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Biology 1001A
Tom Haffie

Biology Lecture and Reading Objectives for Exams By: River EwingW.LO E.L. 120 150 180 0.037 0.115 0.141 0.010 0.011 0.064 to 0.036 to 0.063 to 0.088 to 0.1 14 to 0.140 Frequency of ccR5-s32 allele Copyright 2004 Poarson Prentice all, Inc. W.LO E.L. 120 150 180 0.037 0.115 0.141 0.010 0.011 0.064 to 0.036 to 0.063 to 0.088 to 0.1 14 to 0.140 Frequency of ccR5-s32 allele Copyright 2004 Poarson Prentice all, Inc.Lecture Two: Evolution and HIV General global distribution of HIV infections. Largely apparent in sub Saharan (below the sahara) Africa. Highe rates in Russia with very low rates in both Europe, north America and south America. Low rates in south East Asia. General temporal trends in HIV infection rates. (not quite sure what it is asking) Factors that explain why no cure or universal vaccine has been developed for HIV/AIDS. 1. Because the HIV virus has such a high mutation rate that no vaccine has been able to successfully stay in pace with the virus. 2. Lacking education and contraception in highly effected areas. Reasons why viruses are not considered “alive”. Not considered alive because they do not have their own metabolism, and they do not reproduce on their own, they use the hardware of a host to do all the heavy lifting. Reasons why anti-viral drug therapies often have serious side effects. This is because generally anti-viral drugs attackthe protein layer outside of the cell which may also seriously damage the protein layer of cells in the body. To rectify this drugs try to attack steps that are unique to the virus. Major steps in life cycle of HIV. Produced by a host cell, floats around and attaches to a potential host cell, then releases its contents into the host; Including reverse transcriptase (turns the viral RNA back into DNA) and the viral RNA which gets turned into DNA and then integrated into the cells local DNA. Specific role of integrase and reverse transcriptase in retroviral life cycle. Reverse transcriptase takes the Viral RNA and turns it into the Viral DNA. Integrase takes the viral DNA and integrates it into the host cells DNA. Mechanism of action of AZT. AZT fools thymidine and tricks the virus into using it instead thus stopping the DNA synthesis of the Viral DNA. Reasons why effectiveness of AZT decreases over time. This is because the HIV virus mutates so rapidly that it can recognize the drug more and more effectively as time goes on with its quick mutation. Rationale for multi-drug (drug cocktail) approach to treating viral infections. This is because it is likely that HIV can mutate rapidly to resist a single type of drug, however, it is highly unlikely that it will be able to undergo several mutations all at once to be able to avoid all of the drugs. This greatly increases the changes of slowing virus progression. Principles of evolution of HIV: variation, heritability, differential reproduction, change in genotype of population. (not sure what its asking) Role of CCR5-Δ32 mutation in human resistance to HIV infection. evolutionary response to HIV? (unlikely, because HIV in Europe has not been a strong past selective pressure.) Could be chance and history? Or strong past selective pressure. It is hypothesized that the black death or bubonic plague could have caused this gene to rise in Europe and other places effected while not so in Africa. The distribution maps between the black death and allele expression are similar. The allele itself works by causing a mutation in the human cells protein coat and makes it very difficult for the HIV virus to attach to host cells. Global distribution of CCR5-Δ32 allele.Likely explanations of modern distribution of CCR5-Δ32 allele. evolutionary response to HIV? (unlikely, because HIV in Europe has not been a strong past selective pressure.) Could be chance and history? Or strong past selective pressure. It is hypothesized that the black death or bubonic plague could have caused this gene to rise in Europe and other places effected while not so in Africa. The distribution maps between the black death and allele expression are similar. In multiple choice format, identify... 1. The general mechanisms by which vaccines protect against diseases. Vaccines cause the immune system to produce antibodies for the specific disease that it is targeted against. This causes the immune system to react much more quickly and therefore more effectively when confronted with a viral infection. 2. Why developing a vaccine against HIV is relatively challenging, compared to other diseases. This is because it mutates so quickly and has such a fast generation time. As well, HIV is a retrovirus with no proof reading mechanism in its genome so its mutation rate is extremely high. 3. Why people are encouraged to get a flu vaccine each year (as opposed to one time only). This is because each year the flu changes, so there is essentially a new flu each year, which the previous flu vaccine did not cover. Lecture Three: Origin of Life On multiple choice exams, you should be able to identify… age of the Earth. 4.6 billion years age of start of life on Earth. Life on earth dates back as far as 3.5 billion years domains of life. (Might not be what question is asking) but it can be split into Bacteria, Archaea and Eukaryotes Characteristics of LUCA 1. cells made of lipids 2. Genetic system based on DNA 3. DNA to RNA to Protein transfer of information 4. common system of protein assembly 5. ATP 6. Glucose & Glycolysis. (these are shared by all life now which supports the idea of a LUCA) Characteristics shared by all domains of life: Order, Harness and utilize energy, Reproduce Respond to stimuli, Exhibit homeostasis, Growth and development, Evolve reason why the term “prokaryote” is inappropriate. The term “prokaryotes” is a bad term, two reasons, Bacteria and Archaea are not evolutionarily related. Also, prefix “pro” means before, and prokaryotes are before the nucleus. However, there is no evidence to support that the nucleus was derived from a cell without one. There is a strong hypothesis now that LUCA was proto- eukaryotic. Some evidence suggests that there was a selective pressure for reductive evolution, or streamlining, thus, removing the nucleus for simplicity (benefits may include; reproducing faster, evolving faster, quicker generation times) which results in quicker adaptation. reductive evolution explanation for rise of bacteria and archaea.. See end of above answer advantages of evolutionary simplification (streamlining). See end of above answer relationship between homochirality and life. All life is homochiral, meaning they only accept one form of a molecule. (see slide show for a clearer explanation. All life uses only one chiral form. All life uses d-sugars and L-amino acids. Example of chirality is your hands, where they cannot be superimposed on one another.reasons why we think RNA was the first of the three molecules of the Central Dogma to evolve. In an early environment it is possible that cells could have existed that contain only RNA. This is because RNA can sufficiently do the job of DNA and Proteins in a cell. It is also a simpler system when just RNA is used so it is likely that RNA systems were developed first and then DNA and Protein were added later to the system because they offered and advantage. It would have taken longer for Proteins and DNA to come in because evolution has travelled in a direction favoring increased complexity for a number of years. force that drives RNA folding. (not sure, doesn’t specify) characteristics of a ribozyme. A ribosome is 2/3 RNA and the rest is protein. This is called a rubonucleicprotein. These must all come together to produce something functional. mechanism whereby a ribozyme cleaves RNA. (Not sure) characteristics of amino transferase activity. (again not really sure how this works) a transferase is an enzyme that catalyzes the transfer of a functional group (e.g., a methyl or phosphate group) from one molecule (called the donor) to another (called the acceptor) reasons why a ribosome is considered a ribozyme. ( not quite sure of this one) however, Wikipedia says, Since their catalytic core is made of RNA, ribosomes are classified as "ribozymes advantage that protein has over RNA as a catalyst. With just RNA replication is never prefect, therefore there was a high mutation rate. RNA led to the formation of proteins. Protein turns to be superior to RNA for its specific functionality. The single-stranded nature of protein molecules, together with their composition of 20 or more different amino acid building blocks, allows them to fold in to a vast number of different three-dimensional shapes, this is also because protein has 20 amino acid building blocks where RNA only has the four. advantage that DNA has over RNA as a repository for genetic information. DNA is much more stable than RNA so it is more reliable when storing genetic information. It is not prone to breaking apart or having high levels of mutation as is RNA. chemical basis for the advantage that DNA has over RNA as a repository for genetic information. Thymine replaces Uracil, (look in textbook). DNA is much more stable than RNA. The OH group on RNA makes the RNA very reactive and can cause it to be broken down. DNA does not have this and because of it is more stable. In multiple choice format, identify… 1.characteristics shared by all life. Display order, Harness and utilize energy, reproduce, respond to stimuli, exhibit homeostasis, growth and development, evolve. 2. in what way properties of life are "emergent". (??) This is because as things move from non- living to living they begin to show the characteristics of life; And so these characteristics are said to be emergent. 3. characteristics of the "habitable zone" of a solar system. This is the zone described as the distance from the sun where liquid water can be sustained. 4. conditions of a primitive Earth. Hypothesized to be a reducing atmosphere. 5. types of molecules that were, and were not, synthesized by the Millar-Urey experiment. Macromolecules essential to life were created including amino acids, fatty acids, purine and pyrimidine components of nucleic acids, glyceraldehyde, ribose, glucose, fructose, and phospholipids which form the lipid bilayers of biological membranes. What were not produced was polymers. Which are needed for the formation of life. Monomers were created but the chains of monomers (or polymers) were not. 6. characteristics of mimivirus that suggest it should be considered to be alive. It can be infected by other viruses and it can get sick. It is a massive virus and has over 900 coding proteins. It was originally mistaken for a bacteria because of its size. 7. characteristics of virophage. Virophages are satellite viruses that inhibit or impair the reproduction of the auxiliary virus. As any satellite virus, virophages depend on the coinfection oftheir host by another virus. Similarly to other satellite viruses, the virophage jeopardizes the reproduction of the auxiliary virus. Examples are the Sputnik virophage and the Organic Lake virophage. Lecture Four: Biodiversity most recent common ancestor (MRCA) for a given group(s), given a phylogenetic tree. I can do that (try on trees) why the idea that “humans are descended from chimps” is inaccurate. This is because Humans have an extinct common ancestor with chimps. order of main branching events in tree of life (dates not testable). (see power point) cause of global catastrophe associated with mass extinction 65 mya. There is Solid evidence that it was a meteorite that struck the earth and caused a mass extinction. relative proportion of protostome vs. deuterostome species. (??) greater than 1 million protostomes information provided by genetic relatedness vs. traditional groupings of organisms (“reptiles”, “fish”) the words reptiles and fish generally grouped animals based on what they looked like. Now through genetic relatedness we can see that these groups are very innacurate and generally meaningless because members of some “groups” are very distantly related to other members. distribution of multi-cellularity in tree of life. Perhaps one of the most important evolutionary developments after the evolution of cells was the capacity of different cells to function together collectively: multicellularity. Several grades of multicellularity are known in both prokaryotes and eukaryotes representing a wide range of inter-cellular relationships. In prokaryotes, multicellularity remains relatively simple (for example, filaments in microbial mats are composed of chains of linked cells, but each cell still functions as an individual). Multicellular eukaryotes (fungi, plants, and animals) are more integrated and able to grow to a larger size. Multicellularity at its most complex level sees cells differentiating to form specialized tissues and organs in the "true" animals (Eumetazoans) and land plants. why estimating numbers of species is uncertain. This is because not all species form fossils so there is no way to tell from the past what has become extinct that we do not know about. role of similarities due to common descent (DNA genome) vs. convergence (eyes) in constructing a phylogenetic tree. Some similarities occur because of common decent in the genome (in regard to species they sort of come with it) in terms of convergence, there are some traits that have developed individually multiple times regardless of common descent eyes are a good example. 1. significance of "tree thinking" to evolutionary theory This gives rise to the idea of a LUCA and common decent. This is a large portion of the theory of evolution. 2. most recent common ancestor of two or more groups, given a phylogenetic tree (just test it out) 3. which groups are more versus less closely related to one another, given a phylogenetic tree (yep) 4. whether rotating internal nodes on a phylogenetic tree changes the information conveyed (no they do not, as long as the branches remain the same. 5. contemporary and ancestral species on a phylogenetic tree (yes) top is contemporary and below that is ancestralLecture 5: Why Evolution is True characteristics of a scientific theory a concept that attempts to explain phenomenon observed in the natural world. A theories finding is repeatedly confirmed multiple times and confirmed through observation and experimentation. components of the theory of evolution, Evolution by natural selection entails that genes are passed on from generation to generation, also, survival of the fittest, that species react to change within their environment, species have more offspring than are needed to survive so only the fittest reproduce and only those traits get passed on. evidence for "descent with modification" Fossil record, all of the striking similarities between all life ex. Chirality, DNA, RNA, protein and The central dogma of biology. examples of homology and why they support the idea of evolution an example of homology is a bats wings and the arms of primates. They share common bone structures. The same can be said for horse legs and human hands. They support evolution because they very clearly show a common ancestry between animals. examples of vestigial traits and why they support the idea of evolution These support the theory of evolution because there is no reasons that they would be there other than common descent. Role of fossil record as evidence for evolution and example of a vestigial trait is the human appendix. ( It doesn’t do anything anymore) 1. how Darwin's theory of evolution differed from that proposed by Lamarck Lamarck believed that if an animal needed to develop a trait, then they would develop it over their own lifetime and pass it down. This is like the giraffe theory. If a Giraffe needed to reach to tall trees, it would stretch its neck and pass its long neck trait to its offspring. However, Darwin believed that sometimes a mutation resulted in a giraffe having a long neck. That way, the giraffe could reach the trees better, and get more food, and be more likely to survive and reproduce than all of the other giraffes. Eventually, the trait would be passed down until most giraffes had long necks. (Lamarck believed that traits developed over lifetime, Darwin thought that they were genetic) 2. meaning of catastrophism, gradualism, uniformitarianism Catastrophism is the theory that there are local catastrophes that wipe out local species, when the area is repopulated there are slightly different species that repopulate it. Gradualism is the theory that the earth changes gradually over long periods of time. (more geographical it seems) uniformitarianism. Uniformitarianism is the assumption that the same natural laws and processes that operate in the universe now have always operated in the universe in the past and apply everywhere in the universe. e belief in or the policy of change by gradual, often slow stages 3. difference between relative versus absolute ages of rock formations and the fossils they contain. Relative ages of rock are in relation to the species before and after them. Absolute ages of rock are in relation to how old they are in time. 4. approximate age of a fossil or rock formation, given the half-life of a radioisotope and the proportion of starting isotope that has decayed take the half-life and multiply it by how many times the half life has occurred. 5. why most living things never form fossils Organism only leave fossils in very rare conditions. First, the body must be buried immediately after death. This usually only happens in swamps or sand pits. Then they must be exposed too little air because even some air pockets in the soil will allow the bacteria to breathe and thus not create a fossil. If this is met then the organism creates afossil. However the fossil can be destroyed because of shofting plates of being pulled so ar underground that they melt. Lecture 6: Genome Variation In multiple choice questions, identify non-nuclear genomes in typical plant and animal cells. Mitochondria have genomes inside. As well as chloroplasts. So plants have three different genomes, the mitochondrial genome, nuclear and chloroplast. It is also in the mitochondria in animal cells. As well as the nucleus. trend in C value from prokaryotic vs. eukaryotic cells. There is no relationship the c value is all over the map for both. relationship between C value and organismal complexity there is no relationship it is a misconception relationship between C value and ploidy if an organism has a higher ploidy then it has a higher coefficient in front of the c value for copies in the cell. Ie. A diploid organism may have 2c or 4c copies in each of its cells. distribution of linear vs. circular chromosomes in the various domains of life. The bacteria and Archaea have circular chromosomes. Mitochondria and chloroplasts have circular chromosomes just as bacteria and Archaea. Eukaryotes do not have circular chromosomes they are all linear. The role of nucleosomes in DNA packaging in chromosomes nucleosome are the product of Histomes and DNA attaching and is the first step in packaging DNA. The nucleosomes are then wound into a thread. They are then further wound by other proteins into large structures known as chromosomes. general trends in costs of DNA sequencing Going down. Rapidly since 2007. Starting to plateau. But generally it is getting much much cheaper with time. relative distribution of various components of genome sequence ("junk" vs. essential DNA) 1. meaning of "C-value". This is the amount of DNA contained in one copy of an organism’s genome. 2. "paradox" or "enigma" associated with C values The paradox is that the C value has no correlation to the complexity of the organism as seems logical. 3. meaning of haploid (n) and diploid (2n) Haploid means there is one copy of the chromosomes carried in the cell my the organism while diploid means that there are two copies of every chromosome in the cells of the organism. 4. relationship between C and n as measures of genome size. (??) kind of a dumb question? 5. proportion of the human genome that codes for protein. There is only 2% of the human genome that is protein coding. Lecture 7: Genome Replicationbasic structure of double-stranded DNA (ATCG) double helix structure made with a phosphate backbone. 5’ and 3’ ends, 3’ end is reactive because it has a free OH group. This means that it is the one that gets extended in replication. components necessary for DNA synthesis All of the Replisomes (learn what they all are and the function of each). What else? Is it obvious? direction of elongation of a given DNA strand 3’ end structure of a replication bubble Replication bubble is just two forks there are leading and lagging strands on the same strand of dna in a replication bubble just going opposite ways (see diagram) relationship between replicated DNA and metaphase chromosomes Replicated DNA is semi conservative, and a part of each old DNA strand is in each side of the metaphase chromosome. There is one DNA molecule per side of chromosome in metaphase and they are wound tightly. why chromosomes shorten at each replication (see YouTube link in next question makes a lot more sense) On the leading strand, DNA polymerase can make a complementary DNA strand without any difficulty because it goes from 5' to 3'. However, there is a problem going in the other direction on the lagging strand. To counter this, short sequences of RNA acting as primers attach to the lagging strand a short distance ahead of where the initiation site was. The DNA polymerase can start replication at that point and go to the end of the initiation site. This causes the formation of Okazaki fragments. More RNA primers attach further on the DNA strand and DNA polymerase comes along and continues to make a new DNA strand. Eventually, the last RNA primer attaches, and DNA polymerase, RNA nuclease and DNA ligase come along to convert the RNA (of the primers) to DNA and to seal the gaps in between the Okazaki fragments. But in order to change RNA to DNA, there must be another DNA strand in front of the RNA primer. This happens at all the sites of the lagging strand, but it does not happen at the end where the last RNA primer is attached. Ultimately, that RNA is destroyed by enzymes that degrade any RNA left on the DNA. Thus, a section of the telomere is lost during each cycle of replication at the 5' end of the lagging strand. mechanism by which telomerase adds telomeres to chromosomes 1. purine and pyrimidine base-pairing in DNA/RNA Purines are double-ring molecules (bases), while pyrimidines are single-ring molecules (bases), and all DNA is made up of just four chemicals: (A) Adenine (purine) (T) Thymine (pyrimidine) (C) Cytosine (pyrimidine) (G) Guanine (purine). There is not enough room in the double helix for two purines to bond and the prymidines are too small to get close enough to each other in the double helix to form a bond. Thus, they must bond with the opposite molecule. 2. outcome of the classic Meselson and Stahl experiment The outcome of the experiment showed that DNA replication was semi-conservative. 3. direction of movement of DNA polymerase on the template strand On the template strand DN polymerase moves from the 3’ to the 5’ end. 4. meaning of semi-conservative, semi-discontinuous, leading and lagging strand Semi conservative means that half of the old DNA in in each of the daughter DNA’s. so, the DNA splits and then copies of each strand are built onto the pre-existing one. Semi-discontinuous means that bcause DNA can synthesize in only one direction it has to be semi-discontinuous because it can only go so far during replication (lagging strand) leading strand and lagging strand are the two ways that DNA is synthesized near the replication fork. See the diagram for a clearer explanation. 5. general action of proteins in Fig. 12.15. (SEE TEXTBOOK) page 272 for an explanation of all of the Replisomes. (Need to know this). Lecture 8: Inheritance of Sameness mechanisms that ensure "inheritance of sameness" 1. Complementary base paring during replication 2. Pairing is always antiparallel 3. Extend 3’ end of base pairs 4. Proof reading mechanismslocation of actively cycling cells in multicellular animals/plants Perhaps the question means which cells replicate quickest or the most? (stems cells, blood cells) function of rapid cycling cells at various stages of the life cycle ??? examples of situations in which cells would be programmed to die by apoptosis Perhaps the cell has acquired too many mutations and should not continue to replicate poor copies. There are too many cells in a give area. The cell isn’t functioning well or efficiently anymore. main features of each stage of mitosis with respect to cytoskeleton and chromatin ??? main features of chromosome anatomy (brush up on chromosomes) composition of microtubules, intermediate filaments and microfilaments (not sure look on slides) interaction between spindle fibers and kinetochores The kinetochores grap on to the spindle fiber, which is like a rope, and climb up it to the poles of the cell. The spindle doesn’t do any pulling the kinetochore actually blimbs the rope and dissolves it behind it. role of motor proteins in chromosome segregation The motor protein keneto chore grabs onto the rope and pulls in separate directions thus splitting the chromosome into its chromatids and they then travel to the poles of the cell. role of cell cycle checkpoints Cell cycle checkpoints regulate the cell cycle to make sure nothing is happening too fast and that everything has happened and is in place before the next stage begins. implications for cell division if various components malfunction (ie. what if drugs prevent microtubule polymerization?) If drugs prevented microtubule polymerization then the cells would not be able to effectively divide because they could not pull the chromosomes to the poles of the cells, which would stop division. 1. stages and main characteristics of the stages of mitosis. (brush up on mitosis) 2. stage of cell division, given a micrograph of a dividing cell. (look at pictures and relate them to the stage in mitosis. practice 3. role and mechanism of the mitotic spindle. Just acts as a rope for the chromosomes to pull themselves with. 4. role of cell cycle check points. They stop things from happening too quickly and make sure everything is correct before proceeding. (I don’t really know, look it up) 5. changes in amount of DNA throughout the cell cycle DNA is duplicated in S phase so there is twice the mass of DNA during that phase. Then it splits into two cells so the amount goes back to normal. Lecture 9: Origin of Variation Pt. 1 different types of genomic variation among humans types of variation include SNP’s where a single base pair is different, as well as CNV’s where large sections of the chromosome have an abnormal number of copies (this can include deletion or addition of copies) LINES and SINES and retro elements. structure of IS elements, transposons, retrotransposons and retroviruses. The Insertion Sequence elements code for Transposase which makes cuts in the backbone of a target sequence this initiates the element being able to move. This part of Transposons, if there are two, can hold a sequence in between and essentially move that sequence around the genome with or without making a copy of itself. Retrotransposons are transcribed by RNA polymerase produces an RNA copy, this copy is in the “air” and is transcribed back to DNA and is then integrated back into the genome at a new site. Retroviruses can move within the genome Sometimes these viruses undergo a mutation and cannot get out of the cell so they are stuck in the genome and can move around the genome. These are called endogenous retrovirus which are essentially junk DNA. types of evidence that would be useful in determining how long the human genome has been infected by a given mobile element. How many people have this sort of mobile element. What demographics it is spread across. Perhaps the fossil record of humans, Look at close relatives such as the great apes, is it present there? role of mobile elements in genetic disease Mobile elements, when moving around in the genome, can cause genes to be expressed differently and cause genetic disease because the code is being jumbled around and can lead to some sort of a harmful “mutations”why it is that mobile elements can be considered to be "biological mutagens". This is because they are something that causes a mutation in the genetic code, while they are not chemical or physical (such as UV light) they are biological and so… Biological mutagens. why African populations have more unique SNPs than other populations (ie. Asian or Caucasian). African people have the most diversity in terms of SNP’s so we can interpret this as meaning that the African population is the oldest. They had the most time to develop these differences. And we can also infer that the human population must have originated from Africa. (People of African origin are much more different from each other. Than people of other descents). 1. mechanism of proofreading and likely result of proofreading defects DNA polymerase which has a built-in proofreading mechanism and can work “backwards” to correct its mistake. (Works by the deformities in the double helix that a mismatch causes). 2. mechanism of mismatch repair Repair enzymes scan and remove so it can be filled back in if there is DNA damage. 3. differences among insertion sequences, transposons and retrotransposons IS sequences are the edges that are inverse repeat sequences and are what causes the mobile element to be able to move by breaking the DNA backbone. If two are close together and there is some sequence in the middle we call this a transposon. And it can move from one place in the Genome to another. Retrotransposons are transcribed into RNA and then back to DNA on another part of the genome. 4. implications of insertion of mobile elements into DNA This means that Junk DNA will accumulate over time and that there is a risk of genetic disease or complications in gene expression whenever a mobile element moves as it changes the DNA code. 5. why transposons are not actually "jumping" genes Because they are never in the air, they transposition form one point on the genome directly to another. 6. basic structure of retrovirus genome “or provirus” contains the inverse repeat sequences on each end as well as three main segments. Gag gene pol gene and env gene (see page 206) essentially coding for viral proteins, reverse transcriptase and integrase and proteins associated with RNA core. Lecture 10: Origin of Variation pt. 2 difference between DNA damage and mutation DNA Mutation is a change in the double stranded sequence of NDA while damage is for example, a mismatch of base pairs. (UV light is also an example of damage. mechanism by which tautomeric shifts in DNA bases leads to alternative base pairing THIs is because the nucleic acids (ATCG) change their bond structure naturally and sometimes take on a slightly different form with a differently bonded reactive part and then will pair with the wrong base ie. A with C and T with G. This occurs naturally but not very often. This is because after a tautomeric shift if it is not repaired and the DNA replicates one of the strands of the semi conservative replication will have an SNP or a single pair mutation. So, it takes a full replication for the damage from tautomeric shifts to become mutations. mechanism by which unstable base analogues cause mutation Some chemicals are very similar to ATCG and can cause mutations by being replaced instead of the regular base pairs. They often fool DNA polymerase. They are usually unstable and dangerous. mechanism by which UV light damages DNA UV causes some T and T bases when next to each other to bond covalently between the carbons. mechanism by which UV-induced DNA damage can be repaired This is repaired by Photolayse and white light (Which is a protein that undoes the covalent bonding). Placental mammals do not have this function so they use the good olf cut and paste method which is less efficient. mechanism by which strand slippage gives rise to indel mutations Strand slippage gives rise to mutations because when there is a strand slippage and the strands separate, depending on which strand the slippage is one a addition or deletion can occur. types of damage caused by ionizing radiation possible implication of changing the location of genes in the genome This can cause geneticdisease and can also directly relate to how a gene is expressed, either not enough or way too much and can be deadly. typical structure of gene families Gene families are usually arisen from genes that are repeated and have the mutated to create similar functions and are generally placed fairly close together on the chromosome. PAX-6 and the HOX genes are good examples of gene families. reasons why gene duplication might be beneficial over evolutionary time This can be beneficial by creating gene families in the sense that a gene duplicates and now there is a potential for them to do slightly different function that for example, may be more tailored to each stage of development. They could also serve as a backup for mutations if it is a crucial gene. 1. mechanism of proofreading DNA polymerase double checks. 2. mechanism of mismatch repair Repair enzymes scan for abnormalities and correct errors. 3. basic structure of STR regions that makes them useful for DNA fingerprinting STR regions are regions usually composed of non-coding DNA which is repeated different numbers of times in different alleles for an individual. This allows for much variation between individuals and allows for specific DNA fingerprinting (except DNA in identical twins). 4. basic structure of gene families Gene families such as the HOX or Pax-6 genetic toolboxes are close together in the chromosome and regulate the expression of thousands of other genes. They are common amongst all animals and even many plants and some fungi, showing that these have been conserved by evolution for millions and millions of years. Lecture 11: Meiosis reason why meiosis I is "reductional" and meiosis II is "equational" Meiosis I is reductional because it halves the number of chromosomes in a cell so that the daughter cells are haploid. Meiosis II is equational because it keeps the same haploid value. changes in C and n during meiosis Cells start meiosis as diploid but the n value gets halved and the end being haploid. Cells start mitosid (being diploid) with a value of 4C, and after meiosis I they are 2C. After meiosis II they are C. mechanism of recombination during prophase The recombination mechanism in prophase is crossing over. role of cohesin and synaptonemal complex Cohesin is responsible for holding the two sister chromatids together and the synaptonemal complex occurs in meiosis and is responsible for holding the homologous pairs together. how homolgues pair in order for all non-sister chromatids to participate in recombination They lie “on top on one another” and are super imposed so that crossing over can take place at any point between the chromosomes. mechanism by which recombination creates new combinations of alleles This mechanism is crossing over and it causes new combinations of alleles to take form because the homologous pairs of chromosomes have different alleles and are not identical. So, by swapping parts of them new combinations appear. mechanism by which recombination creates copy number variation (CNV) This happens when there is an unequal crossing over between homologous pairs. Ie. A big chunk of one chromosome is swapped and a small chunk of the other is swapped. randomness of alignment of homologous pairs at metaphase I: This just means that regardless of the other homologous pairs each individual chromosome in a pair could go to either daughter cell (and the second of that homologous pair would go to the other). relationship between distance separating genes and the likelihood of recombination between them The closer genes are together on a chromosome the less likely it is that they will be separated in recombination. way in which meiosis can be thought of as a kind of DNA "repair". That is, how can you inherit mutations on both homologues of chromosome 6 but give a chromosome 6 with no mutations to your offspring? This is because of crossing over that the alleles can be shuffled. In lucky instances the mutations or bad alleles can all end up in one cell at the end of meiosis I and then there is potential for the mutations to not be passed on (the same is true for if they were isolated during meiosis II)mechanism by which errors in MI or MII give rise to aneuploid products of meiosis Non dysjunction occurs when a homologue fails to separate in meiosis I. This means that of the funal cells two will be n+1 and two will be n-1. A misdivision is when chromatids fail to separate in meiosis II this means that two of the final cells will be normal (n) and two of the cells will be n-1 and n+1 alternatively. 1. products of meiosis in animals vs. plants, fungi and algae In animals the product is Gametes in plants it is spores and in fungi/algae it is spores. 2. timing of meiosis in vertebrate life cycles It happens when the organism is producing gametes whether that be during most of the life (human males), or before birth (human females). 3. main differences between meiosis and mitosis: Mitosis creates genetically identical daughter cells which are still diploid; While meiosis creates genetically different daughter cells which are haploid. 4. characteristics of homologous chromosomes Homologous chromosomes are copies of each other as in the y carry the same genes however, they have different combinations of alleles of those genes. Lecture 12: Inheritance of Variation mechanisms that are, or are not, random with respect to generation of genetic diversity Crossing over is random. Mutations are NOT random. difference between somatic and germ line mutation with respect to evolutionary processes Somatic mutations are not expressed in the offspring because they are not turned into gametes. However, when there is a mutation in the germ line or gametes then that is passed onto the offspring because those are the cells that will eventually grow into a new individual. opportunities for genetic variation to be introduced into the germ line In mothers physical mutation from the eggs sitting around and being exposed to their surroundings for too long or During the stages of meiosis in either the father or mother or during the very early divisions of the zygote. way in which inheritance of polygenic traits show that inheritance is not "blended" This is because many genes contribute to one characteristic, so there are many factors influencing the expression of a single characteristic. Height it gives the appearance of being blended in actuality it is just the combination of many alleles. Ex. There is a large range of height because of the expression or absence of many different kinds of alleles. characterisitics of Mendel's work that set him apart as a genetic researcher He actually quantified the expression of genes and counted while assessing the probability of having a certain type of phenotype. This allowed him to create a basic model that holds true to this day components of Mendel's explanatory model Mendel’s law of segregation showing that traits did not blend. He said that for each organism has two alleles one inherited from each parent. He proposed the gene. Showed the statistical nature of inheritance. distribution of progeny, given parental genotypes in monohybrid and sex-linked crosses red and white eyed flies experiment. Know how X and Y chromosomes are distributed and how it effects the f1 and f2 populations. parental genotypes, given distribution of progeny in monohybrid and sex-linked crosses Same as above. Also for both do the basic punnett square and figure out all information about the crosses. It shouldn’t be hard. location of various alleles on homologues know where alleles are placed on the homologues. I.e. Same locus. segregation of various alleles during meiosis How alleles are segregated during meiosis. In crossing over, and in meiosis two where it splits again. number of different gametes produced, given parental genotype all combinations of alleles are created with one from each parent. 1. arrangement of genes and alleles on homologous chromosomes in a dihybrid organism The locations and Locus and how that works. 2. how independent assortment creates 4 different products of meiosis from a dihybrid parent Independent assortment means that all the alleles of a gene are assorted independently of everyother gene in order to randomize the combinations. 3. application of the sum and product rule of probability sum and product rule of probability. Just know them. Lecture 13: Inheritance in Populations general pathway of eukaryotic membrane protein production. Each of the Alleles will be transcribed into two different MRNA’s (carryi
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