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Ribosomes, Transcription, and Translation
The genetic information stored in DNA is a living archive of instructions that cells use to accomplish the functions of life. Inside each cell, catalysts seek out the appropriate information from this archive and use it to build new proteins — proteins that make up the structures of the cell, run the biochemical reactions in the cell, and are sometimes manufactured for export. Although all of the cells that make up a multicellular organism contain identical genetic information, functionally different cells within the organism use different sets of catalysts to express only specific portions of these instructions to accomplish the functions of life.
How Is Genetic Information Passed on in Dividing Cells?
When a cell divides, it creates one copy of its genetic information — in the form of DNA molecules — for each of the two resulting daughter cells. The accuracy of these copies determines the health and inherited features of the nascent cells, so it is essential that the process of DNA replication be as accurate as possible (Figure 1).
One factor that helps ensure precise replication is the double-helical structure of DNA itself. In particular, the two strands of the DNA double helix are made up of combinations of molecules called nucleotides . DNA is constructed from just four different nucleotides — adenine (A), thymine (T), cytosine (C), and guanine (G) — each of which is named for the nitrogenous base it contains. Moreover, the nucleotides that form one strand of the DNA double helix always bond with the nucleotides in the other strand according to a pattern known as complementary base-pairing — specifically, A always pairs with T, and C always pairs with G (Figure 2). Thus, during cell division, the paired strands unravel and each strand serves as the template for synthesis of a new complementary strand.
What Are the Initial Steps in Accessing Genetic Information?
RNA molecules differ from DNA molecules in several important ways: They are single stranded rather than double stranded; their sugar component is a ribose rather than a deoxyribose; and they include uracil (U) nucleotides rather than thymine (T) nucleotides (Figure 4). Also, because they are single strands, RNA molecules don't form helices; rather, they fold into complex structures that are stabilized by internal complementary base-pairing.
mRNA is the most variable class of RNA, and there are literally thousands of different mRNA molecules present in a cell at any given time. Some mRNA molecules are abundant, numbering in the hundreds or thousands, as is often true of transcripts encoding structural proteins. Other mRNAs are quite rare, with perhaps only a single copy present, as is sometimes the case for transcripts that encode signaling proteins. mRNAs also vary in how long-lived they are. In eukaryotes, transcripts for structural proteins may remain intact for over ten hours, whereas transcripts for signaling proteins may be degraded in less than ten minutes.
Cells can be characterized by the spectrum of mRNA molecules present within them; this spectrum is called the transcriptome . Whereas each cell in a multicellular organism carries the same DNA or genome, its transcriptome varies widely according to cell type and function. For instance, the insulin-producing cells of the pancreas contain transcripts for insulin, but bone cells do not. Even though bone cells carry the gene for insulin, this gene is not transcribed. Therefore, the transcriptome functions as a kind of catalog of all of the genes that are being expressed in a cell at a particular point in time.
What Is the Function of Ribosomes?
Ribosomes are complexes of rRNA molecules and proteins, and they can be observed in electron micrographs of cells. Sometimes, ribosomes are visible as clusters, called polyribosomes. In eukaryotes (but not in prokaryotes), some of the ribosomes are attached to internal membranes, where they synthesize the proteins that will later reside in those membranes, or are destined for secretion (Figure 6). Although only a few rRNA molecules are present in each ribosome, these molecules make up about half of the ribosomal mass. The remaining mass consists of a number of proteins — nearly 60 in prokaryotic cells and over 80 in eukaryotic cells.
Within the ribosome, the rRNA molecules direct the catalytic steps of protein synthesis — the stitching together of amino acids to make a protein molecule. In fact, rRNA is sometimes called a ribozyme or catalytic RNA to reflect this function.
How Does the Whole Process Result in New Proteins?
After the transcription of DNA to mRNA is complete, translation — or the reading of these mRNAs to make proteins — begins. Recall that mRNA molecules are single stranded, and the order of their bases — A, U, C, and G — is complementary to that in specific portions of the cell's DNA. Each mRNA dictates the order in which amino acids should be added to a growing protein as it is synthesized. In fact, every amino acid is represented by a three-nucleotide sequence or codon along the mRNA molecule. For example, AGC is the mRNA codon for the amino acid serine, and UAA is a signal to stop translating a protein — also called the stop codon (Figure 7).
Molecules of tRNA are responsible for matching amino acids with the appropriate codons in mRNA. Each tRNA molecule has two distinct ends, one of which binds to a specific amino acid, and the other which binds to the corresponding mRNA codon. During translation , these tRNAs carry amino acids to the ribosome and join with their complementary codons. Then, the assembled amino acids are joined together as the ribosome, with its resident rRNAs, moves along the mRNA molecule in a ratchet-like motion. The resulting protein chains can be hundreds of amino acids in length, and synthesizing these molecules requires a huge amount of chemical energy (Figure 8).
In prokaryotic cells, transcription (DNA to mRNA) and translation (mRNA to protein) are so closely linked that translation usually begins before transcription is complete. In eukaryotic cells, however, the two processes are separated in both space and time: mRNAs are synthesized in the nucleus, and proteins are later made in the cytoplasm.
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18 Protein Synthesis I: Transcription
Andrea Bierema
Learning Objectives
Students will be able to:
- Explain the processes necessary for transcription to begin.
- Explain how DNA is transcribed to create an mRNA sequence.
- Describe the role of polymerase in transcription.
- Recognize that protein synthesis regulation (i.e., changes in gene expression) allow cells to respond to changes in the environment.
- Explain which gene-expression regulatory factors are at play for transcription.
This chapter focuses on how transcription works; that is, how information coded in the DNA molecule is read to create an mRNA sequence. Please see the previous chapter for a general overview of transcription and DNA and RNA bases before continuing to read this chapter.
The Process of Transcription: A First Look
Let’s first look at a basic overview of what the process of transcription looks like. At the beginning of the following video, you will see that transcription is regulated by a variety of proteins. By “regulation”, we mean that certain proteins are needed for transcription to start and some proteins can even prevent transcription from happening. Transcription is happening throughout your body all of the time, but not every gene is constantly being transcribed in every cell; it is regulated by different proteins and depends on which proteins your body needs in which cells.
For closed captioning or to view the full transcript see the video on YouTube . Or click on the “YouTube” link in the video.
Now that you have watched a basic overview of transcription, test your knowledge with the following activity in which you will place the following transcription steps in the correct order.
Role of the Polymerase
The polymerase is an enzyme—and a protein—that aids in the transcription process. The polymerase was depicted in the previous video. Now let’s look more closely at what is happening within the polymerase in relation to the steps described previously.
Transcription Regulation
The overview above depicted components of transcription regulation. Basically, there are proteins that have to bind to the DNA, and each other, before the polymerase can begin transcription.
There are many steps along the way of protein synthesis and gene expression is regulated. Gene expression is when a gene in DNA is “turned on,” that is, used to make the protein it specifies. Not all the genes in your body are turned on at the same time or in the same cells or parts of the body.
For many genes, transcription is the key on/off control point: if a gene is not transcribed in a cell, it can’t be used to make a protein in that cell.
If a gene does get transcribed, it is likely going to be used to make a protein (i.e. expressed). In general (but not always) the more often a gene is transcribed, the more protein that will be made.
Various factors control how much a gene is transcribed. For instance, how tightly the DNA of the gene is wound around its supporting proteins to form chromatin can affect a gene’s availability for transcription.
Proteins called transcription factors, however, play a particularly central role in regulating transcription. These important proteins help determine which genes are active in each cell of your body.
Transcription Factors
More information
In bacteria, RNA polymerase attaches right to the DNA of the promoter. You can see how this process works, and how it can be regulated by transcription factors, in the lac operon and trp operon videos.
What has to happen for a gene to be transcribed? The enzyme RNA polymerase , which makes a new RNA molecule from a DNA template, must attach to the DNA of the gene. It attaches to a spot called the promoter .
The RNA polymerase can attach to the promoter only with the help of proteins called general transcription factors . They are part of the cell’s core transcription “toolkit,” needed for the transcription of any gene.
How do Transcription Factors Work?
Turning Genes on in Specific Body Parts
Some genes need to be expressed in more than one body part or type of cell. For instance, suppose a gene needed to be turned on in your spine, skull, and fingertips, but not in the rest of your body. How can transcription factors make this pattern happen?
A gene with this type of pattern may have several enhancers (far-away clusters of binding sites for activators) or silencers (the same thing, but for repressors). Each enhancer or silencer may activate or repress the gene in a certain cell type or body part, binding transcription factors that are made in that part of the body. 1,2
Example: Modular Mouse
As an example, let’s consider a gene found in mice, called Tbx4 . This gene is important for the development of many different parts of the mouse body, including the blood vessels and hind legs. 3
During development, several well-defined enhancers drive Tbx4 expression in different parts of the mouse embryo. The diagram below shows some of the Tbx4 enhancers, each labeled with the body part where it produces expression.
Evolution of Development
Enhancers like those of the Tbx4 gene are called tissue-specific enhancers: they control a gene’s expression in a certain part of the body. Mutations of tissue-specific enhancers and silencers may play a key role in the evolution of body form. 4
How could that work? Suppose that a mutation, or change in DNA, happened in the coding sequence of the Tbx4 gene. The mutation would inactivate the gene everywhere in the body and a mouse without a normal copy would likely die. However, a mutation in an enhancer might just change the expression pattern a bit, leading to a new feature (e.g., a shorter leg) without killing the mouse.
Transcription Factors and Cellular “Logic”
Can cells do logic? Not in the same way as your amazing brain. However, cells can detect information and combine it to determine the correct response—in much the same way that your calculator detects pushed buttons and outputs an answer.
We can see an example of this “molecular logic” when we consider how transcription factors regulate genes. Many genes are controlled by several different transcription factors, with a specific combination needed to turn the gene on; this is particularly true in eukaryotes and is sometimes called combinatorial regulation. 5,6 For instance, a gene may be expressed only if activators A and B are present, and if repressor C is absent.
- Activator A is present only in skin cells
- Activator B is active only in cells receiving “divide now!” signals (growth factors) from neighbors
- Repressor C is produced when a cell’s DNA is damaged
A Closer Look
After reading through this section, view the following video, which depicts many of the regulatory factors described above.
Now that you have learned some of the basics, check out this example that applies what you learned to a specific case study.
The video above briefly describes the laboratory part of this research. To learn more about what this research looks like, check out the “ Stickleback Evolution Virtual Lab .”
Lactose Example
If you are still a little unsure of how switches work, then check out this HMMI Biointeractive interactive . The ability to digest lactose as an adult is a rare phenomenon in mammals. It evolved twice in humans—in Africa and Europe.
Now let’s test your understanding of transcription regulation!
Optional: Take the quiz below the simulation as you work your way through it. Note that if you are using your mouse to scroll down, it may not work at this point—use the scrolling bar at the right edge of your web browser instead.
The Process of Transcription: A Detailed Look
This chapter began with an overview of transcription and then focused more deeply on the role of the polymerase and regulatory proteins. Now watch the following video. It is an in-depth version of the first video of this chapter, incorporating aspects described throughout this chapter.
- Gilbert, S. F. (2000). Anatomy of the gene: Promoters and enhancers. In Developmental biology (6th ed.). Sunderland, MA: Sinauer Associates. Retrieved from https://www.ncbi.nlm.nih.gov/books/NBK10023/#_A751_ .
- Gilbert, S. F. (2000). Silencers. In Developmental biology (6th ed.). Sunderland, MA: Sinauer Associates. Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK10023/#_A777_ .
- Menke, D. B., Guenther, C., and Kingsley, D. M. (2008). Dual hindlimb control elements in the Tbx4 gene and region-specific control of bone size in vertebrate limbs. Development , 135 , 2543-2553. http://dx.doi.org/10.1242/dev.017384 .
- Wray, Gregory A. (2007). The evolutionary significance of cis -regulatory mutations. Nature Reviews Genetics , 8 , 206-216. http://dx.doi.org/10.1038/nrg2063 .
- Reece, J. B., Urry, L. A., Cain, M. L., Wasserman, S. A., Minorsky, P. V., and Jackson, R. B. (2011). Combinatorial control of gene activation. In Campbell Biology (10th ed., pp. 37). San Francisco, CA: Pearson.
- Reményi, Attila, Hans R. Schöler, and Matthias Wilmanns. (2004). Combinatorial control of gene expression. Nature Structural & Molecular Biology , 11 (9), 812. http://dx.doi.org/10.1038/nsmb820 . Retrieved from http://www.nature.com/scitable/content/Combinatorial-control-of-gene-expression-16976 .
Attributions
This chapter is a modified derivative of the following articles:
“ Regulated Transcription ” by Molecular and Cellular Biology Learning Center, Virtual Cell Animation Collection, CC BY-NC-ND 4.0.
“ Transcription ” by Molecular and Cellular Biology Learning Center, Virtual Cell Animation Collection, CC BY-NC-ND 4.0.
“ Transcription Factors ” by Khan Academy, CC BY-NC-SA 4.0. All Khan Academy content is available for free at ( www.khanacademy.org) .
An Interactive Introduction to Organismal and Molecular Biology, 2nd ed. Copyright © 2021 by Andrea Bierema is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License , except where otherwise noted.
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Protein synthesis
Protein synthesis n., plural: protein syntheses Definition: the creation of protein.
Table of Contents
Protein synthesis is the process of creating protein molecules. In biological systems, it involves amino acid synthesis, transcription, translation, and post-translational events. In amino acid synthesis , there is a set of biochemical processes that produce amino acids from carbon sources like glucose .
Not all amino acids are produced by the body; other amino acids are obtained from the diet . Within the cells, proteins are generated involving transcription and translation processes. In brief, transcription is the process by which the mRNA template is transcribed from DNA.
The template is used for the succeeding step, translation. In translation, the amino acids are linked together in a particular order based on the genetic code. After translation, the newly formed protein undergoes further processing, such as proteolysis, post-translational modification, and protein folding.
Proteins are made up of amino acids that are arrainged in orderly fashion. Discover how the cell organizes protein synthesis with the help of the RNAs. You’re more than welcome to join us in our Forum discussion: What does mRNA do in protein synthesis?
Protein Synthesis Definition
Protein synthesis is the creation of proteins. In biological systems, it is carried out inside the cell. In prokaryotes , it occurs in the cytoplasm . In eukaryotes , it initially occurs in the nucleus to create a transcript ( mRNA ) of the coding region of the DNA . The transcript leaves the nucleus and reaches the ribosomes for translation into a protein molecule with a specific sequence of amino acids .
Protein synthesis is the creation of proteins by cells that uses DNA , RNA , and various enzymes . It generally includes transcription , translation , and post-translational events, such as protein folding, modifications, and proteolysis.
The term protein came from Late Greek prōteios , prōtos , meaning “first”. The word synthesis came from Greek sunthesis , from suntithenai , meaning “to put together”. Variant : protein biosynthesis.
Forum Question: Where does protein synthesis take place? Best Answer!
Prokaryotic vs. Eukaryotic Protein Synthesis
Proteins are a major type of biomolecule that all living things require to thrive. Both prokaryotes and eukaryotes produce various proteins for multifarious processes and functions. Some proteins are used for structural purposes while others act as catalysts for biochemical reactions.
Prokaryotic and eukaryotic protein syntheses have distinct differences. For instance, protein synthesis in prokaryotes occurs in the cytoplasm. In eukaryotes, the first step (transcription) occurs in the nucleus. When the transcript (mRNA) is formed, it proceeds to the cytoplasm where ribosomes are located.
Here, the mRNA is translated into an amino acid chain. In the table below, differences between prokaryotic and eukaryotic protein syntheses are shown.
Genetic Code
In biology, a codon refers to the trinucleotides that specify for a particular amino acid. For example, Guanine-Cytosine-Cytosine (GCC) codes for the amino acid alanine .
The Guanine-Uracil-Uracil (GUU) codes for valine. Uracil-Adenine-Adenine (UAA) is a stop codon. The codon of the mRNA complements the trinucleotide (called anticodon) in the tRNA.
What is the Genetic Code? “The genetic code is the system that combines different components of protein synthesis, like DNA, mRNA, tRNA…” More FAQ answered by our biology expert in the Forum: What does mRNA do in protein synthesis? Come join us now!
mRNA, tRNA, and rRNA
mRNA , tRNA , and rRNA are the three major types of RNA involved in protein synthesis. The mRNA (or messenger RNA) carries the code for making a protein. In eukaryotes, it is formed inside the nucleus and consists of a 5′ cap, 5’UTR region, coding region, 3’UTR region, and poly(A) tail. The copy of a DNA segment for gene expression is located in its coding region. It begins with a start codon at 5’end and a stop codon at the 3′ end.
tRNA (or transfer RNA), as the name implies, transfers the specific amino acid to the ribosome to be added to the growing chain of amino acid. It consists of two major sites: (1) anticodon arm and (2) acceptor stem . The anticodon arm contains the anticodon that complementary base pairs with the codon of the mRNA. The acceptor stem is the site where a specific amino acid is attached (in this case, the tRNA with amino acid is called aminoacyl-tRNA ). A peptidyl-tRNA is the tRNA that holds the growing polypeptide chain.
Unlike the first two, rRNA (or ribosomal RNA) does not carry genetic information. Rather, it serves as one of the components of the ribosome. The ribosome is a cytoplasmic structure in cells of prokaryotes and eukaryotes that are known for serving as a site of protein synthesis. The ribosomes can be used to determine a prokaryote from a eukaryote.
Prokaryotes have 70S ribosomes whereas eukaryotes have 80S ribosomes. Both types, though, are each made up of two subunits of differing sizes. The larger subunit serves as the ribozyme that catalyzes the peptide bond formation between amino acids. rRNA has three binding sites: A, P, and E sites. The A (aminoacyl) site is where aminoacyl-tRNA docks. The P (peptidyl) site is where peptidyl-tRNA binds. The E (exit) site is where the tRNA leaves the ribosome.
Protein Biosynthesis Steps
Major steps of protein biosynthesis:
- Transcription
- Translation
- Post-translation
Transcription is the process by which an mRNA template , encoding the sequence of the protein in the form of a trinucleotide code, is transcribed from DNA to provide a template for translation through the help of the enzyme, RNA polymerase.
Thus, transcription is regarded as the first step of gene expression. Similar to DNA replication, the transcription proceeds in the 5′ → 3′ direction. But unlike DNA replication, transcription needs no primer to initiate the process and, instead of thymine, uracil pairs with adenine.
The steps of transcription are as follows: (1) Initiation, (2) Promoter escape, (3) Elongation, and (4) Termination.
Step 1: Initiation
The first step, initiation, is when the RNA polymerase, with the assistance of certain transcription factors, binds to the promoter of DNA. This leads to the opening (unwinding) of DNA at the promoter region, forming a transcription bubble . A transcription start site in the transcription bubble binds to the RNA polymerase, particularly to the latter’s initiating NTP and an extending NTP . A phase of abortive cycles of synthesis occurs resulting in the release of short mRNA transcripts (about 2 to 15 nucleotides).
Step 2: Promoter escape
The next step is for the RNA polymerase to escape the promoter so that it can enter into the elongation step.
Step 3: Elongation
During elongation, RNA polymerase traverses the template strand of the DNA and base pairs with the nucleotides on the template (noncoding) strand. This results in an mRNA transcript containing a copy of the coding strand of DNA, except for thymines that are replaced by uracils. The sugar-phosphate backbone forms through RNA polymerase.
Step 4: Termination
The last step is termination. During this phase, the hydrogen bonds of the RNA-DNA helix break. In eukaryotes, the mRNA transcript goes through further processing. It goes through polyadenylation , capping , and splicing .
Translation is the process in which amino acids are linked together in a specific order according to the rules specified by the genetic code. It occurs in the cytoplasm where the ribosomes are located. It consists of four phases:
- Activation (the amino acid is covalently bonded to the tRNA ),
- Initiation (the small subunit of the ribosome binds to 5′ end of mRNA with the help of initiation factors)
- Elongation (the next aminoacyl-tRNA in line binds to the ribosome along with GTP and an elongation factor)
- Termination (the A site of the ribosome faces a stop codon)
Post-translation Events
Following protein synthesis are events such as proteolysis and protein folding . Proteolysis refers to the cleavage of proteins by proteases. Through it, N-terminal, C-terminal, or the internal amino-acid residues are removed from the polypeptide.
Post-translational modification refers to the enzymatic processing of a polypeptide chain following translation and peptide bond formation. The ends and the side chains of the polypeptide may be modified in order to ensure proper cellular localization and function. Protein folding is the folding of the polypeptide chains to assume secondary and tertiary structures.
Watch this video about Protein Translation:
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Further reading.
- Protein Synthesis. (2019). Retrieved from Elmhurst.edu website: http://chemistry.elmhurst.edu/vchembook/584proteinsyn.html
- Protein Synthesis. (2019). Retrieved from Estrellamountain.edu website: https://www2.estrellamountain.edu/faculty/farabee/biobk/BioBookPROTSYn.html
- Protein Synthesis. (2019). Retrieved from Nau.edu website: http://www2.nau.edu/lrm22/lessons/protein-synthesis/protein-synthesis.htm
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Last updated on August 25th, 2023
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