BLAST Lab

January 30, 2013

Intro to Cladistics

http://www.ucmp.berkeley.edu/clad/clad4.html

 

Gene Files are here:

https://drive.google.com/folderview?id=0BzhhMp8wJzcUOHBkakprSWpvYU0&usp=sharing

 

BLAST homepage

http://blast.ncbi.nlm.nih.gov/Blast.cgi

 

Your own search:

http://www.ncbi.nlm.nih.gov/gene

 

Worm Challenge

November 25, 2012

testing

Contact Information

September 22, 2009

To Contact:

email:  chinnc@galileoweb dot org

phone:  415-749-3430  ext: 3103

mail:  c/0

Galileo Academy

1150 Francisco St

San Francisco, CA 94118

Study Questions

January 19, 2006

Review Questions for Biology – C. Chinn

 

Directions:  These will be the questions on your Final exam, for semester one.  You do not have to turn these in, but you should try to do them with out the book if you can.  Most of these questions will be multiple choice.

 

  1. What is a hypothesis? 
  2. To be useful in science, a hypothesis must be?
  3. What is a controlled experiment? 
  4. What is a scientific theory? 
  5. If a microscope has an objective of 10x and a eyepiece of 10x, what is the power of magnification?
  6. How are multicellular and unicellular organisms alike?  How are they different? 
  7. What are the characteristics of all living things? 
  8. What is an ionic bond? 
  9. What is a covalent bond?
  10. What are hydrogen bonds?
  11. What is cohesion between water molecules?  What is adhesion of water molecules?   
  12. What pH is acidic, what pH is neutral, what pH is basic?
  13. What are some types of carbohydrates?
  14. What are types of lipids?
  15. What are 2 things that can affect how well an enzyme works?
  16. What are the three parts of the cell theory?
  17. What is the difference between a prokaryote and eukaryote?
  18. Which part of the cell does cellular respiration?
  19. Which part of the cell does photosynthesis?
  20. Which part of the cell makes proteins?
  21. Which part of the cell contains the genetic information?
  22. What are cell membranes made out of?
  23. What is diffusion?
  24. What is osmosis?
  25. If a cell with lots of solutes inside is placed in distilled (pure) water, what will happen to the cell?
  26. What is the difference between active and passive transport?
  27. What is the difference between an autotroph and a heterotroph?
  28. What is ATP used for?
  29. What is the formula for photosynthesis?
  30. What comes out of photosynthesis?
  31. What comes out of cellular respiration?
  32. What are 2 reasons why a cell might need to divide?
  33. What is cancer?
  34. What are stem cells?
  35. If you cross a TT (Tall Plant) with a  tt(short) plant, what are the possible offspring?
  36. Can two Brown eyed parents (B) have a blue eyed child (bb)?
  37. What is the shape of DNA?  Who discovered this shape? 
  38. What are the three parts of a nucleotide?
  39. What is GTC-CAA-CCT-ACC transcribe to in mRNA?
  40. For the same DNA sequence, what amino acids does that sequence code for?
  41. What are the base pairing rules?
  42. What does tRNA do?
  43. What is a frame shift mutation?  What are 2 ways you can have a frameshift?

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DNA Quizzes

December 6, 2005

Directions: 

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

2)  McGraw Hill http://highered.mcgraw-hill.com/sites/0070271348/student_view0/chapter13/chapter_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: 

http://www.accessexcellence.org/RC/VL/GG/genetic.html

Animations: 

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!

http://science.nhmccd.edu/biol/bio1int.htm

Cancer Assignment

November 30, 2005

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)

Questions:

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)

 

Punnett and Pedigree

November 7, 2005

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    

 

Signed-off By:                     

 

2.  University of Cincinatti   http://biology.clc.uc.edu/courses/bio105/geneprob.htm

 

Signed-off By:                  

 

3.  University of Virginia   http://www.people.virginia.edu/~rjh9u/pedhint.html

 

Signed-off By:                 

 

4.  Ohio State University   http://www.mansfield.ohio-state.edu/~sabedon/biol1128.htm

 

Signed-off By:                 

Biotech Syllabus

November 3, 2005

Biotechnology 1 Syllabus 

                           

Mr. Chinn and Ms. Chu        

Galileo Academy of Science & Technology

Office/Room: 103

Contact: 749-3430 ext: 3103  Email: misterchinn@yahoo.com                                                      teacher_chu@hotmail.com

Office Hours:

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.

 

Prerequisites:

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.

 

 

Course Outline:

 

Fall Semester

 

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.

 

Spring Semester

 

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)

b.      PCR

c.      Transformation

 

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.”

 

General Rules

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.

 

Consequences

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.

 

Grading Policies

 

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.

 

Grading Scale

A        100% to 90 %

B        89% to 80%

C        79% to 70 %

D        69 to 60%

F        Below 60%

 

Homework Assignments

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%)

 

Binder Check

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.

 

Extra Credit

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.

 

SPECIAL NOTE:

 

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”. 

 

Biology Syllabus

October 26, 2005

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

Webpage:   http://www.galileoweb.org/chinn/

 

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:

 

Fall Semester

Biochemistry, the chemistry of life

Cell Biology, Energetics (Photosynthesis,Cellular Respiration), Cell Division

Genetics and Biotechnology

Spring Semester

Origins and Changes over Time

Diversity of Life

Botany and Zoology

Physiology

 

Evaluation: Grading in this course will be based on the following:

Tests and Quizzes:  15%

Homework:  15%

Laboratory Reports:  20%

Class work:  40%

Participation: 10%

 

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. 

 

Consequences:

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.

 

Materials:

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.

Mitosis Quizzes

October 25, 2005

Cell Division Online Quizzes

Directions: Type in or click on the following links to quizzes.

Mitosis Quizzes:

1.  Biology in Motion  q    Score:

http://biologyinmotion.com/cell_division/

* Note:  The computer lab may have trouble with this site, but you should be able to get through.  Also note:  Sometimes it’s hard to get the chromosomes to “stay” where they’re supposed to stay, just keep trying.

Meiosis Quizzes

2.  Discovery Channel’s Teacher site     q  Score:

http://school.discovery.com/quizzes15/biolessonscom/MitosisandMeiosis.html

3.  Prentice Hall ( a biology book publishing company) q  Score:

http://www.phschool.com/science/biology_place/biocoach/meiosis/quiz.html

4. Michigan College of Science and Technology

http://www.cst.cmich.edu/users/benja1dw/bio101/tools/quiz/mitosis.htm

5. Darien Public Schools

http://www.darienps.org/teachers/otterspoor/reviewquiz/mitosis_review_quiz.html

6.  Palomar College

http://anthro.palomar.edu/biobasis/quizzes/bioquiz2.htm

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