04/10/2022

IV. NUCLEIC
ACIDS
J e ssebel V . G a d o t, R C h .

What are they ?

THE 3RD TYPE OF
MACROMOLECULES
THE CHEMICAL LINK
BETWEEN GENERATIONS
THE SOURCE OF GENETIC
INFORMATION IN
CHROMOSOMES

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Nucleic Acids
1. Nucleic Acid and Building Blocks
2. Types and Functions of Nucleic Acids
3. DNA and Inheritance

Definitions
Nucleic acids are polymers of nucleotides

Nucleotides are carbon ring structures containing nitrogen linked to a

5-carbon sugar (a ribose)
5-carbon sugar is either a ribose or a deoxy-ribose making the
nucleotide either a ribonucleotide or a deoxyribonucleotide

In eukaryotic cells nucleic acids are either:

Deoxyribose nucleic acids (DNA)

Ribose nucleic acids (RNA)

Messenger RNA (mRNA)

Transfer RNA (tRNA)
Ribosomal RNA (tRNA)

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1. Nucleic Acid and Building Blocks

Nucleic acids are composed of nucleotide monomers, which themselves
are built from:
 a phosphate group,
a sugar, and
a nitrogenous base

- The bases are of two types:

1. pyrimidines (single ringed) and
2. purines (double ringed).

What are they made of ?

Simple units called nucleotides, connected in long chains
Nucleotides have 3 parts:
1- 5-Carbon sugar (pentose)
2- Nitrogen containing base
(made of C, H and N)
3- A phosphate group ( P )
The P groups make the links that unite the sugars (hence a
“sugar-phosphate backbone”

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The Bases

The Ribose Sugar

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Formation of Nucleoside and

Nucleotides
Nucleosides and nucleotides are combinations of a base with a sugar.

A nucleoside is an N-glycoside formed between a base and a sugar

(usually ribose or deoxyribose).
A nucleotide is a phosphate ester of a nucleoside.
DNA nucleotides are more stable to acid hydrolysis of the
glycosidic bond, which is one reason that DNA has superseded RNA as
the main genetic storage molecule; it is less prone to mutation.

https://microbenotes.com/nucleic-acids-nucleosides-and-nucleotides/

Nucleotide Structure
Despite the complexity and diversity of life the structure of DNA is
dependent on only 4 different nucleotides

Diversity is dependent on the nucleotide sequence

All nucleotides are 2 ring structures composed of:

5-carbon sugar : b-D-ribose (RNA)
b-D-deoxyribose (DNA)

Base Purine
Pyrimidine

Phosphate group A nucleotide WITHOUT a phosphate group is a

NUCLEOSIDE

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Formation of Nucleoside and

Nucleotides

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Comparison

Nucleotide Composition

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2. Type and Functions of

Nucleic Acids
1. DNA - deoxyribonucleic acid
2. RNA - ribonucleic acid

Nucleic Acid Function

DNA
Genetic material - sequence of nucleotides encodes
different amino acids
RNA
Involved in the transcription/translation of genetic
material (DNA)

Genetic material of some

viruses

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Two types of Nucleotides

(depending on the sugar they contain)

1- Deoxyribonucleic acids (DNA)

The pentose sugar is Deoxyribose (has
just an hydrogen in the same place--- H)
Deoxy = “minus oxygen”

2- Ribonucleic acids (RNA)

The pentose sugar is Ribose (has a
hydroxyl group in the 3rd carbon---OH)

Nucleic Acids
DNA and RNA are nucleic acids, long, thread-like polymers
made up of a linear array of monomers called nucleotides

All nucleotides contain three components:

1. A nitrogen heterocyclic base
2. A pentose sugar
3. A phosphate residue

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Chemical Structure of DNA vs RNA

Ribonucleotides have a 2’-OH
Deoxyribonucleotides have a 2’-H

Pentose Sugars
There are two related pentose sugars:
- RNA contains ribose
- DNA contains deoxyribose
The sugars have their carbon atoms numbered with primes to
distinguish them from the nitrogen bases

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Nucleotide Structure - 4
Base-Sugar-PO42-
4
3 5N

2 6
O 1
N
5’
O P O C O
O 4’ 1’

3’ 2’

OH

Monophosphate

Nucleotide Function

Building blocks for DNA and RNA

Intracellular source of energy - Adenosine triphosphate
(ATP)

Second messengers - Involved in intracellular

signaling (e.g. cyclic adenosine monophosphate
[cAMP])
Intracellular signaling switches (e.g. G-proteins)

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Nucleotide Structure - 4
Phosphate Groups
Phosphate groups are what makes a nucleoside a
nucleotide
Phosphate groups are essential for nucleotide
polymerization
Basic structure:

O P O X

Nucleotide Structure - 4
Phosphate Groups
Number of phosphate groups determines nomenclature

Monophosphate O
e.g. AMP
O P O CH2
Free = inorganic
phosphate (Pi) O

Diphosphate O O
e.g. ADP
O P O P O CH2
Free = Pyro-
O O
phosphate (PPi)

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Nucleotide Structure - 4
Phosphate Groups

Triphosphate O O O
e.g. ATP
O P O P O P O CH2
No Free form exists O O
O

NUCLEIC ACIDS (DNA and RNA) Notes

DNA – Deoxyribonucleic Acid

•DNA controls all living processes including
production of new cells – cell division
•DNA carries the genetic code – stores and
transmits genetic information from one
generation to the next
•Chromosomes are made of DNA
•DNA is located in the nucleus of the cell

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Nucleotide Structure - 1
Sugars
HOCH2 OH
O
Generic Ribose
Structure Ribose
5’
HOCH2
O OH OH
4’ 1’

3’ 2’
HOCH2 OH
O

N.B. Carbons are given numberings as a

prime

Deoxyribose
OH H

Purine and Pyrimidine

Pyrimidine contains two pyridine-like nitrogens in a six-
membered aromatic ring
Purine has 4 N’s in a fused-ring structure. Three are basic like
pyridine-like and one is like that in pyrrole

BASED ON MCMURRY, ORGANIC CHEMISTRY, CHAPTER 28,

6TH EDITION, (C) 2003
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Nucleotide Structure - 2
Bases - Purines
NH2

Adenine N
N
A
N
N
N 6 H
7 5 1 N
8
9 4 2 O
3
N N N
NH
G
Guanine N N NH2
H

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Nucleotide Structure - 3
Bases - Pyrimidines
O

H3C
Thymine NH
T
N O
4
3 5 N H
2 6 NH2
1
N
N

C
Cytosine N O
H

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Nitrogen Bases
The nitrogen bases in nucleotides consist of two general types:
- purines: adenine (A) and guanine (G)
- pyrimidines: cytosine (C), thymine (T) and Uracil (U)

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Nucleotide Structure - 4
Bases - Pyrimidines
Thymine is found ONLY in DNA.
In RNA, thymine is replaced by uracil
Uracil and Thymine are structurally similar

Uracil O

4
3 5 N NH

2 6
U
1
N N O
H

Heterocycles in DNA and RNA

Adenine, guanine, cytosine and thymine are in DNA
RNA contains uracil rather than thymine

BASED ON MCMURRY, ORGANIC CHEMISTRY, CHAPTER 28,

6TH EDITION, (C) 2003
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Hydrogen Bonding Interactions

Two bases can hydrogen bond to form a base pair
For monomers, large number of base pairs is possible
In polynucleotide, only few possibilities exist
Watson-Crick base pairs predominate in double-stranded
DNA
A pairs with T
C pairs with G
Purine pairs with pyrimidine

一、the building block molecule of

nucleic acid--nucleotide

In RNA:
AMP、CMP、GMP、TMP
In DNA:
dAMP、dCMP、dGMP 、dUMP

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How DNA Works

1- DNA stores genetic information in
segments called genes
2- The DNA code is in Triplet Codons
(short sequences of 3 nucleotides each)
3- Certain codons are translated by the
cell into certain Amino
acids.
4. Thus, the sequence of nucleotides in
DNA indicate a sequence of Amino
acids in a protein.

Functions of
Nucleotides and Nucleic Acids
Nucleotide Functions:
◦ Energy for metabolism (ATP)
◦ Enzyme cofactors (NAD+)
◦ Signal transduction (cAMP)

Nucleic Acid Functions:

◦ Storage of genetic info (DNA)
◦ Transmission of genetic info (mRNA)
◦ Processing of genetic information (ribozymes)
◦ Protein synthesis (tRNA and rRNA)

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2. Type and Functions of

Nucleic Acids
1. DNA 2. RNA
RNA has several functions and is found in the nucleus, cytosol
DNA stores and mitochondria.
genetic information Messenger RNA (mRNA) carries genetic information obtained
used for the from DNA to sites that translate the information into a protein.
synthesis of
proteins including Transfer RNA (tRNA) carries activated amino acids to sites
enzymes and is where the amino acids are linked together to form polypeptides.
found in the Ribosomal RNA (rRNA) is a structural component of
nucleus and ribosomes, which serve as the sites for protein synthesis.
mitochondria.
Small nuclear RNA (snRNA) is a component of small nuclear
ribonucleoprotein particles.
These particles process heterogeneous RNA (hnRNA, the
immature form of mRNA) into mature mRNA.
In some viruses, HIV, influenza, polio, RNA functions as the
storage house of genetic information.

Types of RNA

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Messenger RNA (mRNA)

Its sequence is copied from genetic
DNA
It travels to ribsosomes, small granular
particles in the cytoplasm of a cell
where protein synthesis takes place

BASED ON MCMURRY, ORGANIC CHEMISTRY, CHAPTER 28,

6TH EDITION, (C) 2003
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Ribosomal RNA (rRNA)

Ribosomes are a complex of proteins
and rRNA
The synthesis of proteins from amino
acids and ATP occurs in the ribosome
The rRNA provides both structure and
catalysis

BASED ON MCMURRY, ORGANIC CHEMISTRY, CHAPTER 28,

6TH EDITION, (C) 2003
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Transfer RNA (tRNA)

Transports amino acids to the
ribosomes where they are joined
together to make proteins
There is a specific tRNA for each
amino acid
Recognition of the tRNA at the anti-
codon communicates which amino acid
is attached
BASED ON MCMURRY, ORGANIC CHEMISTRY, CHAPTER 28,
6TH EDITION, (C) 2003
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Transfer RNA
Transfer RNA translates the genetic code from the messenger
RNA and brings specific amino acids to the ribosome for protein
synthesis
Each amino acid is recognized by one or more specific tRNA
tRNA has a tertiary structure that is L-shaped
 - one end attaches to the amino acid and the other binds
to the mRNA by a 3-base complimentary sequence

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The Structure of tRNA

BASED ON MCMURRY, ORGANIC CHEMISTRY, CHAPTER 28,

6TH EDITION, (C) 2003
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Different Structure of Nucleic

Acids
1. Primary Structure
2. Secondary Structure

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Primary Structure
The sequence or order of the
nucleotides defines the primary
structure of DNA and RNA.
The nucleotides of the polymer
are linked by phosphodiester
bonds connecting through the
oxygen on the 5' carbon of one to
the oxygen on the 3’ carbon of
another.
The Oxygen and Nitrogen atoms
in the backbone give DNA and RNA
"polarity"

Example of RNA Primary Structure

In RNA, A, C, G, and U are linked by 3’-5’ ester bonds between
ribose and phosphate

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Primary Structure of Nucleic Acids

The primary structure of a nucleic acid is the nucleotide sequence
The nucleotides in nucleic acids are joined by phosphodiester
bonds
The 3’-OH group of the sugar in one nucleotide forms an ester bond
to the phosphate group on the 5’-carbon of the sugar of the next
nucleotide

Generalized Structure of DNA

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Example of DNA Primary Structure

In DNA, A, C, G, and T are linked by 3’-5’ ester bonds between
deoxyribose and phosphate

Discovering the structure of DNA

Erwin Chargaff – (1905-2002)

• Columbia University, NY
• Investigated the composition of DNA
• His findings by 1950 strongly
suggested the base-pairings
of A-T & G-C
• Met with Watson and Crick in
1952 and shared his findings
• “Chargaff’s rule” A = T & C = G

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Nucleic Acid Structure

The double helix
First determined by Watson & Crick in 1953

Most energy favorable conformation for double stranded DNA to

form
Shape and size is uniform for all life (i.e. DNA is identical)

Without anti-parallel base pairing this conformation could not

exist
Structure consists of “major” grooves and “minor” grooves

Major grooves are critical for binding proteins that regulate DNA
function

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The paired strands are coiled into a spiral called

A DOUBLE HELIX

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17
PO4
ThePOstrands
4

separate PO4
PO4

PO4 PO4

PO4 PO4

PO4
PO4

PO4
PO4

PO4
PO4

PO4
PO4

Secondary Structure
A purine base always pairs with a pyrimidine base or more specifically
Guanosine (G) with Cytosine (C) and Adenine (A) with Thymine (T) or
Uracil (U)

The G-C pair has three hydrogen bonds while the A-T pair has two
hydrogen bonds.

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Secondary Structure
DNA:
The secondary structure of
DNA consists of two
polynucleotide chains
wrapped around one
another to form a double
helix. The orientation of the
helix is usually right handed
with the two chains running
antiparallel to one another

Properties of a DNA
double helix

The strands of DNA are antiparallel

The strands are complimentary

There are Hydrogen bond forces

There are base stacking interactions

There are 10 base pairs per turn

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Secondary Structure: DNA Double Helix

In DNA there are two strands of nucleotides that wind together in a
double helix
 - the strands run in opposite directions
 - the bases are are arranged in step-like pairs
 - the base pairs are held together by hydrogen bonding
The pairing of the bases from the two strands is very specific
The complimentary base pairs are A-T and G-C
 - two hydrogen bonds form between A and T
 - three hydrogen bonds form between G and C
Each pair consists of a purine and a pyrimidine, so they are the same
width, keeping the two strands at equal distances from each other

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Model of DNA:
•The model was developed
by Watson and Crick in
1953.

•They received a nobel prize

in 1962 for their work.

•The model looks like a

twisted ladder – double
helix.

Complementarity
The sequence of bases on each strand are
arranged so that all of the bases. on one
strand pair with all of the bases on another
strand, i.e. the number of guanosines
always equals the number of cytosines and
the number of adenines always equals the
number of thymines.
There are two grooves, one major and one
minor, on the double helix. Proteins and
drugs interact with the functional groups
on the bases that are exposed in the
grooves .

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Complementarity
The structural forms of DNA can differ in four aspects: the
"handedness" (right or left), the length of the helix turn, the number of
base pairs per turn, and the difference in size between the major and
minor grooves. The most common structural form of DNA is the B-form

Complementarity of DNA strands

Two chains differ in sequence
(sequence is read from 5’ to 3’)
Two chains are complementary
Two chains run antiparallel

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Secondary Structure
RNA:
The secondary structure of RNA consists of a single polynucleotide.
RNA can fold so that base pairing occurs between complementary regions.
RNA molecules often contain both single- and double-stranded regions.
The strands are antiparallel and assume a helical shape.
The helices are of the A-form.
The structure of t (transfer) and r(ribosomal) RNA consists of multiple, single
stranded, stem-loop structures.
The stems consist of helices formed by bas pairing of complementary regions
within the RNA.
The secondary structure of tRNA and rRNA are important for their biological
functions, mRNA also assumes some degree of secondary structure but not to
the same extent as tRNA and rRNA.

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Secondary Structure

Secondary Structure
oSome of the bases in DNA and RNA can be chemically modified via methylation.
oEnzymes, similar to pro teases, called exo- and endo-nucleases can cleave RNA
and DNA.
oExonucleases cleave nucleic acids from the ends.
oEndonucleases recognize specific sequences of duplex DNA and cleave at a
specific site within or near the recognized sequence.
oThe sequences that are recognized range from four to eight base pairs in
length.
oThe resulting fragments can be joined to other fragments to create new
combinations of DNA sequences.

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Denaturation/Renaturation of
DNA
DNA can be denatured into single strands and renatured back into a
double helix.
Reversible denaturation is essential for the biological processes of
replication and transcription; and for molecular biological techniques
such as Southern blotting and polymerase chain reactions (PCR's).
There are three ways to denature DNA:
1. enzymatically,
2. chemically or
3. with heat.

Heat Denaturation of DNA

The denaturation of DNA via heat can be followed with a
spectrophotometer set to a wavelength of 260 nm.
Absorption increases with increasing heat breaking the hydrogen
bonds that hold the strands together, unstacking and exposing the
bases.
This effect is called the hyperchromic effect.
The temperature at which 50% of the DNA is denatured is called the
melting temperature or Tm.

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Renaturation of DNA
For renaturation to take place the two strands of DNA must contact one
another to initiate base pairing. Once this happens the two strands
quickly reassociate along their entire length.
Several things influence renaturation:
1. complexity,
2. DNA concentration,
3. cation concentration - Cations such as sodium, potassium and
magnesium decrease the intermolecular repulsion of the negatively
charged phosphate backbones of the two DNA strands.
4. temperature. Renaturation will only occur if the temperature is
below the Tm, however if the temperature is too low the rate of
renaturation will decrease.

Hybridization of DNA and RNA

Hybridization can occur between complementary strands of nucleic
acids derived from different sources.
The double stranded nucleic acid that forms is a heteroduplex and the
extent of heteroduplexes indicates homology between the two nucleic
acid sources.
For example, humans and mice mix with ,a very small fraction of the
DNA renaturing but humans and chimpanzees give greater than 98%
homology.
DNA and RNA can also hybridize with one another to form
heteroduplexes.

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DNA and RNA

The study of the replication and expression of genetic information
involves a unidirectional flow from DNA to RNA to Protein:

28.11 Nucleic Acids and

Heredity
Processes in the transfer of genetic information:
Replication: identical copies of DNA are made
Transcription: genetic messages are read and carried out of
the cell nucleus to the ribosomes, where protein synthesis
occurs.
Translation: genetic messages are decoded to make proteins.

BASED ON MCMURRY, ORGANIC CHEMISTRY, CHAPTER 28,

6TH EDITION, (C) 2003
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The central dogma of

molecular biology.

DNA and
RNA
Study of genetics will
examine these
processes in relation
to the diagram
shown

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4. DNA and Inheritance

Until the 1940s biologists argued about whether DNA or
protein was the molecule of heredity.
 Nuclei observed to divide when cells reproduced
themselves.
 Large amounts of both DNA & protein in the nucleus.
 Many though protein was most likely molecule of
heredity.
 Proteins made of 20 different amino acids- could have
more variety than DNA (made of only 4 different bases).

4. DNA and Inheritance

Pneumonia bacteria have a transforming factor.
 Pneumonia bacteria (Streptococcus pneumoniae) exist in 2 forms:
◦ o R (rough): harmless.
◦ o S (smooth): "wild type", causes disease.
◦ • The S type is coated with a polysaccharide which makes it infective and gives the
colonies a smooth appearance.
 Frederick Griffiths about 1928 studied the R & S strains by injecting them
into mice.
◦ o S injected into mice -> pneumonia -> death.
◦ o R injected into mice -> harmless.
◦ o Also, boiled S injected into mice -> harmless (bacteria killed by boiling).
◦ o The Griffiths did a strange experiment and got a strange result:
◦ • Boiled S + live R injected into mice -> pneumonia -> death.
◦ This was not expected because boiled S and live R were harmless by themselves.
◦ Took blood samples and found live S in the dead mice.
◦ Concluded that some factor, a "transforming principle“ from the dead S had converted
some R bacteria into S bacteria (a genetic change).

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4. DNA and Inheritance

4. DNA and Inheritance

The transforming factor was found to be DNA.
 Oswald A very wanted to know the nature of the transforming principle.
 Spent many years purifying transforming principle from killed S bacteria.
 Finally determined it was DNA 1944.
 First clear cut evidence for hereditary role of DNA.

Bacteriophage DNA changes the hereditary functions of bacteria.

 Bacteriophage are a type of virus that attacks bacteria.
 Consist of DNA with a protein coat.
 When virus attacks bacterium its DNA is inserted, but not its protein.
 Viruses alter genetic function of bacteria so that they make virus proteins
and DNA.
 Again DNA shown to have a genetic function.

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4. DNA and Inheritance

By the early 1950s, it was believed that the secret of heredity was in the
structure of DNA.
 Many laboratories began studying the structure of DNA, hoping to find the
secret of heredity.
 The basic composition of DNA was known.
 A sugar-phosphate backbone, with 4 nucleotide bases (A, C, G & T)

 Chargaff had measured th~ base composition in DNA from many species and
found that always A = T and C = G.
 X-ray diffraction pictures made by Rosalind Franklin showed that the DNA
structure was a helix (2 or more molecules spiraling around each other); the
structure appeared to have a uniform thickness.

Nucleic Acid Structure

“Base Pairing”
RNA [normally] exists as a single stranded polymer
DNA exists as a double stranded polymer

DNA double strand is created by hydrogen bonds between nucleotides

Nucleotides always bind to complementary nucleotides

A T (2 H-bonds)

G C (3 H-bonds)

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Practice DNA Base Pairs

ATTACA
CTAAT T

Storage of DNA

In eukaryotic cells (animals, plants, fungi) DNA is stored

in the nucleus, which is separated from the rest of the
cell by a semipermeable membrane
The DNA is only organized into chromosomes during
cell replication
Between replications, the DNA is stored in a compact
ball called chromatin, and is wrapped around proteins
called histones to form nucleosomes

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REFERENCES:
1. Gajera, H.P. (2008). Fundamentals of Bicohemistry A Textbook.
International Book Distributing
2. http://www.vanderbilt.edu › Chemistry . Chapter 28: Nucleosides,
Nucleotides, and Nucleic Acids.
3. https://microbenotes.com/nucleic-acids-nucleosides-and-nucleotides/

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