Unit 5- Nucleic Acids

Nucleic Acids
 Nucleotides
 Nucleotides are the monomers of nucleic acids

 They are energy rich compounds

 They provide energy for metabolic processes

 They are a part of enzyme cofactors e.g.

NAD - nicotinamide adenine dinucleotide

FAD – flavin adenine dinucleotide

 They act as secondary chemical messengers in response to hormones

 A nucleotide consist of three portions

(a) a nitrogenous bases – purine and pyrimidine

common purine bases – adenine and guanine

common pyrimidine bases – cytosine, uracil, thymine

 Uracil

http://www.uic.edu/classes/bios/bios100/lecturesf04am/nucleotides.jpg
 Nucleotides
(b) A sugar – deoxyribose or ribose

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 Nucleotides
(c) One or more phosphate groups
 Nucleotides
 Some common nucleotides include-

ATP – adenosine triphosphate

ADP – adenosine diphosphate

AMP – adenosine monophosphate

GTP – guanosine triphosphate

UTP – uridine triphosphate

CTP – cytidine triphosphate

 Nucleotides

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 Nucleosides
 A nucleoside consists of a nitrogenous base covalently attached to a sugar(ribose or

deoxyribose) but without the phosphate group

 When a nucleoside is phosphorylated a nucleotide is formed

 In naming the nucleosides

(a) The purine NSs end in "-sine" : adenosine and guanosine

(b) The pyrimidine NSs end in "-dine" : cytidine, uridine, deoxythymidine
(NS – nitrogen sugar complex)
 Nucleic Acids
 There are two types of nucleic acids

(a) DNA – deoxyribonucleic acid

(b) RNA – ribonucleic acid

 They provide genetic information

 Both nucleic acids are found in plants and animals

 Viruses contain either RNA or DNA but not both

 Nucleic Acids - DNA
 It is found in the chromatin of the cell nucleolus and also outside the nucleus i.e. in the

mitochondria and chloroplast

 It contains genetic information in a segment called the genes

 It contains information (blue print) that is used to construct other cell components

 The DNA is made up of nucleotide monomers and the structure consists of two strands that

are entwined

 The structure is described as a double helix (proposed by Watson and Crick)

 The helix is formed through the pairing of the nitrogenous bases in the nucleotide
http://ghr.nlm.nih.gov/handbook/illustrations/dnastructure.jpg
 Nucleic Acids - DNA
 The double helix is also called the B-form DNA or B-DNA

 This form is very stable

 There also exists different variations in DNA helix structure i.e. A-DNA and Z-DNA

 Both forms are converted into the B-DNA at normal physiological conditions
 Main Differences in Variations
A-DNA B-DNA Z-DNA
Right handed helix Right handed helix Left handed helix

Helix has a hollow core Helix has a solid core Helix has a solid core – more
tightly packed
Appears when the DNA is Occurs at normal Occurs when there is very
dehydrated physiological conditions high salt concentration
 Nucleic Acids – DNA Structure
 The backbone of the DNA is comprised of a deoxyribose sugar linked by phosphodiester

bridges

 The 3' hydroxyl group of the sugar is linked to the 5' hydroxyl group of another sugar by

a phosphodiester bond

 The linking of the sugars maintains the structure of the DNA

 The strands run anti parallel to each other, i.e. one strands run in the 3' → 5' direction

and the other strand runs in the 5' → 3' direction

http://fig.cox.miami.edu/~cmallery/150/gene/16x3DNA.jpg
 Nucleic Acids – DNA Structure
 The nitrogenous bases found in DNA are adenine (A), thymine (T), cytosine (C) and

guanine (G)

 They carry the genetic information

 Adenine is paired with thymine and vice versa by 2 hydrogen bonds (double bond) A = T

 Guanine is paired with cytosine by 3 hydrogen bonds (triple bond) G C

 The GC pair is more strongly held together than the AT pair due to the triple bonds that

holds the latter pair together

 The pairing of the bases is referred to as complementary base pairing

 The two helices are complementary to each other. They are not identical

 There must exist equal amounts of complementary bases

 Nucleic Acids – DNA Structure
 The DNA helix can be bent or super coiled

 This flexibility allows DNA to be wrapped around proteins

 Allows the DNA to be compact into smaller volumes

http://upload.wikimedia.org/wikipedia/commons/thumb/e/e4/DNA_chemical_structure.svg/350px-DNA_chemical_structure.svg.png
 Nucleic Acids - RNA
 RNA is present in the cytosol of the cell and in the nucleolus

 It is formed from DNA by a process called Transcription

 The molecule consist of

(a) a phosphate group

(b) a nitrogenous base – adenine (A), uracil (U), cytosine (C) and guanine (G)

(c) sugar – ribose

 Similar to DNA, the nitrogenous bases in RNA carries the genetic information and

sugar-phosphate serves to maintain the structure of the molecule

 Nucleic Acids – RNA Structure
 The structure is single stranded and runs in the 5' → 3' direction

 However because base pairing can occur, the molecule can fold on itself in the form of a

hairpin

 During base pairing adenine pairs with uracil and guanine with cytosine

A U G C

 The hairpin formation does not require the molecule to have equal amounts of

complementary base pairs

http://www.makingthemodernworld.org.uk/learning_modules/biology/01.TU.03/illustrations/01.IL.09.gif
http://en.wikipedia.org/wiki/Image:Ciliate_telomerase_RNA.JPG
Differences Between DNA and
RNA
 DNA RNA
Found in the chromatin of the nucleus Found mainly in the cytoplasm and to a lesser
extent in the nucleolus

Sugar – 2 deoxyribose Sugar – ribose

Nitrogenous bases are A, T, C and G Nitrogenous bases are A, U, C and G

Double stranded Normally single stranded

The A/T and G/C ratio is 1 Complementary base pairs ratio not necessary

Base pairing occurs throughout the molecule Base pairing occurs at specific locations

Can replicate and transcribe Does not replicate or transcribe

 Types of RNA
 There exist three RNA forms

ribosomal RNA – rRNA

transfer RNA – tRNA

messenger RNA – mRNA

 They differ from each other by size, function and stability

 Types of RNA - rRNA
 It is the most abundant and makes up 80% of the RNA in the cells

 It is also the most stable form

 The molecule has a higher GC content than AU content

 In the cytoplasm rRNA combines with proteins to form ribosomes

http://img.sparknotes.com/figures/F/f88cd44dc6a50ffa6b94cdb9d213894e/ribosome.gif
 Types of RNA - tRNA
 It occupies 15% of the total RNA in the cell

 It is the smallest polymeric form

 It functions as a carrier of activated amino acids to a growing polypeptide chain (protein

synthesis)

 It binds to specific amino acids

 All tRNA molecules have a three fold clover leaf configuration

 Types of RNA - tRNA

 The 3' end contains the CCA

sequence. Amino acids bind to this

end via esterification

 The anticodon region base pairs to the

corresponding codon region on the

mRNA molecule

 Each tRNA molecule contains a

specific anticodon triplet

http://universe-review.ca/I11-21-tRNA1.jpg
 Types of RNA - mRNA
 Otherwise called template RNA

 Comprises 5% of RNA in the cell

 It is synthesized on the surface of the DNA template

 It carries genetic information from the nuclear DNA to the cytosol

 It is used as a template for protein synthesis

 If the mRNA carries the code for a simple protein it is called monocistronic

 If it carries the code for more than one kind of protein it is polycistronic
 Genetic Code
 The sequence of bases that encodes a functional protein is called the gene

 The relationship between the base sequence and the amino acid sequence in a particular

protein is called the genetic code

 A codon consists of 3 nitrogenous bases

http://www.mun.ca/biology/scarr/MGA2-03-28.jpg
Consequences of Altering the Nucleotide Sequence
Frameshift Mutation
Genetic Flow
 This is the flow of genetic material

form DNA to proteins

 It is described as the central dogma

 DNA Replication
 This is a duplication of genetic material

 During replication the hydrogen bonds holding the nitrogenous bases together are broken

(helicase) causing separation of the strands

 Each separated strand serves as a template for the synthesis of a new strand that is

complementary to the parent strand

 The enzyme DNA polymerase moves along each template of the open helix reading the

nucleotide in the template

 The enzyme ligase then joins the complementary nucleotide in the new strand

 DNA polymerase is only able to move in the 3' → 5' direction, therefore the enzyme

moves in the opposite direction along the two strands

 (Remember the strands run opposite to each other, i.e. one strand runs in the 3' → 5'

direction and the other in the 5' → 3' direction

 DNA Replication
 Other proteins are needed in the process -:

(a) to unwind the helix

(b) to keep the strands separated

(c) to join the segments together after into a continuous strand

 When the process is completed there would be two identical molecules of double

stranded DNA

 Each molecule will contain one strand that was obtained from the parent strand

 This form of DNA replication is described as semi conservative because half of the

DNA molecule comes from the parent

http://www.uic.edu/classes/phar/phar331/lecture4/replication2.jpg
 DNA Replication
 The DNA polymerase is a phenomenal enzyme, in that it is able to reduce the number of

mistakes made in complementary base pairing

 The enzyme contains two active sites i.e. one for polymerization and the other for proof

reading

 If a strand is being synthesized and a wrong nucleotide is selected by the first active site

then the second active site would recognize the error and remove the incorrect
nucleotide

 If the second active site does not recognize the error then this results in a permanent

change or genetic mutation

 Transcription
 This is the process by which RNA is formed from DNA

 The information stored in the DNA molecule is carried by the mRNA molecule

 During transcription the double helix of the DNA temporarily separates

 A complementary strand of mRNA assembles on one of the DNA strand (sense strand)

which acts as a template

 The process is catalyzed by RNA polymerase

 A=U G≡C

U =A C ≡ G
 Transcription
 The strand is synthesized in the 5' → 3' direction

 At the end of the process, the mRNA will contain the complementary genetic

information of the DNA

 The mRNA then leaves the DNA template where it carries the information to the

ribosomes so the synthesis of polypeptides can take place

 N.B mRNA is the only RNA synthesized by a cell

http://fig.cox.miami.edu/~cmallery/150/gene/c7.17.7b.transcription.jpg
 Translation
 Every three consecutive nucleotide on the mRNA is called a codon

 Each codon codes for a particular amino acid

 The mRNA determines the sequence of amino acids in a protein

 This occurs in a process called translation

 It is the most complex process of the cell

 The process requires numerous enzymes, ribosomes, amino acids, mRNA, tRNA and

energy (ATP and GTP)

 Translation
 One of the folds on the tRNA molecule has a specific triplet codon to which an amino acid

is attached

 The amino acid binds covalently to this region

 At least one kind of tRNA is present for each of the 20 amino acid

 Some amino acids have more than one tRNA molecules

 There is a triplet codon called an anticodon located at another folded end of the tRNA

molecule

 The anticodon is the complementary code for the amino acid attached

 E.g. tRNA with valine (GUA) attached will have an anticodon CAU

 When the amino acid is linked to the tRNA molecule, base pairing can occur between the

anticodon region of the tRNA and the mRNA molecule

 Functional Ribosome

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 Translation
 Each triplet codon on the mRNA specifies the insertion of a particular amino acid

 The tRNA carrying the appropriate amino acid can become attached to the mRNA

 Therefore the message on the mRNA is read codon by codon until the synthesis of a

polypeptide chain is completed

 Translation involves three main steps

(a) Initiation (b) Elongation (c) Termination

 Initiation
 During the initiation step, the small subunit of the ribosome binds at the start codon

(AUG) near the 5' end of the strand

 It is then joined by the large subunit of the ribosome and a special initiator tRNA

molecule (i.e. one that codes for met)

 If the message is read at the wrong nucleotide in the start sequence, then the remaining

triplets would be incorrectly read

 The wrong amino acid would be inserted producing a useless polypeptide

Initiation
e.g. correct a.a. order - Met Leu His Pro
mRNA sequence - AUG CUG CAU CCA

mRNA sequence - AUG CUG CAU CCA

Incorrect a.a. order - Ala Ala Ser
 Elongation
 A tRNA with the amino acid bonded to it then base pairs with the mRNA molecule

 This process requires energy

 The preceding amino acid (met) is then linked to the incoming amino acid by a peptide

bond

 The initiator tRNA to which methionine was attached is then released

 The ribosome then moves to the next codon where base pairing between tRNA and

mRNA molecule occurs

 Termination
 The end of the translation occurs when the ribosome reaches a stop codon (i.e. either

UAA, UAG, UGA)

 There exists no tRNA molecule with anticodons for stop codons. Hence there exists no

amino acids that codes for these codons

 Release factors recognize these codons and releases the polypeptide chain from the

ribosome…the process requires energy

 The ribosome then split into its subunit which can be reassembled later for another round

of protein synthesis

 Protein synthesis is an efficient process…i.e. many mRNA molecules can be translated at

the same time as there exist numerous ribosomes

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 Discussion
 Forensic Science
 DNA profiling
 Genetically Modified Foods
 Biotechnology