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As you may know, I have been teaching BIO101 (and also the BIO102 Lab) to non-traditional students in an adult education program for about twelve years now. Every now and then I muse about it publicly on the blog (see, and for a few short posts about various aspects of it - from the use of videos, to the use of a classroom blog, to the importance of Open Access so students can read primary literature). The quality of students in this program has steadily risen over the years, but I am still highly constrained with time: I have eight 4-hour meetings with the students over eight weeks. In this period I have to teach them all of biology they need for their non-science majors, plus leave enough time for each student to give a presentation (on the science of their favorite plant and animal) and for two exams. Thus I have to strip the lectures to the bare bones, and hope that those bare bones are what non-science majors really need to know: concepts rather than factoids, relationship with the rest of their lives rather than relationship with the other sciences. Thus I follow my lectures with videos and classroom discussions, and their homework consists of finding cool biology videos or articles and posting the links on the classroom blog for all to see. A couple of times I used malaria as a thread that connected all the topics - from cell biology to ecology to physiology to evolution.
Audio translation is much more complex than transcription. In audio translation, someone fluent in both the original and target language must translate what is being said into the target language. Translation is extremely subjective and sensitive to context, as anyone who has. It's always intrigued me what the difference is between these two terms. I can guess that translation is a contextual translation whereby the original foreign text is maintained with any language idiosyncrasies intact, whereas transliteration is translating the text verbatim, during which any context may be lost. Any help clearing up this would be appreciated, and an example from another.
I think that worked well but it is hard to do. They also write a final paper on some aspect of physiology.Another new development is that the administration has realized that most of the faculty have been with the school for many years. We are experienced, and apparently we know what we are doing. Thus they recently gave us much more freedom to design our own syllabus instead of following a pre-defined one, as long as the ultimate goals of the class remain the same. I am not exactly sure when am I teaching the BIO101 lectures again (late Fall, Spring?) but I want to start rethinking my class early. I am also worried that, since I am not actively doing research in the lab and thus not following the literature as closely, that some of the things I teach are now out-dated. Not that anyone can possibly keep up with all the advances in all the areas of Biology which is so huge, but at least big updates that affect teaching of introductory courses are stuff I need to know.I need to catch up and upgrade my lecture notes.
And what better way than crowdsource! So, over the new few weeks, I will re-post my old lecture notes (note that they are just intros - discussions and videos etc. Follow them in the classroom) and will ask you to fact-check me. If I got something wrong or something is out of date, let me know (but don't push just your own preferred hypothesis if a question is not yet settled - give me the entire controversy explanation instead). If something is glaringly missing, let me know. If something can be said in a nicer language - edit my sentences. If you are aware of cool images, articles, blog-posts, videos, podcasts, visualizations, animations, games, etc.
That can be used to explain these basic concepts, let me know. And at the end, once we do this with all the lectures, let's discuss the overall syllabus - is there a better way to organize all this material for such a fast-paced class.Today, we continue with the cell - the basic processes of DNA transcription, RNA translation, and protein synthesis. See the previous lectures:Here is the third BIO101 lecture (from May 08, 2006). Again, I'd appreciate comments on the correctness as well as suggestions for improvement.-BIO101 - Bora Zivkovic - Lecture 1 - Part 3The DNA codeDNA is a long double-stranded molecule residing inside the nucleus of every cell. It is usually tightly coiled forming chromosomes in which it is protected by proteins.Each of the two strands of the DNA molecule is a chain of smaller molecules.
Each link in the chain is composed of one sugar molecule, one phosphate molecule and one nucleotide molecule. There are four types of nucleotides (or 'bases') in the DNA: adenine (A), thymine (T), guanine (G) and cytosine (C). The two strands of DNA are structured in such a way that an adenine on one strand is always attached to a thymine on the other strand, and the guanine of one strand is always bound to cytosine on the other strand. Thus, the two strands of the DNA molecule are mirror-images of each other.The exact sequence of nucleotides of all of the DNA on all the chromosomes is the genome. Each cell in the body has exactly the same chromosomes and exactly the same genome (with some exceptions we will cover later).A gene is a small portion of the genome - a sequence of nucleotides that is expressed together and codes for a single protein (polypeptide) molecule.Cell uses the genes to synthesize proteins.
This is a two-step process. The first step is transcription in which the sequence of one gene is replicated in an RNA molecule.
The second step is translation in which the RNA molecule serves as a code for the formation of an amino-acid chain (a polypeptide).TranscriptionFor a gene to be expressed, i.e., translated into RNA, that portion of the DNA has to be uncoiled and freed of the protective proteins. An enzyme, called DNA polymerase, 'reads' the DNA (the sequence of bases on one of the two strands of the DNA molecule) and builds a single-stranded chain of the RNA molecule as a complementary, mirror-image sequence. Again, where there is a G in DNA, there will be C in the RNA and vice versa. Instead of thymine, RNA has uracil (U). Wherever in the DNA strand there is an A, there will be a U in the RNA, and wherever there is a T on the DNA molecule, there will be an A in the RNA.Once the whole gene (100s to 10,000s of bases in a row) is transcribed, the RNA molecule detaches. The RNA (called messenger RNA or mRNA) may be further modified by addition of more A bases at its tail, by addition of other small molecules to some of the nucleotides and by excision of some portions ( introns) out of the chain. The removal of introns (the non-coding regions) and putting together the remaining segments - exons - into a single chain again, is called RNA splicing.
RNA splicing allows for one gene to code for multiple related kinds of proteins, as alternative patterns of splicing may be controlled by various factors in the cell.Unlike DNA, the mRNA molecule is capable of exiting the nucleus through the pores in the nuclear membrane. It enters the endoplasmatic reticulum and attaches itself to one of the membranes in the rough ER.TranslationThree types of RNA are involved in the translation process: mRNA which carries the genetic code, rRNA which aids in the formation of the ribosome, and tRNA which brings individual amino-acids to the ribosome.
Translation is controlled by various enzymes that recognize specific nucleotide sequences.The genetic sequence (nucleotide sequence of a gene) translates into a polypeptide (amino-acid sequence of a protein) in a 3-to-1 fashion. Three nuclotides in a row code for one amino-acid.
There are a total of 20 amino-acids used to build all proteins in our bodies. Some amino-acids are coded by a single triplet code, or codon. Other amino-acids may be coded by several different RNA sequences. There is also a START sequence (coding for fMet) and a STOP sequence that does not code for any amino-acid. The genetic code is (almost) universal.
Except for a few microorganisms, all of life uses the same genetic code - the same triplets of nucleotides code for the same amino-acids.When the ribosome is assembled around a molecule of mRNA, the translation begins with the reading of the first triplet. Small tRNA molecules bring in the individual amino-acids and attach them to the mRNA, as well as to each other, forming a chain of amino-acids.
When a stop signal is reached, the entire complex disassociates. The ribosome, the mRNA, the tRNAs and the enzymes are then either degraded or re-used for another translational event.Protein synthesis - post-translational modificationsTranslation of the DNA/RNA code into a sequence of amino-acids is just the beginning of the process of protein synthesis.The exact sequence of amino-acids in a polypeptide chain is the primary structure of the protein.As different amino-acids are molecules of somewhat different shapes, sizes and electrical polarities, they react with each other. The attractive and repulsive forces between amino-acids cause the chain to fold in various ways. The three-dimensional shape of the polypeptide chain due to the chemical properties of its component amino-acids is called the secondary structure of the protein.Enzymes called chaperonins further modify the three-dimensional structure of the protein by folding it in particular ways.
The 3D structure of a protein is its most important property as the functionality of a protein depends on its shape - it can react with other molecules only if the two molecules fit into each other like a key and a lock. The 3D structure of the fully folded protein is its tertiary structure.Prions, the causes of such diseases as Mad Cow Disease, Scrapie and Kreutzfeld-Jacob disease, are proteins. The primary and secondary structure of the prion is almost identical to the normally expressed proteins in our brain cells, but the tertiary structure is different - they are folded into different shapes. When a prion enters a healthy brain cell, it is capable of denaturing (unwinding) the native protein and then reshaping it in the same shape as the prion. Thus one prion molecule makes two - those two go on and make four, those four make eight, and so on, until the whole brain is just one liquifiied spongy mass.Another aspect of the tertiary structure of the protein is addition of small molecules to the chain.
For instance, phosphate groups may be attached to the protein (giving it additional energy). Also, short chains of sugars are usually bound to the tail-end of the protein. These sugar chains serve as 'ZIP-code tags' for the protein, informing carrier molecules exactly where in the cell this protein needs to be carried to (usually within vesicles that bud off the Rough Enodplasmic Reticulum or the Golgi apparatus).
The elements of the cytoskeleton are used as conduits ('elevators and escalators') to shuttle proteins to where in the cell they are needed.Many proteins are composed of more than one polypeptide chain. For instance, hemoglobin is formed by binding together four subunits. Each subunit also has a heme molecule attached to it, and an ion of iron attached to the heme (this iron is where oxygen binds to hemogolobin). This larger, more complex structure of the protein is its quaternary structure.See animations:Previously in this series:The views expressed are those of the author(s) and are not necessarily those of Scientific American. ABOUT THE AUTHOR(S).
Thegenetic information stored in DNA is a living archive of instructions thatcells use to accomplish the functions of life. Inside each cell, catalysts seekout the appropriate information from this archive and use it to build newproteins — proteins that make up the structures of the cell, run thebiochemical reactions in the cell, and are sometimes manufactured for export. Although allof the cells that make up a multicellular organism contain identicalgenetic information, functionally different cells within the organism usedifferent sets of catalysts to express only specific portions of theseinstructions to accomplish the functions of life. One factor that helps ensure precise is the itself. In particular, the two strands of the DNA double helix are made up of combinations of molecules called nucleotides.
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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. © 2009 All rights reserved.In most multicellular organisms, every cell carries the same DNA, but this genetic information is used in varying ways by different types of cells. In other words, what a cell 'does' within an organism dictates which of its genes are expressed.
Nerve cells, for example, synthesize an abundance of chemicals called neurotransmitters, which they use to send messages to other cells, whereas muscle cells load themselves with the protein-based filaments necessary for muscle contractions. © 2009 All rights reserved.Transcription is the first step in decoding a cell's genetic information. During, enzymes called RNA polymerases build RNA molecules that are complementary to a portion of one strand of the DNA double helix (Figure 3).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. © 2009 All rights reserved.Three general classes of RNA molecules are involved in expressing the genes encoded within a cell's DNA. Messenger RNA (mRNA) molecules carry the coding sequences for protein synthesis and are called transcripts; ribosomal RNA (rRNA) molecules form the core of a cell's ribosomes (the structures in which protein synthesis takes place); and transfer RNA (tRNA) molecules carry amino acids to the ribosomes during protein synthesis. In eukaryotic cells, each class of RNA has its own polymerase, whereas in prokaryotic cells, a single RNA polymerase synthesizes the different class of RNA. Other types of RNA also exist but are not as well understood, although they appear to play regulatory roles in gene expression and also be involved in protection against invading viruses.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. Courtesy of Dr. Abraham Minsky (2014). All rights reserved.Ribosomes are the sites in a cell in which protein synthesis takes place.
Cells have many ribosomes, and the exact number depends on how active a particular cell is in synthesizing proteins. For example, rapidly growing cells usually have a large number of ribosomes (Figure 5).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.Eukaryotic and prokaryotic ribosomes are different from each other as a result of divergent evolution.
These differences are exploited by antibiotics, which are designed to inhibit the prokaryotic ribosomes of infectious bacteria without affecting eukaryotic ribosomes, thereby not interfering with the cells of the sick host. 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, 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).
(1) Translation begins when a ribosome (gray) docks on a start codon (red) of an mRNA molecule in the cytoplasm. (2) Next, tRNA molecules attached to amino acids (spheres) dock at the corresponding triplet codon sequence on the mRNA molecule. (3, 4, and 5) This process repeats over and over, with multiple tRNAs docking and connecting successive amino acids into a growing chain that elongates out of the top of the ribosome.
(6) When the ribosome encounters a stop codon, it falls off the mRNA molecule and releases the protein for use in the cell. Cellular DNA contains instructions for building the various proteins thecellneeds to survive.
In order for a cell to manufacture these proteins,specificgenes within its DNA must first be transcribed into molecules of mRNA;then,these transcripts must be translated into chains of amino acids, whichlaterfold into fully functional proteins. Although all of the cells in amulticellular organism contain the same set of genetic information, thetranscriptomesof different cells vary depending on the cells' structure and functionin theorganism.
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