Nucleotides and nucleic acids

Department of Biochemistry, KMC, DuwakotThursday,

February 4, 2016

Rajesh Chaudhary 1

Nucleotide and Nucleic acids

Thursday, February 4, 2016

2

Nucleoside

Sugar BasePhosphate

DNA RNA

Nucleotides

Nucleic acid

Nucleic acids3

Information flow

DNA RNA

PROTEIN

DNA: storage of

genetic information

RNA: expression of

genetic information

PROTEIN:

Rajesh Chaudhary

Ribose and Deoxyribose |sugar within gene


4

DNA vs RNA


5

DNA vs RNA


6

With exception of few

viruses that contain single-

stranded (ss) DNA, DNA

exists as dsDNA.

The two strands of DNA are

coiled around a common

axis forming helical

structure known as “AXIS

OF SYMMETRY”.

Rajesh Chaudhary

Nucleic acid


7

DNA contains 4

deoxynucleotides:

1. deoxyadenylate (A)

2. deoxyguanylate (G)

3. deoxycytidylate (C)

4. thymidylate (T)

Rajesh Chaudhary

Thursday, February 4, 20168 Rajesh Chaudhary

Rajesh Chaudhary

DNA chain with nucleotide sequence


9


10

Rajesh Chaudhary

Phosphodiester bond

Phosphodiester bonds in DNA or RNA

are cleaved hydrolytically by

chemicals or enzymes such as

nucleases: deoxyribonucleases for

DNA and ribonucleases for RNA.


11

Major grooves Vs Minor groovesAnticancer drug, for example, “Actinomycin D” exerts its cytotoxic effect by

intercalating into the narrow groove of DNA double helical structure.

Structure of DNA


12

Base pairing

Rajesh Chaudhary

13

1. Hydrogen bond

2. Van der Waals force

3. Hydrophobic interaction

4. 3’,5’-phosphodiester bond

What are the stabilizing forces in

DNA?


14

Rajesh Chaudhary

Chargaff’s rule

Thursday, February 4, 2016Rajesh Chaudhary

15

1. The base composition of DNA generally varies from

one species to another.

2. DNA specimens isolated from different tissues of the

same species have the same base composition.

3. The base composition of DNA in a given species does

not change with an organism’s age, nutritional state or

changing environment.

4. In all cellular DNAs, regardless of the species, the total

number of purines is equal to total no. of pyrimidine.

“In any sample of dsDNA, the amount of

Adenine equal the amount of Thymine, the

amount of Guanine equals the amount of

Cytosine, and the total amount of Purines

equals the total amount of Pyrimidines.”

Chargaff Rule


16

-- Lippincott’s Illustrated Review, Biochemistry

Rajesh Chaudhary


17

The simpler representation of

nucleotide sequence

Rajesh Chaudhary

Forms of DNA


18

Forms: A – E and Z-form

B-form: found under low

salt, high degree of

hydration

DNA exists in relaxed & supercoiled

form


19

Circular DNA

Mitochondrial & bacterial

Torsional stress of DNA

Negative supercoiling

Topoisomerase (coils or relaxes)

Rajesh Chaudhary

Melting temperature (Tm)20

Factors influencing

melting temperature:

1. The GC-content of

DNA.

2. Non-covalent cations

3. Formamide

Denaturation of DNA to analyze its

structure


21

How?

Increasing temperature (Tm)

Decreasing salt concentration

10-fold increase in monovalent cation concentration increases Tm by 16.6 0C

Denaturation Increased optical absorbance

Hyperchromicity

Addition of FORMAMIDE

Rajesh Chaudhary

Renaturation of DNA


22

Differences between DNA and RNA


23

DNA RNA

1. Sugar moiety: deoxiribose 1. Sugar moiety: Ribose

2. Usually double stranded 2. Usually single stranded

3. Bases: Adenine, Guanine, Cytosine,

Thymine

3. Bases: Adenine, Guanine, Cytosine,

Uracil

4. DNA is comparatively more stable

then RNA

4. RNA is comparitively less stable then

DNA

5. Follows Chargaff’s rule 5. Do not follow Chargaff’s rule

6. DNA is bigger in size compared to

RNA

6. RNA is comparatively smaller in size

than DNA

Rajesh Chaudhary

Chemical nature of RNA


24

Sugar moiety: ribose rather than 2’-deoxyribose of DNA

ss rather than ds

Doesn’t follow Chargaff's rule

Alkaline treatment: RNA can be hydrolyzed while DNA can’t

Rajesh Chaudhary

RNA types


26

1. Messenger RNA (mRNA) acts as a template

2. Transfer RNA (tRNA) carries AA for protein synthesis

3. Ribosomal RNA (rRNA) structural component of ribosomes

4. Small nuclear RNA (snRNA) helps in RNA processing

Rajesh Chaudhary

RNA


27

Rajesh Chaudhary

mRNA


28

Heterogeneous in abundance, size and stability

Have unique chemical characteristics


7-methylguanosine triphosphate

Cap prevents from 5’-exonuclease as

well as 3’-exonuclease digestion,

stability, recognition by protein

synthesis complex

Poly A tail residue (20-250 nucleotide long)

Rajesh Chaudhary

tRNA


30

Length = 74 – 95 nucleotides

Adaptor for the translation of information

20 species of RNA in each cell to carry 20 AA.

Rajesh Chaudhary

What is common in all tRNA?

31


• (CpCpAoH) terminal

• Added post transcriptionally

• By Nucleotidyl transferase

enzyme

Define specific RNA

Rajesh Chaudhary

tRNA

rRNA


32

Protein synthesis (RNA + Protein) = Polysomes.

MW = 4.6×106

Sedimentation velocity = 80S (60S vs 40S)

Mammalian cells = 2 mitochondria rRNA and 4

Cytoplasmic

Ribosomal RNA


33

Rajesh Chaudhary

Small stable RNA


34

Complexed with protein ribonucleoprotein

Size = 90 – 300 nucleotides

Copies = 100,000 – 1,000,000 per cell

sRNA (mRNA processing and gene regulation)

sRNA = U1, U2, U4, U5, U6 (intron removal and hnRNA to

mRNA)

Rajesh Chaudhary

References35


Nucleotides and nucleic acids

Science

Transcript of Nucleotides and nucleic acids