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Genes and Proteins

Investigation 1 – Concept Day

 

 

 

 

 

 

 

Genes and Proteins: Investigation 1

Concept Day

SLIDE GENES-1-1

In this Investigation, we wish to introduce you to the import concept of molecular biology. More specifically, we will introduce the concept of what has been called the Central Dogma of Molecular Biology (sometimes called the Central Dogma of Biology), which is the idea that “DNA makes RNA makes Protein”.

  • Important Note: Everything that we discuss in this CELL applies to both animal and plant cells.

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SLIDE GENES-1-2

  • This slide introduces the fundamental concept that genetic traits are passed from one generation to the next through parent’s chromosomes.
  • Chromosomes contain all of the information required to make a complete individual. Although half of an individual’s chromosomes come from their father and half from their mother, each individual is an entirely new combination of genetic information that, unless they have an identical twin, has never occurred before and will never occur again!
  • On the left are shown karyotypes of a human male and female. Karyotypes view microscopic images of chromosomes and arrange them in pairs for analysis. Each human has 23 pairs of chromosomes. Thus, each normal human has a total of 46 chromosomes. Each chromosome pair contains genetic information from both the individual’s father and mother. Notice that the final pair of chromosomes, the 23rd pair, determines the sex of the individual. In the 23rd chromosome pair, males have one “x” chromosome and one “y” chromosome, whereas females have two “x” chromosomes.

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SLIDE GENES-1-3

  • This slide shows where chromosomes are located within the cell. You may have seen this graphic representation of an animal cell in another CELL, Cellular Organization. All chromosomes are located within the cell nucleus. Therefore, when a cell nucleus divides at cell division in the process of mitosis (discussed more extensively later in this CELL), an identical number of chromosomes goes to each of the two new cells.
  • The other important aspect of this slide is that it shows that DNA is located within the chromosomes and it is this molecule, DNA (deoxyribonucleic acid), that determines the function of the chromosomes.

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SLIDE GENES-1-4

  • This slide shows the structure and base-pairing characteristics of the DNA molecule. Each DNA molecule is an extremely long strand with a ladder-like conformation. The two “rails” of the ladder are composed of a phosphate/sugar backbone. It is the phosphate of the backbone that gives DNA (and RNA) its negative charge and acidic properties. The sugar component of the backbone is deoxyribose in DNA (Ribose in RNA).
  • The “rungs” of the ladder are composed of pairs of nucleotide bases. As shown, there are four nucleotide bases in DNA: adenine, thymine, guanine, and cytosine. The bases on one side of the DNA molecule interact with the bases on the other side of the molecule in a very specific manner: adenine (A) only binds to thymine (T) and guanine (G) only binds to cytosine (C). There are well over a billion base-pairs in the DNA of each human cell!
  • The sequence of the bases contains the core information of the genetic code. The sequence of the bases is important for a number of reasons. First, the order in which the bases occur will ultimately determine the type of proteins that are made by various regions of the DNA sequence, call genes. There are many thousands of genes on each DNA strand in each of the chromosomes. Second, because bases on one strand can only pair with a particular kind of base on the other, we can always predict what the corresponding base on the other strand will be. That is, if a sequence of bases at a given position on one DNA “strand” is CGAT, as in the upper strand at the right end of the DNA molecule in this slide, then we know that the sequence on the other strand will correspondingly be GCTA.
  • The specific base-pairing characteristic of the DNA molecule has a profound effect on how the molecule replicates (makes an exact copy of itself) as described on the following slide.

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SLIDE GENES-1-5

  • This slide shows the process of DNA replication. This process must occur prior to any cell division so that both new cells each receive the exact same copy of the DNA molecule (we will discuss mutations in the DNA sequence later). We can conveniently breakdown the process of DNA replication into a series of steps.

Replication Steps Chart

 

  • The important final result of the DNA replication process is that the entire DNA molecule faithfully reproduces an exact copy of itself. This is the molecular basis of reproduction. Replication of DNA occurs for every DNA molecule in every chromosome between every cell division in mitosis.

Note: Notice in the slide numerous proteins are shown to cause the various steps in DNA replication. Each of these steps are exceedingly complex and are all active areas of investigation. Most steps involve complexes of many proteins. At this point, we are not introducing these specific proteins and their mechanism of action to you.

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SLIDE GENES-1-6

  • This slide shows the process of transcription. While proteins do much of the important work for cells, they cannot be made directly from DNA. An intermediate step is required in which the DNA molecule makes a molecule called RNA (ribonucleic acid) that retains all of the original base code information from the DNA molecule. The process by which RNA is made from DNA is called transcription. The process of transcription takes place in the cell nucleus, as does DNA replication.
  • While not shown here, transcription is promoted by many different proteins, as was the case with DNA replication. In essence, a specific area of a double-stranded DNA molecule is selected and its base pairs are broken, much like as in the process of DNA replication. However, in the case of transcription, the new bases that bind to the unpaired DNA bases are adenine, guanine, cytosine, and uracil: there is no thymine in RNA molecules; uracil replaces thymine. Therefore, an unpaired adenine base on the DNA strand will bind to a uracil base instead of a thymine base. A new backbone will be formed to join the new sequence of bases into a new RNA molecule. The RNA backbone, like the DNA backbone, is composed of phosphate and sugar. However, in the case of RNA, the sugar is ribose instead of deoxyribose as it is in DNA.
  • Once transcription is complete, the DNA re-pairs and rewinds to form the original twisted helix. Many different areas of a single DNA molecule may undergo transcription at the same time. The stretch of DNA that codes for the transcription of an RNA molecule is a gene and will ultimately produce a specific protein through the process of translation shown on the following slide.

Note: An analogy relating genes to DNA sequence is that of an alphabet. One may think of the bases of a DNA molecule as an alphabet that contains only four letters (A, T, G, and C). In some areas of this long sequence of letters, meaningful words are formed from the letters. These words would be analogous to genes. Much of the DNA molecule consists of a meaningless sequence of bases that don’t code for anything.

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SLIDE GENES-1-7

  • This slide shows the process of protein translation. After they are made in the nucleus from a DNA template, newly formed RNA molecules (call transcripts) leave the nucleus through pores in the nuclear membrane (nuclear pores) and enter the cytoplasm of the cell where important components required for protein synthesis are located. These components are many and include amino acids and ribosomes.
  • The sequence of each RNA molecule transcript is arranged into repeating groups of three bases. The RNA base triplets are called codons. It is this sequence of codons, dictated by the original DNA molecule and inherited through chromosomes from an individual’s parents, that directs the synthesis of thousands of different protein molecules.
  • Ribosomes are very large complexes composed of many different proteins and other molecules. They bind to RNA transcripts in the cytoplasm. The ribosome recognizes the codons (triplets of bases) arranged along the RNA transcript, each of which codes for a specific amino acid (see code on the wheel on the lower left of this slide, which will be discussed in detail in the following slide). There are 20 different amino acids. The ribosome moves along the RNA transcript and forms a chain of specific amino acids in a specific sequence, or order, dictated by the RNA codon sequence.
  • Protein synthesis continues as the ribosome moves along the RNA transcript until a specific codon (the stop codon) is reached. This codon tells the ribosome that the amino acid sequence information for the protein being made is now complete. When reaching the stop codon, the ribosome detaches from the RNA transcript, and the synthesis of that particular protein is complete. The protein is then released from the ribosome.  

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SLIDE GENES-1-8

  • This slide provides more detailed information about the codons of RNA transcripts and which amino acids they code for. It is simple to use. Let’s take an example of the codon GCU. Locate the first letter, G, on the inner circle. From this quarter of the inner circle (turquoise on this wheel), locate the second letter of the codon, C, touching it (blue/purple on this wheel). Third, from this blue/purple C, locate the third letter of the codon, U (green on this wheel) touching it on the outer part of the wheel. Now, look at which amino acid is coded for by GCU: Ala, short for the amino acid alanine.
  • Similarly, GAC codes for Asp (aspartic acid), UCC codes for Ser (serine), CCC codes for Pro (proline), and ACU codes for Thr (threonine). For your convenience, a table of the 3-Letter abbreviations of the twenty amino acids is given below. Notice that a 1-Letter code is also sometimes used.  

imgf000015_0001

  • As noted on the right side of this slide, many amino acids have more than one codon that codes for its insertion into a protein. This is known as redundancy but we will not discuss this concept further at this time.
  • There are two other important types of codons. The first, AUG, not only codes for the amino acid Met (methionine) but is also a signal code to the ribosome to start the translation of a new protein exactly here. AUG is the start codon. Thus, all proteins are initially made with the first amino acid of methionine.
  • The second important types of codons are the stop codons. These tell the ribosome that the end of the protein has been reached and it should stop adding any more amino acids, release the newly formed protein and fall off of the RNA transcript. There are three stop codons: UAA, UAG, and UGA.

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SLIDE GENES-1-9

  • This slide provides an overview of the essential Dogma of Molecular Biology: DNA makes RNA makes Protein. We have gone over these individual steps in this presentation.
  • DNA replication and RNA transcription occur in the cell nucleus. DNA does not leave the nucleus. However, once made, the RNA transcript may be seen in this illustration exiting the nucleus through nuclear pores and entering the cytoplasm where the ribosomes are located. It is here that protein translation occurs. Finally, notice that in a completed protein (pink ribbon on lower right), the sequence of amino acids folds in upon itself to form a very specific three-dimensional structure. The nature of the amino acid sequence and the overall three-dimensional structure of a protein are thought to give proteins their varied functions in cells. All of this function, of course, is ultimately dictated by the DNA sequences that we inherit from our parents.

Note: Little on this or most any other graphic representations of a cell is drawn to scale. For example, although ribosomes are composed of dozens of different proteins as well as other molecules, it is shown in this graphic to be smaller than the single protein molecule at the lower right!

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SLIDE GENES-1-10

  • This final slide simply gives credit to some of the many scientists who were important in the discovery of the structure of DNA. While the credit for solving the structure of DNA is typically mainly given to Drs. James Watson and Francis Crick, their work (published on February 28, 1953) was largely based on the work of those other scientists pictured here. Many people believe that, had she not died prematurely, Dr. Rosalind Franklin would also have received a Nobel Prize for discovering the structure of DNA as did Drs. Watson and Crick.  

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