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Post by Dharshini Selladurai on December 6, 2010

3'-OH on 3' Carbon

3 answers

Last reply by: Dr Carleen Eaton
Tue Sep 17, 2013 4:29 PM

Post by Kendrick Miyano on April 16, 2013

Hello, Dr. Eaton.

If the telomeres shorten after each round of replication, does this mean that they will eventually become too short to replicate? Will the telomeres be broken down and then recycled?

1 answer

Last reply by: Dr Carleen Eaton
Tue Sep 17, 2013 4:33 PM

Post by Vinit Shanbhag on September 11, 2013

Does a Phosphodiester bond formation require energy?

0 answers

Post by Bao Vo on February 10 at 10:43:16 PM

Transcription and Translation video has the wrong Caption. Fix it please

Transcription and Translation

  • Transcription is initiated when RNA polymerase and transcription factors bind to the promoter region of a gene. The promoter frequently includes the nucleotide sequence TATA and is known as a TATA box.
  • Following transcription, the pre-mRNA undergoes processing to form mRNA. Introns are removed through splicing and a 5' cap and a poly A tail are added to the mRNA.
  • The mRNA is transported out of the nucleus to the cytoplasm where translation takes place.
  • Nucleotide triplets, called codons, signify particular amino acids.
  • The three phases of translation are also initiation, elongation and termination.
  • Translation begins at the start codon AUG, which is also the codon for methionine. Transfer RNA (tRNA) delivers the amino acids to the ribosome to be added to the growing polypeptide chain.
  • Translation is terminated when the ribosome encounters a stop codon.
  • Mutations are changes in the DNA sequence. A change in a single base pair is a point mutations. Types of mutations include silent, missense and nonsense mutations.
  • Insertions and deletions result in base pairs being added or eliminated from the DNA sequence. This results in a frameshift mutation.

Transcription and Translation

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.

Advanced Placement Biology

Transcription: Transcription and Translation

Welcome to Educator.com.0000

We are going to continue our discussion of molecular genetics with the topics of transcription and translation.0002

Before we delve into the details, I am going to give you an overview of the process.0011

Recall that the central dogma of molecular biology is the flow of information from DNA to RNA to protein.0015

The genetic information is contained on DNA.0029

A transcript is made of RNA and this is then, transported.0033

A particular type of RNA, mRNA is transported into the cytoplasm, where it is translated into polypeptide and forms of protein.0039

This process, therefore, is called transcription.0050

The use of a DNA template to form RNA, and the process of going from RNA using that RNA transcript to form a protein is translation.0055

When a protein is made based on the information contained in DNA, we say that the gene has been expressed.0071

A person might carry a gene for red hair, and that is just the gene.0079

But the actual protein that makes the hair color red, when that is made, we say the gene is expressed. It is expressed in the form of red hair.0086

Now, looking at these names, transcription and translation, recall that DNA is made from nucleotides. The nucleotide monomers form a polynucleotide.0095

RNA is also made from nucleotide monomers.0108

There are slight differences between DNA and RNA, but the essential code is the same.0112

Therefore, a DNA template is simply copied. It is transcribed to make the RNA.0117

That is much difference between RNA and protein, so with DNA, you are working with nucleotides, with RNA, with nucleotides.0125

With protein, it is an amino acid sequence.0132

In order to go from this one type of code - nucleotides - to another code - amino acid sequence - is actually translation.0135

You are not just copying something. You are actually taking the information and translating it into a different form.0145

We are going to discuss transcription first, and to understand transcription, you need to have RNA structure down.0154

Again, this is a topic that was covered under the nucleic acid and protein lecture earlier on, but I am going to review the essentials right now.0160

Unlike DNA, RNA molecules are single stranded.0169

Another difference between RNA and DNA is that they contain uracil instead of thymine.0173

The essential structure is the same, though.0180

RNA consists of nucleotides. It is a nucleotide sequence, and looking at what a nucleotide is, there is a pentose sugar; so that is a 5-carbon sugar.0182

In the case of RNA, the sugar is ribose.0194

In DNA, this oxygen is gone. It is deoxygenated.0198

It is deoxyribose, so this is ribonucleic acid.0202

The second element is a nitrogenous base.0206

And recall that there are two sets of nitrogenous bases- the pyrimidines, which contain a 6-membered ring, and they are cytosine, thymine and uracil.0210

In RNA, you will find uracil. In DNA, you will find thymine, and cytosine is found in both.0224

For RNA, we are just going to have C and U.0233

The second type of nitrogenous base is the purines.0236

These contain a 6-membered ring fused to a 5-membered ring and consist of G and C, adenine and - excuse me - guanine and cytosine, so C, U, G, C.0243

The other thing to be aware of besides the differences between RNA and DNA is the types of RNA.0267

There are multiple types of RNA. Three main ones we will be focusing on.0275

One is messenger RNA. The other is ribosomal RNA, and the third is transfer or tRNA.0279

Messenger RNA is the type of RNA that is used for translation.0289

It is the transcript to make a protein.0297

Ribosomal RNA is not used to make a protein. The rRNA is itself, the product.0303

Ribosomes are composed largely of ribosomal RNA, so these are component of ribosomes.0309

tRNA or transfer RNA delivers amino acids to the ribosome during translation, and we will be going into detail about all three types of these as we go along.0323

We are going to start out mainly focusing on mRNA. All three of these would be transcribed.0340

DNA would be used as a template to form all three types, but as we talk about transcription, I am going to focus on mRNA.0345

And then, we are going to follow that process of transcription with translation.0352

Transcription is the process through which RNA is synthesized using a DNA molecule as a template.0359

There are three phases. Initiation, elongation and termination are the three phases.0368

We are going to go through each of these phases starting out with initiation.0375

Initiation begins with the binding of RNA polymerase to the promoter region.0379

The region on DNA, where this gets started, is known as promoter.0385

Here, we have the DNA double helix, and you see it is separated out here in order to allow transcription to occur.0392

Transcription for a particular gene occurs using only one of the DNA strands as a template.0401

In this case, here we have DNA, DNA, and then, in brown, it is the RNA; and you can see that this RNA strand is using this DNA as the template.0408

This is the template strand. Another name for template strand, we sometimes call it the sense strand, and the other is the antisense strand.0420

During initiation - I will put this right here - the RNA polymerase binds to the promoter region.0430

Promoter regions are also known as TATA boxes because they have the sequence T-A-T-A.0447

Initially, where this promoter region is, the RNA polymerase binds, is slightly upstream of where the first actual nucleotide will be transcribed.0459

Things start out, RNA polymerase binds to this promoter region, and then, slightly pass that, we will get the actual transcription of RNA.0471

In addition to RNA polymerase, there are other factors that bind to this promoter region.0487

If you take it together, the RNA polymerase plus other proteins known as transcription factors,0493

what you have is something called the transcription initiation complex.0506

And the job of these transcription factors is to help the RNA polymerase bind to the correct region.0516

We have RNA polymerase plus transcription factors. All that binds together to the promoter region to get things started.0525

And it is known as a transcription initiation complex.0531

In eukaryotes, there is actually a different type of RNA polymerase for each of those three types of RNA that I mentioned- tRNA, rRNA and mRNA.0535

We are focusing right now in messenger RNA.0550

The one that is used to transcribe DNA into what will become messenger RNA is known as RNA polymerase II.0551

RNA Pol II transcribes DNA into what is eventually messenger RNA.0559

This has occurred. This binding has occurred.0566

The transcription initiation complex has bound.0569

The next thing that needs to happen is the double helices to unwind.0571

And again, helicases are involved in this unwinding, this separating out so that the RNA can use the template strand.0575

Now, for a particular gene, the same strand is always used as a template.0584

Let's look at this DNA and say that there is a gene here that is being transcribed.0589

Well, that is what is happening, and we see that this is the template strand.0594

There might be another gene over here that needs to be transcribed, and this strand may be the template for that.0599

So, the same template is used for a particular gene, but it might be a different strand that is used for another gene, so that is initiation.0606

The next thing that needs to happen is elongation.0617

The initiation complex has bound. RNA polymerase is ready to go.0619

It is bound to the template strand. These other factors are bound.0623

We found the TATA box. The helix has been separated.0628

What is going to happen is that RNA polymerase is going to proceed in the 5' to 3' direction, just like DNA polymerase.0632

And it is going to form a strand of RNA that is complementary to the template strand.0641

Remember that complementary means that we would have G and C. Those two are complementary.0645

And with DNA, when we would say "OK, A is complementary with T", for RNA we do not have T. We have U.0656

For RNA, it is going to be A, U, G, C as complementary nucleotides.0666

Looking here at what I mean, this is the template strand for this situation.0672

This is the RNA strand. RNA polymerase is going to seed T, and that is going to tell it to add A for the nucleotide in the growing RNA strand.0681

For C, the complementary strand is going to be G. For G on the template, we are going to have C.0692

For A, if this was DNA synthesis, we would have T, but it is not. It is RNA synthesis, so instead, we are going to have U, G, C.0701

A on the DNA gives me U, A, T and so on, and recall that we just produced one strand.0713

We do not need a double helix. RNA is just single-stranded.0725

You will also notice that this is the same sequence almost as the antisense strand.0731

It is complementary to this template strand or sense strand.0736

And it is the same as antisense not a 100% the same because you will see here, I have AA GG CC T.0739

There is no T here. There is U instead, CC and U instead of T and so on.0748

OK, the first step was initiation transcription complex - excuse me - transcription initiation complex bound to the template strand.0756

Now, we have elongation. RNA, polymerase is adding nucleotides one at the time in the 5' to 3' direction.0766

And this is going to go on until a termination sequence is encountered.0774

A typical termination sequence, a common one is A-A-U-A-A-A.0784

RNA polymerase is going along, and then, it encounters a certain sequence on the DNA that is going to be transcribed into this sequence A-A-U-A-A-A.0795

That is the termination sequence.0803

Shortly after that signal, the newly produced RNA is cut free.0805

This newly produced RNA is not mRNA yet. It is actually known as pre-mRNA or sometimes hnRNA, which stands for heterogeneous nuclear RNA.0811

This is the initial transcript produced.0827

Just reviewing, we had initiation. Then, the RNA polymerase is adding nucleotides 5' to 3'.0830

It encounters a certain sequence that when transcribed it forms A-A-U-A-A-A, which is the termination sequence.0836

Shortly after that, the RNA is released from this complex, and it is free.0844

I mentioned that this initial transcript is not messenger RNA.0856

It is not mRNA. It is pre-mRNA.0860

In order to become mRNA, processing needs to occur, and there is several major types of processing.0863

One of them is splicing. The other is the addition of a 5' cap, and the third is the addition of a poly(A) tail.0871

DNA actually contains both coding and noncoding regions.0879

Coding regions can be expressed as a protein, so they can be used as instructions to form a protein.0883

Noncoding regions do not.0891

Let's first look at DNA, and say we have a piece of DNA like this and there is sections that are coding.0895

And there is sections that are noncoding- 1, 2, 3 to add one more.0909

These numbered sections are going to be the coding regions. These are called exons.0922

These sections in between with no number are introns.0928

The coding regions, again, a protein can be formed from those, and one way to remember this is just remember the introns interrupt.0932

They interrupt the coding regions, and the exons are expressed; so remember ex for expressed and/or you can remember interrupt.0940

In the initial transcript, the pre-mRNA, all of these nucleotides are transcribed.0958

We are going to end up with a transcript that has each of these nucleotides represented.0965

Introns, exons, all of it is there so 1, 2, 3 and 4.0972

However, when the ribosome goes to make the protein, it does not need these interrupting regions.0979

In fact, that would disrupt translation, so we need to get rid of these.0987

In order to form actual messenger RNA, these regions are cut out or spliced out, so this is going to be cut out, cut out, cut out.0991

The result is we are going to be left with 1, 2, 3 and 4- just the exons.1004

The introns have been removed, so we spliced those out.1016

This step is splicing, and this step is performed by spliceosomes.1022

Spliceosomes are composed of snRNPs, or they are also called snRNPs plus protein.1032

Now, what are these snRNPs? What does that stand for?1045

What are they made of?1048

Well, sn is small nuclear ribonucleoproteins. That is why it is abbreviated because it is really long.1049

And small nuclear ribonucleoproteins consist of protein plus a special type of RNA called snRNA.1065

snRNA is what is called a ribozyme. This is RNA that acts as an enzyme or it is thought to be.1076

Ribozymes are RNA that acts as an enzyme, and snRNA is believed to be a ribozyme.1095

Ribozymes, RNA that act as an enzyme. It is thought that snRNA is a ribozyme.1106

When snRNA is combined with particular proteins, it is a snRNP.1112

snRNPs plus other proteins form a particular form a spliceosome, and they are responsible for the splicing.1120

In addition to splicing, a couple other changes are made to form mRNA.1125

A 5' cap is added. Let's say this is 5' and this is 3'.1132

This 5' cap is actually a modified guanine molecule that is added to the 5' region, and then, at the other ends, this is a modified guanine for the 5' cap.1137

The poly(A) tail is on the 3'-end. It is just like you would imagine.1156

It is a string of As, and there is a modified guanine here.1161

The purpose of this cap and tail, it is partly to protect the ends. The other purpose is to mark this as mRNA.1167

In the nucleus the pre-mRNA is formed. These modifications occur, and now, it is marked for export from the nucleus.1176

The mRNA is, then, exported form the nucleus.1184

Before we go on and talk about translation, I want to just mention that there is something called alternative splicing.1187

Seeing how this has been spliced - 1, 2, 3 and 4 were spliced together - it is actually possible - let’s say we start out with the same 1, 2, 3, 4 -1195

instead of splicing it like this, it is possible to splice it differently1219

Instead of just taking out the intron, maybe you will cut out number 2.1223

Maybe you will splice that out, and then, what you will end up with is a transcript that contains1228

- and this is would be spliced out because that is an intron - 1, 3 and 4, those exons.1236

And this actually does happen - this type of alternative splicing - quite frequently with the human genome.1248

And what this allows is for a fewer number of genes - less DNA - to be needed to make a huge variety of protein.1255

And a protein like this that contains 1, 3 and 4 is going to be related to this protein, but it is going to be different.1262

Therefore, you can use a series of exons, kind of, mix and match them to create related proteins, and it is a more efficient use of DNA.1268

It could have been spliced with 2, 3 and 4 or just 4 and 1- various different ways for splicing.1277

OK, just to sum up, RNA processing consists of splicing, in which the noncoding regions are removed1284

as well as the addition of a 5- cap and a poly(A) tail to protect the ends and to let the cell know that this is mRNA.1291

Then, it is exported out of the nucleus into the cytoplasm, where translation can occur.1299

During translation, the RNA transcript is used to create a polypeptide. As I said, this occurs in the cytoplasm.1307

Recall that RNA is formed from nucleotides. Proteins are formed from amino acids.1315

How do we get from nucleotides to amino acids? How is that nucleotide sequence interpreted?1322

Well, it is something called codons.1330

Let's look at a particular RNA sequence, and I am going to cluster these in triplets- CUG, GCU, UAC.1335

I am going to cluster them that way, so that it emphasizes the fact that codons are triplets.1347

And reading from the 5' to 3'-end, I would end up with CUG, and that particular triplet specifies leucine. This is saying leucine should be added.1353

When the ribosome encounters this particular triplet, GCU signifies alanine, UAC- tyrosine.1366

This is how RNA - this is mRNA - can be translated into an amino acid sequence.1381

The ribosome is able to, and in the other translation machinery together with the ribosome,1388

are able to interpret a nucleotide sequence and translate it into an amino acid sequence.1393

You certainly do not need to memorize which codons signify particular amino acids. There is just a few things you should know, though.1400

However, AUG has a special job. It is also the start codon.1408

It specifies methionine. Methionine is always the first amino acid added, and AUG is the start codon.1414

There are several other special codons known as stop codons. UAA, UAG and UGA are stop codons.1422

When the ribosome encounters these, it knows translation is complete.1434

The genetic code is what is known as degenerate or redundant. What this means is that an amino acid can be specified by more than one codon.1441

This is best understood for example, so let's look at the codons for arginine.1450

CGA, CGC, CGG and CGU all code for arginine. All of these signify arginine.1455

If the ribosome encounters these, an arginine will be added there.1471

You have probably noticed that the first two - one and two - positions are the same. This third position is different.1476

This third position is known as the wobble position. Then, we will talk more about this in a minute.1484

But for right now, just be aware that the genetic code is redundant.1490

There is more than one codon for a particular amino acid, and it is that third position that changes.1494

Although it is redundant, it is non-ambiguous. There is no confusion about what amino acid to add.1502

When the ribosome gets to CGC, arginine will be added.1509

There is no question of "oh, should a valine be put here or a leucine?". It is very clear.1513

When the ribosome encounters CGG- same thing. Arginine should be added.1518

Looking at a different set of amino acids, let's look at glycine, GGU.1524

Ribosomes sees that it adds glycine- GGC, GGA and GGG. All of these code for glycine.1531

There is no ambiguity. However, there is redundancy.1545

We have more than one codon. It is redundant, not just one codon, one amino acid.1546

It is redundant- non-ambiguous but redundant.1550

We, now, understand how the code in RNA, the nucleotide sequence, is translated by the translation machinery into an amino acid sequence.1558

In order for this to occur, the elements that are required for translation are a messenger RNA transcript,1569

transfer RNA and ribosomes, as well as the amino acids to add.1578

We have got the transcript, got the amino acids, and we have got the machinery to actually carry out the job.1586

The function of tRNA is to deliver the amino acids to the ribosome, and this shows you the structure of transfer RNA.1593

This is a 2-dimensional representation. If you took the 3D, fold it up, tRNA, and flatten it out, you would get the structure.1602

And there is a couple areas on here that you should be familiar with.1610

The 3'- end is the amino acid attachment site.1613

When the tRNA is sitting there with no amino acid attached, we say that it is uncharged.1622

A charged tRNA is covalently bonded to a particular amino acid.1630

A second important site on the tRNA is this sequence, which is called the anticodon- a triplet called the anticodon.1642

This is a 3'-end, and this is the 5'-end; so if you just look at these three, we are going from 3' to 5'.1653

This anticodon can base pair with the complementary sequence on the mRNA, so let's look at mRNA and what sequence would be complementary.1662

A pairs with U. C pairs with G, and A pairs with U.1673

The ribosome is holding an mRNA, and when it gets to this particular codon,1683

the tRNA that is going to be able to pair with it is going to be the one with the anticodon that is complementary.1692

This sequence, this codon, of course, specifies an amino acid.1700

In this case it is cysteine. This is the codon for cysteine.1707

That means that this tRNA is going to be charged with cysteine.1713

If we were talking about arginine, one of the codons is CGC.1719

If there was a CGC down here, where the anticodon for that,1723

if we got a CGC here and the anticodon to compare with that, this would be holding arginine instead.1729

So, the anticodon pairs up with the codon, and whatever that codon specifies is what that type of tRNA is going to be carrying that amino acid.1736

That is how the tRNA gets the correct amino acid to the correct place.1746

Obviously, it is very important that there is a charging done correctly.1752

And the job of making sure that the correct amino acid gets bonded to the correct transfer RNA is performed by enzymes called aminoacyl tRNA synthetases.1758

There are twenty of these. There is one for each type of amino acid, and what this type of enzyme does is it holds on to a tRNA.1776

It also holds on to the amino acid that belongs to that tRNA and catalyzes the attachment of, say in this case, cysteine to this tRNA.1785

Once that is charged, it can deliver its amino acid to the ribosome at the correct place.1796

There are actually 61 codons, but they are not 61 tRNAs.1804

There is actually about 40 in bacteria and about 50 in eukaryotes, so I am going to say there is only 40 to 50 tRNAs.1810

How does that work? Each codon does not have a special tRNA.1819

Well, it has to do with the wobble position that we talked about.1827

Let's revisit arginine that we talked about- the codons for arginine: CGA, CGC, CGG and CGU.1830

In this third position, why is it called the wobble?1850

The reason it is called the wobble is there is some flexibility in the binding of the anticodon to the codon in this 5' or wobble position.1855

Focusing on, let’s say we have a tRNA and going from 3', it is GCG.1866

We would expect it to pair up with an mRNA that goes 5' CGC. That is expected.1880

That is typical Watson Crick base pairing rules is G would go with C, and A would go with T; or in RNA, A would go with U.1892

This is what I expect, that when this codon is encountered, tRNA will float in. It will base pair codon, anticodon, and CGC specifies arginine.1903

This tRNA will be holding an arginine, and argentine will get added- fine.1918

However, let's say I had a different codon. I had an mRNA that contained CGU.1922

Actually, this tRNA anticodon can base pair with this codon. GC, expected, CG, expected, GU, that is not expected, but it is allowed.1933

In this wobble position, in this 5' anticodon position, the rules of base pairing are a little bit more flexible.1946

G in the 5' wobble position can pair with C and U.1956

In the wobble position, if there is a U, it is actually allowed to pair with both A and G.1964

You see how you will not need a single tRNA for every codon.1972

Instead, there could be a tRNA with GCG, and it could add an argentine when it comes upon either this CGC codon or the CGU codon.1977

And that is because of that wobble position.1991

tRNA is one component needed for translation as well as mRNA and, of course, the amino acids.1994

The other very important component is ribosomes, and we talked about this briefly when we talked about cell structure but now delving into more detail.2002

To understand translation, you need to understand various parts of the ribosome.2010

Ribosomes consist of a large subunit, a small subunit and ribosomal RNA.2014

They contain some particular binding sites.2022

Here is the mRNA, so there is a site for the mRNA to attach.2026

There is also several places where tRNA can be located.2030

These three sites are the E-site, which is the exit site. That is a channel that the tRNA can leave through.2035

The A-site which is known as the aminoacyl site.2043

In that site, you would find tRNA attached to an amino acid, the incoming tRNA carrying the next amino acid to be added.2048

The P-site is the peptidyl site. What you would find in that site is the tRNA carrying the growing peptide chain.2058

There will be a tRNA in here, and it is going to have this peptide chain attached.2070

And then, another tRNA will come in carrying the next amino acid to be added.2077

And then, eventually the empty tRNA we will see in a second will leave through this exit site.2084

Just be aware that there is a place for the mRNA. There is an exit site, a peptidyl transfer RNA site and an aminoacyl transfer RNA site.2089

Looking at the steps of translation, we talked about transcription. There are three phases.2102

There are three phases here, as well, and they have the same names- initiation, elongation and termination.2108

Starting of course with initiation, during initiation, the two ribosomal subunits, the mRNA and the first tRNA comes together.2116

The components of translation are assembled. They come together.2128

Initially, the two ribosomal subunits are not together. The small subunit binds first, and it binds upstream of the start codon.2140

The small ribosomal subunit binds upstream of the start codon. It binds to the mRNA upstream of the start codon.2151

Remember that the start codon is AUG, and that is also the codon that signifies methionine. In addition...well, it is OK.2166

So, then, right now, we just got this small subunit, and we have got the mRNA.2188

This small subunit actually, then, after it is bound upstream, it moves downstream until it gets to the start codon.2192

It needs to reach that AUG, and at that point, the large subunit will bind.2204

During initiation, the small ribosomal subunit binds first, binds upstream of the start codon. It moves to the start codon.2208

The large subunit binds. The ribosome is assembled.2216

The other thing that comes into play is that first tRNA, and the first tRNA is known as the initiator tRNA.2219

That is what you are seeing here at the beginning of the process, the initiator tRNA.2232

And since the start codon is AUG, this initiator tRNA is going to be charged with or carrying the amino acid methionine.2236

This process is facilitated by initiation factors, and it requires GTP; so initiation requires GTP, and it is facilitated by initiation factors.2245

In addition to the ribosome, the tRNA, amino acids and mRNA, to get things started, other proteins are needed.2261

And GTP will be hydrolyzed to provide energy for the process.2270

Now, I said that the first amino acid, the one at the start codon, is methionine.2275

And this is going to end up being at the N-terminus because amino acids are put together2280

to form a polypeptide starting at the N-terminus and ending at the C-terminus.2287

However, that does not mean that every single protein ends up with a methionine first2291

because sometimes, the methionine is cleaved off later as part of posttranslational processing.2296

During the translation process, yes, methionine will be added first, but it does not necessarily stay there.2302

Alright, initiation occurred. We have got the ribosome, the mRNA.2310

We have got this initiator, tRNA, ready to go with the methionine.2315

Now, notice that this is in the P-site. That very first tRNA starts off in the peptidyl site.2318

During elongation, what is going to happen is amino acids will be added one at a time, and the order of construction is from the N-terminus to the C-terminus.2328

Here, we have our start codon. The start codon is AUG.2342

Recall that the tRNA that is carrying a codon complementary to AUG is going to be able to come in, hydrogen bond temporarily with the codon.2347

So, here we have the codon. Here, we have the anticodon, and it is going to be carrying methionine.2363

Now, let's say this next codon encodes glycine. There is tRNAs floating around.2368

and eventually, the correct tRNA, the one that is carrying the anticodon complementary to the codon, is going to float in to this A-site.2376

And it is going to be able to hydrogen bond with the codon, and it is coding for glycine; and it is going to be carrying a glycine.2387

I have this methionine charged tRNA in the P-site. Now, I have the next one to be added in the A-site, so P-site.2395

And then, the new amino acid to be added goes in the aminoacyl tRNA site.2408

What happens next during elongation is that the ribosome is going to catalyze the formation of the bond between2416

the peptide chain - right now, there is only one amino acid here, but eventually it will be a chain - in the P-site and the amino acid in the A-site.2427

During that process, this chain...right now, just one amino acid will be transferred to the tRNA on the A-site.2436

GTP is also hydrolyzed during this step. GTP is needed for elongation.2449

OK, so, we had an amino acid on this tRNA.2455

We had the incoming amino acid glycine, and now, a bond is going to be hydrolyzed between these two.2460

Now, we have a little polypeptide chain consisting of methionine and glycine. Next is translocation.2466

Elongation is going to consist of growing the polypeptide chain by catalyzing the polypeptide bond.2478

So we add amino acids and translocate the tRNAs to the next site.2491

This is now empty. It needs to just leave.2503

This tRNA is going to be translocated to this exit site, and it is going to leave.2507

It is going to float off, and it is going to pick up the correct amino acid that is floating around in the cytoplasm, be charged.2513

And then, it can go along and add another methionine where it is needed.2519

This empty tRNA goes to the E-site, and then, it leaves.2525

Now, this is no longer just one amino acid by itself. It is now a peptide chain.2528

Therefore, this tRNA is going to be translocated to the P-site.2533

The mRNA is going to be shifted over until this codon is in the A-site.2538

Let's say that this codes for valine. Let's say it is the codon for valine.2546

Then, this will be shifted to the A-site. The tRNA with the anticodon for valine and carrying valine charged with it will float into the A-site.2554

This peptide chain and this tRNA in the P-site, this one is gone. and the process will continue.2563

The essential points are that the incoming tRNA with the correct amino acid floats in and enters the A-site.2568

The ribosome catalyzes the bonding between the peptide chain on the tRNA on the P-site to the new incoming amino acid.2577

The empty tRNA exits through the exit site, and then, everything is pretty much translocated over one.2588

And the mRNA is being moved along by the ribosome 5'-end first. That is elongation.2598

This is going to continue on until the ribosome encounters a stop codon.2606

At that point, termination will occur.2612

So, along goes...the mRNA has been moved along, moved along, moved along, and then, finally, the ribosome encounters a stop codon.2616

Remember UAA, UAG and UGA.2625

If the ribosome encounters that, it does not specify an amino acid, so there is no tRNA that is going to come along and add an amino acid.2630

Instead, what is going to bind is something called a release factor.2638

The release factor is shaped like a tRNA, and it binds, then, at this A-site.2642

Once we get to a stop codon, the release factor will bind, but it does not add an amino acid.2649

Instead, what it does is it hydrolyzes the bond between the peptide and the last tRNA, so the release factor adds water.2654

Normally, elongation is going along. One amino acid is added to the chain and so on, and so on, and it grows.2668

The release factor does not add an amino acid. It adds water.2676

By adding water here, the peptide strand is released. It has let go.2679

It floats away, and then, this complex disassembles.2685

The mRNA goes off. These two subunits disassociate.2689

The tRNAs go off, and then, they can all go be used to make another protein.2693

Three main steps: initiation, elongation and termination, and termination occurs when a stop codon is encountered.2699

A release factor binds, enters that A-site and adds water instead of adding an amino acid.2707

Many ribosomes can actually translate a single mRNA molecule at once.2717

You will have this mRNA going along, and there will be a bunch of ribosomes bound to it at different points, trailing out these polypeptides.2722

And when you see this complex with a bunch of ribosomes on a single mRNA molecule, it is called a polyribosome or sometimes just a polysome.2741

Recall that once this polypeptide chain is made, a lot of times, we just say "oh the protein has been made", but technically, it is not a protein yet.2754

It is only a polypeptide.2763

The primary sequence of a protein is its amino acid sequence, the primary structure, but it will fold into a 3-dimensional shape to actually become a protein.2765

Right now, that initial product, that amino acid sequence, is just a polypeptide chain.2777

It is going to undergo folding, and we talked in an earlier lecture about the different types of folding; and we talked about protein structure.2784

Recall that there is a secondary structure, which involves a hydrogen bonding between different regions within a polypeptide chain.2795

There were alpha-helices and beta-pleated sheets that was within a single polypeptide chain, and then, there is a tertiary structure.2805

And folding occurs so that this polypeptide chain forms an overall 3-dimensional shape.2821

Sometimes the shape is more globular like with hemoglobin. The shape can also be fibrous like with keratin.2827

Finally, some proteins have a quaternary structure when they are composed of multi-polypeptide chains.2834

Again, if you need to review that, look back in the lecture on proteins and nucleic acids.2842

Finally, some posttranslational modifications may need to occur like the addition of phosphate groups, the cleavage of the sequences.2847

And at that point, you have the final product.2854

You have the polypeptide chain. It is folded up.2856

It had modifications, things added, things removed, and now you have the product.2859

Mutations are changes in DNA sequence, and this was mentioned briefly earlier on when we talked about DNA synthesis.2867

But we want to talk about the implications of mutations on protein structure.2874

Now, initially, maybe DNA polymerase adds the wrong nucleotide, but often, it catches that mistake; or that mistake is repaired quickly by mismatch repair.2881

If it is not repaired and it creates a permanent change in a base pair, then there is mutation.2891

And these mutations are going to be passed along to the daughter cells.2897

Whenever that cell replicates its DNA, and then, the cell divides, that is going to be passed along.2900

If there is a mutation in the cells that will form germ cells, then, that mutation is actually going to be passed along to an organism's offsprings.2907

Point mutations are mutations in a single base pair. They are a change in a single base pair- change in one base pair.2916

There are multiple types of point mutations. They can be substitutions, insertions and deletions.2931

In a substitution, the base pair is changed. It is a different set of nucleotides.2938

However, the number of nucleotides is still the same.2946

Insertions- nucleotides are added. Deletions- they are removed.2950

Let's focus first on substitution mutations. In substitutions, there has been a change to one base pair, but the number is the same.2954

You could have a point mutation that it is a change. It is an adding of a single base pair here.2975

It is just changing the actual nucleotide.2980

For example, looking at DNA, I have got my DNA 5' to 3', and then, I have got the complementary strand.2982

Actually let’s do this slightly differently.2997

Let's say I have DNA 3' TTC to 5', and I am going to have a complementary strand, of course, because it is a double helix.3001

But I am going to focus on this strand, and this, let’s say, is the template strand for a particular gene.3015

When transcription occurs, you are going to end up with an RNA strand that is complementary.3021

T is going to pair up with A. T is going to pair up with A.3027

C is going to signify G.3041

When this is transcribed, the product of transcription, the mRNA is going to be this sequence- AAG.3044

AAG is actually the codon for lysine, so initially, this DNA encoded the information that lysine should go in a particular spot on the protein.3058

Let's say a mutation occurs. This becomes mutated, and you instead end up with DNA template strand 3' TT; but now, the third one is also T.3069

There has been this mutation. C has been changed.3090

There is a change in the DNA sequence. C is changed to T.3094

Now, when RNA polymerase comes along, and it sees this sequence,3098

it is going to say "OK, I need to add a T - excuse me - an A. I need to add an A. I need to add another A".3103

Normally, a G would be added here. Instead, an A was added.3114

There has been a change in DNA sequence. There is a few possible outcomes.3120

As it turns out, it is pretty lucky that the change was here in this third spot because remember that the genetic code is redundant,3124

that there is more than one codon for a particular amino acid.3134

And as it happens, AAG codes for lysine, and AAA codes for lysine.3137

That third position, that wobble position, often if you change that, you get the same amino acid.3143

When the ribosome comes along, and it sees this, it is going to add lysine. If it came along and saw this instead, it is going to add lysine.3150

There is going to be no effect on the protein. The protein is going to be completely normal because the lysine went where it should be.3162

This type of mutation is called a silent mutation, so for substitutions, there are three kinds of substitutions.3168

The first kind, the result is a silent mutation. There has been no change in the amino acid that is specified.3181

When you look at the protein that resulted, it is the same. There has been no change in the amino acid sequence.3193

That is the best case because, then, there is no problem with the protein. The protein will still function correctly.3199

This mutation is silent. It is not expressed in the phenotype.3205

It is there, but it is quiet.3209

The second type of mutation is known as a missense mutation. Let's look at an example.3211

This was first. We had silent, now, missense.3219

Let's say that I have this DNA template strand, and the 3' is GAA and then, 5'-end here.3229

And it would result in a transcribed mRNA that looks like this: 5' CUU to 3'.3238

This is actually a codon for leucine, and let's say a mutation occurs; and we end up with 3' G, but instead of A, we get a T.3251

RNA polymerase comes along and makes an mRNA based on this, and it is going to be 5' C. T is going to specify A, and the A is going to specify U.3270

There has been a change here. There is a change from G to A up here, but it did not really matter because these both coded for lysine.3287

However, CAU does not code for leucine. It actually codes for histidine.3294

There has been an impact then. A different amino acid will be added.3303

If I took this DNA and watch it be transcribed and translated, I would see a protein with a leucine in a certain spot.3307

This DNA used to form this mRNA is going to give a protein with histidine.3314

If there is a change to a different amino acid, that is a missense mutation. There has been a change in one amino acid.3319

Sometimes it is not a big deal.3333

Maybe those two amino acids are similar like they are both hydrophobic, or they are both basic.3335

And maybe they are located outside the active site of an enzyme, or they do not make a big difference in the folding of the protein in the structure.3342

Sometimes, it will not be a major deal. Other times it is.3348

Sickle-cell anemia is a disease that is actually caused by a change in only one amino acid.3353

In sickle-cell anemia, there is a change from glutamic acid to valine. That single change causes a difference in hemoglobin structure.3360

The hemoglobin is abnormal, and hemoglobin is found in red blood cells. It carries oxygen.3376

Under conditions of low oxygen, that hemoglobin causes the red blood cell to be shaped abnormally.3381

It actually causes it to, kind of, flatten out the shape, which is a shape of a sickle, hence the name sickle-cell anemia.3388

The problem is when cells sickle like that, they clump up. They block the smaller blood vessels.3397

And they can cause organs and tissues not to get enough oxygen, which is painful and can actually damage organs and tissues.3403

There are profound effects sometimes from a change of a single amino acid.3411

The other thing to think about is that mutations account for genetic diversity. Often times, these mutations are deleterious.3415

They will cause the protein not to work as well. They will cause the organism not to be as healthy, perhaps.3425

However, sometimes, the protein may function better, or under certain conditions, it is favorable to have that mutation.3432

And when talk about evolution, we will see how the genetic diversity and selection pressure for a particular phenotypes and traits works.3440

So one source of genetic diversity is mutations.3451

We talked about silent and missense mutations. Finally, the third type of substitution mutation is a nonsense mutation.3457

Nonsense mutations result in the change from an amino acid to a stop codon.3467

Perhaps, the DNA template was a CG on the DNA, which codes for cysteine, and we get our mRNA UGC.3478

We end up with cysteine added. Then, there is a mutation.3499

Now, we have DNA that is A, C and then T, so there has been a mutation.3503

This mRNA is, then, going to give me UGA. That is one of the stop codons.3518

Silent mutation- no effect on the amino acid. Missense mutation- a single change in an amino acid.3529

Nonsense mutation is a change from an amino acid to a stop codon,3536

which means that the protein is going to be shorter than it should be and generally, non-functional3540

unless you get very lucky, and this occurred way, way, way at the end. Usually though, this is a major effect.3546

Now, we talked about substitutions, where there has been a change in the amino acid sequence.3554

But another possibility is that amino acids have been - excuse me - nucleotides have been added or removed.3562

These are known as insertions and deletions.3577

Let's say that I have DNA looks like this: AGC, TCA, CTT.3583

Well, there is what is called a reading frame.3601

If you are reading in a book, and you are reading, say, a simple sentence "The boy can see.".3604

The reason this makes sense is you know where to start. You start over here on the left, and you know how to group these, the reading frame.3619

This is a word. This is a word.3625

This is a word. This is a word.3627

The ribosome reads as the same way. This is a codon, codon, codon.3628

If I stuck a letter in here, let's say I put an A right in here, now, the reading frame would be changed if I was reading every 3 it would be TA, EBO, YCA.3633

It would not make sense if I try to group those into words. The same thing can happen here.3651

If there is a mutation, and let’s say we add a T right here, so then, this might have signified just say lysine, valine, histidine.3655

Now, instead of AGC, I have AGT. Let me see.3672

Oh, actually, we need to change that. I will left out the C.3681

Let me change that. If I add a T here, and then, I would have my C still, I would have C, TCA, CTT.3688

There we go. Now that is added.3703

I have, instead of AGC, I have AGT. The C is still there, but now, it is part of the CTC as a codon instead of TCA.3704

Then, I have ACT and so on.3717

The protein from that point downstream is going to be messed up3720

because these amino acids are completely different than the amino acids that should have been specified.3725

And in fact, what often happens in this case, is one of these ends up being a stop codon.3731

So then, the protein is just truncated, so if within insertion or a deletion.3737

If I added an amino acid or excuse me, a nucleotide, if I added a nucleotide or took one out, either way, that would change what is called the reading frame.3743

And when the reading frame is changed, it is known as a frameshift mutation.3760

Adding or deleting insertions or deletions can result in frameshift, and that is a very severe mutation.3766

It could be just a point mutation, where a single base pair is added or a single base pair is removed, or there might be a large segment added or removed.3773

When we talked about chromosomes, we talked a little bit about larger problems that can occur.3783

This is just point mutations, but recall that there could be larger problems.3787

A part of a chromosome could break off, and then, that would be a large deletion. Parts of the chromosomes could be copied- duplications.3792

During miosis, if there is unequal crossing over, you can end up with large segments that are duplicated or large segments that are left out.3801

Mutations can occur spontaneously.3812

DNA polymerase makes a mistake. It is not caught.3816

Mismatch repair does not occur. It just happens sometimes, so these mistakes made during replication that is passed along.3819

Mutations may also be initiated by mutagens.3827

It is not just part of a natural error rate of DNA polymerase, but it is some chemical or physical mechanism that causes damage to the DNA.3830

Mutagens can be chemical. Certain chemicals are known as mutagens, or they can be physical.3839

Physical factors such as excessive exposure to sunlight can be a mutagen. X-rays can be a mutagen.3854

This, then, can result in a change in the DNA sequence, and such changes can actually result in cancer sometimes.3862

And therefore, we also say that certain mutagens or many mutagens are carcinogens.3872

Excessive exposure to a certain chemical can cause a change in the DNA sequence that may cause cancer.3878

We would say that that chemical is carcinogenic. It is mutagenic, and it is carcinogenic.3884

Alright, today, we covered quite a bit. We covered transcription, translation and mutations.3890

Now, we are going to review these concepts.3895

Example one: list three types of processing that are performed on pre-mRNA.3898

Recall that the immediate product of transcription is not mRNA. It is pre-mRNA.3906

In order to form mRNA, processing needs to be done.3913

Three major types are splicing, splicing is the process of removing introns, and they are fusing together the coding regions of DNA- the exons.3918

A second type of processing that occurs is the addition of the 5'- cap. This is a modified guanine nucleotide.3936

There is also the addition of a series of adenines that is the 3' poly(A) tail.3949

And the 5' cap and poly(A) tail protect the ends of the mRNA and signify that it is mRNA destined for export from the nucleus.3958

So, these are three types of processing that occur.3966

The terms below are related to the process of translation. Match each one to its description.3972

First we have elongation- delivers amino acids to the ribosome- that is not elongation.3978

A phase during which amino acids are added to the growing polypeptide chain- that is actually correct.3987

Remember that there are three phases of translation: initiation, elongation and termination.3997

Elongation is the phase during which the amino acids are added.4005

Alright, next, tRNA- delivers amino acids to the ribosome.4010

Well, that is already the correct one. That is the function of tRNA.4018

tRNA is charged with a particular amino acid.4024

When that tRNA encounters the codon that is complementary to its anticodon, it can base pair and it is carrying that amino acid.4027

That amino acid will be added to the growing polypeptide chain by the ribosome.4035

P-site - alright, we already used up A and B - it hydrolyzes the bond between the polypeptide chain and the tRNA once translation is completed.4040

Well, the P-site is just a site. It does not hydrolyze something.4051

D: sequence on tRNA that base pairs to a complementary codon on mRNA.4057

The P-site is not a sequence on the mRNA. Site of the ribosome, where the tRNA bound to the polypeptide is located.4063

This is a site on the ribosome, and E is the correct answer.4073

The P-site is the peptidyl site. It is the site where the tRNA carrying the polypeptide chain is located.4079

Anticodon: we used up E, and we already mentioned that this is a sequence; and that is what an anticodon is.4087

It is a triplet sequence, and it is found on tRNA; and it is going to be complementary to a particular codon on mRNA, so that is D.4098

That leaves us with release factor, which must be C.4110

And does the release factor hydrolyze the bond between the polypeptide chain and the tRNA once translation is competed? Yes.4115

When the ribosome encounters a stop codon, instead of a tRNA entering the A-site,4121

a release factor will enter the release site and add water to the polypeptide chain.4127

The polypeptide chain will be freed from the tRNA it is attached to.4132

Example three: the template strand used for transcription of a gene is shown below.4139

What would the RNA sequence of the transcript be?4144

Note always that you have to pay attention to directionality.4150

Here we have a template strand, so this is DNA; and what this question is asking me is what is the complementary RNA sequence going to be.4154

When you approach these, think about the directionality because sometimes wrong answers will have 5' here and 3' here or something.4162

Make sure that you first write in the directionality- 3' and 5'.4170

Using base pairing rules, I know that A is going to pair with U for RNA. There is no T.4178

That is another mistake that gets made is people put T here.4185

G pairs with C so AT, GC for DNA. For RNA, it is going to be AU, GC.4189

C pairs with G. C specifies G for complementary.4204

T gives us the U. The complementary nucleotide, the T is a U, GC, CG, GC, UGU.4210

This is a sequence that would be found in the transcript. This would be the template strand.4224

And then, the other strand on DNA, the antisense strand, would have this sequence except that the Us would be replaced with Ts.4232

Describe the three types of substitution mutations that can occur. Substitution means that there is a change in a single base pair.4243

And there are three possible types of substitutions: silent mutations, missense mutations and nonsense mutations.4251

In silent mutations, the result is another codon that specifies the same amino acid.4265

Although the DNA sequence is changed by look, it is changed to a sequence that specifies for a codon for the same amino acid as the original sequence.4282

A missense mutation- change to a codon for a different amino acid.4294

A change has occurred in the DNA sequence, and it is going to result in a codon that for example instead of specifying for valine, it specifies for glycine.4307

There is going to be a single amino acid change in that protein.4317

Nonsense mutation is change to a stop codon, initially, a DNA sequence coded for an amino acid.4320

The codon was for an amino acid. Its change in sequence results in a stop codon in that place.4332

So, these are the three types of substitution mutations.4339

That concludes this lesson on transcription and translation.4343

Thanks for visiting Educator.com.4347