I posted it on Intense Cogitation solely as an exemplar. Using ideas or words from this without acknowledgement is plagiarism. If you have any questions about this, please leave a comment.

The Canadian short story “Exiled” by Shizuye Takashima beautifully illustrates the tragic story of Japanese-Canadian internment during World War II. The protagonist, a female Japanese-Canadian child, describes this riveting tale through a series of journal entries from 1942. These journal entries are organized into three seasons: spring, summer and autumn. At the same time, the protagonist changes in terms of complexity. This causes one to wonder: what does the author achieve by linking character development to seasons? Takashima uses the seasons to reflect on the rise and fall of the complexity of the protagonist, which draws the reader into this captivating story. It also reinforces the theme that all good things come to an end. In terms of the protagonist, spring represents the birth of her identity, summer reflects the growth of her identity, and autumn highlights the slow decay of her identity. Essentially, each season illustrates a pivotal moment in the protagonist’s life.

Spring is a season of birth. It is the season where everything comes to life—plants and animals are born, and a temperate climate returns. This connotative meaning of spring makes it an excellent parallel for the birth of the protagonist’s identity.

The first journal entry from March 1942 exemplifies this idea; it documents the emergence of the protagonist. Although the child appears to be simple and flat at the beginning, Takashima does this to highlight the fact that there is room for progress. Near the beginning of the entry, she states, “Mass evacuation for the Japanese!” (44). This illustrates the simple mentality of the child, since she does not realize the severity of the situation. The internment process is referred to as an “evacuation” (44), which is extremely ironic. The child describes the forced relocation of Japanese-Canadians with a word that has a positive connotation, highlighting her simple understanding of the issue at hand. Her poor grasp of the world around here is exemplified through the disparity between her views on relocation and the views of others. She notes that “The older people are very frightened. Mother is so upset; so are all her friends. I, being only eleven, seem to be on the outside” (44). Evidently, the protagonist’s lack of depth manifests itself in her reaction to the situation at hand; she does not realize why everyone around her is acting this way. In addition, her use of simple diction in the passage above further reinforces her lack of complexity. Overall, the author portrays the protagonist as a rather clueless child, but this allows her to have room for growth.

Growth occurs in the following journal entry, much like the appearance of new leaves on a tree. The protagonist begins to develop a sense of self, which is a sign of sophistication. She watches her father board the train “at the train station” (44), and notices that her mother is silent. She reacts with firm determination: “I look at her. I see tears are slowly falling … I turn away, look around” (45). At last, the main character appears to be actively responding to events happening around her instead of merely listing the facts. In addition, she appears to be developing a sense of self. Takashima conveys this burgeoning self-identity with the repetition of the word “I” at the beginning of the sentences mentioned above. This is significant since she rarely referred to herself in the previous entry. Evidently, the protagonist is becoming increasingly complex, as demonstrated by her blossoming sense of self and hints of independent action. In essence, the author gives the reader some glimpses of the child’s complexity, which makes the story even more gripping.

Although both of these journal entries are relatively devoid of details of spring itself, the essential point still remains: the protagonist is becoming increasingly dynamic, which is consistent with the connotative meaning of spring. However, the lack of details about spring may be a literary feature. This lack of information about the setting likely reflects the protagonist’s flatness at the beginning of the story. Nevertheless, the protagonist begins as a simple, flat character, and later becomes a budding plant that is ready to develop into a truly complex character.

After spring comes summer, a season in which the hottest and longest days of the year occur. Since summer appears to be the season with the most intensity, it is possible that the epitome of character development may occur in this season for the protagonist.

The first journal entry in this season involves the destruction of the world around the protagonist, and her development regardless of that fact. She notes that David, her brother, is “taken away” (45). As he leaves, she wonders “what [David] thought as his time came to leave” (45). This clearly shows that the main character is able to comprehend what is happening around her, and that she is beginning to understand the plight of others, making her less egocentric relative to the previous section. Moreover, she mentions, “my house is empty. What we can sell, we do for very little money … We are not supposed to own anything! The government takes our home” (45). The repetition of “we” clearly shows that she is realizing her place in her family. Along with her reaction to David’s departure, it is evident that she now understands that the events happening in the world are having a direct effect on her and her family. The short, choppy sentences in the previous excerpt reinforce the description of the harsh environment around her, making her progress all the more remarkable. The destruction of the world around the child is intended by the author; it causes her to face difficult challenges, which forces her to adapt by being more knowledgeable and complex. Evidently, the author’s ironic use of a crumbling environment in a season of prosperity forces the protagonist to be more complex.

The author then proceeds to thrust her into an even more disturbing environment: the Exhibition grounds. Takashima’s powerful use of imagery highlights the protagonist’s growing complexity and limitations. The reader is immediately immersed in an atmosphere of despair; instead of “bright balloons and sugar candy”, the protagonist and her family are greeted with “tension and crying children… [along with] the unmistakable foul smell of cattle” (45). Japanese-Canadians are being detained on this site, which used to house animals. The sensory input overloads the protagonist, and she wants to “turn and run” (46). She likens the Exhibition grounds to “the hell-hole [her] Sunday school teacher spoke of with such earnestness” (46). Although the protagonist is becoming increasingly sophisticated, there is only so much that she can handle; Takashima uses this scene to illustrate the full extent of the child’s emotional capacity. At the same time, this shows how far she has progressed; in spring, she would not have acted in such a dynamic fashion. Afterwards, her encounter with Mrs. Abe makes her uncomfortable again. When “a curious head [poked] in from the drawn, frail curtain” (46), Mrs. Abe becomes extremely angry, and this rage accidentally manifests itself into a glare aimed at the child. As a result, she “[begins] to feel uncomfortable” (46) and leaves. Yet again, the growth of the protagonist is reflected in her reaction to uncomfortable situations; instead of being passive, like in spring, she now actively reacts to external stimuli and develops emotional responses. Takashima’s clever use of an unnerving environment clearly forces her to bring complex aspects of herself to the forefront.

Although both of these journal entries do not necessarily convey a sense of summer, there are still references to summer hidden in the background. The day of the Exhibition grounds visit is described as being a “very hot summer day” with a “strong, summer July sun” (45). This foreshadows the protagonist’s growth during that day. Like the sun, the child had an extremely strong day in terms of character development—her reaction to a strange environment was explored, and previously unknown aspects of her character were revealed, such as her emotional side. There is unmistakable growth in the development of the protagonist, and this growth is clearly mirrored by the fierceness of various aspects of summer, especially heat.

However, the protagonist begins to decline in complexity as autumn comes, since it is a season of slow, but gradual decay. The beginning of the end is foreshadowed: her family is waiting for “[their] notice to go to the camps.” (46). Likewise, a similar fate awaits the protagonist.

The first entry of autumn involves the protagonist’s escape from regular life. She joins her sister Yuki in watching a movie, which is an atypical event. The curfew mandates that “all Japanese have to be indoors by ten P.M.” (46), and she and Yuki have to hurry home when the movie finishes. As they sprint home, Yuki refers to her as “Shichan” (46). In Japanese, the suffix “chan” is a honourary term for females only. Thus, the protagonist is female. By revealing the gender of the character, Takashima removes a layer of complexity—no longer is the protagonist shrouded in a fog of uncertainty and mystique. After this riveting adventure, Shichan escapes reality yet again by retreating into isolation. She looks outside the window and notices that “one by one the lights in the city vanish” (47), which can be interpreted as a metaphor for her gradual decline into simplicity; lights are often associated with ideas or intelligence. In both these instances, Shichan relinquishes control, much like a leaf falling from a tree in fall. Clearly, her deterioration parallels the slow decay that happens in autumn.

By the last journal entry, titled “An end to waiting”, Shichan has come full circle in terms of character development—she is right back where she started. When she visited the Exhibition grounds, she saw firsthand how horrific the living conditions were at a Japanese internment camp. However, she is excited about going to an internment camp. She claims that it is due to her reunion with her father, since “families will be back together” (47) at the camp, and reassures herself with the thought of a scenic view from the camp. She feels “secretly happy for [she loves] the mountains” (47) and reassures herself that a lake will be a suitable replacement for “the roaring sea” (47). Her reaction to prison camps resembles her reaction to relocation in spring, suggesting that she has lost the complex identity that she has fostered. The sheer insanity of Takashima’s writing at this stage encourages the reader to read more, in order to rationalize what they have just read. This burst of optimism in the face of such an ominous fate is similar to the last gasp of air that a person takes before they die: only in this case, it is the complexity of the protagonist that is dying. Amazingly enough, this entire entry is still consistent with the season of fall: the protagonist’s complexity has decayed past the point of no return.

The idea of autumn is clearly conveyed in both of these entries, as the protagonist becomes increasingly simplistic until she comes full circle. However, autumn is nearly described as being similar to summer. According to Shichan, the “fresh autumn air feels nice” (47) and the “sun’s warm rays reach [them]“. Instead of descriptors that illustrate cold and decay, Shichan chooses to use words that illustrate warmth and happiness. This could be attributed to the fact that autumn is similar to summer in this story, since both seasons involved significant character development, albeit in different directions. Nonetheless, the general idea of fall is reflected in the character’s actions.

Although descriptions of the seasons themselves may not have reflected the character of Shichan very accurately, the idea behind each season still generally mirrored the character. The protagonist developed a rudimentary identity in spring, expanded that identity in summer, and lost that identity in fall. Essentially, the character came full circle, reinforcing the theme that all good things come to an end. This theme is reinforced by the destruction of the protagonist’s once-glorious environment and her eventual detainment at a Japanese internment camp. Overall, Takashima transforms a complex tale of Japanese internment into a simple and engaging story of a girl in British Columbia by using the seasons as a mirror of the characterization of the protagonist.

Just a quick post: I came across a wonderful English teacher’s website that has many resources and sample papers for IB English Paper 1 and Paper 2, for both HL and SL. If you click on Paper 1 or Paper 2 on the left side of his website, you will see grading rubrics, examiner’s reports, useful tips, step by step guides, and sample essays.

Here are some quick links to some resources you may find useful on Intense Cogitation:

• Tips for IB English Paper 2
• Writing a Commentary
• TPCASTT – A Method of Analyzing Poetry
• Qualities of an Aristotelian Tragic Hero
• (love song, with two goldfish) – analysis of May 2010 paper 1 commentary

Shakespearean play resources:

• Oedipus: The Tragic Hero Readers’ Theatre Script
• Hamlet by William Shakespeare: Act I Commentary Outline
• Analysis of the Significance of Cameo Appearances by Minor Characters in “Macbeth”

Death of a Salesman:

• Key Quotes, Ideas and Themes in Death of a Salesman
• Death of a Salesman Readers Theatre

Other plays/stories:

• Short story: The Chmarnyk: Water Imagery and Pathetic Fallacy
• Short story: Use of the Seasons as a Mirror of Character Development in “Exiled” – IOP script
• Poem: Sonnet XXVIII (My Letters!) by Elizabeth Barrett Browning — A Presentation
• Novel: A Candid Discussion on “The Handmaid’s Tale”
• Novel: A Political Novel: One Day in the Life of Ivan Denisovich [essay]
• Novel: Analysis of Anita Desai’s “Fasting, Feasting” [Readers Theatre script]

Comedy:

• The Keats Enigma
• How to Kill A Mockingbird

Introductory Statistics Midterm 1 Sheet (PDF)

Introductory Statistics Midterm 1 Sheet (docx)

This cheat sheet was for my first introductory statistics midterm. We were allowed to bring 1 page, double-sided (‘cheat sheet’) into the exam with any formula, example or definition. It’s somewhat condensed, so it might be a bit confusing to understand. Feel free to customize it for your class. Please keep the credit to Intense Cogitation.  It should be useful if you are studying for IB Maths (for the statistics portion of the syllabus) or a 1oo-level statistics course.

The sheet has about 1700 words at font size 8, with page margins of 0.25 inches. If your printer cannot print 0.25 inch margins, you may have to edit the sheet. If the text is too microscopic, you can make it larger, but do note that the text will exceed 2 pages. I have included both versions (PDF and docx) in case either file format doesn’t work.

Main topics covered:

1. Basic statistics definitions / qualitative vs quantitative data
2. Measures of centre – range, median, mode, mean, variance, standard deviation
3. Bivariate data, regression line calculations
4. Probability – definitions, permutations, combinations, union, independent, dependent, total probability, conditional probabilities, Bayes theorem
5. Probability distributions (mostly discrete)- binomial, Poisson, hypergeometric, continuous random variable

If you have any comments, let me know!

Macroeconomics Final Sheet (docx)

For my introductory macroeconomics final, we were allowed to bring in 4 pages of formulas and definition (‘cheat sheet’) for our final exam. The class was for Canadian macroeconomics, so there may be references and allusions to unfamiliar institutions. I’m not sure if you’ll find it helpful because I really condensed it for my needs, but feel free to customize the sheet so it it’s suitable for your class. Please keep the credit to Intense Cogitation link in the file.

Main topics covered:

1. What is economics?
2. Economic markets
3. Macroeconomic cycles and growth
4. Unemployment and inflation
5. Expenditure and production
6. The Multiplier
7. The Aggregate Supply, Aggregate Demand model
8. Understanding Growth, Unemployment, Inflation and Cycles
9. Finance, Saving and Investment
10. Money and the Financial System
11. Exchange rates and international finance
12. Government budgets and fiscal policy
13. Bank of Canada monetary policy

The sheet has about 8500+ words at font size 5.5-6 on 2 pages, double sided (4 pages) with 0.25 inch margins. If your printer cannot print 0.25 inch margins, you may have to edit the sheet. I also recommend printing it in colour so it’s easier to see some of the graphs. If the text is too microscopic, you can make it larger, but do note that the text will exceed 4 pages. I have included both versions (PDF and docx) in case either file format doesn’t work.

NB: The graphs in the file are property of their respective copyright owners. They are used for demonstration/educational purposes only. Any infringement is not intentional.

If you have any comments, let me know!

May 2012 IB students: good luck on your IB exams!

Salutations from everyone at Intense Cogitation, the most popular IB student blogs on the Internet! We have a wide range of content, including university course notes, university course study guides, IB advice, IB notes, university help, technology-related posts, and much more. We’re always excited for content from our visitors, so if you want to contribute, just contact us via the Contact Us link at the top.

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To IB or not to IB, that is the question

I hope everyone is studying for their IB exams next month!

Whilst you’re studying, here are some links that you might find helpful/interesting:

• Mr Simon Porter has a list of IB physics past papers and mark schemes from 2007-2010 for multiple timezones in SL and HL. Some years seem to have only mark schemes, so you might want to look around.
• IB Memes is the largest IB memes page on Facebook, so you might want to check out the page if you’re on a study break!
• Here’s an article that was published in the Washington Post about transfer credits for American universities, so some of you may find this relevant.

For those of you who are well into your revision, do you have any study tips? What’s your favourite method for revising for exams?

Here are some basic notes on the Aggregate Demand-Aggregate Supply (AD-AS) model. Once I’m finished my Introductory Macroeconomics courses, I plan on posting some more economics notes.

Thanks to Taras for supplying the notes.

• The AD-AS model tries to predict & explain fluctuations in aggregate economic activity and inflation
  • It works well in situations of full employment and unemployment, allowing it to explain long-term growth trends and corresponding fluctuations.
  • The AD-AS model is an extension of the microeconomic supply-demand model, using total output (GDP) and average price level (P) rather than individual market quantity and price.

Aggregate Demand

α = proportional/related to

• AD is the quantity of domestic GDP people want to purchase given:
  • Price (P α (1/AD))
  • Household Income (H α AD)
  • Government Spending (G α AD)
  • Exports (E α AD)
  • Interest Rate (I α (1/AD))
  • Exchange Rate ($C α (1/AD))
  • The AD curve is a negative relationship between average price level (P) and real GDP (Y)
    • Change in P causes a movement along the AD Curve
    • Change in other factors causes a AD Curve shift

Aggregate Supply

• The AS is the amount of GDP that all firms in the economy are willing to supply.
• It is mostly dependent on factor costs, the biggest of which is cost of labour.
  • In the short-run, factor costs are fixed
  • In the long-run, factor costs aren’t fixed
  • Anything that will change the cost of production will cause a shift in the supply curve.

For other articles on the Extended Essay on Intense Cogitation, please see our helpful articles on The Extended Essay Outline and Sample sources for an Extended Essay – The American Civil War

This is my Extended Essay in History of the Americas that I wrote to fulfill my diploma requirement. It received a final grade of A. Please use this only as an exemplar — any academic misconduct is frowned upon.  As a warning, please do not use any portion of this sample in any academic coursework; this is only to give you a general idea of what an extended essay is like. Usage without permission is strictly prohibited, and is a violation of relevant intellectual property laws.

STRATEGIC VALUE OF THE CONFEDERATE IRONCLAD Virginia IN THE AMERICAN CIVIL WAR

Table of Contents

Abstract.. 1

1. Introduction.. 3

2. The Blockade.. 4

2.1 The Battle of Hampton Roads. 5

2.2 Strategic Analysis. 9

3. The Peninsular Campaign.. 10

4. The Defence of Norfolk.. 12

5. Conclusion.. 15

Appendix 1 – Map of the Area Around Hampton Roads. 19

1. Introduction

On April 12^th, 1861, the American Civil War began when Confederate forces fired on Fort Sumter. This war would eventually produce “more carnage than any other war in American history, before or since” (Brinkley 399). In this bloody conflict, the sea soon became a contested area, primarily because the Union quickly blockaded Confederate ports. However, both the United States of America and the Confederate States of America struggled to create wartime navies at the beginning of the conflict. The Union Navy had only twelve vessels available for immediate use, whereas the Confederacy had virtually none (Commager 796). To combat this disadvantage, Confederate Secretary of the Navy Stephen R. Mallory developed an audacious plan.

His radical plan involved the construction of powerful armoured warships, known as ironclads. Soon after Fort Sumter, he wrote:

I regard the possession of an iron-armored ship as a matter of the first necessity. Such a vessel at this time could traverse the entire coast of the United States, prevent all blockades, and encounter, with a fair prospect of success, their entire navy . . . But inequality of numbers may be compensated by invulnerability; and thus not only does economy but naval success dictate the wisdom and expediency of fighting with iron against wood. (qtd. in Beringer 145-46)

Mallory believed that it would be a strategic move to build a small fleet of ironclads instead of a navy of wooden ships because of the invulnerable nature of the ironclad. Shortly after Mallory’s remarks, the Confederates enacted this plan by converting the Merrimack, a captured Union vessel, into the ironclad Virginia at the Gosport Navy Yard in Norfolk,Virginia (“Lincoln and His Admirals” 132).

The Virginia was evidently a critical naval strategic asset for the Confederate war effort, and thus had many expectations. These expectations naturally took the form of important Confederate strategic goals. This leads to the question: to what extent did the ironclad Virginia benefit the Confederacy by achieving strategic goals?

Although she was a remarkable vessel, the Virginia was ultimately unsuccessful in her quest to benefit the Confederacy strategically. She failed to achieve three vital strategic goals: the destruction of the suffocating Union blockade, the suspension of McClellan’s Peninsular Campaign, and the defence of the Gosport Navy Yard at Norfolk. Despite her efforts, the blockade fleet still remained at Hampton Roads, McClellan’s Peninsular Campaign still occurred, and the Union still managed to capture the ship yard at Norfolk. In essence, this ironclad was unable to make any significant difference in the war. Because she was unable to achieve the aforementioned strategic goals, the Virginia was of little strategic use to the Confederacy.

2. The Blockade

The destruction of the blockade quickly became a vital strategic goal for the Confederacy. The Union Navy’s blockade of Confederate ports had the potential to devastate the Confederate war effort. During the spring of 1861, General-in-Chief Winfield Scott developed a plan to slowly suffocate the Confederate States through a naval blockade, which would later be known as the “Anaconda Plan” (J. McPherson 334). On April 19^th, 1861, one week after Fort Sumter, the Anaconda Plan was partially adopted by the Union when President Abraham Lincoln officially blockaded all ports in the Confederate States (E. McPherson 149). This theoretically prevented the Confederacy from importing or exporting any goods, which allowed the Union to exploit its advantage in industrialization.

The South was far behind the North in terms of industrialization. In terms of manufacturing establishments, the South possessed a mere 18,026, while New York State alone possessed 23,236 (Blair 25). The Union factories were also more efficient than their Confederate counterparts; the factories in New York State alone produced about four times more manufactured products than the entire Confederacy (Paludan 105). The disparity between Union and Confederate factories in terms of quantities and efficiency naturally limited the amount of weapons that the South could produce. One county in Connecticut, for example, produced more firearms than the entire Confederacy (Paludan 105). Compared to the North, the South evidently lacked the necessary infrastructure to conduct warfare in an effective manner. Therefore, the Confederacy needed to trade with foreign countries to counter the Union advantage in industrialization. Hence the destruction of the blockade was a vital objective for the South.

In order to achieve this goal, the Confederacy turned to the Virginia. As mentioned in the introduction, Secretary Mallory believed that an ironclad could “prevent all blockades” (qtd. in Beringer 145-46). To accomplish this goal, the Virginia started by attacking the Union blockade fleet at Hampton Roads, which was fairly close to the Virginia‘s home base at Norfolk (see Appendix 1 for a map). In essence, Hampton Roads was a trial for the Virginia, since the outcome of the battle would demonstrate the power of ironclad ships. Despite Secretary Mallory’s faith in ironclad ships, the Virginia failed to achieve the strategic goal of the destruction of the blockade; she did not succeed at the Battle of Hampton Roads.

2.1 The Battle of Hampton Roads

Hampton Roads was home to a Union blockade fleet (Simpson 58), which made it extremely attractive for the Virginia to attack. Before the Virginia steamed towards Hampton Roads, Captain Franklin Buchanan sent a message to Secretary Mallory that read:

“I contemplate leaving here to appear before the Enemy’s Ships . . . I feel confident that the acts of the Virginia will give proof of the desire of her officers and crew to meet the views of the Department as far as practicable.” (qtd. in Konstam 137)

Evidently, the goal of the Virginia‘s attack on the ships at Hampton Roads was to demonstrate her potential by destroying the Union blockade fleet there, which would meet the expectations of the Department of the Navy. Although the Virginia initially experienced success at the Battle of Hampton Roads, she was ultimately unable to achieve the strategic goal of the destruction of the blockade; the strategic situation remained unchanged in the end.

On March 8^th, 1862, the Virginia steamed towards the Union fleet anchored in Hampton Roads. A telegram from John Wool, a Union general in the region, to Secretary of War Edwin M. Stanton succinctly described the grim events of that day:

The Merrimack [the Union designation for the Virginia] came down from Norfolk to-day, and about 2 o’clock attacked the Cumberland and Congress. She sunk the Cumberland, and the Congress surrendered. The Minnesota is aground and attacked . . . the St. Lawrence just arrived and going to assist . . . Probably both will be taken . . . It is thought the Merrimack . . . will pass the fort to-night.

(“Official Records” 4-5)

Although the telegram presents the battle from a Northerner’s perspective, the telegram appears to be fairly objective. The facts of the battle are presented in a relatively neutral fashion, which makes it an intriguing piece of historical evidence in the aftermath of such violence, especially since it was among the first telegrams sent to the Union government in regards to the devastation at Hampton Roads.

As illustrated by the telegram, the situation was evidently grim: the Virginia routed Union forces at Hampton Roads on this day. However, the telegram mentions that the Minnesota was only aground, and not destroyed. Thus, the Virginia would have to return on the following day to complete her destruction of the Union blockade fleet stationed at Hampton Roads. Overall, the day appeared to have ended on a strongly positive note for the Confederacy; the Virginia was one step away from destroying the Union blockade.

Moreover, the Virginia was barely damaged, which reinforces Secretary Mallory’s claims that ironclads were invulnerable. Despite the intense battle that had happened at Hampton Roads, shots fired from Union ships and shore batteries rebounded “from her iron sides as if they had been of india (sic) rubber” (Rhodes 112). Thus, Secretary Mallory’s dream of ironclads destroying the Union fleet appeared to be coming true. In fact, only crew exhaustion and the falling tide prevented the Virginia from finishing off the Minnesota on that day (“Decision at Sea” 117). The Virginia was ostensibly close to achieving her strategic goal of decimating the Union blockade at Hampton Roads.

However, the Union also had an ironclad, which had the potential to counter the Confederacy’s perceived advantage in the aftermath of Hampton Roads. The Monitor arrived at Hampton Roads around 11 P.M. (Commager 806), just in time to see the Congress explode (“Decision at Sea” 117). The Union ironclad would undoubtedly serve to protect the Minnesota and the remaining remnants of the Union fleet from the Virginia, because the Union could not afford to let the Confederacy seize a massive strategic victory by annihilating an entire Union blockade base.

On the following morning, the Virginia returned to Hampton Roads to finish her mission. She soon found the “queer-looking Monitor guarding the stranded frigate [Minnesota]” (qtd. in Scharf 167). Despite the presence of the Monitor, the Virginia still intended to destroy the Minnesota. However, neither ironclad was able to inflict serious damage on the other. Union Secretary of the Navy Gideon Welles received the following telegram from his subordinate, G.V. Fox, which describes the battle in a concise manner:

The Monitor met them at once and opened her fire, when all the enemy’s vessels retired, excepting the Merrimack. These two ironclad vessels fought part of the time touching each other, from 8 a.m. to noon, when the Merrimack retired. Whether she is injured or not it is impossible to say . . . The Minnesota kept up a continuous fire and is herself somewhat injured.

She was moved considerably to-day, and will probably be off to-night. The Monitor is uninjured and ready at any moment to repel another attack.

(“Official Records” 6)

Like the previous telegram, this one is also from a Union perspective, and is also included in the U.S. government’s official records of the war. However, this telegram also appears to be a valid historical resource, since the facts given are consistent with facts mentioned in secondary sources, such as the book Duel of the Ironclads. The historical significance of the second day of the Battle of Hampton Roads is the shattered image of the Virginia’s invulnerability, which casts doubt on the strategic effectiveness of the ironclad.

In the end, the tactical picture was fairly impressive. The Virginia managed to destroy the USS Cumberland and USS Congress, damage the USS Minnesota, and inflict an estimated 409 Union casualties, according to the Battle Summary page by the American Battlefield Protection Program. With these losses in mind, the Virginia remained the cause for the worst day in the history of the United States Navy until Pearl Harbor in 1941 (qtd. in Holzer and Mulligan 147). However, tactical success did not necessarily translate into strategic success, since the Union retained control of the region.

2.2 Strategic Analysis

The strategic picture was relatively unchanged after the battle. The Virginia was unable to complete her destruction of the blockade fleet, since the Minnesota still remained at Hampton Roads, and the arrival of the Monitor essentially replaced the tactical role of the two Union warships that were sunk on March 8^th. Essentially, the Virginia was unable to destroy the Union blockade fleet at this important Union base, which meant that she was unable to achieve her strategic goal. However, there is another historical interpretation of the events that transpired during this battle.

E. Merton Coulter, Professor of History at the University of Virginia, asserts that “the Confederacy gained potential control of [Hampton Roads and the surrounding] Bay and even theoretical control of the high seas” because the Virginia was “impervious to the most terrific punishment the Federal wooden ships could inflict” (306). This interpretation appears to exaggerate some aspects of the Virginia‘s capabilities. For instance, it claims that one ship—the Virginia—controlled the area around Hampton Roads because it was essentially invulnerable. However, this interpretation fails to account for the innate weaknesses of the Virginia. Lieutenant Jones, a member of the crew, wrote about the Virginia‘s condition prior to battle:

The lower part of her shield forward was only immersed a few inches instead of two feet as intended, and there was but one inch of iron on the (lower) hull . . . The Virginia was unseaworthy; her engines were unreliable, and her draft, over 22 feet, prevented her from going to Washington . . . (qtd. in Konstam 139)

The Virginia was clearly not suited for battle, much less controlling the high seas. This casts further doubt on the Virginia’s ability to achieve strategic goals. Thus, Coulter’s interpretation is rather limited for this battle.

In essence, the Virginia was unable to accomplish the strategic goal of destroying the Union blockade. She attempted to accomplish this goal by attacking the Union fleet stationed at Hampton Roads, but her attempt ultimately ended in failure—the Union blockade fleet was still stationed at Hampton Roads when the Virginia departed. Furthermore, her innate weaknesses, such as her deep draft, essentially restricted her to Hampton Roads, preventing her from attacking the Union blockade at different locations. Therefore, the Virginia was unable to benefit the Confederacy in this regard.

3. The Peninsular Campaign

Besides the blockade, the Union had another major strategic plan: the Peninsular Campaign. Led by General George B. McClellan, this plan proposed the capture of Richmond by moving up the Virginia Peninsula (Linedecker 199). Thus, the Confederates needed to interfere with this campaign.

Richmond, the Confederate capital, was an important Confederate industrial city. Important Confederate war industries were established in Richmond, including the famous Tredegar Iron Works. According to “A Guide to the Tredegar Iron Works Records” by the University of Virginia, Tredegar was “virtually the sole source of heavy guns, projectiles, gun carriages . . . wheels and axles for railroad rolling stock, furnace machinery, and a variety of other products for Confederate munitions factories and navy yards.” Moreover, this was the same industrial establishment that produced iron plating for the Virginia since it was the closest foundry to Norfolk. If it were captured by the Union, the Confederacy would face a weapons production dilemma and Secretary Mallory’s hopes of creating a small ironclad fleet would be dashed. Therefore, the protection of Richmond became a strategic objective because of the city’s industrial and political importance. By extension, the suspension of the Peninsular Campaign became a strategic goal of the Confederacy.

The principal means by which the Virginia interfered with this campaign was through intimidation. Lincoln’s government was too focused on the destruction that had happened on March 8^th after General Wool’s telegram arrived on March 9^th; in response to that telegram, President Lincoln met with Secretary of War Stanton, Secretary of the Navy Welles, Secretary of State William H. Seward, General McClellan and others in the President’s office (Davis 113). Lincoln’s secretary noted that Stanton was “fearfully stampeded. He said they would capture our fleet, take Ft. Monroe, [and] be in Washington before night” (qtd. in Thomas 179). He went on to say that the Virginia would “destroy every vessel in the service . . . disperse Congress, destroy the Capitol and public buildings” (qtd. in “Lincoln and His Admirals” 137). Even President Lincoln occasionally glanced outside, as if he were expecting the Virginia to attack Washington at any moment (Davis 133). This clearly highlights the psychological effect of the Virginia on the upper echelon of the Union government; these men believed that the Virginia could essentially change the strategic picture of the war.

Their continued fear of the Virginia is reinforced by the fact that Secretary Welles sent every usable ship to Hampton Roads to transport the Army of the Potomac down to Virginia, including ships designed to ram the Virginia (Tucker 175). It is interesting to note that the expedition occurred when the Virginia was undergoing repairs. Tucker also notes that McClellan requested that Flag Officer Goldsborough use his warships at Hampton Roads to attack Confederate defences, but naturally he declined: the Virginia could make an appearance at any time, and weakening his force would put his other ships in danger (176). Clearly, the Virginia‘s mere presence in the area negatively impacted the Union campaign.

However, the strategy of intimidation could not last forever. On April 11, 1862, the Virginia was finally ready for battle after spending weeks in dry dock for repairs, and Mallory ordered the Virginia to interfere with the Peninsular Campaign by attacking Union transport ships (Tucker 176). Once again, the Virginia steamed towards Hampton Roads. This time, Union forces did not challenge the Virginia because it could jeopardize the Peninsular Campaign. If the Virginia gained control of the area, then the Union’s Army of the Potomac would be cut off from its primary supply line. The Union therefore shifted to a strategy of avoidance because the North could not afford to lose valuable ships to the Virginia, such as the Monitor. This strategy essentially neutralized the Virginia. The Virginia had an average speed of 5 knots (Konstam 48), which meant that virtually any Union ship in the region could outrun her. Furthermore, she could not attack ships that were under the protection of the guns at the local fort, such as the Monitor (Tucker 176). In fact, a crewman on the Monitor stated that “I believe the Department [of the Navy] is going to build us a big glass case to put us in for fear of harm coming to us” (Konstam 182). By altering its strategy, the Union effectively prevented the Virginia from achieving the strategic goal of interrupting the Peninsular Campaign.

Since the Virginia was unable to attack any ship, she was therefore unable to interfere with the Peninsular Campaign. Therefore, there was very little for the Virginia to do, since she failed to break the blockade and delay the Peninsular Campaign. There was only one vital strategic goal remaining: the defence of Norfolk.

4. The Defence of Norfolk

Throughout this tumultuous time period, the city of Norfolk was home to one of the Confederacy’s most valuable naval assets: the Gosport Navy Yard. Besides its role as the Virginia‘s home port, Norfolk was also important to the Confederacy in other ways. The shipyard was the one of the largest naval construction and repair facilities in the entire country (J. McPherson 279). It was located close to the industrial centre of Richmond, which allowed quick transport of manufactured goods from Richmond to the shipyard. Furthermore, Gosport was one of only two shipyards located in the entire Confederacy; the other being New Orleans (Konstam 2). If Norfolk fell, then the Confederates would not have a major shipyard along their entire Atlantic coastline. Norfolk was clearly an important part of the Confederate war effort, and needed to be defended. Thus, the defence of Norfolk was an important strategic goal for the Confederacy. To this end, the Confederates enlisted the Virginia as a part of their defence plan, but she failed to defend the ship yard from being captured by the Union.

During the spring of 1862, the Peninsular Campaign did not make significant progress, as previously mentioned. McClellan managed to land his troops on Confederate soil while the Virginia was being repaired, but he was held up at Yorktown. From Lincoln’s view point, the Union had forgotten about the menace that was the Virginia (Oates 326). The only logical way to defeat the Virginia with minimal direct contact would be to attack the city of Norfolk, which, as mentioned above, contained the Gosport Navy Yard. Capturing the shipyard would deprive the ironclad of a home. However, the Virginia was unable to prevent this disaster for the Confederacy.

The Virginia had the potential to stop an attack. When Union forces began to attack locations near Norfolk not long after the Battle of Hampton Roads, the mere appearance of the Virginia caused the U.S. fleet attacking Sewell’s point (see Appendix 1 for map of area) to move away quickly (“Lincoln and His Admirals” 151). This is another clear example of the Virginia‘s psychological capability. While defending Norfolk, the Virginia‘s psychological effect had more power than it did during her attempt to thwart McClellan’s Peninsular Campaign; the Union could not simply run away if it wanted to attack Norfolk. Thus, the Virginia had the ability to defend the city of Norfolk from a naval assault through her psychological effect.

At around the same time, McClellan began to march up the Virginia Peninsula, and engaged Confederate forces at Yorktown. After being surrounded by an overwhelming number of Union troops, Confederate forces were strategically redeployed to Richmond on May 4th; this left Norfolk isolated (Oates 326). President Lincoln decided to visit the front lines and found out that no one had tried to attack Norfolk, home of the infamous ironclad. With this in mind, he soon led an amphibious assault on Norfolk, which was not obstructed in any shape by the Virginia. In fact, there was no Confederate response to the beach landing. Evidently, the Virginia, with all her potential, did not stop the Union force.

According to Professor Craig L. Symonds of the U.S. Naval Academy, the lack of response was due to a simple reason: the Confederates “had planned to abandon Norfolk in any case once the Confederate army had evacuated the Yorktown line” (“Lincoln and His Admirals” 155). This interpretation highlights the idea that the Confederates decided that the Virginia was ultimately less powerful than the Confederate Army. This illustrates the Virginia‘s slow decline; she was originally designed as a major strategic weapon, but by May 1862, she was just another ship that could not even defend her home. Thus, Symonds’ interpretation of the events at Norfolk appears to have merit.

In essence, the Virginia theoretically had the capability to defend Norfolk, but she was ultimately disregarded. This line of thought likely stemmed from her inability to break the blockade and delay McClellan’s campaign. Therefore, the Virginia‘s past ineffectiveness prevented the Confederates from considering her as an integral part of Norfolk’s defence, which prevented her from achieving this strategic goal. Granted, the odds of an overland attack were extremely high, but the Virginia may have had the potential to assist Norfolk. In the end, she failed to accomplish any of her strategic goals.

5. Conclusion

The story of the Virginia is indeed a most riveting one. Her journey began at a captured Union shipyard in Norfolk, and this journey reached its climax at the engrossing Battle of Hampton Roads. However, her adventure came to an end when she was destroyed by Confederate troops after the fall of Norfolk.

At one point, Secretary Mallory considered her to be a powerful strategic weapon. He claimed that after she attacked New York City, “peace would inevitably follow. Bankers would withdraw their capital from the city. The Brooklyn navy yard and its magazines and all the lower part of the city would be destroyed, and such an event, by a single ship, would do more to achieve our immediate independence than would the results of many campaigns” (qtd. in Davis 78). This quote illustrates the Virginia‘s initial expectations.

However, she ultimately failed to accomplish any of the strategic goals outlined in the introduction. Each of these goals was of vital importance to the Confederacy. She initially attacked the Union fleet at Hampton Roads, and finished the day with some measure of success, but she was ultimately prevented by the Monitor from completely destroying the blockade in that region. Afterwards, the Virginia attempted to halt McClellan’s Peninsular Campaign which threatened the Confederate capital. To avoid destruction, Union ships merely avoided her or outran her. Once again, she failed to accomplish a strategic goal. When all else failed, she attempted to defend her home base at Norfolk, but her disappointing performance in the past caused the Confederates not to consider her as a serious contender for the defence of Norfolk.

In all these events, the Virginia may have made a difference, but it was not to the extent that the Confederacy expected. After all, strategic goals have the potential to benefit one side significantly and potentially alter the course of a war. This brings Secretary Mallory’s statement in the introduction to mind yet again; however, the Virginia was unable to fulfill any of the expectations he outlined in his statement.

In fact, the Virginia may have detrimentally affected the Confederate war effort. Historian John Elwood Clark viewed the ironclad program as an expensive failure. He claims that the Confederacy foolishly “diverted one-quarter of . . . [its] iron production” (66), since the ironclads were “often underpowered . . . struggled to make headway against tidal or river currents . . . design flaws rendered many unseaworthy . . . only half saw action” (67). Even though the Virginia was unable to benefit the Confederacy in a meaningful fashion, the fact that multiple interpretations still exist a century and a half after the Virginia‘s birth suggests that this topic is worthy of continued exploration.

Works Cited

A Guide to the Tredegar Iron Works Records, 1801-1957. 2 September 2009 <http://vip.lib.virginia.edu:8080/cocoon/vivaead/published/lva/vi00494.bioghist>.

Battle Summary: Hampton Roads, VA. 31 July 2009 <http://www.nps.gov/history/hps/abpp/battles/va008.htm>.

Beringer, Richard E. Why the South Lost the Civil War. Athens: University of Georgia Press, 1986.

Blair, Dr. William A. “Extremists at the Gate.” Sheehan-Dean, Aaron, et al. Struggle for a Vast Future. Oxford: Osprey Publishing Ltd., 2006.

Brinkley, Alan. The Unfinished Nation: A Concise History of the American People. New York: Alfred A. Knopf, Inc., 1997.

Clark, John Elwood. Railroads in the Civil War: The Impact of Management on Victory and Defeat. Baton Rouge: Louisiana State University Press, 2004.

Commager, Henry Steele. The Blue and the Gray. New York: The Bobbs-Merrill Company, Inc., 1950.

Coulter, E. Merton. A History of the South: The Confederate States of America 1861-1865. Vol. VII. Baton Rouge: Louisana State University Press, 1950.

Davis, William C. Duel Between the First Ironclads. Garden City: Doubleday & Company, Inc., 1975.

Foote, Shelby. The Civil War, A Narrative: Fort Sumter to Perryville. New York: Vintage Books, 1986.

Holzer, Harold and Tim Mulligan. The Battle of Hampton Roads: New perspectives on the USS Monitor and CSS Virginia. New York: Fordham University Press, 2006.

Konstam, Angus. Duel of the Ironclads. Oxford: Osprey Publishing Ltd., 2003.

Linedecker, Clifford L. Civil War A to Z: The Complete Handbook of America’s Bloodiest Conflict. New York: Ballantine Books, 2002.

McPherson, Edward. The Political History of the United States of America, During the Great Rebellion. Washington, D.C.: James J. Chapman, 1882.

McPherson, James M. Battle Cry of Freedom. New York: Oxford University Press, Inc., 1988.

Oates, Stephen B. With Malice Toward None: The Life of Abraham Lincoln. New York: Mentor, 1977.

Official Records of the Union and Confederate Navies in the War of the Rebellion, Series I. Vol. VII. Washington, D.C.: Government Printing Office, 1898.

Paludan, Phillip Shaw. A People’s Contest: The Union & Civil War, 1861-1865. 2nd Edition. Lawrence: University Press of Kansas, 1996.

Rhodes, James Ford. History of the Civil War. New York: The Macmillan Company, 1917.

Scharf, John Thomas. History of the Confederate States Navy from Its Organization to the Surrender of Its Last Vessel. New York: Rogers & Sherwood, 1887.

Simpson, Brooks D. America’s Civil War. Wheeling: Harlan Davidson, 1996.

Symonds, Craig L. Decision at Sea. New York: Oxford University Press, 2005.

—. Lincoln and His Admirals. New York: Oxford University Press, Inc., 2008.

Tucker, Spencer. A Short History of the Civil War at Sea. Wilmington: SR Books, 2002.

Appendix 1 – Map of the Area Around Hampton Roads

Battle of Hampton Roads, VA. Digital image. Civil War Preservation Trust. 28 Nov. 2009

<http://www.civilwar.org/battlefields/hampton-roads/maps/hampton-roads.jpg>.

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Contents

• The Bacteria
• Archaea and Eukarya
• The Fungi
• Genetics Fundamentals
• Genetic Exchange
• Viruses and Prions
• Genomics

The Bacteria

• Evolution of three domains
  
• Bacterial morphology – very diverse
  
  • These unique features (eg. Flagellum, etc) are used to group/categorize microbes
    
  • There are three major types (which each replicate by binary fission)
    
    • Coccus (round)
    • Bacillus (tube-like, rods)
    • Spiral
• Bacterial replication by binary fission
  
  • Dividing in the centre equally
    
  • Depending on how it happens, you can get different morphologies
    
• Coccus
  

1. Streptococcus – don’t separate, stay joined as they divide
2. Diplococcus – stay in twos
3. Tetrads – divide and stay together in fours
4. Sarcina – divide down longitudinal plane (eight cells, two tetrads that are stacked on top of each other)
5. Staphylococcus – replicate in different planes (random)

• The bacillus (rods) – also divide by binary fission
  
  • Depending on end result, you can get two different types)
    
  • Streptobacillus – chain of bacilli
    
  • Coccobacillus – shortened bacillus structure, combination of coccus and bacillus
    
• Spirals – not based on division, just based on morphology (what they look like)
  
  • Vibrio – comma shaped
    
  • Spirillum – spirals but inflexible (any pic prob)
    
  • Spirochete – flexible spirals (any pic prob)
    
• Bacterial structure has many layers
  
  • Cytoplasm
    
    • Many small molecules (amino acids, nucleotides, ions, cofactors) floating around
      
    • Enzymes/proteins for maintaining the organism
  • Nucleoid
    
    • Nuclear material is concentrated in the nucleoid (no distinct nucleus)
      
    • Not a compartment; just a location
      
    • DNA (a lot) is present in a covalently closed circular duplex (supercoiled)
      

    • The DNA structure is circular, therefore no chromosomes
      
      • Hence, it bundles up in this compact form
        
  • Ribosomes
    
    • Read mRNA, create proteins
      
    • In bacteria, ribosomes form polyribosomes to translate mRNA into protein simultaneously as DNA is being transcribed into mRNA
      
    • Bacteria: 70S ribosomes
      
      • 30S (bottom) subunit and 50S (top) subunit (does not equal 70 = expected)
        
      • S = sedimentation coefficient in centrifugation
        
  • Cytoplasmic membrane – phospholipid bilayer
    
    • Proteins are embedded in the membrane (eg. Transporters)
      
    • Connected to each other with ester linkages between the heads
      
  • Cell wall
    
    • Two major components: peptidoglycan and in some bacteria, outer membrane
      
    • Gram + has a lot more peptidoglycan, Gram – has less but has an outer membrane
      

Gram +ve / Gram -ve

• Gram + cell wall
  
  • Made up of largely peptidoglycan = very thick
    
  • Periplasm – small gap between cytoplasmic membrane and cell wall
    
• Gram – cell wall
  
  • Outer membrane is the outermost layer
    
  • Peptidoglycan is sandwiched between the cytoplasmic membrane and the outer membrane
    
  • Periplasm surrounds the peptidoglycan
    

• Gram staining
  
  • Crystal violet is added and seeps into bacteria – turns everything PURPLE
  • Iodine is added as a mordant
  • Ethanol is used for decolorization
    • Gram + stays purple, Gram – clears
  • Use Safranin, a counterstain, to distinguish between the two types
    • Gram – turns pink
  • Therefore, Gram +ve = purple, Gram -ve = pink
    
• What’s happening in the gram stain?
  
  • Crystal violet penetrates in
    
  • Mordant forms complexes with the ions of crystal violet –> trapping crystal violet in large complexes to make it hard to leave
    
  • Ethanol washes away outer membrane of Gram -ve and dehydrates water
    
    • By dehydrating water, the peptidoglycan SHRINKS
      
    • Gram +ve still has some peptidoglycan left since it had a lot to begin with, but Gram -ve loses almost all of its peptidoglycan
      
    • Crystal violet complex remains in Gram +ve since it’s still stuck on the peptidoglycan and hasn’t been washed away
      
• Peptidoglycan differences
  
  • Gram +ve
    
    • N-acetylmuramic acid (NAM) is bonded to N-acetylglucosamine (NAG)
      
    • Forms long strands and forms bridges with pentaglycine crosslink (glycine residues)
      
  • Gram -ve
    
    • Still have long chains of NAM and NAG
      
    • However, there is a direct crosslink (a direct bond) with no residues in between
      
• Teichoic acid anchors – Gram +ve
  
  • Peptidoglycan is attached to the cell membrane and held together with teichoic acid anchors
    

  • Lipoteichoic acid attaches the peptidoglycan to the lipids in the actual cell membrane
    
  • Teichoic acid anchors hold the peptidoglycan layer together
    
• Lipoprotein anchors – Gram -ve
  
  • Lipoproteins anchor the thin peptidoglycan layer to the outer membrane to provide stability
    

• LPS – Lipid + Sugar (saccharide)
  
  • In humans, the virulence is determined by the O-polysaccharide
    
  • This allows bacteria to attach to the cell
    
  • Eg) E coli has O:157
    

Components (cont.)

• Fimbrae/Pili
  
  • Extend from bacterial cell (can be extended) to attach to a surface
    
  • Bacteria can use the pili to reel themselves in by retracting their pili
    
  • Ie) used to attach / move (via gliding)
    

• Capsule
  
  • An outer layer that forms just around the cell
    
  • Made of extracellular polymeric substances – sugars, proteins (polypeptides)
    
  • Very important for attachment and protects them
    
  • Some bacteria have sheaths – made of sugars and amino acids
    
• Flagellum
  
  • Used in motility
    
  • Variety of different “conformations” and numbers
    
  • Monotrichous – single flagellum from single point
    
  • Peritrichous (perimeter) – multiple flagellum coming out from around the cell
    
  • Amphitrichous (amphibian)- flagella from both ends
    
  • Lophotrichous (mound/hill) – tuft of flagella at one end
    
  • Amphilophotrichous – tuft of flagella at both ends
    
• Flagellum of Gram -ve
  
  • Has evolved to include specific proteins to anchor to the inner/outer membranes and the thin peptidoglycan layer
    
  • Very complex structure
    
• Flagellum of Gram +ve
  
  • Embedding proteins are also adapted
    
  • Anchored in cell membrane also
    
  • Simpler in structure than Gram -ve
    
• Flagellar filament
  
  • Middle is hollow
    
  • Looks like spiral staircase
    
  • Assembly:
    
    • Pieces go through the middle and come out on top – pieces are assembled spirally
      
• Type III secretion system
  
  • Injects virulents into host
    
  • It seems to be related to the flagellum – specialized form
    
    • Seems to have had a common ancestor structure with the flagellum
      
  • The flagellum probably came first because it is more ubiqutous
    
  • Flagellum is hollow inside –> useful structure for adaptation into injection
    

Taxis

• Taxis – movement or orientation directly towards / away from a stimulus
  
  • Eg) magnetotaxis in Magnetospirillum
    
  • Eg) Phototaxis – bacteria align in specific pattern for optimal photosynthesis
    
  • Eg) chemotaxis – move towards chemical / chemical gradient (Agrobacterium tumefaciens)
    
    • Agrobacterium goes towards leaking compounds in soil to find plant
      

Archaea and Eukarya

• Evolution of three major domains: Archaea, Bacteria, Eukarya
  
  • Bacteria are their own distinct domain; Eukarya are considered to be an offshoot of Archaea
    
  • However genetic information was exchanged between all groups
    
• Archaea – general information
  
  • Have layers like bacteria
    
  • Components are very similar to bacteria; similar appearance; small differences in structural components (ie. to allow them to survive extreme conditions)
    
  • Cytoplasm
    
    • Ribosomes
      
    • Macromolecules: DNA, RNA, proteins
      
    • Small molecules: amino acids, nucleotides, ions, cofactors
      
    • Enzymes: metabolic processes
      
    • DNA is found in a nucleoid
      
• DNA of Archaea
  
  • Like bacteria – covalently closed circular duplex (supercoiled)
    
    • Compacting is done so the massive amount of DNA does not fill up the entire cell
      
    • Similar limitations as bacterial DNA
      
  • Supercoiling controlled by gyrase and helicase – introduce + or – supercoiling
    
• Ribosomes of Archaea
  
  • DNA -> mRNA -> proteins (made through ribosomes)
    
  • Simultaneous transcription and translation
    
    • Polyribosomes translate mRNA into protein; attach at gene sequences whilst DNA is being transcribed into mRNA
      
  • Ribosomes are essential for protein synthesis
    
  • 70S ribosomes (like bacteria)
    
    • 50S subunit (top), 30S subunit (bottom)
      
    • They are a bit different even though they are both 70S — same function though
      
    • Ribosomes from Archaea can be substituted with ribosomes from Eukarya, even though Eukarya have 80S ribosomes
      
      • Bacterial ribosomes can not be substituted for Eukaryotic ribosomes!! Only Archaea!!
        
• Plasma membrane = cytoplasmic membrane
  
  • Remember: ester linkages in bacteria
    
    • Major parts: hydrophilic head, hydrophobic tails (unbranched fatty acids)
      
  • Archaeal membrane – lipid bilayer
    
    • Ether linkages
      
    • Different fatty acid (branched)
      
      • Purpose: stronger in extreme environments (where Archaea thrive)
        
  • Archaeal membrane – lipid monolayer
    
    • Still ether linkages and branched fatty acid
      
    • However, fatty acids are directly connected with each other (less sliding)
      
      • WHY? Better stability in extreme conditions and higher bond strength
        
      • Archaea live in high stress (high temp and high pressure) environments so they need stability
        
  • Ether bond is more energetically stable than the ester bond
    
• Comparison of Peptidoglycan in bacteria and archaea
  
  • Bacteria: have NAM and NAG
    
    • Gram +ve – pentaglycine crosslinks
      
    • Gram -ve – direct links
      
  • Archaea cell wall – pseudomurein
    
    • Have NAG still
      
    • Have TAL (N-acetyl-talosaminouronic acid) instead of NAM
      
    • Still the same chain, same orientation of peptidoglycan
      
    • Direct connection, almost like Gram -ve
      
• Many archaea lack a traditional cell wall
  
  • Some use other types of physical structures
    
  • Can have cell wall and/or sheath
    
  • Sheath – like capsule
    
  • S layer – like sheath
    
    • Functions like chain mail – forms a lattice
      
    • Extra reinforcement for extreme environments
      
• Archaeal flagella
  
  • Fimbra/pilus (singular) – used for gliding
    
  • Flagellum may have evolved from archaeal pilus – but it could be the opposite also
    
  • Pili grow from the base – not pushed through hollow tube
    
    • Protein is added closest to the membrane from a single point (like a plant)
      
    • Flagellum of archaea grow in the same way – by adding subunits to base
      
  • Hence, bacterial flagella/pilus are very different from archaeal ones
    
• Comparison: bacterial flagella
  
  • Bacteria have hollow flagella
    
  • Subunits go through hollow tube, added to top (grow at the tip, not the base)
    
  • Type III secretion system – inject virulent proteins
    
  • May have evolved from a protein exporter since bacteria already had a structure to export protein – common ancestor?
    
• Flagella comparisons
  
  • Archaea: assemble from base, solid
    
  • Bacteria: assemble from tip, hollow
    

Eukarya

• Large diverse group (plants/animals)
  

• DNA
  
  • Bacterial DNA: supercoiled, circular
    
    • Most have one copy, some have multiple
      
  • Eukaryotic DNA: chromosomes
    
    • Different packing – wrapped around histones instead of supercoiled
      
    • Not circular
      
    • 2 copies of DNA at least
      
      • Diploid (animals), Polyploid (tetra, hexa, etc. in plants)
        

• Eukaryotes have specialized organelles
  
• Eukaryotes have 80S ribosomes (bacteria/archaea have 70S)
  
  • Archaeal ribosomes work in eukarya, not bacterial ribosomes
    
• Mitochondria
  
  • Involved in cellular respiration -> create energy in the form of ATP (“power plants”)
    
  • Have circular DNA, ribosomes, membranes
    
• Chloroplasts – plants
  
  • Make food for plants
    
  • Harvest energy from light, use CO2 to make sugars
    
  • Have membranes, DNA, ribosomes
    
    • Suggests that mitochondria and chloroplasts are of bacterial origin
      
  • Have very specialized compartments
    
• Photosynthetic bacteria
  
  • Chloroplasts/plant cells resemble cyanobacteria
    
    • However, cyanobacteria have no special compartment, they are the special compartment!
      
  • DO NOT CONFUSE WITH ALGAE
    
    • Some algae are eukarya, some are cyanobacteria
      
• Endosymbiotic theory
  
  • Start off with ancestral prokaryote
    
  • Nuclear area formed in it and it ingested other organisms to survive
    
  • One day, it ingested an ancestral mitochondrion
    
    • It somehow found a way to survive in the cell, as it was beneficial to both organisms
      
    • Efficient energy exchange
      
  • Plants had a second event where chloroplasts were engulfed
    
• Chloroplast ancestor related to the 2 cocci based on DNA (Synechococcus and Prochlorococcus)
  
• Mitochondria ancestor is related to rickettsia
  
  • Pathogen that remains as an intracellular pathogen
    
    • Has pathogen to enter and persist in cells
      
• Eukaryotes – ester linkages (resembles bacteria more than archaea)
  
• Flagella
  
  • Flagella structured very differently in eukarya than bacteria/archaea
    
  • Have microtubules that run the whole way through
    
    • Microtubules can slide within the flagellum for whip-like motion
      
  • Characteristic 9+2 structure for eukarya
    
    • 9 around, 2 in middle
      
  • Flagellum are very long, cilia are shorter and more numerous, like hair
    
• Quick review
  
  • Ester linkage – bacteria, eukarya
    
  • Mitochondria – eukarya only, endosymbiotic theory
    
  • DNA – supercoiled in bacteria/archaea, chromosomes in nuclear region in eukarya
    
  • Ribosomes – 70S in bacteria/archaea, 80S in eukarya
    
  • Flagella
    
    • Bacteria: hollow, built from top
      
    • Archaea: solid, built from base
      
    • Eukarya: (?), 9+2 structure with microtubules through whole length
      

Tree of life

• Three-domain tree – one ancestor into 3 distinct groups
  
• Eocyte tree – eukaryotes evolved from archaea (e. offshot of archaea)
  
  • Eocyte is group within archaea
    
• Web of life – no real ancestor
  
• Ring of life – fusions and mixtures (can’t really trace common ancestor)
  

The Fungi

• Belong in Eukarya
  
• Found virtually everywhere; very diverse
  
• One of the most abundant organisms on the planet
  
• Have medical, agricultural, ecological (nutrient recycling) relevance
  
  • Eg) decimated plant, breaking down wood, ceiling tiles, lichens, yeast infection
    
  • Can form very specific associations with plants (mutualism) – eg. Fungus extending root system
    
• Fungal body
  
  • Mycelium – entire fungal body (singular)
    
  • Mycelia – multiple fungal bodies (plural)
    
• General biology
  
  • Hypha – individual strand in fungal body
    
  • Hyphae – multiple strands
    
  • Mycelium – many hypha
    
  • A fungus has only one type of hyphae, not both (either coenocytic or septate)
    
  • Septum - single wall
    
  • Septa – many walls
    
  • Septate hypha – walls between the cells create individual compartments; seem like individual “cells” with nucleus inside
    
  • Coenocytic hypha – no septa; continuous – nuclei are freely distributed – no physical separation
    
• Fungal growth and reproduction
  
  • Side note: bread mold = usually penicillin
    
  • Fungi spread very quickly from a single point of infection – usually a single spore
    
  • From one spore, they get a single hypha that branches
    
    • Additional hypha and branching from that point give you the whole fungal mycelium
      
  • Hyphae are very good at pushing through a substrate – very strong
    
  • When the mycelium is growing it can produce billions and billions of spores
    
  • Conidia (plural) – Conidium (singular) – asexually produced spores
    

  • A fungal mycelium can take over an entire substrate very quickly (eg. Orange); white parts = growing edge of mycelium, whereas the green = spores
    
• Fungal nutrition
  
  • The fungi spreads throughout the food source
  • Secretes enzymes to break substrate down
  • Enzymes break down specific products
  • Broken down products are absorbed by fungus
  • Enzymes are targeted for specific substrates that they can digest
    

• Fungal identification
  
  • Before DNA… reproductive structure and spore morphology
    
    • Penicillin has “hands” for the reproductive structure
      
• Major fungal groups
  
  • Zygote = resting spore
    
    • Can survive for a long time
      
    • Once conditions are right, they undergo asexual reproduction
      
  • Chytridiomycota (chytridiomycetes)
    
    • Known largely for being parasites and feeding off other organisms
    • Generally aquatic
    • Produce motile spores
    • Responsible for massive die off of frogs
    • Lifecycle:
      
      • Once conditions are right, zygote undergoes asexual reproduction
        
      • Produces structures that look like mycelium (sporangium?) that produce motile zoospores (these infect hosts, like frogs)
        
        • Zoospores move to a source through chemotaxis
          
      • In the host, spores attach and lose their flagellum
        
        • Begin to extend into the host and derive nutrition
          
      • Once somewhat mature, they produce spoers in host
        
      • These spores are gametes (male and female)
        
      • When gametes fuse via conjugation zygote is formed
        
  • Zygomycota – common soil fungi
    
    • Fairly common on fruits, vegetable
    • Do not produce a lot of complex enzymes – can only breakdown simple substrates (simple sugars)
    • Grow very fast and absorb very quickly
    • Coenocytic – no septa in hyphae
    • Worst competitive fungus – colonize only simple sugar substrate, but do not compete well
    • Very thin spore structures
      
    • Common species: Rhizopus, Mucor
      
    • Lifecycle
      
      • Have sexual/asexual cycles
        
      • Sexual cycle involves 2 types that form sexual spores (+ and -)
        
      • Asexual cycle forms more asexual spores that germinate to create a mycelium to repeat the cycle
        
  • Glomeromycota – arbuscular mycorrhizae
    
    • Forms mutualisms – Both partners benefit
    • Endomycorrhizae enter the actual cells
      • Arbuscular mycorrhizae because they send tentacle like structures into cells – that’s where the nutrient exchange happens
      • Forms arbuscules – nodes?
    • Mycorrhizae extends the root system
      • Fungus grows a lot faster than the plant, so it can absorb more nutrients for the plant
      • Under nutrient-limiting conditions, it can make a huge difference (small plant vs large plant grown)
  • Ascomycota – common soil fungi
    
    • Common soil fungus – everywhere
    • Aspergillus – puffy black spores
      • Aspergillus flavus produces aflatoxin
        • Present in canned corn, fresh corn, peanut butter
        • Processed by liver to produce carcinogenic compounds (before processing: not carcinogenic, after processing: carcinogenic)
        • Carcinogenic because it binds to DNA
        • However, it takes a lot to succumb to aflatoxin
    • Alternaria – teardrop with septa spores
    • Penicillium – skeleton hands spores
    • Fusarium – crescent moon shaped spores
    • Trichoderma – overtakes lab plate in a day; runs everything over
      
    • Asexual and sexual reproduction
      
      • One spore forms mycelium which forms even more spores
        
      • 2 types of sexual spores
        
      • Sexual structure is apothecium (cup-like) which produces sexual spores
        
      • Can produce many different structures
        
    • 8 spores (sexual) in ascus
      
    • Nematode-trapping fungi
      
      • Soil fungi that can capture nematodes for extra nutrients
        
      • Nematode comes along, hyphae senses it and rings clasp around nematode
        
      • Hypha tightens, and begins to grow into nematode
        
      • Digests it from the inside out
        
    • Human disease
      
      • Stachybotrys – causes black mould in building
        
        • Loves paper
          
        • Usually growing on paper in drywall – produces cellulase to digest it
          
        • Spores can grow in lungs and spread
          
      • Trichophyton – Athlete’s foot / jock itch
        
        • Loves humans, adapted to skin / nails / hair
          
        • Have keratinase to digest it
          
    • Yeast
      
      • Can produce asca and sexual structures
        
      • Saccharomyces – budding yeast
        
        • Bud off from parent, becomes separate cell
          
      • Schizosaccharomyces – splits into 2 evenly down the middle (binary fission)
        
  • Basidiomycota
    
    • Have asexual and sexual reproduction
    • 2 types that give rise to sexual spores
      • Sexual spores come in form of mushroom
      • Mushroom = sexual structure
      • Underneath the mushroom cap are gills – have millions of spores within
      • Mushrooms can produce hallucinogenic compounds or produce toxins (easily confused)
    • Fairy rings – ring of mushrooms around plant
      
      • Usually a single inoculation point in middle
        
      • Reproduction happens at edge of mycelium -> mushrooms
        
      • Usually around plants, form ectomycorrhizae
        
    • Plant pathogenic fungi
      
      • Rusts
        
        • Often have 2 hosts
          
        • Can produce up to 5 different types of spores
          
        • When plant is infected, infection stays localized to one location
          
      • Smuts
        
        • One host
          
        • Usually 2 different types of spores
          
        • Overtakes entire plant
          
    • Human disease
      
      • Fungi that are found in birds nests are hotspots for 2 pathogens
        
        • Cryptococcus and histoplasma (through inhalation)
          
        • Cryptococcus have outer layer that makes them sticky
          
        • Histoplasma have projections that make it sticky
          
        • Germinate in lungs
          
    • Largest organism
      
      • Armillaria root disease – largest organism on earth
        
      • Almost 10 square kilometres (6000 hockey rinks, 1600 football fields)
        
      • Discovered by finding out that different samples in the area had same DNA
        
• Ectomycorrhizae
  
  • Present in ascomycota, basidiomycota, zygomycota
    
    • Not glomeromycota
      
    • Form on outside of the actual cells to exchange nutrients
      
    • Can also stay in between cells; never enter the actual cell
      
• Batrachochytrium (a type of chytridiomycete)
  
  • The main agent that is killing frogs
    
    • Zoospores swim and penetrate frogs
      
    • Start growing inside frog
      
    • Produce spores in specialized structures
      
    • Motile zoospores are produced again
      
    • Frog eventually dies
      
  • Frogs have a protective slime coating that protects their skin from elements and pathogens
    
    • The chytrid causes the coating to disintegrate, weakening them
      
  • When frog is infected, odd behaviour
    
    • Can’t eat well
      
    • Legs are in odd position -> unable to sit properly
      
    • Lose ability to right themselves (can’t put themselves back up) – succumb to heat, UV
      

Genetics Fundamentals

• Review: basic structure of bacteria/archaea
  
  • Pili, DNA, Ribosomes, Cell Wall, Plasma Membrane, Flagellum
    
• Overview:
  
  • DNA replicates (loop) – 2 copies of DNA, one for each daughter cell
    
  • Transcription to RNA (DNA to RNA)
    
  • Translation to Protein (RNA to protein)
    
• Structure of DNA
  
  • 4 bases: A, T, C, G
    
    • A = T (double hydrogen bond)
      
    • C G (triple hydrogen bond) = stronger bond
      
  • Has major grooves and minor grooves
    
  • Adenine and Guanine are purines (two rings)
    
  • Cytosine and Thymine are pyrimidines (one ring) (both have y in name)
    
• DNA binds in a specific way to form the double helix
  
  • Each sugar bonds to a phosphate on each base
    
    • Direction is determined by which carbon the phosphate binds to
      
    • The phosphate will bind to either Carbon 3 or Carbon 5 on the sugar group
      
    • Start numbering on sugar from where it connects with the nucleotide group
      
  • One strand goes 5′ to 3′, the other goes 3′ to 5′
    
  • Order is always Base -> Sugar -> Phosphate -> Base -> Sugar -> Phosphate
    
• Genetics – Informational Molecules
  

Replication

• Replicate DNA strand to begin transcription and translation
  

• Binary Fission
  
  • As bacteria are dividing, they need to create a copy of DNA for daughter cell
  • Take original DNA -> Separate it into two strands
  • Make copy of each strand (complementary)
• Chromosome Replication
  
  • A bacterial chromosome = circle
  • There is a specific spot called the origin of replication
  • A theta structure is formed as the DNA begins to replicate
    • Bidirectional replication – proceeds in both ways
  • The replicated DNA then “peels off” the original strand = 2 identical molecules formed

1. Replisome
   

• DNA helicase – unwinds DNA at origin
  
  • This creates a lot of winding pressure since the strand is being twisted around
    
• DNA gyrase – unwinds to release winding pressure from helicase
  
• DNA primase – synthesizes RNA primer that serves as starting point of synthesis for new strand
  
• DNA polymerase III does the actual reading of every nucleotide using the dark green strand as template (complementary base)
  
  • DNA polymerase III can read 3′ to 5′ and synthesizes 5′ to 3 for leading strand – CONTINUOUS
    
• For the bottom strand (lagging strand), the template given is already 5′ to 3′ WHICH IS BAD since polymerase needs to synthesize in opposite direction
  
• DNA primase synthesizes RNA primer
  
• DNA binding proteins bind to the primer
  
• Typewriter motion happens
  
  • Ie) Okazaki fragments – piece by piece synthesis
    
  • Does a piece -> lets strand go (to go back) -> synthesizes another piece; DISCONTINOUS
    
  • Synthesizes until it reaches previous RNA primer -> unlatches -> strand scooches in and process repeats
    

• Bidirectional replication – two complexes going in different directions
  
• ALWAYS RESULT IS 5′ TO 3′
  

The Gene

• Gene – many regulation signals that trigger functions
  
• Codon - group of 3 nucleotides, each codes for a single amino acid
  
• Start codon / stop codon – tells translation where to begin and start
  
• Open reading frame – between stop/start codon; includes start/stop codon
  
  • Everything in codons
    
• Promoter region – upstream of start codon
  
  • Activates gene expression
    
  • Turns on during transcription to tell transcription where to begin
    
• Terminator – terminates transcription (turns off gene)
  
• Ribosome binding site – binds the ribosome and interacts with ribosome
  

Open Reading Frame (ORF)

• Start/Stop codon are part of open reading frame
  
• NEEDS TO HAVE START AND STOP CODON
  
• EVERYTHING NEEDS TO BE IN CODONS
  

Transcription

• Promoter
  
  • Upstream of start codon
    
  • A specific DNA strand that activates gene
    
  • Proteins bind to promoter to activate gene
    
  • Sigma factors activate genes – turns them on
    

• How transcription starts
  
  • RNA polymerase (core enzyme) binds to promoter region and gets ready for transcription
    
  • Sigma factor recognizes the DNA strand and binds with RNA polymerase at promoter region
    
  • Sigma factor opens up strands so RNA polymerase can begin its work
    
  • Sigma factor is released (not needed anymore)
    
  • RNA polymerase synthesizes mRNA (from promoter to terminator)
    
    • Final mRNA strand is 5′ to 3′ (like DNA)
      
    • Bottom strand of NDA is used as template
      
    • Therefore mRNA = same as top strand of DNA since bottom strand is the template
      
  • mRNA generated has everything between promoter and terminator, including ribosome binding site
    
• RNA
  
  • Virtually same as DNA, except thymine is replaced by uracil (a pyrimidine)
    
• Quick check – transcription
  
  • Completely ignores start/stop codon and does not check for mutations
    
  • Does not require anything other than promoter or terminator
    

Translation

• Now that we have mRNA, we can translate it to a protein
  
• mRNA to protein
  
  • Ribosome reads mRNA and translate it to a protein
    
  • Also involves rRNA and tRNA
    
  • Ribosome associates with mRNA and reads it codon by codon to make the protein
    
  • Protein detaches and ribosome detaches into its subunits
    
• mRNA = messenger RNA
  
• rRNA = ribosomal RNA
  
• tRNA = transfer RNA
  
• rRNA – functions to help associate ribosome with mRNA
  
  • Ribosome binding site is a specific sequence that helps ribosome bind to a strand
    
  • A sequence on the rRNA will bind to the mRNA
    
• tRNA – transfer RNA
  
  • Helps bring in a specific amino acid for protein synthesis to ribosome
    
  • The amino acid is kept on top
    
  • Anticodon loop on the bottom of the tRNA finds the complementary codon on the ribosome, and then adds the amino acid to the growing polypeptide chain
    
  • tRNA is not as specific as we think – sometimes it might bond with multiple codons, even though they’re not exactly the complementary of its anticodon
    
    • Last position = wobble position = some variance
      
• Wobble position on tRNA
  
  • tRNAs don’t discriminate as much
    
  • For instance, you can get 6 different variations that code for the same amino acid
    
  • Genetic redundancy – 64 codings for 20 amino acids
    

Translation – protein synthesis steps

• Ribosome has 3 sites
  
  • E-site, P-site, A-site
    
  • Exit site, Peptide site, Acceptor site
    

1. Codon is recognized by tRNA on P-site of ribosome
   
2. Second tRNA comes in on A-site
   

• Peptide bond forms between 2 amino acids so far = protein growing
  
  • Protein growing on p-site
    

1. Next amino acid comes in when there is a shift (ie. P-site tRNA moves to E-site, A-site tRNA to P-site) and lands on A-site
   
2. 1st tRNA gets bumped into exit site and exits
   

Protein

• Protein gets released from translation
  
• Stop codon is recognized by termination factor and translation stops
  
• Protein forms 3D structure
  
• In bacteria, transcription and translation is simultaneous
  
  • As the DNA is transcribed into mRNA, polyribosomes read it directly
    

Genetic Exchange

• Gene structure: Promoter -> Ribosome binding site -> Start codon, Open Reading Frame, Stop Codon -> Terminator
  
• Genetic structure = similar in Bacteria/Archaea
  
  • Transcription
    
    • Start: Promoter
      
    • Stop: Terminator
      
    • How it works: RNA uses bottom strand as the template (the 3′ to 5′ strand) IN ORDER to make the mRNA product (5′ to 3′)
      
      • Therefore, mRNA will be identical to top strand except for T and U being interchanged
        
  • Translation
    
    • Start: Start codon / Ribosome binding site (but begins translating at start codon until it reaches stop codon)
      
    • Stop: Stop codon
      
• Eukaryotes have “junk” DNA
  
  • Exons = good (coding)
    
  • Introns = “spacer”
    

  • Still have promoter / terminator signals
    
  • Only exons are coding
    
    • Therefore not a continuous open reading frame because of the introns
      
  • The final mRNA has only exons with introns cut out
    
  • Gene A has introns / exons
    
    • Hence transcription reads the whole gene (from promoter -> terminator)
      
  • 1st mRNA has introns and exons
    
    • Protein cuts out introns and pastes exons (splicing) to create final open reading frame
      
  • Mature mRNA leaves nucleus, exported into ER
    
  • Cap and poly A tail put onto mRNA -> function as export signals
    
  • ER in cytoplasm has ribosomes, which form the mature protein from the mature mRNA
    
• Bacteria – 1 step (simultaneous transcription and translation), whereas eukaryotes have multiple steps because of organelles
  
• 3 domain comparison
  
  • More commonalities between Archaea and Eukarya even though the Archaea have similar appearance to Bacteria
    
    • Although Bacteria/Archaea have circular chromosomes and only one
      
    • Eukarya/Archaea share a lot more replication structures and techniques and share transcription factors
      
  • Eukarya and Bacteria = Ester linkages
    
  • Archaea = Ether linkages (extreme conditions)
    

Mutations

• Bacterial Replisome – Mistakes?
  
  • Mistakes are often made by DNA polymerases whilst transcribing
    
  • It replicates it almost perfectly, but small errors can accumulate
    
  • Eg) add in incorrect bases
    
  • This leads to mutations
    
• Mutations – substitution
  
  • Mistake with existing information (no insertions/deletions) – sometimes detrimental
    
  • Start codon has very little effect (if it is created by a mutation) – the actual start codon has a special addition to it
    
  • Silent mutation – does not change the amino acid, yields normal protein (because of the redundant codon code so same amino acid is produced) (eg TAC -> TAT)
    
  • Nonsense mutation – eg) stop codon in middle of gene (eg TAC -> TAG)
    
    • Transcription is not affected (since it disregards codons), but translation stops
      
    • Creates incomplete protein
      
  • Missense mutation – changes amino acid, creating faulty protein (eg TAC -> AAC)
    
    • By changing the amino acid, the protein might still have some residual activity or it might be completely non-functional
      
• Mutations – Insertions and Deletions (INDELS)
  
  • Usually more harmful because they always change the amino acids / codons
    
  • Original reading frame = 0
    
  • Insertion (+1) – transcription doesn’t care (disregards codons) but translation does
    
    • Ribosome reads codons
      
    • However, all codons move down 1 letter because of the insertion, therefore the amino acids and the resultant protein change
      
  • Deletion (-1)
    
  • Since the amino acids always change, there is a difference in the final protein
    

Operons – complex genetic structure

• Bacteria are always streamlining their genetic code
  
• Compressed such that genes with similar functions are under the control of the same regulatory elements
  
  • Saves a lot of space
    
  • For example, one promoter can serve multiple genes (since transcription starts at promoter and ends at terminator)
    
  • Multiple ribosome binding sites are kept to allow for multiple simultaneous translations which are very efficient
    
• Operons – co-regulated genes
  
• Cistron - gene
  
• Monocistronic – one gene in final mRNA
  
• Polycistronic – multiple genes on same strand of mRNA
  
• Operons and metabolism
  
  • Operons direct the breakdown of nutrients in environment (eg lactose) into simple sugars
    
• Operons – Lactose Inducer
  
  • The Lac operon has 3 genes – lacZ, lacY, lacA (lacI is the repressor gene)
    
    • lacZ produces beta-galactosidase which breaks down lactose
      
  • LacI is on all the time, repressing transcription
    
    • This is very efficient because the lactose genes are on ONLY when there is enough lactose
      
  • Normally the repressor binds to a special area near the lac Promoter to block transcription (since RNA polymerase cannot move)
    
  • Once lactose (inducer) binds to the repressor, the repressor comes off which allows the RNA polymerase to transcribe and translate the strand into proteins
    
  • This prevents the bacteria from producing unnecessary proteins
    
• Operons – Arginine Repressor
  
  • Operon directs the synthesis of arginine which is used in translation
    
  • Transcription proceeds, gene is translated into protein and arginine is made
    
  • You reach a point eventually where you have excess arginine
    
    • The XS arginine binds to repressor and causes repressor to bind to the arg Operator to block RNA polymerase
      
  • Ie) once enough, production is stopped
    
  • Once the concentration dips down again, the arginine dissociates and process resumes
    
    • Arginine constantly in flux
      

Horizontal Gene Transfer – Conjugation

• Horizontal gene transfer = lateral gene transfer
  
• Very common in Archaea/Bacteria to have horizontal gene transfer, rare in Eukarya
  

1. Transformation – DNA from environment
2. Conjugation – Bacteria to bacteria transfer
3. Transduction – transfer mediated by viruses

• Plasmids
  
  • Self-replicating circular pieces of DNA
    
    • Code for various genes
      
    • Can move between bacteria
      
    • Independent of chromosomes
      
  • Multiple copies of plasmids per cell (up to 500 copies) – can also have up to a dozen separate plasmids
    
  • Function independently – have own replication mechanism
    
    • Origin, replication proteins
      
  • Big chunk of genetic info that can be infused into an organism
    
• Plasmid purpose: Symbiosis, Metabolism, Resistance
  
  • Pseudomonas putida – plasmid directs breakdown of benzenes and toluenes
    
  • Yersinia pestis (black plague) – plasmid caused infection (a lot of the Black Plague genes were plasmid-encoded; remove plasmid, remove disease)
    
  • Plasmids carry genes in symbiosis
    
    • To facilitate association with host (+/- relationship)
      
  • Metabolic genes
    
    • Break down compounds, acquire energy
      
  • Resistance genes
    
    • Antibiotic resistant genes can move between bacteria
      
• Conjugation Mechanism
  
  • Direct exchange between 2 cells via physical conduit
    
  • Donor (has plasmid) encounters cell without plasmid
    
  • Pilus connects donor and recipient
    
    • Conduit = pilus (conjugated pilus, not pili for gliding)
      
    • Genes needed to synthesize pilus and the conduit are all coded by the plasmid
      
  • Pilus reels in recipient, retracts
    
  • Pore develops between the two cells
    
  • Plasmid in donor is replicated and one of the strands moves through the pore into the recipient
    
  • Both cells (or just recipient) make the plasmid double stranded again
    
• Plasmids encode surface exclusion proteins and display them on surface (if both have them, the exclusion proteins prevent the pili from forming)
  

Viruses and Prions

• Explain why the answer is not A, B, C, etc.
  
• 70 minutes for exam
  
• Horizontal gene transfer – bacteria picking up DNA from other organisms
  

Transformation

• Homologous (similar) recombination
  
  • Bacteria in environment can pick up pieces of DNA in their immediate vicinity
    
  • DNA is often degraded (nutrition for bacteria), so it doesn’t necessarily remain intact
    
  • However, it is possible that it is not degraded and is incorporated into the DNA of bacteria
    
  • If the DNA is kept (donor DNA), endonuclease (protein) nicks/cuts one strand in the middle
    
  • A single stranded binding (SSB) protein (in replication / DNA synthesis – lagging strand) binds to the single cut strand
    
  • Organism produces RecA protein that helps incorporate unwound DNA donor strand into a host
    
  • RecA helps create a cross-strand junction
    
  • The junction can be cut horizontally or vertically to get 2 double strands
    
• RecA helps incorporation of strand, but it requires the incoming strand to have some similar DNA identity to the recipient
  
• Transformation – Transposons
  
  • Transposons are jumping genes that can cut themselves out of DNA and move to another location (selfish genes)
    
    • Selfish genes because they only reproduce; no obvious advantages
      
    • Too much transposition could be a problem by killing the cell
      
  • 2 types of transposons?
    
    • IS2 (Insertion Sequences / IS Elements)
      
      • Simplest – they have one gene in centre that codes for a transposase enzyme
        
      • Transposase enzyme that is produced can recognize the special borders of the IS elements and cuts at the borders
        
      • The piece is picked up, moved and then reinserted somewhere else
        
    • Multiple IS elements could surround gene
      
      • Transponsase can cleave many different ways (not specific – just cuts as a border)
        
      • The transposon could transpose again only if they still have the functional transposase gene
        
      • Different from IS elements since they carry other genes in addition to transposons (like antibiotic resistance genes)
        
• Transformation – Mechanisms of Transposition
  
  • Conservative transposition - only one copy – cut from original, paste into target (original doesn’t have it anymore, starts to degrade or re-ligased)
    
  • Replicate transposition – copy of original transposon or IS is pasted (both still have the sequence)
    

Transduction

• Involves viruses, especially bacteriophages
  
  • Phage attaches to bacterial host, injects DNA into host
    
  • DNA is then used for:
    
    • Replication (for progeny)
      
    • Transcription and translation (to produce needed proteins)
      
      • All proteins necessary for reproduction are produced by the cell’s machinery using bacteriophage DNA
        

1. Bacterial DNA is chopped up in the process -> pieces of bacterial DNA may be accidentally packaged with phage DNA
   
2. Many bacteriophages are assembled
   
3. Host lyses (bursts) via viral enzymes
   
4. Progeny infects another host
   

• Follows same process, but those progeny inject phage + original host DNA into the new host
  
  • Has introduced new strand of DNA tht may go into homologous recombination if it is similar enough and the new host survives
    

Inheritance

• Horizontal gene transfer - between cells (ie. Incoming DNA)
  
• Vertical gene transfer – happens over course of bacterial reproduction (evolution)
  
  • As species diversify, similar genes are found to be present that are not from horizontal gene transfer in that generation
    
  • Hence, it was acquired through inheritance (ancestors); stays within lineage
    

Viruses

• Have medical relevance
  
• Virus – element that requires a host – similar to IS elements in the sense that they are not really alive
  
• Come in a variety of different flavours
  
  • Naked virus vs enveloped virus
    
• Basic structure: nucleic acid surrounded by protein shell
  
  • Protein shell = nucleocapsid / capsid
    
  • Capsomers – subunits of the protein shell
    
• Enveloped viruses are a nucleocapsid surrounded by a membrane envelope (usually membrane of host)
  

Viral structure

• 2 major viral structures
  
  • Helical – capsomers have specific region where nucleic acid is held inside
    
    • CAPSOMER HOLDS DNA
      
  • Icosahedral - 20 sides
    
    • At each node there are 5 capsomers, everywhere else there is 6
      
    • DNA is inside the protein shell
      

• Viruses are very diverse
  
  • Can have enveloped / naked viruses
    
  • Can have DNA and RNA viruses
    
  • Many combinations
    
• Viral types
  
  • + strand = 5′ to 3′ (top)
    
  • - strand = 3′ to 5′ (bottom)
    
  • Bacteriophage have dsDNA
    
    • Transcription of bottom strand to get mRNA+ -> translation -> protein
      
  • Goal is always mRNA+ from whatever the virus has originally
    
    • Need -ve strand as template
      
  • Eg) ssDNA(+) – cannot use + strand as a template, need bottom strand
    
    • Make other strand, then get dsDNA intermediate and then transcribe bottom strand to get mRNA+
      
  • Eg) dsRNA(+) – directly transcribe bottom strand to mRNA+
    
  • Eg) ssRNA(+) – already mRNA+, no transcription needed
    
  • Eg) ssRNA(-) – transcribe minus strand to get mRNA+
    
  • Eg) ssRNA(+) retrovirus – use own reverse transcriptase enzyme (often very sloppy which generates more beneficial mutations) that takes RNA and converts it into a DNA intermediate. Bottom strand used as template to get mRNA+
    

Bacteriophage (dsDNA)

• Some have just head, some have just head and tail
  
  • Capsid contains DNA
    
  • Tail fibres attach to host membrane
    
  • Tail pins help anchor virus as it infects
    
• Infection mechanism
  

1. Phage attaches to membrane with tail fibres
   
2. Tail pins are used to anchor bacteriophage
   
3. Bacteriophage injects DNA (DOES NOT ENTER CELL)
   
4. Tail lysozyme dissolves through membrane and peptidoglycan
   

• Diagram is a gram negative cell
  
• Once DNA is in, there are 2 routes
  
  • DNA is replicated for progeny
    
  • DNA is transcribed and translated (reproduction / assembly / gene expression)
    
  • Many phage code their own proteins, like transcription enzymes, etc.
    
  • These proteins are used to make more phage DNA – most of it is kept for progeny, some reused for more translation
    

1. Virus assembles spontaneously and becomes mature phage particle
   

• It is a very well timed process – each triggers the next set of events
  
• Three major stages
  
  • Early – start things off
    
  • Middle – replication, sigma factors, translation
    
  • Late – final assembly
    

• Lytic vs lysogenic cycles
  
  • Lytic (most cells DO NOT enter lytic pathway)
    
    • Infection (DNA replication, etc)
      
    • Assembly
      
    • Phage particles lyse cell to get released
      
  • Lysogenic
    
    
    • DNA comes in and integrates into host DNA
      
    • Remains dormant as piece of DNA – prophage
      
    • When cell divides, the prophage is treated as part of the bacterial chromosome
      
  • Eg) cholera toxin encoded by prophage – eliminate phage, no more cholera
    
    • Originally there was no toxin in that bacterium – phage introduced it
      
    • Hence phage are very influential
      
• Plaques – lytic
  
  • Lytic cycle causes lysing of bacterial cells
    
  • Plaques form on lawn of bacteria when they are lysed by the phages
    
    • Ie) holes develop on the plate where bacteria have died because of phage
      

Influenza

• Three types
  
  • A – many animals (seasonal flu)
    
  • B – humans, seals
    
  • C – humans, pigs
    
• Influenza A is very well represented by aquatic birds (eg. Duck, geese) – very prevalent
  
• Influenza A has not jumped very well to humans directly from wild birds because of special unique receptors on human cells
  
  • However, pigs can be infected by wild strains
    
  • Can jump to humans via pigs
    
  • Therefore pigs are reservoirs
    
  • Route from pig to humans is unknown
    
• Evidence that it came from domesticated chickens to humans, not yet from wild birds
  
  • Agriculturally related?
    
• Influenza A virus structure
  
  • Has a nucleocapsid which surrounds the nucleic acids in the middle
    
  • Has envelope (to aid in infection)
    
  • Has 8 different RNAs
    
    • 11 genes scattered on 8 RNAs all over the place
      
  • Outer membrane has H and N proteins
    
• Infection
  
  • H and N are critical for attaching to host and escaping from host
    
  • H bonds to sialic acid sugars on cell surfaces
    
  • Virus enters cell, not injected
    
  • RNA is injected into the cell – 2 routes
    
    • Replicate RNA
      
    • Transcribe and translate genes to get functional proteins
      
  • H and N proteins migrate to cell membrane and embed themselves in it
    
  • Virus buds off cell, taking the H and N proteins as part of its own envelope
    
• Antigenic Drift
  
  • Viruses are prone to mistakes
    
  • Antigenic drift describes mutations (small changes in the nature of the H and N)
    
  • Normally there are 3 H types and 2 N types in humans
    
    • In wild, many different variants between H and N proteins (very different)
      
    • Variants can be combined in any combination
      
    • These variants are known to infect humans
      
    • Eg) H1N1 / H5N1 etc
      
  • In the wild – 16 H variants, 9 N variants
    
    • Antigenic shift – different mixture of H and N
      
    • H1N1 vaccine – immune to H1N1 in that year
      
      • Antigenic drift causes it to change year to year
        
• Influenza Review
  
  • Hemagglutinin (H) binds to sialic acid sugars (receptors) on cell surfaces
  • Virus enters cell and releases RNA into cell
  • RNA takes two paths
    • Replication (progeny need RNA for their structure)
    • Transcription and translation (to make required proteins)
  • Some of the replicated RNA migrate to the cell membrane bud off

  • H and N are transcribed proteins
    
  • They embed in the membrane
    
  • Neuraminidase (N) helps in exit
    
• Antigenic Drift (sloppy replication) – subtle
  
  • Changes in the virus due to mutations
    
  • Mistakes can be made in replication and protein production
    
  • Can get different mutations in different parts of RNA genome
    
  • Leads to antigenic drift -> mutations in RNA
    
  • Mutation helps virus escape the immune system
    
• Antigenic shift – more dramatic
  
  • Switching of the H (16 types) and N (9 types) markers
    
  • Shift describes how viruses mix and match those
    
  • Eg) pigs can be infected by both avian and mammalian flu, therefore pig = reservoir
    
    • Pig might get H5N2 and produce H1N2 and H5N1
      
      • If 2 viruses infect the same cell, mixing and matching happen
        
  • Apparently there is a mechanism that prevents H1H1 or other crazy variants from forming
    
• The next pandemic?
  
  • H1N1 – easily spread, rarely fatal (common)
    
    • H1-H3 bond to sialic acid sugars in nose/mouth since they have specific receptors
      
    • H1 to H3 is usually in humans, not the other ones
      
      • However, there are always mutations and antigenic shift
        
  • H5N1 – spreads slowly, often fatal
    
    • Shouldn’t be in humans, but gets in somehow
      
    • H5N1 is a problem because it is not cell-specific – infects a lot of different tissues
      
    • Spreads very slowly and does not discriminate
      
    • Right now it doesn’t move easily between humans, for now
      

Genomics

• Genomics – study of entire genetic complement of organism (focus on many/all genes)
  
  • Very powerful because you can determine biology, physiology, ecology and evolution from its genomic sequence
    
  • Useful when organism is hard to study directly
    
• Can reveal basic physiology
  
  • Can see entire metabolic sequence based on genome by identifying what proteins are produced and then placing them in the grand scheme of things
    
• Bacterial genome
  
  • Major chromosome = circular
    
  • Plasmids
    
  • Need to take both into account when sequencing
    
• Genome sequencing and assembly
  
  • Construction of DNA library by obtaining bacteria, culturing bacteria and extracting all DNA from bacteria
    • Chromosome is very big, so we cannot sequence it continuously; there is a limit
  • Therefore, DNA is chopped up into smaller sequences so it is easier to process
  • Chopped up sequences are cloned by putting them into cloning vectors (special plasmids)
    • Each vector has a small piece of the original DNA
  • The little pieces are later extracted and then sequenced
• Sequencing
  
  • Each piece sequenced is a fragment of the original, forming a genomic library
    
  • Sequence random pieces and assemble them by looking for an overlap
    • Nowadays, usually done with a software program that will look for overlaps and reconstruct original molecule piece by piece
  • Original strand is obtained (ideally)
  • However, you often just get contigs – a bunch of overlapping sequences
    • Don’t get the whole genome assembling perfectly
    • Need to order the contigs
  • Once you order the contigs, you can put them together to get the original sequence to reconstruct the original circular molecule
• Polymerase Chain Reaction (PCR)
  
  • A method to connect contigs
    
  • Amplifies a specific region of DNA (must have / know part of the sequence already)
    
    • Need to start off with original template
      

1. Heat up DNA to denature it at 94 degrees — the two strands separate
2. Add single stranded pieces of synthesized DNA (primer) –> anneal to corresponding sequence at 50-70 degrees depending on primer
3. Polymerization - (72 degrees) Add in bases (dNTP) and polymerase; the polymerase will add the bases in region between primers until it completes the two strands
4. Strands are constructed, and then used to repeat the cycle again too get many more copies; ie) each new strand becomes a template strand

• Need to do it 30-35x to get lots of sample
  
• Polymerase does 5′ to 3′ synthesis in both cases always
  
• PCR uses dNTP bases
  

• Gel electrophoresis
  
  • Detection limits for DNA are very low, so we need a lot of sample
    
  • Gel is how we visualize DNA
    
  • Left hand side – ladder to measure size of DNA fragmenet
    
  • How this works:
    
    • Gel separates DNA via electricity that causes the DNA to migrate through the gel
      
    • The smaller the fragment, the faster it migrates
      
• ddNTPs vs dNTPs
  
  • Each individual base is connected to the next group with OH in dNTP
    
  • In ddNTP, it’s just H (not OH)
    
• Normally if you have OH it serves as the connection for the next phosphate group to bind to
  
  • The elimination of that O prevents the addition of the next base, terminating the chain
    
  • Useful in sequencing
    

Sequencing – Traditional Sanger Sequencing (max 1000 bases, usually 700-800 is common)

• ddNTP terminates chain
  
• Get 4 tubes of ddNTP for each base (eg. ddGTP, etc)
  • Each tube has all the dNTPs, but they have ONE of each ddNTP

1. In PCR, bases are added
2. Sometimes some of the ddNTPs will be incorporated instead of a dNTP, causing the chain to terminate

• You still get one fragment, but you get distinct bands (completely random) in gel electrophoresis
  
• Band length corresponds to where that particular base is
  
• You can identify the shortest band in gel electrophoresis and conclude that it is one of the first bases (eg if it is T, then one of the first bases should be T) – this corresponds to the DNA
  
• Very slow way of sequencing – one by one almost
  

Modern Sanger Sequencing

• Slight modification
  
• Fluorescent dyes to label bases
  
• Laser reads the fluorescent ddNTPs
  
• Sequencing output
  
  • New output – software does all the work
    
  • Each peak = particular base
    

Annotations

• Once you have the complete DNA sequence, need to annotate it
  
• Annotation – define features in genome and tell where the genes are
  
  • Find open reading frames (start codon to stop codon) in general
    
  • However, not all ORFS are necessarily genes….
    
  • Therefore, the program will find every single start/stop, but there are a bunch of potential starts
    
  • Algorithms will determine which genes are most likely
    
• BLAST – comparison tool that uses central database to determine if your particular sequence has been identified as a gene by someone else
  • Basic Local Alignment Search Tool
  • Paste in DNA, select algorithm, search
  • Typical output: input vs match in gene
    
  • Pretty output: shows bands that represent shared genes between organisms
    
  • Many DNA sequences for microbes added and to be added
    
• Once you have the final annotation, create map of the genes
  
  • Can have genes going forwards and backwards
    
  • Sometimes top strand is coding region, sometimes bottom strand
    

Comparative and Evolutionary Genomics

• Once you have the entire genome, you can do comparisons
  
• Comparative and evolutionary genomics
  
  • Look at different strands and see how they’re evolving through full genome comparisons
    
  • For instance, blocks of same colour indicate that region is the same
    
    • Can detect insertions / deletions / substitutions / inversions
      
    • Can tell if whole regions / genes are acquired or lost – eg) polymerase in all strains, disease or virulence gene in some strains only
      
• Inversions – pieces of DNA may flip between top and bottom strand
  
  • Ie) top strand might become coding region or vice versa
    
• Core region = found in all strains
  
• Flexible region = found in some strains
  
• Genomic islands – came in through horizontal gene transfer because of flexible genome
  
  • Often encode for disease/resistance/biosynthetic/catabolic genes
    
  • Considered to be foreign, and usually can be identified
    
  • Often have IS elements or transposons associated with them
  • GC content (% of G or C) is different in genomic island than in surrounding sequence
  • Inserted near tRNA and scattered throughout genome
    • Addvantage: core gene -> since trNAs are more conserved and are core, this guarantees the success of genomic islands

Functional genomics – DNA microarrays

• Looking at what is happening in the whole organism and all the processes
  
• Microarrays – what’s happening in cell at DNA/RNA levels
  
  • A slide that has tiny spots
    
  • Each spot corresponds to a single gene – can have hundreds or thousands of spots
    
  • Genes are arrayed in single stranded form
    
• Microarrays are used to find out how closely related unknown genome is to known genome by finding genes they have in common
  
  • Extract DNA from organism
  • Make DNA single stranded and wash it over slide – genes will fall into tiny spots
  • Wash over slide of known with unknown
    • If they are similar / complementary, they will bind to each other (hybridization)
  • Use solvent to wash away excess that do not bind
  • Remaining binding spots are shared genes
• If you make a couple of microarrays from a known strain, and wash it over with multiple unknowns, you can easily compare multiple organisms
  

RNA microarrays

• Same approach with RNA
  
• However, point of this is to identify which genes are produced in response to an event or turned in
  
• For instance, bacterial RNA in salt vs no salt environments – which genes are turned on?
  
  • Hybridize both on same microarray
  • If they overlap, they have a certain colour
    • Easily see which genes are turned on under certain circumstances