Closed 1/14/10

 

Totaled 1/10 /10 Mr F

 

Restored to "lost" version  and I cut and pasted all the "new" stuff back in.  I have a record of all changes made so we should be good to go.  Check the main page for midterm and wiki point project.

 

Totaled 1/5 /10 Mr F

Totaled 12/22 Mr F

 

Watson and Crick made two seperate assumptions about protein synthesis.

Watson- Sequential Hypothesis

Crick- Central Dogma (OOPS! too general a topic for dogma, there are some exceptions)

 

 

Protein synthesis is the process in which cells build proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi-step process, beginning with amino acid synthesis and transcription of nuclear DNA into messenger RNA which is then used as input to translation.

 

DNA vs. RNA

 

What is RNA's purpose?

RNA molecules carry out the process of making proteins - fits between DNA and proteins, as figured out in the Sequential Hypothesis and Central Dogma. It has three types: Messenger RNA (mRNA), which carries the DNA code from the nucleus to the rest of the cell, ribosomal RNA (rRNA) and transfer RNA (tRNA), which transfers each amino acid to the ribosome as it is specified by the coded messages in mRNA. 

 

DNA-

• Double helix
• Deoxyribose (stable)
• Long strands
• Base pairs of A-T and C-G
• Found ONLY in the nucleus

RNA-

• Single stranded
• Ribose (less stable)
• Generally shorter
• C-G and A-U  **Uracil instead of Thymine**
• Found in nucleus and the cytoplasm

 

 

This video is a rap on dna replication but mostly protein synthesis. i guess if you learn this song it might help you remember how to do protein synthesis

 

Unique Features of RNA and DNA

 

The helix geometry of DNA is that of B-form. DNA is also protected by the body from enzymes that harm it and it is susecptabe to damage through exposure to Ultra Violent rays. RNA on the other hand is of A-form and strands of it are continually broken down and reused. It is also more resistant to damage from Ultra Violent rays. 

'

This is a really good video which talks about the differences between RNA and DNA clearly and simply. 

 

Transcription Unit: DNA strand promoter region to termination

-Initiation: [TATA] box (Double Hydrogen Bonds, so it is weaker) , DNA opened using helicase forming replication eye, attach RNA polymerase. This RNA polymerase creates a strand to match the parent strand of the DNA it has stuck to.

-Elongation: ATP activates RNA polymerase, nucleotides get added and RNA is built 5' - 3', after RNA is built the DNA rewinds back up

-Termination: Stops everything, factors and enzymes released, now we have pre mRNA

-RNA Processing:  5' end capped which provides protection from enzymes.  3' end has poly A tail.

• Protection and recognization
• Removal of introns
• Splicing together exons with spiceosomes

 

This video, although made a really long time ago is really memorable and i think will really help in learning the process of protein synthesis. it's a bunch of hippies and its realy descriptive and colorful.

 

 

Here is a really cool video to help explain the central dogma process discovered by Crick:

 

I found it very helpul in my understanding of the central dogma and it's really cool visually!

 

 

Here is a video that describes protein synthesis and the translation process. 

 

 

http://www.youtube.com/watch?v=NJxobgkPEAo

This link has a step by step video of the process of protein synthesis.

 

 

 

http://www.youtube.com/watch?v=983lhh20rGY

This is a cooler video on protein synthesis which gives you a more general idea of the process.

 

http://www.elmhurst.edu/~chm/vchembook/584proteinsyn.html

This link is to a website with a breakdown of Protein synthesis, step by step with pictures and diagrams.

 

as stated above, the difference between the dna code and rna genetic code is that the thymine in the DNA sequence is subsituted out for Uracil. the diagram below shows how the RNA fits right in where the opposing strand of DNA would fall into place

 

This photo shows how transcription and translation relate in protein synthesis. 

 

This picture shows the different combonations that make up the Translation stage.

 

This image is broken down into sequencial steps that are easy to follow.  I found this image helpful in learning where in the cell each step takes place.

 

Here is a quick animation of protein synthesis.

 

Protein Synthesis       Legend: Process whereby DNA encodes for the production of amino acids and proteins. This process can be divided into two parts: 1. Transcription Before the synthesis of a protein begins, the corresponding RNA molecule is produced by RNA transcription. One strand of the DNA double helix is used as a template by the RNA polymerase to synthesize a messenger RNA (mRNA). This mRNA migrates from the nucleus to the cytoplasm. During this step, mRNA goes through different types of maturation including one called splicing when the non-coding sequences are eliminated. The coding mRNA sequence can be described as a unit of three nucleotides called a codon. 2. Translation The ribosome binds to the mRNA at the start codon (AUG) that is recognized only by the initiator tRNA. The ribosome proceeds to the elongation phase of protein synthesis. During this stage, complexes, composed of an amino acid linked to tRNA, sequentially bind to the appropriate codon in mRNA by forming complementary base pairs with the tRNA anticodon. The ribosome moves from codon to codon along the mRNA. Amino acids are added one by one, translated into polypeptidic sequences dictated by DNA and represented by mRNA. At the end, a release factor binds to the stop codon, terminating translation and releasing the complete polypeptide from the ribosome. One specific amino acid can correspond to more than one codon. The genetic code is said to be degenerate.

 

Here is a helpful picture that shows protein synthesis in an easy to understand way.

It also helps for you to visulize the processes taking place with the DNA in the nucleus and the RNA in the cytoplasm.

 

 

This image is useful in that every object is labeled well.  It is clear that A attaches to U, rather than T.  Also, it shows where each object is in the process.  For example, the ribosomal subunits, messenger RNA and anitcodons are placed with each other.

 

The Three Roles of RNA in Protein Synthesis:

 

• 1

  Messenger RNA (mRNA) carries the genetic information copied from DNA in the form of a series of three-base code “words,” each of which specifies a particular amino acid.

• 2

  Transfer RNA (tRNA) is the key to deciphering the code words in mRNA. Each type of amino acid has its own type of tRNA, which binds it and carries it to the growing end of a polypeptide chain if the next code word on mRNA calls for it. The correct tRNA with its attached amino acid is selected at each step because each specific tRNA molecule contains a three-base sequence that can base-pair with its complementary code word in the mRNA.

• 3

  Ribosomal RNA (rRNA) associates with a set of proteins to form ribosomes. These complex structures, which physically move along an mRNA molecule, catalyze the assembly of amino acids into protein chains. They also bind tRNAs and various accessory molecules necessary for protein synthesis. Ribosomes are composed of a large and small subunit, each of which contains its own rRNA molecule or molecules.

  Translation is the whole process by which the base sequence of an mRNA is used to order and to join the amino acids in a protein. The three types of RNA participate in this essential protein-synthesizing pathway in all cells; in fact, the development of the three distinct functions of RNA was probably the molecular key to the origin of life. How each RNA carries out its specific task is discussed in this section, while the biochemical events in protein synthesis and the required protein factors are described in the final section of the chapter.

 

 

 

 

http://www.wisc-online.com/objects/index_tj.asp?objID=AP1302

 

>>  This is a link to an activity with animations that shows the process of protein synthesis. It shows the process and how proteins are finally produced. 

 

 

 Here is a video that shows the difference between trascription and translation. And also shows the process of protein synthesis.

 

 

This is a video that does a good job emphasizing when T is replaced with U, and it also covers where the process takes place.  It's in the form of a dance and song, so it's catchy.

 

This video really helped me because there are not too many words on each slide-it is broken down simply, which makes the process easy to understand.  The end of this video also contains information about translation.

 

 

RNA

 

Ribonucleic acid is a biologically important type of molecule that consists of a long chain of nucleotide units. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA is very similar to DNA, but differs in a few important structural details: in the cell, RNA is usually single-stranded, while DNA is usually double-stranded; RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom); and RNA has the base uracil rather than thymine that is present in DNA.

RNA is transcribed from DNA by enzymes called RNA polymerese and is generally further processed by other enzymes. RNA is central to protein synthesis. Here, a type of RNA called messanger RNA carries information from DNA to structures called ribosomes. These ribosomes are made from proteins and ribosomal RNAs, which come together to form a molecular machine that can read messenger RNAs and translate the information they carry into proteins. There are many RNAs with other roles – in particular regulating which genes are expressed, but also as the genomes of most viruses.

 

RNA contains ribonucleotides of adenine, cytidine, guanine, and uracil; DNA contains deoxyribonucleotides of adenine, cytidine, guanine, and thymine. Because 4 nucleotides, taken individually, could represent only 4 of the 20 possible amino acids in coding the linear arrangement in proteins, a group of nucleotides is required to represent each amino acid. The code employed must be capable of specifying at least 20 words (i.e., amino acids).

 

Process whereby DNA encodes for the production of amino acids and proteins.

1. Transcription

Before the synthesis of a protein begins, the corresponding RNA molecule is produced by RNA transcription. One strand of the DNA double helix is used as a template by the RNA polymerase to synthesize a messenger RNA (mRNA). This mRNA migrates from the nucleus to the cytoplasm. During this step, mRNA goes through different types of maturation including one called splicing when the non-coding sequences are eliminated. The coding mRNA sequence can be described as a unit of three nucleotides called a codon.

2. Translation

The ribosome binds to the mRNA at the start codon (AUG) that is recognized only by the initiator tRNA. The ribosome proceeds to the elongation phase of protein synthesis. During this stage, complexes, composed of an amino acid linked to tRNA, sequentially bind to the appropriate codon in mRNA by forming complementary base pairs with the tRNA anticodon. The ribosome moves from codon to codon along the mRNA. Amino acids are added one by one, translated into polypeptidic sequences dictated by DNA and represented by mRNA. At the end, a release factor binds to the stop codon, terminating translation and releasing the complete polypeptide from the ribosome.

 

 

 

Following video is on translation.

 

In transcription an mRNA chain is generated, with one strand of the DNA double helix in the genome as template. This strand is called the template strand. Transcription can be divided into 3 stages: Initiation, Elongation and Termination, each regulated by a large number of proteins such as transcription factors and coactivators that ensure the correct gene is transcribed. 

 

Steps of Transcription:

 

Step 1: Initiation

 

At promoter region (TATA box) DNA is opened forming a replication eye.  RNA polymerase attaches.

 

Step 2: Elongation

 

• ATP actiuates RNA polymerase and RNA nucleotides added (Using U instead of T).
• DNA goes from 3 to 5 and RNA builds from 5 to 3.
• RNA seperates from DNA template.
• DNA reforms behind RNA polymerase.

 

 

Step 3: Termination

 

• Stops the elongation, and stops the transcription.
• All factors and enzymes are released.
• RNA is released as "pre mRNA".
• Transcription unit= DNA strands from the promoter region to the termination process.

 

 

Step 4: RNA Processing

 

• 5 end capped.  Protected from enzymes.
• 3 end has a ploy A tail added.
• Removal of introns.

 

Here's a really helpful video on transcription. It's from youtube and its cartoons of the transcription process.

 

 

Introns were believed to be non coding pieces of DNA  that needed to be removed from the mRNA, but scientists are now learning more about Introns and what they do.

 

 

This image from the powerpoint in class really helped me understand the splicing of the RNA process.

mRNA Summary

• Copy the code from DNA
• IT's a temporaty copy and is not meant to last
• "real" cde is locked in the nucleous
• mRNA now leaves the nucleus and is headed for Translation 

 

http://highered.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/0072437316/120077/micro06.swf::Protein%20Synthesis

^ You are going to need to copy and paste this website into your URL address.

This website is kind of difficult to understand with the wording, but if you watch the steps, after a while you can understand what is going on.  

 

more on DNA Transcription

      Once the messenger RNA moves into the cytoplasm, the DNA's information gets transcribed into the mRNA.  As we know, T changes to U.  When DNA makes mRNA, the pattern continues on.  Where the first pairing on DNA would be T-A, the pattern would continue on to mRNA, where the first pairing would be U-A.  (T-A-U-A).  The ends follow the same pattern.  If on top, the DNA ends went from 3' to 5', then the mRNA's ends on top would also go from 3' to 5'.  If there are any blanks in the pairings or ends, it is easy to fill them in based on the information in the DNA and mRNA. 

 

   Here is an example I made of this process:

 

   Here is an example of missing terms I made.  See if you can fill them all in!

 

This is the universal genetic code which determines the sequence of nucleotides in RNA and DNA. Three adjacent nucleotides are known as a codon; each codon represents one amino acid. There are 64 codons possible.

 

This chart can be used by looking at the a pair of 3 nucleotides, starting with the first nucleotide find the corresponding letter on the left (the first position) and then use the second position to line up with the first position, finally corresponding the last nucleotide with the third position.

 

More about Introns ---

• An intron is a DNA region within a gene that is not translated into a protien
• Non coding peices of DNA that need to be removed from the RNA ("old idea" -- maybe old code)
• Introns are removed from the RNA through the process of splicing
• Introns may do more than we think!

 

mRNA summary ---

• mRNA is a copy of the DNA code (or original "cookbook") in the nucleus/ or a chemical blueprint
• It is a temporary copy that is not made to last
• mRNA is transcribed from a DNA template

 

Here is a really good video that explains the splicing of introns from the RNA strand. It clearly shows different protiens working together to break and reconnect the RNA strand.

 

 

Big Stop.  A very large chunk of the section has been erased. Do nt add more until it gets fixed.  1/8/10 7:00 am Mr F

 

Here is the "essay" (notes) we wrote today in period 9:

 

     DNA carries the code into the nucleus, where mRNA needs to transcribe the DNA.  mRNA is temporary, and not meant to last, but it gets reused afterwards. tRNA anticodons match with codons, then the anticodons leave for the cytoplasm. Amino acids are attatched to the tRNA bond with peptide bonds.  The 5 end is capped to protect from enzymes, and the 3 end has a poly tail added, with 100-200 adenines.  During RNA processing it stops elongating and transcribing, and the RNA polymerase attatches. 

 

http://www.biostudio.com/demo_freeman_protein_synthesis.htm

This is a demonstration of protein synthesis that walks you through the entire process. It is really easy to follow and if you have questions on a part of the demonstration, you can rewind and watch again. 

 

http://www.teachersdomain.org/resource/tdc02.sci.life.cell.lp_prosyn/ 

This is a link to a website (teachers domain) that includes a couple different resources that break down protein synthesis into steps and explain each part. There is also a video on the link above that shows protein synthesis and describes each step and why it happens.  

---

 

 

 

 

Legend:

Process whereby DNA encodes for the production of amino acids and proteins.

This process can be divided into two parts:

1. Transcription 

Before the synthesis of a protein begins, the corresponding RNA molecule is produced by RNA transcription. One strand of the DNA double helix is used as a template by the RNA polymerase to synthesize a messenger RNA (mRNA). This mRNA migrates from the nucleus to the cytoplasm. During this step, mRNA goes through different types of maturation including one called splicing when the non-coding sequences are eliminated. The coding mRNA sequence can be described as a unit of three nucleotides called a codon.

 

Transcription is the result of 4 processes:

     First is Initiation: in this stage, the TATA box is found as a place to break the double helix and form a replication bubble. Then RNA Polymerase attaches.

     Second is Elongation: This process is fairly self explanatory. The chain elongates, building on to the protein.

     Next is Termination: At this stage, a certain sequence of nucleotides tells the tRNA to stop, UAA for example.

     Finally, RNA Processing: Here, the protein is capped and a tail is added to it to keep enzymes from consuming it. Introns are removed and exons are spliced together using spliceosomes.  A spliceosome is a complex of specialized RNA and protein subunits that removes introns from a transcribed pre-mRNA (hnRNA) segment. This process is generally referred to as splicing.

 

MUTATIONS: There are many mutations that can occur during protein synthesis. AMong possible mutations are:

     Frameshift mutations: Which changes the sequence reading frame

     Nonsense mutations: causing a stop codon where there shouldnt be one.

     Missense mutations: A mistake resulting in the exhange of one amino acid for a different one, or change the properties of the amino acid.

 

Effects of Mutations:

-Insignificant: mainly point substitution mutation

     -functionally equivelant amino acid change-"nuetral mutation"

-Harmful-some point substitution mutations may result in harmful effects

     -"null mutations": a null mutation, or null allele is a copy of a gene that is completly lacking that specific genes normal function. This type of mutation is caused by a complete absence of a gene product, or the expression of a non functional gene product.

     -altered or lost protein function

-Beneficial:

     -significant for evolution

 

Mutations are changes in the DNA sequence and can be caused radiation, viruses, transposons, and mutagenic chemicals. Aside from these outside factors mutations can also be a result of an error in meiosis or DNA replication. Mutations in the DNA sequence can either have no effect, alter the product of a gene, or prevent the gene from functioning. In multicellular organisms mutations can be subdivided in to germ line mutations. These can be passed on to decendents through reproductive cells.

 

Here is a super informative video about different DNA and RNA mutations. I learned alot by watching this, and it's simple and easy to understand. 

 

Here is a quiz that you can take to help yourself study for the upcoming test. 

http://www.cst.cmich.edu/USERS/BENJA1DW/bio101/tools/quiz/dnarna.htm

 

     One example of a point mutation is sickle cell disease which is caused by a single cell mutation (a missense mutation) in the beta-hemoglobin gene that converts a GAG codon into a GUG, which encodes the amino acid valine rather than glutamic acid.

 

     Two other well known dieases which are caused by insertion are Huntington's Disease ( a neuro-degenerative disease) and Myotonic Dystrophy.

 

     On the other hand, one disease which is caused by deletion  is von Willebrand's Diease, a coagulation disease which show flaws in one's blood.

 

     A mutation is not necessarily a bad thing for an organism. Sometimes when an error occurs during transcription from the already jumbled DNA sequence a better result can occur. We demonstrated this in class on Friday when we used letters of the alphabet in subsitution for codons; particualarly when 'Hallo' became 'Hello'.

 

     To specify, there are four main types of DNA mutations:

1. Point Substitution - This is when one codon is substituted for another, or replaced by a different codon.  This is not neccessarily always harmful because it does not mess up the reading frame, and is just one glitch in the very long amino acid chain.  Sometimes, the particular protein (such as glycine) could remain the same since there are many different combinations for it. 

2. Elimination - In this case, one codon is removed from the chain, and this is always a big change since it screws up the reading frame and the entire DNA sequence is changed, reading differently.

3. Insertion - This is when a codon is added to the amino acid change, also screwing up the reading frame.  This changes the entire DNA sequence, and can stop the completion of the amino acid chain all together if a stop codon is inserted.

 

Here is a clear explanation of these types of mutations, showing how they happen:

 

 

DNA mutations can be repaired through several different methods. One of which involves using one of the strands of DNA as a template to correct the damaged strand. This obviously only works if only one of the strands in the double helix is defective. There is a number of excision molecules that are used to remove the damaged nucleotide and replace it with an undamaged one that is complementary to that DNA strand

 

This video explains and clearly shows how mutated DNA strands can be fixed.

 

This is a quiz on protein synthesis and could really help you study for the test tomorrow!!

http://www.cst.cmich.edu/USERS/BENJA1DW/bio101/tools/quiz/dnarna.htm