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BIOL 1201 Lecture Notes - Lecture 1: Reductionism, Atom, Scientific Method

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violeteagle17
3 May 2016
School
LSU
Department
Biological Sciences
Course
BIOL 1201
Professor
Bill Wischusen

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Document Summary

Assume the future is like the past. Generalization or model (make sense of the pattern) **prereading for next class- pages 46 to 57. The new observations are combined with the old in order to make the best model possible. Our model is sometimes far from reality but as our process progresses, it gets better and we get to a point where the relationship is very similar and close to perfect. It has very little validity: theory- has been tested many times and is always supported. It becomes something that we think has a great deal of value. Example: gravity: law- nothing more than a theory that continues to be tests and always supported. There are very few things referred to as laws in biology. Most things in biology has exceptions to them (messy). Characteristics of living systems- none of these individually define what it"s like to be alive.

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Related Questions

2.Conclusion:

What have you learned from your study?

Interpret your data/ results:

Do your results support of disprove your hypothesis?

Compare and contrast your result with those of previous research.

Significance of the results: “Big Picture”

What is the global impact of your results?

What questions remain unanswered?

What kinds of experiments can come out of your study?

i have lab for biology and i need help with the Lab Report

the lab name is Bacterial Transformation Lab

1. Introduction:

Introduce the background and the nature of the problem your experiment is investigating.

Summarize the current knowledge of your subject.

Use examples of other research that have examined the same or a similar topic as your experiments.

Ending your introduction:

State your hypothesis

State your predictions

Give a brief statement about how you tested your hypothesis.

please help me with it is important for my lab class tomorrow

that is the lab i put the info please help me for the intro and for number 2 please be clear please

i would be happy if you help me it is due tommorrow i realy need your help on the intro and number 2 please be clear and show clear work hope you do it because it is due tomorrow

Bacterial Transformation Lab

Genetic engineering is one of the newest applications of basic knowledge in biology. It involves the isolation of specific genes from one organism and the insertion of those genes into a second organism of the same, or even different, species. Remember that a gene is a piece of DNA which codes for a product, usually a protein, which gives an organism a particular trait. The development of these techniques has generated considerable excitement and answered many questions, but it has also raised questions. Many scientists and others see genetic engineering as offering opportunities to make life better, for example, by exploring how genes are regulated, by curing diseases of genetic origin, by adding desirable traits to agricultural crops such as the ability to fix nitrogen in corn and pest resistance in cotton, and by genetically altering bacteria with genes enabling them to digest oil spills.

For almost 100 years, it has been possible to isolate DNA from cells, but only in the last 40 years or so has its function been understood. Your textbook discusses the work of such investigators as Fred Griffith and Oswald Avery, who demonstrated that if DNA was isolated from a pneumonia-causing strain of bacteria and added to cultures of nonvirulent bacteria, the recipient cells were transformed into virulent types that caused pneumonia. These transformation experiments were the first to show that genes could be artificially transferred in the laboratory. Since the time of those experiments (Avery's work was done in the 1940s), our knowledge of gene structure, function and control has increased astronomically. The application of this knowledge has created the field of genetic engineering.

Modern genetic engineering techniques depend on three critical factors:

A suitable host organism in which to insert the foreign gene;

A vector to carry foreign genes into the host; and

A means of isolating the host cells that have taken up the foreign gene.

The host organism

The most commonly used host organism is the gut bacterium Escherichia coli (E. coli). Its chromosome is a single large circular DNA molecule, called the genomic DNA, containing about 4 x 106 base pairs. Not every cell will take up foreign DNA when exposed to it, but E. coli grows rapidly, dividing in less than 20 minutes, so that a single cell can give rise to a billion genetically identical descendants in a matter of 10 hours. Thus, a few transformed cells can provide a large number of offspring within a day. The strain we are using is K-12.

The vector

A vector is a DNA molecule used as a vehicle to carry genes from one organism to another. This DNA molecule can be modified by gene-splicing techniques using restriction enzymes and ligases so that it carries the genes of interest (essentially a cut-and-paste operation). Sometimes viruses are used as vectors, but for E. coli, plasmids are often used. A plasmid is a small circular DNA molecule containing 1000 to 200,000 base pairs. Plasmids exist naturally in many strains of E. coli and other bacteria. Plasmids replicate as the cell grows, independent of replication of the genomic DNA. These plasmids are transmitted to each of the product cells during cell division. Plasmids carrying genetic information that is beneficial to the host cell are maintained in a given population by natural selection. Plasmids frequently carry genes that confer antibiotic resistance, an obvious benefit.

When E. coli cells are exposed to plasmids or any other foreign DNA, some of the cells, called competent cells, will take up the DNA. We can induce cells to become competent by treating them with divalent cations, such as Ca++, followed by a brief exposure to high temperature, called a heat shock treatment. Exactly how this treatment causes cells to become competent is not understood, but it is described as making the membranes "leaky" so that large DNA molecules (like plasmids), which would not normally pass through the cell membrane, can enter the cell. This treatment does not make all cells competent, but it greatly increases the number of competent cells. Once in a cell, the plasmids replicate and are passed to the product cells during cell division.

The selective medium

The last requirement for genetic engineering is a means of isolating host cells that have taken up the gene of interest. The techniques used depend on the growth requirements of the host organism. For example, each species of bacteria has particular nutrient requirements. The composition of the growth medium (agar or broth) can be modified to allow growth of only certain bacteria -- for example, by adding or removing nutrients or other chemicals from the medium mixture. This modified medium is called a selective medium, because it selects for the growth of only some species. By introducing an antibiotic such as ampicillin into the medium in which the bacteria are grown, you will select for growth of only those bacteria carrying the antibiotic-resistance gene on newly acquired plasmids. In a matter of days, billions of antibiotic-resistant cells, all with the plasmid, can be grown.

Genetic engineers use a modification of this technique to insert a foreign gene into E. coli. In simplified terms, the plasmid (already carrying an ampicillin resistance gene) is modified by inserting the gene of interest. The gene of interest has been isolated from another source; for example, the gene for human insulin has been isolated from the human genome. The modified plasmid, carrying the inserted gene, is then mixed with competent E. coli and the bacteria are placed in a medium containing ampicillin. Only those cells that have the plasmid will grow in the medium, and they are also the cells carrying the insulin gene (in their plasmids). These selected cells can now be used to manufacture insulin, which can be used for insulin therapy by diabetics.

The genes

In the following experiment, you will insert a plasmid into E. coli. The plasmid you will use carries the gene bla, which codes for a protein (beta-lactamase) that is secreted by the bacteria, inactivating the ampicillin in the agar and allowing for bacterial growth. The plasmid also carries an indicator gene. The indicator gene we are using was isolated from a bioluminescent jellyfish, Aequorea victoria. It codes for Green Fluorescent Protein (GFP).

The GFP gene has been modified to include a regulator system that can be used to control the expression of the gene. Gene expression in all organisms is carefully regulated to allow for adaptation to differing conditions and to prevent wasteful overproduction of unneeded proteins. The genes involved in the breakdown of different food sources are good examples of highly regulated genes. For example, the sugar arabinose is both an energy source and a carbon source for bacteria. The bacterial genes that make digestive enzymes to break down arabinose for food are not expressed when arabinose is not in the environment. But, when arabinose is present, these genes are turned on. When the arabinose runs out, the genes are turned off.

Arabinose initiates transcription of these genes by promoting the binding of RNA polymerase. In the genetically engineered pGLO DNA, some of the genes involved in the breakdown of arabinose have been replaced by the jellyfish gene GFP. When bacteria with this plasmid are grown in the presence of arabinose, the GFP gene is turned on and the bacteria glow green in UV light. When arabinose is absent form the growth medium, the GFP gene remains turned off and the colonies appear white. This is an example of the central molecular framework of biology in action: DNA ? RNA ? protein ? trait.

In summary, you will render E. coli cells competent to take up plasmid DNA. The plasmid carries two identifiable phenotypic markers:

The beta-lactamase or bla gene codes for resistance to the antibiotic ampicillin. We will use this to select for bacteria that have taken up the plasmid.

The pGLO gene codes for Green Fluorescent Protein (GFP), which is switched “ON” if arabinose is present.

Safety Procedure

For your own safety and the safety of others, it is essential that you follow all instructions about handling bacteria and disposal of materials. When you finish work for the day, swab your table with disinfectant. WASH YOUR HANDS thoroughly with soap before leaving the lab for any reason, and at the end of the day after you have cleaned your table. Report any spills to your instructor.

List of Materials

Prepared agar plates (2 LB, 2 LB/amp, 1 LB/amp/ara)

Transformation solution (50 mM CaCl2, pH 7.4)

LB broth

1 pack of inoculation loops

Sterile transfer pipets

1 foam microtube holder w/ tubes

E. coli starter plate

1 red biohazard bag for loop disposal (common use – Loops/pipets only - NO PAPER!!!)

Andrea Smith was taking notes for her biology exam. Her professor has told her that the exam would cover, in part, the di erences between sexual and asexual reproduction. As she reviewed her notes and prepared for today’s class, she was thinking about her own reproductive dilemma. If only asexual reproduction were the case for humans, maybe she wouldn’t be in this mess. Or at least there wouldn’t be questions about who was the father of her twins. “Dwelling on it isn’t going to help me prepare for class, and right now I have got to nish this chapter on animal reproduction,” she thought. She tried to concentrate and forget about her current dilemma as she feverishly typed on her notepad:

Asexual or sexual reproduction: 3 types of asexual reproduction: (1) ssion: separation of a parent organism into two or more individuals of equal size, (2) budding: growth of new individuals from outgrowths of existing organisms, and (3) fragmentation accompanied by regeneration: the breaking of the body into several pieces, some or all of which develop into new complete individuals through the regrowth of lost body parts. NOTE: Be able to explain the di erences between sexual and asexual reproduction!

She suddenly let out a long sigh. “It’ll be ne,” she thought. “I just hope that none of my family or friends watches the show. What was I thinking when I agreed to this? But that’s what Xavier wanted, and I will do whatever it takes to prove he is the father. Besides I am going to need the money if I have to take care of these babies on my own!”

e next day in class she was feeling even more nervous and was becoming increasingly angry as she thought about her current situation. Her thoughts were interrupted by the sound of her professor’s voice:

“OK, class,” her teacher was saying, “that wraps up asexual reproduction. Let’s move on to reproductive cycles
and patterns. Most animals exhibit cycles in their reproductive activity. Reproductive cycles are often controlled
by hormonal and environmental cues. Animals may reproduce either exclusively asexually or sexually while other animals alternate between the two methods. For example, some animals can lay eggs of two types, depending on
the environment and/or season. One egg type matures only if it is fertilized while the other type does not require fertilization for development, a process called parthenogenesis. Some animals, and in rare cases humans, have both male and female reproductive systems. Some hermaphrodites can fertilize themselves, but most must mate with a member of the same species. Please look over these handouts and answer the questions that follow.”

As the other students read through the assignment, Andrea was thinking: “I’m dealing with a case of sexual reproduction that no doubt started with the fertilization of my egg with, hopefully, Xavier’s sperm. at reminds me, I need to make sure I go over internal and external fertilization again in my notes. I’m not sure I completely understand it.”

All this started the night Xavier had come came over to talk to Andrea about their break-up. He had smelled and looked so good that evening. e events of that night had left Andrea wondering if there was really some truth to that stu about pheromones, which Andrea has learned in her class were chemical signals released by one organism that in uence the behavior of another individual of the same species. Even though Andrea had met someone else and had

“An Unusual Case of Animal Reproduction” by Powell and Tillman Page 1

been seeing Neo for a while, she hadn’t been able to resist Xavier. Neither she nor Xavier had behaved like themselves that night. It was unlike them not to use some barrier method of contraception. As the class wrapped up, Andrea’s mind was still on her upcoming appearance on a daytime talk show. In some ways she was dreading it; but she was determined to prove what she believed she had known all along: at Xavier was the father of her twins.

Questions

1. What is the di erence between asexual and sexual reproduction?
2. List and de ne some types of asexual reproduction. Give one example of each. 3. What is the di erence between parthenogenesis and hermaphroditism?
4. What is the di erence between internal and external fertilization?
5. What is the function of pheromones?

NATIONAL CENTER FOR CASE STUDY TEACHING IN SCIENCE

“An Unusual Case of Animal Reproduction” by Powell and Tillman

Page 2

Part II – The Pregnancy

“I can’t believe it has come to this! Airing our dirty laundry on national television. I never thought Xavier would let things get so out of hand.”

It was late and Andrea was so upset she couldn’t sleep. She tried studying for the upcoming exam, but she couldn’t concentrate. She decided to get an early start on packing. She was so angry with Xavier. How could he have left her pregnant and alone, she thought, as she neatly added her new dress to the bag? How could he think that their babies might belong to someone else? She grabbed her journal, about to add it to the bag, but instead sat in her cozy corner chair and began to read:

January 12, 2007

I’m pregnant with twins! Sometimes it’s still hard to believe because it was so unexpected. I feel like I am about to pop! I know that Xavier is the father of my babies and I can’t wait for us to be a family. But he has doubts about it all because he knows that I met someone else during the brief time that we split up. And he wants to be sure that he is the father before we can move on. But what if it is Neo, the new guy I met? ere’s a slight chance but I doubt it. I know the exact time of conception. It was the night Xavier came over to talk about our relationship. It was a little over a week after that night that the pregnancy test detected the increase in HCG. I guess I just missed him so much.

I do regret that Xavier hasn’t been around much during the pregnancy. He has missed the development of our babies. In the past months, I have heard the babies’ heartbeats and felt them moving around. I wish he would come back because it’s obvious that I am pregnant now. Hopefully we can talk through our di erences and get back together before the pregnancy gets di cult—the frequent urination and back pain my OB/GYN keeps warning me about. I know there is no way he will ever let me go through labor alone. I only pray the contractions are not more than I can bear. Xavier seems committed to the idea of a paternity test. Hopefully it won’t come to that, but if it does, we’re going to a daytime show to gure all this out.”

“Wow! at seems like a lifetime ago,” she thought. “Now we have these beautiful twins and we don’t seem any closer to becoming the real family I dreamed about. Well this will all be over in a couple of days. I am 110% con dent that the twins belong to Xavier, not Neo. I can’t wait to see the look on Xavier’s face and hear him apologize once he sees the results of the paternity test!”

Questions

1. What does Andrea mean by time of conception?
2. How is HCG used to determine pregnancy?
3. List some changes that occur with the fetus/mother during the 1st, 2nd, and 3rd trimesters. 4. What hormones are responsible for inducing and regulating labor?
5. What trimester is Andrea in during this journal entry?

NATIONAL CENTER FOR CASE STUDY TEACHING IN SCIENCE

“An Unusual Case of Animal Reproduction” by Powell and Tillman

Page 3

Part III – The Results

Andrea replayed the words over and over again in her mind: “Xavier, you ARE the father!” She was ecstatic. Finally, she could breathe, knowing that Xavier was the father of her babies. en she heard what the host had to say next...

“Neo...YOU ARE the father!”
Andrea looked around in disbelief. She heard herself saying, “What do you mean? You just said Xavier was the father!

If Xavier is the father, how can he be the father?” she asked as she pointed toward Neo.

“Well, this is a rst, even for our show. But it appears that your twins were fathered by both of these men.”

“I can’t believe it. e rst time I do something like this and I end up with twins and two fathers! Not only did I expose myself to potentially deadly STDs, but now I have two children, whom I have no doubt that I will be raising alone, and I have put my school career in jeopardy,” Andrea thought.

She still couldn’t believe this was really happening to her. How was it possible that her TWINS have di erent fathers? What were the events that must have happened within her body that could lead to these circumstances? She grabbed her

journal from her bag and ipped back to the entry describing her feelings the day she found out she was having twins:

August 23, 2006

I just came back from another Dr’s appointment. Dr. Blossom informed me that I am having two babies— twins—fraternal. I don’t know if they are boys or girls yet. One could be a boy and the other a girl. I still can’t believe this has happened. Xavier has to be the father. He has to be! I will have to just play the hand I have dealt myself. How stupid was I? I was going to practice abstinence after Xavier and I broke up...and I certainly wasn’t planning on meeting and getting involved with Neo! I can’t believe that Neo and I didn’t use a condom either. And it’s no excuse that we had been drinking. I just got caught up in the moment with Xavier—going down memory lane and things got all sentimental. I could have at least thought to use the rhythm method and kept track of when ovulation may occur. is has to be the most irresponsible thing I have ever done! Why did I stop taking my birth control pills anyway? And I have no idea where I put that diaphragm. Undoubtedly, some people will judge me as the type of woman who should have a tubal ligation that would permanently prevent any pregnancy.

Everything hit her at that very second. She closed her journal and just sat there for a moment. Andrea was reminded that she had stopped taking the pill the month before she became pregnant. She remembered that physicians recommend that a woman wait at least one cycle after she stops taking the pill before becoming pregnant because there is a chance that multiple ovulations may occur. Did it have something to with oogenesis? Andrea was so confused she just couldn’t keep things straight in her mind. She thought about it for a minute to let it all sink in.

Andrea sat back and thought about the lecture on animal reproduction the week before. She pulled out her lecture notes on the menstrual cycle, the basic foundation of everything that she was going through.

Questions

1. Describe the two types of cycles that occur in female mammals (menstrual vs. estrous).

2. Compare and contrast the sterilization techniques (vasectomy and tubal ligation) and the temporary and reversible methods discussed in the case.

3. What are the functions of GnRH, FSH, LH, estrogen, and progesterone?

4. How can the paternity results be explained? Your answer should consider the amount of time before and after ovulation a woman is at risk for pregnancy and how long sperm can survive in the reproductive tract. Your discussion may include the following terms: ova, oogenesis, and fertilization, etc.

•

Image in title block dervied from licensed image © CLIPAREA.com—Fotolia.com, ID #21458691. Case copyright held by the National Center for Case Study Teaching in Science, University at Bu alo, State University of New York. Originally published December 8, 2011. Please see our usage guidelines, which outline our policy concerning permissible reproduction of this work.

NATIONAL CENTER FOR CASE STUDY TEACHING IN SCIENCE

“An Unusual Case of Animal Reproduction” by Powell and Tillman Page 4

Andrea’s Lecture Notes: The Female Reproductive Cycle

(I) e female reproductive cycle involves both the uterus and the ovaries:

Menstrual cycle = uterine cycle
• Refers to the speci c changes that occur in the uterus

Ovarian cycle
• Cyclic events in the ovaries that regulate the menstrual/uterine cycle

(II) Hypothalamus secretes gonadotrophin-releasing hormone (GnRH) which stimulates the anterior pituitary to secretefollicle stimulating hormone (FSH) and luteinizing hormone (LH) into the blood. FSH and LH regulate the ovarian cycle.

~OVARIAN CYCLE:

Folicular Phase

FSH and LH stimulate a follicle to grow

e growing follicle releases estrogen

Ovulation

• An LH surge triggers ovulation

Luteal Phase

LH stimulates ruptured follicle to become corpus luteum

Corpus luteum secretes estrogen and progesterone, which inhibits LH and FSH secretion from the pituitary

Corpus luteum disintegrates

Estrogen and progesterone levels decrease, releasing the inhibitory e ect on the hypothalamus and the

pituitary

FSH and LH are released and a new cycle begins

(III) Ovarian hormones, estrogen and progesterone, regulate the uterine (menstrual) cycle ~UTERINE CYCLE:

Proliferative Phase

• increasing estrogen levels causes the uterine lining (endometrium) to thicken: prepares the uterus for

implantation of the blastocyst

Secretory Phase
• increased levels of estrogen and progesterone following ovulation maintains the endometrium by increasing

blood supply and growth of endometrial glands that secretes nutrients

Menstrual Flow Phase
• decreased levels of estrogen and progesterone cause the uterine arteries to spasm, depriving the endometrium

of blood: endometrium disintegrates, resulting in menstruation

Based on the information in the case study, Animal Reproduction, please answer the following questions.

Andrea is pregnant and is trying to calculate the time of conception.What is time of conception and how is it determined?

What are the functions of GnRH, FSH LH, estrogen and progesterone in pregnancy?

Andrea is having twins but the babies have two different fathers.Explain the difference between fraternal and identical twins.Which are these?How could the babies have different fathers?