Chapter 17 Reading Journal

What are the three steps of transcription?
First it starts with a transcription unit this is the whole strand of DNA that is transcribed into RNA. 1. Initiation is when the RNA polymerase binds to the promoter. In eukaryotes it must first receive help from transcription factors so that the polymerase can bind. 2. Elongation: is when the polymerase moves along the strand of DNA producing a strand of RNA with the complementary sequence. 3. Termination: the terminator sequence of DNA causes the RNA to be released and then it detaches ready for modification before translation.

What is the difference between a codon and anti-codon and what do they do?
A codon is a sequence of three bases on an mRNA molecule that will be translated into a protein. The anti-codon is the complementary strand on the tRNA that allow the codon to bind. Codons come into the tRNA at the A site where amino acids are added and then the amino acids from the codon in the P site to the codon in the A site. Then the Codon in the A site shifts to the P site while that codon moves to the E site and exits so that the whole process may start again.

What are the different types of mutations?
Point mutations change only one base in a sequence and they account for either missense or nonsense mutations. Missense is when the codon still makes a protein though that protein may be dysfunctional. Nonsense is when a normal codon is turned into a stop codon so that no protein is made. Insertions and deletions are the adding and removal of certain sequences, if these come in threes they are often not very harmful but if not they can cause a frame shift and through off all the codons down the line.

Facts:
-Mutagens are substances that cause mutations in DNA sequences
-In modification mRNA gets a 5’ cap and poly-A-tail
-RNA splicing takes out the introns which are the portions of the RNA that don’t code for anything so they are removed
-Many codons code for the same proteins even when they have a different last base this is called the wobble effect
-The template strand is the strand of DNA that the polymerase binds to in order to make the RNA strand



This is the codon table, used to determine what amino acid a certain codon makes and then from there what amino acid sequences and therefore proteins a certain strand of DNA or RNA will produce once translated.

Summary:
DNA codes for RNA which then translates into proteins this is how something goes from being a gene to being expressed, if the protein of a certain gene isn’t made then that gene isn’t being expressed. First DNA is transcribed into a complementary RNA sequence after the RNA is processed and modified it is translated into a protein although some RNA is never translated but still useful in its transcribed form. RNA polymerase allows the synthesis of RNA after it attaches to the promoter. Translation uses a ribosome small and large subunit and tRNA that allows the codons to attach to the anti-codon. Mutations with the DNA cause problems in the organism because they effect protein production by either stopping it or changing it into different proteins that aren’t as useful to the cell. RNA doesn’t have to be modified in bacteria like it does in eukaryotes because it doesn’t have to be packaged to pass the nuclear envelope.

Chapter 18 Reading Journal

What are oncogenes and proto-oncogenes?
Proto genes are the ones that code for normal cell growth and once a mutation occurs in these type of genes they turn into oncogenes where they produce more proteins than normal and become cancerous. Though cancer can also be a result of a decreased function of genes that inhibit cell division.

What’s the difference between a repressible and inducible operon?
Repressible operons are typically turned on typically building some type of molecule but when enough of that molecule is produced it binds to the repressor activating which then binds to the activation site and block the production of that molecule until the concentration goes down again. Example would be the lac operon. Inducible operons are typically off but the production of a certain other molecule (inducer) will bind to the repressor deactivating allowing the activation site to be open and the production of whatever this gene makes which would typically be something used to break down a molecule. An example of this would be the tryp operon.

What is DNA methylation and histone acetylation and what is the function for the cell?
DNA methylation makes a chromosome more tightly packed because it makes the DNA more attracted to itself therefore limiting gene expression. Histone acetylation is when amino groups are added to histone proteins decreasing the attraction and making them unwind more. Genes in an area like this are more likely to be expressed. The mechanisms of cell specializing utilize these two types of increased or decreased expression.

Facts:
- Cell differentiation is how cells go from being blank in the zygote to being specialized to take on specific functions in the organism
- Morphogenesis is how cells organize into things like tissues and organs
- Apoptosis is the programmed suicide of a cell that occurs once DNA is too damaged
- The P53 gene is an important tumor-suppressor meaning that it prevents cancer by regulating the cell cycle
- The operon has the operator, promoter, and the genes of the operator all within it




This shows how through alternate splicing the same gene can give rise to several different codons and therefore proteins. In this way gene expression can help to preserve space within the genome by using one gene for several uses by just expressing it different ways.

Summary:
Operons are used so that cells don’t use their energy making molecules they don’t need at that exact moment. These can be either up repressible inducible operons and they are like off and on switches for a particular gene. Gene expression is regulated from the time a cell is in the zygote well into its developed life through methods such as alternate splicing, mRna degradation, chromatin modification, and protein processing. The use of many non-coding RNA molecules is to help with gene expression. Cells differentiate so that only certain genes this is the reason that liver cells and skin cells are not the same they different regulations of gene expression aid with this.

Chapter 19 Reading Journal

What is the difference between the lysogenic and lytic life cycle?
In the lytic life cycle the virus attaches to the cell inserts its genome replicates many times until there are so many new viruses that they bust out of the cell killing it in the process this is quick and effective because there are many new viruses in a short amount of time but slightly inefficient since it also kills the host. In the lysogenic life cycle the virus enters its genome into the host’s genome so that the cell continues functioning as normal except that it is also producing new viruses that are released without killing the cell this relationship can be relatively symbiotic for a while.

What is a retrovirus?
This is a virus that uses RNA as it’s genome and uses reverse transcriptase to convert the RNA into DNA and then implement it into the genome of the animal cell its infecting. HIV is this type of virus and due to the complex nature of using reverse transcriptase and its ability to change its markers on the outside of the cell so often allows it to go undetected for long periods of time.

What are prions and viroids?
Viroids are circular RNA molecules fairly short that infect plants most often they are able to reproduce within host cells. Even though they don’t code for proteins they seems to effect regulatory genes and mess up their function. Prions are misfolded proteins that cause the other proteins they encounter to misfold as well. They often cause brain disorders.

Facts:
-A viruses host range limits the type of cells they can infect and typically the host range in very small
- Viruses aren’t considered alive because they cannot reproduce without a host
-The capsid is the protien shell that encases the genetic material of a virus
-Viruses that infect bacterial are called bacteriophages or just phages
- As humans we come in contact with viruses on a daily basis and if it weren’t for our cells ability to recognize them as foreign we would all be in grave danger




This is a diagram of the basic structure of the virus with the genetic material enclosed in the capsid the tails are used to attach to cells and the sheath to be injected so that the genetic material will be put into the host cell.

Summary:
Viruses use enzymes and ribosomes along with a genome to utilize a host cell in order to reproduce. They either use the lysogenic or lytic life cycle to reproduce. Viruses either use RNA or DNA as their genetic material if they use RNA they have to use reverse transcriptase to turn it into DNA first. Viruses can infect all sorts of animals as well as plants. Outbreaks of newly evolved viruses that humans don’t have immunities to yet can be very dangerous.

Chapter 20 Reading Journal

What is PCR?
This is a way to copy small portions of DNA in a test-tube. It is used when the DNA sample is impure, because when this is the case this method copies strands more quickly than cloning could.

What is the process of PCR?

First the DNA is heated so that the strands separate. Then the DNA is cooled so that primers designed to adhere to certain portions of the strand attach to their complementary strand. Once the temperature is raised only slightly this time polymerase binds and new DNA is synthesized this marks the end of cycle one. Cycle two starts by heating and denaturing the newly formed DNA strands. Primers bind to all four strands once the temp has cooled and then new strands are formed again. This same cycle continues forming more DNA molecules and the more cycles the higher percentage of the molecules are of the desired portion of DNA.

What are GMOs and how do they relate to our everyday lives?
This is a genetically modified organism this can either be through artificial selection or even using genes from another species. These organisms whether animals or plants are often used for food. Most of the agriculture in the US is made of GMOs but it is not required that they are labeled as such. In other countries especially European ones these foods have been banned because many are concerned that since they are not natural they also aren’t healthy to consume. Some are also concerned that these organisms will take a toll on the environment and crossbreed with the natural versions of similar organisms.

Facts:
-Scientists are using stem cells to research regulatory genes and various diseases since stem cells are sort of a blank slate cell.
- Totipotent cells are mature cells that can go back to an un-differentiated state and then become different specialized cells
- Scientists are now able to clone entire organisms as well as single cells
- Gel electrophoresis measures the size and charges of different dna sequences because they arrange themselves differently within the gel based on these factors
- A genomic library is the complete set of plasmid containing cell clones each containing segments from the original genome.


This is the process of magnifying a small bit of DNA as describes in questions one and two. The process of denaturing and recombining to duplicate a selected portion of the strand over and over until it is more accurate.

Summary: DNA cloning and other DNA technologies are used to study genomes and develop new products and possibly studying diseases. Eukaryotic DNA can be cloned within a bacterial plasmid by splicing it and then inserting the strand of DNA wanted then the cell clones itself making more copies of the strand. DNA is analyzed through methods such as gel electrophoresis, DNA sequencing, and analyzing gene expression and function. Cloning and other DNA technologies have uses in the medical field, in crime scene investigation, environmental cleanup and even creating new organisms for food sources.

Chapter 21 Reading Journal

How do the genome sizes vary between species?
Some animals have relatively large genomes with few genes. For instance flies have a genome twice the size of a nematodes, yet the nematode has over 6,000 more genes than a fly. Humans have a genome 10 times the size of both these animals but they have about the same number of genes as the nematode. The reason this can still provide the human with a large enough variety of proteins is that many of these genes are able to be spliced into different proteins through the use of alternate splicing of exons.

What are the three stages of genome sequencing?
1. Linkage map: markers are found all along the chromosomes recombination frequencies are used to determine the distances between them. These markers can be either genes, STRs or RFLPs.
2. Physical map: a physical distance between markers is determined. Then fragments of DNA are replicated so they can be overlapped to determine the order of them within the chromosome.
3. DNA sequencing: The ultimate goal is to know the nucleotide sequence of each chromosome. Now there are machines and computer programs that are able to help with this process

What is the effect of hox gene expression during development in crustaceans and insects?
Over time through the evolution of four different expressions of hox genes the different body shapes of these organisms has developed. This can be seen in the difference of body shape of the shrimp and grasshopper. The hox genes expression is responsible for morphological differences of species.

Facts:
- evo-devo is the study of evolutionary development biology
- Multigene families are collections of two or more identical or very similar genes
- In the human genome only 1.5% of it actually codes for rRNA and tRNA
- Genomics is the study of a whole set of genes within a species
- Bioinformatics is the application of computational methods to storage and analysis of biological data



This is a mapping of protein interactions. This is the statistically likely interaction between all the proteins found in an organism as predicted and mapped by a computer program.

Summary:
Scientists have begun to map genomes in order to determine things about animals their relationship to each other and the evolution of them. Databases and Internet tools help to pick out the sequences within a genome that actually code for a protein or the likely hood that one will. Some genomes are larger than others with smaller amounts of coding DNA this is a result of alternate splicing, transposable DNA, and repeating sequences. Alternation within structure of chromosomes, duplications, rearrangement of genes ect give the variety of genes that allows for evolution and study of these changes help the trace of evolution. The difference between expressions of genes such Hox genes change the developmental stages of organisms and change their body shapes.

Chapter 22 Reading Journal

What where the main theories about life on earth before Darwin?
Greek philosophers believed that all organisms were perfectly suited to their environment and they were organized by a scale of complexity called “scala naturae”. Then many people believed in creation that all organisms were made by god for a certain purpose. George Curvier believed that all changes in living organisms happened because large natural disaster killed off certain species but no new species were being created “Catastrophism”. James Hutton believed that everything changed gradually and the same mechanisms of change were still operating “gradualism”. Charles Lyell proposed uniformitarianism was influence by Hutton said that there was a constant level of change in the geological features of the earth. This meant the earth had to be very old and influenced Darwin in his idea of evolution being changes with species over time. Lamarck believed in a sort of evolution but he believed that the characteristics organisms obtained during their life could be passed along and the features not used would get weaker with the generations.

What is Darwin’s general theory?
Natural selection/ descent with modification
He believed that most organisms would reproduce until they overused their environmental resources and therefore those best suited to their environment would have a better chance of surviving to pass along their inherited traits to offspring. Because of this certain traits would become more prominent while others would leave a population. A population was the smallest unit of evolution and this also meant that all creatures were related to each other by a common ancestor.

What are Homologous structures, analogous structures and vestigial organs?
Homologous structures are structures that are the same in different species but they have different functions this shows a common relationship between all life. Vestigial structures have little to no use in a species but they are left over from their ancestors so they are still present. Analogous structures shows no relationship between organisms but are rather similar structures that arose from different species evolving to similar environments separate from each other.

Facts:
- Covergent evolution- is when organisms evolve separately to similar environments
- Biogeography- the geographic distribution of species this gives a lot of evidence for evolution
- Endemic species are those found only in a specific location and nowhere else in the world (typical to islands)
- Artificial selection- when humans breed animals for desired characteristics
- Darwin believed in decent with modification and because everything came from a common ancestor it could be organized into a tree of life



This shows how the same bones are used for different functions amongst mammals the homologous structures also show that all mammals are related in some way all the way from the bat to the human.

Summary:
There were many different theories about life on earth and the changes of the earth itself. The theory of evolution had been proposed by Darwin came up with a mechanisms through which it would be plausible. He went on a voyage in the Beagle and studied the birds on the Galapagos Islands and their common relation to each other and came up with the theory of natural selection. Much evidence such as fossil record, direct observation (bacterial resistance to drugs), homology, and biogeography supports the theory of evolution.

Chapter 23 Reading Journal

What maintains genetic variation amongst organisms?
Variation is maintained in some ways by having two alleles determine the singular phenotypic expression. Geographical separation between populations produces more variation by evolving to different environment. Mutations give population’s new alleles to work with and sexual recombination and fertilization is also accountable for genetic variation.

What is the Hardy- Weinberg equation/ assumptions and how is it used?
P+Q=1 P^2+ 2pq + q^2=1 P= % of dominant allele q= % of recessive alleles P^2= homo-dominant 2pq=heterozygous q^2= homo-recessive. Assumes that these ratios will remain the same so long as the population meets the following criteria: 1. Large population (no genetic drift) 2, Isolation (no gene flow) 3. No net mutations 4. Random mating (no sexual selection) 5. No natural selection. This is used to measure the rate at which a population is evolving because if it defies these criteria the ratios will be changing and therefore we can deduce that it is evolving.

What are the different mechanisms for evolution?
Natural selection- where certain characteristics that benefit an organisms in relation to their environment increase in frequency because of their higher survival rate.
Genetic Drift- Allele frequencies change at random based on a smaller population either most of it dying out or a small group being separated from the rest
Gene Flow- The movement of certain alleles in or out of a population because certain organisms with their gamete move in or out. In plants this can happen merely from the wind blowing
Facts:
- Genetic drift can occur in one of two ways bottleneck effect (natural disaster kills off most the population or founders effect (small group within the population gets separated from the whole)
- Natural selection is the only evolutionary mechanism that makes an organism more suited to their environment
- Balancing selection is when two variations of genotype are maintained through selection
- Neutral variation occurs when mutations cause neither a positive or negative effect
- Sexual selection often encourages phenotypes that have nothing to do with the organisms ability to survive in their environment.



Directional selection is when the environment favors the extreme of a characteristic so the trend moves towards the extreme. Disruptive is when the environment favors both extremes so the trend moves away from the average in both directions. Stabilizing selection is when the average makes for more successful organisms so the trend moves towards the average and away from both extremes.
Summary: Genetic variation is rampant there is variation within a population, between populations, between the organisms in different geographical locations ect. Mutations introduce new alleles into a population but the most genetic variation within a population comes from crossing over, independent assortment, and fertilization. Populations of species have a gene pool, which is the combination of all their alleles when the frequencies of these alleles are changing evolution is occurring. The hardy-Weinberg principle assumes that allele frequency is remaining the same and is used to compare to the actual and measure evolution rates. Allele frequencies are changed by: natural selection, genetic drift, and gene flow. Natural selection is the only change in a allele frequency that is guaranteed to improve the population, however it will never make the perfect organism because it has to work with the variation already present it doesn’t create new characteristics.