Essential Knowledge 1.B.1

Cytoskeleton - only found in eukaryotic cells, this structure acts as muscle and skeleton for cells, aiding with movement and stability.

Mitochondria - eukaryotic cells aquired mitochondira via the endosymbiotic theory (A big cell ate a little cell but didn't digest it because the little cell could help it function better by producing energy for the big cell) and this membrane bound organelle produces evergy that is used by countless activities that occur within the cell.

Endomembrane System - this postal service of different materials a cell creates and uses consists of the nuclear envelope, ER, golgi apparatus, plasma membrane, as well as other organelles.

These conserved core processes and features support the idea of common ancestry for all organisms, because ALL eukaryotic cells have these features. This suggests that at some point in time, all organisms with eukaryotic cells originated from a single ancestor, and evolution/ natural selection lead to the 'birth' of new species.

Essential Knowledge 1.A.2:

Peppered Moth Questions

21.)

22.)
The color of the moth increases chance of survival because it allows the moth to blend into their surroundings, making it harder for predators to spot them. So, in a dark polluted forest, dark colored moths will survive better because birds cannot spot them.

23.)
Natural Selection is the process of evolution favoring the 'more fit to live' over the weak. This means that organisms that are better able to adapt to their surroundings, are more likely to survive and produce offspring. So in the case of a dark polluted forest that is home to peppered moths, the dark colored moths will be a greater percentage of the population than the light colored moths because the dark color increased chance of survival, allowing the moths to blend into their environment.

24.)
If there were no predators in the forest, peppered moths would not feel the pressure of natural selection because there is no force that is weeding out the 'weak'. As a result, the population will either stay the same, as there is no reason to favor any colored moth since there are no pressures acting on survival based on the ability to camouflage.

Using peppered moths, explain and justify how an evolutionary change in population is related to a change in the environment. What role do humans play in this change? What is the impact in the future of this change?
Take a look at the forest in which the peppered moth normally lives in, and observe the appearance of the trees and the appearance of the moths. The peppered moth lives in a light colored forest, and most of the population is light colored to blend in and hide from predators. But when such a forest starts to become polluted, and the trees start to turn dark, this influences the population to change in order for the species to continue to survive. Now, in this dark polluted forest, you will find dark moths in greater numbers than light moths. This is how an evolution change in population is related to a change in the environment. Humans play a role in this by unnaturally introducing materials in to the world that make it hard for species to survive, often driving them to extinction. The future of this change can eventually change the entire environment of the Earth, as well as lead to the extinction of humans. All species and all environments are they way they are, because they need to interact with one another in they way they do, in order for this Earth to exist as it does.

Brave New World?

Explain the key ideas that make PCR possible.

DNA must first be denatured through the use of heating and annealing, this is followed up by the extension of the separates strands of DNA, thereby replicating the DNA. This is repeated again and again. Since the DNA generated will be used as a template for replication, this is why PCR becomes exponentially amplified, as the number of DNA produced and uses as a template is growing exponentially.

Genetic Engineering Techniques

Briefly discuss the following genetic engineering techniques - include a model of each and explain how each can be used to manipulate DNA

Gel Electrophoresis

This is an indirect method to quickly analyze and compare genome. The use of a gel that acts as a molecular sieve. Separates nucleic acids or proteins by size. A current is applied through the gel, which causes the molecules to move accordingly depending on attraction. The end result has molecules sorted into bands by size, and this allows for the mapping and comparison of genetic material.   

http://sciencefair.math.iit.edu/techniques/gelelectrophoresis/

Plasmid-based Transformation

Plasmids [found in bacteria] are small circular DNA molecules that replicate separately from bacterial chromosomes. So, these units are very useful in carrying foreign DNA into cells, with the intent to insert a particular gene into the aforementioned cells. The end result of this, leads to the cells producing whatever protein is coded for in the plasmid DNA.

https://en.wikipedia.org/wiki/Transformation_(genetics)

Polymerase Chain Reaction (PCR)

This is a method to reproduce many copies of a specific segment of DNA. This three-step cycle involves heating, cooling, and replication. It serves to produce an exponentially growing population of identical DNA molecules.

https://www.quora.com/profile/Amina-Zaid

Restriction Enzyme Analysis of DNA

Enzymes are used to cut DNA to produce fragmented DNA that can be used for gel electrophoresis. This is very useful when comparing two different DNA molecules.

Lytic and Lysogenic Cycles

Compare and contrast the differences between lytic and lysogenic life cycles of a virus.

The lytic cycle is a reproductive cycle of a phage, that results in destroying the host cell. This cycle produces new phages by using the host cell to replicate itself. Once the phages have assembled within the host cell, they will digest and break through the host’s cell wall. The lysogenic cycle replicates the phage’s DNA and incorporates it into the DNA of the host cell. Every time the host cell divides, it will replicate this phage DNA along with its own DNA. These two cycles are connected, because a cell in the lysogenic cycle can be triggered to move into the lytic cycle and will start reproducing the actual phages. Phages that can do this are known as temperate phages, phages that can only utilize the lytic cycle are known as virulent phages.

https://sites.google.com/site/namoshomeworksite/ap-biology/virus

Viruses

Develop a model and explain the components of a virus.

There are various forms of viruses, these are small infectious particles consisting nucleic acid which is enclosed in a protein coat known as a capsid, and sometimes also an envelope membrane. Depending on the nucleic acid contained in the virus, it will either be a DNA or an RNA virus. Capsids can have various structures, as a result, can form different looking viruses.

Take a look at some different types of viruses below.

Mastering Biology | Pearson; Campbell Biology

Cancer Hands

Compare and contrast the role of oncogenes, proto-oncogenes, and tumor suppressor genes in cancer.

Oncogenes are cancer causing genes, and proto-oncogenes are normal cellular genes that are responsible for normal cell growth and division. So proto is good, once the proto is gone, we’ve got cancer on our hands. Not actually, I mean you can get cancer nearly anywhere.. ANYWAYS,

tumor suppressor genes are responsible for repairing damaged DNA, controlling cell adhesion, and inhibiting the cell cycle when necessary. They also prevent uncontrolled cell growth/division.

DNA Methylation and Histone Acetylation

Describe the impact of DNA methylation and histone acetylation on gene expression.
DNA methylation adds methyl groups to specific bases in DNA, which leads to turning off the transcription of some genes. This typically causes long-term inactivation of a gene. For example, the gene for humans to grow tails has been methylated, we only have a tailbone and cannot grow tails. Histone acetylation adds acetyl groups to the lysines in histone tails that are positively charged. [See “Wiggly Purple Guys” under Ch 16 & 17] This functions to loosen up the chromatin structure, so that transcription can be initiated. Also, methylation in chromatin can cause it to condense more. Phosphate groups added to methylated amino acids also can loosen up wound up chromatin.

Why Repressing Stuff can be Good

Explain the role of repressor genes in operons and why they are important.

Repressors genes are important for these segments of DNA code for repressor proteins. Repressor proteins are necessary for the proper functioning of operons, repressors make sure operons are only active when they need to be, and not otherwise.

Inducible vs Repressible

Compare and contrast an inducible operon and a repressible operon. Include an example of each.

Inducible: The lac operon is an example of an inducible operon. It is usually off, but can be induced to turn on when needed. In these operons, there is an active operon always attached to the operator of the operon, until an inducer attaches to it and causes it to change shape and detach. This allows for RNA polymerase to go through reading the operon, to create the protein it codes for. The lac operon codes for enzymes that are used to hydrolyze and metabolize lactose. So, this operon will only be active when there is lactose present. When lactose is present, allolactose is the inducer which will inactivate the repressor attached to the operator.  

http://biology-forums.com/index.php?action=gallery;sa=view;id=11503

Repressible: The trp operon is an example of a repressible operon. It is usually turned off, but can be repressed when it is not needed. These operons are turned off by the binding of a repressor protein, that may need a corepressor in order to be activated, to the operator of the operon. In the trp operon, tryptophan is coded for. When there is tryptophan present in the cell and does not need to be synthesized, this acts as a corepressor and causes the operon to be blocked and turned off.

http://www.slideshare.net/kindarspirit/18-regulation-of-gene-expression

Oper-on or Oper-off?

Describe the structure of an operon. Include a model with your discussion.

An operon is a segment of DNA that includes an operator, a promoter, and a stretch of functionally related genes. Operons are regulatory switches for the production of specific proteins that are only needed during certain times.

https://diaryofanalevelstudent.wordpress.com/2013/02/23/the-lac-operon/

Frameshift

Develop a model which explains how point and frameshift mutations can impact a protein.

Frameshift mutations include deletions and additions. With the addition/deletion of one nucleotide pair in a gene, this can cause a shift in an entire series of codons, leading to the creation of an incorrect or malfunctioning protein.

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Modifying RNA

Explain how eukaryotic cells modify RNA after transcription and why it is necessary.
Both ends of the transcript are altered to include a 5’ cap on the 5” end, and a poly-A tail on the 3’. These modifications facilitate the export of mRNA from out of the nucleus into the cytoplasm, protect mRNA from hydrolytic enzymes, and help ribosomes attach to the 5’ end of the strand. Enzymes that modify the original RNA transcript into mRNA within the nucleus also cut out interior sections of the molecule before allowing it to exit the nucleus.

Process of Transcription and Translation

Develop a model and explain the process of transcription and translation.
In an eukaryotic cell:

Transcription occurs in the nucleus of the cell. There are three steps; initiation, elongation, and termination. RNA polymerase attaches to the promoter segment of DNA and moves downstream, laying down corresponding RNA bases along the template strand of DNA in the 5’ to 3’ direction. Once the segment of DNA has been transcribed, the RNA polymerase detaches and the DNA rewinds, leaving a completed RNA transcript.

Mastering Biology | Pearson; Campbell Biology

Translation typically occurs in ribosomal units that are free floating within the cytoplasm. mRNA is fed through the ribosomal complex, and tRNA brings corresponding

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Gene Expression, Transcription, Translation

Compare and contrast the key terms gene expression, transcription, and translation.
Gene Expression: Process that includes transcription and translation; this is the process by which DNA directs protein synthesis

Transcription: Creating RNA from DNA; mRNA coding

Translation: Creating a polypeptide using information coded in mRNA

Wiggly Purple Guys

Develop a model and explain how DNA is packaged into a chromosome.

DNA is wound around histones, and these histone packages condense to form a chromosome.

Mastering Biology | Pearson; Campbell Biology

Mastering Biology | Pearson; Campbell Biology

Replication, Transcription, Translation

Compare and contrast the difference between replication, transcription, and translation.
Replication: Copying DNA

Transcription: Creating RNA from DNA; mRNA coding

Translation: Creating a polypeptide using information coded in mRNA

Replication Bubble

Develop a model which explains the major steps to replication, specifically a replication bubble.

To form a replication bubble, Helicase will come in first at the origin point of said replication bubble, and will unwind the two strands by breaking hydrogen bonds between nitrogenous bases. Single-strand binding proteins keep the fork open, and topoisomerase makes sure the DNA strands do not become damaged from the stress of unwinding. Topoisomerase does its job by breaking and swiveling pieces of DNA, which will later be rejoined. Next, primase comes in and places an RNA primer at the 5’ end of the leading strand, and on the 5’ end of each Okazaki fragment of the lagging strand. This allows new DNA to be created in the 5’-3’ direction. DNA polymerase III places new nucleotides on the parental DNA that complements the template in the 3’ to 5’ direction. So, the new DNA is formed in the 5’-3’ direction, but the new nucleotides are placed starting at the 3’ end of the old DNA strand that is being used as a template. DNA polymerase II removes any RNA nucleotide primers that were placed in the leading and lagging strand(s), replacing them with DNA nucleotides. Lastly, DNA ligase will clean up the disjointed areas and make sure all the Okazaki fragments, breaks in DNA sequencing, etc. are glued and smoothed out. At this point, the DNA strand will be fully replicated. Multiple replication bubbles occur at the same time, which is why DNA can be replicated so quickly, otherwise the time it would take for this to happen via one single replication bubble would be too great.

Mastering Biology | Pearson; Campbell Biology

Structure of DNA and Nucleotides

Explain the structure of DNA and nucleotides. Include a model of your explanation.

DNA is shaped as a twisted ladder; a double helix. Hydrogen bonds connect corresponding nitrogenous bases with one another, forming the rungs of the ladder.

Mastering Biology | Pearson; Campbell Biology

Rosalind Franklin took a photograph of the X-ray diffraction of DNA. This photo is what helped Watson and Crick understand that DNA has a helical shape, and the width of this helix suggested that the molecule is made up of two strands. The width also provided a basis which allowed Watson was able to estimate the spacing of nitrogenous bases along DNA.

http://biology-forums.com/index.php?action=gallery;sa=view;id=398

Nucleotides are subunit of DNA that build up the twisted helical shape, each nucleotide consists of a sugar-phosphate group attached to a nitrogenous base.

Mastering Biology | Pearson; Campbell Biology