Assume that a length of axon membrane of about 10 cm is excited by an action potential (length excited nerve speedpulse duration 50 m/s2.0 ms 10 cm). In the resting state, the outer surface of the axon wall is charged positively with K ions and the inner wall has an equal and opposite charge of negative organic ions, as shown in Figure P18.41. Model the axon as a parallel-plate capacitor, and take C 0A/d and Q CV to investigate the charge as follows: Use typical values for a cylindrical axon of cell wall thickness d 1.0108 m, axon radius r 10m, and cell-wall dielectric constant 3.0. (a) Calculate the positive charge on the outside of a 10-cm piece of axon when it is not conducting an electric pulse. How many K ions are on the outside of the axon? Is this a large charge per unit area? [Hint: Calculate the charge per unit area in terms of the number of angstroms (2) per electronic charge. An atom has a cross section of about 12 (1 1010 m)] (b) How much positive charge must ow through the cell membrane to reach the excited state of 30mV from the resting state of 70mV? How many sodium ions (Na) is this? (c) If it takes 2.0ms for the Na ions to enter the axon, what is the average current in the axon wall in this process? (d) How much energy does it take to raise the potential of the inner axon wall to 30 mV, starting from the resting potential of 70 mV?
Chapter 13: Translation and Proteins I. Polyribosomes: many ribosomes. These are found on most transcripts a. On one strand of mRNA there are multiple ribosomes attached that are translating. As soon as the shine Dergano sequence is exposed, another ribosome will attach. b. NOTE: transcription and translation will occur at the same time in prokaryotes i. In Eukaryotes, these do not occur in the same place. 1. There is a separation between nucleus (where transcription takes place) and cytoplasm (where translation takes place). II. Comparison between Prokaryotic and Eukaryotic Translations a. Genetic Code: this is conserved. i. Prokaryotes: fMet is an initiator amino acid. To start, the fMet will be first placed into the P site to help align the start codon. ii. Eukaryotes: do not have fMet. A normal Met is used as an initiator to makes sure the start codon is placed in the right spot. 1. A specialty tRNA is used to get everything started b. Transcription and translation occur simultaneously in prokaryotes. i. As the shine Dergano sequence is exposed, another ribosome will attach. c. mRNA life span i. Prokaryotes: short lived 1. Since transcription and translation occur in the same place, mRNA does not need to stay alive as long. Can be measured in minutes ii. Eukaryotes: live longer 1. Since there is a division, the life span of mRNA needs to be longer, can be measured in hours. iii. The longer the transcript is present in a cell, the more protein it can make d. Ribosomal subunits: differences create differences in initiation i. Prokaryotes: smaller in size, though still two subunits ii. Eukaryotes: larger in size, though still two subunits 1. Changes how we initiate e. Genotype and Environmental impact Phenotype i. Garrod: suggested that genes are encoded enzymes (he was the first to suggest this) 1. Was studying what we know as genetic diseases now 2. Noticed they were being passed down within families from one generation to the next 3. Though this was due to a protein that was not working correctly a. Made a connection between heredity and proteins, this was long before we knew that DNA was the genetic material ii. Beadle and Tatum: experimentally proved what Garrod was trying to say 1. Used bread mold, easy to grow in lab setting and the vegetative form is haploid (allows to see recessive mutations easily) 2. They were the first to make a connection that if you mutate genetic material, then you will case a gene to not be present, which leads to an enzyme not being created, which will lead to a phenotype missing 3. Theory: One-gene, one-enzyme hypothesis. Each gene encodes a separate enzyme a. Later changed to one-gene, one-polypeptide i. Sometimes many polypeptides are used to interact to create a functional product f. Beadle and Tatum experiment: i. Exposed spores to UV radiation 1. Knew that this would cause the spores to mutate (prototroph will become auxotroph). 2. This was done in complete media ii. They then switched the spores to minimal media 1. Looked to see if the spores could grow or not 2. Have to have the wild type allele to be able to live, if the spores can make it all on their own, then they will grow in minimal media. Meaning that they did not mutate 3. If they die, then they have mutated (auxotroph) iii. Switched to supplemental medium to see what the spores need to live, to see what they are mutant for. 1. If they live when something is added, then that is what they are missing, what they are deficient in. 2. The experiment showed that they grew in the medium with amino acids added to it. This means that they cannot create a certain amino acid iv. They then put the spores in medium with a certain type of amino acids to see what amino acid they are lacking. 1. Discovered it was tyrosine g. Sickle Cell Anemia i. Helped to adopt the change of the Beadle and Tatum hypothesis ii. Several groups studied sickle cell, they made the connection that it was hereditary iii. Later, another group discovered that there is a single amino acid changed, resulting in a completely different phenotype h. Proteins are your friend (unless they are prions) i. Proteins are needed, but also needed to be made correctly ii. You want the primary structure to be correctly made, but also need the other structures (secondary, tertiary, etc.) to be made properly as well iii. Function is tied to structure iv. Proteins can be enzymes, structural, signal transducers, other or combinations v. Structures: 1. Primary: the actual sequence made during translation, the polypeptide chain 2. Secondary: interactions between neighboring amino acids, usually H-bonds. This is the first interaction after being formed a. Beta sheets or alpha helix 3. Tertiary: forms the 3D structure of the protein. Results from interactions of the secondary structures a. In this form, they are ready and functional proteins (most of them) some need another structure 4. Quaternary: multiple polypeptides interacting a. Different kinds of subunits interacting together. This is the final stage and the protein is ready to go and is functional i. What are proteins made of i. Made up of 20 common amino acids 1. The bases of the protein is amino acids ii. 20 amino acids: similar core structure. 1. Carbon, amino, and carboxyl groups 2. The R group is what gives the amino acid its own characteristics and identification a. R groups can characterize the proteins, can be polar or nonpolar iii. Mutations and amino acids: 1. If the amino acid switched in has common characteristics, size, or folding, then the result may not be a drastic change. If they are not similar, then the resulting change can be huge iv. Peptidyl transferase: transfers from A site to P site and makes peptide bonds 1. Peptide bonds hold all amino acids together v. Amino group and carboxyl group will give directionality 1. Amino end is the first amino acid 2. Whatever is closes to the stop codon is the carboxyl end vi. Structure is important because it will define how well a protein will do its job or what job it will do 1. Active site: if the site is not formed correctly due to not being folded right (the structure), then it will not be able to grab onto what it is supposed to grab on to and will not be able to do the job a. Change the structure and change the function 2. Different changes can have different impacts a. People can have mutation in the same gene, but will result in different phenotypes 3. Changes in or around the active site will result in a greater change in function. j. Post translational modifications: i. Molecular chaperons: proteins start to fold as soon as they leave the ribosome (they are more stable folded). A molecular chaperon can come and hold off the folding until a certain point to help the protein achieve the correct formation. This can also help the protein get into the right location ii. Signal sequence: other proteins will recognize and put the signal sequence where they need to go. Once they are there, they will cut off that sequence and allow the protein to fold into the correct shape k. Antibiotics: these can target differences between prokaryotic and eukaryotic mechanisms i. If we understand the differences between prokaryotic and eukaryotic then we can use the differences as a target for antibiotics 1. Wipe out replication = cell death 2. If we the differences, we can shut down transcription and translation of prokaryotic cells and not interfere or hurt the eukaryotic ones. l. Prions, Mad Cow, and You i. Prusiner: discovered that Scrapie in sheep was caused by infectious proteins ii. Some proteins fold and get transcribed correctly, but then for some reason they will change configuration 1. This happens with prions. A regular protein is made correctly but then some change will occur. This results in a prion (most are neurologically related, located in the brain) to switch 2. Examples: Scrapie in sheep. Kuru in humans 3. All have this regular protein that has been changed 4. If it switches, it will have the exact same RNA, DNA and amino acids, but the difference will be in the folding. This causes it to not be used right 5. Kuru: if a normal protein bumps into a misfolded one (the prion), the normal will change into the prion. This will continue to bounce into others, causing the prion to form a. Infectious protein b. Shows how much structure is important c. If individual has this and someone comes in contact with the infected brain (or even a blood transfusion) then the other individual will become infected 6. Scrapie: if you come in contact with the brain of an infected sheep, you will develop issues 7. These prions are not going through the central dogma, a protein is still being made correctly, just changing after being developed. iii. Some can be inherited Chapter 14: Gene Mutation, DNA Repair, and Transposition I. Mutations impact life in several ways a. Mutation: change at DNA level in genetic information that will be passed onto the next generation i. Can be passed into daughter cells through mitosis or individuals through sexual reproduction b. Mutations can be good, allows for diversities, though most are bad. c. We can use mutations to understand how different genes function. i. Where genes are located ii. When something goes wrong in a gene, what affect does it have on phenotype II. Somatic Mutations vs. Germ-Line Mutations a. Classifications of mutations i. These classifications are not mutually exclusive ii. Can be classified in multiple classifications b. Tissue type change: i. Does it occur in somatic tissue or germ-line 1. Somatic mutations: arise in somatic (non-sex) cells. They are passed to daughter cells through mitosis a. They divide mitotically b. Through mitosis, the daughter cells can have the mutation, but just on a region of the skin surface c. Will not be super dramatic, if occurs in the wrong spot or tissue it can become cancerous though. 2. Germ-line mutations: arise in cells that produce gametes and are passed to future generates a. Occur in tissues that are passed onto the next generation of an organism. b. Passed onto a brand new individual c. Germ-line will result in the entire organism having the mutations, not just in a region (like seen in somatic) III. Spontaneous Mutations vs. Induced Mutations a. Mutations can be caused, however, there are two types of mutations, each classified by how they are caused b. Spontaneous Mutations: occur without a real cause, nothing is interfering with DNA to cause the mutation i. Example: replication errors that are not caused or fixed. c. Induced Mutations: outside facts influence/causes the mutation i. Can be naturally or artificially induced ii. Naturally induced: is something we cannot escape, such as UV light. It naturally occurs. iii. Artificially induced: a chemical that results in a change at nucleotide level, usually something that can be avoided. It does not occur naturally. d. Mutation Rate: can be determined to see how much a mutation in one generation will occur i. Can be tricky to calculate ii. Can vary between two different organisms iii. Some genes within organisms will have a higher mutation rate than others IV. Types of Mutations a. Base/base pair substitution or Point Mutation: a single nucleotide is altered. L i. Occurs at the sequence level ii. Looking at a change in a gene will help us understand phenotypic change caused by mutations. However, mutations can occur outside a gene as well iii. Transition: replaces a like for a like 1. A purine replaces a purine 2. A pyrimidine replaces a pyrimidine iv. Transversion: replaces unalike bases 1. A purine replaces a pyrimidine and vice versa b. Insertion/Deletion: this is the most frequent type of mutation i. Insertion: inserting a new base ii. Deletion: deleting a new base iii. Any time you add or take out bases, you can change the reading frame 1. Frameshift mutations: occur when insertion or deletion take place V. Frameshift Mutations a. A frameshift mutation is much more detrimental b. If had to choose between having a point mutation or a frameshift mutation, always choose point mutation! c. Point mutation: only going to change the exact location where the mutation is put in or switched out. i. It is a single point that is mutated d. Deletion/Insertion: everything to follow after the point of deletion or insertion will be messed up i. The rest of the polypeptide will be changed, wrong amino acids incorporated. (refer to slide 7 for an example) VI. Mutations can have a number of different outcomes. a. When talking about mutations, it is usually talking about forward mutations. b. Forward mutations: wild allele is changed to a mutant allele i. Can have different mutations, what affect does it have on amino acids ii. Missense Mutation: single base changed that results in the incorporation of a different amino acid iii. Nonsense mutation: single base change that results in a stop codon being created 1. Stops the process of translation, no amino acid is put in, and the polypeptide chain stops growing, lose everything after that point 2. In general, this is worse than missense mutation because it results in the loss of material. iv. Silent Mutation: changes the base resulting in a different codon, but results in the same amino acid being incorporated. This is due to the wobble effect. c. Reverse mutations: goes from mutant allele to a wild allele i. A true reverse mutation will completely undo whatever forward mutation occurred 1. Insert a T to be mutant, so the reverse would delete the T d. Look at what affect it was on proteins ability to do its job i. Neutral change: if changes amino acid, but not how the protein functions ii. Loss of function mutation: prevents protein from doing is job properly 1. Could be a scale. Go from not working well but still working to being null a. Null: complete loss of function b. Haploinsufficiency: protein working, just not enough production 2. Recessive when passed through generations, will not interfere with other allele even if it is wild type iii. Gain of function mutation: production of a new trait, protein takes on a new job. Protein could do something completely different or still doing the same task just at the wrong time 1. The protein could be seen in a tissue that it is not supposed to be seen in 2. Tends to be dominant. If a protein is being made at a different point in time, this will occur no matter what the other allele is (even if it wild type) VII. Phenotypic Classifications a. How we classify the change within an organism. These different classifications can overlap, a change can be classified in multiple classifications b. Visible: is what we see, such as pigmentation c. Nutritional: loss of ability to make certain amino acids or vitamins d. Biochemical: interrupts any pathway that is involved in a biochemical reaction e. Behavioral: identify a mutation changes how an organism acts f. Regulatory: protein itself is not mutated, able to create a polypeptide that folds into a functioning protein, changes how it is expressed, cannot control expression correctly g. Lethal: changes essential process, change prevents organism surviving h. Conditional: expressed only under certain environmental conditions i. Temperature sensitive: type of conditional mutant, the environmental condition is temperature j. Conditional mutations have been instrumental in studying lethal mutations VIII. Suppressor Mutations a. Hides the impact of another mutation. Allows us to return to wild type phenotype but will not fix the mutation, instead it hides it with a second mutation b. Intergenic Mutations: the second mutation occurs in a separate gene i. If there is a mutation in gene A, then the second mutation will be in gene B to hide the initial mutation (mutated gene A causes white eyes, mutation in gene B causes red eyes which is the normal phenotype) c. Intragenic mutations: the second mutation occurs in the same gene i. First mutation changes a codon from AAT to AAA. Resulting in the amino acid change from Leu to Phe. The second mutation changes AAA to GAA. Resulting in the amino acid change from Phe to Leu. This is due to the wobble effect d. These are not reverse mutations, because reverse mutations fix the initial mutation while suppressor mutations hide the initial mutation. The initial mutation is still present in the suppressor mutations.