Molecular genetics

What do proteins create?

Phenotypes

Explain how retroviruses modify the central dogma.

Retroviruses are able to transcribe RNA into DNA through the use of an enzyme called reverse transcriptase and then insert that DNA into the host. Retroviruses such as HIV use RNA to carry genetic information. Retroviruses have a RNA genome rather than a DNA genome. These viruses convert their RNA genome into DNA for the purpose of replication. Following genome replication, the DNA is transcribed back into RNA and then translated into protein. The conversion of RNA → DNA violates the information flow of the central dogma, which states DNA → RNA →protein.

Transformation

Since DNA is interchangeable, human DNA can be inserted into the plasmid of bacteria, and bacteria can make copies

Central dogma

Take the DNA and copy a gene into messenger RNA though transcription, which takes place in the nucleus. Messenger RNA moves out through nuclear pores and grabs onto a ribosome and makes proteins through process called translation

Explain how the experiments that each of the following people/groups performed provided evidence that DNA is the genetic material. Oswald Avery, Maclyn McCarty, and Colin MacLeod

They looked at Griffith's experiment and tried to figure out what the transforming factor was. They found RNA, Protein, and DNA. They used enzymes that broke down each of those to see if they could transform the bacteria again. Added ribonuclease and broke down RNA and it was still able to transform. They added enzymes to break down proteins and they were still able to transform. They added deoxyribonuclease which breaks down DNA and then they couldn't transform. They figured out that DNA was the transforming factor.

Eyes

To read it we use DNA sequencer Its like a PCR machine. Have everything it has (primer polymerase etc.) but we also have four special letters called dideoxynucleotides. They have a specific color. The stop points have color. Then these fragments are run through gel electrophoresis.

Negative control

Trp operon.

The extended phenotype

A beaver has a number of different phenotypes, a flattened tail, extended teeth, tiny arms which are all created by DNA but beavers also produce a beaver damn. This isn't created by genes but is an extension of them.

What is every 3 letters in an mRNA called?

A codon

Regulatory gene

A gene on the DNA that regulates another gene somewhere farther down

Describe how proteins can be altered once they have been synthesized at the ribosome and what organelles are involved.

After a protein has been made by a ribosome, it is processed by other organelles. The rough ER helps with folding the protein. The golgi apparatus packages the protein in vesicles and modifies it. It could be altered in one of those organelles.

Explain how the "one-gene-one-protein" hypothesis was derived by Beadle and Tatum. Why has this hypothesis been refined to "one gene-one polypeptide," and now "one gene-one (protein) domain?"

Beadle and Tatum used bread mold to figure out this hypothesis. They found that mold that was exposed to radiation lost the ability to produce essential nutrients, which slowed and even stopped mold growth. They found that mold growth could be restored by providing the mutated mold with a specific supplement. They figured out that each mutation inactivated the enzyme needed to synthesis the nutrient. ---> one gene carries the directions for making one protein. It changed to one gene one polypeptide because the genes don't make the protein they make the polypeptide chain....also their are proteins that have more than one polypeptide making them up. One protein domain...a gene coding for a specific functional area of a protein...ex: coding for an active site for a protein.

Gene regulation : when

Can regulate genes along any step (transcription, translation, etc) In general regulation happens from DNA to mRNA.

Structure of DNA

Chromosomes DNA is wrapped around histone proteins which are swirled around other proteins and eventually you get to the structure of the chromosome. Prokaryotic chromosome: is loose not in a chromosome. It is also a loop. They also have plasmids.

Francis Crick coined the term "central dogma" with regard to the relationship between DNA and RNA. Explain what Crick meant by this.

Crick was talking about transcription and translation. DNA-->RNA-->Proteins Take the DNA and copy a gene into messenger RNA through transcription, which takes place in the nucleus. Messenger RNA moves out through nuclear pores and grabs onto a ribosome and makes proteins through process called translation. Why it's called central dogma: Wanted to suggest that the new assumption was more powerful. An idea for which there is no reasonable evidence is what he thought dogma meant.

DNA replication

DNA has to be copied every time a cell replicates. Unzip the double helix of the DNA and now you have two strands. You can only add new letters on the 3 prime end and so on one side DNA polymerase, which is an enzyme that adds new bases to the other side of DNA, runs really smooth (leading strand), and on the other side, it has to back stitch

Central dogma

DNA makes RNA: transcription RNA makes proteins Proteins make phenotypes Phenotypes make you

How do mistakes happen

DNA polymerase copies DNA but occasionally makes mistakes. We can get mutations through radiation. We can get mutations through chemicals (carsinogens)

Transcription

DNA unwinds and RNA polymerase moves down the DNA and copies the information. Complimentary bonding. mRNA detaches and DNA zips back up. Initiation, elongation, termination Put a 5 prime cap on one side of the mRNA and a poly A tail, which is a bunch of adenines in a row. And get rid of introns, sections that don't actually code for a gene. They we will splice together the mRNA. mRNA goes out to cytoplasm.

Ruler/measuring device

Gel electrophoresis Inside you have a gel. Wells on one side to insert the DNA. A positive charge on the opposite end. And a negative charge on the other side so the DNA is going to migrate across that gel. DNA has a negative charge so positive charge will pull it across.

Hydrogen bonds

Glue...found within DNA

Trp operon

Has five genes right next to each other. It is off when tryptophan or when that chemical is present. Tryptophan is an amino acid so we need it to make proteins. So when typtophan is present, we don't need to make it. Tryptophan fits in the repressor and gives it a shape the blocks the RNA polymerase or the making of those proteins. If you are not getting tryptophan in your diet, the repressor is going to change shape and allows RNA polymerase to attach on and make those 5 proteins and then those proteins make more tryptophan.

The lac operon.

Have three genes on the strand right next to eachother. The lac Z, Y and A gene. They each make a protein and help break down lactose. Above that is a regulatory sequence called a promoter that's where RNA polymerase grabs on. They have an operator between the promoter and the genes. The operator is like an on off switch and regulates whether or not we turn the genes on or don't. a repressor plugs right into the operator and as long as the repressor is on there, RNA polymerase can't get on. When lactose isn't present, we want it to be off. But when lactose is present, lactose fits into the repressor and it changes the confirmation or the shape of that protein and the repressor no longer fits into the operator. RNA polymerase now fits on and it runs down and makes each of the mRNAs for each of those lac genes. Each of those makes a protein and those break down the lactose. Now the lactose is gone, the repressor goes back to its shape and returns to the operator.

Explain what would happen to the process of gene expression if the gene for RNA polymerase was mutated.

If its mutated it would make the mRNA incorrectly or differently which would change the protein that is made.

Pachinko machines

If we take a small fragment of DNA its going to work its way farther down through that pachinko machine sooner than one of these big fragments. We use gel electrophoresis.

Describe how the following tools are used to study or modify organismal genomes: Gel electrophoresis

Inside you have a gel. Wells on one side to insert the DNA. A positive charge on the opposite end. And a negative charge on the other side so the DNA is going to migrate across that gel. DNA has a negative charge so positive charge will pull it across.

What does a tRNA do?

It grabs onto its amino acid it bonds to the ribosome and then drops off its amino acid. And then it flows out into the cytoplasm to grab the next amino acid. tRNA has three letters on the bottom of it, the anicodon that bonds to the codon in the mRNA.

Describe the characteristics of the DNA molecule that make it a good information-bearing molecule.

It has the same bases. (universal bases). Easy to copy because of hydrogen bonds and nucleotide base pairing Its really small. Their protected by a phosphate sugar backbone so it's hard to damage It's self replicating...able to make copies of itself to pass on the information while also staying in tact

Sickle cell anemia

Just a change in one letter in DNA Leads to changes in amino acids

Explain how the experiments that each of the following people/groups performed provided evidence that DNA is the genetic material. Erwin Chargaff

Looking at different organisms and studying the amount of As, Ts, Cs, and Gs. He found that amount of A and T is exactly the same. Chargaff's rule

Each amino acid has a tRNA synthetase enzyme that is responsible for attaching it to a tRNA molecule. Explain what would happen if there was a mutation in the gene encoding one of these enzymes.

Lower end of tRNA is anti codon and other end is amino acid. You need enzymes to bind an amino acid to the tRNA so the tRNA can bring it to the ribosomes. If the enzyme wasn't there you would be missing an amino acid.

Can have mistakes in the cell cycle

Mistakes in meiosis in meiosis 1. Chromosomes will fail to separate and eventually you could have not just haploid but could have 4n or 3n. can lead to a new species, sterility, or disorders.

Three types of mutations

Neutral: changed the DNA but it doesn't effect the organism (might be in introns) Beneficial: help an organism Harmful: hurt an organism. If mutation occurs within a gene, 70% of the time that change within the gene is going to cause a harmful mutation. If its outside the gene only 7% of the time is it harmful. point shift: silent: one base substituted and no change to protein nonsense mutation: codes for a stop significant change missence mutation: base change codes for a different amino acid frameshift: inserts a base

Positive control

Operator turns on when lactose is present and off when it isn't.

Define operon. Explain how bacterial cells use operons to control gene expression.

Operon: a unit made up of linked genes that is thought to regulate other genes responsible for protein synthesis. Inducible: lac operon. In the presence of lactose, lactose binds to the inhibitor and it changes shape and leaves the lac operon so that RNA polymerase can continue to make the mRNA of the enzymes that break down lactose Repressible: Trp operon. It is always on. In the presence of tryptophan, it no longer needs to be on because if would be a waste to make more tryptophan. So, tryptophan binds to a repressor and changes its shape so that it can attach to the operon so that RNA polymerase can't move down the gene and make the mRNA.

Copy machine

Polymerase chain reaction The PCR. We need a primer which is a little section of DNA that will grab onto the DNA it will allow the polymerase to drive down the DNA. We need nucleotides. You put it in the PCR. It heats it really quickly then cools it then heats it. As it heats it DNA is unzipped. Primer is added and bonds to the complimentary sides of the DNA now the taq polymerase grabs on. Taq polymerase adds bases and creates new strand of DNA. This cycle continues.

Describe how the following tools are used to study or modify organismal genomes: Polymerase Chain Reaction (PCR)

Polymerase chain reaction. The PCR. We need a primer which is a little section of DNA that will grab onto the DNA it will allow the polymerase to drive down the DNA. We need nucleotides. You put it in the PCR. It heats it really quickly then cools it then heats it. As it heats it DNA is unzipped. Primer is added and bonds to the complimentary sides of the DNA now the taq polymerase grabs on. Taq polymerase adds bases and creates new strand of DNA. This cycle continues.

Describe the structure of a eukaryotic chromosome. How does it compare to a prokaryotic chromosome?

Prokaryotic Chromosomal DNA in cytoplasm Circular chromosome/ loop shape Made only of DNA no histone proteins Eukaryotic Chromosomal DNA in nucleus only Linear chromosomes (looks like an x) DNA tightly coiled around histone proteins

Explain the relationship between protein synthesis and an organism's phenotype.

Proteins eventually create phenotypes. Just by changing one gene a little bit, the phenotype can be drastically different. If one gene of a peppered moth is changed a little, it can be dark colored instead. Changes in the DNA create changes in the mRNA, which create changes in the proteins which create changes in the phenotypes.

Translation

RNA moves out into cytoplasm and feeds through a ribosome. Every three letters RNA is going to match on three letters of a tRNA and that tRNA is going to bring in one amino acid (building blocks of proteins).

RNA vs. DNA

RNA: single helix DNA: double helix Both made of sugar, phosphate, base RNA has ribose sugar DNA has deoxyribose sugar BACKBONE: RNA: ribose sugar attached to a phosphate attached to a ribose sugar attached to a phosphate etc. On the inside attached to the sugar is the nitrogenous base. In RNA it's adenine, guanine, uracil, and cytosine. In DNA it's A, T, C, G.

Explain how repressible operons differ from inducible operons. Use the trp and lac operons as examples.

Repressible: can be turned off in the presence of a substance: trp operon Inducible: can be turned on in the presence of a substance: lac operon

Explain why DNA replication is considered to be semiconservative. Why is the leading strand replicated continuously, while the lagging strand is replicated discontinuously?

Semiconservative DNA replication: Produces two copies of one of the strands...one is the original and one is the new copy.The two new strands will join together and then the two old ones will zip back together. Using part of the old molecule to make the new molecule. Leading strand is replicated continuously because RNA polymerase can only continuously add nucleotide bases in the 5' to 3' direction. The other strand goes in the 3' to 5' direction and can only make several fragments called okazaki fragments. Ligase is needed to join the fragments.

Explain how the experiments that each of the following people/groups performed provided evidence that DNA is the genetic material. Frederick Griffith

Take rough strain of streptococcus pneumonia inject it into the mouse and mouse would be happy. Injected the smooth/ virulent type into a mouse and it would die. Injected an evil smooth strain and heated it up before and when injected into the mouse, the mouse was okay. When he took the rough strain, which normally doesn't hurt anything and mixed it with the heat killed smooth strain which normally doesn't hurt the mouse at all, the mouse died. He learned that there was a transforming factor. Something was being transferred from the dead smooth strain to the live rough strain and transforming it to virulent.

Explain why the peanut plant in Mr. Anderson's DNA and RNA video is able to express a gene from B. thuringiensis (Bt).

The peanut plant can express a gene from B. thuringiensis because DNA is the same and can be transferred from one organism to another.

Restriction enzymes

The sissors They come from bacteria. They methylate their DNA. Add a methyl group to all of their DNA from the bacteria to protect it. Then create restriction enzymes, which chop up or cut DNA. It cuts foreign / viral DNA. EcoR1: scans the DNA until it finds a specific sequence and it cuts it in half. Once the enzyme is gone, the two DNA strands come right back together again because of hydrogen bonds.

Explain how the experiments that each of the following people/groups performed provided evidence that DNA is the genetic material. Alfred Hershey and Martha Chase

Used sulfur in one experiment and in this they used a red dye to dye the bacteriophages in the experiment. They infect the bacteria, blend it all up, precipitate it out and see what color came out. It's important they used sulfur because it is found in proteins, but not in DNA (many people thought proteins were the transforming factor). They used a different dye to dye phosphorous, which is found in DNA, but not in proteins. They showed the only one doing the transforming was the green dye. That means it was the phosphorous, so proteins were not responsible for transforming. Conclusion: DNA was hereditary material

Regulatory sequence

Usually found just above the gene. Regulatory gene secretes a regulatory protein which can then grab onto a regulatory sequence.

Describe how viruses are able to cause tumors and cancer in human cells, such as HPV that causes cervical cancer.

Viruses inject their own DNA or RNA into the cell and then the cell will reproduce and pass down the new DNA. The viruses can now use all the other machinery like ribosomes to make their virus and rapidly reproduce.

Gene regulation

We have a gene and upstream of that is a regulatory sequence. Ex: the TATA box (called this because you have a thymine adenine thiamine adenine). Is a sequence above the gene that allows the RNA polymerase to get on. We have a regulatory protein coming from somewhere else, another regulatory gene.. ex: TATA binding protein. TATA binding protein grabs onto the TATA box and it allows RNA polymerase to grab on and actually express that gene.

Transcription

We have our DNA. We have a gene, a portion we want to make a protein out of. The enzyme RNA polymerase drives down the DNA and as it does that it makes a copy behind itself which becomes the messenger RNA. The DNA will stay within the nucleus. The RNA can leave the nucleus and make proteins.

How does it work in us?

We use transcription factors. RNA polymerase can't get on until we have a number of transcription factors present. Transcription factors allow the attachment of RNA polymerase. Other transcription factors hold RNA polymerase in place and we aren't actually making the gene. In order to make the gene the DNA upstream of that will have to fold. More transcription factors will attach to the folded part and that folded part folds even more and then activates the RNA polymerase

Describe how the following tools are used to study or modify organismal genomes: Plasmids

bacteria can share genetic information through plasmids and give them a new trait. Since DNA is interchangable, we can cut it out and insert it into bacteria. Scientists have inserted human genes into the bacteria's plasmid and the bacteria can make copies and proteins. We will be able to grow human proteins in plants which could transform medicine.

Describe how the following tools are used to study or modify organismal genomes: Restriction enzymes:

enzymes that cut DNA at a specific place. The enzyme scans the DNA and looks for a specific sequence of nucleotides. Then, it cuts the strands.

Translation

mRNA moves through a ribosome. A ribosome has two parts, a small subunit (the bottom part) and a large subunit on the top. The mRNA flows right though the ribosome. Every three letters in the mRNA codes for one amino acid. Amino acids are on top of transfer RNA. The job of tRNA is to transfer amino acids from the cytoplasm to the ribosomes so we can attach ribosomes onto the growing polypeptide chain which is going to become a protein.