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Here are some exercises to help you understand the week 2 objectives
Be able to identify carbons and hydrogens in organic compounds
Watch this video
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. Geometric isomers are distinguished by having a double bond and a different arrangement of atoms around he double bondd
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
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 carbohydrates 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
Here is a second activity for 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
Here is a protein structure review
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
Membranes
Review of Lipid and Membrane structure
the above structure is a lipid. Note the polar head (top) and hydrophobic tails (bottom). One of the tails is bent due a a double bond.
Lipids arrange themselves in bilayers as described here
Note the round heads oriented toward the outside (water) and the tails oriented toward each other (inside of membrane). This limits transport of many types of molecules (See below)
This image shows the lipid bilayer along with proteins carbohydrates
Functions for membrane proteins
Transport of substances across membranes: the following types of substances can be transported across lipid bilayers without the help of proteins
(1) Non-polar compounds including gases such as oxygen and carbon dioxide and larger compounds such as steroids
(2) Water and some very small polar compounds. Water travels slowly
Reception. Membrane proteins help detect internal signals (such as insulin) and external signals (such as sugar, for taste buds). Binding of the compound on the outside triggers a series of reactions that leads to a response.
Recognition For example self vs nonself immune reactions are determined by membrane proteins and or carbohydrates. The difference between blood types A,B AB and O is determined by different carbohydrates.
Formation of organs like liver and stomach can depend on membrane proteins sticking like cells together.
Junction formation Gap, Tight and Adhesion junctions are made of membrane proteins
Role of cholesterol
In cold temperatures, cholesterol breaks up phospholipid packing (in a manner similar to unsaturated fats. This makes the membranes more fluid)
At high temperature, cholesterol limits the lateral movement of phospholipids, thus making the membrane less fluid.
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:
This video covers membrane transport including endo and exocytosis
Crash Course, Membranes and Transport
Here is a video (also linked inthe open stax text showing how receptor mediated endocytosis regulates cholesterol level
We learned about this in the last unit, but you should review this here.
Test Your Self on Membrane transport
Be able to describe the effects of insulin signalling
Insulin signalling involves a number of processes that we have studied. In a later unit we will tie them together.
(1) A protein binds to a membrane receptor
(2) Vesicles containing glucose transporters travel via exoctyosis to the membrane
(3) Glucose enters the cell through the glucose channels
(4) Glucose is converted to glycogen
Here is a video showing the process (except for 4)
For each unit, you should read the book links 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 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 distinguish between inductive and deductive reasoning
Watch the following video
Inductive vs deductive reasoning
Go through the slide show below
Slide show: Deductive reasoning
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!)
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?
Be able to order the levels of biology
This video with embedded questions should be helpful
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 determine how many bonds an atom can form
Example oxygen
Step 1 determine the number of valence (outer shell electrons) 6 for oxygen
Step 2 If the number of valence electrons is 1-4, then that is the number of bonds it can form.
If the number of valence electrons is 5-8 then 8-# of valence electrons = the number of bonds
So for oxygen the number is 8-6=2.
There are exceptions to this rule and you may have learned them in chemistry class, but for this class you do not need to worry about most of them. (Phosphorous can sometimes form 5 bonds and that is found in some important biological molecules).
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 are a couple of other activities to help you review bonds types:
http://www.classtools.net/connect/201508_T8ah6X
Bond Types Branching Questions
Example what is the molarity of 20 g of NaOH in .5L of solution?
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 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
