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Notes on Nucleic Acids and Nucleotides

DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are nucleic acids which are polymers of

nucleotides. Electron carries such as FAD, NAD, and NADP are dinucleotides. High energy phosphate

carriers such as ATP, CTP, GTP, and UTP are single nucleotides.

The Nucleotide Structure

Nucleotides are the basic components of nucleic acids. Each nucleotide consists of three components:

1. Pentose Sugar: Each nucleotide contains a five-carbon sugar. The pentose is ribose for ATP, FAD,

NAD, NADP, and RNA. The pentose is deoxyribose for DNA.

2. Nitrogenous Base: Each nucleotide contains one nitrogenous base which may be either a purine or a

pyrimidine.

Pyrimidinesconsist of a 6-membered ring containing C and N (i.e. cytosine, uracil, and thymine)

Purinesconsist of a 6-membered ring fused to a 5-membered ring (i.e. adenine and guanine)

3. Phosphate Group: Each nucleotide contains one (MP), two (DP), or three (TP) phosphate groups.

The letter code for the nitrogenous base plus the letter code for the number of phosphate groups can be

used to designate a nucleotide (ex. A nucleotide with adenine and two phosphate groups is ADP).

If more than one phosphate group is attached to the nucleotide, the extra phosphates are weakly bonded to

the nucleotide and can be easily hydrolyzed to release the energy used to make the bonds and make that

energy available to other processes in the cell. Due to the higher number of bonds in triphosphatenucleotides, triphosphate groups arethe primary energy source.

UTP =>used in biosynthetic reactions involving addition of sugars.

GTP =>used to provide energy for protein shape changed by G proteins involved in receptor-triggered

reaction sequences and protein synthesis.

Positional Nomenclature

Locations of atoms on nucleotides are specified relative to the carbon atoms in the pentose ring.

1. The purine or pyrimidine is attached to the 1 C on the sugar.

2. The phosphate group is attached to the 5 C on the sugar.

3. The hydroxyl groupon the 3 C on the sugar is reacted with the phosphate group on the adjacent

nucleotide when a nucleotide is added to a DNA or RNA chain.

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Nucleotide Base Pairing

Nucleotides may base pair with complementary nucleotides by forming H bonds between their

nitrogenous bases. Stable base pairs consist of a purine paired with a pyrimidine. Two patterns of base

pairing occur naturally. An adenine base pairs with uracil or thymine by forming two hydrogen bonds. A

guanine base pairs with cytosine by forming three hydrogen bonds.

There are three nucleotide functions in cells:

- Nucleotide triphosphates transport energy from energy-generating chemical reactions to energy-

consuming reactions within the same cell.

- Nucleotide triphosphates serve as monomers for the synthesis of RNA and DNA.

- Nucleotides may be modified into chemical signals for use within a cell.

RNA Structure

RNA is a polymer of ribonucleotides. The purine bases in RNA are adenine and guanine while thepyrimidine bases in RNA are cytosine and uracil. RNA consists of a single linear chain of nucleotides.

However, RNA chains may fold and form base pairs between regions of the same chain where

complementary sequences occur.

RNA Functions

Messenger RNA (mRNA) codes for the amino acid sequence (primary structure) of polypeptide chains in

proteins.

Transfer RNA (tRNA) carries amino acids (as aminoacyl groups on the tRNA) into protein synthesis and

uses the nucleotide sequence in a mRNA to determine where to insert the amino acid carried by the tRNAinthe forming polypeptide chain.

Ribosomal RNA (rRNA) form the structural framework for the ribosomal subunits, and a loop of one of

the rRNA molecules appears to be capable of catalyzing the formation of peptide.

Several ribonucleicprotein (RNP) particles contains small RNA molecules are involved in RNA and

protein processing. Small nuclear ribonucleicproteins (snRNPs) which contain RNA molecules remove

introns (DNA regions within a gene that is not translated into a protein) from mRNA in eukaryotes.

DNA Structure

DNA is made of deoxyribonucleotides. The purine bases in DNA are adenine and guanine. Thepyrimidine bases in DNA are cytosine and thymine. The nucleotides within a single DNA chain or strand

are joined by covalent bonds linking the 3 carbonon one nucleotide with the phosphate on the 5 carbon

of the adjacent nucleotide.

A DNA molecule usually consists of two linear chains of nucleotides and is referred to as double-stranded

(although some viruses have single-stranded DNA).

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The two chains or strands in a DNA molecule are paired by H bonds between complementary base pairs

(A-T, G-C).

Genetic Information Flow in Cells

Genetic information (genotype) is stored in cells in the form of the sequence of deoxyribonucleotides in

DNA. The double-stranded nature of DNA allows repair of damage as long as both strands are not

damaged in the same location.

Genetic information is transmitted from cell to cell during mitosis and from parent to offspring since the

deoxyribonucleotide sequence in newly formedDNA molecules during DNA replication.

Conversion of genetic information into a cellular phenotype requires a sequence of events.

Transcription (RNA Synthesis). The deoxyribonucleotide sequence in regions of DNA (genes) codes for

the ribonucleotide sequence in mRNA. The bases in RNA can hydrogen bond to the bases in DNA, so

one base in DNA specifies one base (complementary to it) in RNA.

Translation (Protein Synthesis). The ribonucleotide sequence in regions of DNA (genes) codes for

(serves as a templatefor) the ribonucleotide sequence in mRNAs codes for the amino acid sequence in

proteins (polypeptides). A three nucleotide codon in the mRNA base pairs with the complementary three

nucleotide anticodon on an aminoacyl tRNA to allow the aminoacyl group onthe aminoacyl tRNA to be

added to the polypeptide being synthesized. A three nucleotide unit in mRNA functions as one codon to

specify one amino acid in a polypeptide (a polypeptide in turn forms all or part of a protein).

The proteins form cellular structures and/or perform or catalyze cell functions. Proteins directly or

indirectly produce the phenotype of a cell.

Protein Structure

Proteins are made of 20 different types of amino acids which share a common backbone structure

consisting of an amino groupcovalently bonded to a carboxylic acid (carboxyl) group. Each of the 20

different types of amino acids differs in the side chain structure attached to the alpha carbon.

One amino acid in a polypeptide chain in a protein is specified by a sequence of three nucleotides in a

messenger RNA (mRNA). This three nucleotide codon is translated through the mediation of a transfer

RNA (tRNA). The amino acid sequence of each polypeptide chain (its primary structure) interacts with

the polypeptides environment and with other functional components in the cell. In which the polypeptide

was made to determine further modifications and eventual assembly of a functional protein.

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Protein Function

Structural proteinsform all or parts of cell structures such as ribosomes, chromosomes, mitotic spindles,

and cell membranes.

Enzymesare almost all proteins and are required to catalyze most chemical reactions in cells, including

DNA synthesis, RNA synthesis, protein synthesis, carbohydrate synthesis, and lipid synthesis. Most

cellular reactions will not occur under normal intracellular conditions without access to the appropriate

enzyme.

Transport proteinsserve as carriers or channels to allow molecules to move across cell membranes.

Signal or regulatory proteinsrespond to changes in a cell by changing their interactions with critical

components such as DNA, thereby altering cell functions.