1. Nucleic Acids: How Structure Conveys Information
Chapter 9

2. Levels of structure in Nucleic Acids
Primary – Order of bases in polynucleotide sequence
Secondary – Three-dimensional conformation of the backbone
Tertiary – Supercoiling of molecule
Quaternary - Interaction between DNA and proteins
Order of bases in DNA is the genetic code. It contains information necessary to produce the correct amino acid sequence in cell’s proteins

3. What are nucleotides? Monomers of Nucleic acids – Nucleotides
Consists of nitrogenous base, sugar and phosphoric acid residue
Covalently bonded
RNA (Ribonucleic Acid)
DNA (Deoxyribonucleic Acid)

4. Pyrimidine and Purine Bases

5. Other Bases Less common bases/Unusual bases
Principally but not exclusively, in transfer RNAs
Most of these bases are methylated

6. What are Nucleosides?
Nucleoside: a compound that consists of D-ribose or 2-deoxy-D-ribose covalently bonded to a nucleobase by a β-N-glycosidic bond
Lacks phosphate group
It is a compound that contains a base linked to a sugar by a covalent bond or base forms a glycosidic linkage with sugar. When the sugar is β-D-ribose the resulting compound is ribonucleoside and when the sugar is β-D- deoxyribose then the resulting compound is deoxyribonucleoside.
When phosphoric acid is esterified to one of the hydroxyl groups of the sugar portion of a nucleoside then a nucleotide is formed. Monophosphate, diphosphate or triphosphate

7. Nucleotides
A nucleoside in which a molecule of phosphoric acid is esterified with an -OH of the monosaccharide, most commonly either the 3’-OH or the 5’-OH
Polymerization leads to nucleic acids. Linkage is repeated (3’,5’-phosphodiester bond)
Name based on parent nucleoside (any base ) with a suffix “monophosphate”

8. DNA - 1° Structure
Deoxyribonucleic acids : a biopolymer that consists of a backbone of alternating units of 2-deoxy-D-ribose and phosphate
the 3’-OH of one 2-deoxy-D-ribose is joined to the 5’-OH of the next 2-deoxy-D-ribose by a phosphodiester bond

9. DNA - 1° Structure “d” used to designate “deoxy”
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
A,G,C, and T

10. Secondary structure of DNA
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 double helix model of DNA 2°structure was proposed by James Watson and Francis Crick in 1953

11. How is the base pairing of DNA complementary?
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

12. How is the base pairing of DNA complementary?
G-C base pair comprised of 3 hydrogen bonds

13. Are there other possible conformations of double helix DNA?
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

14. Are there other possible conformations of double helix DNA?
B-DNA
considered the physiological form
a right-handed helix
10 base pairs per turn (34Å) of the helix

15. Are there other possible conformations of double helix DNA?
Z-DNA
a left-handed double helix
may play a role in gene expression
Alternating purine and pyrimidine sequences

16. Z-form is derivative of B-form
Produced by flipping one side of the backbone 180˚ without disturbing the backbone covalent bonds or hydrogen bonds

17. Differences between three forms
Both A and B-DNA are right-handed helices
• Z-DNA is left handed
• Z-DNA occurs in nature, usually consists of alternating purine-pyrimidine bases
• Methylated cytosine found also in Z-DNA

18. Tertiary structure of DNA
Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling
Circular DNA: a type of double-stranded DNA in which the 5’ and 3’ ends of each stand are joined by phosphodiester bonds
Supercoiling- Further coiling and twisting of DNA helix

19. What are Topoisomerases?
Enzymes that can change supercoiled state of DNA – TopoIsomerases
Class I and Class II
DNA gyrase

20. How does prokaryotic DNA supercoil into its tertiary structure?
Class I: cut the phosphodiester backbone of one strand, pass the end through, and reseal
Class II: cut both strands, pass some of the remaining DNA helix between the cut strands, and reseal
DNA gyrase introduces negative supercoils into DNA

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

22. How does eukaryotic DNA supercoil into its tertiary structure?
Histone: a protein, particularly rich in the basic amino acids Lys and Arg; found associated with eukaryotic DNA
five main types: H1, H2A, H2B, H3, H4
Chromatin: DNA molecules wound around particles of histones in a beadlike structure
Topological changes induced by supercoiling accommodated by histone-protein component of chromatin.

23. Chromatin • Each “Bead” is a nucleosome
• Nucleosome consists of: DNA wrapped around histone core

24. Denaturation of DNA Denaturation: disruption of 2° structure
most commonly by heat denaturation (melting)
absorbance at 260 nm
Hyperchromicity
midpoint of transition (melting) curve = Tm
the higher the % G-C, the higher the Tm
renaturation is possible on slow cooling

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

26. Principal Kinds of RNA Six kinds of RNA – messenger RNA (mRNA)
transfer RNA (tRNA)
ribosomal RNA (rRNA)
small nuclear RNA (snRNA)
micro RNA (miRNA)
small interfering (siRNA)

27. Structure of RNA
RNA
nucleotides joined by phosphodiester bonds between the 3’-OH of one pentose and the 5’-OH of the next
the pentose unit is D-ribose
the pyrimidine bases are uracil and cytosine
RNA is single stranded

28. Central dogma theory

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

30. 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
Also the shape of clover leaf which is considered as secondary structure of RNA. Shows hydrogen bonding among certain bases. The hydrogen bonded portions of the molecules are called stems and non-hydrogen bonded portions are called loops. Some of the loops have modified bases. Aminoacids bind to 3’ end of tRNA

31. Ribosomal RNA- rRNA Only a few types of rRNA exist in cells
ribosomes consist of 60 to 65% rRNA and 35 to 40% protein
prokaryotes and eukaryotes - ribosomes consist of two subunits
analyzed by analytical ultracentrifugation - sedimentation coefficients - expressed in Svedberg units (S)
a ribonucleic acid found in ribosomes, the site of protein synthesis. Among the subunits in pro and eukaryotes – ribosomes consist of two subunits – one is larger than the other. particles characterized by sedimentation coefficients .

32. Messenger RNA - mRNA
A ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteins
Present in cells in small amounts (5-10 %)
Very short-lived

33. Small nuclear RNA (snRNA)
Found in nucleus of eukaryotes
Small ( nucleotides long)
Forms complexes with protein - small nuclear ribonucleoprotein particles (snRNPs)
snRNPs help with processing of initial mRNA transcribed from DNA
recently discovered RNA - in nucleus of eukaryotes

34. Small interfering RNA (siRNA)
Used in RNA interference
Eliminate expression of an undesirable gene

35. This project is funded by a grant awarded under the President’s Community Based Job Training Grant as implemented by the U.S. Department of Labor’s Employment and Training Administration (CB ). NCC is an equal opportunity employer and does not discriminate on the following basis:
 against any individual in the United States, on the basis of race, color, religion, sex, national origin, age disability, political affiliation or belief; and
 against any beneficiary of programs financially assisted under Title I of the Workforce Investment Act of 1998 (WIA), on the basis of the beneficiary’s citizenship/status as a lawfully admitted immigrant authorized to work in the United States, or his or her participation in any WIA Title I-financially assisted program or activity.

36. Disclaimer
This workforce solution was funded by a grant awarded under the President’s Community-Based Job Training Grants as implemented by the U.S. Department of Labor’s Employment and Training Administration.  The solution was created by the grantee and does not necessarily reflect the official position of the U.S. Department of Labor.  The Department of Labor makes no guarantees, warranties, or assurances of any kind, express or implied, with respect to such information, including any information on linked sites and including, but not limited to, accuracy of the information or its completeness, timeliness, usefulness, adequacy, continued availability, or ownership.  This solution is copyrighted by the institution that created it.  Internal use by an organization and/or personal use by an individual for non-commercial purposes is permissible.  All other uses require the prior authorization of the copyright owner.