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NUCLEIC ACIDS

-consists of a base and a sugar covalently linked

9.1 LEVELS OF STRUCTURE IN NUCLEIC ACIDS

together

Primary structure

-lacks phosphate group

-order of bases in the polynucleotide sequence

-the base forms a glycosidic linkage with sugar

*base=

Secondary structure

one/two

ring

nitrogenous

base

-3 dimensional formation of the backbone

compound

Tertiary Structure

-when the sugar is B-D-ribose, the resulting compound

-supercoiling

is a ribonucleoside

2 PRINCIPAL TYPES:

-when the resulting sugar is a B-D-deoxyribose, the

a.) DNA

b.) RNA

9.2 COVALENT STRUCTURE OF POLYNUCLEOTIDES

resulting compound is a deoxyribonucleoside

-the glycosidic linkage is from the C1 carbon of the
sugar to the N1 nitrogen of pyrimidines or to the N9

Monomer
-smallest single unit of the polymer

nitrogen of purines.
*when a phosphoric acid is esterified to one of the

Nucleotides
-monomers of nucleic acids
-an individual nucleotide consists of

hydroxyl groups of the sugar portion of a nucleoside, a

nucleotide is formed
-a nucleotide is

a.) nitrogenous base

nucleoside with the suffix monophosphate added

b.) sugar

-*the 5 nucleotides are most commonly encountered in

c.) sugar
d.) phosphoric acid residue
- covalently bonded together

nature
-the polymerization of nucleotides gives rise to nucleic
acids.

Nucleic acid bases

-linkage between monomers in nucleic acids involves

1.) Pyrimidine
a. Cytosine
i. Found both in RNA and DNA
b. Thymine
i. Substituted for Uracil
c. Uracil
i. Occurs only in RNA

formation of two ester bonds by phosphoric acid.

9.3 THE STRUCTURE OF DNA

-A always have the same amount as T, G with C
-The sugar-phosphate backbone is the outer part of the
helix
- the chain runs in an anti-parallel directions, 3-5 and
5-3

2.) Purine
a. Adenine
b. Guanine
i. Both are found in DNA and RNA
Nucleoside

named for the parent

- base pairing is complementary

-A&T G&C
-The inside diameter of the sugar-phosphate backbone
of the double helix is about 11A (1.1 nm)

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-distance between points of attachment of the bases to

-single stranded DNA tends to form structures in which

the two strands of the sugar phosphate backbone is the

the bases can stack

same for the two base pairs

-hydrophobic bases interact with each other via pi-cloud

-The outside diameter of the helix is 20A, length of one

electrons

complete turn of the helix along its axis is 34A.

-each base pair is rotated 32owith respect to the

-contains 10 base pairs

preceding one

Grooves

Propeller twist

-empty spaces

-base-pairing distances are less optimal, but the base

Large major groove & smaller minor groove

stacking is more optimal

both can be sites at which drugs or

-water is eliminated from the minor groove contacts

polypeptides bind to DNA

with bases

-At physiological pH, each phosphate group of the

Sideways

backbone carries a negative charge..

-allows them to interact better with the bases above

- + charged side chains such as NA or Mg must be

and below them.

associated with DNA in order to neutralize the negative

*The DNA molecule has a length considerably greater

charges

than its diameter

Histones

*basic unit for studying DNA structure is actually a

+ charged proteins in the cell nucleus

dinucleotide with its complementary pairs

B-DNA

PROKARYOTIC

-principal form that occurs in nature

-DNA is circular and forms supercoils

A-DNA

-negative supercoil : underwound strands

-11 base pairs that are not perpendicular to the helix

- + supercoil : overwound strands

-originally found in dehydrated DNA samples

- - supercoiling introduces torsional stress that favors

*they are both right handed helices

unwinding of the right handed B-DNA double helix

Z-DNA

- + supercoiling overwinds such helix

-left handed, winds in the direction of the fingers of the

left hand

Topoisomerases

-purine and pyrimidine can also be found in the Z form

-enzymes that are involved in changing the supercoiled

-plays a role in gene expression

state of DNA

-derivative of the B form of DNA

a.) Class I

B form of DNA

-cut the phosphodiester backbone of one strand

-normal, physiological DNA form

of DNA, passs the other end through, reseal the

Base stacking

backbone
b.) Class II

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- cut both strands of DNA, pass some of the

- the string portions consists of DNA complexed to

remaining DNA helix between the cut ends, and then

some H1 histones and non-histone proteins

reseal it.

- about 30-50 base pairs

Nucleosome

DNA gyrase
-

-DNA wrapped around a histone core

Bacterial

topoisomerase

that

introduces

-octamer

supercoils into DNA

-

Tetramer

9.4 DENATURATION

Class II topoisomerase

-energy must be added to a sample of DNA to break the

Cuts both strands of DNA

hydrogen bonds and to disrupt the stacking interactions

*evidences from electron micrographs show coiled

- usually carried out by heating the DNA in solution

structures in circular DNA

-conversion of double stranded to single stranded DNA

*Ultracentrifugation can be used to detect supercoiled

Melting

DNA because it sediments more rapidly than relaxed

form.

of ultraviolet light

EUKARYOTIC
-DNA is complex
-

Can be monitored by observing the absorption

abundant

Base absorb light at 260nm wavelength region

Way to obtain single standed dna

*when DNA is replicated, it first becomes single

positively

charged

side

chains

at

stranded so that the complementary bases can be

physiological pH.

aligned

Chromatin

Hyperchromicity

-formed by electrostatic attraction between the

As the DNA is heated and the strand separate,

negatively charged phosphate groups on the DNA and

wavelength of absorption does not change but

positively charged groups on the proteins

the amount of light absorbed increases

-histones

*GC base pair- has 3 hydrogen bonds ; higher melting

- are the principal proteins

temp ; more hydrophobic ; stacks better ; affects

- H1, H2A, H2B, H3, H4

melting point

-lysine and arginine

*AT base pair- 2 hydrogen bods

-includes 2 molecules of each type of histone except H1.

Renaturation

-can

be

modified

by

acetylation,

methylation,

phosphorylation, and ubiquitinylation

Possible on slow cooling where separated

strands can recombine

Ubiquitin

9.5 Principal kinds of RNA and their structures

-degrades other proteins

Transfer RNA (tRNA)

Spacer regions

Smallest of 3 important kinds of RNA

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-

Can be found in every living cell

Single-stranded poly nucleotide chain (73-90

residues)

Order of bases in mRNA specifies the order of

amino acids in the growing protein

Sequence of 3 bases of mRNA directs the

Molecular mass of 25,000 Da

incorporation of a particular amino acid into the

Substitutes Uracil for Thymine

growing polypeptide chain in protein synthesis

A helical form ; predominant form in DNA

Cloverleaf structure; 2ndary tRNA structure

because of hydrogen bonding between bases

Directs protein synthesis while it is being

transcribed

Eukaryotic mRNA

Stems

Splicing out intervening sequences (introns)

Exons will be contiguous to each other

H bonded portions of the molecule

Loops
-

Small Nuclear RNA(snRNA)

Non H-bonded portions

-tertiary structure is necessary for tRNA to interact with

Found only in the nucleus of eukaryotic cells

- involved in the processing of initial mRNA

enzyme that covalently attaches the amino acid to the

transcription products to a mature form

2 or 3 end ; Xray diffraction

suitable for export from the nucleus to the

Ribosomal RNA (rRNA)

cytoplasm for translation

Large; only a few types exist

Micro RNA(miRNA)

Ribomes are 60-65% of total weight

Protein is 35-40%

discoveries

Analytical ultracentrifugation
-

Monitors the dissociation and reassociation of

ribosomes

-oldest evolutionary relationships between

bacteria and bacteriophages

Small interfering RNA (siRNA)

motion of the particle is characterized by

sedimentation

coefficient

expressed

in

Svedberg Units

Main players in RNA interference

Transcription
-The process by which the order of bases is passed from

S value
-

Small interfering RNAs that are most recent

DNA to RNA
increases

with

the

mol.weight

of

the

Ribosomes

sedimentating particle but is not directly

-sites for assembly of the growing polypeptide chain in

proportional

protein synthesis

*e-coli

Translation

- 70S.

-The order of bases in mRNA specifies the order of

-produces 30S light subunit ; & a 50S heavy

amino acids in the growing protein

subunit
Messenger RNA(mRNA)

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- A sequence of three bases in mRNA directs the
incorporation of a particular amino acid into the
growing protein chain