BISSMILLAH AHRAHMAN AR-RAHEEM.

NUCLEIC ACIDS :

Introduction:

Frederic Miesher in 1869, isolated an acidic compound from the nuclear material of SALMON sperms, and named it as NUCLIEN which is now called NUCLEIC ACID.

Jones in 1920 proved the fact there are two types of nucleic acids, i.e., Deoxy ribo nucleic acid (DNA) and Ribonucleic acid (RNA).

In 1935 J. D. Watson and F. H. C Crick, on the basis of information's available not only proposed the “Double helical” structure of DNA but also suggested what Crick termed “central dogma of molecular genetics”, which states that genetic information flows from DNA to RNA to protein.

The Double Helix (1953)

© Dr Kalju Kahn USBC Chemistry and BiochemistryPublic Domain image

Central Dogma

DNA RNA amino acids proteins

CENTRAL DOGME :

1. 1.Replication:The copying of the DNA to form identical daughter molecules.

2. 2. Transcription :The process by which the genetic message in DNA is transcribed in the form of m RNA to be carried to the ribosome

3.Translation: The process by which the message is decode by the ribosome's, where m RNA is used as a template in directing the specific amino acids sequence during protein biosynthesis.

Nucleic acids

Two types; DNA RNA The building blocks

of nucleic acids are called NUCLEOTIDES

Nucleic Acids

Chemical Composition

Elements: C, H, O, N, and P.

There are 2 types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

Nucleotide

Nucleotides: monomers of nucleic acids. All nucleic acids consist of many nucleotides

bonded together. Nucleic acids are polynucleotide. Their building blocks are nucleotides

Monomers

nucleotides, are made up of three parts:(a) Phosphate (phosphoric acid)(b) N-base (Nitrogenous base)(c) Sugar ~ ribose or deoxyribose

NUCLEOTIDE STRUCTURE

PHOSPATE SUGAR

Ribose or Deoxyribose

NUCLEOTIDE

BASEPURINES PYRIMIDINES

Adenine (A)Guanine(G)

Cytocine (C)Thymine (T)Uracil (U)

© 2007 Paul Billiet ODWS

RIBOSE DEOXYRIBOSE

CH2OH

H

OH

C

C

OH OH

C

O

H HH

C

CH2OH

H

OH

C

C

OH H

C

O

H HH

C

© 2007 Paul Billiet ODWS

BASES

Purines: adenine, guanine (double ring) Pyrimidine: thymine, cytosine (single

rings)

Purines & Pyrimidines

Adenine

CytosineGuanine

Thymine

© 2007 Paul Billiet ODWS

The bases always pair up in the same wayA purine with a pyrimidine

Adenine forms a bond with Thymine

and Cytosine bonds with Guanine

Adenine Thymine

Cytosine Guanine

DNA Structure

Sugar= Deoxyribose Specific Base Pairing

Adenine-Thymine Guanine-Cytosine

Forms a double Helix Structure

RNA structure

Sugar= Ribose Thymine gets

replaced by Uracil Single stranded

DNA RNA

Structure/shape

Double helix or α-helix

Linear, single strand

# of strands

2 1

Sugar Deoxyribose Ribose

N-bases A, T, G, C A, U, G, C

Structural (and functional) Comparison of DNA & RNA

Functions

DNA is used to store genetic information It is replicated before cell division

DNA is very important so it is stored in the nucleus.

It never leaves the nucleus Your DNA stores the code for your

proteins, which exhibit your “traits” The DNA gets converted to RNA in order

to move out into the cytoplasm

Functions

In the cytoplasm it meets up with the ribosome, where it can synthesize proteins

Stores genetic information. Maintains growth and repair.

Controls all cellular activities.

Contains protein codes.

Ensures each daughter cell & gamete receives exact genetic information.

1.GENE SEQUENCING TECHNIQUE (Gel Electrophoresis) 2. GENETICALLY ENGINEERED PRODUCTS• Insulin for diabetes • Factor IX for curing hemophilia B• -Macrophage colony-stimulating factor (GM-

CSFGRANULOCYTE) for stimulating the bone marrow after a bone marrow transplant

• Tissue plasminogen activator (TPA) for dissolving blood clots

• Angiostatin and Endostatin for trials as anti-cancer drugs.

3. HUMAN GENOME PROJECT 4. GENE THERAPY particularly AMNIOCENTESIS AND

MUCH MORE!!!

NUCLEIC ACIDS (DNA)

Nucleic Acid:

Nucleic acids are non-prorein nirogeneous bases made up of Monomeric units called nucleotides.

These are molecules through which organisms are described through their continuation.

TYPES OF NUCLEIC ACIDS: DNA RNA

DNA :

Abbreviation of deoxyribonucleic acid. It is a polymer of Deoxyribo nucleotide. This thread like structure is a combination

of large number of nucleotide units joined together.

This Polynucleotide contains genetic information that gives rise to chemical and physical properties of organisms.

Location and Isolation:

LOCATION: It can be found in chromosomes

(specifically nucleus), mitochondria and chloroplast of the cell.

It is present in every living organism because it contains genetic material.

ISOLATION: From viruses, bacteria, thymus gland,

spleen, blood, hair, skin, etc

Size of DNA:

Size shows great variation. Only 1.7µm long in simple structure of

simian virus with 5 or 6 genes. and can also extend to 2M in Human DNA.

The size of human DNA inside the chromosome is just 200 nm.

Structure of DNA:

The sub-units are called nucleotides

Each nucleotide is made up of

a pentose sugar called deoxyribose

a phosphate group -PO4 and

Nitrogenous bases

DNA is a very large molecule made up of a long chain of sub-units

Deoxyribose

Deoxyribose is almost the same as RNA but lacks one oxygen atom

Phosphate Group :

Negatively charged Phosphate group is present to whole positively charged protein molecule.

P OO

O

O

Structure of the DNA-continued

c. Nitrogenous base: There are four different bases which are divided into two groups.

i) Pyrimidines: These are single rings each with six sides. They are Cytosine and Thymine .

ii) Purines: These are double rings comprising a six-sided and a five-sided ring. They are Adenine and Guanine.

Adenine always pairs with Thymine, with the help of two hydrogen bonds and Guanine always pairs with Cytosine with the help of three hydrogen bonds. This makes the two chains

complimentary to each other.

The most common organic bases are

Adenine (A)

Thymine (T)

Cytosine (C)

Guanine (G)

The bases

The deoxyribose,

adenine

deoxyribose

PO4

the phosphate and one of the bases

Combine to form a nucleotide

Nucleotides

PO4

PO4

PO4

PO4

A molecule of DNA (polymer) is formed by millions of nucleotides joined together by phospodiester bonds into a long chain bycondensation reactions.

sugar-phosphate backbone

+ bases

Joined nucleotides

In fact, the DNA usually consists of a double strand of nucleotides

The sugar-phosphate chains are on the outsideand the strands are held together by hydrogen bondsbetween the bases

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

2-stranded DNA

The bases always pair up in the same wayA purine with a pyrimidine

Adenine forms a bond with Thymine

and Cytosine bonds with Guanine

Bonding 1

Adenine Thymine

Cytosine Guanine

PO4

PO4

PO4

thymine

PO4

PO4

PO4

PO4

adenine

cytosine

PO4

guanine

Bonding 2

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

PO4

Pairing up

The paired strands are coiled into a spiral called

A DOUBLE HELIX

sugar-phosphatechain

bases

THE DOUBLE HELIX

Types of DNA :

Two types; Circular DNA Non-Circular DNA CIRCULAR DNA : In Eukaryotes: The ends of DNA are

cohesive,so they join forming a circular DNA.eg.mitochondria,chloroplast,tec.

In Prokaryotes: mostly it is in the form of PLASMID whose replication donot depends on genomic DNA.eg.bacteria.

NON-CIRCULAR DNA: The two anti parallel strands of DNA twist

around each other to form helical structure of double helix.

FUNCTIONS OF DNA

DNA has 2 major functions:

1. Replication in dividing cells, allowing accurate copying of DNA for cell division.

2. Carrying the information for protein synthesis in all cells.

REPLICATON OF DNA:

Steps of DNA Replication

1) DNA must unwind and break the hydrogen bonds

2) Each strand is used as a template (blueprint)

3) Two new strands of DNA are formed from the original strand by the enzyme DNA Polymerase

During replication, an enzyme called helicase “unzips” the DNA molecule along the base pairing, straight down the middle.Another enzyme, called DNA polymerase, moves along the bases on each of the unzipped halves and connects complementary nucleotides.

What do we mean by complementary nucleotides?

DNA polymerase

Replication fork

Growth

Growth

New strandOriginal strand

DNA polymerase

New strandOriginal strand

Replication fork

Nitrogenous bases

Because of Chargaff’s rule, only the correct, complementary bases will fit, so chances are good that the DNA polymerase will make a perfect copy.

Mistakes happen! Mutation!

Is this frog likely to survive long in the wild?

Transcription- how RNA is madeJust as DNA polymerase makes new DNA, a similar enzyme called RNA polymerase makes new RNA.

RNA polymerase temporarily separates the strands of a small section of the DNA molecule.

This exposes some of the bases of the DNA molecule.

Along one strand, the RNA polymerase binds complementary RNA nucleotides to the exposed DNA bases.

An exposed thymine on the DNA strand hooks up with an RNA nucleotide with an adenine; an exposed cytosine on the DNA hooks up with an RNA nucleotide with a guanine base; an exposed adenine DNA base will hook up with URACIL!

As the RNA polymerase moves along, it makes a strand of messenger RNA (mRNA).

It is called messenger RNA because it carries DNA’s message out of the nucleus and into the cytoplasm.

mRNA is SINGLE STRANDED!When the RNA polymerase is done reading the gene in the DNA, it leaves.The separated DNA strands reconnect, ready to be read again when necessary. mRNA moves out of the nucleus and finds a ribosomeOn the ribosome, amino acids are assembled to form proteins in the process called translation.

Hydrogen bonds

Nucleotide

Sugar-phosphate backbone

Key

Adenine (A)

Thymine (T)

Cytosine (C)

Guanine (G)

HISTORY OF DNA :

Griffith’s Experiment

Was trying to develop a vaccination for the pneumococcus bacteria. 

Vaccine- a prepared substance from killed or weakened disease causing agents used to prevent future infections

He was working with two strains of bacteria. 

Rough - bacteria had a rough appearance in culture, non-virulent (doesn't kill)

Smooth - bacteria had a  smooth appearance in culture, virulent (kills)

Control(no growth)

Dies of pneumonia Lives Lives Dies of pneumonia

Disease-causing bacteria (smooth

colonies)

Harmless bacteria (rough

colonies

Heat-killed, disease-causing bacteria (smooth colonies)

Heat-killed, disease-causing bacteria (smooth colonies)

Harmless bacteria (rough colonies)

Live, disease-causingbacteria (smooth colonies)

DNA as hereditary materialThe Genetic Material is DNA – Alfred Hershey and Martha Chase, 1952Previously, scientists thought that proteins were the hereditary moleculeHershey and Chase worked with viruses that infect bacteria called bacteriophages

Through a series of experiments, they were able to show that DNA, not protein, is the hereditary molecule.

Martha Chase (left) & Alfred Hershey (right)

Virus Structure

DNA is locatedin the head.

The outside and tailof the virus ismade out of protein.

Virus ATTACKS!!

Bacteriophages ATTACK!!

Hershey – Chase Experiment – DNA in Viruses

Bacteriophage with phosphorus-32 in DNA

Bacteriophage with sulfur-35 in protein coat

Phage infectsbacterium

Radioactivity inside bacterium

Phage infectsbacterium No radioactivity inside

bacterium

Hershey & Chase Experiment

Concluded that the DNA of viruses is injected into the bacterial cells, while the viral proteins remain outside

The injected DNA molecules cause the bacterial cells to produce more viruses

DNA is the hereditary material – not proteins.

Wilkins and Rosalind Franklin

M.H.F. Wilkins and Rosalind Franklin, early 50’sWilkins and Franklin studied the structure of DNA crystals using X-rays.They found that the crystals contain regularly repeating subunits.The X pattern produced by DNA suggested that DNA contains structures with dimensions of 2 nm, 0.34 nm, and 3.4 nm. The dark structures at the top and bottom indicate that some structure was repeated, suggesting a helix.

Rosalind FranklinX-ray diffraction image of DNA

Watson and Crick

James Watson and Francis H.C. Crick, 1953Watson and Crick used Chargaff's base data and Franklin’s X-ray diffraction data to construct a model of DNA.The model showed that DNA is a double helix with sugar-phosphate backbones on the outside and the paired nucleotide bases on the inside, in a structure that fit the spacing estimates from the X-ray diffraction data.Chargaff's rules showed that A = T and G = C, so there was complementary base pairing of a purine with a pyrimidine, giving the correct width for the helix.The paired bases can occur in any order, giving an overwhelming diversity of sequences.

Watson & Crick with their model of DNA

Chargaff’s rules:

Base pairing rule is A-T and G-C Thymine is replaced by Uracil in RNA Bases are bonded to each other by

Hydrogen bonds Discovered because of the relative

percent of each base; (notice that A-T is similar and C-G are similar)

Erwin Chargaff

Backbone alternates with phosphate and sugar (deoxyribose)with the nucleotides formingthe rungs or steps of the ladder

The backbone of it all…

A C G G T A

TEMPLATE STRAND

T TG C C A

The backbone is made of alternating sugars and phosphates.

- Remember: Sugar ALWAYS attaches to the Nitrogen base

So Remember:

DNA Chromatin Chromosomes

Chromosome

Supercoils

Coils

Nucleosome

Histones

DNA

double

helix

FUNCTIONS OF DNA :

-Stores genetic information.-Maintains growth and repair.-Controls all cellular activities.-Contains protein codes.-Ensures each daughter cell & gamete receives exact genetic information.

RIBONUCLEIC ACID

INTRODUCTION:

Ribonucleic acid usually called as RNA, is a biologically important type of molecule that consists of a long chain of nucleotide units.

It is a single stranded chain of nucleotides that contains genetic information and it functions for the synthesis of proteins and also to transfer genetic information from one generation to the next.

HISTORY OF RNA :

Nucleic acids were discovered in 1868 by Friedrich Miescher, who called the material 'nuclein' since it was found in the Nucleus.

Nuclein was shown to have acidic properties, hence it became called nucleic acid

The role of RNA in protein synthesis was suspected already in 1939.

Severo Ochoa won the 1959 Nobel Prize in Medicine after he discovered how RNA is synthesized.

Carl Woese realized RNA can be catalytic in 1967 and proposed that the earliest forms of life relied on RNA both to carry genetic information and to catalyze biochemical reactions—an RNA world.

In 1990 it was found that introduced genes can silence homologous endogenous genes in plants, now known to be a result of RNA interference.

In same year, the discovery of gene regulatory RNAs has led to attempts to develop drugs made of RNA, like siRNA, to silence genes.

STRUCTURE OF RNA :

Found in the nucleus and cytoplasm.

Linear, single strand of nucleotides.

Contains the sugar, ribose.

N-bases include adenine, uracil, cytosine and guanine.

Backbone is of ribose sugar-phosphate.

The sub-units are called nucleotides

Each nucleotide is made up of

a pentose sugar called ribose

a phosphate group -PO4 and

a nitrogenous base

RNA is a large molecule made up of a long chain of sub-units

*RNA structure: single-strand moleculeNote: Backbone consists of alternating P-S-P-S-P- etc…

Ribose

Ribose is a sugar, like glucose, but with only five carbon atoms in its molecule

The most common organic bases are

Adenine (A)

Uracil (U)

Cytosine (C)

Guanine (G)

The bases

The deoxyribose,

adenine

ribose

PO4

the phosphateand one of the bases

Combine to form a nucleotide

Nucleotides

PO4

PO4

PO4

PO4

A molecule of RNA is formed by millions of nucleotides joined together into a long chain .

sugar-phosphate backbone

+ bases

Joined nucleotides

REPLACEMENT OF URACIL

•The base thymine is replaced by •Uracil (pyrimidine) in RNA.

•Uracil bonds with adenine.

Types of RNA :

There are three types of RNA in a cell.Ribosomal RNA (rRNA)Messenger RNA (mRNA) Transfer RNA ( tRNA)

•Their main function is to make proteins after taking instructions from the DNA.•They are temporarily present in the cell.

from to to make up

also called which functions to

also called also calledwhich functions to

can be

RNA

Messenger RNA Ribosomal RNA

Transfer RNA

mRNA Carry instructions

rRNACombine

with proteins

tRNABring

amino acids toribosome

DNA Ribosome Ribosomes

Messenger RNA :

Also known as mRNA. Messenger RNA is a single long chain of

nucleotides It is a molecule of RNA encoding a

chemical "blueprint" for a protein product. mRNA istranscribed from a DNA template,

and carries coding information to the sites of protein synthesis: the ribosomes.

WORKING OF MRNA :

 In mRNA as in DNA, genetic information is encoded in the sequence of nucleotides arranged into codons consisting of three bases each.

Each codon encodes for a specific amino acid, except the stop codons that terminate protein synthesis.

Click icon to add picture

RIBOSOMAL RNA :

It is also known as rRna.

Ribosomal RNA is the central component of the ribosome, the protein manufacturing machinery of all living cells.

Ribosomal RNA - continued

Ribosomal RNA has two units, one large and the other small.

. Large subunit

Small subunit

Ribosomal RNA

(rRNA)

The function of the rRNA is to provide a mechanism for decoding mRNA into amino acids and to interact with the tRNAs during translation.

The tRNA then brings the necessary amino acids corresponding to the appropriate mRNA codon.

Working mRNA is sandwiched between the small

and large subunits and the ribosome catalyzes the formation of a peptide bond between the 2 amino acids that are contained in the rRNA.

The ribosome also has 3 binding sites called A, P, and E.

The A site in the ribosome binds to an aminoacyl-tRNA (a tRNA bound to an amino acid).

The amino (NH2) group of the aminoacyl-tRNA, which contains the new amino acid, attacks the ester linkage of peptidyl-tRNA (contained within the P site), which contains the last amino acid of the growing chain, forming a new peptide bond.

The tRNA that was holding on the last amino acid is moved to the E site, and what used to be the aminoacyl-tRNA is now the peptidyl-tRNA.

A single mRNA can be translated simultaneously by multiple ribosomes.

TRANSFER RNA :

Transfer RNA (abbreviated tRNA) is a small RNA molecule (usually about 74-95 nucleotides) that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation.

act as adapter between nucleotides codons and amino acids. They pick up free amino acids in cytoplasm and carry them into the ribosomes where polypeptide chain is elongated.

Transfer RNA

Each tRNA carries an amino acid

As each codon of the mRNA molecule moves through the ribosome, the corresponding amino acid is brought into the ribosome by the tRNA.

Each tRNA molecule has three unpaired bases (anticodons)which are complimentary to mRNA codons

There are 20 different tRNAs, for the different aminoacids.

Differences between DNA and RNA

DNARNA

Structure: Double stranded

Sugar: DeoxyriboseBases: Adenine Guanine Cytosine Thymine

Structure: Single-stranded

Sugar: RiboseBases: Adenine Guanine Cytosine Uracil

Translation- the Ultimate Goal!

•Going from mRNA to the final product

Why are proteins needed?

Immune system Muscles move bones Cell membranes Enzymes For repair of broken cells Growth of organisms

Decoding the Information in DNA

How does DNA (a twisted latter of atoms) control everything in a cell and ultimately an organism? DNA controls the manufacture of all cellular

proteins including enzymes A gene is a region of DNA that contains the

instructions for the manufacture of on particular polypeptide chain (chain of amino acids)

DNA is a set of blueprints or code from making proteins

How do you get from DNA to Proteins?

TRANSCRIPTION – the synthesis of RNA under the direction of DNA

TRANSLATION – the actual synthesis of a protein, which occurs under the direction of mRNA

Where does this happen?

Where is the DNA?

Protein synthesis – the manufacture

of proteins

Where are proteins made

in the cell?

Translation: Protein Synthesis

mRNA combines with a ribosome and tRNA and makes a protein

Remember: mRNA carries the codon (three base sequence

that codes for an amino acid) tRNA carries the anticodon which pairs up with

the codon tRNA brings the correct amino acid by reading

the genetic code

tRNA (transfer RNA)

tRNA carries (or transfers) the correct amino acid to the codon on the mRNA.

tRNA has an ANTICODON that can attach to mRNA’s codon.

Translation

GUA UCU GUU ACC GUAmRNA

•mRNA carries the same message as DNA but rewritten with different nitrogen bases.

•This message codes for a specific sequence of amino acids

•Review..Amino acids are the building blocks of…

• PROTEINS

Translation

GUA UCU GUU ACC GUAmRNA

•Codon: a sequence of 3 nitrogen bases on mRNA that code for 1 amino acid

• It’s a TRIPLET code

•Example: This strand of mRNA has 5 codons, so it would code for 5 amino acids.

Translation

GUA UCU GUU ACC GUAmRNA

•These codons are universal for every bacteria, plant and animal on earth

•There are 64 codons which code for all 20 amino acids on earth.

Translation

GUA UCU GUU ACC GUAmRNA

•The mRNA molecule travels to the ribosomes where the mRNA codes are “read” by the ribosomes•Ribosomes hold the mRNA so another type of RNA, transfer RNA (tRNA) can attach to the mRNA

Ribosome

Translation

GUA UCU GUU ACC GUAmRNA

RibosomeC UA AG A

Translation

GUA UCU GUU ACC GUAmRNA

C UA AG A CA A

Codons match up

with anticodons to create a

protein

Protein formation

Amino acids link together to form a protein

The new protein could become cell part, an enzyme, a hormone etc.

SO:

Say the mRNA strand reads: mRNA (codon) AUG–GAC–CAG-UGA tRNA (anticodon) UAC-CUG-GUC-ACU

tRNA would bring the amino acids: Methionine-Aspartic acid-Glutamine-stop

1)mRNA is transcribed in the nucleus and leaves the nucleus to the cytoplasm

2) mRNA attaches to the ribosome3)The codon on the mRNA is read by

the anticodon on the tRNA4) tRNA brings the amino acid as it

reads mRNA5) The amino acids are joined together

to form a polypeptide (protein)6) When a stop codon is reached (UAA,

UAG, UGA) protein synthesis stops

What if things go wrong?

MUTATION!!! If transcription or translation were to

copy the wrong sequence, the incorrect amino acid could be added

This would change the overall protein structure and could make the protein ineffective

Sickle cell anemia is caused by a single amino acid difference in the hemoglobin protein sequence

Gene Mutations

Point Mutations – only occur at a single point in the DNA sequence – only changes a few amino acids

Frameshift Mutations – shift the entire “reading frame” – change ALL the amino acids

Mutations

Substitution – one base replaces another

Insertion – an extra base is inserted

Deletion – loss of a single letter (makes entire base disappear!)

Chromosomal Mutations

Change in the number or structure of chromosomes

Ex. – Deletion, Duplication, Inversion, and Translocation

Deletion

Duplication

Inversion

Translocation