Early DNA info

Early Stuff


Molecules:
Functional groups. Don't memorize lots of details. For example, if you read the word "acetate," you should know 'that must be an acid that's lost it's proton." but you would not need to know how to draw it.
  1. Carbonyl in either keto or aldehyde along with Nitrogens: good H-bond acceptor . Just don't be scared if you see one.
  2. OH in an alcohol and NH in amine: Good H bond donor and the O or N can be an acceptor. You should know this.
  3. Organic acid protonated or deprotonated (-ate ending). Know it is a defining part of an "amino acid."
  4. OH in organic acid NOT an alcohol.
  5. Amino, the other defining part of an amino acid.
  6. Unsaturated C=Bonds in either cis or trans and the importances of cis in biology. Know how these effect fatty acids.
  7. Phospho groups especially importance in ATP and chemistry of DNA and RNA
Bigger substituents:
  1. Purine (Big) and pyrimidine (small) bases in DNA and RNA. GC has three bonds and is more heat-stable. A-T has 2 and is less heat stable.
  2. Ribose and deoxyribose in the ring form (be able to spot 5' and 3' in DNA or RNA).
  3. Fatty acids (a good place to think about saturate and unsaturated bonds in cis and trans).
  4. The importance of stereoisomers in biology: that the mirror form of molecules may not work or bind the same way. You won't need to recognize these distinctions. But, if I ask about D or L forms being different in Biology.
  5. Polymers: Made by dehydration reaction (dehydration synthesis…take out H2O) and taken apart by hydrolysis (add water).
  6. Structure of starch, cellulose and glycogen and what they do in which type of organism (plant or animal). Particularly, remind yourself of the differences in hydrogen bond patterns in cellulose and starch, and how that derives from the beta versus alpha 1-4 link
  7. Amino acid structure. Identify amino, carboxyl and alpha carbon as well as the "R" group. You don't have to memorize the amino acids.
  8. Lipids. Recognized sterols versus fatty-acid lipids. Recognize fat versus phospholipid. Know basic roles. (Phospholipids in the membrane, Cholesterol regulating membrane fluidity and used as basis for hormones).
Macromolecules. General: know what each is made of. Imagine questions like "If I add labeled nitrogen, where will that end up?" (amino acids and DNA/RNA). "If I add labeled phosphorous, where will that end up?" (DNA and RNA, mainly).fa
  1. In proteins, know primary, secondary, tertiary and quaternary structure and how they relate to each other.
  2. Know alpha helix and beta strand (recognize in structure...ribbon representation, for example) and that hydrogen bonds involving carbonyl and amino groups in the "Backbone" lead to these secondary structures. The main point here is denaturing at higher temperature disrupts H-bonds, unfolds tertiary and eventually secondary structure, but does not break (hydrolyze) the peptide bonds of the backbone.
  3. Know the types of interactions that lead to tertiary structure (more H-bonds, hydrophobic interactions; salt bridges (ionic interactions) and covalent S-S bonds when Cysteine is involved).
  4. In carbohydrates...covered above
  5. In lipids...bilayer formation and the basic structure of the bilayer
  6. Nucleic acid: recognized 5' and 3' ends. Describe chemical polarity and the notion of "antiparallel."
Enzymes:
  1. Review my blog on the various steps. Minimally, we have to consider an on-rate, catalytic rate and an off rate, all of which can be modified by mutation, changed by interaction with another protein, and selected and fine-tuned by evolution (or a bio engineer), so that each enzyme would differ in the details. To be clear, I don't need you to know details, just THAT these things happen because of changes to the fine shape of the protein. It's important in the context of questions involving drugs or mutations and how they affect things as well as how proteins regulate each other. Again…this is not a lot of memorization. The whole idea that modifications to a protein or interactions with other molecules, including proteins, will alter function. This is how drugs work and how biology is regulated.
  2. Saturation kinetics and what the graph means. Remember that the graph flattens out when the initial concentration of substrate saturates the enzyme. Adding more doesn't increase the rate because all the enzyme is occupied. It's already going at its maximum rate.
  3. Know how to show Km and Vmax and what the effect of competitive and non-competitive inhibitors are. In particular, how the binding of product leads to the most basic kind of feedback inhibition. This seems like a lot for what will likely be worth a point or two. Don't study the hell out of this. Basically, just recognize how the graphs of activity are affected and have an idea of why.
  4. "Affector molecules," often other proteins, can alter any of an enzyme's attributes: binding to substratee; catalytic rate; off rate of product....any of it. (This will be critical as we look at regulation of cell cycle etc…discussed in "7a"). This idea is mentioned above as well.
Cells. Brief, one or two sentence description/definition of:
  1. Plasma membrane
  2. Nucleus
  3. Nucleolus
  4. Mitochondria
  5. Centrosome/Centriole/MTOC
  6. Endoplasmic reticulum (Rough and smooth)
  7. Golgi
  8. Transport vesicles
  9. Exo/endocytosis
  10. Actin/microfilaments
  11. Tubulin/microtubules
  12. Intermediate filaments
  13. Chloroplast (plant)
  14. Cell wall (plant)

Know the key differences between prokaryote and eukaryote and between plant and animal cells.

When you think about these structures and what they do, focus on what would happen if a chemical or disease or mutation screwed them up. Remember all the questions I ask about things like "This drug allows ions to pass through lipid bilayers" or this mutation causes vesicle transport to be blocked. Think about "what will happen if…" or "what could be the cause of…" types of questions.
Also, assume there will be a question about osmosis and hypertonic/hypotonic solutions. Remember that plant cells like to be in hypotonic solution because that swells them up to fill the cell wall well. Animal cells like to be in "isotonic" (same salt concentration).
Cellular structure, greater detail:
  1. Membrane trafficking and protein transport (how does a protein synthesized in the ER get secreted or put in the membrane?
  2. A key thing everyone forgets: not all proteins are synthesized on Rough ER. Cytoplasmic and nuclear proteins are synthesized by free ribosomes in the cytoplasm.
  3. Role of the three components of the cytoskeleton. The proteins main proteins that make them up and how each does different, sometimes overlapping things in the cell.
  4. Cell-surface and cell-cell interface: Gap junctions; tight junctions; desmosomes and other adhesions always interact with cytoskeleton.. Interaction with the extracellular matrix.
Respiration and Photosynthesis: The main big question that will likely cover this will be on the second, group effort day.
Respiration: Three components of the process and where the small and big payoff of ATP happen. Know the molecule from each step that is important for the next.
Glycolysis: know the rate-limiting early step (phosphofructokinase) and why that might be important. Know the general points:
  1. 2ATP in, 4 out for a net 2 gain
  2. There are also 2NADH created, which is also a good energy source and, if O2 is around, can lead to more ATP.
  3. If no oxygen, the NADH must be oxidized to NAD+ by some sort of fermentation.
  4. Pyruvate transported to the mitochondria for the next steps
Citric Acid cycle: Main products are some ATP and GTP through substrate-level phosphorylation and NADH. CO2 released mostly in this cycle.
NADH feeds into electron transport which leads to the pumping of protons across membrane. The protons feed the next step. Final recipient of the electrons is Oxygen, resulting in water as a product.
Protons drive the ATP synthase.
Structure of the mitochondria (inner/outer membrane and intermembrane space...what happens where and where the main components are). As always, I like to ask structure-function questions. I love to compare photosynthesis to respiration (the water-oxygen-electron connection is a favorite). But, I've recently given you one of those. I will keep it basic on this test.
Photosynthesis
General structure of a leaf: stoma; cuticle; chloroplast; thylakoid; grana; That's enough silly names.
Light harvesting complex...other pigments that feed energy to:
The reaction center, specialized chlorophyl.
Basic Z scheme: Photons excite electron in PSII, which are sent down an electron transport chain off to PSI. Splitting water (Oxygen production) replaces the electrons in PS II (Apparently, this portion of PSII is the only biological case where water is oxidized...cool). Electrons travel down and H
+ is pumped into the Thylakoid lumen. The electron is passed to PSI, where it is hit with another photon and excited to a higher level than the first photon hit. The big win here is the passing of the electrons to the higher-energy NADPH2.
Protons drive ATP synthase and NADPH
2 feeds into the calvin cycle, where, almost the reverse of Citric Acid cycle, NADPH2 is oxidized to NADP and CO2 is reduced by addition to growing carbon chain.
Circular flow...just in PSI. Gets some protons pumped, but no NADPH
2.

The number one thing you should know about me and how I view this course is that I want you ALL to succeed. I want to write a test that gives each of you the chance to shine, and challenges each of you to do more than you think you can. We'll see if I'm good enough to do that.

Study Guide for recent stuff and other guidelines.

You can review the previous test. Assume that the level of detail, particularly for the first test, will be lower, but that you will be expected to put things together.

For Cell Signaling:


Know the general scheme: Ligand binding; transduction; cellular response
Know in
very general terms what GPCR, RTK, and apoptotic pathways do.
Know the role of G-proteins as timers
The main thing is to be able to
read a diagram and answer questions like "what would happen if this protein was removed, or that protein was over-expressed?"
Know what a "cascade" is and what second messengers are.
Know the importance of "off switches."

For Meiosis and Mitosis:


Be able to recognize/name the basic phases.
Know the role and names for the: chromosome; homologous chromosomes; sister chromatid; centrioles (spindle-pole bodies); Kinetochore; Centromere; kinetochore and non-kinetochore microtubules; motor proteins (dynein).
Know the key differences between mitosis (replicate once, divide once, generate two cells with
identical DNA to the parent) and meiosis (replicate once, divide twice, separation of homologous chromosomes at anaphase I, separation of sister chromatids at meiosis II, generate four cells with exactly ½ the DNA of parent—one copy of each gene). Be able to follow that out on a diagram.

For Cell Cycle:


Know: names and roles of MPF; Cyclin; and Cyclin-dependent Kinase (CDK).
Know the purpose of a "check point" and at least where the main ones are. Be able to correlate the time of expression of a cyclin with a particular checkpoint.
Know the phases G1; G0; S; G2 and M.

Important connections:


Respiration and photosynthesis. This will be mainly on the group day. But know the basics.
Cell signaling and cell cycle.