4th

Exams

5th

READING DAY

Available in 110! Bring questions and review sheets

6th

Exams

7th

Biology Exam

Report to MP room next to Gym (Dress for heat!)

8th

2nd languages

Makeup exams

11

April 30-

Period 1: Mechanics of Translation-

Nucleotides into Amino Acid Language

Vocabulary:

AUG- or Start

Reading frame

Codon

Stop codon

UTR- untranslated region (before AUG and after STOP)

mRNA

But where does this occur in the cell? What bring the correct amino acid?

HW: Please "translate" the second gene into the primary order of amino acids.  Some did not do first gene correctly yet- be sure that both are completed.

Honors Project

May 1st

Art Fundementals Field Trip to Grounds for Sculpture

Only period 3/4 will have class, sub will be there

3

HONORS PLACEMENT TESTING FOR NEXT YEAR'S COURSES- Period 7 see Mr. Coe if a conflict. If you missed the testing, please see Mr. Coe about rescheduling another opportunity to take the test.

Section 12: worked on finding the ORF of a DNA sequence.  please be sure that you have finished the analysis of your DNA and marked introns and exons.

Section 1/2 meeting tomorrow at 8:30 in room 104

Section 34/ 5/8: reviewed hw and reviewed translation.

ppt  for translation

Videos to support understanding

For Honors Students: RNAi video and how it affects gene transcription

Translation video

Lame overall video of protein synthesis, RNA polymerase is WAY too small here! yucky music.

 FOR HW- Review and attempt the following questions. Please look them up, find videos, etc. Make some attempt for understanding these concept prior to class tomorrow.

What are introns?

What are exons?

WATCH/ DO animation on RNA splicing linked here.

Do prokaryotes have introns?

Alternative Splicing?

What if you wanted a eukaryotic gene such as insulin to be manufactured by bacterial cell?  What would you have to do to human version of the DNA sequnce to make it usable in bacteria?

4

 Special ANNOUNCEMENT: Section 1/2 meeting tomorrow at 8:30 in room 104.

(O'Mara off campus during headmasters break tomorrow!)

5/6

TEST: DNA Structure and Mol Bio.

Bring a copy of test to class on MONDAY.

NO outside class discussion or collaboration of any type, including online chats, Facebook groups, google, etc

Test Link

9    English Field  Trip - Students leaving at 10:30

O'Mara covering a study hall for Form III

10 Special Schedule (Friday Schedule) combined rehearsal

Antoine DuBourg Concert

28  Memorial Day!

No Classes!

29

Yearbook

Final Lab of the semester

Digest plan due today! 

Tubes should be labeled with information

TEST link here

Diagrams for question 9/0! - soooo sorry!

You are NOT allowed to work together unless you are in class. You are not to discuss the test outside of class in any way shape or form. By clicking the above link you agree to abide by the honor code. Bring copy of test to class tomorrow for work in small groups. 

You will complete your restriction digests and then work on your tests. SUbmissions due preferably Wednesday by midnight but Thursday night is acceptable with permission.

Review Sheet for Final Exam

30

Special Schedule

Restriction Digests

Work on test in class

31

Special Schedule

Running gels for restriction digests during class

HW; Review gel pictures linked here.

Section 1/2

PDF of gel annotation- courtesy of Nate and Stephanie

Section 1/2

1914 Matt, Rahul, Evan, Nate, Claire, Ruthie

1915 Images of gels Clay Nat, Russell, Rahul Mat

Section 3/4

PDF gel annotation first gel

1917( LM, GA),

second gel 1918: Gabby, Caitlin)

PDF annotation of third gel-

image 1920 (Lori & Anthony)

Section 5/8

PDF Annotation of Gel Big Box  Leah, Ricky, Julian C, Kyle, Charlie, Kirmser

Section 5/8 Big gel

Section 58 Small gel

MARKER LADDER IMAGE

JUNE 1

Reivew DAY

Bring diagrams for review (See Monday for link)

You should have worked on your review sheet at least somewhat this week.

June 2/3

Work on Review Sheet

I will be in on Tuesday for Reading day and ready and willing to answer questions.

d.

Moday April 2

Cellular Respiration

What is the big picture for cell respiration? 

Is how is this similar or different to photosynthesis?

The raw ingredients for cellular respiration

the mitochondria: Find a labeled drawing of the mitochodria. Be sure that you the following in your diagram: Matrix, Inner membrane, cristae, intermembrane space, outer mitochondrial membrane.

Cellular Respiration occurs in 3 major pieces

1 Glycolysis- where does that occur in the cell? Read carefully the PDB molecule of the month article on the glycolyis enzymes and their function

2. Krebs Cycle (annoying music)- where does that occur?

3 Electron Transport Chain- where is that found? Try to identify what goes into each piece and what exits each stage. How does each stage connect to each other. Which stage has significant similarities to photosynthesis?

MY ALL TIME FAVORITE Video of cell respiration

watch and learn!!!

Khan Academy- overview of cell respiration kind of boring and long...but decent. Let me know what you think.

Tuesday

3

Cellular Respiration Continues

Glycolysis

Kreb

ETC

HW: Wrkst Handed out in class. Please complete using notes

Section 56 & 34: google doc needed of collecting and averaging data.

Wednesday 4

Cell respiration Continues

Lab 12: yeast metabolism lab Create google doc for data collection and trends.

Thursday 5th

PPT for Cell Respiration here.

This weekend- print out the ppt and review. Add to the diagrams and make them "tell the story" of cell respiration.

Review carefully the packet that I handed out earlier this week. Special deal will be offered to each class. I would suggest you talk and compare answers before Tuesday.

8

POSTER

IN CLASS:

Using the your resources, not the internet,

create a poster that details the entire process of cell respiration. We will brainstorm a few minutes in the beginning of class for vocab/ concepts to be included on the poster. If you get done early- find your photosythesis poster and double check it.

Review carefully the packet that I handed out last week. week. Special deal will be offered to each class. I would suggest you talk and compare answers before TOMORROW>

9

Review

Double check your posters!

Check other people's posters

Packet special deal offer today!

10

Test:

Photosynthesis & Cell Respiration including Fermentation

 You will be allowed to use your POSTERS only.

16

Genetically Modified foods continues.

Please check out the following sites and compare the different definitions of Genetically Modified Foods.

FDA commission report. What is their defination of GMO food?

Another govt agency. What is their definitionof GMO?

Check out wikipedia too.!

This website keeps track of the currently introduced biotech foods. How many different types of corn? What was the earliest food that was biotech'ed? 

GMO debate video- organic farming vs biotech.

17

Honors projects due (old date)

See Honorsbiology.com for updated date.

DNA structure and function

 DNA structure and function ppt

Vocabulary:

antiparallel

5' to 3'

base pairing

complementary bases

Review the following links:

LONG DNA video- background- some info on Watson and Crick

Lame DNA structure- there is a mistake at 1:10ish, can you find it?

DNA structure video

DNA Structure website-what is a nucleoside?

DNA packing video

How many AT base pairs in this image of DNA?

How does complementary bases play an important role in DNA replication?

LAST ONE: This is a jmol tutorial on DNA structure and function. Please read complete the following document in conjunction with completing the tutorial. Due Wednesday.

18

DNA Replication

HW: Review your notes from class then complete the questions below

The following questions should be answered in some form in your notebook:

What is an Okazaki Fragment?

Good video on the process of DNA replication. What is the difference between leading and lagging strand?

More complicated video! Now, can you pick out discontinous and continous synthesis?

PDB: DNA Polymerase

Review the paragraph about accuracy? How accurate is DNA polymerase and what mechanisms are in place to keep the accuracy of the enzyme?

Another Flash animation of DNA replication, shows all the proteins, including the one that lays down the RNA primer.

19

HONORS PROJECTS DUE! NEW DATE!!!!

LEAVING FOR ASBMB at 8th period

Worksheet on DNA replication

And PCR

20 In Service Day

NO Classes

ASBMB

21/22

ASBMB

23

ASBMB

NO School-Headmaster Day off!

24

Section 1/2:

Thymine Dimers and Children of the Night. What can you suggest as a fix for this problem? Investigate gene therapy!

Section 3/4. 5/6:

Comparison of PCR and DNA Replication. What  are the shared pieces? How are they different?

Can you find the PCR song?

5/6: Complete DNA replication diagram

25

Section /12

Review of Primers and understanding Primer construction with DNA structure

Finding information in DNA sequence

Section 3/4 & 5/6

Primer construction with DNA structure

HW:

Molecular Biology Introduction!

What is the definition of molecular biology?

Transcription and Translation, what is transcription and translation?

Transcription Basic

Transcription video DRY

Transcription videoMedium more extraneous details

Translation

27

Gene hunting Prokaryotes

We worked on a piece of DNA today that is from a prokaryotic genome.  (Honors students: should be able to compare a prokaryotic genome to eukarytotic genome!)

We discussed the elements of a gene

1. Promotor Sequence

2. Coding region

3 Terminator region

You should be able to discuss the function of each and  all of the above should be isoloated on DNA given out in class.

This link will have promotor sequence and terminator sequence

For Monday: Please isolate the (with pencil) all of the above and try to complete the mRNA transcript for the coding region.

30

Honors Project III Comes out.

1

Art Fundementals Field Trip!

Mrs O'Mara on trip!

April 30-

Period 1: Mechanics of Translation-

Nucleotides into Amino Acid Language

Vocabulary:

AUG- or Start

Reading frame

Codon

Stop codon

UTR- untranslated region (before AUG and after STOP)

mRNA

But where does this occur in the cell? What bring the correct amino acid?

HW: Please "translate" the second gene into the primary order of amino acids.  Some did not do first gene correctly yet- be sure that both are completed.

Honors Project

May 1st

Art Fundementals Field Trip to Grounds for Sculpture

Only period 3/4 will have class, sub will be there

3

HONORS PLACEMENT TESTING FOR NEXT YEAR'S COURSES- Period 7 see Mr. Coe if a conflict.

9    English Field  Trip - Students leaving at 10:30

10 Special Schedule (Friday Schedule) combined rehearsal

Antoine DuBourg Concert

28  Memorial Day!

No Classes!

Monday 5th

Membrane Dynamic begins!

1.Fluid Mosaic Model of the Cell Membrane- what is fluid about a lipid bilayer? What is meant by mosaic part?  What are the pieces that make up the mosaic?

Proteins have an important part in cell the functional role of cell membrane. What are the different roles that proteins play?

Supple membrane

2. How do particles move across a membrane? How do different particles move across the membrane?

Facilitated diffusion slow mo

Large particle/bulk transport

What are three types by observing the video.

Read in your Book:

Page 363-369 Up to the Fluidity of the lipid bilayer

Read the Membrane Protein section on page 372-373- especially the drawings.

Carefully at the drawings on 380-381

Carefully observe the drawing on page 384

Ppt

Fluid Mosaic Model, Extracellular Fluid,  Intracellular Fluid, Gradient, Law of diffusion,

Wed 7th

Potato Cores are in solution will be massed first tomorrow.

You will then need to graph % change

% Change=  (Final mass- Initial Mass)/

Initial Mass * 100

You will need to create spread sheet that

(HINT: start on this tonight)

1)  Records the Masses of initial and final

2) Show % change as a function that works in your spread sheet

3) Graph the % change of  your potato cores. The graph should have a title, labeled correctly, and have appropriate axis labeled.

4) Write a conclusion with a statement of the trend with a biologically plausible explanation of the trend. You should include the terms hypertonic, isotonic, and hypotonic in your discussion. What is the approximate solute concentration in potatoes?

Complete the WS on osmosis & water balance. Be sure that you have pictures

BRING COMPUTERS TO CLASS TOMORROW

Thurs 8th

Worksheet due in class today.

Take a crack at the quiz to be given in class tomorrow.

Fri 9th

Quiz on Cell Parts and Membrane Dynamics

26

Cell Energy Processes

Photosynthesis & Cell Respiration

Photosynthesis 1st! Why? Which came first photosynthesis or cellular respiration?

Photosynthesis Review Flalsh Animation- Complete the puzzles at the end of the animation

Photosynthesis-youtube video

Photosynthesis Review site

Review Lab 3 and Lab 4- Click through both labs to get a sense of the process of photosynthesis.

Lab Bench

Related Vocab that should be in your notes.

• Autotrophs/producers- Are you a producer? Explain?
• Leaf Structure (vocab)- Where is the primary area for photosynthesis? What is the structure for allowing gasses in and out of the leaf?
• Summary Reaction...know it.
• Visible Light spectrum
• Light and Dark Reaction- what goes into to each? Why the name? Can you find another name for each.

light and dark reaction

ppt on ingredients for photosynthesis

8

27

Cell Energy Processes

Capturing the light....

The light reaction and the dark reaction

What are the products of the light reaction? Where is it located?

Where is the dark reaction reaction? What are the products of the dark reaction?

Relook at the summary reaction and see how the light and dark reaction fit into this equation.

Review the chlorophyll demo we did today and see if you can place it in the ppt. Where would it occur?

Section 58 work on graphing assignment

Setion 34 graphing assignment assigned today DUE monday

28

Cell Energy Processes

Section 12 Graphing assignment assigned today due monday.

Can an animal photosynthesize?

Read this link about the green sea slug!

A photosynthetic animal!!!!

Today you received a packet with diagrams.

Please attempt to label the diagrams carefully for class tomorrow.

Work on the graphing assignment. Please see me ahead of deadline if you would like help.

29

Cell Energy Processes

30

Cell Energy Processes

Section 56- Graphing assigment due

February 6th

Giants WIN!!!!

HONORS LETTER DUE

Go over test!

Enzyme sheet for HW linked here.

Enzyme Project Assigned- Please choose ONE enzyme (that is not listed on the hw) and construct a paragraph about its role. You should discuss itsmetabolic role and include  a discussion of substrate binding. Please include a discussion of the products that are formed too.

You also need to include two images of your protein, rendered from the viewer on from one of the PDB's ID cited in the MOM article.  One view must show secondary structure. Each image must include a caption that state the PDB id and the what the file is.. The assignment should not more than one page long and should be 50% image. Try to use a WHITE background instead of black. You will be graded on your text explanation of your protein, your images, and your ability to follow directions.

Please include the NAME of your enzyme on the top of the page in bold.

7th

Read:

Enzymes: Wikipedia artlicle

PPT for Enzymes

Enzymes Animation

Enzyme You Tube Animation- enzyme/substrate complex.

What is the enzyme-substrate complex? How does that relate to specificity and lock and key?

8th

Enzyme Lab

Catalase

9th

Catalase graph

10th Protein Project DUE

Second catalase experiment

13

HONORS PROJECT COMES OUT TODAY!!!

GRAPHING with excel- you will be expected to produce two graphs from excel, you will be required to turn email your excel file with your data table and graphs in the file AND turn in two graphs- 1- enzyme concentration, 2- your investigated variable experiment. You will need to turn an excel file via email and a hardcopy of both graphs. Both should have labeled axi, titles, correct units and a sentence or two that states the trend or the conclusion to be drawn from the graphical interpretation of the data. Each person turns in their OWN work though you may help each other construct excel file, every student must make their own excel file and send it to me.

Swim meet away , not around for CP

14

Finish enzyme discussion

and statement of trends

 You will need to email me the excel file containing both sets of data analysis for both experiment.

You will need to create a work document  with two graphs each graph should have a statement that desribes the trend and include a biologically plausible explanation of the trend. Besure that your graph is done correctly. .

15

Graphs due

Animotos continues

ANIMOTO of  enzyme concepts

http://animoto.com/create - register for the free version...use your Pingry email.

You will be responsible for creating a 30sec film on ONE aspect of enzyme function.

You and one partner will be responsible for a 30 second video using the above software link. Your film must illustrate or explain in clay animation (using a cell phone that takes pictures) one specific enzymatic concept but you will need to include text that has the appropriate vocabulary for this unit. I will supply the play dough! Good luck  and have fun!

Film choices:

1) competitive and non competivie inhibition of enzyme function, include example

2) Induced fit, include a discussion of active site and substrate, and example

3) How ph OR salt OR heat affect enzyme and enzyme's activity

4) a specific enzmatic reaction

5) How enzyme concentration can affect the rate of reaction.

Ranney Swim Meet- Mrs. O'Mara NOT around CP

16

Animotos

17

Animotos due

Open notes quiz of enzymes (25 points)

21 The YANKED back day off..classes to be held

Living and non living

What is a living thing?

What is the dividing line between living and non living?

CELLS!

Review Animations from class

and ppt (links inside ppt)

HW: redo graph option, be sure that you submit and staple your OLD graph on top and your new and improved version underneath.

Have power printed so that you can take notes on the slides.

22

Cells!

Fish tank and making slides

23

Cheek Cells and Onion

24

Cheek and Onion

Biozone Packet Complete through the PLANT CELL PAGE

2

Out sick!

Worked on sub packet.

28

Slides continues

29

Slides

Thursday March 1st

Part of a cell

ppt

Friday march 2

Quiz: CELLS! ppt, open notes, open "tray"