Month: June 2016

Be able to determine whether a compound is oxidized or reduced in an oxidation reduction reaction.

In some reactions, electrons are transferred from one atom or molecule to another or they get closer to one atom than another (they form polar bonds). The atom (or molecule) receiving the electron is said to get reduced (remember electrons have a negative charge so gaining electrons makes their overall charge more negative). The atom (or molecule) losing the electrons is said to be oxidized. The following can help you remember

Oxidation is loss of electrons, Reduction is Gain (OIL RIG)

2K + Cl₂→2KCl  in KCl, K has a positive charge (K⁺)  thus is oxidized relative to K,

In KCl, Cl has a negative charge (Cl^–) thus is reduced relative to to Cl₂.

Some more rules:

Losing Hydrogen =oxidation

Gaining Hydrogen =reduction

Losing oxygen=reduction

Gaining oxygen=oxidation

Example

6CO₂ + 6H_2O→C₆H₁₂O₆ + 6O₂ (Equation for photosynthesis)

Carbon dioxide gains hydrogen and is reduced

Water loses hydrogens and is oxidized

Try the following (more on the group worksheet)

In the following reactions which compound or element is oxidized and which is reduced?

2Ca + O₂ →2CaO

CH₃CH₂OH + 3O₂ → 2CO₂ + 3H₂O

For the following know (1) Where they occur (2) what is produced and what is used (ATP, NADH, carbon dioxide etc)—Glycolysis, Krebs Cycle(including the preparation step) , Oxidative Phosphorylation

Here are some useful exercises on Glycolysis the Krebs Cycle and Oxidative Phosphorylation

Glycolysis

Kreb Cycle

Electron Transport Chain

Know the order of events in respiration

In the activity below you will see terms as well as steps. Drag “step 1” to the process which is the first step among those listed. If you are correct, the step and process will disappear. Continue until all of the steps are gone. How fast can you do this?

Respiration Order

Here are some more review activities

Review Game 1

This is best done with “Wordshoot”

Review Game 2

 

Be able to rank the energy levels for different components.

Remember the rules of thermodynamics.  If 1 molecule of compound A is used to make 10 molecules of compound B, then (if there are no other energy sources) compound A must have more energy per molecule than compound B. Use this worksheet to help you:

Energy levels

Energy levels key

Be able to compare respiration and fermentation.  When does fermentation occur? What purpose does it serve?

This video will be useful. A key point is that the purpose of fermentation is to produce NAD⁺ so that glycolysis can continue.

[youtube https://www.youtube.com/watch?v=4yupGRlB0iA]

 

For each of the following, know where they are made and where they use  (The light cycle or Calvin Cycle): ATP, NADPH, NADP+, Oxygen, Carbon Dioxide, Sugars.

There is a table in the group worksheet for this.

Here is a video quiz on the light cycle.

Light Cycle video quiz

Be able to draw out and analyze experiments as shown on the photosynthesis worksheet. See the group worksheet. You also look at this experiment which is relevant to both chapters 9 and 10

Chemiosomotic Principle Experiment

Be able to interpret an action spectrum and distinguish it from an absorbance spectrum

Plants move toward light. The image below shows how the relationship between the wavelength of light and the degree of movement. This is an action spectrum, because it measures a plant response as a function of wavelength. This can be compared to an absorbance spectrum which measures absorbance of light as a function of wavelength (like our first lab). What would you predict about the absorbance spectrum of a pigment that was responsible for the response in the graph below? What would be a good title for this graph. (Answer these questions and submit as a reply to this blog for worksheet credit)

 

Be able to diagram a chloroplast and show where the Calvin cycles and light cycles take place.

Use this link to diagram and a label chloroplast and a mitochondrion and fill in the table in the  second slide. Each of these 3 can be done for worksheet credit. To draw freehand use the “scribble” function which can be found using the tiny arrow next to the diagonal line under “tools”.  This exercise is similar to the cell drawing exercise we did in class. The site we used can not be use for this exercise since it goes away when closed.

Chloroplast/mitochondrion drawing

The table is useful for this objective:

Be able to compare respiration with photosynthesis. Which processes do they have in common?

 

 

 

Some problems for this section can be found on the worksheet for this week. These can be used for credit. 

To understand the basic energy rules, view the slideshow which is on D2l (it is also linked here)

Energy Rules

Enzymes:  First watch this video and answer the questions. Do not click on the “next” button when prompted, the video will advance automatically here.

https://edpuzzle.com/embed/media/55836053ddd82e833b378cbe

Know what substrates are and how they relate to enzyme catalyzed reactions.

Example what is the substrate in this enzyme catalyzed reaction described in the video?

The substrate is the reactant (or reactants) in a reaction involving an enzyme. The reactant fits into the active site of an enzyme which in this reaction is trypsin. Note that the enzyme is shown above the arrow.  Doing this helps remind you that the enzyme is not changed by the reaction. One enzyme can do many reactions (like a machine)

 

Know how enzymes catalyze biological reactions, specifically their effects on activation energy and their mechanism of action.

View this activity

Enzyme Mechanism

This shows how enzymes speed up reactions: They can get molecules closer to each other and in the right orientation.

Another concept in how enzymes speed up reactions is activation energy. Imagine you have a homework assignment due next week. You could do it now, or you could put it off until right before it is due.  The activation energy is the energy needed to get the process started. Note that the homework might take you an hour whether you do it now or later. The activation  energy is just what it takes to get started. Enzymes decrease activation energy as shown in the diagram below.

By Originally uploaded by Jerry Crimson Mann, vectorized by Tutmosis, corrected by Fvasconcellos – en:Image:Activation2.png, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=1407225

Note that that the ΔG (The overall energy) does not change whether or not the enzyme is present. Enzymes also have no effect on the equilibrium of a reaction; adding an enzyme does not shift the reaction to the left or right.  It does change how quickly the reaction reaches equilibrium.

 

Know what active and allosteric sites are.

We have already mentioned active sites, they bind to the substrate(s) of a reaction. Some enzymes also have allosteric sites. These do not bind to substrates but they bind to compounds that can turn on (activators) or turn off (inhibitors) an enzyme.

One example is important in insulin control of blood sugar.  There is an enzyme that converts glucose to glycogen. This enzyme only works when insulin is present (this is when you just ate a meal; your body wants to convert the glucose you ate to glcyogen to store for later. When insulin binds to insulin receptor a chain reaction occurs (like the following dominoes shown here)

In the reaction an enzyme called a kinase becomes active and kinases add phosphates to other proteins some of which are enzymes. Adding a phosphate to the enzyme which turns glucose to glycogen makes it active. The phosphate is added to an allosteric site which is not near the active site. However, when the phosphate is added, the enzyme changes it shape into an active form. This is shown here

By aussiegall – [1], CC BY 2.0, https://commons.wikimedia.org/w/index.php?curid=4428411

Note that some compounds can inhibit by binding to the allosteric site and some can activate an enzyme by binding to an allosteric site as illustrated in this video
[youtube https://www.youtube.com/watch?v=WAZXqhtduFw]

Know what competitive and non-competitive inhibition is and how it relates to active and allosteric sites.Know how one can distinguish these inhibitors

Many drugs can inhibit enzyme function by binding to the active site. Here is an example

HIV Drug Action

The key point here is that the inhibitor binds very strongly to the active site preventing the substrate from binding. Because both the inhibitor and substrate bind to the same site, the binding is said to be competitive.  If the concentration of substrate increases, the inhibitor is less effective.

Non-competitive inhibitors bind to the allosteric site.  Adding more substrate has no effect on allosteric inhibitors since the inhibitor changes the active site to be “closed”.

Know what feedback inhibition is and how it can be used to control amino acid synthesis.

 
http://www.powtoon.com/embed/ehIHXeADNit/

Do  Problem #7, page 161.

 

 

 

 

 

Be able to list and recognize the principles of the cell theory
This video is useful and fun.

History of the Cell Theory

Be able to give applications of GFP

. In order to examine moving structures in living cells scientists took advantage of a jelly fish which makes a protein which glows green in fluorescent light. This protein is called GFP.(Green fluorescence protein) Using molecular tricks, one can fuse the GFP protein to other proteins. Where ever that other protein is, there will be a green signal. This video shows an example:

GFP in c. elegans development

In this video, a protein associated with chromosomes is labeled green. First, you can see the nucleii from the 2 parents  fuse together. Then the embryo starts cell division and you can follow the nucleii as this happens. The organism is C. elegans which is a tiny worm.

 

Cell Parts. Here are some activities to help you remember cell parts and functions

Here is a review video

Tour of the cell

Cell Parts

(Click on the flag and then, when prompted, click on the red dot associated with the structure)

Two structures that easily get confused are the nucleus and the nucleolus

By OpenStax College – Anatomy & Physiology, Connexions Web site. http://cnx.org/content/col11496/1.6/, Jun 19, 2013., CC BY 3.0, https://commons.wikimedia.org/w/index.php?curid=30131201

Note the difference.

The function of the nucleolus is to help make ribosomes

The nucleus stores the chromosomes which have the genetic information for a cell. The nucleus is also needed for cell division and contains the nucleolus.

Know the pathway that membrane and secreted proteins take to get to or through the cell membrane. Know what happens at each step.

This was mentioned briefly in the last chapter. I recommend the video in Mastering Biology (Tour of the cell and the HW activities). Be sure to be able to draw out the pathway.

 

Know the functions of cytoskeletal proteins including microtubules microfilaments and intermediate filaments.  Be able to give examples of how these elements contribute to movement of cells and of structures within cells and how they are involved in structure and shape of cells.

 

here is a video on cilia function

Cilia Function

 

Be able to give examples of how human disorders relate to defects in specific cell structures and/or proteins.

Here is a video on lysosomal storage disease

Lysosomal Storage Disease

This boy has a condition called EBS (Epidermolysis Bullosa Simplex), which causes severe blistering. This is a genetic condition which can be caused by defects in a number of proteins including keratin (an intermediate filament protein in the skin) and in components of the anchoring junctions. Based on what you have read about the functions of these components, why might a defect in them results in the blistering condition?

 

By Paulo Henrique Orlandi Mourao – Own work, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=9793806

These are red blood cells  from someone who has a defect called Hereditary Spherocytosis. Normal red blood cells are disc shaped. In the microscope, they will usually shown a clearer area in the center. Abnormal red blood cells are rounder and do not have the clear area in the center.  Depending on the severity of the disease, the patient will have different numbers of normal and rounder red blood cells. The condition is genetic and is due to defects in a number of proteins which are known to associate with actin. Based on what you know about actin, explain the effect of the defect on the cells.

 

By Filip em – Own work, CC BY 2.5, https://commons.wikimedia.org/w/index.php?curid=3838971

 

The left shows the cross section from a normal flagellum and the right shows a defective flagellum in a case of Kartagener’s syndrome which is due to a defect in dynein protein.    Male individuals who have this genetic condition are sterile, and individuals of both sexes who have this condition have breathing difficulties. Why might these symptoms appear? (Hint see the video on cilia).  Another effect of this condition is that the organs of the body are on the wrong side! This by itself does not seem to cause any serious problems, since other causes of this condition do not have medical consequences.

 

Extracellular Matrix; In addition to what is in the book, you may find this video quite informative

. Extra Cellular Matrix

 

Here is a useful review activity

Review Activity

Use the “Scatter’ Function to do a speed test.

 

Here are some exercises to help you understand the week 2 objectives

Be able to recognize and give functions for the following biomolecules: Monosaccharides, disaccharides, polysaccharides. Fats, phospholipids, steroids. Amino acids, proteins.

The following exercise will help you recognize the key differences between carb0hydrates and lipids.Click on the green flag and observe which structures are lipids and which are carbohydrates.
Click next and then click the appropriate button
Continue hitting next and choosing the correct button

Carb and Lipid Test

It is also recommended to do the mastering bio activities in the study area for chapter 5.

Here is a second activity for carbs and lipids

Carbs and lipids

Be able to distinguish primary, secondary, tertiary and quaternary structure

This can be difficult for people to remember.  A few key points

1. The levels represent interactions within a protein. They do not necessarily represent steps in protein folding .
2. You should know (1) What types of bonds are used and (2) What parts of the amino acids are involved. Be sure you can identify R groups and the backbone portions of amino acids.

3. Read the the section on 4 levels of protein structure in chapter 5.4

4. Do the activity on protein folding in Mastering Biology

5. Watch the following video and answer the embedded questions:
https://edpuzzle.com/embed/media/575adfdf98ce82292d1b1a4d

 

Here is a review of macromolecules you need to know

https://edpuzzle.com/embed/media/54e792d9073086a942ceed2f

Be able determine whether an environment is hypotonic, isotonic or hypertonic to a cell.

Be able to predict what will happen if a plant or animal cell is put in a hypotonic, isotonic or hypertonic environment.  .

Example:

• A cell with an internal NaCl concentration of . 1M is put into a solution of .01 M NaCl. The salt can not cross the membrane. What happens?
• 
• 
• Note:  Problems like the first one may appear in exams and quizzes. Problems like the second one will appear in Mastering Biology and the Group Worksheet.

Be able to describe the signal pathway that determines how insulin regulates blood sugar.

The following exercise (insulin game) requires little understanding of the insulin pathway itself, you should be able to put the steps together logically.  This exercise is tricky in that if you get a step incorrect you have to start from the beginning. Note; One of the steps, exocytosis, is covered in more detail in Chapter 6 (And we will cover it in the next unit). For now, you just need to know that membrane proteins go from membrane bound structures called vesicles to the outer membrane. Here is a short video to help

https://edpuzzle.com/embed/media/5507787130ee9e3e5fb4c500

Insulin game

Directions

1. Click on the Green Flag
2. Click on the buttons in the correct order of events. If you make a mistake, you need to start again. Note that the buttons shading will change if you do it correctly, so you can remember which buttons you already pressed.

If you complete this, take a screen shot and send it to me for 2 extra credit points!

For each unit, you should read the book and look at the objectives in the folder. For some of the objectives, it is helpful to have worked examples and problems to try. In addition, there are some objectives that may require different approaches than in the book or in the Mastering Bio exercises. Therefore, this class will have a blog that will go over these particular objectives. For each unit there will be a blog post.

Chapter 1

Be able to draw and interpret evolutionary trees

In this diagram, particular genes are being compared to each other, but one can also see the relationships between organisms. For example, the bees are closest to each other and the wasp is closer to the bees than any other organism and then the vinegar fly (fruit fly)  is closer to the remaining organisms.  Now think about what common features the bee ans wasp might have that the fly does not and what common features the insects have that the other organisms do not. These common features would be found in the common ancestor (which could be found at the branch points) of the different species.

Now draw a tree using the following animals: Mouse, Parrot, Bat, Snake, Crab. What features would the common ancestors have in common?

Be able to identify proper controls to test a hypothesis. 

The key points to remember here are that (1) The control condition is identical to the experimental condition except for the variable to be tested and (2). If one wants to know what the effect of the variable is, the control lacks that variable. Example: There is research suggesting that the attention span of fruit flies can be measured. (Really!)

[youtube https://www.youtube.com/watch?v=L8Bd_p8pbQI]

Supposed you wanted to determine whether Ritalin increased the attention span of the flies. What control would you use? The control would be flies not given the drug.  The experimental group would be the flies given Ritalin.

Now try this one:

Recently, there have been some reports that dogs could tell whether a person had cancer by sniffing their urine.

How might you test whether this is possible? What controls would you use?

 

Chapter 2

Be able to determine the atomic number and atomic mass given the number of protons and neutrons and vice versa.

Rules to remember

(1) The atomic number of an atom is equal to the number of protons. This is equal to the number or electrons unless the atom is an ion.

(2) All atoms of the same element have the same atomic number but they may differ in  the number of neutrons (isotopes)

(3) The mass number is the number of protons plus the number of neutrons (The mass of the electron is too small to affect the atomic mass).

Examples:  An atom of nitrogen has a mass number of 15. How many protons and neutrons does it have?

Answer: Nitrogen has has an atomic number of 7, therefore it has 7 protons. 15=neutrons +7, so the atom has 8 neutrons.

Using the rules for placing electrons in shells, be able to draw an electron shell diagram

Rules

(1) The first shell can hold 2 electrons, the second and third can hold 8 each (Most biologically relevant atoms have no more than 3 shells. K and Ca have 4 shells, but they only have one or two electrons in their 4th shell

(2). Electrons are never put in a shell unless the shells below them are full.

Example: Magnesium has an atomic number of 12. Draw a shell diagram

It would have 2 in the first shell, 8 in the second and 2 in the third.

By Peo at the Danish language Wikipedia, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=7364211

Do not worry about the SPDF designation for this class. (SPDF designations indicate position, shell diagrams refer to energy levels)

Now try this one: Draw an energy diagram for phosphorous, atomic number 15.

Be able to distinguish the bond types including covalent, ionic, and hydrogen bonds. Recognize the difference between polar and non-polar bonds. 

When categorizing terms,  sometimes it is useful to make a tree diagram, like our evolutionary trees. Just as in the evolutionary tree, in this diagram bonds that are grouped have features in common with bonds that are not grouped. For example The covalent bonds share electrons, while the ionic and hydrogen do not. What do hydrogen and ionic bonds have in common that is not in common with the covalent bonds?

Another consideration for classifying bonds is where there are found. Covalent bonds are within molecules. Hydrogen bonds are usually between  molecules (But they can be within some large molecules such as proteins). Ionic bonds can be between atoms in an ionic compound and sometimes between molecules or within large molecules.

You should know that bonds between the same atom are non-polar and bonds between carbon and hydrogen are non-polar. Biologically important polar bonds that you should know are C-O, O-H and N-H.

Here is another activity to help you review bonds types:

http://www.classtools.net/connect/201508_T8ah6X

Be able to calculate the molecular weight of a compound given a molecular formula

The molecular mass of a compound is simply the sum of the masses of the atoms.

Example: What is the mass of SO₂?

Sulfur has a mass of 32 and oxygen has a mass of 16 (rounded off). There is one Sulfur and 2 Oxygen atoms. Thus the Mass is 32 + 2(16)= 64. The units are Daltons or g/mole.

Now try this one. What is the mass of NaOH?

Chapter 3

Be able to determine moles from grams and molecular formula

A mole of substance will have the number of of g equal to its molecular mass or atomic mass (for atoms).

Example How many moles is 5 g of NaOH?

(1) Find the mass of NaOH Na=23 O=16 H=1. one mole=40 g

5 g X 1mole/40 g= .125 moles of NaOH

Be able to determine concentrations given chemical formulas and grams of material

Example what is the molarity of 20 g of NaOH in .5L of solution?

Step 1 determine the molecular mass (40 g/mole from the question above)

Step 2 determine the number of moles 20 g X 1 mole/40 g= .5 moles

Step 3 Divide the number of moles by the volume of solution in L .5 moles/.5L = 1mole/L or 1M

Try this one. Beer is usually around 5% ethanol (50 g/L).  What is the molarity of ethanol in beer. Ethanol has a formula of   C2H6O

Given pH, [H⁺] or [OH^–] calculate the other 2

Rules (1) pH=-log[H⁺]

if the pH is 2 the [H⁺] =.01M. If the [H⁺] is .00001 the pH is 5.

Rules (2)

[H+]  [OH-] =10^-14

If the [OH-]=.001M, then the  [H+] =10^-14/.001 =10^-11 

Then the pH=11.

Be able to predict how the change in concentration of a substance will affect an equilibrium reaction

View the following videos. The second one has embedded questions
[youtube https://www.youtube.com/watch?v=wlD_ImYQAgQ]

https://edpuzzle.com/embed/media/575070b7e37454f56e6c8cc9

Be able to determine whether 2 structures are isomers and whether they are structural, geometric or enantiomeric isomers.

For 2 structures to be isomers, they have to have the same molecular formula

Watch the video. Note that geometric isomers are a type of diastereomers

 

Be able to identify functional groups.

Click on the green flag to start. The faster you do this, the higher your score
//scratch.mit.edu/projects/embed/112453626/?autostart=false