Essential Cell Biology gy

Third Edition

Chapter 7 From DNA to Protein: How Cells Read the Genome

Copyright Garland Science 2010

Genetic information directs the synthesis of protein

This flow of g genetic information in cells from DNA to RNA to protein is so fundamental that it has been termed the central dogma of molecular biology. The central dogma of molecular biology was first articulated in 1958 by Francis Crick, who discovered DNA structure with James Waston Waston.

Transcription: copy the nucleotide sequence q of DNA into RNA. Translation: use the information in RNA to make protein.

(I) F From DNA t to RNA

Genes can be expressed with different efficiences

Gene A is transcribed and translated much more efficiently than gene B. This allows the amount of protein A in the cell to be much higher than that of protein B

The chemical structure of RNA differs slightly from that of DNA

(A) RNA contains the sugar ribose, which differs from deoxyribose the sugar used in DNA deoxyribose, DNA, by the presence of an additional OH group. (B) RNA contains the bases adenine (A), guanine (G), cytosine (C), and uracil (U), which differs from thymine (T), the equivalent base in DNA, by the absence of a CH3 group. (C) The chemical linkage between nucleotide in RNA is the same as that in DNA.

Uracil forms a base pair with adenine

(Despite the absence of a methyl group, uracil has the same base-pairing properties as thymine. thymine Thus, UA base pairs closely resemble T-A base pairs.

RNA molecules can form intramolecular base pairs and fold into specific structures
RNA is single-stranded, but it often contains short stretches of nucleotides that can base pair with complementary sequences found elsewhere on the same molecule. The conventional (Waston-Crick) base-pair interaction (A) and nonconventional base-pair interaction (green) (e (e.g., g A A-G) G) shown in (B), (B) allow an RNA molecule to fold into a three-dimensional structure that is determined by its sequence of nucleotides. Structure of an actual RNA molecule that is involved in RNA splicing (C).

Movie: RNA structure

Transcription produces an RNA complementary to one strand of DNA

The nontemplate strand of the DNA (the top strand) is sometimes called the coding strand because its sequence is equivalent to the RNA product product. The RNA chain produced by transcription is called the transcript and has nucleotide sequence exactly complementary to the template strand.

DNA is transcribed by the enzyme RNA polymerase

The RNA polymerases catalyze the formation of the phosphodiester bonds that link the nucleotides together and form the sugar sugar-phosphate phosphate backbone of the RNA chain chain. The RNA polymerase moves along the DNA, unwinding the DNA helix in front of it. Using an exposed DNA strand as a template, the polymerase adds nucleotides one by one to the RNA chain at the polymerization site site. As it moves along the DNA template, the polymerase displaces the newly formed RNA, allowing the two strands of DNA behind the polymerase to rewind. A short region of hybrid DNA/RNA helix (about nine nucleotides in length) therefore forms only transiently, causing a window window of DNA/RNA helix to move along the DNA with the polymerase.

Movie: Transcription

Transcription can be visualized in the electron microscope

The micrograph shows many molecules of RNA polymerase simultaneously transcribing two adjacent genes genes. Molecules of RNA polymerase are visible as series of dots along the DNA with the transcripts (fine threads) attached to them. The ribosomal RNAs (rRNAs) transcribed from the genes shown in this examples are not translated into protein but instead used directly as components of ribosomes, the machines on which translation takes place. The p particles at the 5 end ( (the free end) ) of each rRNA transcript p are believed to be ribosomal proteins that have assembled on the rRNA.

Types of RNA produced in cells

Signals in the sequence of a gene determine where bacterial RNA polymerase starts and stops transcription
Bacterial B t i l RNA polymerase l contains t i a subunit b it called ll d the th sigma i factor f t (yellow) ( ll ) that th t recognizes the promoter (green) on the DNA. Once transcription has begun, the sigma () factor is released and the polymerase continues synthesizing the RNA without it. Chain elongation continues polymerase y encounters until the p a termination signal (terminator or stop site) (red) in the DNA. There the enzyme halts and releases both the DNA template and the newly made mRNA. The polymerase then g reassociates with a free sigma factor and searches for another promoter to begin the process again.

Bacterial promoters and terminators have specific nucleotide sequences that are recognized by RNA polymerase
The Th first fi t nucleotide l tid t transcribed ib d i is d designated i t d as: +1 ( (start t t site) it ) The asymmetry of the promoter with the conserved -35 sequence located upstream of the -10 sequence, orients the RNA polymerase and determines the direction of transcription. p Terminator is the stop signal for transcription.

Some genes are transcribed using one DNA strand as a template, whereas others are transcribed using the other DNA strand
The direction of transcription is determined by the orientation of the promoter at the beginning of each gene (green arrowheads). The g genes transcribed from left to right g use the bottom DNA strand as the template, whereas those transcribed from right to left use the top strand as the template. Here about 0.2% or 10,000 nucleotide pairs of the E.coli chromosome is shown.

The three RNA polymerase in eucaryotic cells

While bacteria contain a single type of RNA polymerase, eucaryotic cells have three RNA polymerase I, I II, II and III. III The bacterial RNA polymerase (along with its sigma subunit) is able to initiate transcription on its own, whereas eukaryotic RNA polymerases require the assistance of a large set of accessory proteins. Principal among these are the general transcription factors, which must assemble at each promoter along with the polymerase before the polymerase can begin transcription. The mechanisms that control transcription initiation in eucaryotes are much more elaborate than those in procayotes. procayotes Eucaryotic transcription initiation must take into account the packing of DNA into nucleosome and more compact forms of chromatin structure.

Eucaryotic RNA polymerase II requires general transcription factors for transcription initiation
(A) Many promoters contain a DNA sequence called the TATA box. (B) The TATA box is recognized and bound by the general lt transcription i ti f factor t TFIID through th h one of f it its subunit called TATA binding protein (TBP), (C) The TATA box-binding of TFIID then enables the adjacent binding of TFIIB, one of the general transcription factors. (D) The rest of the general transcription factors including TFIIH as well as the RNA polymerase itself assemble bl at t th the promoter t t to form f a complete l t transcription initiation complex. (E) TFIIH then pries apart the double helix of DNA at the transcription start point point, using the energy of ATP hydrolysis, allowing the template strand to be exposed. TFIIH also phosphorylates the long polypeptide tail of RNA polymerase II, releasing it from the general factors f so it can begin the elongation phase of transcription.

TATA-binding protein (TBP) binds to TATA box sequences and distorts the DNA

TBP is i the th subunit b it of f the th general transcription factor TFIID that is responsible for recognizing and binding to the TATA box sequence. The unique DNA bending caused by TBP may help attract tt t the th other th general l transcription factors. TBP is a single polypeptide chain that is folded into two very similar domains. Its eight sheets sit atop the DNA helix like a saddle on a horse.

Movie: TATA-binding protein (TBP)

The mRNA molecules transcribed in the nucleus move out into the cytoplasm through nuclear pores for translation

Phosphorylation of RNA polymerase II allows RNA-procession proteins to assemble on its tail

Eucaryotic RNAs are transcribed and processed simultaneously in the nucleus. nucleus Capping at the 5 ends with a guanine (G), polyadenylation at the 3 3 ends with poly-A tail, and splicing are modifications made to RNA during processing.

Eucaryotic mRNA molecules are modified by capping and polyadenylation

The ends of eucaryotic mRNA are modified by the addition of a cap at the 5 end (7-methyl guanine (G)), and by cleavage of the primary transcript at 3 end through an enzyme that cuts the RNA chain at a particular sequence of nucleotides and d th the fi finished i h d off ff b by a second d enzyme th that t adds dd a series i of f repeated t d adenine d i (A) nucleotides (poly-A tail) to the cut end.

Eucaryotic mRNA molecules are modified by capping and polyadenylation

The structure of the cap at the 5 end of eucaryotic mRNA molecules. Note that unusual 5-to-5 linkage of the 7-methyl guanine (G) to the remainder of the RNA. ,

Eucaryotic and bacterial genes are organized differently

A bacterial gene consists of a single stretch of uninterrupted nucleotide sequence that encodes the amino acid sequence of a protein. In contrast, the coding sequences of most eucaryotic genes (exons) are interrupted by noncoding sequences (introns). Note: Promoters for transcription are indicated in green.

Most human genes are broken into exons and introns

(A) The -globin gene, encoding one of the subunits of the oxygen-carrying protein hemoglobin hemoglobin, contains 3 exons exons. (B)The Factor VIII gene, which encode for a protein (Factor OO) that functions in the blood-clotting pathway, contains 26 exons. Mutations in this large gene are repsonsible for the most prevalent form of hemophilia. hemophilia