DNA and Protein (Structure and Functions)

A. Zulfa Juniarto

Introduction

DNA carries the genetic information of a cell and consists of thousands of genes. Each gene serves as a recipe on how to build a protein molecule. Proteins perform important tasks for the cell functions or serve as building blocks. The flow of information from the genes determines the protein composition and thereby the functions of the cell.
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DNA is the physical carrier of inheritance. It is like a giant book of information containing all the instructions for building and maintaining a living organism.

Replication followed by cell division is the answer to one of life's most interesting questions: How can the union of a single sperm and an egg become a five-trillion-cell baby, all containing the same DNA?

DNA stands for deoxyribonucleic acid which is a structure of sugar, phosphate and a base combined into a complex double helix

The helix makes a complete turn every 3.4 nm and there are about 10.5 base pairs per turn.

The building blocks of DNA are the 5carbon sugar deoxyribose linked together by phosphodiester bonds forming two strands of sugar-phosphate backbones on the outside of the double helix

On the outside of the double helix the spaces between the intertwined strands form two helical grooves of different widths described as the major groove and the minor groove.

The sequential arrangement of base pairs in a DNA molecule can be sensed via the major groove and the minor groove as a surface pattern of hydrogen donors, hydrogen acceptors and hydrophobic patches

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DNA-binding proteins that form DNA sequence specific complexes usually recognize their cognate DNA segment via a DNA-binding domain which has a surface pattern complementary to the pattern of the major and/or minor groove of that particular DNA segment.

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The human genome contains 3x109 base pairs of DNA divided into 23 chromosomes which if linked together would form a thread of 1-2 meter with a diameter of 2 nm. This DNA codes for about 105 different proteins. In fact only about 2-4 % of the total coding capacity in the human DNA is used for coding of different genes, the rest of it probably has other more structural and organizational functions.

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Chromatin

The DNA double helix in the cell is packaged by special proteins called histones to form a protein/DNA complex called chromatin

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The structural unit of chromatin is the nucleosome. It consists of a central protein complex, the histone octamer, and two turns of DNA, about 146 base pairs, which are wrapped around the histone octamer complex.

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There are four different types of core histones which form the octamer containing two copies each of H2A, H2B, H3 and H4.

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There is a linker histone, H1, which contacts the exit/entry of the DNA strand on the nucleosome. The nucleosome together with histone H1 is called a chromatosome. Chromatosomes are held together by the continuous DNA strand, thus forming linker DNA of 30-50 base pairs in length.

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The Gene

A functional and inheritable element in the genome is referred to as a gene and usually codes for a protein. In some cases genes also code for RNA molecules that are not translated to protein, e.g. ribosomal RNA.

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The gene regulatory segment, of which the proximal part is referred to as the promoter, usually consists of many different DNA segments defined by their particular base pair sequences Each individual segment, usually involving about 6-12 base pairs of DNA, serves as a binding target for a DNA binding protein which functions as a transcription factor
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Furthermore, the DNA binding capacity of various transcription factors is usually regulated via cellular signals through extracellular hormones and receptor pathways or via cell interactions with the environment. In this way a particular stimulus in the surrounding of a cell will trigger the binding of a set of transcription factors to a certain set of genes,

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RNA

Like DNA, the RNA molecule, is built up by nucleotides linked together in a chain. There are some differences though :

The RNA molecule is single stranded The four bases in the DNA nucleotides are adenine, guanine, thymidine and cytosine. In RNA thymidine is replaced by uracil. The sugar in DNA is deoxyribose. In RNA it is ribose.

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There are three major types of RNA: 1) mRNA, messenger-RNA, which transfer the information about the aminoacid sequence from the DNA to the protein synthesis. 2) rRNA, ribosomal-RNA, which builds up the ribosome together with proteins. 3) tRNA, transferRNA, which transfer aminoacids to the ribosome for protein synthesis.

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Transcription

After transcription has been initiated RNA polymerase II, together with the necessary transcription elongation factors, travels along the DNA template and polymerizes ribonucleotides into an RNA copy of the gene The polymerase moves at a regular speed (approximately 30 nucleotides per second) and holds on to the DNA template efficiently, even if the gene is very long

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RNA Processing

The primary transcription product of a gene is therefore called a precursor of mRNA, pre-mRNA.
Both ends of the pre-mRNA are modified. An additional nucleotide, a 7-methylguanosine is added to the 5'-end to form a cap-structure. This process is called capping. The 3'-end of the premRNA is cleaved and polyadenylated. The premRNA is cut at a specific site and 150-200 adenylate residues are added to the 3'-end to form a poly(A)-tail. The third major modification is splicing.

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Translation

Translation is the actual synthesis of a protein under the direction of mRNA the ribosome, provides the basic machinery for the translation process. The major role of the ribosome is to catalyse coupling of amino acids into protein according to the sequence specified by the mRNA. The amino acids are brought to the ribosome by tRNA (transfer RNA) molecules.

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Initiation formation of the initiation complex between mRNA, charged tRNA and the ribosome translation begins at a specific codon, the initiation codon (AUG)

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Elongation the growing polypeptide chain is attached to an amino acid in the P site the next codon to be read is present beneath the A site the tRNA bearing the next amino acid to be inserted enters the A site a peptide bond is formed between the new amino acid and the growing chain, transfering the chain to the tRNA in the A site the ribosome moves down one codon moving the peptide-tRNA to the P site and the cycle repeats
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Termination translation of a particular protein ends when the ribosome encounters one of three termination codons (UAG, UAA or UGA)

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Replication
Formation of the leading strand

3' 5' Newly synthesized leading strand 5' DNA polymerase III 5' 3'

Replication fork

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