DNA StructureDNA Replication

TranscriptionTranslation

ProteinsEnzymes

DNA STRUCTUREDNA is a polymer. The monomer units of DNA are nucleotides, and the polymer is known as a "polynucleotide." Each nucleotide consists of a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to the sugar, and a phosphate group. There are four different types of nucleotides found in DNA, differing only in the nitrogenous base. The four nucleotides are given one letter abbreviations as shorthand for the four bases.

A is for adenineG is for guanineC is for cytosineT is for thymine

PURINE BASESAdenine and guanine are purines. Purines are the larger of the two types of bases found in DNA. The 9 atoms that make up the fused rings (5 carbon, 4 nitrogen) are numbered 1-9. All ring atoms lie in the same plane.

PYRIMIDINE BASESCytosine and thymine are pyrimidines. The 6 atoms (4 carbon, 2 nitrogen) are numbered 1-6. Like purines, all pyrimidine ring atoms lie in the same plane.

DEOXYRIBOSE SUGARThe deoxyribose sugar of the DNA backbone has 5 carbons and 3 oxygens. The carbon atoms are numbered 1', 2', 3', 4', and 5' to distinguish from the numbering of the atoms of the purine and pyrmidine rings. The hydroxyl groups on the 5'- and 3'- carbons link to the phosphate groups to form the DNA backbone. Deoxyribose lacks an hydroxyl group at the 2'-position when compared to ribose, the sugar component of RNA.

Components of the DNA Nucleotide

Bonds seen in a DNA structure

DNA HelixThe three-dimensional structure of DNA was discovered in 1953 by Watson and Crick in Cambridge, using the experimental data of Wilkins and Franklin in London, for which work they won a Nobel prize. Ms Franklin however died before the award and the Nobel Prize is never awarded posthumously.The main features of the structure are:DNA is double-stranded, so there are two polynucleotide stands alongside each other.The strands are antiparallel, i.e. they run in opposite directions thus 5' to 3' is parallel to 3' to 5‘.The two strands are wound round each other to form a double helix.The two strands are joined together by hydrogen bonds between the bases.The bases therefore form base pairs, which are like rungs of a ladder.The base pairs are specific. A only binds to T (and T with A), and C only binds to G (and G with C). (A with U in RNA)These are called complementary base pairs (or sometimes Watson-Crick base pairs). (A-T and G-C)This means that whatever the sequence of bases along one strand, the sequence of bases on the other stand must be complementary to it.

RNA (Ribonucleic Acid)Ribonucleic acid (RNA) is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate.

RNA is very similar to but differs in a few important structural details:

Point of Difference DNA RNA

Number of strand Double stranded Single stranded

Sugar in Nucleotide Deoxyribose Ribose

Nucleoside base A, T, C, G A, U, C, G

Enzymes involved in DNA ReplicationHelicase – unwounds a portion of the DNA double helixSSB - prevents degradation and base pair re-annealment (single-stranded DNA binding proteins)DNA Polymerase III – creates the leading strand (5’-3’)RNA primase – creates the lagging strand/RNA primers on the other parent strand (3’ – 5’) and is attached onto the DNA strand by RNA primaseDNA polymerase I - replaces the RNA primersExonucleases – either DNA polymerase I or III – finds and removes the RNA primersDNA ligase – adds phosphate in the remaining gaps of the phosphate-sugar backboneNucleases – removes wrong nucleotides from the daughter strand

TRANSCRIPTIONAim: to produce a complementary copy of DNATakes place in the nucleusSteps:

1. RNA Polymerase moves the transcription bubble, a stretch of unpaired nucleotides, by breaking the hydrogen bonds between complementary nucleotides.

2. RNA Polymerase adds matching RNA nucleotides that are paired with complementary DNA bases.

3. RNA sugar-phosphate backbone forms with assistance from RNA polymerase.

4. Hydrogen bonds of the untwisted RNA+DNA helix break, freeing the newly synthesized RNA strand.

5. If the cell has a nucleus, the RNA is further processed (addition of a 3' poly-A tail and a 5' cap) and exits through to the cytoplasm through the nuclear pore complex.

TranscriptionDNA Strands:

Antisense strand – serves as template

Sense strand – contains the promoter and terminator regions

RNA polymerase attaches to it

Unzips the DNA strand

Reads the sense strand

Provide the ribonucleosides/base pairs

TRANSLATIONTranslation occurs in the cytoplasm where the ribosomes are located. Ribosomes are made of a small and large subunit which surround the mRNA.Transfer RNA (tRNA) molecules are 75 - 95 nucleotides long and have four arms and three loops. True to its name, tRNAtransfers amino acids to the site of the growing protein chain (polypeptide). Each tRNA molecule recognises a specific, three base-pair mRNA code or codon (the DNA form of a codon is called a triplet and the sequence on the tRNA is called an anticodon). Since there are three bases and four possible nucleotides, there can be up to 64 (4x4x4) possible tRNA molecules. Three of these tRNA molecules recognise "stop" or termination codons which have been named amber (UAG), opal (UGA) and ochre (UAA).

The codon indicates which amino acid is to be added and the amino acid is attached to the tRNA molecule at the acceptor arm. Most amino acids are represented by more than one codon. This means that the expected protein can still be synthesised, even when a degree of mutation occurs in the DNA or mRNA.

There are 20 essential amino acids, however they can be combined in any order, just like the four nucleotides. This permits the production of the many different proteins which let organisms grow and function.

Name1-Letter

NicknameTriplet

3-Letter Nickname

Glycine G GGT,GGC,GGA,GGG Gly

Alanine A GCT,GCC,GCA,GCG Ala

Valine V GTT,GTC,GTA,GTG Val

Leucine L TTG,TTA,CTT,CTC,CTA,CTG Leu

Isoleucine I ATT,ATC,ATA Ileu

Serine S TCT,TCC,TCA,TCG,AGT,AGC Ser

Threonine T ACT,ACC,ACA,ACG Thr

Cysteine C TGT,TGC Cys

Methionine M ATG Met

Glutamic Acid E GAA,GAG Glu

Aspartic Acid D GAT,GAC,AAT,AAC Asp

Lysine K AAA,AAG Lys

Arginine RCGT,CGC,CGA,CGG,AGA,AG

GArg

Asparagine N AAT,AAC Asn

Glutamine Q GAA,GAG Gln

Phenylalanine F TTT,TTC Phe

Tyrosine Y TAT, TAC Tyr

Tryptophan W TGG Trp

Unknown X xxx

Proline P CCT,CCC,CCA,CCG Pro

Terminator * TAA,TAG,TGA End

TranslationStep 1 - Initiation

When the large ribosmalsubunit,small ribosomal subunit, mRNA and the tRNAcarrying a methionine come together in the cytoplasm, the ribosome becomes active and the synthesis of a polypeptide, or "translation", is initiated. The AUG codon binds at the protein binding site (P) of the ribosome and AUG is always the first codon of an mRNA.

Step 1 – Initiation continued….The next complementary tRNAwill bind at the attachment binding site(A) of the ribosome. The adjacent amino acids are then joined by a peptide bond via a peptidase enzyme. Thus the polypeptide chain begins to grow and as it does, it is passed to the next tRNA currently occupying the A site.

Translation:Step 2 - Elongation

ELONGATIONThe ribosome then moves 1 codon down the mRNA in a 5' to 3' direction. This is achieved by atranslocase enzyme. As the process of ribosome translocation continues, the "old" tRNA is released to bind another amino acid and go in search of a new codon. The binding of a new aminoacid is mediated by an enzyme called amino-acyl-tRNAsynthase

Translation:Step 3 - Termination

TERMINATION

The process continues along the mRNA until a stop codon is reached. While there is no tRNA for a stop codon, there is an enzyme called release factor which cleaves the polypeptide chain resulting in a new protein.

Step 3 – Termination continued ….Finally, the entire complex is disrupted, the ribosome separates and the mRNA is released to be used again or degraded. Translation occurs at multiple sites along an mRNA so that many ribosomes can be seen by electron microscopy bound to a single mRNA strand with many polypeptide chains forming from each.Once DNA is synthesized, DNA polymerase III and DNA polymerase I act as quality control checkers by proofreading the newly synthesized daughter strand –either of the two enzymes function as an exonucleases – these are enzymes that remove incorrectly-placed nucleotide sequences and replace them with the correct ones