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Introduction
A cell builds the proteins it needs from instructions encoded in its genome.
The flow of information in the cell is as follows:
Transcription in Bacteria
Transcription
RNA polymerase performs this synthesis by transcribing only one strand of DNA, called the template strand. The other DNA strand is called the non-template strand. The sequence of the non-template strand matches the sequence of the RNA, except that RNA has uracil (U) in place of thymine (T). Transcription consists of three phases:
RNA 5
Hydrogen bonds form between complementary base pairs
DNA template
Bacterial RNA polymerase is a large, globular enzyme with several interior channels.
A holoenzyme Prokaryotic RNA polymerase is a holoenzyme made up of the core enzyme, which has the ability to synthesize RNA, and a sigma subunit
Holoenzyme
Core enzyme
10 box
+1 site Sigma
Active site
Downstream DNA
RNA polymerase
1. Initiation begins
Sigma binds to promoter region of DNA.
Next, sigma opens the DNA double helix and the template strand is threaded through the RNA polymerase active site.
An incoming ribonucleoside triphosphate (NTP) pairs with a complementary base on the DNA template strand, and RNA polymerization begins.
+1 site
+1 site
Non-template strand
RNA
RNA NTPs
2. Initiation continues
Sigma opens the DNA helix; transcription begins.
Zipper Rudder
Downstream DNA
3. Initiation is complete
Sigma releases; mRNA synthesis continues.
During the elongation phase of transcription, RNA polymerase moves along the DNA template and synthesizes RNA in the 5' 3' direction.
Transcription ends with a termination phase. In this phase, RNA polymerase encounters a transcription termination signal in the DNA template. This signal codes for RNA forming a hairpin structure.
RNA polymerase
Downstream DNA
DNA
The promoters in eukaryotic RNA are more diverse and complex than are bacterial promoters.
The promoters recognized by each type of RNA polymerase differ. Many promoters recognized by RNA polymerase II include a sequence called a TATA box analogous in function to the prokaryotic 10 and 35 boxes. In eukaryotes, transcription is followed by several important RNA processing steps.
The RNA made in the nucleus was much longer than the mRNA molecules found in the cytoplasm ,
Seems the protein-coding regions of eukaryotic genes are interrupted by noncoding regions. Exons are the coding regions of eukaryotic genes that will be part of the final mRNA product. The intervening noncoding sequences are called introns, and are not in the final mRNA. Therefore, Eukaryotic genes
Promoter
Exon 2
Exon 3 3
The transcription of eukaryotic genes by RNA polymerase generates a primary RNA transcript that contains exons and introns. Introns are removed by splicing.
Small nuclear ribonucleoproteins (snRNPs, pronounced snurps) form a complex called a spliceosome.
snRNPs 3 Exon 2
Exon 1
Intron
Excised intron A
Exon 1 Exon 2
3 Mature mRNA
Primary RNA transcripts are also processed by the addition of a 5' cap and a poly (A) tail.
With the addition of cap and tail, processing is complete; the product is a mature mRNA. The 5' cap serves as a The poly (A) tail extends the life of an mRNA by protecting it from degradation.
5
5 untranslated region
Coding region
3 untranslated region
Translation
In translation, the sequence of bases in the mRNA is converted to an amino acid sequence in a protein.
of mRNA
Ribosome translates mRNA as it is being synthesized by RNA polymerase
Protein 1 1 1 Ribosome RNA polymerase Start of gene (3 end of template strand) End of gene (5 end of template strand)
Hypothesis 2: Adapter molecules hold amino acids and interact with mRNA codons.
Amino acids
The adapter molecule was later found to be a small RNA called transfer RNA (tRNA).
A tRNA covalently linked to its corresponding amino acid is called an Enzymes called aminoacyl tRNA synthetases.
For each of the 20 amino acids, there is a different aminoacyl tRNA synthetase and one or more tRNAs.
Each tRNA.
Experimental Evidence that Amino Acids Are Transferred from tRNAs to Proteins
Experimental Evidence that Amino Acids Are Transferred from tRNAs to Proteins
Experimental Evidence that Amino Acids Are Transferred from tRNAs to Proteins
structure.
The CCA sequence at the 3' end of each tRNA is the The triplet loop at the opposite end of the cloverleaf is the anticodon that base pairs with the mRNA codon. The cloverleaf structure of tRNA folds over to produce a molecule with an L-shaped tertiary structure. .
Anticodon
Codon 5 mRNA
There are 61 different codons but only about 40 tRNAs in most cells.
To resolve this deficit, Francis Crick proposed the wobble hypothesis. This hypothesis proposes that the anticodon of tRNAs can still bind successfully to a codon whose third position requires a nonstandard base pairing. Thus, one tRNA is able to base pair with more than one type of codon.
Large subunit
Large subunit
Aminoacyl tRNA
Anticodon
All three tRNAs are bound at their anticodons to the corresponding mRNA codon.
The A site of the ribosome is the acceptor site for an aminoacyl tRNA. The P site is where a peptide bond forms that adds an amino acid to the growing polypeptide chain. The E site is where tRNAs no longer bound to an amino acid exit the ribosome.
Initiation
Initiation factor
Initiation factor
Aminoacyl tRNA
Initiation
Once the small ribosomal subunit is bound to the mRNA, the initiator aminoacyl tRNA binds to the AUG sequence.
The large subunit binds and completes the initiation complex.
Elongation
At the start of the elongation phase, the initiator tRNA is in the P site, and the E and A sites are empty.
An aminoacyl tRNA binds to the codon in the A site via complementary base pairing between anticodon and codon. .
Ribosome
Peptidyl site
tRNA
Aminoacyl site
3
Start codon
After peptide bond formation, the polypeptide on the tRNA in the P site is transferred to the tRNA in the A site.
The ribosome translocates down the mRNA by three nucleotides, and the tRNA attached to the growing protein moves into the P site.
3. Translocation
Ribosome moves down mRNA. The tRNA attached to polypeptide chain moves into P site. The A site is empty.
The A site is now available to accept a new aminoacyl tRNA for binding to the next codon.
The tRNA that was in the P site moves to the E site, and if the E site is occupied, that tRNA is ejected.
6. Translocation
Ribosome moves down mRNA. The tRNA attached to polypeptide chain moves into P site. Empty tRNA from P site moves to E site, where tRNA is ejected. The A site is empty again.
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Elongation
Polyribosomes, strings of translating ribosomes, assemble along an mRNA to increase the rate of protein production.
Ribosomes
Polyribosomes
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Termination
TERMINATION OF TRANSLATION
Release factor
TERMINATION OF TRANSLATION
mRNA 5
TERMINATION OF TRANSLATION
Large subunit
5 mRNA
Small subunit
TERMINATION OF TRANSLATION
Release factor
TERMINATION OF TRANSLATION
mRNA 5
TERMINATION OF TRANSLATION
Large subunit
5 mRNA
Small subunit
Post-Translational Modifications
Most proteins go through an extensive series of processing steps, collectively called posttranslational modification, before they are ready to go to work in a cell.
Molecular chaperones speed folding of the protein. Folding determines a protein's shape and therefore its function.
Point Mutations
A single base change is called a point mutation. Point mutations can result from errors in DNA replication.
3 5
Original DNA
5 3
DNA replication
Point Mutations
A point mutation that causes a change in the amino acid sequence of the protein is called a missense mutation. Such mutations are often deleterious, meaning they reduce an individuals fitness.
For example, sickle-cell disease results from a missense mutation in the hemoglobin gene. Mutations that do not change the amino acid sequence of the protein are known as silent mutations. Mutations that change the amino acid to a similar amino acid and therefroe there is not phenotypic change are called neutral mutations.
Sickle-Cell Disease Results from a Point Mutation in the Gene for Hemoglobin
DNA point mutation can lead to a different amino acid sequence. DNA sequence 5 of non-template (coding) strand Amino acid sequence Normal Normal red blood cells DNA sequence 5 of non-template (coding) strand Amino acid sequence Mutant Sickled red blood cells 3 3 Phenotype
Chromosome-Level Mutations
Chromosome-Level Mutations
Figure 12-6bc
Key Concepts
Inside ribosomes, mRNAs are translated to proteins
via intermediary molecules called transfer RNAs. Transfer RNAs carry an amino acid and have a threebase-pair anticodon, which binds to a three-baselong mRNA codon. The amino acid carried by the transfer RNA is then added to the growing protein via formation of a peptide bond.
Key Concepts
After the enzyme RNA polymerase binds to a
specific site in DNA with the help of other proteins, it catalyzes the production of an RNA molecule. The base sequence of the RNA produced is complementary to the base sequence of the DNA template strand.
regions called exons, while others are encoded by gene regions called introns. During RNA processing, introns are removed and the ends of the RNA receive a cap and tail.
Key Concepts
Inside ribosomes, mRNAs are translated to
proteins via intermediary molecules called transfer RNAs. Transfer RNAs carry an amino acid and have a three-base-pair anticodon, which binds to a three-base-long mRNA codon. The amino acid carried by the transfer RNA is then added to the growing protein via formation of a peptide bond.