Nucleic Acids: How Structure Conveys Information

Chapter 9

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

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)

Pyrimidine and Purine Bases

Other Bases

Less common bases/Unusual bases

Principally but not exclusively, in transfer RNAs

What are Nucleosides? Nucleoside: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

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)

DNA - 1° Structure

Deoxyribonucleic acids :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

DNA - 1° Structure

“d” used to designate “deoxy”

Primary 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

A,G,C, and T

Secondary structure of DNA

Double helix: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

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

How is the base pairing of DNA complementary?

G-C base pair comprised of 3 hydrogen bonds

Are there other possible conformations of double helix DNA? A-DNAA-DNA

a right-handed helix, but thicker than B-DNA

11 base pairs per turn of the helix

has not been found in vivo

Are there other possible conformations of double helix DNA?

B-DNAB-DNA considered the

physiological form

a right-handed helix

10 base pairs per turn (34Å) of the helix

Are there other possible conformations of double helix DNA? Z-DNAZ-DNA

• a left-handed double helix

• may play a role in gene expression

• Alternating purine and pyrimidine sequences

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

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

Tertiary structure of DNATertiary structure of DNA

Tertiary structure:Tertiary structure: the three-dimensional arrangement of all atoms of a nucleic acid; commonly referred to as supercoiling

Circular DNA: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

What are Topoisomerases?

Enzymes that can change supercoiled state of DNA – TopoIsomerases

Class I and Class II

DNA gyrase

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

Super DNA Coiled Topology Double helix can be considered to a 2-

stranded, right handed coiled rope Can undergo positive/negative supercoiling

How does eukaryotic DNA supercoil into its tertiary structure? Histone: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:Chromatin: DNA molecules wound around particles of histones in a beadlike structure

Topological changes induced by supercoiling accommodated

by histone-protein component of chromatin.

Chromatin

• Each “Bead” is a nucleosome

• Nucleosome consists of: DNA wrapped around histone core

Denaturation of DNA

Denaturation: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

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

annealing

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)

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

Central dogma theory

RNA molecules are classified according to their structure and function

Transfer RNA-tRNA

the smallest kind of the three RNAs

a single-stranded polynucleotide chain between 73-94 nucleotide residues

carries an amino acid at its 3’ end

intramolecular hydrogen bonding occurs in tRNA

Ribosomal RNA- rRNARibosomal 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)

Messenger RNA - mRNAMessenger RNA - mRNA

A ribonucleic acid that carries coded genetic information from DNA to ribosomes for the synthesis of proteinsPresent in cells in small amounts (5-10 %)Very short-lived

Small nuclear RNA (snRNA)

Found in nucleus of eukaryotes

Small (100-200 nucleotides long)

Forms complexes with protein - small nuclear ribonucleoprotein particles (snRNPs)

snRNPs help with processing of initial mRNA transcribed from DNA

Small interfering RNA (siRNA)

Used in RNA interference Eliminate expression of an undesirable gene

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-15-162-06-60). 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.

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.