Termination
Termination of translation occurs when the ribosome comes to one of the three stop codons, for which there is no tRNA. At this point, a protein called a release factor binds to the A site. The release factor causes the addition of a water molecule to the polypeptide chain, resulting in the release of the completed chain from the tRNA and ribosome. The ribosome, release factor, and tRNAs then dissociate and translation is complete. The process of translation is summarized in Figure below.
Figure 8.17
Summary of translation. Notice the mRNA segment within the ribosome. A tRNA anticodon binds to the appropriate codon, bringing the corresponding amino acid into the ribosome where it can be added to the growing polypeptide chain.
Post-Translational Modification and Protein Folding
The events following protein synthesis often include post-translational modification of the peptide chain and folding of the protein into its functional conformation. During and after synthesis, polypeptide chains often fold into secondary and then tertiary structures. These levels of organization were discussed in the chapter titled Chemical Basis of Life. Briefly, the primary structure of the protein is determined by the gene. The secondary and tertiary structures are determined by interactions between the amino acids within the protein (Figure below).
Many proteins undergo post-translational modification, allowing them to then perform their specific function. This may include the formation of disulfide bridges or attachment of any of a number of biochemical functional groups, such as phosphate groups, carbohydrates or lipids. Certain amino acids may be removed, or the polypeptide chain may be cut into two pieces. Lastly, two or more polypeptides may interact with each other, forming a functional protein with a quaternary structure.
Figure 8.18
The four stages of protein folding.
Lesson Summary
“DNA makes RNA makes protein” is the central dogma of molecular biology.
Transcription is the transfer of the genetic instructions from DNA to RNA.
Translation is the process of using the information in the mRNA to order amino acids into a polypeptide.
Transcription begins with the binding of RNA polymerase to the promoter of a gene.
Newly transcribed eukaryotic mRNA is not ready for translation; this mRNA requires extensive processing, including splicing and polyadenylation.
A codon is a three base code for one amino acid.
Start and stop codons signal the beginning and end of translation.
There are three stop codons.
The reading frame is the frame of three bases in which the mRNA is read.
The genetic code is universal.
Translation involves the interactions of the three types of RNA.
After the protein is made, it must fold into its functional conformation.
Review Questions
What is meant by “DNA → RNA → Protein?”
Describe transcription.
List some of the modification mRNAs undergoes before translation.
Define introns and exons.
Describe mRNA splicing.
Describe the role of the Genetic Code in translation.
What is a reading frame?
Discuss what is meant by the universal genetic code.
Explain translation.
What is protein folding?
Further Reading / Supplemental Links
Transcription Animation
http://www-class.unl.edu/biochem/gp2/m_biology/animation/gene/gene_a2.html
Campbell, N.A. and Reece, J.B. Biology, Seventh Edition, Benjamin Cummings, San Francisco, CA, 2005.
Biggs, A., Hagins, W.C., Kapicka, C., Lundgren, L., Rillero, P., Tallman, K.G., and Zike, D., Biology: The Dynamics of Life, California Edition, Glencoe Science, Columbus, OH, 2005.
Nowicki S., Biology, McDougal Littell, Evanston, IL, 2008.
The National Health Museum:
http://www.accessexcellence.org/RC/VL/GG/rna_synth.html
Genetic Science Learning Center:
http://learn.genetics.utah.edu/units/basics/transcribe/
Kimball’s Biology Pages:
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Codons.html
The National Health Museum:
http://www.accessexcellence.org/RC/VL/GG/genetic.html
The National Health Museum:
http://www.accessexcellence.org/RC/VL/GG/protein_synthesis.html
http://en.wikipedia.org
Vocabulary
5' cap
A modified guanine nucleotide added to the 5’-end of the pre-mRNA; crucial for recognition and proper attachment of the mRNA to the ribosome.
A site
Within the ribosome; binds a tRNA with an attached amino acid.
alternative splicing
Process by which pre-mRNA messages can be spliced in several different configurations, allowing a single gene to encode multiple proteins.
E site
Within the ribosome; contains the tRNA that no longer has an attached amino acid.
editing
The process of changing the nucleotide sequence of an mRNA to allow the mRNA to produce multiple proteins.
elongation
The segment of transcription that the further addition of RNA nucleotides; also refers to the process during translation of adding additional amino acids to the growing polypeptide chain.
exon
The region of a gene that contains the code for producing a protein.
frameshift mutation
Mutation that disrupt the reading frame by insertions or deletions of a non-multiple of three nucleotide bases.
gene
A segment of DNA that contains the information necessary to encode an RNA molecule or a protein.
genetic code
The code in which the language of nucleotides is used to create the language of amino acids.
initiation
The start of transcription; signaled by the transcription initiation complex formed by the promoter, transcription factors, and RNA polymerase; also refers to the start of translation.
intron
Long region of DNA that has no identified function; separates exons.
P site
Within the ribosome; contains the tRNA with the growing polypeptide chain attached.
pre-mRNA
Newly transcribed eukaryotic mRNA; not yet ready for translation.
polyadenylation
The addition of a string of adenines to the mRNAs 3’-end; signals the termination of translation in eukaryotes.
reading frame
The frame of three bases (codon) in which the mRNA is translated.
Rho-dependent termination
Involves a protein factor (Rho), which destabilizes the RNA-DNA hybrid, releasing the newly synthesized mRNA from the elongation complex.
ribosome
Non-membrane bound organelle; site of protein synthesis.
RNA polymerase
The enzyme that reads a template strand of DNA during transcription to synthesize the complementary RNA strand.
splicing
The process by which introns are removed from pre-mRNA.
spliceosome
RNA-protein complex that usually performs splicing of the pre-mRNA.
termination
The end of transcription; involves the detachment of the RNA from the DNA template; also refers to the end of translation when the ribosome comes to one of the three stop codons, for which there is no tRNA.
transcription
The process that uses the DNA sequence to make an mRNA molecule.
translation
The process of converting the language of nucleotides (in the mRNA) into the language of amino acids.
Points to Consider
We know what happens when everything goes right. The result is a correctly made protein that functions properly and maintains homeostasis.
However, what happ
ens when things do not go right? What can lead to a protein not being made correctly or not functioning correctly?
Can you think of possible mechanisms that may that can interfere with protein synthesis?
How can a change in the DNA sequence lead to a different protein?
Lesson 8.3: Mutation
Lesson Objectives
Define mutation.
Describe common causes of mutation.
Describe common types of mutation.
Illustrate common chromosomal alterations.
Discuss potential outcomes of point mutations.
List and describe three common types of point mutations.
Discuss consequences of effect-on-function mutations.
Discuss the significance of germline and somatic mutations.
Explain why some mutations are harmful and some beneficial.
Discuss the saying, “Without beneficial mutations, evolution can not occur.”
Introduction
You have learned that an allele is an alternative form of a gene. Most, if not all genes have alternative forms causing the resulting protein to function slightly differently. But are there alleles that cause proteins to function dramatically differently or not function at all? A mutation is a change in the DNA or RNA sequence, and many mutations result in new alleles. Some of these changes can be beneficial. In fact, evolution could not take place without the genetic variation that results from mutations. But some mutations are harmful. There are also chromosomal mutations, large changes with dramatic effects.
Causes of Mutation
Is it possible for mutations to occur spontaneously, or does there have to be a cause of the mutation? Well, the answer is that both are possible. A spontaneous mutation can just happen, possibly due to a mistake during DNA replication or transcription. Mutations may also occur during mitosis and meiosis. A mutation caused by an environmental factor, or mutagen, is known as an induced mutation. Typical mutagens include chemicals, like those inhaled while smoking, and radiation, such as X-rays, ultraviolet light, and nuclear radiation. Table below lists some spontaneous mutations that are common.
Common Spontaneous Mutations Tautomerism a base is changed by the repositioning of a hydrogen atom
Depurination loss of a purine base (A or G)
Deamination spontaneous deamination of 5-methycytosine
Transition a purine to purine, or a pyrimidine to pyrimidine change
Transversion a purine becomes a pyrimidine, or vice versa
Types of Mutations
In multicellular organisms, mutations can be subdivided into germline mutations, which can be passed on to descendants, and somatic mutations, which cannot be transmitted to the next generation. Germline mutations change the DNA sequence within a sperm or egg cell, and therefore can be inherited. This inherited mutation may result in a class of diseases known as a genetic disease. The mutation may lead to a nonfunctional protein, and the embryo may not develop properly or survive. Somatic mutations may affect the proper functioning of the cell with the mutation. During DNA replication, the mutation will be copied. The two daughter cells formed after cell division will both carry the mutation. This may lead to the development of many cells that do not function optimally, resulting a less than optimal phenotype. Various types of mutations can all have severe effects on the individual. These include point mutations, framehift mutations and chromosomal alterations.
Keep in mind, some mutations may be beneficial or have no effect. Mutations that have no effect will not affect the expression of the gene or the sequence of amino acids in an encoded protein.
Chromosomal Alterations
Chromosomal alterations are large changes in the chromosome structure. They occur when a section of a chromosome breaks and rejoins incorrectly, or does not rejoin at all. Sometimes the segment may join backwards or reattach to another chromosome altogether. These mutations are very serious and usually lethal to the zygote or embryo. If the embryo does survive, the resulting organism is usually sterile and thus, unable to pass along the mutation.
The five types of chromosomal alterations are deletions, duplications, insertions, inversions, and translocations (Figure below).
Deletions: removal of a large chromosomal region, leading to loss of the genes within that region.
Duplications (or amplifications): lead to multiple copies of a chromosomal region, increasing the number of the genes located within that region. Some genes may be duplicated in their entirety.
Insertions: the addition of material from one chromosome to a nonhomologous chromosome.
Inversions: reversing the orientation of a chromosomal segment.
Translocations: interchange of genetic material between nonhomologous chromosomes.
Figure 8.19
Chromosomal alterations. Deletion: the blue segment has been removed; Duplication: the blue segment has been duplicated; Inversions: the blue segment has been reversed; Insertion: the yellow segment has been removed from chromosome 4 and placed into chromosome 20; Translocation: a green segment from chromosome 4 has been exchanged with a red segment from chromosome 20.
Point Mutations
As the name implies, point mutations occur at a single site within the DNA. Lets go back to our earlier example from lesson 8.2:
THE BIG FAT CAT ATE THE RED RAT.
A change at any one position could result in a sequence that does not make sense. Such as:
THE BIG FAT SAT ATE THE RED RAT.
As shown above, point mutations exchange one nucleotide for another and are known as base substitution mutations. These mutations are often caused either by chemicals or by a mistake during DNA replication. A transition exchanges a purine for a purine (A ↔ G) or a pyrimidine for a pyrimidine, (C ↔ T), and is the most common point mutation. Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T ↔ A/G). Point mutations that occur within the protein coding region of a gene are classified by the effect on the resulting protein:
Silent mutations: which code for the same amino acid.
Missense mutations: which code for a different amino acid.
Nonsense mutations: which code for a premature stop codon.
These mutations may result in a protein with the same function, with altered function, or with no function. Silent mutations, as they code for the same amino acid, will have no altered effect on the protein. Missense mutations may have a minor effect or a dramatic effect on the protein. Nonsense mutations usually have the most dramatic effet. Depending on the position of the premature stop codon, nonsense mutations may result in an unstable mRNA that cannot be translated, or in a much "smaller" protein without any activity.
Deletions and Insertions
As pointed out earlier, a deletion or insertion in the DNA can alter the reading frame. Deletions remove one or more nucleotides from the DNA, whereas insertions add one or more nucleotides into the DNA. These mutations in the coding region of a gene may also alter splicing of the mRNA (splice site mutation). Mutations which alter the reading frame are known as frameshift mutations. Splice site mutations and frameshift mutations both can dramatically change the mRNA, altering the final protein product.
Effect-on-Function Mutations
For a cell or organism to maintain homeostasis, the proteins work in a highly defined and regulated manner. It may take just one protein not working correctly to interrupt homeostasis. A protein having more or less activity than normal, or a different activity or function, may be enough to interrupt homeostasis. Mutations that may result in altered function of the gene product or protein are loss-of-function and gain-of-function mutations, as well as dominant negative mutations.
Loss-of-function mutations result in a gene product or protein having less or no function. Gain-of-function mutations result in the gene product or protein having a new and abnormal function. Dominant negative mutations have an altered gene product that acts in a dominant manner to the wild-type gene product.<
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Significance of Mutation
Imagine the coding sequence (broken up into codons) TAC CCC GGG. This is a fairly generic coding sequence. It transcribes into the following mRNA: AUG GGG CCC, which would translate into start-glycine-proline. As glycine is encoded by four codons (GGG, GGA, GGC, GGU), any change in the third position of that codon will have no effect. The same is true for the codon for proline. But what about changes in the other nucleotides in the sequence? They could have potentially dramatic effects. The effects depend on the outcome of the mutation. Obviously any change to the start codon will interrupt the start of translation. Turning the simple glycine into the nonpolar (and relatively large) tryptophan (UGG codon) could have dramatic effects on the function of the protein.
Once again, a mutation is the change in the DNA or RNA sequence. As discussed earlier, in multicellular organisms, mutations can be subdivided into germline mutations and somatic mutations. Germline mutations occur in the DNA of sex cells, or gametes, and are therefore potentially very serious. These mutations can be passed to the next generation. Somatic mutations, which occur in somatic, or body, cells, cannot be passed to the next generation (offspring). Mutations can be harmful, beneficial, or have no effect. If a mutation does not change the amino acid sequence in a protein, the mutation will have no effect. In fact, the overwhelming majority of mutations have no significant effect, since DNA repair mechanisms are able to mend most of the changes before they become permanent. Furthermore, many organisms have mechanisms for eliminating otherwise permanently mutated somatic cells.
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