Chapter 11

We will begin chapter 11 when you return from break. You have been emailed the first part of the packet for section 11.1.

Please print this out and bring it to class on Tuesday. You will also need to read pages 208-209 BEFORE coming to class on Tuesday Feb 3.


We will be taking notes on gene regulation in prokaryotes as well as watching some video clips.

Never Say Prove Again!

I thought we talked about this the last time you submitted lab reports, but perhaps we didn't or it slipped your mind...

In science you can never really PROVE anything; you can disprove a theory and you can find support for a hypothesis but you can't PROVE it. Hopefully this classy James Bond movie poster will help you remember.

More Practice for the midterm

Don't be this guy...

Be this guy...

Thanks to Dr. Madoka Gray-Mitstumune of UMB Fredricton there are tons of review questions, lecture notes and vocab lists for our book here.

REMEMBER: THIS IS NOT OUR COURSE, JUST A SIMILAR COURSE AS AN ADDITIONAL RESOURCE FOR MORE PRACTICE.

Mid Year Study Guide

Here it is....what you've been waiting for....

Review your lab reports!!! The graphs and results and discussion questions are included on the mid-year.

Chapter 1

What is a hypothesis?

What is a theory?

What is the scientific method?

What is a controlled experiment? Why is it important?

What are the 3 domains? What are the kingdoms?

What are the 7 characteristics of living things?

Chapter 2

What is an element? a molecule? a compound?

What is the atomic number of an element? The mass number?

What is an isotope? A radioactive isotope?

What is an ionic vs. a covalent bond? A polar vs. nonpolar covalent bond?

What are hydrogen bonds? Why are they important in molecules, especially water?

What is the pH scale? What represents acidity vs. alkalinity?

What is a solute, solvent and solution?

Chapter 3: Organic Molecules

1. What is an organic compound?
2. What is an isomer? Be able to recognize structural isomers.
3. Functional groups – what are they? What are they characteristic of (i.e. alcohols, ketones, aldehydes, etc.)? What class of macromolecules are they present in – carbohydrates, lipids, proteins, nucleic acids?
4. What are the building blocks of each of the classes of molecules? How many are there?
5. What is dehydration synthesis? What is hydrolysis?
6. Carbohydrates:
1. What elements make up carbohydrates? What is their function? What is an example?
2. Monosaccharides – glucose, fructose, galactose
3. Polysaccharides - What are starch, glycogen and cellulose made from? Where is each found?
4. Be able to recognize a carbohydrate.
7. Lipids:
1. Why are lipids grouped together?
2. What elements primarily compose fats? What are the examples of lipids – fats, waxes, phospholipids, steroids – and what is the function of each type?
3. Be able to recognize a triglyceride molecule.
8. Proteins:
1. Know the general functions of proteins (structure, contractile, storage, defense, transport, communication, enzymes)
2. Describe the structure of a protein. What elements are in proteins? What functional groups are present?
3. What are some examples of proteins?
4. Know the four levels of the protein’s structure: primary (amino acid sequence), secondary (alpha helix and pleated sheets), tertiary (overall shape – globular vs. fibrous), and quaternary (relationship between multiple polypeptide chains). Do all proteins have all four layers?
9. Nucleic Acids:
1. What are the subunits of the nucleotide (sugar, phosphate group and a nitrogenous base)

Chapter 4: A Tour of the Cell

1. What is the difference between a prokaryotic and eukaryotic cell? Which is more complex?
2. Make a list (or a chart) of all the cell organelles mentioned in the chapter. What is the function of each? Where in the cell is it found?
3. Draw a plant cell and an animal cell. How are they similar? How are they different?
4. How are the chloroplasts and the mitochondria similar? How are they different?

A. MEMBRANE STRUCTURE AND FUNCTION

1. What is selective permeability?

2. Why are membranes important within the cell?

3. What is the cell membrane composed of and how is its structure helpful in its function?

4. Define the terms: passive transport, diffusion, osmosis, facilitated diffusion, active transport. Give biological examples of each of these processes.

5. What is tonicity? Why is it important? Give an example of a biologically important situation of a hypotonic solution. Of a hypertonic solution. Of an isotonic solution.

6. What is a concentration gradient? What does it mean to travel down a gradient? Against a gradient? Are concentration gradients independent of one another?

7. What is the importance of concentration gradients within our body?

8. What type of solution is healthiest for animal cells? For plant cells?

9. What are the processes that transport very large molecules?

B. ENERGY AND THE CELL

10. Describe an exergonic and an endergonic reaction.
11. What is energy coupling? How does it help a cell perform work?
12. What is cellular metabolism?
13. How does the structure of ATP make it a “high energy” molecule?
14. What is the process by which the 3^rd phosphate group is cleaved off of the ATP molecule?

C. ENZYMES

15. What do enzymes do for a reaction? Why are they important for life?
16. How specific are enzymes and their shapes for their substrate? Where does the substrate bind with the enzyme?
17. What is the “induced fit” model?
18. What is a negative feedback loop?

Chapter 6

GENERAL INFORMATION

What is aerobic respiration?

What is anaerobic respiration? How much ATP does it produce?

What is cellular respiration? How much ATP does it produce?

What are redox reactions? What is oxidation (gain or loss of electrons?)? What is reduction (gain or loss of electrons?)?

Explain in term of cellular respiration why we breathe oxygen, and exhale carbon dioxide?

What is the difference between substrate level phosphorylation and chemiosmotic (or oxidative) phosphorylation?

GLYCOLYSIS

Where does glycolysis occur?

What are the net (Total/overall) products of glycolysis?

Why do we invest energy to make glycolysis occur?

How much of the energy available in a glucose molecule is harvested as ATP in glycolysis?

If oxygen is present, where does pyruvic acid go? What happens to it?

If oxygen is not present, where does pyruvic acid go? What happens to it?

Why would yeast choose to perform anaerobic respiration, as in our lab, even though oxygen was available to them?

FERMENTATION

What is the purpose of fermentation? (What does it recycle for glycolysis to continue?)

When does fermentation take place?

What does a build up of lactic acid cause in our bodies?

KREBS CYCLE

Where does the Krebs cycle take place?

What are the net (Total/overall) products of the Krebs cycle? For each acetyl coA molecule? For each glucose molecule?

How is pyruvic acid changed before it will enter the Krebs cycle?

What is the primary energy carrier that is produced in the Krebs cycle?

ELECTRON TRANSPORT CHAIN (SYSTEM)

Where does the electron transport chain take place?

What are the net (Total/overall) products of the ETC?

What molecules enter the electron transport chain?

What specifically happens to the electrons in the ETC? What is the final electron acceptor in this system? What happens to that product after it initially accepts electrons?

How is the transport of H+ ions linked with the ETC? Why is this important?

What does the proton gradient drive the ATP synthase? Why does it only happen at this specific location in the membrane (i.e. why can’t the H+ ions move across the membrane at any point)?

Chapter 7 - Photosynthesis

What is the path an electron takes through photosynthesis?

What is the balanced equation for photosynthesis? What is reduced and what is oxidized?

What is an autotroph? A producer? (What are we?)

Why is chlorophyll green? What wavelength (in nm) does it reflect?

Describe the anatomy of a leaf. What is the stomata and what happens here? The thylakoid – what is present and what occurs? The chloroplasts – what happens here? The grana? The stroma – what happens here?

What are the light reactions? What happens and what is created?

What is the dark reaction? What happens and what is created?

What is a photosystem? What is the difference between Photosystems I and II?

What is the reaction center? What are antenna molecules? Where do the electrons come from that are put into the photosystem and eventually move to the primary electron acceptor?

What are the differences between the electron transport chains in the mitochondria and the ETCs in the thylakoid?

How many times the Calvin cycle have to turn to produce on G3P? one glucose? How much CO2, ATP and NADPH does each of these consume?

How do plants store their excess sugar?

What is carbon fixation?

Chapter 8 - Mitosis and Meiosis

1. Know the multitudinous definitions that are in the chapter: sexual reproduction, asexual reproduction, life cycle, chromosomes, chromatin, sister chromatids, centromere, cell cyle, mitosis, mitotic spindle, kinetochore, cleavage furrow, cell plate, anchorage dependence, density-dependent inhibition, cell cycle control center, tumor, malignant vs. benign tumors, metastasis, somatic cell, homologous chromosom, autosomes, diploid, haploid, gametes, fertilization, zygote, meiosis, crossing over, chiasma, genetic recombination.

2. karyotype, trisomy 21 (Down’s syndrome), nondisjunction, deletion, duplication, inversion, translocation. You do NEED to know these terms, this is a correction from the first email.

3. What are the four phases of mitosis and meiosis? What similarities exist in these phases between mitosis, meiosis I and meiosis II? What makes them different? Which one process (mitosis, meiosis I and meiosis II) is most different from the others? Explain your answer.

4. How much time of the entire cell cycle is spent in Interphase? M phase?

5. How does cytokinesis differ for plant and animal cells?

6. What are the three functions of mitosis? Briefly describe each.

Chpt 9 – Patterns of Inheritance

1. Mendel’s principles
1. Dominant vs. recessive traits
2. Genotype s. Phenotype
3. Parental, F1 and F2 generations
2. Punnett Squares and the rules of probability
1. Monohybrid cross – define and know expected ratios
2. Dihybrid cross - define and know expected ratios
3. Family Pedigrees
3. Variations of Mendel’s Patterns
1. Incomplete dominance
2. Codominance
3. Sex linkage
4. Pleiotropy
5. Polygenic inheritance
4. Chromosomal basis of inheritance
1. Chromosomal theory of inheritance
2. Sources of variation
3. Linked genes

Chapter 10 Test

Today (and tomorrow) students will have a test on chapter 10. A friendly reminder that I will only preview labs if they are sent to me before 7pm this evening.

HHMI on HIV & AIDS

Today C blocked wrapped up chapter 10 by learning about HIV from the HHMI Holiday Lecture Series.

To watch some of the animations we watched in class, click here.

Homework: Review for your test and work on your lab reports.

pGLO Lab Report Rubric

This lab report should follow the following guidelines:

1. No more than 3 pages, 1.5 spacing (not 1.3 etc), Size 12, Times New Roman Font, 1.5 inch margins and page numbers.

2. See The Guide to Writing Scientific Papers for additional formatting details.

RUBRIC

Title 3 points

Includes the environmental factors that were manipulated (1 pt).

The parameter that was measured (1pt)

The specific organism that was studied (1pt).

Introduction 12 points

Purpose (2 pts)

Relevant background information (5 pts)

hypothesis (5pts)

Materials and Methods 5 points

You only need to write one sentence for this section. "See Bacterial Transformation: The pGLO System from BIO-RAD pages 14 and 15"

Results 10 points

Here the researcher presents summarized data for inspection using narrative text (4 pts)

You must include a tables and/or figures to display summarized data (6pts)

Formatting of table 5 points

All tables and/or graphs have…

Title (1pt)

A description explaining what is presented (4 pts)

Discussion 20 points

Here, the researcher interprets the data in terms of any patterns that were observed (5 pts)

An explanation of how the results differed from those hypothesized (5 pts)

Describe the evidence that indicates whether your attempt at performing a genetic transformation was successful or not (this is question number 4 in the Lesson 3 Review Questions). (5 points)

Include at least 3 sources of error AND explanation for the impact these would have, as well as ways to eliminate them in a future experiment. (5 pts)

Conclusion 7 points

This section simply states what the researcher thinks the data mean, and, as such, should relate directly back to the problem/question stated in the introduction.

Acknowledgments 3 points

In this section you should give credit to people who have helped you with the research or with writing the paper. If your work has been supported by a grant, you would also give credit for that in this section.

Literature Cited 3 points

This section lists, in alphabetical order by author, all published information that was referred to anywhere in the text of the paper. It provides the readers with the information needed should they want to refer to the original literature on the general problem.

Spelling, Grammar & Formatting 5 points

Report is free from spelling and grammatical errors. All section headings are in bold and centered.

Total possible score: 73 points

Happy Mish!

Happy Mish everyone, enjoy your holiday!

Please bring your packets to class tomorrow so we can wrap up chapter 10.

A block: Test on Thursday
C & D blocks: Test on Friday

Hello from Mount Washington

Today has been a packed day on the mountain. Here's a basic summary of what we've done...

Took the Cat up to the summit
Safety Overview
Tour of the station
Walk around the summit a few times
Headed up to the tower to be the highest point for miles around

Factoid for the day: There is 20% less oxygen at the summit or at the base.

Click here for the webcams for the mountain.

Chapter 10 wrap up for D block & Lab Analysis for C block

Today D block will wrap up Chapter 10 by learning about HIV & AIDS. We will continue to learn about HIV and AIDS next week.

D block your Chapter 10 test will be on Friday January 23rd.

C block analyzed their pGLO lab today and.........there was SUCCESSFUL TRANSFORMATION!

MLK Day

There were no classes today because of MLK day. Instead listened to guest speakers in both Chapel & Mem Hall.


C Block please make sure that you bring your lab notebooks to class tomorrow as we will be analyzing the pGLO experiment to see if it worked.

D Block please make sure you bring your packet to class.

Lab 9: Bacterial Transformation Using pGLO

Today C block did a great job setting up the pGLO transformation. Now all we have to do is wait for the bacteria to grow and see if our experiment worked. Click here for the post with the video for the protocol as well as the prelab requirements.

If you are confused about what is going on in this lab check out this PDF which has easy to understand information plasmids, vectors, bacterial transformations and more.

The next time class meets we will look at the plates so make sure you bring your lab notebook to class.

Conroy Visitor

Today Christopher Buckley spoke as the winter Conroy Visitor, as a result C block did not have class today.

D block wrapped up the bulk of chapter 10 by creating a review (pictorial, written or some combination of the two) of DNA replication, transcription & translation.

A block finished through sections 10.14 and for homework needs to create a summary review of DNA replication, transcription & translation.

A & D blocks also voted to move their chapter 10 test up, so to have more time to review for the mid-year exam. After C block votes tomorrow I will update the calendar.

(image from Men's Vogue)

Plugging away with Chapter 10

Today students had a quiz on sections 10.1 through 10.7. Overall the results were very good, many people earned a 100%.

C block: make sure that you complete the prelab for Wednesday and come prepared to focus in lab.

A & D blocks: please bring your books to class tomorrow.

All classes: Watch the short Translation Animation

Lab 9: Bacterial Transformation Using pGLO

In your class on Blackboard under course documents, the PDF for next week's lab (Jan 14 for C block and Jan 17 for A & D blocks) is posted.


BEFORE coming to lab you need to print this document and paste/tape/staple it into your lab notebooks, as well as fill in the table of contents, write a purpose and answer the lesson 1 focus questions (there are only 4 questions) You will be graded on this.

3. You will also need to read the procedure. In the PDF it is pages 6 & 7 (the actual printed page numbers are 14 & 15. Who knows, you might just have a prelab quiz on this...

If you are reading the procedure and think, "I have no idea what I am supposed to do" then I HIGHLY recommend watching the 4 minute video clip below which demonstrates most of the procedure.

Watch more Google Video videos on AOL Video

You will be doing a formal write up on this, so it is a good idea to take extra care in preparing for this lab.

Lab 8: Strawberry DNA Extraction (Sat).

To read about the Strawberry DNA extraction click here.

Help on Blackboard: In case you "lost" the chapter 10 packet it is posted on Blackboard. There is also a supplementary PowerPoint on DNA replication, transcription & translation if you would like additional review.

Extra Help

I am on duty this Saturday night in Wing. If you'd like extra help please stop by BEFORE 10:00pm (after 10:00 my mind starts to go....). Rather than showing up and saying, "I don't get it" please bring specific questions as well as your chapter 10 packet.

DNA Replication

Today (A block) and tomorrow ( C and D blocks) we will be learning about DNA replication and transcription. We first heard about DNA replication when we learned about the cell cycle (Chapter 8). Recall that DNA is replicated during the S phase of the cell cycle. But how does it actually happen?Transcription
In order to make proteins, DNA must first be transcribed into a strand of messenger DNA. This mRNA can leave the nucleus and head for a ribosome.

Homework:
A & D block: Complete the DNA Replication WebQuest which has been emailed to you. This is due in class on Monday. You also have your prelab to complete due on Saturday.

C block: Complete the DNA Replication WebQuest which has been emailed to you. This is due in class on Monday.

Reminder: You will have a quiz on Monday in class on Sections 10.1-10.7. You will NOT be allowed to use any notes and the quiz will not take the whole period, so please make sure you bring the packet.

Success in Lab

C Block had a very successful lab today. There is no homework this evening, however in the event that you have some extra time (and a burning desire to get ahead) you can read 10.4 through 10.7 in the book on DNA replication.

Lab 8: Strawberry DNA Extraction

In lab this week we will be extracting DNA from strawberries. C block you have been emailed the procedure along with the information below.

Read the lab, cut it out and tape/glue/staple it into your lab notebook. You will receive a 10 point homework grade for the following:

4 points: Completing the table of contents in your lab notebook (date, title, page numbers)

4 points: In PEN Write a 2-3 sentence purpose IN YOUR OWN WORDS

2 points: The procedure is NEATLY taped/glued/stapled into your lab notebook BEFORE coming to class. There should be no pages of the lab hanging outside of your lab notebook.

DNA review and Start of Chapter 10

We started off class today with students writing down their New Year's resolutions. These include:
* Be well prepared for class and speak more
* Review my notes on the same day I learned the material to reinforce what I learned
* Ask questions in class when I do not understand something
* Study in chunks rather than cram
* Arrive to class on time / don't bag

My New Year's resolutions are to give smaller, more frequent assessments and to do a better job of putting in attendance the day it happens.

Next we...
1. Reviewed the differences between DNA and RNA
2. Learned how experiments showed that DNA (not protein) is the genetic material by watching this video clip.
3. Examined the structure of DNA to understand how the strands are antiparallel with a 5' and 3' end.

NOTE: D block even got ahead of schedule completing an overview of 10.5

Homework All Classes: Read pages 182-183 in your book and write down three things you learned. There is space for you to do this on page 1 of the packet.

C Block: check your email this evening for information about tomorrow's lab.

New Year's Resolutions & A Busy January

Happy New Year Everyone! When we return you will be asked to write down a new year's resolution for class. Please think carefully about what you would like to improve.

You have been emailed the packet for chapter 10. The trial run of the packet for chapter nine seemed to go well, so we'll keep doing this. Please print this out and bring it to class on Tuesday.

January is a very busy month, we don't have nearly as much class time as you might think. Below is a calendar with the plan for the month. Click on the picture to make it larger.