Chapter 17 BIO Transcription & Translation

Transcription: X–directed synthesis of X: ribosmal RNA, tRNA, and messenger RNA 

Translation: X–directed synthesis of a X (X)

How do genes (DNA) direct the synthesis of proteins (amino acids)?

- DNA is a double stranded molecule that stays in the X, proteins are made outside in the X 

- DNA is transcribed into X (in the X) 

- X goes outside of the nucleus and is translated into X (in the X)

- X is the link between DNA and protein

Structure of RNA:

- X sugar, base on the # carbon, and phosphate on the # carbon, so when you make a polymer you will have a X bond between the 3’ and 5’. Again 3’ means the OH on the 3 carbon, and the 5’ is the longest beginning of the rna. The bases of DNA are the same except with RNA X pairs with X instead of X. 

THREE types of RNAs are involved in protein synthesis

(and many more are involved in other regulatory roles, in Ch 18!)

1. X: contains information to specify 1 or more protein 

2. X: will act as a connector between the mRNA and the amino acid, and it carries the amino acid in based on the information on the mRNA 

3. X: physical structure that can bind both the mRNA, travels along the mRNA and brings in tRNAs, based on how well they fit with the codon 

Transcription: X–directed synthesis of X: ribosmal RNA, tRNA, and messenger RNA 

Translation: X–directed synthesis of a X (X)

How do genes (DNA) direct the synthesis of proteins (amino acids)?

- DNA is a double stranded molecule that stays in the X, proteins are made outside in the X 

- DNA is transcribed into X (in the X) 

- X goes outside of the nucleus and is translated into X (in the X)

- X is the link between DNA and protein

Structure of RNA:

- X sugar, base on the # carbon, and phosphate on the # carbon, so when you make a polymer you will have a X bond between the 3’ and 5’. Again 3’ means the OH on the 3 carbon, and the 5’ is the longest beginning of the rna. The bases of DNA are the same except with RNA X pairs with X instead of X. 

THREE types of RNAs are involved in protein synthesis

(and many more are involved in other regulatory roles, in Ch 18!)

1. X: contains information to specify 1 or more protein 

2. X: will act as a connector between the mRNA and the amino acid, and it carries the amino acid in based on the information on the mRNA 

3. X: physical structure that can bind both the mRNA, travels along the mRNA and brings in tRNAs, based on how well they fit with the codon 

Overview of Transcription and Translation: The triplet code

1. X of # X unwinds

2. X X will pass through in a #’ to #’ direction 

3. X carries info

5. X information

End Result: a X, specified by the information in X!

- By the end of this process you will have an X copy, the RNA that is made the information is going to be carried into the X and it will be X, the mRNA goes out into the X, the information on the mRNA is read in groups of # called X, and they are read 1 at a time within the X, and the information that is on the mRNA codon an X X is brought in to match the codon 

- Translation happens in the X, synthesis of mRNA is in X and splicing is in the X 

Transcription and RNA Splicing

- X directed synthesis of X 

- RNA splicing, once the mRNA is made, depending on the cell mRNA regions are removed and they are not always removed in an identical manner,  regions will be looped out and then it will be snipped tohgetehr and make a final processed X, while that is going on something called a # X and a X X tail are added to help it get out of the nucleus as well as protect it. So 1. TX 2. RNA X 3. X activation, meaning these are molecules that to get into the process of protein synthesis, they need to pick up an X X and bring some information in with them, when you eat amino acids, those are the building blocks where one tRNA will pick up one amino acid an enzyme reaction will happen and then they can get into protein synthesis 

- On the X, there will be a very specific sequence and it is called the X box X, this is a huge signal to the cell that says X X come and bind here, so RNA polymerase initially binds there and will go down. There will be a #’ prime end of the RNA and it will need the #’ OH to keep on going, X X can start its own synthesis unlike X X so it does not need a X. There will be a template strand, where the DNA will directly code and it directly provides the information to make the mRNA, there will also be a nontemplate strand and little pieces of mRNA can be made off of it to X the mRNA

Overview of Transcription and Translation: The triplet code

1. DNA of 1 gene unwinds

2. RNA polymerase will pass through in a 5’ to 3’ direction 

3. RNA carries info

5. Codon information

End Result: a Protein, specified by the information in DNA!

- By the end of this process you will have an mRNA copy, the RNA that is made the information is going to be carried into the cytoplasm and it will be spliced, the mRNA goes out into the cytopalsm, the information on the mRNA is read in groups of 3 called codons, and they are read 1 at a time within the ribosome, and the information that is on the mRNA codon an amino acid is brought in to match the codon 

- Translation happens in the cytoplasm, synthesis of mRNA is in nucleus and splicing is in the nucleus 

Transcription and RNA Splicing

- DNA directed synthesis of RNA 

- RNA splicing, once the mRNA is made, depending on the cell mRNA regions are removed and they are not always removed in an identical manner,  regions will be looped out and then it will be snipped tohgetehr and make a final processed RNA, while that is going on something called a cap and a poly A tail are added to help it get out of the nucleus as well as protect it. So 1. Transcription 2. RNA Splicing 3. tRNA activation, meaning these are molecules that to get into the process of protein synthesis, they need to pick up an amino acid and bring some information in with them, when you eat amino acids, those are the building blocks where one tRNA will pick up one amino acid an enzyme reaction will happen and then they can get into protein synthesis 

- On the DNA, there will be a very specific sequence and it is called the TATA box TATAAA, this is a huge signal to the cell that says RNA polymerase come and bind here, so RNA polymerase initially binds there and will go down. There will be a 5’ prime end of the RNA and it will need the 3’ OH to keep on going, RNA polymerase can start its own synthesis unlike DNA polymerase so it does not need a primer. There will be a template strand, where the DNA will directly code and it directly provides the information to make the mRNA, there will also be a nontemplate strand and little pieces of mRNA can be made off of it to modulate the mRNA

RNA processing and RNA Splicing 

- The RNA before it can get out into the nucleus, has to be polished off, processing and splicing. 

- A #’ cap is added where it started and the cap is a modified X nucleotide, where phosphates like GTP will be connected to the front.

- A poly A tail is added to the #’ end, means many 5–250 X nucleotides added in 3’ end. Protects the X 

- The Cap and tail protect RNA and help it exit the X safely

- A typical mRNA in eukaryotes is going to hav regions called X which means intervening sequence and will be X out of the RNA, and will be removed from the final RNA. The X will stay in. All introns have been removed, becomes pure X RNA with X and X. 

- The pre-mRNA is “spliced” to REMOVE X, joining X`1

- Now the fully spliced mRNA will have a #’ X (X region), which is the X region, and it will help the X find its position on the X and position itself. 

- Start codon is a specific sequence of nucleotides X

- From the X codon to the X codon, ignoring everything else, will be made into a X

- X splicing allows variation where exons from one and introns form another can come together 

- Who does the splicing? X enzymes, X, create a X

RNA processing and RNA Splicing 

- The RNA before it can get out into the nucleus, has to be polished off, processing and splicing. 

- A 5’ cap is added where it started and the cap is a modified guanine nucleotide, where phosphates like GTP will be connected to the front.

- A poly A tail is added to the 3’ end, means many 5–250 adenine nucleotides added in 3’ end. Protects the RNA 

- The Cap and tail protect RNA and help it exit the nucleus safely

- A typical mRNA in eukaryotes is going to hav regions called introns which means intervening sequence and will be spliced out of the RNA, and will be removed from the final RNA. The exons will stay in. All introns have been removed, becomes pure exon RNA with cap and tail. 

- The pre-mRNA is “spliced” to REMOVE introns, joining EXONS

- Now the fully spliced mRNA will have a 5’ UTR (untranslated region), which is the untranslated region, and it will help the mRNA find its position on the ribosome and position itself. 

- Start codon is a specific sequence of nucleotides AUG

- From the start codon to the stop codon, ignoring everything else, will be made into a protein

- Alternative splicing allows variation where exons from one and introns form another can come together 

- Who does the splicing? RNA enzymes, ribozymes, create a spicosomes

tRNAs and activation via Aminoacyl-tRNA synthetases

- tRNAs are small pieces of X, made from X into X by transcription but they do not get made into X, if you put them into the X they spring and create a 3 dimensional shape, we said that RNA cannot form a X X, but it can be complimentary to other nucleotides. Will have a #’ and #’ ends. The #’ end ends in X because that is what the cell needs to attach an X X right there. The tRNA has a clover shape, looks like a bobby pin, that is created from X bonds. One of the bobby pin ends is the X, the action end. AT the 3’ CCA end an X X will attach based on the X

- Ther eis a process that cells go through to get connected to their amino acids, when we say there is an aminoa acid attached at the end of the tRNA, how do they know which amino acid to pick up. There is a set of enzymes, one for every amino acid, the enzyme is called X-tRNA X, an enzyme that will synthesize a combination of an X X and a tRNA, it will bring in a X and inserts itself into that enzyme, that also has room for a very specific X X and it will click them in with the help of X. Each enzyme will recognize the specific codon which is a grouping of 3 nucleotides, so it will have an active site that will recognize the shape of the anticodon, and it will allow it to fit in and it will use an ATP molecule to make a phosphorylated intermediate, when that is snapped into the enzyme, the hydroylsis of that X, then allows the proper amino acid to come and get connected to the #’ here at the X. tRNA activation, getting correct X X attached to them and that is based on the X region, 1 for every amino acid

- Attaching 1 amino acid to 1 trna based on the anticodon usinf this enzyme

tRNAs and activation via Aminoacyl-tRNA synthetases

- tRNAs are small pieces of RNA, made from DNA into RNA by transcription but they do not get made into proteins, if you put them into the cytoplasm they spring and create a 3 dimensional shape, we said that RNA cannot form a double helix, but it can be complimentary to other nucleotides. Will have a 5’ and 3’ ends. The 3’ end ends in CCA because that is what the cell needs to attach an amino acid right there. The tRNA has a clover shape, looks like a bobby pin, that is created from hydrogen bonds. One of the bobby pin ends is the anitocodon, the action end. AT the 3’ CCA end an amino acid will attach based on the anticodon

- Ther eis a process that cells go through to get connected to their amino acids, when we say there is an aminoa acid attached at the end of the tRNA, how do they know which amino acid to pick up. There is a set of enzymes, one for every amino acid, the enzyme is called Aminoacyl-tRNA synthetases, an enzyme that will synthesize a combination of an amino acid and a tRNA, it will bring in a tRNA and inserts itself into that enzyme, that also has room for a very specific amino acid and it will click them in with the help of ATP. Each enzyme will recognize the specific codon which is a grouping of 3 nucleotides, so it will have an active site that will recognize the shape of the anticodon, and it will allow it to fit in and it will use an ATP molecule to make a phosphorylated intermediate, when that is snapped into the enzyme, the hydroylsis of that ATP, then allows the proper amino acid to come and get connected to the 3’ here at the CCA. tRNA activation, getting correct amino acid attached to them and that is based on the anticodon region, 1 for every amino acid

- Attaching 1 amino acid to 1 trna based on the anticodon usinf this enzyme

Cracking the genetic code – the Codon Chart

- X is the genetic material that will specify proteins 

- How letters of nucleotides end up specifying a sequence of protein 

- They knew there were # amino acids and # bases, has to be read in groups of 3# 

- # nucleotides of DNA, read # at a time when it makes RNA, # or # different codons -

More than enough to specify the ~# known amino acids. # different ways you can align nucleotides, 

All possible combinations of codons are used 61 specify amino acids; # are stop codons

The genetic code is X: All living organisms, and viruses, use this same genetic code to make protein

The genetic code is redundant: There are many synonymous codons, with the 3rd position allowing ‘wobble’ at the 3’ end of the codon 

Coronavirus Edition

- RNA virus, comes in as a piece of RNA. Spike, envelope, membrane, and nucleocaspid protein

- It has this spike protein on the outside, there is a receptor that a lot of people hav eon outside of their cells, the receptor called X converting enzyme which regulate sblood pressure, the X protein fits on that receptor, once it docks the receptor lets inside. When it gets into the cell, the X starts to uncoat from the RNA and leaves behind the naked viral RNA. There is enzyme called the X dependant X polymerase. The RNA can now be used to make X and a X snaps on and creates more coronavirus proteins

Cracking the genetic code – the Codon Chart

- DNA is the genetic material that will specify proteins 

- How letters of nucleotides end up specifying a sequence of protein 

- They knew there were 20 amino acids and 4 bases, has to be read in groups of 3. 

- 4 nucleotides of DNA, read 3 at a time when it makes RNA, 43 or 64 different codons -

More than enough to specify the ~20 known amino acids. 64 different ways you can align nucleotides, 

All possible combinations of codons are used 61 specify amino acids; 3 are stop codons

The genetic code is universal: All living organisms, and viruses, use this same genetic code to make protein

The genetic code is redundant: There are many synonymous codons, with the 3rd position allowing ‘wobble’ at the 3’ end of the codon 

Coronavirus Edition

- RNA virus, comes in as a piece of RNA. Spike, envelope, membrane, and nucleocaspid protein

- It has this spike protein on the outside, there is a receptor that a lot of people hav eon outside of their cells, the receptor called angiotensin converting enzyme which regulate sblood pressure, the spike protein fits on that receptor, once it docks the receptor lets inside. When it gets into the cell, the nucleocapsid starts to uncoat from the RNA and leaves behind the naked viral RNA. There is enzyme called the RNA dependant RNA polymerase. The RNA can now be used to make proteins and a ribosome snaps on and creates more coronavirus proteins

What is Translation? Preview The X-directed synthesis of a X

- X RNA physically forms the structure of the ribosome, the X will bring in the amino acids, the ribsomal RNA will create the structure of the ribosome

- The physical link between a gene and a protein!

How is Translation Initiated?

- This is happening in the X, the X just has came out of the cytplasm and met by a small subunit of the X, and an initiator X, so an X codon on the mRNA #’ to #’, the initiator tRNA will have the X going #’ to #’ and the anticodon will be X and it would have an attached X amino acid on the tRNA. So the codon AUG woul dbe complimentary to the anticodon UAC, when that UAC bearing X comes into that enzyme it puts methionine and it will require X to close the large subunit over. You will have the initiator tRNA. X stands for the acceptor, accept the incoming X, X site is where the X bond is built X site, X site once the tRNA has done its work it will go to the exit site

- RIbosome is getting ready to look at codon 4, a new X will be recruited and it will be bearing the correct X X to match that codon, making a protein is an energy expensive process, a new tRNA brought in? A new X spent. The bond that join the amino acid to the tRNA has to be cut for a brief moment in time in the P site it will not be connected to anything, and at this point the bond that is broken will transfer this amino acid over to the incoming amino acid in the A site and at the same time the ribosome will switch down to another 3 nucleotides. The enzyme that does this reaction in severing the connection between the tRNA and it moves it over the P site: X, detached the amino acid at the X site and joins it to the amino acid to the X site, making a peptide bond, it is a X, made within the ribosome where X bonds are formed. So amino acids will be severed from tRNA in the X site and flipped to the incoming tRNA in the X site.  The first amino acid and the tRNA is the bond made by the X X tRNA enzyme. While the first amino acid and the second amino acid is a X bond made by X. Then it goes to the E site, a new tRNA will ve recruited to the free A site

How is Translation Terminated? 

- Finally ribosome will reach the stop codons on the X: UAG, UAA< or UGA and a X factor will be recruited in and hydrolyzes everything, it cuts the X away from the X, the subunits will push apart this is an energy requiring process using # X. And as long as the mRNA is still intact, the process can continue 

Polyribosomes: mRNA half-life is very short, so many ribosomes cluster on the

same mRNA simultaneously, forming a X, making many proteins off the same = mRNA in a short time.

What is Translation? Preview The RNA-directed synthesis of a protein

- RIbosomal RNA physically forms the structure of the ribosome, the tRNA will bring in the amino acids, the ribsomal RNA will create the structure of the ribosome

- The physical link between a gene and a protein!

How is Translation Initiated?

- This is happening in the cytoplasm, the mRNA just has came out of the cytplasm and met by a small subunit of the ribosome, and an initiator tRNA, so an AUG codon on the mRNA 5’ to 3’, the initiator tRNA will have the anticodon going 3’ to 5’ and the anticodon will be UAC and it would have an attached methionine amino acid on the tRNA. So the codon AUG woul dbe complimentary to the anticodon UAC, when that UAC bearing tRNA comes into that enzyme it puts methionine and it will require ATP to close the large subunit over. You will have the initiator tRNA. A stands for the acceptor, accept the incoming tRNA, P site is where the peptide bond is built peptidyl site, E site once the tRNA has done its work it will go to the exit site

- RIbosome is getting ready to look at codon 4, a new tRNA will be recruited and it will be bearing the correct amino acid to match that codon, making a protein is an energy expensive process, a new tRNA brought in? A new ATP spent. The bond that join the amino acid to the tRNA has to be cut for a brief moment in time it will not be connected to anything, and at this point the bond that is broken will transfer this amino acid over to the incoming amino acid and at the same time the ribosome will switch down to another 3 nucleotides. The enzyme that does this reaction in severing the connection between the tRNA and it moves it over the P site: peptifyltransferase, detached the amino acid at the P site and joins it to the amino acid to the A site, making a peptide bond, it is a ribozyme, made within the ribosome where peptide bonds are formed. So amino acids will be severed from tRNA in the P site and flipped to the incoming tRNA in the A site.  The first amino acid and the tRNA is the bond made by the amino acetyl tRNA enzyme. While the first amino acid and the second amino acid is a peptide bond made by peptidyltransferase. Then it goes to the E site, a new tRNA will ve recruited to the free A site

How is Translation Terminated? 

- Finally ribosome will reach the stop codons on the mRNA: UAG, UAA< or UGA and a release factor will be recruited in and hydrolyzes everything, it cuts the polypeptide away from the tRNA, the subunits will push apart this is an energy requiring process using 2 GTP. And as long as the mRNA is still intact, the process can continue 

Polyribosomes: mRNA half-life is very short, so many ribosomes cluster on the

same mRNA simultaneously, forming a polyribosome, making many proteins off the same = mRNA in a short time.

Proteins made in the RER 

- There are a set of amino acids that comes out early in the synthesis of the protein called a X X, short segment of 3-4 X X, once it appears in the X it will be recognized by something called the X X particule SRP, and it will grab on to the X X and grabs onto the whole ribosme, and the mRNA has to pull the whole complex to the ER membrane, and it docks to the X complex and opens a pore in the ER, and as the ribosome is moving along the RNA and creates a longer protein the protein will begin synthesizing in the X

Coupled transcription and translation in bacteria

- bacteria do not have a X, so they can simultaneously do X and X 

- Prokaryotes=no X

Proteins made in the RER 

- There are a set of amino acids that comes out early in the synthesis of the protein called a signal peptide, short segment of 3-4 amino acids, once it appears in the cytoplasm it will be recognized by something called the signal recognitional particule SRP, and it will grab on to the signal peptide and grabs onto the whole ribosme, and the mRNA has to pull the whole complex to the ER membrane, and it docks to the translocation complex and opens a pore in the ER, and as the ribosome is moving along the RNA and creates a longer protein the protein will begin synthesizing in the ER

Coupled transcription and translation in bacteria

- bacteria do not have a nucleus, so they can simultaneously do transciritpn and translation 

- Prokaryotes=no introns

Errors in DNA: The molecular basis of sickle-cell disease: a X mutation

- # X is changed. 

- In the mutant DNA, the template strand has an A instead of a T.

The mutant mRNA has a U instead of an A in one codon.

The sickle-cell hemoglobin has a valine instead of a glutamic acid.

Base-pair substitution

- 1 nucleotide is swapped fo another in the DNA 

Silent Mutation: Change in nucleotide has NO effect on X (wobble) - we have these all over our genome! Ex: GGC to GGU = both are Gly, 3rd position changed no effect. Amino acid stays the same? Silent mutation 

Missense Mutation: Change in nucleotide specifies a new amino acid. Change in nucleotide and in amino acid. 

Ex: X X disease: GAA (Glu) to GUA (Val).

Ex: X: GGA (Gly) to AGA (Arg).

NonSense Mutation: Change in nucleotide creates a premature X Codon, truncating protein, X protein 

Ex: X: UGC (Cys) to UGA (stop).

Base-pair insertion or deletion (Indels)

- You add or subtract 

Frameshift causing immediate X: X - a #-X X at codon 22

causes a stop, resulting in a loss of this tumor supressor protein. # X pair X 

Frameshift causing mX iX: Ex: X and X X Insertions and/or deletions: Ex: X The biggest gene in our genome - 2 million bp! 1 deletion of nucleotide 

Insertion or deletion of 3 nucleotides: no X but X or X amino acid

Ex: X - a common # base pair X Phe508 causes a loss of one (crucial) X X and non-functional X protein, enite X gone.

Errors in DNA: The molecular basis of sickle-cell disease: a point mutation

- 1 nucleotide is changed. 

- In the mutant DNA, the template strand has an A instead of a T.

The mutant mRNA has a U instead of an A in one codon.

The sickle-cell hemoglobin has a valine instead of a glutamic acid.

Base-pair substitution

- 1 nucleotide is swapped fo another in the DNA 

Silent Mutation: Change in nucleotide has NO effect on aa (wobble) - we have these all over our genome! Ex: GGC to GGU = both are Gly, 3rd position changed no effect. Amino acid stays the same? Silent mutation 

Missense Mutation: Change in nucleotide specifies a new amino acid. Change in nucleotide and in amino acid. 

Ex: Sickle cell disease: GAA (Glu) to GUA (Val).

Ex: Achondroplasia: GGA (Gly) to AGA (Arg).

NonSense Mutation: Change in nucleotide creates a premature Stop Codon, truncating protein, shortening protein 

Ex: Phenylketonuria: UGC (Cys) to UGA (stop).

Base-pair insertion or deletion (Indels)

- You add or subtract 

Frameshift causing immediate nonsense Ex: BRCA1 - a 2-bp deletion at codon 22

causes a stop, resulting in a loss of this tumor supressor protein. 2 base pair deletion 

Frameshift causing missense Insertions: Ex: Huntingtons and Fragile X Insertions and/or deletions: Ex: DMD The biggest gene in our genome - 2 million bp! 1 deletion of nucleotide 

Insertion or deletion of 3 nucleotides: no frameshift but extra or missing amino acid

Ex: CF - a common 3 base pair deletion Phe508 causes a loss of one (crucial) amino

acid and non-functional CFTR protein, enite codon gone.

COVID-19 Continued

- RNAs will be made into new X, making the X proteins as well as little RNA X, now the viral proteins have to go through the X and will begin to bud out of the cell through X and spread the infection. 

- Inhibtis the transcitipion of the viral RNA: antiviral remdeivir because it looks like the viral RNA but it doesn’t recognize certain aspects of it, blocks the X dependent X polymerase

COVID-19 Continued

- RNAs will be made into new proteins, making the spike proteins as well as little RNA genome, now the viral proteins have to go through the ER and will begin to bud out of the cell through exocytosis and spread the infection. 

- Inhibtis the transcitipion of the viral RNA: antiviral remdeivir because it looks like the viral RNA but it doesn’t recognize certain aspects of it, blocks the RNA dependent RNA polymerase