dna and protein gc

8/21/2019 DNA and Protein GC

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DNA and Protein(Structure and

Functions)A. Zulfa Juniarto


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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 genesdetermines 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 containingall the instructions for building andmaintaining a living organism.

Replication followed by cell division is theanswer to one of life's most interestingquestions: How can the union of a singlesperm and an egg become a five-trillion-cell

baby, all containing the same DNA?


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DNA stands for deoxyribonucleic acid

which is a structure of sugar, phosphate

and a base combined into a complexdouble helix


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The helixmakes a

complete turn

every 3.4 nmand there are

about 10.5

base pairs

per turn.


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The building blocks of DNA are the 5-

carbon sugar deoxyribose linked together

by phosphodiester bonds forming twostrands of sugar-phosphate backbones on

the outside of the double helix


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On the outside of the double helix the spacesbetween the intertwined strands form two helicalgrooves of different widths described as themajor groove and the minor groove.

The sequential arrangement of base pairs in aDNA molecule can be sensed via the majorgroove and the minor groove as a surfacepattern of hydrogen donors, hydrogen acceptors

and hydrophobic patches


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http://nobelprize.org/medicine/educational/dna/a/replication/dna.html


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DNA-binding proteins that form DNA

sequence specific complexes usually

recognize their cognate DNA segment via aDNA-binding domainwhich 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 3x109base pairsof

DNA divided into 23 chromosomes which if linked

together would form a thread of 1-2 meterwith 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

histonesto form a protein/DNA complexcalled chromatin


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The structural unit of chromatin is the

nucleosome.

It consists of a central protein complex, thehistone octamer, and two turns of DNA,

about 146 base pairs, which are wrapped

around the histone octamer complex.
http://nobelprize.org/medicine/educational/dna/a/replication/dna.htmlhttp://nobelprize.org/medicine/educational/dna/a/transcription/histoneoctamer_nucleosome.htmlhttp://nobelprize.org/medicine/educational/dna/a/transcription/histoneoctamer_nucleosome.html


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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, whichcontacts the exit/entry of the DNA strand onthe nucleosome.

The nucleosome together with histone H1is called a chromatosome.

Chromatosomes are held together by the

continuous DNA strand, thus forming linkerDNA of 30-50 base pairs in length.


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The Gene

A functional and inheritableelement 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 theproximal part is referred to as the promoter,usually consists of many different DNA

segments defined by their particular basepair sequences

Each individual segment, usually involving

about 6-12 basepairs of DNA, serves as abinding target for a DNA binding proteinwhich functions as a transcription factor


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Furthermore, the DNA binding capacity of

various transcription factors is usually

regulated via cellular signalsthrough

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 triggerthe binding

of a set of transcription factors to a certainset of genes,


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RNA

Like DNA, the RNA molecule, is built up bynucleotides 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 isribose.


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There are three major types

of RNA: 1) mRNA,

messenger-RNA, whichtransfer the information about

the aminoacid sequence from

the DNA to the protein

synthesis. 2) rRNA,

ribosomal-RNA, which buildsup the ribosome together with

proteins. 3)tRNA, transfer-

RNA, which transfer

aminoacids to the ribosomefor 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 ribonucleotidesinto 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 istherefore called a precursor of mRNA, pre-mRNA.

Both ends of the pre-mRNA are modified. Anadditional nucleotide, a 7-methylguanosine isadded to the 5'-end to form a cap-structure. Thisprocess is called capping. The 3'-end of the pre-mRNA is cleaved and polyadenylated. The pre-mRNA is cut at a specific site and 150-200adenylate residues are added to the 3'-end toform a poly(A)-tail. The third major modification issplicing.
http://nobelprize.org/medicine/educational/dna/a/splicing/splicing_endmaturation.htmlhttp://nobelprize.org/medicine/educational/dna/a/splicing/splicing_endformation.htmlhttp://nobelprize.org/medicine/educational/dna/a/splicing/principle.htmlhttp://nobelprize.org/medicine/educational/dna/a/splicing/principle.htmlhttp://nobelprize.org/medicine/educational/dna/a/splicing/splicing_endformation.htmlhttp://nobelprize.org/medicine/educational/dna/a/splicing/splicing_endmaturation.html


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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 theribosome 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.
http://nobelprize.org/medicine/educational/dna/a/gene.htmlhttp://nobelprize.org/medicine/educational/dna/a/translation/ribosome.htmlhttp://nobelprize.org/medicine/educational/dna/a/translation/trna.htmlhttp://nobelprize.org/medicine/educational/dna/a/translation/trna.htmlhttp://nobelprize.org/medicine/educational/dna/a/translation/ribosome.htmlhttp://nobelprize.org/medicine/educational/dna/a/gene.html


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Initiation

formation of the initiation complex

between mRNA, charged tRNA and theribosome

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, transferingthe chain to the tRNA in the A site

the ribosome moves down one codon movingthe peptide-tRNA to the P site and the cyclerepeats


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Termination

translation of a particular protein ends

when the ribosome encounters one ofthree termination codons (UAG, UAA or

UGA)


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DNA polymerase III

Newly

synthesizedleading strand

3'

5'

5'Replication fork

3'

5'

Formation of the leading strand

Replication


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