Central Dogma of Molecular Biology

Dr.Aida Fadhel Biawi , 2013

Enzymes in DNA replication

Helicase unwinds parental double helix

Binding proteinsstabilize separatestrands

DNA polymerase III binds nucleotides to form new strands

Ligase joins Okazaki fragments and seals other nicks in sugar-phosphate backbone

Primase adds short primer to template strand

DNA polymerase I (Exonuclease) removes RNA primer and inserts the correct bases

Proofreading

• DNA polymerases proofread newly made DNA, replacing any incorrect nucleotides

Nuclease

DNApolymerase

DNAligase

A thymine dimerdistorts the DNA molecule.1

A nuclease enzyme cutsthe damaged DNA strandat two points and thedamaged section isremoved.

2

Repair synthesis bya DNA polymerasefills in the missingnucleotides.

3

DNA ligase seals theFree end of the new DNATo the old DNA, making thestrand complete.

4

Accuracy of DNA Replication

• The chromosome of E. coli bacteria contains about 5 million bases pairs

– Capable of copying this DNA in less than an hour

• The 46 chromosomes of a human cell contain about 6 BILLION base pairs of DNA!!

– Takes a cell a few hours to copy this DNA

– With amazing accuracy – an average of 1 per billion nucleotides

Protein Synthesis

• The information content of DNA is in the form of specific sequences of nucleotides along the DNA strands

• The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins.

• The process by which DNA directs protein synthesis, gene expression includes two stages, called transcription and translation.

Transcription and Translation

• Cells are governed by a cellular chain of command– DNA RNA protein

• Transcription– Is the synthesis of RNA under the direction of

DNA– Produces messenger RNA (mRNA)

• Translation– Is the actual synthesis of a polypeptide, which

occurs under the direction of mRNA– Occurs on ribosomes

Transcription and Translation• In a eukaryotic cell the nuclear envelope separates transcription

from translation• Extensive RNA processing occurs in the nucleus

Eukaryotic cell. The nucleus provides a separatecompartment for transcription. The original RNAtranscript, called pre-mRNA, is processed in various ways before leaving the nucleus as mRNA.

(b)

TRANSCRIPTION

RNA PROCESSING

TRANSLATION

mRNA

DNA

Pre-mRNA

Polypeptide

Ribosome

Nuclearenvelope

Transcription

• RNA synthesis– Is catalyzed by RNA

polymerase, which Separates the DNA strands and hooks together the RNA nucleotides.

– Follows the same base-pairing rules as DNA, except that in RNA, uracil substitutes for thymine

RNA

• RNA is single stranded, not double stranded like DNA• RNA is short, only 1 gene long, where DNA is very long and

contains many genes• RNA uses the sugar ribose instead of deoxyribose in DNA• RNA uses the base uracil (U) instead of thymine (T) in DNA.

Synthesis of an RNA Transcript

• The stages of transcription are– Initiation– Elongation– Termination

PromoterTranscription unit

RNA polymerase

Start point

53

35

35

53

53

35

53

35

5

5

Rewound

RNA

RNA

transcript

3

3Completed RNA transcript

Unwound

DNA

RNA

transcript

Template strand of DNA

DNA

1 Initiation. After RNA polymerase binds to

the promoter, the DNA strands unwind, and

the polymerase initiates RNA synthesis at the

start point on the template strand.

2 Elongation. The polymerase moves downstream, unwinding the

DNA and elongating the RNA transcript 5 3 . In the wake of

transcription, the DNA strands re-form a double helix.

3 Termination. Eventually, the RNA

transcript is released, and the

polymerase detaches from the DNA.

• Promoters signal the initiation of RNA synthesis

• Transcription factors help eukaryotic RNA polymerase recognize promoter sequences

TRANSCRIPTION

RNA PROCESSING

TRANSLATION

DNA

Pre-mRNA

mRNA

Ribosome

Polypeptide

T A T AAA AATAT T T T

TATA box Start point TemplateDNA strand

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Transcriptionfactors

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35

Promoter

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355

RNA polymerase IITranscription factors

RNA transcript

Transcription initiation complex

Eukaryotic promoters1

Several transcriptionfactors

2

Additional transcriptionfactors

3

Synthesis of an RNA Transcript - Initiation

• Sense strand, or coding strand, is the segment of double-stranded DNA running from 5' to 3' that is complementary to the antisense strand of DNA, which runs from 3' to 5'. The sense strand is the strand of DNA that has the same sequence as the mRNA, which takes the antisense strand as its template during transcription, and eventually undergoes translation into a protein.

Promoter, a regulatory region of DNA usually located upstream of a gene, providing a control point for regulated gene transcription .

Upstream and downstream (DNA)

• In molecular biology, upstream and downstream both refer to a relative position in DNA or RNA. Each strand of DNA or RNA has a 5' end and a 3' end, so named for the carbons on the deoxyribose (or ribose) ring. Relative to the position on the strand, downstream is the region towards the 3' end of the strand. Since DNA strands run in opposite directions, downstream on one strand is upstream on the other strand.

Synthesis of an RNA Transcript - Elongation

Elongation

RNApolymerase

Non-templatestrand of DNA

RNA nucleotides

3 end

C A E G C A AU

T A G G T T AA

CG

U

AT

CA T C C A A T T

G

G

3

5

5

Newly madeRNA

Direction of transcription(“downstream”) Template

strand of DNA

• RNA polymerase synthesizes a single strand of RNA against the DNA template strand (anti-sense strand), adding nucleotides to the 3’ end of the RNA chain

• As RNA polymerase moves along the DNA it continues to untwist the double helix, exposing about 10 to 20 DNA bases at a time for pairing with RNA nucleotides

• Specific sequences in the DNA signal termination of transcription

• When one of these is encountered by the polymerase, the RNA transcript is released from the DNA.

Synthesis of an RNA Transcript - Termination

• Several mechanisms of regulating transcription termination have been discovered in bacteria and eukaryotes.

• RNA polymerase itself plays a role in the two principal mechanisms of transcription termination that occur in E. coli.

• An additional protein, a transcription-termination factor called Rho, is required in one mechanism. That mechanisms is commonly referred to as Rho-dependent termination.

Transcription Overview

• Most eukaryotic mRNAs aren’t ready to be translated into protein directly after being transcribed from DNA. mRNA requires processing.

• Transcription and RNA processing occur in the nucleus. After this, the messenger RNA moves to the cytoplasm for translation.

• The cell adds a protective cap to one end, and a tail of A’s to the other end. These both function to protect the RNA from enzymes that would degrade

• Most of the genome consists of non-coding regions called introns

1- Non-coding regions may have specific chromosomal functions or have regulatory purposes.

2- Introns also allow for alternative RNA splicing

• Thus, an RNA copy of a gene is converted into messenger RNA by doing 2 things:

– Add protective bases to the ends

– Cut out the introns

Post Transcriptional RNA Processing

RNA Processing - Splicing

• The original transcript from the DNA is called pre-mRNA.

• It contains transcripts of both introns and exons.

• The introns are removed by a process called splicing to produce messenger RNA (mRNA)

Alteration of mRNA Ends

• Each end of a pre-mRNA molecule is modified in a particular way– The 5 end receives a modified nucleotide cap– The 3 end gets a poly-A tail

A modified guanine nucleotideadded to the 5 end

50 to 250 adenine nucleotidesadded to the 3 end

Protein-coding segment Polyadenylation signal

Poly-A tail3 UTRStop codonStart codon

5 Cap 5 UTR

AAUAAA AAA…AAA

TRANSCRIPTION

RNA PROCESSING

DNA

Pre-mRNA

mRNA

TRANSLATIONRibosome

Polypeptide

G P P P

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1 - Capping - the 5’ end of the pre-mRNA is capped with a 7-methyl guanosine nucleotide.

Capping is required to:

1- Protect the RNA transcript from degradation 2-Plays an important role in mRNA transport to the cytoplasm 3- Initiation of protein synthesis.

CAP5’ 3

’

2- Polyadenylation - the 3’ end of the pre-mRNA is cleaved and a stretch of adenosines are added to the end of the molecule.

Use of alternative polyadenylation sites can result in :

1- Insertion or deletion of sequences that control the stability of the mRNA.

2-The polyA tail is also involved in translation termination.

CAP5’ 3’

An

3- Pre-mRNA splicing - intron-exon junctions (also referred to as splice sites) in the pre-mRNA, the intronic sequences are excised and the exons are ligated to generate the spliced mRNA.

AnCAP5’ 3’

The enzyme that catalyzes intron excision is a ~ 3 MDa complex

pre-mRNA spliced mRNA

spliceosome

Assembly and structural dynamics of the spliceosome, one of the most complex molecular machines in the cell

However, multiple introns may be spliced differently in different circumstances, for example in different tissues.

3 541 2

1 2 3 5Heart muscle

1 43 5Uterine muscle

Thus one gene can encode more than one protein. The proteins are similar but not identical and may have distinct properties.

This is important in complex organisms

mRNA mRNA

Splicing

mRNA

Typical human gene structure: 90-95% intron / 5-10% exon average Intron 3500bp / average exon 150

Thus expression of a gene with an intron requires an extra step to remove the intron

protein

translation

DNA GE

transcription

NE

mRNA

RNA splicing

intron

pre-mRNAintron

exon 1 exon 2

The human genome sequencing project (Venter et al., 2001) estimated the number of human genes to be between 30,000-40,000, which is much less than the previous estimates .

There are 130 thousands types of proteins.

Monocistronic versus polycistronic mRNA

• An mRNA molecule is said to be monocistronic when it contains the genetic information to translate only a single protein chain (polypeptide). This is the case for most of the eukaryotic mRNAs.

• On the other hand, polycistronic mRNA carries several open reading frames (ORFs), each of which is translated into a polypeptide. These polypeptides usually have a related function .

• polycistronic transcription units characteristic of bacteria.

• Polycistronic mRNA refers to a messenger RNA which encodes two or more proteins. Polycistronic messenger RNAs participates in the process of protein synthesis (translation) in prokaryotes.

Polycistronic mRNA

Monocistronic mRNA

Types of RNA

Genetic information copied from DNA is transferred to 3 types of RNA:

mRNA

Copy of information in DNA constitutes ( 2%) , 100,000 KINDS.

rRNA

Most of the RNA in cells is associated with structures known as ribosomes, the protein factories of the cells.(80%), FEW KINDS

It is the site of translation where genetic information brought by mRNA is translated into actual proteins.

Types of rRNA :

In prokaryotic :( 23S,16S,5S)In Eukaryotic: ( 28S,18S, 5.8S and 5S).

Note: S ( Svedberg) is a unit refers to the molecular weight and shape of the compound .

tRNA

Brings the amino acid to the ribosome that mRNA coded for. (15%), 100 KINDS.

It has 4S in molecular weight.

Structure of tRNA