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    Medium, 4 examples, 5 practice questions

  • Translation is the process of synthesizing a protein from an mRNA transcript.
  • Translation occurs in the cytoplasm.
  • Eukaryotic 80S ribosomes are comprised of the 60S and 40S subunits; Prokaryotic 70S ribosomes are comprised of the 50S and 30S subunits.
  • The major steps of translation are: charging of the tRNA, initiation, elongation, and termination.
  • Stop codons, signaled by a codon on the mRNA, recruit release factors instead of a tRNA, and result in the release of the polypeptide chain from the ribosome.


The process of making DNA form RNA is called:
  • Replication
  • Transcription
  • Translation
  • Reverse transcription
In eukaryotes, where does translation take place?
  • Nucleus
  • Nucleolus
  • Cytoplasm
  • Golgi body
Each complete ribosome has all of the following sites, EXCEPT:
  • Aminoacyl site
  • Exit site
  • Peptidyl-tRNA site
  • DNA binding site
In prokaryotes, the 30S subunit binds to the Shine-Dalgarno sequence (AGGAGG) near 5’-end of the mRNA via homology to what?
  • 16S rRNA
  • TATA box
  • Aminoacyl site
  • 23S rRNA
Which of the following recognizes STOP codons in eukaryotes, resulting in the release of the polypeptide chain from the ribosome?
  • tRNA
  • eRF1
  • RF1
  • eRF3

*These practice questions are only helpful when you work on them offline on a piece of paper and then use the solution steps function to check your answer.



Lecture Slides are screen-captured images of important points in the lecture. Students can download and print out these lecture slide images to do practice problems as well as take notes while watching the lecture.

  1. Intro
    • Lesson Overview
      • Linking Transcription to Translation
      • Overview of Translation
      • Ribosome and Ribosomal Subunits
      • Major Steps of Translation
      • “Charging” of tRNA
      • Translation Initiation - Prokaryotes
      • Example 1
        • Translation Initiation - Eukaryotes
        • Translation - Elongation
        • Example 3
          • Translation - Termination
          • Example 4
            • Review of Translation
              • Consequences of Altering the Genetic Code
              • Genetic Code
                • Consequences of Altering the Genetic Code
                • Intro 0:00
                • Lesson Overview 0:06
                • Linking Transcription to Translation 0:39
                  • Making RNA from DNA
                  • Occurs in Nucleus
                  • Process of Synthesizing a Polypeptide from an mRNA Transcript
                  • Codon
                • Overview of Translation 4:54
                  • Ribosome Binding to an mRNA Searching for a START Codon
                  • Charged tRNAs will Base Pair to mRNA via the Anticodon and Codon
                  • Amino Acids Transferred and Linked to Peptide Bond
                  • Spent tRNAs are Released
                  • Process Continues Until a STOP Codon is Reached
                • Ribosome and Ribosomal Subunits 7:55
                  • What Are Ribosomes?
                  • Prokaryotes
                  • Eukaryotes
                  • Aminoacyl Site, Peptidyl tRNA Site, Empty Site
                • Major Steps of Translation 11:35
                  • Charing of tRNA
                  • Initiation
                  • Elongation
                  • Termination
                • “Charging” of tRNA 14:35
                  • Aminoacyl-tRNA Synthetase
                  • Class I
                  • Class II
                  • Important About This Reaction: It Is Highly Specific
                  • ATP Energy is Required
                • Translation Initiation - Prokaryotes 18:56
                  • Initiation Factor 3 Binds at the E-Site
                  • Initiation Factor 1 Binds at the A-Site
                  • Initiation Factor 2 and GTP Binds IF1
                  • 30S Subunit Associates with mRNA
                  • N-Formyl-met-tRNA
                  • Complete 30S Initiation Complex
                  • IF3 Released and 50S Subunit Binds
                  • IF1 and IF2 Released Yielding a Complete 70S Initiation Complex
                  • Deformylase Removes Formyl Group
                • Example 1 25:11
                • Translation Initiation - Eukaryotes 29:35
                  • Small Subunit is Already Associated with the Initiation tRNA
                  • Formation of 43S Pre-Initiation Complex
                  • Circularization of mRNA by eIF4
                  • 48S Pre-Initiation Complex
                  • Example 2
                • Translation - Elongation 44:00
                  • Charging, Initiation, Elongation, Termination All Happens Once
                  • Incoming Charged tRNA Binds the Complementary Codon
                  • Peptide Bond Formation
                  • Translocation Occurs
                  • tRNA Released
                • Example 3 47:11
                • Translation - Termination 55:26
                  • Release Factors Terminate Translation When Ribosomes Come to a Stop Codon
                  • Release Factors Are Proteins, Not tRNAs, and Do Not Carry an Amino Acid
                  • Class I Release Factors
                  • Class II Release Factors
                • Example 4 57:40
                • Review of Translation 1:01:15
                • Consequences of Altering the Genetic Code 1:02:40
                  • Silent Mutations
                  • Missense Mutations
                  • Nonsense Mutations
                • Genetic Code 1:06:40
                • Consequences of Altering the Genetic Code 1:07:43
                  • Frameshift Mutations
                  • Sequence Example

                Transcription: Translation

                Hello, and welcome back to

                Today, we are going to talk about translation.0002

                As an overview, first thing we need talk about is how we can link transcription to translation.0007

                After that, we will just give an overview of translation and going to it all the way through.0013

                First, we will talk about ribosomes and their ribosomal subunits.0018

                Then, we will go through each part of translation, starting with the charging of tRNA,0022

                all the way through to initiation, elongation, and termination of translation.0027

                Finally, we will briefly talk about the consequences of altering the genetic code.0033

                Transcription, once again, to remind us from last time, is making RNA from DNA.0042

                We synthesize RNA complementary to DNA.0052

                This is going to occur in the nucleus; this is important to remember.0059

                Translation is the process of synthesizing a polypeptide from an mRNA transcript.0069

                It synthesize polypeptide from mRNA transcript.0080

                If we have our tRNAs, our rRNAs, those are not going to be made in a protein.0084

                You are not going to translate those RNAs.0089

                Obviously, our non-coding RNAs, you will not translate either.0092

                Our mRNA transcripts are the ones that are going to go through translation very often.0096

                We have our mRNA being translated into 5 prime to 3 prime direction,0104

                just as if we were talking about DNA synthesis happening in a 5 prime to 3 prime.0109

                Meaning, the next base is added to the 3 prime end.0114

                mRNA is translated 5 prime to 3 prime, 3 bases at a time.0119

                This is important to know, 3 bases at a time which we call a codon.0125

                Each 3 base pair unit or each 3 base unit on an mRNA is called a codon.0134

                Each one of those codons will code for a specific amino acid or a stop.0143

                The mRNA gets translated 3 bases at a time, by base pairing with a tRNA, having a complementary anti-codon.0150

                Your codon and your anti-codon will match up via a base pair.0164

                An example being, let us say UAG, your codon, your mRNA, would match up with AUC on your tRNA.0171

                Remember, we would have a hydrogen bond between there.0194

                Translation is going to occur in the cytoplasm.0202

                It will either occur inside ribosomes that are located on the rough endoplasmic reticulum0209

                which the endoplasmic reticulum is studded with ribosomes, that is why it is called the rough endoplasmic reticulum.0214

                We also have the smooth ER.0223

                It is going to be either in the rough ER or in the cytocell itself.0225

                If we look at this depiction down here, we can see that here is our nucleus.0231

                We have transcription occurring in the nucleus, DNA being made into RNA.0240

                In this case, we are looking at mRNA.0245

                That mRNA can leave the nucleus into the cytoplasm.0248

                At which point are right here, this is our ribosomes and it is going in this direction.0253

                Our ribosome can be the site of protein synthesis by reading the mRNA,0261

                one codon at a time and recruiting our tRNAs to come in and0268

                add its individual amino acid to the growing polypeptide chain shown here.0277

                We will go over each one of these steps of translation today and0284

                hopefully we will have a very good understanding, by the end of this unit.0289

                As an overview, what is happening in translation?0296

                First things first, we have a ribosome binding to an mRNA molecule.0299

                It is going to bind to it and it is going to search for the start codon.0308

                A start codon, this is going to be found on the mRNA.0314

                Your start codon is going to be AUG.0318

                Remember, this is on the mRNA.0323

                This AUG will code for methionine.0327

                Inside the ribosome, charged tRNAs, that means they are carrying an amino acid,0337

                will base pair to the mRNA via the complementarity found between the anti-codon on that tRNA and the codon on the mRNA.0345

                This is important, codon on the mRNA and anti-codon on the tRNA.0357

                The next step is, we have the amino acids being transferred from the tRNA and0368

                being linked to the growing polypeptide chain via a peptide bond otherwise known as an MI bond.0373

                This growing polypeptide is still being associated with the ribosome itself.0384

                Spent tRNA, tRNAs that no longer have an amino acid because it has already given its amino acid and0391

                let it attach to the growing polypeptide chain, the spent tRNAs get released from the ribosome via the E site or the exit site.0398

                We will talk about that later.0410

                The process of bringing in a new tRNA having a peptide bond being synthesized and0414

                a growing polypeptide continuing in its synthesis, we will continue until you reach a stop codon.0422

                Once again, remember it is a codon, it would be found on the mRNA.0430

                Our stop codons are UAA, UGA, and UAG.0435

                We continue until we reach a stop codon.0449

                What will happen is instead of a tRNA coming in, we have a protein called a release factor coming in.0451

                What that does is, it basically hydrolizes or cleaves the polypeptide,0459

                releasing it from the ribosome and allowing it to fold into its final tertiary shape.0465

                Those are our main steps, that is our overview.0473

                Let us first start with what ribosomes are and what the subunits are.0477

                First of all, a ribosome is a nucleoprotein.0483

                It is made up of several proteins, as well as ribosomal rRNA.0489

                Remember, our rRNAs + many proteins will make up our ribosome.0494

                We have different ribosomes in eukaryotes and prokaryotes, but they serve basically the same function to synthesize proteins.0513

                Let us first look at our prokaryotes.0522

                Our prokaryotes, the overall ribosome, it is a same thing as if we were looking down here, it is a 70S.0524

                What that is, an S is a density unit, it is a Svedberg unit.0533

                We have the small subunit which would be down here being a 30S small subunit.0542

                The large subunit which is the top part, the bigger part, would be the 50S subunit.0550

                In our prokaryotes, the rRNA that is included in the 30S or the small subunit is our 16S rRNA, as well as several proteins.0559

                Our 50S contains the 5S and 23S rRNA, as well as our protein subunits.0570

                It is important we have this 23S rRNA and this is our ribozyme.0579

                It is our peptidyl transferase.0585

                In eukaryotes, we have what is called an 80S ribosome, it is a little more dense.0603

                We have our small subunit including our 18S rRNAs, as well as proteins and that is called the 40S subunit.0609

                We have our large subunit being the 60S subunit and that contains 3 different rRNAs, our 5S, our 58S, and our 28S rRNA.0618

                Our 28S rRNA is also the ribozyme found in the eukaryotic ones.0628

                That is the peptidyl transferase enzyme in eukaryotes.0637

                Each ribosome fully functional, full unit ribosome, our 70S and 80S.0642

                Each complete ribosome has 3 different very important sites.0649

                We have the A-site.0654

                The A-site which can be found right here, is known as the aminoacyl site or the acceptor site.0656

                We have that P site which is known as the peptidyl site, the peptidyl tRNA site.0665

                This is where we are actually making the new peptide bond.0670

                The A-site is where the new tRNA will come in.0675

                And then, we have the E-site which is the emptier exit site and that would be not only here,0678

                but this would be the E-site right here.0684

                That is where the spent tRNAs are leaving the ribosome, so they are being released.0687

                Let us talk about the major steps of translation again.0697

                First of all, we have the charging of the tRNA, followed by initiation, elongation, and termination.0700

                In activation or charging, the proper amino acid is esterrified to the tRNA by its carboxyl group to the 3 prime OH of the tRNA.0707

                Remember, a bond between a carboxylic acid and an alcohol makes an ester.0724

                If you remember, our tRNA, our cloverleaf structure, we have the CCA at the 3 prime end.0738

                That A is where we are going to esterify the amino acid.0752

                Let us say for example, this would be methionine.0758

                Methionine would be added right there.0763

                Next, we would have initiation.0768

                Initiation would involve the small subunit of the ribosome binding to the 5 prime end of mRNA,0770

                with the help of initiation factors which we will abbreviate as IF.0781

                The next step would be elongation and that is going to happen when we have the next aminoacyl tRNA.0789

                This is the charged tRNA.0797

                When the next one comes in, bind to the ribosome along with the GTP because you need a lot of energy for this to occur.0801

                When we have energy and a charged tRNA coming in, as well as elongation factor, we can allow elongation to occur.0813

                We are lengthening the polypeptide, longer and longer.0823

                Finally, we have termination occurring, when we have the acceptor site of the ribosome encountering a stop codon on the mRNA.0827

                Remember, our stop codons are UAA, UAG, and UGA.0838

                When this happens, we have the releasing factor.0846

                If it is eukaryotes, it is ERF1.0850

                If it is prokaryotes, it is just RF1 or RF2.0854

                And that will cause the release of the polypeptide chain from the ribosome because it is hydrolyzing it and basically, releasing it.0859

                We will get more into the release factors, as we hit the termination section in this presentation.0867

                Let us start with the first step, the charging of our tRNA.0876

                We have an enzyme called aminoacyl tRNA synthetase.0880

                And, that is going to catalyze a two step reaction0887

                that results in the covalent attachment of the carboxyl group of an amino acid to the ribose of the adenosine of the CCA.0891

                This is, let us say CCA.0913

                We have the carboxyl group of an amino acid.0919

                Let us say we have methionine.0925

                We are going to say its carboxyl group.0928

                Each carboxyl group is going to attach via an ester bond to the adenosine on this 3 prime end.0933

                This is 3 prime, this would be 5 prime.0946

                Once again, this is a tRNA.0951

                We have an ester bond.0956

                We have our covalent attachment.0968

                Right here, it is an ester bond between the ribose of the adenosine0973

                found on the 3 prime end of the tRNA and the carboxyl group, in this case methionine but it can be any amino acid.0979

                How is this occurring?0989

                It is a two step reaction, we are not going to get in all the detail.0992

                We have that esterification.0996

                We have two different types of aminoacyl tRNA synthetase enzymes.0998

                We have class 1 and that attaches the amino acid to the 2 prime hydroxyl group of the ribose.1002

                We have class 2 that attaches the amino acid to the 3 prime hydroxyl of the ribose.1012

                The end result is the same, we have an ester bond between our tRNA and the amino acid, it is just where it is occurring.1019

                What is very important about this reaction is that it is highly specific.1030

                The reason that it is highly specific is because, let us say this anti-codon, it has to be specific, hopefully, for the methionine.1038

                This would be specific for the methionine, whatever that 3 base pair sequence would be.1049

                If for some reason, we have a different amino acid, the methionine being attached to the specific tRNA.1055

                What will happen is, when this tRNA properly base pairs with our mRNA,1066

                which has the codon for the methionine, this is supposed to hydrogen bond together.1072

                If this amino acid is not methionine, we are going to add the improper amino acid to the growing polypeptide chain,1079

                even though we have proper base pairing between the codon and anti-codon.1090

                This, the whole reason that this is a highly specific reaction is that we have high fidelity of our translation.1095

                Because if we start adding in amino acids that are not supposed to be attached to the specific tRNA according to the anti-codon,1101

                then we are going to mess up that protein and could really detrimentally hurt that cell.1114

                The last thing I want you to know about our charging is that we have ATP energy being required.1122

                Once we have charged our tRNA, we can continue on with initiation.1129

                Let us start with our prokaryotes, our bacteria and virus section.1137

                Let us look at it, first of all, we have initiation factor 3 binding the small subunit, the 30S, at E-site, the exit site.1145

                The whole reason that it does this is so that the 50S subunit cannot bind.1160

                If we have the exit site here, we have IF3 binding and that does not allow the full 70S ribosome complex to be constructed.1174

                The IF3 protein binds the 30S subunit after the previous round of translation is finished, so that you cannot rebind.1205

                Next, we have IF1 binding the 30S subunit at the A-site.1215

                This would be the P and that would be the A.1229

                We have IF1 and that prevents any tRNAs from binding because the tRNAs are going to come in at the A-site.1233

                Next, we have IF2 and GTP binding IF1.1249

                And then finally, we have our 30S, the small subunit, let us draw that.1265

                This is the 50S, this is the 30S.1271

                Our 30S subunit will then associate with the mRNA.1277

                It will do that by binding to what is called the Shine-Delgarno sequence which has a consensus sequence of AGG, AGG.1281

                It is near the 5 prime end of the mRNA.1292

                The mRNA, let us draw it in purple.1296

                The mRNA will bind to the 30S subunit using its Shine-Delgarno sequence.1304

                The Shine-Delgarno sequent has homology to the 16S rRNA that is found in the 30S subunit.1333

                We have the 16S rRNA.1344

                Once that happens, we have a special tRNA coming in.1359

                We have a tRNA that is carrying an N formylated methionine.1367

                By the way guys, what a formyl group, it is just a C double bond OH.1374

                When it is bound to an R group, we just call it an aldehyde.1382

                It is a formylated methionine, it has this group attached to it, binds to the mRNA at the proper start site, the AUG.1396

                That is facilitated by our IF2 and GTP that is already there.1408

                That helps position the start codon in the P-site.1414

                The P-site is where we are going to have the peptidyl transferase reaction.1418

                That is where we are actually going to catalyze the synthesis of that peptide or MI bond.1423

                At this point, once we have this tRNA, this formylated methionine tRNA bound in there,1429

                we have a complete 30S initiation complex.1437

                After this occurs, IF3 will be released letting the 50S subunit bind.1446

                Remember, IF3 was the one that did not allow the 50S subunit to bind, after the previous round of translation.1454

                What happens next, we have IF1 and IF2 being released.1464

                Now, we have a fully formed 70S initiation complex that has both an empty A-site and an empty E-site.1468

                We have this N formylated methionine tRNA in the P-site.1477

                This formylated methionine, we do not have to worry too much about1486

                because we have an enzyme called deformylase that removes these formyl group from that tRNA,1489

                either during or after translation.1500

                We do not see the formylated version in the mature protein.1502

                Let us draw out this prokaryotic initiation complexes.1512

                First off, let us draw out the 30S initiation complex.1518

                First off, we have a 30S ribosomal subunit.1542

                We have the E-site, the P-site, the A-site.1560

                We are going to have our IF3 protein binding the E-site and that make sure that the 50S subunit cannot associate with the 30S.1569

                We then have IF1 binding the A-site.1591

                We also have IF2 and GTP binding IF1.1600

                We will then have the mRNA coming in, binding the ribosome via homology to the 16S rRNA.1612

                The 16S rRNA is binding to the Shine-Delgarno sequence found on the mRNA.1632

                Finally, we will have that formylated tRNA coming in and binding to the P-site.1639

                We will say this is, we will just call it met-I for the initiation.1652

                It is a formylated one, it is a special one.1668

                That is our 30S initiation complex.1672

                Let us look at our 70S initiation complex.1675

                Remember, S is a Svedberg, it is a density unit.1687

                What we have now is our 30S, it still has its exit site, its peptidyl site, and its acceptor site.1697

                We have the mRNA properly in there.1711

                We have lost IF3, now we can have our 50S subunit binding.1720

                IF1 and IF2 have left, as well.1736

                We still have our original tRNA with that initiation special methionine in there.1739

                Remember, the anti-codon of the tRNA is going to base pair complementary with the codon on the mRNA.1756

                This is our 70S initiation complex.1771

                What about translation initiation in eukaryotes?1778

                Same concept, a little more complicated.1782

                In eukaryotes, the small subunit, our 40S, is actually already associated with the initiation tRNA, before it is recruited to the mRNA.1787

                And then what we do, we will form what is called a 43S pre-initiation complex.1802

                What that consists of is the following.1811

                We have the 40S subunit, the ribosomal subunit.1815

                That is going to bind to the 5 prime cap of the eukaryotic mRNA.1818

                Remember, the eukaryotic mRNA has the 5 prime cap.1823

                What we have after the 40S subunit binding to the cap, we have eukaryotic initiation factor 1 binding to the E site.1829

                We have EIF5 binding to EIF1.1839

                EIF1-A binding to the A-site.1843

                EIF3 binding to that one, EIF1-A.1846

                And then, EIF2 and GTP binding the initiator methionine tRNA and recruiting that to the peptidyl site, the P-site.1850

                Part of eukaryotic translation initiation is the circularization of the mRNA.1868

                This occurs via a complex called EIF4.1875

                It is EIF4-A, EIF4-G, EIF4-E.1880

                EIF4-A will bind to the upstream region of mRNA.1885

                Let us draw this up, as we are talking about it.1890

                First off, we have the mRNA that we are going to draw.1895

                We will denote that it has a cap right here.1903

                EIF4-A will bind to an upstream region on mRNA.1911

                Let us say, here is A.1921

                EIF4-G binds to the poly-A tail via hydrogen bonding.1928

                EIF4-E binds to the 5 prime cap.1940

                What this allows is for, let us say where the start codon is.1949

                Remember, this is all upstream.1956

                Let us say the start codon is right there.1958

                Here is your start.1961

                Remember, our start codon is AUG.1965

                AUG codes for methionine.1968

                What we can have by circularizing this, we actually allow ribosomes to bind in several different places.1978

                Small subunit, large subunit, all the way up until our stop codon.2011

                Our stop codons are UAG, UGA, or UGG.2031

                Sorry, not UGG, UAA.2055

                UAG, UGA, UAA.2059

                These do not code for a tRNA, and therefore, do not code for an amino acid.2065

                It codes for a release factor.2072

                Each of these ribosomes can bind to the circularized mRNA, making what we call a polyzome.2081

                What we will have is a little bit of protein.2094

                As it goes further along, it will get longer and longer.2100

                These are all different ones.2105

                These are all proteins.2112

                Those are all being made, being synthesized, translation is occurring at that time.2122

                What we are doing is we are making several different proteins or probably the exact same protein.2126

                We are making several copies of the protein from a single mRNA.2133

                If we have multiple ribosomes translating, we are getting multiple copies of the protein from a single mRNA.2138

                We talked about the 43S initiation complex.2151

                Let us move to the 48S pre-initiation complex.2155

                The 48S pre-initiation complex is the 43S.2160

                We talked about plus the addition of the circularized mRNA with the EIF4-E, G, and A subunits.2165

                The 48S pre-initiation complex will scan the mRNA, 5 prime to 3prime, looking for the AUG with the correct reading frame.2178

                The AUG, meaning it is looking for the start codon in methionine.2187

                It is looking for in the correct reading frame.2193

                At the very end of this unit, we will talk about reading frames.2195

                For right now, let us just move on a little bit.2199

                This right here, looking for the AUG in the reading frame is an ATP dependent process, it is energy using.2205

                It is facilitated by EIF4-4A which actually has helicase activity and EIF4-B.2213

                EIF4-B actually activates EIF4-A.2219

                Once the proper AUG is found, our initiation factors 1, 2, and 5 release which allows EIF4-B and GTP to bind that initiator tRNA.2229

                We lose a bunch of initiation factors and gain one which helps a tRNA bind.2246

                This then, recruits the large subunit to associate making the fully functional 80S ribosome,2255

                with the proper initiator methionine tRNA loaded into the peptidyl site.2266

                Similar to the prokaryotic initiation, we have all the initiation factors get everything ready.2274

                Then, they leave so that you can have the full association of the large and small subunits,2282

                with the proper initiator tRNA in the peptidyl site.2289

                Just as a reminder, we have the cap or if we do not have a cap which is actually fairly common on mRNAs in eukaryotes.2296

                If you do not have a cap, you utilize what is called the kozak sequence with the consensus sequence ACC, AUGG.2305

                Whether it is the cap or the kozak sequence that will help the 40S ribosomal subunit bind to the mRNA.2315

                And then, the 60S subunit will bind at the AUG, as we talked about up here once it has been found.2325

                Let us show what this would look like.2335

                We have our 43S pre-initiation complex.2338

                Here we go, we have our 40S ribosomal subunit with the E, the P, and the A-site.2362

                We have the EIF1 binding here.2379

                This does not allow the 60S subunit combine.2388

                We have EIF5 binding this.2394

                Over here at the A-site, we have EIF1-A binding here, that is blocking the acceptor sites so that we can have new tRNAs coming in.2403

                And then, we have EIF3 binding that.2416

                We have our tRNA coming in here.2426

                This is going to be attached to that specific initiation methionine.2442

                And then, we have our last one, we have EIF2 + GTP bind in here.2447

                That is going to help position the methionine in the proper P-site.2470

                This is the 43S.2474

                Now, if we talk about our mRNA, let us just say here we have our mRNA, our cap here.2477

                I’m going to draw in a non-circularized form just so we can see it easier.2503

                We have EIF4-E down to the cap.2509

                We have EIF4-G bound.2518

                We have the EIF4-A helicase.2527

                And then, we have EIF4-B which activates this helicase bound right here.2535

                This one + this one equals our 48S pre-initiation complex.2544

                Just so we can see one more, let us write out what happens when we have the full association.2574

                We have our 40S, we have our E, our P, our A.2582

                Once we have our initiation factors leaving, that allows us to have association with the large subunit, the 60S.2589

                And then, we have that mRNA coming through.2600

                We have our proper initiation tRNA in the P-site.2610

                We will have an empty E-site and an empty A-site.2620

                And then, we now have the full 80S complex.2623

                And now, it is ready to go through elongation.2630

                The next step, elongation.2642

                This is going to just repeat over and over again.2646

                Elongation, every time a new tRNA comes in, this is the step that is going.2649

                We have charging happening to every tRNA.2655

                We have initiation happening once.2659

                We have elongation happening for every tRNA that is coming in.2661

                We have termination happening once.2665

                We have our incoming charged tRNA, aminoacyl tRNA, being recruited by, if were eukaryotes,2670

                it is EF1-α, elongation factor 1-α.2678

                For prokaryotes, elongation factor-T.2685

                The incoming charged tRNA binds the complementary codon on the mRNA in the A site.2690

                Remember, it is using its anti-codon to bind the codon.2699

                Next, we have peptide bond formation being catalyzed by the enzyme peptidyl transferase.2705

                Remember that is a ribozyme, either the 23S rRNA, if it is prokaryotes.2714

                Or the 28S rRNA, if it is eukaryotes.2723

                The peptide bond formation occurs between the amino acid of the tRNA that is in the A site, it just came in.2730

                And, the C terminal amino acid of the growing polypeptide chain which is attached to the tRNA that is already in the P-site.2740

                I will draw this out in just a couple of slides.2750

                Finally, the growing polypeptide chain gets transferred to the tRNA in the A-site.2755

                We will have what is called translocation occurring.2761

                As I said, translocation occurs and that is enabled by the action of elongation factor 2, if it is eukaryote, EFG, if it is prokaryote.2767

                Translocation moves the tRNA in the P-site.2781

                Now, it does not have amino acid anymore.2785

                It moves it to the E-site.2788

                Remember, the polypeptide chain has been transferred already from the tRNA in the P-site to the tRNA in the A-site.2790

                Now, we do a shift.2799

                The tRNA that was in that A-site, the one that just came in,2801

                now it is attached to the growing polypeptide chain will move to the P-site.2805

                The tRNA that was in the E-site, the exit site, is released.2812

                And, the next charged amino acid which is dictated by the codons in the mRNA will enter into the A-site.2817

                Let us draw this out so that we know what it looks like.2828

                I will draw my ribosomes in blue.2836

                I will label this for us.2846

                We have 40S and we have 60S.2848

                We have the E-site, the P-site, the A-site.2853

                This is our mRNA and it is the 5 prime end.2872

                We are going to redraw this bigger.2883

                We have the E, the P, the A.2926

                We have going to have the same channels in the 60S as well.2930

                Our mRNA, this is 5 prime mRNA.2939

                At first, I’m just going to very simplify what a tRNA looks like.2946

                I’m just going to draw it just like this, attached to, let us say a particular amino acid.2954

                That is what I’m going to say an amino acid looks like.2964

                This is perfectly what we have for initiation.2967

                The next step, as the mRNA stays in one place, the ribosome will actually shift to the right.2974

                We will now go to the next codon.2987

                What we have is or what the next step would be, would be a new charged tRNA coming in2990

                with a different amino acid, let us say.3007

                What we have is called translocation.3015

                As the ribosome moves, what we end up having is a kind of a shift looking like this,3067

                whereas, the tRNA are still bound in the P and A site.3080

                However, they have shifted looking like this.3085

                What we are actually doing in that P site, we are making that peptide bond, if I move it.3088

                What we have done is we have transferred this amino acid, the methionine, to this tRNA.3115

                We have made a peptide bond or MI bond.3127

                Now, we have a growing chain.3131

                As we can see, the first amino acid was the methionine, the blue.3133

                The second amino acid, it could be whatever you want to call it.3138

                Let us just say it is alanine.3141

                We have had that translocation.3144

                The next step would be the full movement to where it looks like this, 40S, 60S, the E, P, A, E, P, A, the 5 prime mRNA.3146

                We have a full movement, as we are translocating.3177

                We have the first tRNA, now without an amino acid attached to it.3198

                It is moved into the E-site.3205

                The last tRNA that has come into the A-site, now has 2 amino acids attached to it.3207

                The growing polypeptide chain is now fully in the P-site.3217

                Now that opens up the A-site for the next tRNA to come in.3222

                Let us see what that looks like, to continue this way.3227

                What we have here, it is going out already.3259

                We now have this one here, that is exited.3269

                We have a new tRNA coming in with another amino acid.3284

                The whole thing will occur all over again.3299

                You can just look, what would happen next would be, this would be the next step.3301

                It would follow to here and then back to here again.3310

                That would continue on over and over again until we hit a stop codon, in which case then we will go through termination.3315

                Now that we are talking about termination, we need to talk about release factors.3327

                These are proteins that will terminate translation, when the ribosome comes to a stop codon.3333

                Remember, stop codon is UAA, UAG, UGA.3340

                The release factors are proteins, they are not tRNAs.3350

                They do not carry an amino acid.3353

                This is very important to understand.3355

                It is so important that I’m just going to highlight it all.3359

                I’m even going to put a red star by it.3367

                There are two classes of release factors.3373

                We have class 1 release factors.3376

                They will recognize stop codons and hydrolize or cleave the polypeptide chain from the tRNA that is found in the P-site.3381

                We have, if we are talking about prokaryotes, these are prokaryotic release factors.3393

                Release factor 1 recognizes UAA and UAG.3405

                Release factor 2 recognizes UAA and UGA.3410

                Eukaryotic release factor 1 will recognize all 3 stop codons.3416

                Class 2 release factors will help release class 1 release factors from the ribosomes.3423

                Class 1 release factors cleave the chain from the tRNA in the P-site.3431

                It allows the protein to leave the ribosome.3439

                Class 2 release factors release the class 1 release factors from the ribosome.3442

                The class 3 release factors are RF3 in prokaryotes or ERF3 in eukaryotes.3450

                I put together a little table so that it might be easier for you guys to understand and have all the information in one place.3462

                This should just say step.3474

                Your tRNA charging, the whole function of that is adding an amino acid to the tRNA.3481

                The protein or the enzyme that is responsible for that is aminoacyl tRNA synthetase.3487

                One thing I want to point out guys, synthetase, a general rule of thumb,3495

                when you see the word synthetase that means it is an enzyme that is making something, synthesizing.3499

                It needs the input of energy, usually ATP or GTP is needed.3508

                If this were synthase, it is an enzyme that is doing a synthesis reaction but does not need the input of energy.3516

                That is just a biochemical aside.3528

                You will learn that in biochemistry.3530

                The next step of translation is initiation.3533

                The recognition of the start site, for eukaryotes that is done by EIF1-A and EIF3.3537

                For prokaryotes, it is IF3.3545

                Recruiting the special initiator methionine tRNA to the P-site, eukaryotes, that is EIF2.3549

                Prokaryotes, that is IF1 and IF2.3556

                For elongation, recruiting all other tRNAs to the A-site, prokaryotes, it is EF1-α, for prokaryotes, EF2, as TU.3561

                For peptide bond formation, whether it is eukaryotic or prokaryotic, the name of that enzyme is peptidyl transferase.3577

                It is a ribozyme, meaning it is a ribonucleic acid that has enzymatic activity.3585

                For you eukaryotes, that is the 28S rRNA and prokaryotes that is the 23S rRNA.3593

                Either one of those are found in the large subunit.3600

                Eukaryotes, that 28S rRNA is found in the 60S subunit.3603

                Prokaryotes, the 23S rRNA is found in the 50S subunit.3608

                Finally, translocation involved in the elongation, that is EF2 for eukaryotes, EFG for prokaryotes.3619

                You are going to need GTP, for each time it translocates.3627

                It is energy requiring.3632

                Finally, termination, this is the recognition of stop codons and the release of the polypeptide chain, that is done with our class 1.3635

                The hydrolization of the polypeptide chain from the tRNA in the P-site,3646

                it is done by class 1 release factors which is ERF1.3653

                If we are talking prokaryotes, RF1 and RF2.3660

                The class 2 release factors which released the class 1 release factors from the ribosomes is ERF3 for eukaryotes and RF3 for prokaryotes.3663

                Let us do a quick review of translation.3677

                Each tRNA with its own anti-codon is attached to a specific amino acid, via the CCA end on the 3 prime.3680

                The amino acids delivered by the tRNAs are joined together to form a polypeptide inside the ribosome.3689

                Remember, the tRNA is utilize the complementary of its anti-codon to the codon on the mRNA.3696

                The ribosome will move along the mRNA and encountered codons3704

                which are 3 base sequences that will tell whatever tRNA to come in and add a specific amino acid.3710

                Multiple ribosomes can translate the same mRNA at the same time, creating a polyzome which I talked about when I circularized the mRNA.3717

                The next thing that happens, we have a charged tRNA entering the A-site, where the anti-codon hydrogen bonds to the codon.3728

                Next, the tRNA translocates to the P-site.3738

                The attached amino acid gets connected to the previous amino acid of the growing polypeptide chain.3743

                And then, the spent tRNA, the one that no longer has amino acid on it, exits from the E-site.3749

                It continues over and over again until a stop codon is reached.3755

                I briefly said that I wanted talk about consequences of altering the genetic code.3764

                We have just a couple slides and I want to explain to you why this is so important.3769

                Our genetic code, if we look back at our codon table which I have on the next slide.3775

                Each 3 unit or each 3 base sequence which we call a codon, codes for a specific amino acid.3780

                Each one of those amino acids are in a protein, for a specific reason.3788

                Maybe they are supposed to make hydrophobic bonds or hydrophilic bonds, ionic bonds, so on and so forth.3794

                If you alter that sequence, if you are adding in an amino acid that should not be there,3801

                you can affect the overall function of the proteins.3808

                There are couple different types of mutations that I want to talk about.3813

                We have first, what are called silent mutations.3817

                These are the types of mutations that we can call no harm, no foul.3821

                These are mutations in the DNA sequence that do not alter the amino acid sequent3825

                due to our degeneracy of the genetic code.3832

                Example, all 4 of these and actually 2 other triplets, all 4 of these code for serine.3835

                If we happen to, instead of what should have been a UCU.3843

                If for some reason, we have a mutation changing the U to a C, or even an A or a G, no harm no foul, we still get a serine.3848

                It is a silent mutation, we do not even see it.3860

                If we get what is called a missense mutation, that is a mutation in the DNA sequence3864

                that leads to a change in the predicted amino acid sequent.3871

                For example, instead of a UGC that is supposed to be added, there is some sort of mutation and3875

                we actually have a G present, instead of a C in that 3rd triplet base.3883

                That changes the cystine to a tryptophan.3888

                Maybe, we were supposed to be making a disulfide bond using our cystines in the protein.3892

                But now, we no longer have that ability, so that can be detrimental.3897

                Missense mutations do not always have to be problematic because, let us say, we have aspartate and it is change to a glutamate.3902

                You still have a negatively charged amino acid.3911

                Maybe, it can participate in the same exact bond that it was supposed to have made.3915

                Missense mutations do not always have to be showing a type of phenotype but they can.3921

                The last one, the most detrimental one, is nonsense mutation.3928

                That is a mutation in the DNA that changes a normal amino acid codon to a stop codon.3933

                This truncates the protein, it makes its smaller.3942

                An example, we have UAU coding for tyrosine.3948

                All we have to do is have that one base changed to UAA being a stop codon.3953

                Maybe, instead of getting a full 6,000 amino acid protein, maybe we only get 60 amino acid protein.3958

                If that is the case, it is not going to be very functional and we are likely going to degrade it and just throw it away.3974

                What can cause even more problems is if, let us say, we get a protein that can still function but it functions in a different way.3980

                And thereby, maybe causing a genetic defect.3993

                Remember that the consequence of altering the genetic code are due to the possibility of changing the triplet code.3997

                Cystine, it is fine, if you change that last one, the U to a C, not a big problem.4007

                But if you change that U or C to an A, that is going to give you a stop codon.4012

                That is an example of a nonsense.4021

                If you change the U to a C right here, that is an example of a silent because it is still going to be cystine.4026

                If you change the U to a G, that is going to give you a different protein or a different amino acid.4034

                That is an example of a missense.4040

                Between these two silent, between these two nonsense, between these two missense.4045

                I want to end with just an example of what a frame shift mutation is, because this can alter the genetic code.4064

                Frame shift mutation is due to the addition or deletion of nucleotides, in other than multiples of 3.4074

                And, that will shift the open reading frame which most often results in truncated protein.4081

                Let us write out a sequence, ACG, this is the mRNA.4087

                UGU, ACA, UGG, AUG, CUG, GUAA.4103

                There are 3 possible reading frames for an mRNA and that is due to the fact that there are 3 bases per codon.4127

                For example, this could be your open reading frame 1.4135

                Red is ORF1, we can have purple being the next reading frame, starting there, that is ORF2.4141

                Let us say green is the next one, ORF3.4154

                That is all we can have because, if we then go to starting at the next one, this UGU, that is still ORF1.4163

                This is important, we have 3 different open reading frames.4173

                If we search down here, we can find that there is an AUG.4177

                We have an AUG that we can find here and AUG that we find here.4183

                Those are start codon.4186

                Then, we can find one UAA, this is a stop codon.4189

                If we look, we can see that if we go red, 33333, this is actually a start codon only for open reading frame 1.4196

                If we look for open reading frame 2, if we go 3333333, this is a stop codon only for open reading frame 2.4228

                If we look over here, open reading frame 3, this is 333, this is a start codon only for open reading frame 2.4260

                This should be in green.4293

                This is important because, let us say for example, we are looking at our 3 possible open reading frames.4308

                We see two different starts and one stop.4321

                Let us say, for example, that we are going to do our translation through open reading frame 3.4324

                We can start here, we have AUG, that is going to be our start, our methionine.4333

                Then, we will have GAU as our next codon.4338

                Then, GCU, then UA, whatever that next one is.4342

                We will write it in as, let us say A.4349

                All the starts and stops are perfect as they are now.4359

                But if we would have a frame shift mutation, either adding in or subtracting bases other day in 3,4363

                you either add or subtract 1 or to 2 bases, that can affect the open reading frame.4372

                If we have in addition of a single base, and if we say we add it right here, frame shift caused by the addition of an A right here.4378

                What that does is, it shifts the open reading frame.4395

                The new one, I’m going to write it in red.4398

                This would be AUG, GAU, GCU, GCA, UAAA.4402

                What we see here, this is open reading frame 3.4418

                What we see is we have a start codon, an amino acid, an amino acid, an amino acid, a stop codon.4426

                This is a truncated protein now.4434

                Instead of going on from maybe 500, 600 thousands of amino acids,4436

                this now is a 4 amino acid polypeptide, once it hits that stop codon.4442

                Likely, this will just be sent to the cellular trash can, the prodiuzome or the lysosome,4453

                and be broken down, degrade it, and you have to restart.4460

                This is how a frame shift can affect the genetic code because this might not be as big of a problem,4463

                if we can overcome the frame shift.4472

                But if not, then maybe this protein is not made at all in the body in its functional form and4474

                that could possibly lead to a disease or cancer, or something.4481

                To where, maybe it is a lethal type of mutation and there is not even life form from it.4485

                That is the end of our unit today, thank you for joining us at I hope to see you again next week.4494