Q5 W104

NH2

N
Nucleic acids types and biological role 8
2
They are heterobiopolymers
9 N 4
N3
H
Consist of
purine
Bases
Purines
Pyrimidines
4
SUGAR
5
N3
Ribose, deoxyribose
2
6
Phosphate
N1
NUCLEOSIDES
pyrimidine
Carbohydrates +base
They have a N-glicosidic bond
Ribonucleosides or 2 deoxyribonucleosides
7

N
HO

5'

3'

HO

HO

O
NH

N
H

thymine (T)
DNA

NH
N
H

uracil (U)
RNA

NH
N

NH2

RNA: X= OH, guanosine (G)

DNA: X= H, 2'-deoxyguanosine (dG)
O

NH2
N

H3C

HO

O
NH

NH
HO

1'

4'
3'

NH2

HO

H3C

cytosine (C)
DNA/RNA

RNA: X= OH, adenosine (A)

DNA: X= H, 2'-deoxyadenosine (dA)

5'

N
H

guanine (G)
DNA/RNA
O

NH

2'

HO

HO

N
H

NH2

1'

adenine (A)
DNA/RNA

NH2

4'

N
H

2'

RNA: X= OH, cytidine (C)

HO

DNA: thymidine (T)

HO

OH

RNA: R= H, uridine (U)

DNA: X= H, 2'-deoxycytidine (dC)

Function:
Adenosine is a inhibitory neurotransmitter
Plays a role in promoting sleep and supressing arousal ith levels increasing within each hour an
organism is awake.
It reduces the chatter between nerve cells and widens the blood vessels to increase the flow of
oxygen.
Caffeine: receptors on the surface cannot tell the difference between adenosine and caffeine.
The caffeine will attach itself to the receptors and adenosine is shut out
Without adenosine to make us
sleepy the brain activity perks up
and makes you more alert.
It also constricts your blood vessels
and makes your head ache
disappear.
Nucleotides:
Phosphoric acid esters of nucleosides
Function:
Build up nucleic acids via
phosphodiester bonds.
They combine with other groups to
form coenzymes
They are used as specific signalling
molecules.
Phosphodiester bonds
Oligonucleotides and polynucleotides

The chemical linkage between the nucleotide unit in nucleic acid is a phosphodiester which
connects the 5 hydroxyl group of one nucleotide to the 3
hydroxyl group of the next nucleotide
Nucleic acid sequence is from left to right 5 to 3 end
Nucleic acids are negatively charged

DNA
Is a polymer of 2 deooxyribonucleotides
Structure
2 deoxyribose
phosphodiester bonds
5->3
4 bases
purine: adenine and guanine
pyrimidine: cytosine and thymine
RNA
Is a polymer of ribonucleotides
Structure
Ribose
Phosphodiester bonds
5->3
4 bases
Purines: adenine and guanine
Pyrimidines: cytosine and uracil
RNA is easily hydrolysed under basic conditions
The reaction leads to the production of 2,3-cyclic
monophosphate intermediate compounds. The enzyme
hydrolisis of RNA by RNA-ases goes in a similar way. As the
DNA has no 2-OH group, it is stable under basic conditions

RNA AND DNA

DNA contains Thymine and RNA contains uracil
This is because Cytosine is deaminated in nonenzimatic
way and forms Uracil. If this happens in DNA, it will be a mutation. The cells have a system for
repair that recognises the mistake and changes the Uracil with Cytosine.

Deamination of Cytosine is not fatal for RNA, its function is not to

store unchanged the genetic information.
The phosphate groups of DNA and RNA are negatively charged
The phosphodiester bond pKa is about 1, so it will be always ionised
and negatively charged under physiological conditions (pH ~7).
The Nucleic acids need complementary in charge ions such as Mg2+,
polyamines, histones and other proteins to balance the charge.
The pentoses are always in b-furanose (cyclic) form
The cyclic form accepts different conformations in which C-2 and C-3
are in exo or endo positions according to the bases and C-5.
The nucleotide bases can rotate around the ribose/deoxyribose
The bases can take both syn and anti conformations, but anti are
preferred. ---
Primary and secondary structures features of DNA

Watson and crick

Watson and crick discovered DNA structure with help of Rosalind frankline and goslings x-ray
diffractions of DNA which showed the helix turn.
H-bonds between Watson-Crick base- pairs stabilise the double helix
The base pairs explain the rule of Chargaff for the
base content of DNA: A = T; G = C
DNA Helix
Double helix has a diameter of 20nm
The base pairs take the center of the helix;
phosphate residues are on the outer surface.
B-form of DNA is right turning double helix with
antiparalel strands
The size of the DNA helix in solution is ~10.5 base
pairs per turn.
The two DNA strands are complementary and
antiparallel
The double helix is held as a result of two types of
interactions between bases
HYDROGEN BONDS
HYDROPHOBIC BONDS/ STACKING INTERACTIONS
Denaturing and renaturing DNA
The division of the two strands of DNA as a result of breaking down the weak bonds /heat or
chemical agents /is called denaturation. The restoring of the double helix is known as
renaturation.
The bonds of the double helix are broken down under high temperature
The temperature of denaturation or melting depends on the pH and the salt concntration
and is increased with the increase of the GC content of the DNA.
When the temperature is low the strands recombine.

Double stranded and single stranded DNA differ in the way they absorb light at 260 nm
Conugated p-electron systems of purine and pyrimidine bases absorb UV light (This is the
reason of UV mutagenic and carcenogenic effect)
The absorption of dsDNA) at 260 nm is smaller that that od ssDNA) or free bases. This
effect is known as hypochromic effect.
Main Structural Features of the B-DNA summary
Right turn helix
Two antiparalel stands, connected with Watson-Crick hydrogen bonds
1 turn of the helix = 34 (3.4 nm)
36o turn betwen residues
Diameter of the helix of 20 (2.0 nm)
Broad Major groove, narrow minor groove
The rule of Chargaff: A = T; G = C
Charged phosphate groups
Bases in anti configuration
The strands denature under high temperature
The structure is dynamic in solution
3 TYPES OF DNA
A,B,Z

Hoogsteen pairs can stabilise the three strand DNA structures

Protonated Cytidine can make two H-bond
with the Guanosine in the G-C couple.
Thymidine can make two H-bonds with
Adenosine in the A-T couple.
Telomeres:
Protect the DNA during replication. G
quadruplex DNA. Made of T-loops
T LOOP:
Telomeres are found at the termini of
chromosomes. The end of a telomere
inserts back into the main body of the telomere to form a T-loop

the

 Tertiary structure of DNA

- cyclic (in bacteria,Mitohondrial)
- linear (in the nucleus of the eukaryotic cells; The
number of molecules depends on the karyotype
DNA COMPACTION --
DNA is observed via karyotyping essentiaal in diagnostics
etc as well
Nucleosomes
One nucleosome is made of DNA wrapped around a
histone core doubles of H2A, H2B, H3 and H4 anf the
larger associated H1.
Its a complete dna structure with histone
REGULATION
Is via chromatin being open or closed. When its
closed it represses transcription and vice versa
DNA FUNCTION is to Carry genetic information,
GENETIC CODE:
Universal, one way, specific, can degenerate. You read
it in triplets.
genes are potions of DNA that carry coding for one
molecule or protein or 1 molecule of RNA

RNA
Contains ribonucleoties
ADENINE BONDS TO URACIL
The primary sequence- is
complimentary to a given part of
DNA

the secondary structure:

short double stranded parts non perfect binding therefore exists
Types of RNA and function in cytoplasm
1. Messenger RNA (m) codes proteins
2% of total RNA
2. Ribosomal RNA (r) builds up ribosomes and participates in protein synthesis
Ribosomal RNA makes up 82% of cell RN

 structural units involved in protein synthesis

ribozymes are RNA molecules that catalyse events in RNA processing.
Hammerhead ribozymes are small viral RNAs with two chains.
3. Transfer RNA (tRNA) transports amino acids and participates in protein synthesis
16% of total RNA
Many of the bases in tRNAs are
methylated or otherwise modified. All
tRNAs have the 3 terminal sequence
-CCA, where the amino acid is carried as
an acyl ester. The anticodon loop is at the
top left.
Types of RNA and function in nucleus
4. Small nuclear RNA (snRNA) participate
in the modification of mRNA
5. Small nucleolar RNAs (sno)
participate in the modification of rRNA, tRNAs, snRNAs
the interfering RNAs are involved as translational repressors and post translational regulators.

Methods to analyse DNA and RNA

Gel electrophoresis
Straining with etidium bromide.
You can use PCR to amplify the amount of DNA crucial in
forensic medicine etc. exponential amplification.
you can verify the PCR product on agrose or separide gel via
electrophoresis
DNA sequences can be determined when DNA polymerase and
dideoxynucleotides are used.
Sangers sequencing was discovered in 1977
Synthesis of DNA with the help of enzyme in the presence of
small quantities of dideoxynucleotides (for example, ddTTP) and high quantities of regular
deoxynuclotides ATP, GTP, CTP and TTP, using a primer and single stranded DNA which will serve
as the template. DNA polymerase synthesise the new strand in the direction 5 -3.
Dideoxynucleotides when incorporated will stop the synthesis of DNA. This will happen at random
places where the corresponding complementary base is met. In such a case every newly
synthesised fragment will finish with ddT,

 The same procedure is repeated with ddC, ddA and

ddG, as different fluorescent dyes are used to mark
the different dideoxynucleotides. All DNA fragments
are mixed and separated according to their size in
electrophoresis.
ANTIMETABOLITES
Purine and pyrimidine analogues used as anti
cancer agents
6-mercaptopurine
6-MP ribonucleotide inhibits purine nucleotide
synthesis and metabolism. This alters the
synthesis and function of RNA and DNA.
5-FU
5-fluorouracil- interferes with cells making DNA
and RNA, which stops the growth of cancer
cells
Fluorouracil is used to treat several types of
cancer including colon, rectum, and head and
neck cancers. It is also used for other types of
cancer, and the skin cream is used for other conditions as well.