Muddiest Points 1/25/2012

  1. Chemistry and the various bonds. (2 people)
    chemical bonds –are bonds between atoms when two atoms share, donate or accept electrons. There are three types of chemical bonds: ionic bonds, covalent bonds, and H-bonds (or hydrogen bonds). Ionic bonds are when one atom donates an electron or electrons to another atom which accepts it (them). A covalent bond is when two atoms share electrons. When talking about covalent bonds, a single bond is made up of a pair of electrons which are shared by both atoms. H-bonds are when two or more molecules are polar and hydrogen has a partial positive charge and another atom has a partial negative charge. This allows the partial negative and partial positive (hydrogen) atoms of two different molecules to be attracted together, creating the hydrogen bond. Chemistry is way too broad a topic to try to cover here, it is a complete science. If you are having trouble with chemistry I suggest you reread the chapter on chemistry and see me during office hours.
  2. Monosaccharides, oligiosaccharides, and polysaccharides. (2 people)
    These are the three types of carbohydrates. Monosaccharides are the simple sugars like glucose and fructose. All the others are made up of these simple sugars hooked together in chains. Oligiosaccharides are short chains of simple sugars (about 2-8, depending on who you ask) and polysaccharides are long chains of the simple sugars. Sucrose (table sugar) and lactose (milk sugar) are oligiosaccharides. Starch, glycogen and cellulose are the three polysaccharides.
  3. Trying to determine the number of protons, neutrons, and electrons in the different elements. And the number of electrons in each layer (shell). Is it 8 electrons max in each shell after the fist shell, or is it specific for each element. To determine the number of protons in an atom, just look up the element’s atomic number (which is the number of protons in the atom). If an atom changes its number of protons, it because an atom of a different element. If the atom is electrically neutral, the atomic number is also the number of electrons in the atom (note, that the atom can loose or gain electrons, in which case it is not electrically neutral). Determining the number of neutrons is more difficult. The only way to do this is to look up the atomic mass and subtract the atomic number, the remainder is the number of neutrons.
    The number of maximum electrons in each shell of an atom is 2 for the innermost shell and 8 for all other shells. This is the model we are using. Now, each element has a different number of electrons in its electrically neutral atom, so that most atoms will not have its shells full with electrons. Hydrogen has one electron, Helium two (so its first shell is full), Lithium has 3 electrons (2 in the innermost shell, 1 in the outer shell), Beryllium has 4, Boron 5, carbon 6, nitrogen 7, oxygen 8, fluorine 9, and neon 10 (so it has full electron shells). Only the Noble Gases (Helium and Neon listed here) have full electron shells.
  4. Chemistry is a muddy point. The student suggested having a periodic table on the overhead would make the lesson flow better. My lesson on chemistry does have a periodic table in it, check my lesson notes. I also pointed out (and used) the periodic table on the wall in our classroom. We are very fortunate to have our classroom, because this is the only room with a periodic table on the wall.
  5. What makes a molecule polar? Polar molecules are molecules where atoms share electrons unequally to form a polar covalent bond between the atoms. For us, this is when Hydrogen forms a bond with Oxygen or Nitrogen. Because the electrons are not shared equally, on atom is partially positive (for us it is always Hydrogen) and one atom is partially negative (either Oxygen or Nitrogen). Recall that electrons carry a negative charge and because they are not being shared equally, this gives both atoms a partial charge. If the molecule only has nonpolar covalent bonds (where the electrons are shared equally), the molecule is nonpolar. Now because polar molecules dissolve in water and ionic molecules (where the molecule has an ionic bond instead of a covalent bond) also dissolve in water and nonpolar molecules do not, sometimes ionic molecules are called “polar”. This is not literally correct but is commonly done just to make two groups, polar and nonpolar molecules. It would be more correct to say “polar and ionic molecules” or “hydrophilic molecules”, but partially because of laziness, the word polar is used.
  6. A basic overview of what we’re going to discuss would make all the details of the lectures more understandable.
    Cell biology is complex and not available visually... it is really important to understand how deep we are going with each topic. If you check my lecture notes, you will note that I start each with a preview or an overview outline. If you are the type who wants to understand the big picture first before jumping into the details, you might try doing the reading before the lecture. In Bi 112, we simply do not have time to go over the big picture, talk about the general concepts and then go back and go into the specific details the way they do in Bi 101 and 102. No, I am afraid we have to talk about each topic as we go, going into each with both the details and the big picture, and then move onto the next topic. I do not like it either, but I have to cover the material of two terms in this one course.
  7. The textbook is so dense. What of the info is relevant for tests and quizzes? If you are having trouble with the textbook, please try reading the objectives and chapter summaries before doing the actual reading (these are the most important parts of the readings). In the reading, I want you to see the big picture and walk away with overall concepts. I will not be testing you or minute details of the reading. The most important information will be covered in lecture. With the lecture, you should know the minute details.
  8. The structures of proteins. How the bonds break or form in protein structure levels. Please see my examples page, it has a video on the 4 levels of protein structure that I think you will find helpful. In the first level, there are no bonds in the protein, it is simply the sequence of amino acids. In the 2nd level of protein structure, it is nearby amino acids which are interacting (can be H-bonds, or ionic bonds, or repulsion between a polar R-group and a non-polar R-group). In the 3rd level of protein structure, it is amino acids that may be far away from each other which are interacting (can be H-bonds, or ionic bonds, or repulsion between a polar R-group and a non-polar R-group, or sulfur bonds).
  9. No specifics, but if feels like we bounce? from this thing to that really quickly. This is a blank, it looks like a blank? I am not sure I am reading this correctly. I suspect that this student feels like we are jumping around a lot and quickly talking about one topic before moving onto the next. Sorry, yes that is what we will be doing in Bi 112 because we will be covering Bi 101 and 102 in one term.
  10. The polypeptides. Polypeptides are chains of amino acids. When a protein is being made, amino acids are added onto the growing chain, one at a time. When the chain is growing, we call it a polypeptide. When it stops growing (no more amino acids are added), we call it a protein.
  11. The 4 building blocks –carbs, proteins, etc. How they have sub-groups.
    The 4 building blocks are what cells make their molecules from. The 4 building blocks are simple sugars (or monosaccharides), fatty acids, amino acids, and nucleotides. This 4 building blocks are the monomers (1 unit) that make up the polymers (many unit) of life.
    The 4 polymers of life (also called the 4 molecules of life) are carbohydrates, lipids/fats, proteins, and nucleic acids. Carbohydrates are made up of simple sugars, fats and phospholipids are made up fatty acids and glycerol (other lipids are not), proteins are made up of amino acids, and nucleic acids are made up of nucleotides.
  12. Have more videos (I am working on it, see my examples page).
  13. Outline of nucleotide and nucleic acid. What makes up a nucleotide? Let us start with nucleic acids, these are polymers of nucleotides. There are two nucleic acids, DNA and RNA. The nucleotides are the monomers that make up DNA and RNA (each are made up of 4 different nucleotides). Nucleotides are made up of a sugar (ribose of deoxyribose, a phosphate group, and a nitrogen containing base.
  14. How to read a ring form of the molecule. Look for the points in the ring, each point is the position of a carbon atom. Off of this carbon atom there will be hydrogen or oxygen atoms.
    I also have a hard time coming up with the name or code of a new bond. I am not sure what you mean, so please speak to me during office hours about this one.
  15. In class exercises seem to help. Thank you, I think they help too.

Muddiest Points and Concerns (numbers mean that more than one person asked about it), 2/2/2012

  1. 4 people. Endocytosis. I’ll try and review this. There are 3 types of endocytosis that all do the same thing, bring something inside the cell, forming a vesicle inside the cell, they just do it in different ways. The 3 types are:
  1. Bulk-phase (pinocytosis) endocytosis
  2. Receptor-mediated endocytosis
  3. Phagocytosis (phagocytic edocytosis)
  1. How energy is spent through ATP. This is a topic that we will get to (Energy and Enzymes Lesson). Essentially, the 3rd phosphate bond comes off
    (ATP --> ADP + P) which releases the energy in the bond. The cell uses this energy for its needs.
  2. The difference between passive and active transport. The big difference is that passive transport is for free, it occurs without the cell spending any energy. Active transport costs the cell 1 ATP molecule to move one molecule across the membrane. The other main difference is that passive transport works by diffusion, molecules move down their concentration gradients. Active transport occurs against a molecule’s concentration gradient, the molecule is pumped from an area of low concentration to an area of high concentration.
  3. The function of receptor proteins and R groups. Their function is to bind to a signal molecule (if one is present) and then take the signal inside the cell to change the activity of the cell. My example was a growth hormone binds to a receptor protein on the muscle cell of a child. The signal is taken into the cell and causes the cell to divide; this makes the child’s muscle grow.
    I assume you mean R groups in amino acids. This is the variable region of an amino acid that determines which amino acid you have. There are 20 different R groups that make up each of the 20 different amino acids in people. They can vary from being just one hydrogen atom to being a bunch of carbon atoms in a ring that has other atoms off of the ring.
  4. Hypertonic versus hypotonic. Tonicity is defined by the concentration of the solute (the substance that dissolves, such as salt or sugar) in a solution. Solutions also have a solvent which for us is usually water. Hyper means above, so a hypertonic solutions is one that has more solute in it than the other solution. You always have two solutions that you are comparing when you talk about the tonicity, such as the inside and the outside solutions of a cell. Such as when the cell is put in brine, the solution outside the cell is hypertonic to the solution inside the cell. Hypo means below, so a hypotonic solutions is one that has less solute than the other solution. In our example of a cell put into brine, we can say that the solution inside the cell is hypotonic to the solution outside the cell.
  5. Protons and glucose crossover. Also the different classes and functions? I am sorry, but I do not understand your question. Please speak to me and then maybe I will be able to answer this.
  6. Protein transport. Rushed last bit? I am not sure I understand. We did discuss that there are two types of transport proteins, passive and active transport. We spent a fair amount of time on this. See #3 above for the main differences between these two.

Concerns:

  1. I worry about using the words “weak in science” for struggling students. This could undermine their confidence. Answer, what do you suggest? Struggling in science would undermine their confidence as well. I think you may also be missing my point, that if you are a student who is considering taking bi 112, that you should evaluate your own strengths and weaknesses and ask yourself, should I take bi 101 before taking bi 112? Too many students ignore this and then suffer or end up taking bi 112 a second time. It costs less taking bi 101 before bi 112 and you get credit for both classes compared to taking bi 112 a second time. I try to be upfront from the beginning and try to give good advice. I am surprised that the student advisors at PCC suggest “you bi 112 students should realize that you might have to take bi 112 a second time.” I know this because they used to come to all the bi 112 classes to give 15 minutes of advice. This advice is costly and you only get credit for the class one time.
  2. (2 people) Go slightly slower. Sometimes we have just too much to cover, we are covering the material of two classes in one term. This is the only introductory biology most of you will ever have. (When I was an undergrad, introductory biology was 3 terms!) Yet, if you request me to repeat something, or to keep the screen up longer, I will.
  3. Extra pictures and examples. Videos are good! Please check out my extra examples page. I am working on one for the second midterm and it should have more videos (I hope).
  4. It is confusing having short notes and they being so different than the notes you show in class, which we get later. Sorry, that is not my intention. If you are confused, please ask me a question and I will gladly clarify something. I also want you to ask yourself “Why does my instructor make two sets of notes? It is a lot more work for him to make two instead of one. If he makes a change, he has to do it on two sets of notes, which is more work than if he only had one set. Why does he go to all that extra trouble for us? Why is he not lazier?
  5. (2 people) More videos. Please check out my extra examples page. Finding good videos is really hard and time consuming, so if you have any suggestions, please send them to me. Most of mine that I use in the lecture come from an old textbook that we no longer use at PCC. Technically, I should not be using them.
  6. More real examples. Substances we are familiar with or recently learned. Sorry, I am not familiar with what you are familiar to, and I suspect that everyone has at least a slightly different background, so that what one student is familiar to may be different for another. I do try to give examples that I hope you understand, but due to time constraints, I cannot give many for each topic. Still, I would be interested in a list from you providing a column for the topic and a second column for your suggested examples for that topic. I am always collecting examples. Please also check out my extra examples page and see if it is helpful.
  7. Pictures are good. Thanks!