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NUCLEIC ACIDS AND PROTEIN SYNTHESIS

NUCLEIC ACIDS Nucleic acids are biological molecules which carry all the information to form new cells hence whole organisms and therefore are involved in inheritance. They are the information molecules of the cell. Examples of nucleic acids are Deoxyribonucleic acid (DNA) and ribonucleic acids(RNAs).

Types of RNA:
1. Messenger RNA - mRNA - a single uncoiled strand that transmits information from DNA to the ribosomes during protein synthesis. 2. Transfer RNA - tRNA - a single folded strand that bonds with a specific amino acid. 3. Ribosomal RNA - rRNA - a globular form that is the major constituent of the ribosomes.
Structure Of Nucleotides Basically nucleic acids are made up of nucleotides which are the building blocks or monomers which undergo condensation polymerization to form a polynucleotide. Below is a simplified structure of a nucleotide-the building block for nucleic acids.

A nucleotide is made up of 3 molecules joined together by condensation reaction where two molecules of water are eliminated. These molecules are; i) Pentose sugar.

2 ii) iii) A Nitrogen -containing base. Phosphoric acid

The nucleotides that make up the DNA are called Deoxyribonucleotides while those that make up RNA are called Ribonucleotides. Nucleic acids are acidic because of the phosphate group (from phosphoric acid) present in nucleotides. Phosphate ions/groups are available in cytoplasm of the cells. The pentose sugar found in DNA is called Deoxyribose sugar while the one in RNA is called Ribose sugar. Deoxyribose sugar lacks an oxygen atom at carbon number 2 of the sugar. It therefore has one oxygen less in the molecule compared to Ribose sugar.

H Ribose sugar Deoxyribose sugar

Nitrogen –containing bases are of two types. These are; i)purine bases- these contain two Nitrogen -containing rings. Purine bases examples are Adenine (A) and Guanine(G). ii)Pyrimidine bases-these contain one nitrogen-containing ring. Pyrimidine bases are Thymine(T) ,Cytosine (C) and Uracil (U). Purines and pyrimidines are bases because of the basic properties of the nitrogen present in their rings.

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Polynucleotide strand formation Nucleotides get linked together through condensation reaction to form polynucleotide strands (Nucleic acids).The hydroxyl part of the sugar of one nucleotide bonds to the phosphate of the next nucleotide. This results to a polynuleotide strand which has a hydroxyl group at one end and a phosphate group on the other end. The polynucleotide is therefore made up of a sugarphosphate backbone with bases projecting from the back bone (spine). In RNA, A,U, C and G bases undergo condensation reaction to form polynucleotide (RNA) which may remain as long thread-like molecules or may be folded into complex shapes. Condensation is catalyzed by RNA polymerase enzymes. In DNA A,T,C and G bases undergo condensation reaction to form polynucleotide (DNA) strand Condensation is catalyzed by DNA polymerase enzymes.

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Double Helix structure of DNA

DNA is a massive molecule made up of two antiparallel polynucleotide strands (DNA Strands).One strand is 5’ while the other is 3’ strand. This means that one strand runs in 5’3’ direction while th other 3’5’ direction , hence antiparallel. 5’ means phosphate group is attached to the carbon number 5 0f sugar in the first nucleotide of the chain. 3’ means the phosphate is attached to the carbon number 3 of sugar in the first nucleotide of the chain. The two antiparallel strands are held in place by hydrogen bonds formed between complementary base pairs according to base pairing rule Bases will be complementary only if they can form hydrogen bond between them. The base pairing rule states that a purine from one strand pair through Hydrogen bond formation with a pyrimidine from the other strand. A pairs with T while C pairs with G. Since the DNA is a very large molecule containing millions of nucleotides/bases, it twists on itself every 10 base pairs. This forms a massive double helix structure

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5 that resembles a spiral stair case or a twisted ladder where the steps are hydrogen bonds between complementary base pairs. THEREFORE ,the hydrogen bonds between complementary base pairs occurring between the two strands determine/contribute to the double helical structure of DNA. DNA REPLICATION DNA is the only molecule which has the ability to replicate i.e. to make copies of itself, exactly . This feature is very important because it allows the DNA pass on genetic information from one cell to another or generation to another. The mechanism involved in DNA replication is semi- conservative replication where each of the antiparallel DNA strands act as templates which result to daughter DNA strands having one parent DNA strand retained . Semi-Conservative Replication Of DNA The following steps are followed during semi-consevative replication of DNA ; i)DNA double helix unwinds and the two antiparallel strands unzip as hydrogen bonds get Brocken by DNA helicase enzymes. ii) Each of the DNA strand act as template. iii)The exposed bases attract free complementary DNA nucleotides resulting to formation of hydrogen bonds between complementary bases. iv)DNA ligases and DNA polymerases join the DNA nucleotides together to form new DNA strands. NB:DNA adds new nucleotides in the 5’ 3’ direction.

v)Two daughter DNAs are formed identical to the parent DNA( original piece).The new DNA molecules automatically coils up to form the double helix due to the hydrogen bonds between the two complementary strands.

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MATHEW MESELSOHN AND FRANKLIN STAHL CLASSIC EXPERIMENT Meselsohn and Stahl carried out their classic experiment to prove their semi conservative theory of DNA replication in 1958.

Three theories/ Hypothesis that existed were: 1. The parent DNA molecule breaks into segments and new nucleotides fill in the gaps precisely (fragmentation theory). 2. The complete parent DNA molecule acts as a template for the new daughter molecule, which is assembled from new nucleotides. The parent molecule is unchanged (conservative hypothesis).

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3. The parent DNA molecule separates into its two component strands, each of which acts as a template for the formation of a new complementary strand. The two daughter molecules therefore contain half the parent DNA and half new DNA (semi-conservative hypothesis).

Procedure/method: In their experiment they grew the bacterium E.coli in the presence ofAmmoniumchloride containing radioactive 15N(heavy nitrogen) until a culture was obtained in which all the DNA was labelled with 15N. The assumptions was that Nitrogen used will become part of DNA. A subculture of this labelled bacterium was then transferred for growth in the presence of normal 14N(light nitrogen). The generation time of E.coli is known, so it was possible to take samples of this growing subculture after exactly one, two, three generations and so on.

Each sample had its DNA extracted and the isolated DNA was then centrifuged in a caesium chloride solution (high viscosity) at 40,000G for 20 hours, causing the DNA to sediment out. The heavier the DNA, the further it moved down the centrifuge tubes. 15N DNA is heavier than 14 N DNA. Mixed 14N and 15N DNA is intermediate in mass between the two. The original 15N DNA moved to the lowest position in the tube. After one generation all the DNA moved to an intermediate position, indicating the presence of only mixed 14N and 15N DNA. This was because the DNA in this generation contained one strand of the parent molecule and one new 14N strand. Had the conservative hypothesis been true, two DNA masses would have been visible, one heavy and the other light. In the second generation half the DNA was intermediate and half was light, for the same reason.

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THE GENETIC CODE A gene is a part of DNA which has nucleotide/base sequence which code for a polypeptide chain. The DNA make a chromosome through coiling around proteins especially histones. THE GENETIC CODE IS; A Triplet Code This means it is made up of 3 bases. The set of these 3 bases either in DNA or RNA is called a codon. . The `dictionary ‘of genetic code is more often shown for RNA than for DNA

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9 codons, because RNA codons are the one directly involved in with amino acids during protein synthesis. During protein synthesis some codons code for beginning or ending of a particular amino acid sequence or for a particular amino acid in the polypeptide chain. A non-overlapping code Genetic code is non-over lapping. This means that the codons follow each other like beads on a necklace and are read one codon at a time i.e. 3 bases at a time. E.g. the base sequence UUUAGC has 2 non-overwrapping codons i.e. UUU which code for phenylalanine and AGC which code for serine. If DNA is overwrapping, then the base sequence UUUAGC can give the following codons; UUU, UUA, UAG and AGC. This could allow only a small DNA to be made( economical) but a disaster if a point mutation occurs because 2 amino acids will be affected. Amino acids to be coded for side by side will be very limited. A Degenerate Code/ Redundant Code This means that DNA has more information than it requires. For example in a codon/ triplet code it is the first 2 nucleotides/bases that matter which amino acid is being coded for in all amino acids e.g. serine (UCA, UCC, UCGand UCU except methionine (AUG) and tryptophan (UGG). This feature is important because any mutation occurring to the last base/nucleotide has no effect because only the first 2 nucleotides/bases matter.

PROTEIN SYNTHESIS

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10 Protein synthesis involve the following 2 main steps; i)DNA Transcription ii)DNA code translation DNA TRANSCRIPTION .

Transcription is the transfer of information from DNA into an RNA molecule. To transcribe is to copy.

Transcription process Since DNA is a very large molecule which can’t leave the nucleus and not all the DNA is used to make required protein, then a small molecule (messenger RNA-mRNA) must be formed to carry the exact DNA information/message for protein synthesis in ribosomes in the cell cytoplasm. i)The gene (part of DNA) needed for particular protein synthesis unwinds/unravels as DNAdirected RNA polymerase also called RNA polymerase break down the hydrogen bonds between complementary base pairs.. ii) The 5’ prime DNA strand (antisense /coding strand ) is used as template strand where it provides the template for ordering the sequences of nucleotides/bases in an RNA transcript. iii)Free RNA nucleotides are attracted to the exposed DNA nucleotides on 5’3’ strand according to base pairing rule i.e. A pairs with U (uracil), C with G .

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11 iv)The 5’3’ strand is read by RNA polymerase in the 3’͢ 5’ direction and therefore The new RNA is synthesized/ polymerised in the 5’͢ 3’ direction forming 3’5’ strand which is similar to DNA sense/non-coding strand( it makes sense as it is the one directly involved in protein synthesis in ribosomes). v)The 3’5’ prime MRNA is called pre-mRNA and must undergo the following post-transcriptional changes; a) Removal of introns (sections of mRNA i.e. DNA which don’t code for proteins) to be left with exons (protein coding regions).. b)RNA Splicing where exons are joined to form single RNA molecule by enzyme complexes called spliceosomes. Exons can be joined in different ways .Some exons may be removed as well .This results to an RNA code different from original DNA code . c)Capping the ends of mRNA so that it is not attacked by enzymes. NB: post transcription changes results to formation of an enormous varieties of proteins more than genes available !

start codon

ribosome

mRNA

tRNA Transfer RNA

Translation process

It is made up of RNA coiled to form a clover leaf shape through hydrogen bonds between complementary base pairs .It has a unit of 3 bases (anticodon) at one end of molecule and a site for attachment of amino

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12 acid. It’s function is to pick amino acids from cytoplasm and arrange them on ribosome surfaces during protein synthesis.

Ribosome structure Ribosomes are made up of ribosomal RNA and proteins .r RNA is synthesized in nucleus under the control of nucleoli.It moves to cytoplasm and combine with proteins to form ribosomes. Ribosomes have one larger and one smaller sub unit. The function of ribosomes is to hold together mRNA, tRNA and the enzymes controlling the process of protein synthesis.

TRANSLATION Translation is the transfer of information from mRNA molecule into a polypeptide. This involves a change of language from nucleic acids to amino acids. Translation occurs in ribosomes found in cytoplasm. Translation process i) mRNA go to the cytoplasm ii)Ribosome subunits surround mRNA at the start codon( AUG )which code for methionine and then reads it. iii) tRNA bound to Methionine come to the ribosome surface and it’s anticodon form hydrogen bonds with corresponding mRNA codon. iv)The mRNA start to move toward stop codons step by step exposing/reading mRNA codons as more tRNA with corresponding anticodons bring amino acids to ribosome surface. v)Hydrogen bonds link tRNA to ribosomes while Enzymes link amino acid together by peptide bond. The process continues until stop codons I.E.UAA,UAC or UGA (don’t code for amino acids)are read signaling the end of polypeptide chain. NB: Depending on ribosome and mRNA sequence, mRNA may be read once or repeatedly resulting to several identical chains. All new polypeptides start with methionine because of the nature of the start codon. However, methionine may be removed by enzymes for the protein to be modified.

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