Presentation on theme: "Today is Thursday, January 8 th, 2015 Pre-Class: DNA makes…what? In This Lesson: Protein Synthesis (Lesson 2 of 3)"— Presentation transcript:
Today is Thursday, January 8 th, 2015 Pre-Class: DNA makes…what? In This Lesson: Protein Synthesis (Lesson 2 of 3)
Today’s Agenda The Central Dogma Transcription Translation Mutations Arts and Crafts The Longest Word Ever Where is this in my book? – Chapters – NOTE: This lesson can get very complicated. – USE YOUR TEXTBOOK AND ESPECIALLY THE GLOSSARY.
By the end of this lesson… You should be able to describe in full detail how a DNA gene becomes a protein and thus a trait. You should be able to explain how those genes are turned on and off. You should be able to analyze the effects of a mutation on the genetic code.
The Big Idea Remember those experiments to determine whether DNA or proteins were the basics of heredity? – Damn skippy you do. Well, as you know, there’s a very close relationship between proteins and DNA. So close, in fact, that it is perhaps even more of a “core idea” to biology than is evolution. – We call it the central dogma (of biology). The word “dogma” is usually used to describe the underlying principles of a religion that are never doubted. That should tell you something about how big a deal this is.
The Central Dogma NOTE: DNA Replication does not have to happen before transcription. DNATraitProteinRNA Transcription Translation Replication
The Central Dogma DNATraitProteinRNA Transcription Translation Nucleus (if eukaryotic) Ribosome
Big Ideas from the Big Idea From the central dogma it should be obvious that: – This is the mechanism for DNA to endow an organism with traits. – The nucleus speaks in DNA, the ribosome speaks in RNA. – DNA gets a whole lot of credit but it’s protein that does all the work.
Where We’re Going Following the central dogma, we’re going to review how we get from DNA to RNA to protein. Then we’ll look at what happens when something goes wrong (as usual).
The Origin of Traits So you can see that strong early evidence for the effect of genes and role of proteins was provided by metabolism. If the DNA responsible for production of particular enzymes is non-functional, the damaged metabolic pathway will reveal itself with a particular phenotype. Here’s what I mean…
The Origin of Traits All of this phenotypic analysis led researchers to develop the one gene, one enzyme hypothesis. – Damaged DNA will express itself in the form of a nutritional disorder, allowing the gene to be mapped. – Of course, this isn’t entirely true for all genes, but it helped in the early days.
The Process Okay, let’s start reviewing the process of transcription. Transcription is the creation of mRNA from DNA. RNA (including mRNA) has three main differences from DNA. Do you remember them?
About RNA… RNA is another kind of nucleic acid. – Ribonucleic acid. It is usually single-stranded, DNA is double-stranded. Instead of having Deoxyribose, it has Ribose. Instead of having Thymine, it has Uracil.
Mmm, sugar! Sugar differences: – Deoxyribose is missing an oxygen.
Compare and Contrast Using these pictures and your notes, organize a T-chart comparing DNA and RNA.
Here’s what I got… DNARNA BasesA, C, G, TA, C, G, U SugarDeoxyriboseRibose StrandsTwoOne
Types of RNA There are several types of RNA out there as well, with the main three being: – mRNA (messenger RNA) – tRNA (transfer RNA) – rRNA (ribosomal RNA) Remember these and watch for them to arise later throughout transcription and translation. FYI, all three are made from DNA.
The Process of Transcription Just like in replication, the DNA is unwound, but this time by RNA polymerase. RNA nucleotides begin to be added to a new mRNA strand. – This time, not by DNA polymerase but… – RNA polymerase again! (the enzyme that does it all) Key: Every time the mRNA molecule would have a T, a U for Uracil is placed instead. – Uracil is also a pyrimidine.
Transcription ---H--- Deoxy- ribose P Thymine Deoxy- ribose P Cytosine Deoxy- ribose P Adenine RNA Polymerase breaks H-bondsStrands move apartRNA Polymerase makes mRNA mRNA exits nucleusDNA re-coils Deoxy- ribose P Thymine Deoxy- ribose P Guanine Deoxy- ribose P Adenine Ribose Adenine P Ribose Guanine P Ribose Uracil P Ribose Adenine P Ribose Guanine P Ribose Uracil P ---H---
Transcription Details Instead of a replication bubble, RNA polymerase opens a transcription bubble. RNA is polymerized 5’ to 3’, just like DNA. The strand of DNA that is used for transcription is the antisense strand (or template strand or reading strand). The strand of DNA not used for transcription is the sense strand (or coding strand). – It has the same sequence as the mRNA strand.
---H--- Deoxy- ribose P Thymine Deoxy- ribose P Cytosine Deoxy- ribose P Adenine Deoxy- ribose P Thymine Deoxy- ribose P Guanine Deoxy- ribose P Adenine Ribose Adenine P Ribose Guanine P Ribose Uracil P Ribose Adenine P Ribose Guanine P Ribose Uracil P ---H--- Sense Strand Antisense Strand
Practice Gene Expression – Transcription POGIL – Up to first STOP sign – we’re going to go over this one!
The Road Ahead It’s about to get complicated up in hurr… What I’m going to do is give you some key vocabulary words now, then repeat them exactly later on. You can write them now, later, or in context as I reach the concepts during the presentation.
One other thing… Much of the focus of this lesson, more so than when you covered this in previous biology classes, is concerned with control. How does a cell control transcription? How do we prevent, say, digestive stomach enzymes from being manufactured in the brain? – Your brain cells have those genes, after all. – Every cell has all the genes.
Vocabulary Summary [same as later] Promoter – DNA region where RNA polymerase attaches and transcription starts. Operator – Prokaryotic DNA region to which a repressor may bind. Repressor – A protein that attaches to DNA and blocks transcription. Prokaryotes: Near or in promoter. Eukaryotes: Could be near the promoter, could be far away. Activator – A protein that attaches to DNA and aids transcription. Prokaryotes: Near or in promoter. Eukaryotes: Could be near the promoter, could be far away. Terminator – Prokaryotic DNA region that signals transcription to stop. Closest eukaryotic equivalent is the polyadenylation signal.
Transcription Details Like DNA replication, we know a bit more about transcription from studying prokaryotes, but it’s similar in eukaryotes too. Here’s the sequence: 1.Initiation There’s going to be a lot on this one. 2.Elongation 3.Termination
1. Initiation: Prokaryotes Meet Barry the Bacterium. – He’s E. coli, just so we’re clear. He likes lactose. – The sugar found in milk. He doesn’t get it all the time, though, and he needs a special group of enzymes to digest it. Barry’s got a “choice” to make. Mmmmm! I lurrves me some lactose!
Barry’s Choice Help a bacterium out. Barry can do one of two things: – Barry can make those lactose-related enzymes all the time, and then use them every once in a while when he gets some lactose. – Barry can wait till he gets lactose, then make some of those enzymes. Which makes more sense biologically? – To put it another way, do you get all the groceries you need for the year or get them on an as-needed basis periodically?
Barry Made the Right Choice Transcription and translation cost energy, so it’s best to do them only when necessary. Prokaryotes use something called a repressor to block several genes for lactose- related enzymes, which we collectively call the lac operon. If I were a real bacterium, I wouldn’t have a face.
Simulation PhET: Gene Machine – lac Operon
About Operons Operons are groups of genes controlled by a single region of DNA called a promoter. – The promoter is simply an area upstream of the genes where RNA polymerase can bind to the DNA. In between the promoter and the genes is the operator. – The operator is a stretch of DNA responsible for allowing or denying transcription. How? lac z lac y lac a Lactose-Related Genes Operator Promoter
About Operons Attached to the operator may be a repressor, which is a protein molecule that simply blocks RNA polymerase. Here’s the cool part: – For the lac operon, the presence of lactose removes the repressor. – RNA polymerase is then able to transcribe the relevant genes, which includes an enzyme that degrades lactose. Thus, this is negative feedback. Lactose removes the repressor so RNA polymerase makes lactase, which removes lactose. lac z lac y lac a Lactose-Related Genes Operator Promoter Repressor RNA Polymerase Lactose RNA Polymerase
Removing the Repressor Repressor leaving mRNA.
Other Uses of Operons In the previous case, the presence of lactose stimulated a gene to be expressed. Sometimes the absence of a substance will start gene expression. For example, the trp operon controls five genes that make tryptophan, an amino acid. The repressor detaches when tryptophan is not present. – This is also an example of negative feedback. trp e trp d trp c Tryptophan-Producing Genes Operator Promoter Repressor trp b trp a Tryptophan RNA Polymerase
Trp Operon Metaphor Think of the trp operon like a generator you’d hook up to a house or to a building. You don’t want it running most of the time, unless you’re out of power. – Then you want it on. In the same way, the trp operon is off when the cell is getting tryptophan, but when tryptophan runs out, the operon is activated. – Once the cell makes enough tryptophan, the amino acid (tryptophan) itself will reactivate the repressor and turn the operon off again.
Operon Regulation Inducible operons are those that are turned on when an inducer is present. – For the lac operon, its repressor is deactivated by the presence of allolactose (the inducer). Allolactose’s presence deactivates the repressor. Repressible operons are those that are turned off when something is present. – For the trp operon, tryptophan’s presence activates the repressor.
Positive versus Negative Control Both the trp and lac operons are examples of negative control. – Why negative? – Because an active repressor switches them off. Positive control is when the presence of something activates an activator. – An activator is something that will promote the attachment of RNA polymerase. – An activator turns the genes on.
Initiation in Eukaryotes Eukaryotes are similar, but may sometimes use an activator and transcription factors that need to bind to get things started. – We still use repressors, too. Sometimes. – We do not use operons, or at least they haven’t been discovered in us yet. Instead, we use little complexes that together are called transcription units. They’re similar to operons.
1. Initiation: Eukaryotes A bunch of transcription factors bind to a promoter upstream of the actual gene and signal RNA polymerase II to bind. – Transcription factors are proteins that turn transcription on and off. – How do they know where to bond? The promoter region has in it a TATA box. The TATA box is actually a stretch of “TATA” followed by “A.” Combined, the RNA polymerase and transcription factors make up the transcription initiation complex.
Video! Transcription – Advanced
Further Eukaryotic Differences Okay, here’s where it gets a little complicated. – Note that these next few slides will not be covered on the test. Eukaryotes have two major “curveballs” thrown into the transcription process: – The most obvious one is the nucleus. – The second one is the structure of chromatin. Remember that chromatin is DNA wrapped around spherical histone proteins. The histone/DNA complex is called a nucleosome. https://www.broadinstitute.org/files/news/images/2010/chromatin_states_2a.png Chromatin video
Eukaryotic Initiation The first thing that needs to happen is that the histones need to get out of the way. – Yep, enzymes do it. – Histone acetylation (adding acetyl groups) opens the DNA for transcription. – Histone methylation (adding –CH 3 methyl groups) closes the DNA and makes transcription less likely. Remember from way back in our organic chemistry stuff – methyl groups tend to inactivate stuff.
Eukaryotic Initiation Sometimes genes themselves are methylated. – The “letters” are not changed, but they’re “tagged” with –CH 3 groups. – This methylation stays with the genes and can be passed on to offspring. – This is the foundation of epigenetics (inheritance via means other than the nucleotide sequence of DNA). – Epigenetic inheritance is reversible and explains genomic imprinting. Remember that? When a set of one parent’s genes are shut down?
Back to Initiation Eukaryotic DNA has a lot of control elements, which are sections of DNA to which transcription factors bind. – Transcription factors, not RNA polymerase itself. These control elements can be all over the place in the DNA strand. – Proximal control elements are near the gene promoter. – Distal control elements are far from the gene promoter. Groups of distal control elements are called enhancers. Key: All of these components need to come together to start transcription.
So what’s the difference? Prokaryotes’ operons tend to be relatively simple. Eukaryotes’ genes may be regulated by myriad combinations of control elements and transcription factors, allowing for all kinds of different gene expression. – Yep, genetics is complicated and awesome.
Initiation Summary Prokaryotes – RNA polymerase attaches to a promoter and transcribes genes. – It may be stopped by a repressor attached to the operon. Eukaryotes – Transcription factors (proteins) bind to the promoter. The promoter has a region in it called the TATA box. – Once the transcription factors have bonded, then RNA polymerase II can bind.
2. Elongation RNA polymerase transcribes DNA into mRNA as it unwinds. – Speed is ~20 bases a second. Typical genes are bases total. – Error rate is ~1 in 100,000 bases. However, since this is mRNA and not a more permanent DNA, error checking generally isn’t worth it.
3. Termination RNA polymerase stops at a termination sequence. – This is different for prokaryotes and eukaryotes – more on this on the next slide. RNA GC hairpin turn
3. Termination Eukaryote Difference In prokaryotes, RNA polymerase releases at the termination signal (called the terminator). In eukaryotes, RNA polymerase II eventually reaches a polyadenylation signal. – The signal is “AAUAAA.” It then sails past the signal for hundreds of nucleotides. – The actual mRNA (not RNA polymerase II) is cut free after about 10 to 35, however. – RNA polymerase II makes more mRNA that just gets degraded until enzymes catch up to it and release it.
Further Differences In eukaryotes, transcription is accomplished using three different RNA polymerase enzymes: – RNA Polymerase I makes rRNA. More on that later. – RNA Polymerase II makes mRNA. What we just learned. – RNA Polymerase III makes tRNA. More on that later. They function differently by only responding to certain promoter sequences in the DNA.
Vocabulary Summary [same as before] Promoter – DNA region where RNA polymerase attaches and transcription starts. Operator – Prokaryotic DNA region to which a repressor may bind. Repressor – A protein that attaches to DNA and blocks transcription. Prokaryotes: Near or in promoter. Eukaryotes: Could be near the promoter, could be far away. Activator – A protein that attaches to DNA and aids transcription. Prokaryotes: Near or in promoter. Eukaryotes: Could be near the promoter, could be far away. Terminator – Prokaryotic DNA region that signals transcription to stop. Closest eukaryotic equivalent is the polyadenylation signal.
Okay, time for a “kindabreak.” Here’s what you need to do: – Get a piece of masking tape long enough to write the words “APproPRIAteLY JOinED” on it. – Write the words “APproPRIAteLY JOinED” on it exactly like that, leaving slightly more space between the letters than you normally would. – Now tear the piece of masking tape between letters of different cases (i.e. between “o” and “P”). – Tape only the lower case letters to your desk in sequence. – What did you spell?
mRNA Processing In prokaryotes, all of the mRNA that is transcribed is used, but in eukaryotes, there are stretches of DNA that are transcribed into mRNA but are later removed. – Introns are the parts of the mRNA removed. These parts interrupt (like your CAPITAL letters). – Exons are the parts of the mRNA that are kept. These parts are expressed (like your lower case letters).
Why introns? So why make introns at all if they’re just going to be removed? It turns out that different combinations of introns and exons, even from the same stretch of DNA, can ultimately make different proteins. – This is called alternative RNA splicing. – Case in point: As you’ll see in your POGIL, humans have 25,000 genes but make 100,000 proteins. – Introns/exon combinations explain the variability.
mRNA Processing The original, complete mRNA molecule is called the primary mRNA transcript (or pre-mRNA): Then the introns are excised (confusing?) using spliceosomes. – Spliceosomes are proteins composed of small nuclear ribonucleoproteins, or snRNPs (pronounced “snurps”). Once edited, the mRNA is known as the mature mRNA transcript: But what are those things on the ends?
Further Processing A 5’ cap and a poly-A tail are then added. – The 5’ cap is a GTP molecule for protection/signaling. – The poly-A tail is a stretch of 50 to 250 “A” bases for protection and aid in transport out of the nucleus. The poly-A tail is added by poly A polymerase. Remember the polyadenylation signal?
Further Processing In order, a completed eukaryotic mRNA molecule has: – 5’ Cap – Leader (space between cap and start codon) – Start Codon (AUG – methionine – more later) – Stop Codon (UAA/UAG/UGA – more later) – Trailer (space between stop codon and poly-A tail) The polyadenylation signal sequence is in the trailer. – Poly-A Tail Note: Technically, this mRNA processing happens virtually instantaneously as mRNA is transcribed.
One last thing on RNA splicing… It appears that the sequence of exons in a protein leads to different domains once the peptide is completed. – Domains are different functional sections of the protein.
Whew. That’s a lot. Let’s recap: – Spliceosomes animation
Stop Codons, Trailers, and Terminators In case you’re wondering: – A stop codon tells the ribosome to stop translating – that’s not a part of transcription. – A trailer is a region of “concluding mRNA.” It’s not made into proteins. – A termination signal ends production of the intended mRNA strand. In eukaryotes, RNA polymerase II keeps going and makes a new strand that has no 5’ cap so it gets degraded. Eventually, enzymes catch up to RNA polymerase and detach it from the DNA.
Sidney Altman Yale University Thomas Cech University of Colorado Aside: RNA Self-Splicing? Remember when we talked about ribozymes, those little bits of RNA that can act as enzymes? Well, they’re capable of self- splicing, suggesting that they act as an enzyme. As we learned before, ribozyme RNA may be one of the earliest adaptations of life. – This stuff was discovered in the 1980s by Sidney Altman and Thomas Cech.
What happens to the mRNA strand? In case you’re wondering, the mRNA strand, upon exiting the nucleus, is… …IMMEDIATELY IN PERIL! Enzymes called exonucleases break down the mRNA strand starting at the 3’ end. – That poly-A tail makes a lot of sense now, right? – The poly-A tail prevents the “good” parts of the mRNA strand from being immediately degraded. The free RNA bases can be used again during another round of transcription.
Practice Gene Expression – Transcription POGIL – Finish it – we’re going to go over it!
Now then… …let’s get to the actual protein synthesis. Up until this point we’ve talked about the process of transcription, or processes associated with transcription like RNA splicing. – Remember, transcription is DNA mRNA. Now let’s cover the next step: mRNA Protein. And which organelle is responsible for protein synthesis? – That’s right, ribosomes. – Good job [insert student name here].
Translation Going from mRNA to protein is the process of translation. In prokaryotes, since there is no RNA processing, transcription and translation happen simultaneously. Transcription Translation mRNA Protein Bacterial Chromosome
Translation in Prokaryotes As the mRNA strand grows, ribosomes attach to it and create protein. – By the way, a group of ribosomes reading mRNA concurrently is called a polyribosome.
Translation in Eukaryotes In eukaryotes, the process takes a bit longer due to two main “separations:” – Time mRNA must be processed. It takes about an hour to go from DNA to protein. – Location Eukaryotes have nuclei; the mRNA must exit the nucleus before translation can begin.
Translation in Eukaryotes Here’s a nice summary image. Look for things that are familiar.
Translation: The General Process Translation can be summarized in two general steps. Obviously, these each have their own details, but it really comes down to this: 1.mRNA exits the nucleus through a nuclear pore. 2.Two halves of a ribosome assemble on the mRNA and use its “instructions” to make protein. Some quick reminders: – Protein monomer = amino acid. – Protein polymer = polypeptide.
Universal Genetic Code Here’s where you need a reference table. Universal Genetic Code [found in Fact Sheets]
Codons Every three mRNA bases read by the ribosome is called a codon. Each codon “codes for” a particular amino acid. – Except for the three stop codons. Example: AUG CCC GAU UCG UGA – AUG = Methionine (always the start) – CCC = Proline – GAU = Aspartate – UCG = Serine – UGA = [STOP]
Translation Example Here’s my mRNA sequence: – CGGAUGCUGAAGUGAGGC Now here it is with the codons separated: – CGG | AUG | CUG | AAG | UGA | GGC Now here it is when the amino acids linked together: – Methionine-Leucine-Lysine Notice how I did not start at the beginning (not a start codon) and stopped at the stop codon.
Aside: The Discovery of Codons Francis Crick (that Crick) determined the triplet codon concept. In the 1960s, Marshall Nirenberg and Har Gobind Khorana figured out that codons were linked to particular amino acids. – They made a synthetic mRNA strand of entirely U’s. – UUU was then determined to code for phenylalanine. KhoranaNirenberg
Codons Take a look at your universal genetic code sheet. Here are some things to note: – Because there are 4 different bases and 3 letters in a codon, there are 64 different possible codons. 4 * 4 * 4 = 64. – The code is redundant (sometimes called degenerate). Most amino acids are linked to multiple codons. – For many amino acids, only the first two letters are important. Take a look at the letter combinations that make proline, for example. Once you get the first two letters, the last doesn’t matter. We’ll look further into this concept when we explore “wobble.”
Practice Gene Expression – Translation POGIL – Up to first STOP sign – we’re going to go over it!
Translation So how do codons code for amino acids? – With another form of RNA called tRNA (transfer RNA). tRNA averages around 76 nucleotides of RNA in length. – Transfer RNA has a cloverleaf structure and has two especially important parts: An amino acid attachment site. A three-base anticodon.
Anticodons As you might have guessed, the anticodon on tRNA is the opposite of the codon on mRNA. – Example codon: AUG – Corresponding anticodon: UAC Thus, tRNA appears at the correct codon because it has, to use the old expression, the other half of the BFF necklace. – tRNA brings to the growing polypeptide the correct amino acid.
Wobble A moment ago I mentioned how there are (in some cases) many codons for the same amino acid. Part of the reason why is that the third base in each codon may not be entirely necessary. Crick (yep, him) discovered that the third base doesn’t have the same base-pairing “strictness” as the other two bases do.
Wobble Furthermore, tRNA actually has other bases besides A, U, C, G that sometimes act like wild cards. – Mainly I, for inosine. I serves as a “match” for A, U, or G. The third base is therefore “wobbly” and isn’t quite so essential. – It’s actually called “the wobble base.”
Wobble First or Second Letter in mRNA (5’ to 3’) First or Second Letter in tRNA (3’ to 5’) AU UA CG GC Third Letter in mRNA (5’ to 3’)Third Letter in tRNA (3’ to 5’) A or GU UA U or CG GC U, C, AI
Last thing on wobble… In case you need more evidence for wobble, keep in mind that there are 61 different mRNA codons (excluding “stop”), yet 45 different tRNA molecules. Explain that one without using wobble…
Replication, Transcription, Translation DNA Antisense Strand DNA Sense Strand mRNA Codon tRNA Anticodon Amino Acid TTGAAC UUGAsparagine AGTTCAUCAAGUSerine TCGAGC UCGSerine ACATGTUGUACACysteine ACCTGGUGGACCTryptophan
tRNA tRNA is “loaded” with amino acids by an enzyme called aminoacyl tRNA synthetase. – ATP is hydrolyzed to AMP and the energy from those bonds is stored in the tRNA-amino acid bond. – It’s unstable and high-energy, so the amino acid can “pop off” easily. That’ll be important later.
Aminoacyl tRNA Synthetase Notice how two phosphate groups are used to “load” a tRNA molecule with an amino acid.
Summary Okay, let’s do a little recap. DNA is used to make mRNA in transcription. mRNA is processed. – Addition of 5’ cap. – Addition of poly-A tail. – Removal of introns. mRNA exits the nucleus. tRNA matches every three bases on the mRNA (a codon) with its own anticodon (three tRNA bases) and brings over the appropriate amino acid.
Coordination But wait…where is all this happening? How is this process being coordinated? Key: The process of translation is governed by the ribosome. – Ribosomes are made of a third kind of RNA called rRNA. – They have two parts – a large and a small subunit. – They also have three “sites” used in reading the mRNA. Let’s look closer…
Aside: Ribosome Differences Turns out that ribosomes are slightly different in prokaryotes and eukaryotes. Widely-used antibiotics Streptomycin and Tetracyclin work by disabling prokaryotic ribosomes.
Ribosome Sites A Site – Aminoacyl-tRNA site – tRNA in this site has the amino acid waiting to be added to the polypeptide chain. Memory Device: The A site has the awaiting amino acid as it arrives. P Site – Peptidyl-tRNA site – tRNA in this site has the polypeptide chain. Memory Device: The P site has the polypeptide as it polymerizes. E Site – Exit site – tRNA in this site does not have an amino acid and will leave the ribosome.
Large Ribosomal Subunit (rRNA) E Site A Site P Site Small Ribosomal Subunit (rRNA) tRNA U A C tRNA U A C Translation Mechanism MET tRNA U A U tRNA U A U A U GACCA U A G CA U G A AUG A U C AUG U ISO MET A U GACCA U A G CA U G A AUG A U C AUG U tRNA U A U tRNA U A U tRNA U A C tRNA U A C tRNA G G G tRNA G G G PRO mRNA This process continues until a stop codon is reached, at which point the mRNA strand, tRNA units, and rRNA subunits all are released. Start Codon (Methionine)
Translation Sequence The process of translation is divided into three steps similar to transcription. (leave room in your notes for more!) 1.Initiation mRNA, tRNA, rRNA come together. 2.Elongation Amino acids are added as the polypeptide grows. 3.Termination The stop codon is reached.
1. Initiation Details Initiation factors are small proteins that bring together tRNA and the small rRNA subunit at the start codon of mRNA, methionine. The large subunit arrives just afterward.
2. Elongation Details Elongation factors bring the correct tRNA into the A site. rRNA catalyzes the formation of a peptide bond between the two amino acids (A site and P site). – GTP is used for power. The ribosome moves down the mRNA and the third tRNA exits from the E site.
3. Termination A protein known as a release factor binds to codons UAA, UAG, and UGA – the stop codons. Water is added to the end of the polypeptide chain to end it. Proteins may then undergo post-translational modification before they are functional.
A reminder… Remember what the rough endoplasmic reticulum does? – The rough ER makes proteins…for export from the cell. – Free ribosomes, on the other hand, make proteins that stay local. Key: Translation is slightly different for ribosomes attached to the rough ER as compared to free ribosomes.
The Ultimate Goal If a ribosome is producing a protein made for secretion, the cell adds a signal peptide. – A signal peptide attaches to the forming polypeptide and acts as…a signal. – Key: This occurs while the ribosome is making the polypeptide – the process stops briefly.
The Ultimate Goal A signal-recognition particle (SRP) can then interact with the signal peptide and guide the ribosome to the ER. – This explains how the rough ER becomes rough. – Ribosomes move to it!
Practice Gene Expression – Translation POGIL – Up to second STOP sign – we’re going to go over it!
The Big Picture “Label” everything you can by talking it out with your partner. DNA RNA polymerase RNA processing Poly-A Tail Amino acids tRNA Aminoacyl tRNA synthetase Large and small rRNA subunits E P A sites Polypeptide Nuclear pore 5’ Cap
Semi-Closure We’re not done yet, but here’s a sort of philosophical thought for you: – “What is a gene?” Previously I’ve said it’s a stretch of DNA that codes for a particular protein, but that’s not entirely accurate. – Some genes code for multiple proteins. – Some genes code for RNA (not proteins). – Some genes overlap. – What about those promoters and control units and stuff?
The Currently-Accepted Definition According to your book: “A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule.”
Genes and Proteins Let’s review something else too – the idea that humans make around 100,000 proteins from 25,000 genes. How? – Different combinations of introns and exons. – The protein domains (the exons that are combined) may be combined in different ways. – Post-translational modification can change the protein in different ways. Those are important concepts! ;)
Aside: The Longest Protein/Word The longest protein known to us right now is called Titin in short. It’s got between 27,000 and 33,000 individual amino acids on it. Multiply this by three to get a rough estimate of how many mRNA nucleotides are involved. What does it do? – Helps you contract muscles. And now…the full chemical name, which…again…was shortened to “Titin.” – Note: Next slide in size 1.9 font. – uprise/2009/longest-word/ uprise/2009/longest-word/