PHAROS UNIVERSITY FACULTY OF ALLIED MEDICAL SCIENCE

BIOCHEMISTRY 1 (MGBC-101)

Dr. Tarek El Sewedy

Department of Medical Laboratory Technology

Faculty of Allied Medical Sciences

Lecture19/12/2013

Nucleic Acids Structure and Function

By the end of this lecture, students will learn:

Recognize the structure of nucleosides and nucleotide.

Identify functions of nucleotides.

Recognize the structure of DNA and RNA.

Learn Polymerase chain reaction (PCR)

Identify the biological importance of DNA and RNA.

Intended Learning Outcomes

Lecture Content• Nitrogenous bases (Purines and Pyrimidines)

• Nucleosides

• Nucleotides

• Nucleic acids (DNA and RNA) Structure and

function

• Polymerase chain reaction

Nucleic Acid StructureA. Nitrogenous

Base +

Ribose Sugar =

B. Nucleosides

Nucleosides+

Phosphate =C.

Nucleotides

Nucleotide +

Nucleotide=

D. Nucleic AcidDNA & RNA

A. Nitrogenous BasesPurines and pyrimidine

• Purines and pyrimidine bases are nitrogen-containing heterocycles compounds whose rings contain both carbon and Nitrogen (hetero atoms).

• The smaller pyrimidine has the longer name and the larger purine the shorter name

• Nucleosides consist of nitrogenous base bound to a ribose (RNA) or

deoxyribose sugar (DNA) via a glycosidic bond.

B. Nucleosides

C. Nucleotidesconsists of a nucleoside (Nitrogenous base and sugar) bonded to one or more phosphate groups.

Nucleotides monophosphates

Base Nucleoside

Nucleotide

Adenine Adenosine Adenosine M.PGuanine Guanosine Guanosine

M.PCytosine Cytidine Cytidine M.PThymine Thymidine Thymidine M.P

Uracil Uridine Uridine M.P

Nucleotides Biological functions

1. Nucleotides are the monomers or building blocks of nucleic acids (DNA

and RNA).

2.Adenosine triphosphates ATP is the central cellular energy source.

3.Forming important coenzymes such as NAD+, NADP+, FAD and co A.

4. Intermediates in lipids, carbohydrates and protein biosynthetic reactions.

5.Cyclic nucleotides are 2nd messenger and regulators of many cellular metabolic

pathways.

Adenosine tri-phosphate (ATP)energy source for many reactions in living organisms.

Phosphates are well-known high-energy molecules, meaning that high levels of energy are released when the phosphate groups are removed

D. NUCLEIC ACIDS DNA & RNA

They carry genetic information within cells.

They are usually either single-stranded or double-stranded.

They are polymers of nucleotides.

They are made of three components,

1. nitrogenous bases (purines and pyrimidine)

2. 5-carbon sugars (Ribose in RNA or deoxyribose in DNA)

3. phosphate groups.

D. NUCLEIC ACIDS

Forms of Nucleic acids

TWO-STRANDED

DOUBLE HELIXSINGLE STRANDEDRNADNA

Adenine, guanine, and cytosine are found in both RNA and DNA, while thymine occurs only in DNA and uracil only in RNA.

Deoxyribose Sugar Ribose Sugar

*Difference between Ribose and Deoxyribose

THE CHEMICAL NATURE OF RNA DIFFERS FROM THAT OF DNA

(1) In RNA, the sugar moiety to which the phosphates and purine and pyrimidine bases are attached is ribose rather than the 2′-deoxyribose of DNA.

(2) The pyrimidine components of RNA differ from those of DNA. Although RNA contains the ribonucleotides of adenine, guanine, and cytosine, it does not possess thymine. Instead of thymine, RNA contains the ribonucleotide of uracil.

(3) RNA exists as a single strand, whereas DNA exists as a double-stranded.

(4) Since the RNA molecule is a single strand its guanine content does not necessarily equal its cytosine content, nor does its adenine content necessarily equal its uracil content.

Base pairing

• Base pairing between Adenosine (A) and Thymidine (T) involves the formation of two hydrogen bonds.

• Three hydrogen bonds are formed between Cytosine (C) and Guanosine (G)

Structure Characteristics of DNA* Double helix

* The bases occupy the

centeral core of helix

* Sugar –phosphate run

along external backbone.

* Complementary base

pairing (G binds C),(A binds

T)

* The length of DNA is

measured by bp and Kb.

FUNCTION of DNA-The Main Function of DNA can be summarized in:

Carrying the genetic information for all biological functions of the cell.

FUNCTION OF RNA

Messenger RNA (mRNA)

Transfer RNA (tRNA)

Ribosomal RNA (rRNA)

RNA plays essential role in Protein BiosynthesisThrough the 3 types mentioned above

DNA similarity *Although the structure of DNA is the same throughout all species of plants,

animals and microorganisms, each individual organism looks different. This is due to the DNA base pairs sequence. Not only does this order make you a human rather than a dog or a monkey, it also makes each person unique.

*Sequences of DNA differ from person to person, but every cell within the same person contains the same sequence of DNA. So, your hair, blood, skin and all of the other cells in your body are exactly the same at the molecular level.

The DNA Double Helix Can Be Reversibly Melted (Denatured)

* Inside cells During DNA replication the two strands of the DNA must be

separated from one another by enzymes called helicases that uses

chemical energy (from ATP).

* In the laboratory, DNA can be disrupted by heating DNA. The heating

disrupts the hydrogen bonds between base pairs and thereby causes the

strands to separate.

*Separated complementary strands of nucleic acids spontaneously

reassociate to form a double helix when the temperature is lowered below

T m. This renaturation process is sometimes called annealing.

*The ability to denature and reanneal DNA in the laboratory provides a

powerful tool for some molecular biology techniques such as Polymerase

chain reaction (PCR).

Polymerase Chain reaction

• PCR allows scientists to amplify and analyze bits of DNA from

trace amounts of DNA samples.

• PCR is an essential element in DNA fingerprinting and in the

sequencing of genes and entire genomes. Basically, It’s like a

technique to photocopy pieces of DNA. In a matter of a few

hours, a single DNA sequence can be amplified to millions of

copies.

* PCR Procedures

*Typically, PCR consists of a series of 20-40 repeated temperature changes, called cycles, with each cycle commonly consisting of 3 discrete temperature steps1. Denaturation.

2. Annealing.

3. Extension.

PCR Procedures*Stage one is a hot stage

called denaturation At 90◦C temperature opens up the DNA for copying.

*Stage two is a cooling or annealing that permits the DNA to attach to chemicals needed to copy it.

* Stage three is a warm temperature cycle called the extension. It encourages the growth of the DNA strand.

Requirements for PCR

* DNA template that contains the DNA region (target) to be amplified.

* Two primers that are complementary to the 3' (three prime) ends of each of the sense and anti-sense strand of the DNA target.

* Taq polymerase or another DNA polymerase with a temperature optimum at around 70 °C.

* Deoxynucleoside triphosphates dNTPs, the building blocks from which the DNA polymerases synthesizes a new DNA strand.

* Buffer solution, providing a suitable chemical environment for optimum activity and stability of the DNA polymerase.

Applications of PCR

*Medicine: Detection of mutations in genes causing tumor.

*Infectious disease: early diagnosis of viruses such as AIDS.

*Forensic: Human DNA fingerprinting.

*Research: identification of certain DNA or RNA regions.

*Study Question*Write three points about :

*i-Function of nucleotides*1-*2-*3-*Correct the incorrect word:*Nucleosides are made from a ring of nitrogen, carbon

and oxygen atoms together with a six-carbon sugar.*DNA is polymer of nucleotides and contains ribose

sugar.

1-Nucleotide consists of*a-Sugar+ Nitrogenous base+phosphate group*B- Nitrogenous base+phosphate group.*C- Sugar+ Nitrogenous base

2- DNA is polymer ofa-Nucleosideb-Nucleotidesc-Nitrogenous base

Choose:

Principles of Biochemistry, Donald J. Voet, Judith G. Voet, Charlotte W. pratt; Willey, 3rd ed.

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