5’ catbon atom of another; • the sugar molecules deoxyribose in DNA • and ribose in RNA. • Hydrolysis of phosphodiester bonds can be catalyzed by the action of phosphodiesterases Dr Siham Gritly 32
  • 33. Sequences of RNA and DNA structures The chemical linkage between monomer units in nucleic acids is a phosphodiester Dr Siham Gritly 33
  • 34. phosphodiester, connects the 5’-hydroxyl group of one nucleotide to the 3’-hydroxyl group of the next nucleotide. Dr Siham Gritly 34
  • 35. Formation of phosphodiester bonds Formed by Polymerase and Ligase activities Dr Siham Gritly 35
  • 36. classes of nucleic acids 1-Deoxyribonucleic acid DNA • Deoxyribonucleic acid (DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms (with the exception of RNA viruses). • The DNA segments carrying this genetic information are called genes . • Genes (specific regions of DNA molecules) contain the hereditary information of an organism. Dr Siham Gritly 36
  • 37. • When organisms reproduce The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription. • Within cells DNA is organized into long structures called chromosomes, (packaged form of the DNA). • During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes (46). • Within the chromosomes, chromatin proteins such as histones compact and organize DNA. Dr Siham Gritly 37
  • 38. DNA structure and function • DNA structure is the well-known double helix formed by Watson-Crick base-pairing of C with G and A with T. • This is known as B-form DNA, and is the most favorable and common state of DNA; • its highly specific and stable base-pairing is the basis of reliable genetic information storage. Dr Siham Gritly 38
  • 39. Structure of DNA naturally occurring DNA molecules are double- stranded Watson-Crick model for the structure of DNA Dr Siham Gritly 39
  • 40. Tertiary Structure of DNA: Supercoils. Each cell contains about two meters of DNA. DNA is “packaged” by coiling around a core of proteins known as histones. The DNA-histone assembly is called a nucleosome. Histones are rich is lysine and arginine residues Dr Siham Gritly 40
  • 41. the Watson-Crick model • James Watson and Francis Crick proposed a model for the structure of DNA. • This model predicted that DNA would exist as a helix of two complementary antiparallel strands, wound around each other in a rightward direction and stabilized by H- bonding between bases in adjacent strands. Dr Siham Gritly 41
  • 42. • They proposed that in any given molecule of DNA,;- • the concentration of adenine (A) is equal to thymine (T) • and the concentration of cytidine (C) is equal to guanine (G). • This means that A will only base-pair with T, and C with G. According to this pattern, known as Watson-Crick base-pairing, the base-pairs composed of G and C contain three H-bonds, whereas those of A and T contain two H-bonds. This makes G-C base-pairs more stable than A-T base-pairs. Dr Siham Gritly 42
  • 43. Base pairing model Dr Siham Gritly 43
  • 44. Base pairs are stabilized by H-bonding Dr Siham Gritly 44
  • 45. the base-pairs composed of G and C contain three H- bonds, whereas those of A and T contain two H-bonds. Dr Siham Gritly 45
  • 46. Watson-Crick base-pairing of C with G and A with T Dr Siham Gritly 46
  • 47. Complementarity of strands in the DNA double helix -Adenine (A) and thymine (T) always pair together (A–T), -cytosine (C) and guanine (G) always pair together (C–G). In other words, A and T are complementary bases, as are C and G. Dr Siham Gritly 47
  • 48. Replication of DNA as suggested by Watson and Crick Replication: process by which DNA is copied itself Dr Siham Gritly 48
  • 49. Two polynucleotide strands, running in opposite directions (anti-parallel) and coiled around each other in a double helix. The strands are held together by complementary hydrogen- bonding between specific pairs of bases Dr Siham Gritly 49
  • 50. REPLICTION, TRANSCRIPTION AND TRANSLATION Dr Siham Gritly 50
  • 51. Function of DNA • 1-store of genetic information; • genetic information is the source of information for the synthesis of all protein molecules. The information is copied or transcribed into RNA molecules • Proteins are then synthesized in the process involving the translation of the RNA Dr Siham Gritly 51
  • 52. • 2-DNA provides the inherited information by the daughter cell. DNA provide template for the replication of information into daughter DNA molecule Dr Siham Gritly 52
  • 53. 2-Ribonucleic acid RNA • Ribonucleic acid RNA is a long unbranched macromolecules consisting of nucleotides joined by 3’ to 5’ phosphodiester bonds. It is the same as DNA but it possesses different characteristic • RNA differ from DNA in that it is a single strand do not contain regions of double helical structure Dr Siham Gritly 53
  • 54. • RNA contain ribose sugar instead of 2- deoxyribose that present in DNA • contain four major bases • 1-purine bases;-Adenine and Guanine • 2-pyrimidin bases;- Cytosine and Uracil • RNA contain Uracil instead of thymine • RNA pairs Adenine with Uracil and Cytosine with Guanine Dr Siham Gritly 54
  • 55. Structure of RNA RNA molecules are single-stranded RNA contain Uracil instead of thymine RNA pairs Adenine with Uracil and Cytosine with Guanine Dr Siham Gritly 55
  • 56. Ribonucleic acid (RNA) functions • Ribonucleic acid (RNA) functions in converting genetic information from genes into the amino acid sequences of proteins. RNA translates the DNA message to a format that can be read by ribosomes, or the cellular organelles that assemble proteins (process known as translation). RNA also plays a role in engage the correct amino acids to the protein meeting sites. Dr Siham Gritly 56
  • 57. types of RNA • The three universal types of RNA include • 1-transfer RNA (tRNA), transfer RNA serves as the carrier molecule for amino acids to be used in protein synthesis, and is responsible for decoding the mRNA. • 2-messenger RNA (mRNA), messenger RNA acts to carry genetic sequence information between DNA and ribosomes, directing protein synthesis • 3-ribosomal RNA (rRNA). ribosomal RNA is a major component of the ribosome, and catalyzes peptide bond formation. Dr Siham Gritly 57
  • 58. RNA & DNA structures Dr Siham Gritly 58
  • 59. PHOSPHODIESTER BOND LINK NUCLETIDES Dr Siham Gritly 59
  • 60. references Murry K. Robert, Granner K. daryl, Mayes A. peter, Rodwell W. Victor (1999). Harpers Biochemistry. Appleton and Lange , twent fifth edition • A. Burtis, Edward R. Ashwood, Norbert W. Tietz (2000), Tietz fundamentals of clinical chemistry • Maton, Anthea; Jean Hopkins, Charles William McLaughlin, Susan Johnson, Maryanna Quon Warner, David LaHart, Jill D. Wright (1993). Human Biology and Health. Englewood Cliffs, New Jersey, USA: Prentice Hall. pp. 52–59 Dr Siham Gritly 60
  • 61. references • Nelson DL, Cox MM (2005). Lehninger's Principles of Biochemistry (4th ed.). New York, New York: W. H. Freeman and Company. • Matthews, C. E.; K. E. Van Holde; K. G. Ahern (1999) Biochemistry. 3rd edition. Benjamin Cummings. • Naik Pankaja (2010). Biochemistry. 3ed edition, JAYPEE • Maitland, Jr Jones (1998). Organic Chemistry. W W Norton & Co Inc (Np). p. 139. ISBN 0-393- 97378-6. Dr Siham Gritly 61
  • 62. Pentose sugar Dr Siham Gritly 62