1. Nucleic Acids: DNA and RNA
Principles of Biochemistry (BCH 3000)
Nucleic Acids: DNA and RNA
Dr. Syahida Ahmad
Department of Biochemistry
Faculty of Biotechnology & Biomolecular Sciences
UPM

3. Introduction
Nucleic acids play main roles in the storage, transfer and expression of genetic information
2 types
Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)
DNA
Primarily found in chromosome in the cell’s nucleus, some in mitochondria and chloroplast
Repository of genetic information
RNA
3 types: ribosomal, messenger and transfer
Flow of biological information
DNA  RNA  Proteins  Cell structure and function

5. Components of Nucleotides
Nucleic acids are linear polymers built from four different monomers called nucleotides
Nucleotides has three chemical parts
Heterocyclic compound containing C, H, N and some O (Nitrogenous bases)
5-C carbohydrate (aldopentose)
One, two or three phosphate groups

7. Nitrogenous bases of DNA and RNA
Purine and pyrimidine
Purine
DNA: Adenine (A) and Guanine (G)
RNA: Adenine (A) and Guanine (G)
Pyrimidine
DNA: Thymine (T) and Cytosine (C)
RNA: Cytosine (C) and Uracil (U)

13. Aldopentoses of Nucleic Acids
Two types of aldopentoses are found in the nucleic acids
D-Ribose in RNA
2-D-deoxyribose in DNA
The difference are 2'-OH (RNA) and 2'-H (DNA)
affects secondary structure and stability
Sugars make nucleosides more water-soluble

16. Nucleosides
The linking of a nitrogenous base to an aldopentose through N-glycosidic linkages results in a nucleoside
Named bases by adding -idine to the root name of a pyrimidine or osine to the root name of a purine
Pyrimidine - Cytidine and Uridine
Purine – Adenosine and Guanosine
Synthetic nucleosides used for treatment of certain diseases
E.g. 3’-azidodeoxythymidine (AZT) and 2’,3’-dideoxyinosine (DDI) for treating AIDS patients

19. Drugs for treating AIDS

20. Nucleotides
Forms when a phosphoryl group (-PO2-3) is linked to a carbohydrate -OH group on the nucleoside
Common ester linkage is the –OH group on C-5’ of the pentoses
Adenosine 5’-monophosphate (5’-AMP) – one phosphate
Adenosine 5’-diphosphate (5’-ADP) – two phosphate
Adenosine 5’-triphosphate (5’-ATP) – three phosphate
Central to energy metabolism
Other nucleoside triphosphates
Guanosine triphosphate (GTP) – drives protein synthesis
Uridine triphosphate (UTP) – drives carbohydrates metabolism
Cytosine triphosphate (CTP) – drives lipid synthesis

24. Nucleic Acids DNA and RNA
Forms when nucleotides are linked together through their phosphate groups
5’-phosphate group of one nucleotide is linked to the 3’-OH group of the next nucleotide
3’,5’-phosphodiester bond
Sequence is always read 5' to 3'
Backbone of DNA (and RNA) consists deoxyriboses (or riboses) and phosphate groups

25. DNA
Consists of two polynucleotides strands folded into a double helix (double stranded)
Stabilized by H bonds - Base pairs arise from H bonds
Nucleotides contain a phosphate, a 2-Deoxyribose sugar, and one nitrogen base (A,T,C, or G)
The secondary structure (3D) was elucidated by Watson and Crick in 1953
Complementary base pairing
Guanine with Cytosine (G-C)
Adenine with Thymine (A-T)
Contain sugar
2-deoxyribose
Make up chromosomes in the nucleus
DNA, lacking 2'-OH is more stable than RNA
This makes sense - the genetic material must be more stable
RNA is designed to be used and then broken down

30. RNA Single stranded (a template copy) Complementary base pairing
Guanine with Cytosine (G-C)
Adenine with Uracil (A-U)
Contain sugar
Ribose
Three types of RNA
Ribosomal RNA (rRNA) - the basis of structure and function of ribosomes
Messenger RNA (mRNA) - carries the message
Transfer RNA (tRNA) - carries the amino acids

32. DNA & RNA Differences? Nucleotides strands
DNA: double stranded (double helix)
RNA: single stranded
Complementary base pairing
DNA: A-T, G-C
RNA: A-U, G-C
Sugar
DNA: 2-D-deoxyribose
RNA: D-Ribose
Classes of Nucleic Acids
DNA - one type
RNA – rRNA, mRNA and tRNA

33. Amino Acids 20 amino acids are exist in nature
Linked together in a process called protein synthesis in the cytoplasm to make polypeptides (subunits of proteins)
DNA contains the instructions for making proteins but is too large to leave the nucleus
mRNA codon table tells what 3 bases on mRNA code for each amino acid (64 combinations of 3 bases)
Methionine (AUG) on mRNA is called the start codon because it triggers the linking of amino acids
UAA, UGA,  & UAG on mRNA signal ribosomes to stop linking amino acids together

34. Genetic Code (RNA) Amino Acid 3 Letter Abbreviation Codons Alanine Ala
 GCA GCC GCG GCU
 Arginine
 Arg
 AGA AGG CGA CGC CGG CGU
 Aspartic Acid
 Asp
 GAC GAU
 Asparagine
 Asn
 AAC AAU
 Cysteine
 Cys
 UGC UGU
 Glutamic Acid
 Glu
 GAA GAG
 Glutamine
 Gln
 CAA CAG
 Glycine
 Gly
 GGA GGC GGG GGU
 Histidine
 His
 CAC CAU
 Isoleucine
 Ile
 AUA AUC AUU
 Leucine
 Leu
 UUA UUG CUA CUC CUG CUU
 Lysine
 Lys
 AAA AAG
 Methionine
 Met
 AUG
 Phenylalanine
 Phe
 UUC UUU
 Proline
 Pro
 CCA CCC CCG CCU
 Serine
 Ser
 AGC AGU UCA UCC UCG UCU
 Threonine
 Thr
 ACA ACC ACG ACU
 Tryptophan
 Trp
 UGG
 Tyrosine
 Tyr
 UAC UAU
 Valine
 Val
 GUA GUC GUG GUU
 Start
 Stop
 UAA UAG UGA