1. NUCLEIC ACIDS

2. OBJECTIVES Identify/ recognize nucleic acid
Components in nucleic acid – monosaccharide, nucleobases, phosphoric acid
Differentiate - between 2 types of nucleic acids, DNA and RNA
- between nucleotide and nucleoside
Definition – nucleotide, nucleoside, DNA and RNA

3. Nucleic Acids
Nucleic acid: a biopolymer containing three types of monomer units
a nitrogenous base (nucleobases), either purine or pyrimidine
a monosaccharide (aldopentose), either D-ribose or 2-deoxy-D-ribose
phosphoric acid/phospharyl group
Two types - RNA (Ribonucleic Acid)
- DNA (Deoxyribonucleic Acid)

4. Nucleobases Heterocylic compounds containing C, H, N, and O Nonpolar
Purine and pyrimidine
methyl
1 ring structure
(C)
(T)
(U)
2 ring structure
(A)
(G)

5. Monosaccharide/sugar
Polar
Only  anomer present in nucleic acid
2 type of aldopentoses found
- Ribose (RNA)
- 2-deoxyribose (DNA)
Deoxyribose, derivative of ribose – lacks an oxygen atom at C2

6. Nucleosides
Nucleoside: a compound that consists of D-ribose or 2-deoxy-D-ribose (monosaccharide) covalently bonded to a nucleobase by a -N-glycosidic bond
Covalent linkage forms between N9 of purines or N1 of pyrimidines to C1 (anomeric carbon of ribose or 2-deoxyribose)
Lack phosphate group
Pyrimidine Purine

7. Nucleotides
Nucleotide: a nucleoside in which a molecule of phosphoric acid/phosphoryl group is esterified with an -OH of the monosaccharide, at the 5’-OH
As constituents of cofactors,
Coenzyme A (CoA), flavin adenine dinucleotide (FAD) & nicotinamide adenine dinucleotides (NAD)
Nucleobase, aldopentose sugar and phosphoryl group
Phosphoric acid - polar

8. 5’ = attach to C5 of pentose
SUGAR?

9. NOMENCLATURE of Nucleotide
Based on the nucleoside, plus the phosphate group

10. Nucleotide Sequence
Gene: Sequence of nucleotides that encodes a polypeptide, eventually forming a functional protein
Gene: a discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (RNA in some viruses)
The nucleotide sequence is depending on the bases (nucleobases) present

11. Nucleic Acid: DNA RNA 1. Bases = ATGC 2. Aldopentose = Ribose
Biopolymer, nucleotide as monomer
DNA
RNA
1. Bases = ATGC
2. Aldopentose = Ribose
3. Phosphoryl group
1. Bases = AUGC
2. Aldopentose = Deoxyribose
3. Phosphoryl group
Nucleoside
Naming of nucleotide: if
Base adenine  Deoxyadenosine 5’ monophosphate
Naming of nucleotide: if
Base adenine Adenosine 5’monophosphate

12. Nucleic Acid - DNA and RNA
DNA stands for deoxyribonucleic acid. It is the genetic code molecule for most organisms.
RNA stands for ribonucleic acid. RNA molecules are involved in converting the genetic information in DNA into proteins. In retroviruses, RNA is the genetic material.
NUCLEIC ACIDS ARE POLYMERS OF NUCLEOTIDES

13. DNA
Polynucleotide = DNA and RNA
DNA and RNA are polymers whose monomer units are nucleotides = polynucleotides
Deoxyribonucleic acids, DNA: a biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphoryl group
the 3’-OH of one nucleotide is joined to the 5’ P of the next nucleotide by a phosphodiester bond
Hydrolysis – break bond
Condensation – form bond
3’ 5’ -phosphodiester bond

14. DNA structure Levels of structure
1° structure: the order of bases on the polynucleotide sequence; the order of bases specifies the genetic code
2° structure: the three-dimensional conformation of the polynucleotide backbone = double helix structure
3° structure: supercoiling
4° structure: interaction between DNA and proteins

15. Pg 237, Campbell and Farrel. READ!
DNA - 1° Structure
Primary Structure: the sequence of bases along the pentose-phosphodiester backbone of a DNA molecule
base sequence is read from the 5’ end to the 3’ end
System of notation single letter (A,G,C and T)
5’ – G G C A T T G C G C - 3’
Pg 237, Campbell and Farrel. READ!
On the right
3’ 5’ -phosphodiester bond

16. Segment of DNA Chain 5’-end 3’-5’ link 3’-end guanine thymine cytosine
5’ end – phosphate group is free
3’end – 3’ OH in deoxyribose is free
3’-5’
link
3’-end

17. DNA - 2° Structure
Secondary structure: the ordered arrangement of nucleic acid strands
Double helix: a type of 2° structure of DNA molecules in which two antiparallel polynucleotide strands are coiled in a right-handed manner about the same axis
The chains run antiparallel and are held together by hydrogen bonding between complementary base pairs: A=T, G=C.
DNA double helix

18. DNA structural elements
2 right-handed, helical, polynucleotide chains, coiled around a common axis to form a double helix
2 characteristic: Major groove and minor groove – binding site for drug or polypeptide
2 strands run in opposite direction
(antiparallel)-3’,5’-phosphodiester bridges run in opposite direction
1 base (purine) from single strand link to
1 base (pyrimidine) from other stand (complimentary)
Bases are perpendicular to helix axis
Polarity and non-polarity regions
Aqueous environment – polar, charged, covalent backbone deoxyribose and phosphate groups outside of the helix
Hydrophobic purine and pyrimidine bases avoid water by turning towards the inside of the structure OH P

19. T-A Base Pairing Base pairing is complementary: A=T, GC
A major factor stabilizing the double helix is base pairing by hydrogen bonding between T-A and between C-G
T-A base pair comprised of 2 hydrogen bonds
Complementary base pairing

20. G-C Base Pair G-C base pair comprised of 3 hydrogen bonds

21. Forms of DNA B-DNA considered the physiological form
a right-handed helix, inside diameter 11Å
10 base pairs per turn (34Å) of the helix
A-DNA
a right-handed helix, but thicker than B-DNA
11 base pairs per turn of the helix
has not been found in vivo
Z-DNA
a left-handed double helix
may play a role in gene expression
Z-DNA occurs in nature, usually consists of alternating purine-pyrimidine bases
Methylated cytosine found also in Z-DNA

22. Structural features of A-, B-, and Z- DNA Type A-DNA B-DNA Z-DNA
Helical senses right handed right handed left handed
Diameter (Å) ~26 ~20 ~18
Base pairs/turn
Major groove narrow/deep wide/deep Flat
Minor groove wide/shallow narrow/deep narrow/deep
Pg 294, Concepts in Biochemistry. 3/e 2006 John Wiley & Sons
20 Å

23. DNA - 3° Structure
Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling
Supercoiling- Further coiling and twisting of DNA helix.

24. DNA
DNA can forms tertiary structure by twist into complex arrangement – supercoil
Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each strand (2 polynucleotide chains) are joined by phosphodiester bonds
Can be found in microorganisms (bacteriophages, bacteria)
Circular twisted into supercoiled
DNA - 3° Structure
Supercoil - results of extra
twisting in the linear duplex form

25. DNA Circular DNA: In microorganisms (bacteriophages, bacteria)
Circular twisted into supercoiled DNA - 3° Structure
In eukaryotes, the 3° structure involves histone (protein)- Chromatin: DNA molecules wound around particles of histones in a beadlike structure

26. PROPERTIES OF SUPERCOIL
Supercoiled is less stable than the relaxed form
Compact hence it more easily stored in the cell
Play a regulatory role in DNA replication

27. DNA – threadlike structure
Bacteriophage :
DNA – threadlike structure

28. Super DNA Coiled Topology
Double helix can be considered to a 2-stranded, right handed coiled rope
Can undergo positive/negative supercoiling
Counterclockwise
clockwise

29. DNA - 4° Structure Four stranded form of DNA (quadruplex DNA)
Role in regulating and stabilizing telomeres and in regulation of gene expression
Small molecules such as porphyrins and anthraquinones present, to stabilize the structure
G-quadruplex

30. NUCLEIC ACIDS (2)

31. OBJECTIVES Denaturation of DNA Identify/ recognize RNA
Differentiate between DNA and RNA
Differentiate between mRNA, tRNA, rRNA

32. DNA
Can be disrupted by heat, acids, bases or organic solvents (double helix denatured = unwinding of the DNA double helix)
In nature, the unwinding of the DNA double helix is the important step in DNA replication
Involves the nitrogenous bases

33. Denaturation of DNA Denaturation: disruption of 2° structure
most commonly by heat denaturation (melting- the heat denaturation of DNA)
as strands separate, absorbance
at 260 nm increases
increase is called hyperchromicity-the wavelength of absorption does not change but the amount of light absorbed increases
midpoint of transition (melting) curve = Tm
the higher the % G-C, the higher the Tm
Renaturation/annealing is possible on slow cooling
Principal use in PCR
At the nitrogenous bases

34. Denaturation of DNA Double helix unwinds when DNA is denatured
Can be re-formed with slow cooling and annealing

35. The bases sequences of all types of RNA are determined by that of DNA
consist of long, unbranched chains of nucleotides joined by phosphodiester bonds between the 3’-OH of one pentose and the 5’-P of the next nucleotide
the pentose unit is -D-ribose (it is 2-deoxy-D-ribose in DNA)- the extra OH present in RNA makes this nucleotide more susceptible to hydrolysis than DNA.
the pyrimidine bases are uracil and cytosine (they are thymine and cytosine in DNA)
RNA is single stranded (DNA is double stranded)
The bases sequences of all types of RNA are determined by that of DNA

36. RNA
RNA molecules are classified according to their structure and function

37. RNA structure Levels of structure
1° structure: the order of bases on the polynucleotide sequence; complementary to the DNA template
2° structure: no specific 2° arrangements, but RNA is not completely lacking of regular structure
3° structure:interaction between DNA and proteins

38. RNA- 1° Structure Polymer of nucleotide
Involves single polynucleotide strand

39. All classes of RNA synthesized as single-stranded molecules
RNA- 2° Structure
Loop back onto themselves to fold into conformation containing several different structural elements:
1-hairpin turns
2-right-handed double helixes
3-internal loops
All classes of RNA synthesized as single-stranded molecules
5’P
3’OH

40. Hairpin turn
Loops in the single chain
Right-handed double helixes
- result of intrastrand folding
Trigger by hairpin turn
Antiparallel & stabilized in the same
direction as in DNA
Hold by H bond & stacking interaction
Internal loops
Common in RNA
Structural features that disrupt the
formation of continuous double helix regions

41. tRNA Transfer RNA, tRNA: the smallest kind of the three RNAs
Function: Involves in synthesis of polypeptide, to carry amino acid to site of protein synthesis
Transfer RNA, tRNA:
the smallest kind of the three RNAs
a single-stranded polynucleotide chain between nucleotide residues
carries an amino acid at its 3’ end
intramolecular hydrogen bonding occurs in tRNA
Cloverleaf structure

42. tRNA structure Smallest types of RNA Highly structured
All tRNAs contain between 74 and 93 nucleotides in a single chain
Structural features: hairpin turns, regions of double helix and loops (non-hydrogen bonded portions)
Carriers of specific amino acids used for protein synthesis
Reads the codon message on mRNA and incorporates amino acid into the protein being synthesized
20 amino acid – 20 tRNA

43. The 3D structure of yeast tRNA for phenylalanine
tRNA – 3o structure
To produce tertiary structure, tRNA folds into an L-shaped conformation
The 3D structure of yeast tRNA for phenylalanine

44. rRNA
Ribosomal RNA, rRNA: a ribonucleic acid found in ribosomes, the site of protein synthesis
only a few types of rRNA exist in cells
ribosomes (protein-synthesizing organelles) consist of 60 to 65% rRNA and 35 to 40% protein
in both prokaryotes and eukaryotes, ribosomes consist of two subunits, one larger than the other
analyzed by analytical ultracentrifugation
particles characterized by sedimentation coefficients, expressed in Svedberg units (S)
Sequencing of 16S RNA (small subunit of bacteria rRNA) - identification of bacteria

45. rRNA structure
Secondary & tertiary structures of rRNA display same elements as tRNAs
Secondary structure for E. coli 16S rRNA.

46. mRNA Messenger RNA, mRNA:
Structure: Linear polynucleotide strand
Messenger RNA, mRNA:
a ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteins
present in cells in relatively small amounts and very short-lived (less abundant form of RNA)
single stranded
biosynthesis is directed by information encoded on DNA
Synthesize from DNA, the nucleotide sequence in mRNA is similar with the 5’-3’ strand of DNA, with the exception of U replacing T
5’-3’ DNA sequence is the same with RNA sequence (complementary to 3’-5’DNA) sequence

47. mRNA structure 5’ – G G C A U U G C G C - 3’
Serves as a template for protein synthesis (Carries the transient message for protein synthesis from nuclear DNA to the ribosomes)
Move the information contained in DNA to the translation machinery
Each molecule carries the instruction for each gene (codes for one type of polypeptide product)
5’ – G G C A U U G C G C - 3’

48. Initiation codon
codes for the 1st amino acid in all polypeptide sequences (AUG)
N-formyl methionine in prokaryotes and methionine in eukaryotes
Termination codon
UAA, UAG & UGA
do not code for an amino acid & thus signal the end of protein synthesis
Also called stop codon or nonsense codon