DNA & Proteins Lecture Notes PDF

DNA & Proteins  Genetic Code Before the basic macromolecules were discovered it was thought there was an agent that carried instructions of hereditary Charles Darwin pondered a lot about “genetics” Gregor Mendel discovered the patterns of genetics with studies of plant phe...

DNA & Proteins  Genetic Code Before the basic macromolecules were discovered it was thought there was an agent that carried instructions of hereditary Charles Darwin pondered a lot about “genetics” Gregor Mendel discovered the patterns of genetics with studies of plant phenotypes – Charles Darwin actually did the same experiments, but didn’t have the mathematical mind which could identify his results  Discovery of DNA’s Purpose Frederick Griffith, an army medical officer, in 1928 was attempting to find a vaccine to a bacterium (Streptococcus pneumoniae) He isolated two separate cultures – One had a smooth outer appearance, designated S strain – One had a rough outer appearance, designate R strain  Designed and ran 4 Experiments Fig. 7.2 1. laboratory mice were injected with live R cells. – These did not develop pneumonia 2. laboratory mice were injected with live S cells – S strain was found to be pathogenic 3. S cells were killed by exposure to high temperature – Mice with this strain did not die 4. live R cells were mixed with heat-killed S cells. – These mice died – Blood was found with large amounts of S strained cells  What happened? Did R cells mutate? – If this were true, then chances are it would have occurred with the 1st experiment Were the S cells really alive in the 4th experiment? – If this were true then chances are some would have survived during the 3rd experiment What really happened was the genes involved with making the S strain from the R strain migrated over to the R strain – Bacterial conjugation  Later Studies Further experiments done by other biochemist further supported the evidence put forth by Frederick They changed the strain of inert strains to deadly strains by including dead cells of infectious strains It was widely believed before that proteins were the hereditary molecule – Strains given protein digesting enzymes still developed more proteins – Others they added enzymes that digest DNA and the cells stopped functioning  Viruses Fig. 7.3 In 1952 a group of molecular scientists were experimenting with bacteriophages – Viruses which infect bacteria Viruses observed by electron micrographs show a protein coat with nucleic acids found in the interior It was also shown that when viruses infect cells, the majority of the virus (the protein shell) remains outside the cell – Nucleic acids are injected into the cell  The structure of DNA Rosalind Franklin used what is called x-ray crystallography – A method of shooting x-rays through crystallized matter – How the x-rays are diffracted through the atom lattice of the molecule – Certain atoms show up in particular patterns Watson and Crick used her data to determine the structure of DNA  Fame and Fortune Watson and Crick were later awarded the Nobel Prize for having discovered the structure of DNA Rosalind Franklin was not given any of the credit, though she did the majority of the work – She was a primary researcher in a lab and one of her cohorts took her data and gave it to Watson and Crick – There has been more talk about her work and today she is recognized as being a major contributor to the discovery – Nobel Prizes are not awarded posthumously  DNA The blue prints of protein structure Very stable molecule – Double Helix Structure more stable than RNA single molecule structure Each Gene encodes for one protein – 4 Nucleotides are the information for protein formation (Adenine, Thymine, Guanine, and Cytosine) The sentence is the gene or protein, the letters are the nucleotides, the words are codons – Codons are three nucleotides which encode one amino acid – 64 potential nucleotide combinations, 20 amino acids, so there is some room for redundancy.  DNA Structure Fig. 7.6 & 7.7 Double Stranded and helically shaped – Adds stability Base pair compliments – Thymine binds with Adenine 2 hydrogen bonds – Guanine binds with Cytosine 3 hydrogen bonds Phosphate and Deoxyribose sugar provide the “backbone”  Nucleotides Pyrimidines are single organic rings Purines are double organic rings DNA ladder consists of a pyrimidine bonding with a purine – When two purines are mistakenly put together then the double helix makes a bulge  DNA Backbone Structure The nucleotides along one side of the double helix bond together via phosphodiester bonds – This is a bond between the phosphate of one nucleotide and the sugar of another nucleotide Because the phosphates are so negative they have to align themselves on opposites sides of the DNA molecule  RNA Table 7.1 DNA is the blueprints, RNA is the foreman and the construction workers of protein formation Three types of RNA – Messenger RNA (mRNA) – Transfer RNA (tRNA) – Ribosomal RNA (rRNA) – All made in the nucleus of eukaryotes and the nucleoid region of prokaryotes  RNA and DNA Comparison Fig. 7.10 RNA DNA – Ribose sugar – Deoxyribose (contains one more – Contains thymine, not oxygen than uracil Deoxyribose) – Double-stranded molecule – Contains uracil, not in a double helix thymine configuration – Single-stranded – Genetic material of all molecule prokaryotes and – Genetic material of eukarytoes. Genetic some viruses material of some viruses. Note: both RNA and DNA contain Adenine, Cytosine, and Guanine Basic DNA to Protein Scheme DNA—TranscriptionRNA RNA—TranslationProtein  Transcription The process of changing DNA information into RNA information – Same type of information, nucleotide  nucleotide Same alphabet – One nucleotide difference Thymine in DNA replaced by Uracil in RNA This similar to you re-writing your notes  Translation Taking the information held in the mRNA molecule and changing into Protein information – Nucleotide  Amino Acid formation – Different molecular structure This is the equivalent to a person taking a piece of literature in another language and rewriting it into their native language  mRNA Messenger RNA is the carrier of gene information. – Exports the information of genes from the DNA’s structure so the information can be used to create proteins It represents 5-10% of the total RNA abundance in the cell at any one given time – Gets used and then digested into nucleotides so may be re-used  mRNA structure Consists of a single strand of nucleotides Has a backbone of ribose sugar and a phosphate It is a temporary structure – Digested by RNA polymerases into basic building blocks – The individual RNA nucleotides then can be used to construct new mRNA molecules  Ribosomal RNA This is RNA used to construct Ribosomes – Coupled with proteins – RNA makes up roughly 60-65% of the Ribosome mass – Proteins make up roughly 35-40% of the Ribosome mass rRNA composes 75-80% of all the RNA in the cell at any one give time  Ribosome Structure Consists of two units – A small unit – A large unit These two units are involved with placing amino acids in accordance to the mRNA molecule they are translating  Promoter Transcription begins at a portion of the DNA structure called a promoter – Recognized by RNA Polymerase Found upstream of the gene that is being transcribed  RNA Polymerase RNA polymerase has multiple functions – The main one we are worried about is that RNA polymerase takes RNA nucleotides and builds a mRNA based upon the DNA code of the particular gene – RNA Polymerase I synthesizes rRNA – RNA Polymerase II synthesizes mRNA – RNA Polymerase III synthesizes tRNA There are other RNA Polymerases found in chloroplasts and mitochondria  Construction of RNA DNA is double stranded, but only one strand is used – The promoter has a specific sequence of nucleotides which encodes to that side starting – The other side has an antithesis code that the molecular machinery which will not recognized RNA polymerase takes nucleotides found in the environment and binds them together using the DNA code as the template  mRNA mRNA is not finished with RNA Polymerase II Enzymes attach a cap to the 5’ end – Used for binding the mRNA to the ribosome Enzyme also attach a tail of 100-300 nucleotides to the 3’ end – This “tail” is bound up with proteins as well – Use to pace the destruction of the mRNA molecule by catabolic enzymes  Junk DNA DNA is full of junk material, including within the genes themselves – Exons are portions of the code that are a component of protein information – Introns are portions of the code that need to be excised out of the mRNA Some introns are actually parts that can be re- spliced into the code to create a different protein Good for creating proteins necessary for different cells This is the final editing of the RNA code before it is used for protein synthesis  Genetic Code The genetic code is based upon triplets of nucleotides called codons – Each codon translates to one particular amino acid – For example one codon of a mRNA molecule may have a Uracil, Cytosine, and another Cytosine (in that order) this codes for the amino acid Serine Methionine (AUG) is the start codon – Initiates translation Three codons are used as stop codons – UAA, UAG, and UGA  tRNA These are the RNA molecules which carry specific amino acids They bind to the mRNA putting amino acids in the specific sequence. – They have an anticodon portion, which is the opposite code of that of the mRNA – For example mRNA codon is CUG, then the accompanying tRNA’s anticodon is GAC  tRNA Found in the cytoplasm of the cell Constructed in the nucleus of Eukaryotes and the nucleoid region of Prokaryotes tRNA molecules have a hook which they use to bind to a specific amino acid based upon their anticodon  Ribosomes Provide the substrate with which where protein formation takes place They orient the mRNA and the tRNA molecules so they can more efficiently bond together – Works the same way as an enzyme  Translation Three stages – Initiation – Elongation – Termination At initiation a tRNA carrying the start anticodon binds with the mRNA – Followed by the large and small ribosomal subunits coming together – Creates a initiation complex (combination of mRNA, tRNA, and Ribosome)  Elongation The mRNA molecule passes between the two ribosomal subunits The rRNA molecule has an acidity that allows it to bind amino acids to each other – Found in the center of the large subunit of the ribosome – This regions acts in the same fashion as an enzyme  Termination The three stop codons have no tRNA anti- codons which bind to them. Results in the termination of protein formation There are proteins which recognize these particular codons – They initiate enzyme activity which detaches the mRNA molecule and the amino acid chain from the ribosome  Mutations and Proteins Protein formation is dependent upon the genetic code being correct – Changes in the genetic code can lead to differences in the protein – Silent mutations cause no change in protein formation Changes in proteins that affect cell structure or metabolism can lead to abnormal cells  Point Mutations A point mutation is the result of change in one or a few base pairs. A substitution mutation is a type of point mutation is when the wrong nucleotide is put in place when DNA is being replicated or repaired. Most substitution mutations result in a pyrimidine for a pyrimidine or a purine for a purine Base insertion or Deletions are when one or more nucleotides are either added to the sequence or removed. This results in a frameshift mutation which causes a change in the entire DNA sequence. 3 6  Mutagens Mutagens are external agents which cause mutations. Some common mutagens are U/V light, x-rays, radioactive material, and chemical weapons (such as mustard gas). These all cause changes in organism’s DNA. Interesting observation: Recent research has yielded a rich diversity in our surface oceans. They took a research vessel and collected water every 200 miles as they traveled around the world. They discovered 60-70 million new species of organisms. The same group then started drilling into the crust of the earth. Deep down in the earth they discovered a lot of biomass, but very little diversity. The identical species of bacteria were found both in Colorado and Italy. Leads to a question, does the lack of U/V light in the earth lead to a slower rate of evolution? Still looking for an answer. 3 7  Mutations important for evolution Mutations lead to variation in organisms which allows for populations of organisms to change over time. The result of mutations led to new adaptations which allowed organisms to survive a dynamic world and to create new metabolic processes and later body components. Genes can be replicated within the genome resulting in multiple copies of the same gene. Important evolutionary process because it allows for genes to change through time without interfering with the metabolic processes of the organism. The organism can now produce the original protein and can change the protein at the same time. 3 8  Some Examples of Mutations A single base pair change causes the formation of teeth along a birds beak – Birds do not have teeth because teeth weigh too much Fruit Fly (Drosophila melanogaster): single point mutation in a regulatory gene causes a leg to develop where an antenna is suppose to form – Fig. 7.21 These mutations cause changes in proteins, which cause larger changes in the organism as a whole