Protein Synthesis
In this unit of study, we are going to examine how the cell makes proteins. Remember that there are hundreds of different types of proteins that play important roles in our body (cell structures, enzymes, immunity, hair, eyes, and many more) and so it is our cells' job to make these proteins as needed. Where is the cell getting the information to make proteins? All the information is located in your DNA. Your DNA has information for everything!! And so, it starts with your DNA in the nucleus and ends with proteins made in the cytoplasm of the cell. The picture below summarizes what we will be learning in the next 3 weeks.
The picture on the left is the inside of one cell. The purple circle is the nucleus and any place outside of it is the cytoplasm.
In the nucleus, you see the blue colored DNA. There is a process, called DNA replication, that copies DNA whenever a cell is about to split. So this process doesn't happen very often. But, when it does, it makes a perfect copy of all of your 46 chromosomes!! In the nucleus, you see that there is a red ribbon-like single strand coming out of the blue DNA. That is called a RNA..more correctly..mRNA. mRNA stands for messenger RNA. How did we make the mRNA from the DNA? This process is called Transcription, a process that creates RNAs from DNA. This mRNA now carries the piece of information that will make a protein. The mRNA will travel out of the nucleus and into the cytoplasm. In the cytoplasm, the mRNA meets with ribosomes (brown structures) that "reads" the message called codons and creates the amino acids (purple little circles, squares, triangles, etc). These amino acids are linked together and one long chain of these amino acids give you ONE protein!! Just one!! This process is called Translation. A protein can be made up of 10-100 amino acids long!! |
The Central Dogma is a flow map that will help you remember the sequence of Protein Synthesis: You are going from DNA, RNA, to Proteins.
The Structures of DNA, RNA, and Proteins
DNA is a double helix (double stranded) molecule found in the nucleus. This structure was discovered by two scientists named Watson and Crick. The structure of the DNA is like a twisted ladder composed of nucleotides. Nucleotides are monomers of Nucleic Acids (DNA and RNA) that are the single units of DNA and RNA. One nucleotide is made of 3 parts: Phosphate, sugar, and a base. There are 4 bases: Adenine (A), Thymine (T), Guanine (G), and Cytosine (C). The base is what makes one nucleotide different from another. These nucleotides stack on top of each other to form the double helix and are held together by 2 bonds: Covalent bond and Hydrogen bond. Covalent bonds hold the backbone (Phosphates and sugars) of the DNA together and Hydrogen bonds hold the bases together (A with T and G with C). Looking at the picture on the right below, there are 6 nucleotides on the left and 6 nucleotides on the right.
RNA is a single-stranded nucleic acid that is made in the nucleus but can travel out to the jelly-like space outside called the cytoplasm. There are 3 types of RNA: mRNA (messenger), tRNA (transfer), and rRNA (ribosomal). The structure of RNA is a single-strand made of nucleotides also. However, the sugar of nucleotides is called a Ribose (hence the R in RNA) while DNA's sugar is called Deoxyribose (hence the D in DNA). Another difference is that RNA bases are A, U, G, C instead of A, T, G, C. A pairs with U and G pairs with C. The RNAs are made from DNA.
Proteins are the ultimate molecules that cells make constantly to help the organism's body. Proteins make up so much structures and there are so many different kinds of proteins, each with a specific job in the body. The information in the DNA help code for these proteins. Proteins are made of monomers called Amino Acids. The patterns of these amino acids determine that shape and structure of a protein, hence what protein it is and what it will do.
In the picture on the left, each red circle is an Amino Acid. When they link together, they all make up just ONE protein. Each amino acid is linked to another amino acid by a bond called peptide bond. And so, a protein is also called a polypeptide. A protein does not have to be this shape alone, the chain can wrap up into any shape. The shape of the protein will tell you what protein it is.
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DNA Replication
Now that you know the basic structures of DNA, we can talk about how DNA is replicated. DNA replication occurs right before a cell goes through Mitosis (splitting itself). During DNA replication, all 46 chromosomes are copied in the nucleus. Here is the process:
Step 1: Helicase (an enzyme) unzips the twisted DNA strands and proteins keep the 2 strands untwisted.
Step 2: DNA polymerase (an enzyme) reads the original DNA strand (the nucleotide pattern) and strings together another DNA strand. The enzyme follows the Base Pairing Rule: A pairs with T and G pairs with C. The area that the DNA unzips and DNA polymerase strings the nucleotides is called the Replication fork.
Step 3: The DNA polymerase continues until the whole DNA strands is copied. What you get at the end is 2 DNA strands, each strand consisting of an old and new strand. This is called Semiconservative.
**Note: Replication sites occurs in many places along one DNA, it doesn't start from one end and unzips toward the other end. Many sites are necessary so that the process can occur quickly. If there is only one site, it will take forever. **
Classzone: click on Chapter 8 on the left and interactive button on top, then Animation 1: http://www.classzone.com/cz/books/bio_07/resources/htmls/interactive_review/bio_intrev.html
DNA Replication Animation: http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter3/animation__dna_replication__quiz_1_.htm
Step 1: Helicase (an enzyme) unzips the twisted DNA strands and proteins keep the 2 strands untwisted.
Step 2: DNA polymerase (an enzyme) reads the original DNA strand (the nucleotide pattern) and strings together another DNA strand. The enzyme follows the Base Pairing Rule: A pairs with T and G pairs with C. The area that the DNA unzips and DNA polymerase strings the nucleotides is called the Replication fork.
Step 3: The DNA polymerase continues until the whole DNA strands is copied. What you get at the end is 2 DNA strands, each strand consisting of an old and new strand. This is called Semiconservative.
**Note: Replication sites occurs in many places along one DNA, it doesn't start from one end and unzips toward the other end. Many sites are necessary so that the process can occur quickly. If there is only one site, it will take forever. **
Classzone: click on Chapter 8 on the left and interactive button on top, then Animation 1: http://www.classzone.com/cz/books/bio_07/resources/htmls/interactive_review/bio_intrev.html
DNA Replication Animation: http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter3/animation__dna_replication__quiz_1_.htm
Transcription
Transcription is a process that occurs in the nucleus and it occurs a lot more often than Replication because proteins are always needed. It is a process that uses one of the strand of the DNA, where the information for that protein lies, to make a RNA strand; whether it is an mRNA, tRNA, or rRNA. Most of the time, however, mRNA are made. The DNA strand being use the template. (Remember, a DNA has 2 strands, we are only using ONE of these strands. It will be called the template). In Transcription, not the whole DNA is read but only the parts within the DNA that hold the information to make the desired Protein. Here is the process:
Step 1: RNA polymerase identifies the "starting" point within the DNA to make the desired protein.
Step 2: Once the starting point is identified, RNA Polymerase (enzyme) unzips the DNA strand and it also strings the nucleotides together. This time, however, the Base Pairing Rule is A with U and G with C.
Step 3: The RNA polymerase continues until it reaches the "end" point and what you get is a single strand of RNA that is either an mRNA, tRNA, or rRNA.
The RNA will then travel out into the cytoplasm.
Classzone: click on Chapter 8 on the left and interactive button on top, then Animation 2: http://www.classzone.com/cz/books/bio_07/resources/htmls/interactive_review/bio_intrev.html (This shows Transcription AND Translation)
Step 1: RNA polymerase identifies the "starting" point within the DNA to make the desired protein.
Step 2: Once the starting point is identified, RNA Polymerase (enzyme) unzips the DNA strand and it also strings the nucleotides together. This time, however, the Base Pairing Rule is A with U and G with C.
Step 3: The RNA polymerase continues until it reaches the "end" point and what you get is a single strand of RNA that is either an mRNA, tRNA, or rRNA.
The RNA will then travel out into the cytoplasm.
Classzone: click on Chapter 8 on the left and interactive button on top, then Animation 2: http://www.classzone.com/cz/books/bio_07/resources/htmls/interactive_review/bio_intrev.html (This shows Transcription AND Translation)
mRNA Processing
Before the mRNA strand (which carries the "message" that we want, to make proteins in the cytoplasm), the mRNA strand has to be processed. The reason is because there are alot of "extra" and useless information on the strand and they need to be taken out. We call this process, mRNA processing: a process that cuts out introns (unneeded information) and then splice (join) together the exons (needed information). This process occurs in the nucleus. In the end, what results is a mRNA strand that contains only necessary genetic codes to make a protein. This "clean" mRNA strand now travels out to the cytoplasm for the next process: Translation.
Animation: http://www.youtube.com/watch?v=BpL4dgVGnCk
Animation: http://www.youtube.com/watch?v=BpL4dgVGnCk
Translation
Translation is a process that occurs constantly as well and occurs in the cytoplasm. Once the mRNA is made from Transcription, the message travels out into the cytoplasm where it "docks" with a ribosome (made of rRNA). The ribosomes are in charge of making the proteins. (recall from Unit 1 that the Rough ER has ribosomes attached to it and ribosomes make proteins. Ahhhh, it is all coming together :) ). Here is the process:
Step 1: The ribosome RECOGNIZE the start codon and "read" the message by every codon (3 nucleotides) at a time. Every codon has a matching anticodon located on the tRNAs that are floating in the cytoplasm.
Step 2: The tRNA carries with it specific amino acids. Once the tRNA's anticodon matches and clicks with the mRNA's codon, the tRNA falls off, leaving behind the Amino acid.
Step 3: The Amino acid is quickly bonded to the previous amino acid by peptide bonds. (and so, a protein can also be called a polypeptide). The protein continues to elongate (get longer) as more Amino Acids are added.
Step 4: The ribosome continues to "read" the message until it reaches a "stop" codon. (there are 3 stop codons)
**Note: What kind of amino acid will be produced by codons are determined by using a Codon Table. There are only 20 types of amino acids on Earth).
Step 1: The ribosome RECOGNIZE the start codon and "read" the message by every codon (3 nucleotides) at a time. Every codon has a matching anticodon located on the tRNAs that are floating in the cytoplasm.
Step 2: The tRNA carries with it specific amino acids. Once the tRNA's anticodon matches and clicks with the mRNA's codon, the tRNA falls off, leaving behind the Amino acid.
Step 3: The Amino acid is quickly bonded to the previous amino acid by peptide bonds. (and so, a protein can also be called a polypeptide). The protein continues to elongate (get longer) as more Amino Acids are added.
Step 4: The ribosome continues to "read" the message until it reaches a "stop" codon. (there are 3 stop codons)
**Note: What kind of amino acid will be produced by codons are determined by using a Codon Table. There are only 20 types of amino acids on Earth).
How to read the Codon Table, on the left:
Every codon is every 3 nucleotides on the mRNA strand. Using the picture above, the first 3 nucleotides are GGG. Using the table on the left, G(1st position - G (2nd position) - G (3rd position). 1st position G is the last row in green. 2nd position G is the 4th column in green. 3rd position is the last row in green. If you do this correctly, the Amino Acid from GGG is Gly. Try it yourself. The answers are below: GGG= Gly UUU= Phe UCG= Ser GUC= Val **Note: Many students make the mistake of reading the 3 nucleotides from the anticodon of the tRNA. But please note that the anticodon's purpose is used to pull the right tRNA over to the Ribosome. The message is still on the mRNA NOT the tRNA. Be careful!! |
Practice quizzes and test: http://www.classzone.com/cz/books/bio_07/book_home.htm?state=CA
Translation Animation: http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter3/animation__how_translation_works.html
Translation Animation (shown in class): http://www.youtube.com/watch?v=B6O6uRb1D38
Mutations
Mutation is an event that changes the DNA pattern: by adding, deleting, or substituting one or more nucleotides of the DNA. Mutations can also mean a big part of the DNA or chromosome is changed. For example:
Take a look at the DNA, mRNA, and amino acid patterns of a normal Beta-Globin. The amino acids produced are thr-pro-glu-glu and so on. This pattern of amino acids will give us the protein Beta-Globin.
BUT, a Mutation occurred on the DNA pattern and that affected the mRNA pattern and then the Amino Acid pattern. So now, we have thr-pro-VAL-glu and so on. This change in amino acid pattern result in a DIFFERENT protein or a non-functional beta-globin. If this continues to happen, the cell may have a problem or the body itself. *as long as the amino acid pattern doesn't change, however, then there is no effect because you are still getting the SAME protein. |