We have had some changes to our recipients for this year. Originally we announced that JENNY CHOI – Washington High School, and LILI HUANG – Galileo Academy were to receive the $3600 scholarships.
However, Lili was also the recipient of several other scholarships that took care of 100% of her academic financial needs. She very graciously offered her scholarship to someone else. Deciding who to give the scholarship to was difficult, there were 3 very qualified runner ups. So after careful consideration we decided to give all three runner ups a $2000 scholarship.
So the complete updated list of recipients is:
Jenny Choi -$3600
Tina Chiem – $2000
Kelly Lee – $2000
Mellany Quiroz – $2000
Congratulations to all of these amazing students!!! They are all very deserving and unique.
We also awarded $100 gift cards for applying are (chosen at random) to: Chun Jin Ruan of Galileo and Jia Jian Fu of Washington.
Best of luck with all your future plans and thank you again for applying.
Late in 2015 my father, Henry Chinn, had a massive heart attack. Fortunately he was able to survive and is still with us. Almost losing him made us think about all that he’s done in his life to help us as family and others. With that in mind, we are pleased to announce a new scholarship created in his honor.
SPECIAL ANNOUNCEMENT (1/21/2016)
To help encourage students to apply (even if you don’t think you are the strongest applicant), we are announcing that 2 students will receive a $100 Visa Gift Card! (randomly selected from those who have submitted all parts of the application by March 4th)
(taken from the College Board Laboratory Manual for AP Biology. 2011)
Introduction: A team of scientists has uncovered the fossil specimen in the photo to the right (Figure 3) near Liaoning Province, China. You should make some preliminary observations about this fossil based on its morphological features. Little is known about the fossil. It appears to be a new species. Upon careful examination, small amounts of soft tissue have been discovered. Normally, soft tissue does not survive fossilization; however, rare situations of such preservation do occur. Scientists were able to extract DNA nucleotides from the tissue and use the information to sequence several genes.
You will use bioinformatic methods to support a hypothesis as to the evolutionary relationship between modern organisms and a fossilized organism using DNA collected from soft tissues. You will use BLAST to analyze the information from several genes and determine the most likely placement of the fossil species on the figure on the right.
Form an initial hypothesis as to where you believe the fossil specimen should be place on the cladogram based on the morphological observations you made earlier.
Download the genes:
Gene Files are here: (Save them in a folder on your desktop)
Comparing the Gene to known sequences
Upload each gene sequence into BLAST by following the directions below. You will be doing this for each sequence separately.
- Go to the BLAST site: http://blast.ncbi.nlm.nih.gov/Blast.cgi
3. Click on “Saved Strategies” from the menu at the top of the page. This will allow you to upload your first file.
4. Under “Upload Search Strategy,” click on “Browse” and locate the gene file you just downloaded in the folder on your desktop.
5. Click on “View.”
6. A screen will appear with the parameters for your query already configured. NOTE: Look but do not alter any of the parameters. Scroll down the page and click on the “BLAST” button at the bottom of the page.
7. Collect and analyze the information from your first gene sequence (according to the instructions on the next page). Then do this with the other gene sequences.
Analyze the Results:
The chart (a bunch of horizontal red bars) is a graphical summary of your first sequence. The first line represents the most similar sequence that BLAST was able to pull from the data bases it searched. If you hover over the line, you will see the species of organism that this sequence was derived from. Other, less similar sequences are included from top (most similar) to bottom (less similar).
Scroll down below the graph and notice the list. The species in the list are those with sequences identical to or most similar to the gene of interest. The most similar sequences are first, and as you move down the list, the sequences become less similar to your gene of interest. NOTE: Species with common ancestry will share similar genes. The more similar genes two species have in common, the more recent their common ancestor and the closer the two species will be located on the cladogram.
- Max(imum) Score: the highest alignment score of a set of aligned segments from the same subject (database) sequence. The higher the max score, the closer the alignment.
- Accession: If you click on the Accession number for a particular species listed, you will get a full report, that includes the classification scheme of the species, the research journal in which the gene was first reported, and the sequence of bases that appear to align with your gene of interest. It will identify the gene, in this case it is collagen, that you are working with and you will also see the common name of the organism if it has one!
Build a Cladogram: The results are tedious at best but there is a quick way for you to build a cladogram for the sequences. Click on “Distance tree of results” above the chart.
If you find that your tree seems a bit complicated, go back to BLAST, download the file a second time and go to “Optimize for” and select “Somewhat similar sequences.” The resulting tree will be less complex. If you want to save a picture of your tree, right click on the tree and save it as a .png You can then insert it into a document.
Build a Report for EACH gene:
- List the top 3 different species that this gene might be found in. (look up common names as well – clicking on accession will tell you)
- Identify which protein this is, and a one sentence description of its function.
- List a “Max” score (higher is more similar), and a “Ident” score (100% is perfect match) for each gene
- Sketch a cladogram with the information you gathered from above.
Discussion: Write 3 statements, with evidence and reasoning about the evolutionary relationships discovered in your research. Was your hypothesis correct?
- Choose a species and search for its scientific name, i.e. Panthera pardus
- Search for genes, here http://www.ncbi.nlm.nih.gov/gene
- Click on a gene from the list that comes up. Look for a FASTA link, and click on it. (if no FASTA link go back and find another gene).
- Select and copy the FASTA sequence.
- Go to the BLAST homepage
- select Nucleotide BLAST.
- Paste the FASTA sequence into the box
- Hit BLAST bottom on bottom of page
- Select one of the “hits” that comes up. Write down what species shares some alignment with the gene you searched for.
- Repeat for 2 more genes from step 2.
- Build a report like you did for the 4 genes from above. Try to construct a cladogram from the information you have gathered about the gene you are looking at.
For More Information:
Intro to Bioinformatics: https://www.youtube.com/watch?v=kyXdH-9MWnU
Intro to Cladistics http://www.ucmp.berkeley.edu/clad/clad4.html
Take as many of these quizzes as you have time for. Have someone sign off and write your score down. (Last time I put in at least one question from these sites on the test, so you definitely should practice on these!)
1) Prentice Hall Transcription http://www.phschool.com/science/biology_place/biocoach/transcription/quiz.html
3) ThinkQuest Transcription http://library.thinkquest.org/27819/cgi-bin/quiz.cgi?quiz=6_6
4) University of Connecticutt http://virtual.class.uconn.edu/~virtclas/cgi-bin/quiz/quiz.cgi?/u/bi107vc/public_html/fa02/terry/code.qz
5) Thinkquest Translation http://library.thinkquest.org/27819/cgi-bin/quiz.cgi?quiz=6_8
Amino Acid/Codon Chart:
This is a list of links to animations that might help you visualize the processes better. Our connection at school might be too slow, so you might have to go online at home instead. Also, use headphones if you are in the computer lab!
We are going to start a new project on the topic of cancer. For this assignment you will:
A) Read the following website and answer the following questions about cancer: (write the answers in your lab book)http://cancer.duke.edu/pated/pfrcnews/PFRCNewsletterFebruary04.asp (You can use any website, but this one is pretty good)
1) How many cells do we have in our body?
2) What is a stem cell? How does a liver cell differ from a stomach cell?
3) What is a cell’s main purpose in life?
4) How does cancer get started? (carcinogenesis?)
5) What is a mistake in a cell’s genetic information called?
6) How does a cell usually deal with these mistakes?
7) What is apoptosis?
8) What is the “perfect storm” that can lead to cancer?
9) What is the “secret” to cancer’s success?
10) What is the key to preventing and treating cancer?
B) You will chose a specific type of cancer that you will make a poster to present your research. The way to find a specific type of cancer is to do a search for “types of cancer” and see what you get. I don’t want too many people doing the same type of cancer, so you will have to tell me what type you are doing, and if it’s already taken you might have to chose a new topic.
C) Your report will include:
1) A Nice Looking Title (2 points)
2) An Introduction to what cancer is in general (4 points)
3) An Introduction to the type of cancer you are researching (8 points)
a) What part of the body does it affect?
b) What are the symptoms, how do you know you have it? What are the effects?
c) What are the treatments, what is the survival rate for people with this type of cancer?
4) What organizations, societies, or groups are there to support people with this type of cancer? Where can you find more information about it? (4 points)
5) Your sources. Paste the websites that you used to get your information. (2 points)
Practice with Punnett Squares and Pedigrees
Do you best to do the questions before looking at the answers. Print this page and have someone sign you off that you “completed” the exercise. Who knows, some of these might be on the test! Try all four.
1. Luby’s Bio Help. http://www.borg.com/~lubehawk/psquprac.htm
2. University of Cincinatti http://biology.clc.uc.edu/courses/bio105/geneprob.htm
3. University of Virginia http://www.people.virginia.edu/~rjh9u/pedhint.html
4. Ohio State University http://www.mansfield.ohio-state.edu/~sabedon/biol1128.htm
Biotechnology 1 Syllabus
Mr. Chinn and Ms. Chu
Galileo Academy of Science & Technology
Monday, Tuesday, Friday
3:05 – 3:30
(Or schedule appointments for after school meetings
1st year Biotechnology pathway course description: Biotechnology and Human Genetics (I) is a year-long course, delivered in two modules:
· 1st Semester: We will explore possible careers in the field of biotechnology. You will learn the basic principles and concepts of genetics and genetic engineering techniques.
· 2nd Semester: We will continue our learning of standard laboratory techniques and applications of these techniques in real-life science.
The course will consist of class lectures, pre-lab and post-lab discussions, and weekly laboratories.
Biotechnology & Human Genetics (I) is an upper level elective course offered to students who have completed 1 year of biology and 1 year of chemistry (may be taken concurrently). This course is the first of the 2-year series in the biotechnology pathway. Students who are interested in learning more about biotechnology and possible careers in the field may be selected to continue on for the second year course in the biotechnology pathway.
1. Laboratory safety and career exploration
2. Basic Biochemistry (Review)
3. Basic Cell Biology (Review)
4. Mendelian Genetics
5. DNA Structure
6. Fundamental Biotechnology Techniques & Concepts
a. Pipet and standard laboratory equipment handling
b. Bacteria & Virus (Vector & Plasmid)
c. Gel Electrophoresis
d. Bacterial culture and colony streaking
e. Plasmid preparation
f. Restriction digestion
Quizzes: Announced quizzes
Exams: 2 lab exams and one final exam
Lab book: Required to keep a lab notebook. You will be graded periodically.
1. DNA Replication
2. Protein Synthesis
3. Gene Regulation
4. Human Genetics (Diseases)
5. Bioethics (Risk Analysis)
6. Fundamental Biotechnology Techniques & Concepts
a. Ligation (vector and insert)
Quizzes: Announced quizzes
Exams: One midterm and one final exam
Lab book: Required to keep a lab notebook. You will be graded periodically.
Rules and Policies:
“You Have the Right to Learn, and I Have the Right to Teach.”
In any classroom, rules and policies are created to provide the best and the safest learning environment possible. In addition to following all Galileo and District rules, Mr. Chinn/Ms. Chu’s rules are as follows:
1. Students are to show respect to the teacher and to their fellow students
2. Students should support one another and work together as a team
3. Students are to be on task; no unauthorized experiments or playing with equipment
4. Students are responsible for their own actions at all times
Safety Precautions (Parents must read & sign off) X
Room 103 is used to teach biology and biotechnology all day; therefore, many dangerous pieces of equipment and harmful chemicals are present. For your safety and the safety of others, inappropriate classroom behavior will be dealt with immediately and with harsh consequences. Inappropriate classroom behavior includes, but is not limited to, the following:
1. Any unauthorized experiment or horseplay in class/lab (Absolutely forbidden)
2. Abuse of classroom property, including equipment, lab materials, books, etc.
3. Excessive talking in class that disrupts or distracts from classroom operations (Constructive discussion of relevant science topics during class time in an orderly manner is welcome.)
4. Disrespect shown toward the teacher, either verbally or physically (This will result in an automatic referral out of the classroom)
5. Disruptive behavior toward others, such as paper throwing, name calling, cursing, picking on students, physical threats, etc.
Equipment & chemical handling (Parents must read & sign off) X .
It is important to follow directions on proper handling of equipment and chemicals. All equipments used in biotechnology course are extremely expensive. When a student is found to be responsible for braking equipment (from lack of care), parent conference will be set up and student’s grade may be affected.
Many chemicals used in biotechnology class are harmful if treated improperly. Student must follow instructor’s directions when handling chemicals to avoid contact or accident. Student who shows lack of care when handling chemicals in class will be removed from classroom and parent conference will be set up to discuss dangerous classroom behavior. If no improvement is shown, student will be dropped from the course to ensure the safety of all students and teacher in the class.
When an inappropriate behavior is observed, any one or more of the following actions will be taken:
1. Verbal warning
2. Conference with student
3. Detention and call to parent/guardian
4. Immediate referral to the dean’s office, call to a parent, and parent-teacher-student conference
Other Important Issues
1. Students are expected to be on time as signified by the bell. Habitual lateness will affect your grades.
2. You may use the bathroom during the period. But don’t abuse this privilege, if you are asking to use the “bathroom” everyday, you may be denied permission to leave.
3. Cheating on exams or copying the work of other students will result in a failing grade and a referral to the dean.
4. Parents must excuse all absences. Work missed due to excused absences can be made up for no penalty within two school days after returning to class. Work missed for unexcused absences (cuts) cannot be made up and will adversely affect grades.
General Grading Procedures
Students need to keep track of their own grades. Every 2-3 weeks, class grades will be posted in a designated area using a personal ID number. Your grade will be based on the total number of points you earned throughout the semester. At the end of the semester, the highest total number of points from the two biotechnology classes will be adjusted to 100% and the rest of the students’ grades will be adjusted accordingly as well.
A 100% to 90 %
B 89% to 80%
C 79% to 70 %
D 69 to 60%
F Below 60%
Homework assignments are due on the designated “due dates”. Each day that the assignment is late, there will be a 20% penalty subtracted from the total points earned. Example:
· A 30-point assignment due on Wednesday is turned in on Friday. Let’s say you would have received 24 out of 30 points. But since you handed the assignment in 2 days late, you lose 20% each day (40% total), for a revised score of 14 points (60% of 24).
· Even if you would have scored a perfect 30 points, the highest possible points you can earn on this late assignment is 18 (30 points X 60%)
There will be pop (unannounced) binder checks. You are expected to bring your science binder to class every time class meets. Each binder check is worth 20 points and you will need to have all your work and class notes in chronological order at the time of the pop check. There will be no make-up binder checks whether it is an excused absence or not.
There are only two ways to earn extra credit:
1. By correctly answering extra credit questions on exams
2. By participating in the extra credit activities offered throughout the semester
Important: Do not ask me for an extra credit project at the end of the semester to boost your grades. Your effort for this course is evaluated continuously throughout the semester. You will not be given extra credit to pass this class based on one single project.
Tracking Your Grades
You are also responsible for keeping track of your assignments and grades using your assignment log (this should be in the front of your biotechnology binder). Proof is required when there is a discrepancy between your assignment log and my grade book. Without proof, the grades in my grade book will be final.
You are invited to come ask me questions anytime before, during, or after class. I want to know about your progress so I can help you. Please do NOT wait until the last minute to ask questions. I can also schedule meeting time if that is more convenient for you or your parents/guardian. As always, excuses are only excuses; they cannot get you out of responsibilities in life. If you have been successful using excuses to get you out of trouble in the past, do not expect that to work now in my classroom or later when you graduate into the “real world”.
Course Syllabus Biology
Instructor: Mr. Curtis Chinn
Room 403 (Periods 3-5 including lunch and after school) Room 401(6th Period)
Email: misterchinn @ gmail dot com
Course Overview: This is a first year course in Biological Sciences. The course will be a comprehensive course in biology covering the topics expected by the State of California State and the SF Unified School District. The instruction for course will consist mainly of lectures, discussions, laboratory experiments and independent investigations and research. Textbook used: Biology by Miller and Levine © 2004
Topics Covered in General Biology:
Biochemistry, the chemistry of life
Cell Biology, Energetics (Photosynthesis,Cellular Respiration), Cell Division
Genetics and Biotechnology
Origins and Changes over Time
Diversity of Life
Botany and Zoology
Evaluation: Grading in this course will be based on the following:
Tests and Quizzes: 15%
Laboratory Reports: 20%
Class work: 40%
As you can tell, the class is heavily weighted on in class work. It is vital that every student come to class on time and every day. Class work is NOT busy work, this class will do as much hands-on work as we can. We will do activities, demonstrations, presentations, internet research, laboratory experiments and in class projects. Students can not learn if they are not in class. Tests will be based on participation and completion of these activities.
Participation points are given for students who are paying attention and answering questions when asked. Other participation points are given during the first 5 minutes of class as “Do-Nows”
Rules: All school wide and district rules will be enforced, as stated in the student handbook. In addition to those, the following rules apply to this class.
1) Be Respectful: Students are to show respect to the teacher and other students.
Students show respect by listening and staying on-task, not interrupting, yelling out, or being out of place
2) Be safe: Students must follow all instructions carefully
No unauthorized experiments or playing around will be allowed. Always use the equipemnt properly and take safety precautions. This is for the safety of all students. Please report any unsafe conditions.
3) Be Responsible: Students need to take full responsibility for actions.
Being responsible means that students will get to class every school day on-time, prepared with the necessary supplies, and ready to learn.
Being responsible means that students will do their best in everything they do in order to acheive their full potential in life. This includes doing homework, studying for tests, and seeking help (we all need help in life!)
Being responsible also means that students understand and accept the consequences of their actions and do their best to learn from all situations.
1) Late or Incomplete Homework/Classwork: will recieve PARTIAL credit. Must be completed before the next time homework is checked. If you are late to class when homework is being checked, your homework will be late as well. You will lose 10% for every school day it’s late. If it’s more than 5 days late, it will not be graded.
2) Make-up Work: Students with excused absences will be able to make-up work for full credit (work must be completed the week the student returns. Students with unexcused absences will not be able to make up work and will lose 100% of the points.
3) Unsafe behavior during lab: student will not be allowed to complete the lab and will lose 100% of the points for that lab.
4) Tardiness: Students will not be allowed to make up any work corrected or missed. After 3 tardies a letter will be sent home or a phone call will be made.
5) Cuts/Tardies: More than 3 unexcused absences or 6 tardies per grading period, a “W” will appear on the students report card. More than 6 unexcused absences or 12 tardies per semester, a “U” will appear on the student’s final report card.
6) Disruptive Behavior such as Talking or Yelling Out, Being Out of Place, or being defiant, will result in a warning given. After that, a student may lose 5 participation points. After several disruptive behaviors, a phone call home will be made or a referral will be made to student court/dean.
7) Hats, mp3/CD players, Cell Phones. You will get a warning. If you break it the second time, I will take it away and turn into the Dean’s Office.
8) Eating in class, will be permitted, as long as it’s a small snack (smaller than you hand), and does not disrupt the class. If there is any trash left behind. the privilege of eating will be taken away.
Students are required to have a laboratory notebook (composition book). These can be purchased at most school supply stores or our Lion’s League Student Store. A pencil or pen is also required every day.