Review: Unit 3. DNA, Mutations and rDNA

 What What What!? The end of this unit? Well, one more down, umm... 12 to go. Embarrassing, considering the amount of time I've been working on this,false starts and all.

Unit three test tomorrow, unit four test (aiming for a week from tomorrow) and then, a midterm. I'll be a third of the way through the course. It will be awesome. The pace needs to be picked up though, my scheduled college classes begin in May.

Of course, the rough endoplasmic reticulum is studded with ribosomes... and we all know the ribosomes are active in protein synthesis. ;) According to my biologist friend, the ribosomes on ER are for mRNA translation only.


Quick review:

Nucleotide: Biological building blocks for DNA and RNA. DNA: Made of a Phosphate, a 5-carbon deoxyribose sugar (a pentose sugar) and a base. One of Four bases (listed in the order they pair in)- Adenine, Thymine, Guanine and Cytosine. FOR RNA: Adenine, Thymine, Guanine and Uracil. Bases are either purines or pyrimidines. Purines are Adenine and Guanine. They have a double ring structure. Pyrimidines are Cytosine, Uracil and Thymine. These have a single ring structure. 


DNA: Deoxyribonucleic acid. Our genetic material. Looks like a twisted ladder but it is actually a Polymer of nucleotides joined in the middle (hydrogen bonds) with complementary base pairing. reproduces semi conservatively.The uprights of the ladder are sugar-phosphate-sugar-phospate pattern structure. DNA must replicate with a high degree of accuracy, be able to store information and undergo mutations to control both the development and metabolic activities of the cell and organism.

DNA replication: occurs in the nucleus of the cell. 3 steps: 1. Unwinding: DNA Helicase comes in and unzips [the bases] by breaking the hydrogen bonds that hold them together. 2. Complementary base pairing: Free floating nucleotides pair with the unzipped, now open bases. 3. Joining: DNA Polymerase joins the paired nucleotides and thus, two strands of DNA are born- one side of the DNA's ladder is from the old polymer and the other side of the ladder is new: this is known as semi conservative replication because part of the old strand is always preserved. DNA replicates in this way so that it can replicate with a high degree of accuracy.


RNA: Ribonucleic acid. Structurally the same as DNA with a phosphate, a pentose sugar (ribose) and a nitrogenous base. Adenine, Guanine, Uracil and Cytosine. SINGLE STRANDED IN STRUCTURE. Functions in the synthesis of proteins. Three different tyes of RNA: tRNA: escorts amino acids to mRNA during protein synthesis rRNA: has a structural role, forming most of the ribosome, along with protein. mRNA: messenger RNA carries a coded sequence of bases to the ribosomes for protein synthesis.


Triplet codes: During protein synthesis, amino acids are carried to mRNA dependent which bases are represented and in which order. If you were to supply a singular base at a time, there would not be enough bases to code for all 20 amino acids that must link together to make proteins. By having bases available in triplets, there are enough bases available to code for 64 different bases (this includes start and stop codons). Multiple triplets can code for one amino acid.


Transcription: a strand of DNA is copied to make a strand of mRNA. During Transcription, a segment of  the DNA unwinds and unzips (thank you, helicase) and ONE strand of the DNA is copied from the transcription bubble. Complementary nucleotides pair with the DNA bases using the following bases: Uracil, thymine, guanine and cytosine. A strand of mRNA results.  

Translation: Translation is the process where the sequence of codons formed during transcription becomes the order of amino acids in a polypeptide.Translation begins with rRNA, coming from the nucleus and joining with a protein to form a  ribosomal subunit. Then, the process of translation begins with 1.Initiation: mRNA bonds to two ribosomal subunits. 2. Elongation: tRNA brings amino acids to the ribosomal subunit/mRNA sandwich. These amino acids are the anticodons to the codons on the mRNA. The ribosomal unit has room for two tRNAs. One goes in, bearing an amino acid. That tRNA receives an amino acid chain from the tRNA just leaving the ribosome. That tRNA adds its amino acid and elongates the chain in this manner, passing the chain to the next tRNA to enter the ribosome 3. Termination: A stop codon is encountered on the mRNA. The protein drops off as the ribosome dissociates. Polyribosomes can sometimes form and they all work together along the same mRNA and create multiple copies of the same protein. 



Where transcription copies the sequence of bases from the DNA string to form mRNA, translation translates these base codons to become amino acid polypeptides (protein).


  
Mutation: A mutation is a change in the nucleotide sequence of a gene. 

Point mutation: A change in a specific nucleotide. When one base is substituted for another along the mRNA, different things can happen. There can be a silent mutation where, by luck of the draw, the nucleotide changed ends up coding for the amino acid that was needed in the first place. A Nonsense mutation happens where the codon is changed to become a Stop codon. This makes the resulting protein too short and useless. There is finally, a missense mutation. A missense mutation happens when the codon is a useful amino acid, but it is in the wrong place, affecting the shape of the resulting protein as well as the polarity. This missense mutation is what causes sickle cell disease.  Valine is substituted for glutamate along the protein chain. 

Frameshift mutation: An error on the reading frame or sequence of codons presented for protein synthesis occurs. A base is DELETED along the chain and shifts the codons all down one slot. This deletion changes the entire sequence of codons and confuses the entire meaning of the resulting protein. Frameshift mutations frequently result in severe genetic diseases such as Tay-Sachs disease.

Mutagens: Environmental factors that cause mutations. Mutagens cause cancer and birth defects. Radiation (Xrays) or Organic chemicals (pesticides and compounds in cigarette smoke) are mutagens. Mutations in the body cells will result in cancer. Mutations in the gametes will cause deformities in the offspring. 

Recombinant DNA: Recombinant DNA contains DNA from two or more different sources. rDNA is used to create products that would be difficult to obtain by natural harvesting in mass quantities. These products are things like insulin, hormones, lung surfactant and enzymes. 

To make rDNA: A vector is chosen. In the example here, we will use a bacterium. We remove the plasmid (small DNA molecule) from the bacterium and use resriction enzyme to cleave a space for the gene we want to replicate (insulin, for example) we then isolate the gene for insulin and remove it (again, using the restriction enzyme) the insulin gene is placed into the plasmid and is then sealed together as one unit using DNA ligase. The host cell (bacterium) takes up the recombined plasmid. As the host cell reproduces, the plasmid is reproduced as well, resulting in multiple copies for the rDNA. The resulting rDNA is inspected and if it is found suitable, the product [in this case insulin] is retrieved for use. 

Recombinant DNA

Recombinant DNA (rDNA)
 

Recombinant DNA contains DNA from 2 or more different sources. 

Vector: the means of by which rDNA is introduced into a host cell.
Plasmid: found in the cytoplasm of bacteria, a plasmid is beneficial to making rDNA since it acts as a vector. Plasmids are small accessory rings of DNA. They carry genes not present in bacterial chromosome.
Two enzymes are needed to make rDNA (Next part makes more sense if this here makes sense to you):

Restriction enzyme: cleaves both the plasmid and human DNA.
DNA Ligase: Seals foreign DNA into the opening created by restriction enzyme.


To make insulin:

1. Choose your Vector (host) We will use a plasmid from a bacterium for this.

2. Remove the plasmid from the bacterium.
3. With the help of restriction enzyme, isolate and remove the gene for insulin from the human DNA.
4. Again with the restriction enzyme, cleave a space for the insulin gene in the plasmid.
5. insert gene into vector and seal with DNA ligase.
*******now you have rDNA*************
6. Host cell takes up recombined plasmid.
7. Plasmid is cloned as host cell reproduces.
8. Multiple copies of the cloned gene are replicated and if this cloned insulin gene functions normally (as inspected by an investigator) the product (insulin)  may also be retrieved.


List three specific uses for recombinant DNA or transgenic organisms.
1. Vaccinations
2. Mass production of products to be used in the human body- insulin for example, that would be expensive and harder to achieve by harvesting it from other sources.
3. Growth hormones to produce leaner meat, for slaughter.

Mutagens

 Mutagens are environmental substances that cause mutations. 


Mutations can cause cancer or birth defects. 

Mutagens are factors like radiation (X-rays) or organic chemicals ( certain pesticides or compounds in cigarette smoke). 

Lots of mutagens are carcinogens. Mutations in the body cells will likely result in cancer. 

If the mutation occurs in the sex cells (gametes) then the mutation will occur in the offspring.

Mutation

In order for us to evolve, mutation of our genes is necessary. However, not all of these mutations are beneficial. 

 Define gene mutation.
 A gene mutation is a change in the nucleotide sequence of a gene. 
 Since each new strand of DNA is proofread for errors by DNA Polymerase, it's rare that there is an error in replication. Apparently, the chance that the DNA is repicated incorrectly is about one in 1 billion replicated nucleotides. 

There are two types of mutations that are relevant to this section of coursework: Frameshift and Point mutations. 

A frameshift mutation is an error on the  'reading frame' or sequence of codons that are presented for replication. Since replication begins at a specific point ,when one codon is deleted, the results can be devastating since it shifts the entire row codons down one slot and turns the result into something that doesn't make sense. Imagine you deleted the first letter out of a sentence but kept the spacing the same.
'When is dinner ready?' turns into 'heni sdinne rready?". Nonsensical and it has lost its intended meaning. This is how frameshift mutations occur- by deleting or adding a nucleotide into DNA, rendering it nonfunctional.

A point mutation  happens anywhere along the gene and does not involve a deletion or addition but a change in a specific nucleotide.  

Remember our chart of codons. Each three letters actually stand for a specific amino acid. 61 of them are amino acids, two are Stop codons (describes where termination of synthesis occurs) and one is a Start codon. 

In most instances, replacing one base with another does not have a drastic effect. It can change one codon to another and through luck of the draw, the change results in the same kind of amino acid and life goes on (called a silent mutation)  for instance, CGC is arginine. Substitute CGG and the result is still arginine.
 
In some cases, the codon can be changed to become a stop codon, prematurely ending synthesis and resulting in a too short protein that is non functional (nonsense mutation). 
 
Other times, a missense mutation happens. This is when the meaning of the codon is changed completely when one amino acid is substituted. if CAC is incorporated into the protein instead of UAC, then histidine is added instead of tyrosine. This is disastrous especially since the polarity of the two differ.


Sickle Cell disease is caused by a missense mutation. 
Along the chain, Valine is substituted for Glutamate long the hemoglobin chain. This results in the sickling of the red blood cells and among other things, their premature breakdown-- causing anemia and other complications.

Translation

"Describe the process of translation in protein synthesis, including initiation, elongation, and termination."


Here are two definitions that mean the same thing because I'm annoying like that:

Translation is the process where the sequence of codons formed during transcription becomes the order of amino acids in a polypeptide.

Process by which the sequence of codons in mRNA dictates the sequence of amino acids in a polypeptide.


Where transcription copies the sequence of bases from the DNA string to form mRNA, translation translates these base codons to become amino acid polypeptides.


During translation, the sequence of codons on the mRNA show the amino acids which order to go in to create their polypeptide


Three Steps of translation: 

This is my incomplete Karla ramble:
 
We begin with our mRNA, hanging out in the cytoplasm. It left the nucleus after it had been transcribed and processed (Checked for errors). Here it comes into contact with ribosomal subunits. Two parts of a ribosome (subunits) surround this mRNA, a smaller one and a larger one. The smaller one fuses to the mRNA and the larger one fuses to the smaller one. the mRNA is being fed through this ribosome.

Once surrounded by ribosomes, the mRNA comes into contact with tRNA. tRNA comes bearing an amino acid complementary to the codons on the mRNA. Two tRNA enter the ribosome at a time.  The first tRNA comes in and pairs to the codons. The second tRNA enters the ribosome and receives the peptide from the first tRNA, which leaves the ribosome and makes room for another tRNA amino acid complex to enter the ribosome. Like this, the chain of amino acids grows like a tail, out of the ribosome, each tRNA pairing with a codon and giving its amino acid to the growing chain and leaving to make room for another tRNA amino acid complex to enter.

When the ribosome comes to the stop codon on the mRNA, the ribosome dissociates and falls off the mRNA molecule and is done.

The proper definition of translation:

Three steps and one pre-step to describe rRNA

0. rRNA, also called structural RNA is formed in the nucleolus. There, it join with proteins (made in the cytoplasm) to be a ribosomal subunit. it travels out to the cytoplasm to join just as protein synthesis starts. Each ribosomal sub unit contains proteins and rRNA. One of the proteins in rRNA is the enzyme that joins amino acids together with a peptide bond.

1. Initiation: mRna binds to the smaller of the two ribosomal subunits that join and surround it. 

2. Elongation: One amino acid at a time, the poly peptide begins to form and lengthen.

The ribosome has room for two tRNAs to work in it. The first tRNA goes into the ribosome bearing an amino acid. The tRNA has the anti codon to the codon on the mRNA. This first tRNA gives its peptide to the second tRNA entering the ribosome. In this way, the chain grows and forms the primary structure of the protein molecule. Secondary and tertiary structure come to be after termination.

 3. Termination of synthesis: The ribosome encounters a stop codon on the mRNA. There is no tRNA for this and the ribosome dissociates and falls off the mRNA molecule.

 a polyribosome can sometimes form on a mRNA and form several of the same polypeptides can be formed at the same time.

Transcription

Transcription:

"Describe the process of transcription in protein synthesis. Include the specific roles of DNA and mRNA."

In different contexts, when you transcribe something, you make a copy of it. This is the same in DNA transcription. A copy of a DNA strand is copied an an mRNA molecule is created.


Transcription is making an RNA molecule that is complementary to a portion of DNA. 


Remember the DNA bases- Adenine, Thymine, Guanine and Cytosine.


Again, this is only the part of transcprition that this course calls for. I know there is far more detail to the process, including a 'TATA box', which I find funny but for now, I'll include the information only relevant to my course. 

  

The process of transcription: 

During Transcription a segment of  the DNA unwinds and unzips and ONE strand of the DNA is copied from the transcription bubble. Complementary nucleotides pair with the DNA bases using the following bases: Uracil, thymine, guanine and cytosine. A strand of mRNA results.  

triplet codes

Explain what is meant by a triplet code:


DNA is a long strand of bases. A triplet code is a sequence of three bases along this strand.

 Why three? Diversity. There are four different bases. These bases need to code for all 20 amino acids.

Each triplet of bases stands for one type of amino acid. If each code were only two bases long (a doublet) the codes available would be too limited to provide codes for 20 unique amino acids. 

By having triplet codes in the four bases, we are able to provide codes for 64  different triplets. We only need 20 so some of these triplets are able to be dedicated start and stop codons.

 Codon: three letter unit of an mRNA molecule. 

All 64 codons have been discovered and 3 of  them have been determined to be stop codons.

During transcription, an amino acid is added wherever there is a triplet code.