Download From DNA to Protein

15
FROM DNA TO PROTEIN
Chapter Outline
15.1 THE CONNECTION BETWEEN DNA, RNA, AND PROTEIN
Proteins are specified by genes
The pathway form gene to polypeptide involves transcription and translation
The genetic code is written in three-letter words using a four letter alphabet
15.2 TRANSCRIPTION: DNA-DIRECTED RNA SYNTHESIS
RNA polymerases work like DNA polymerases, but require no primer
Specific sequences of nucleotides in the DNA indicate where transcription of a gene begins and ends
15.3 PRODUCTION OF mRNAs IN EUKARYOTES
Eukaryotic protein-coding genes are transcribed into precursor-mRNAs that are modified in the nucleus
Introns are removed during pre-mRNA processing to produce the translatable mRNA
Introns contribute to protein variability
15.4 TRANSLATION: mRNA-DIRECTED POLYPEPTIDE SYNTHESIS
tRNAs are small, highly specialized RNAs that bring amino acids to the ribosome
Ribosomes are rRNA-protein complexes that work as automated protein assembly machines
Translation initiation brings the ribosomal subunits, an mRNA, and the first aminoacyl-tRNA together
Polypeptide chains grow during the elongation stage of translation
Termination releases a completed polypeptide from the ribosome
Multiple ribosomes simultaneously translate a single mRNA
Newly synthesized polypeptides are processed and folded into finished form
Finished proteins contain sorting signals that direct them to cellular locations
Base-pair mutations can affect protein structure and function
Objectives
After reading the chapter, you should be able to:
1.
Know how the structure and behavior of DNA determines the structure and behavior of the three forms of RNA
during transcription.
2.
Understand the role the three forms of RNA play in determining the primary structure of polypeptide chains during
translation.
3.
Understand the types of mutations and their role in genetic variation.
4.
Explain why the central dogma is too simple a model
5.
Understand the importance of the degeneracy of the genetic code
6.
Understand the sequence and location of the events in transcription and translation
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Key Terms
one gene-one enzyme
hypothesis
degenerate code
exon shuffling
wobble hypothesis
one gene-one
polypeptide
hypothesis
universal code
transfer RNAs
(tRNAs)
RNA polymerases
anticodon
signal peptide (or
signal sequence)
transcription
promoter
signal recognition
particle (SRP)
translation
transcription unit
aminoacylation
(or charging)
aminoacyl-tRNA
mutations
template strand
TATA box
messenger RNA
(mRNA)
precursor-mRNA (premRNA)
aminoacyl-tRNA
synthetase
base-pair substitution
mutations
ribosomes
missense mutation
genetic code
5' cap
codon
ribosomal RNA
(rRNA)
nonsense mutation
poly(A) tail
sense codons
introns
ribosome binding site
frameshift mutation
start codon
mRNA splicing
peptidyl-tRNA
initiator codon
spliceosome
peptidyl transferase
stop codons
ribozyme
nonsense codons
small
ribonucleoprotein
particles
termination codons
alternative splicing
polysome
(polyribosome)
silent mutation
release factor (or
termination factor)
Lecture Outline
15.1 The Connection between DNA, RNA, and Protein
A. Genes specify proteins as demonstrated by alkaptonuria, which is a genetic mutation in a gene for a key
enzyme.
B. The use of Neurospora, a fungi that mutates easily, confirmed that mutations in a gene result in changes in
the protein encoded (Figure 15.2).
C. The one gene–one polypeptide hypothesis represents the analysis of this study.
D. The pathway from gene to polypeptide uses transcription and translation (Figure 15.3).
1. Transcription is the process by which DNA is used to create an RNA copy.
2. Translation is the use of the RNA strand to create a polypeptide.
E. The process of going from “DNA RNA Protein” is called the central dogma (Figure 15.3).
F. The genetic code is written in three-letter words using a four-letter alphabet.
1. The alphabet for DNA is made up of adenine, thymine, guanine, and cytosine (A, T, G, and C).
2. The alphabet for RNA is made up of adenine, uracil, guanine, and cytosine (A, U, G, and C).
3. The genetic code had to be at least three letters coding for one amino acid, and it was proven to be a
triplet code (Figure 15.4).
4. The exact genetic code has 64 possible codons (Figure 15.5).
a. Some codons code for start sites.
b. Some code for stop codons.
c. Only two amino acids, tryptophan and methionine, have a single codon.
d. Most are redundant and are coded by multiple codon combinations.
e. The universal code, with few exceptions, is the same in all living organisms.
15.2 Transcription: DNA-Directed RNA Synthesis (Figure 15.6)
A. RNA transcription is similar to DNA replication.
B. Only one of the two DNA strands acts a template for RNA synthesis.
1. RNA polymerases catalyze the assembly of RNA without a primer.
2. Specific sequences indicate where gene transcription should begin.
C. The structural organization of the gene and the outline of how it is transcribed is depicted in Figure 15.7.
1. A promoter initiates transcription (Figure 15.7, step 1).
2. An RNA polymerase molecule binds to the DNA at the beginning of the gene to be transcribed.
3. The DNA begins to unwind at the front of the RNA polymerase.
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4.
5.
During transcription, RNA nucleotides are base paired one after another with the template DNA bases.
The RNA copy is released when the entire gene has been transcribed. The unwound region of the DNA
rewinds into a double helix.
D. Three main steps of transcription:
1. Initiation: RNA polymerase binds to the promoter, unwinds the DNA, and initiates transcription at the
start point.
2. Elongation: RNA polymerase moves along the DNA, unwinding it and adding new RNA nucleotides
to the transcript in the 5' to 3' direction. Behind the enzyme, the DNA strands reform into a double
helix.
3. Termination: The complete RNA molecule is released from the template DNA, RNA polymerase
leaves the DNA, and the double helix reforms.
E. The promoter of protein-coding genes and transcription initiates and specifies where transcription begins.
1. In eukaryotes, RNA pol II transcribes protein-coding genes.
2. RNA pol I and III transcribe genes for non-protein coding RNAs.
3. Promoters are upstream of the genes and more complex in eukaryotes.
4. A key element in eukaryotes is the TATA box, which is recognized by transcription factors.
F. A protein binding at a termination sequence releases RNA and RNA polymerase from the template and is
called a terminator.
15.3 Production of mRNAs in Eukaryotes
A. mRNAs have noncoding regions that do not code for protein elements.
B. Eukaryotic protein-coding genes make a precursor-mRNA that is modified in the nucleus (Figure 15.8).
C. Modifications of pre-mRNA and mRNA ends include a 5' cap and an mRNA tail.
D. RNA digesting enzymes degrade the poly (A) tail, which extends the functional life of the mRNA.
E. Eukaryotic cells have introns that interrupt the protein coding sequence and exons that are the protein
coding regions.
F. Introns are removed during pre-mRNA processing to produce translatable mRNA (Figure 15.9).
G. Small nuclear ribonucleoprotein plus the pre-mRNA form a spliceosome to “loop out” the intron (Figure
15.9).
H. Introns increase protein variability by alternative splicing and exon shuffling.
1. Alternative splicing can join exons in different combinations to produce different mRNAs from a
single gene (Figure 15.10).
2. Exon shuffling mixes functional regions to allow the evolution of new proteins.
15.4 Translation: mRNA-Directed Polypeptide Synthesis
A. The ribosome binds to the mRNA strand, and tRNA brings amino acids to complex into a polypeptide
(Figure 15.11).
B. Transfer RNAs (tRNA) are small, highly specialized RNAs that bring amino acids to the ribosome.
1. tRNA have a highly distinctive structure (Figure 15.12).
2. It has an anticodon region that binds to the codon and brings an amino acid on the other end.
C. Addition of amino acids to their corresponding tRNAs is called aminoacylation or “charging” (Figure
15.13).
1. There are twenty different enzymes that catalyze this charging, and they are collectively called
aminoacyl-tRNA synthetases.
2. This process requires energy from an ATP molecule.
D. Ribosomes have one large and one small subunit (Figure 15.14).
E. Ribosomes are rRNA-protein complexes that work as automated protein assembly machines (Figure
15.14).
F. Translation initiation brings the ribosomal subunits, an mRNA, and the first aminoacyl-tRNA together
(Figure 15.15).
1. Each step in translation initiation is aided by proteins termed initiation factors.
2. Met-tRNA with GTP bound to it and the small ribosomal subunit form a complex.
3. The complex binds to the 5' cap of the mRNA and scans along it until it reaches the AUG start codon.
4. The large ribosomal subunit binds, and GTP is hydrolyzed, completing initiation.
G. Steps to the elongation phase of translation (Figure 15.16)
1. An aminoacyl-tRNA binds the A site.
2. Peptidyl transferase cleaves the amino acid from the P site tRNA and bonds it to the amino acid on the
A site tRNA.
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The ribosome translocates along the mRNA to the next codon, thereby bringing the tRNA with the
growing polypeptide to the P site and moving the empty tRNA to the E site.
4. When translocation is complete, the empty tRNA in the E site is released, and the cycle is ready to go
again.
Termination releases a completed polypeptide from the ribosome (Figure 15.17).
1. The ribosome reaches a termination codon (UAA, UAG, or UGA).
2. A release factor binds to the termination codon in the A site and causes the ribosome to disassemble.
Multiple ribosomes can simultaneously translate a single mRNA (Figure 15.19).
Newly synthesized polypeptides are processed and folded into a finished form.
1. The final shape is not always random and may require the assistance of a chaperone protein to reach
the correct 3D shape.
2. Some proteins are processed to an inactive form and then wait to be activated.
Finished proteins contain sorting signals that direct them to cellular locations (Figure 15.20).
Base-pair mutations can affect protein structure and function (Figure 15.21).
A missense mutation in a gene for one of the two polypeptides of hemoglobin is the cause of sickle-cell
disease (Figure 15.22).
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