STUDY GUIDE 2
∙ Bacterial Flagella- made of a protein called flagellin & doesn’t have axonemal microtubules
∙ Pericentriolar Material- material around centrioles ∙ Kinesin- plus end directed on cytoplasmic microtubules ∙ Dynein- minus end directed to microtubules ∙ Myosin- plus end directed on microfilaments ∙ Sarcomere- the contractile unit of vertebrate muscle
1. What has axonemal microtubules?
2. What is the purpose of the centriolar microtubules? 3. Two centrioles make up a _____________.
Don't forget about the age old question of What is the difference between concave and convex mirror?
4. What is the purpose of the three different motors on cytoskeletal filaments?
5. What is one difference between kinesin and dynein?
Double helix of filaments
Motor Protein Rules
∙ The head is the motor ∙ The head binds ATP ∙ The head binds to the rails
∙ The tail binds the cargo ∙ The cargo moves in the direction set by the
Don't forget about the age old question of What is nativism?
motor (Kinesin & Myosin + end, Dynein – end)
1. Eukaryotic cilia, eukaryotic flagella, lung cilia, sperm. 2. To serve as a microtubule organization center (MTOC) 3. Centrosome.
4. They are enzymes that hydrolyze ATP to produce energy to move things
5. Kinesin is a tetramer that has quaternary structure and axonal transport. Dynein is a motor protein that moves microtubules into cilia.
∙ Hypertonic Shrinkage- when water from inside the cell flows out of the cell which causes the cell to shrink If you want to learn more check out Who are the members of a construction team?
∙ Isotonic Solution- No visible swelling or shrinking ∙ Hypotonic Solution- when water moves into the cell but the cell can’t expand because of the cell wall
∙ Glycoproteins- proteins with covalently attached sugars
1. What does the extracellular matrix do?
2. How can you stop shrinking?
3. What is the fluid mosaic model?
4. What are the two main types of membrane proteins? What are the two main types of membrane bound proteins? 5. What are integral membrane proteins held in the membrane by?
6. What are peripheral proteins connected to the membrane by?
7. If the protein is in the _______, it’s integral. If the protein is in the ________, it is peripheral.
8. How do you know when something is water soluble? 9. What are two membrane carbohydrates? Don't forget about the age old question of What are the properties of noble gases?
10. The _________ parts extend into the aqueous cell exterior and internal cytoplasm. Hydrophobic side chains interact with the ________ ________ of the membrane. HYPERTONIC HYPOTONIC
∙ Water moves down its Concentration gradient ∙ Water moves out
∙ Cell Shrinks
∙ Water moves into the cell
∙ Cell Swells
∙ Cell soaks up water but doesn’t burst because of cell wall
∙ Nothing: no swelling or shrinking
1. Holds cells together in proper positions, mediates cell to cell interactions within the tissues, regulates shapes & activities of cells, cell growth, signal transduction.
2. Add solutes to the inside to balance solute concentrations or add permeable compound.
3. It proposed that membrane proteins are used to transport nonpermeable compounds & fluid membranes had rapid lateral diffusions of lipids & proteins.
4. Soluble & membrane bound. Peripheral & integral. 5. The distribution of hydrophobic and hydrophilic ide chains on amino acids.
6. Ionic Bonds
7. Pellet, supernatant.
8. If It stays in the supernatant after centrifugation a 100,000g for an hour
9. Glycoproteins and glycolipids.
10. Hydrophilic, lipid core.
LECTURE 14 We also discuss several other topics like What is hydrogen bonding?
∙ Passive Diffusion- No extra energy (-ΔG) coupling needed ∙ Active Transport- Needs energy to make it go
∙ Exoplasmic- Outside
∙ Cytosolic- Inside We also discuss several other topics like What is biological determinism?
1. What are glycoprotein cell receptors?
2. Can a glycolipid be a cell receptor?
3. Do all plasma membrane have the same amounts of lipids, protein and carbohydrates?
4. What does it mean if Δ G is negative?
1. They serve as points of attachments for other cells, infectious bacteria, viruses, toxins, hormones and many other molecules
2. Yes, for toxins
4. The net influx is thermodynamically favored
∙ Vm- voltage across a membrane
∙ Depolarization- a positive going charge in a cell’s membrane potential, making it more positive or less negative inside ∙ Hyperpolarization- a change in a cell’s membrane potential that makes it more negative
1. What additional things must you know if it Is a charged compound?
2. What are the two electrochemical driving forces? 3. Is a polar substance more concentrated on the outside or inside of the cell?
4. What are the two kinds of ion channels?
5. Active transport requires _______ _________ to overcome a positive ΔG with a sufficiently negative ΔG.
ΔG Influx= Wc+We At equilibrium, Wc=We (B/c ΔG=0)
You can get a -ΔG with:
Negative Wc & positive We (driven by chemical forces) Negative We & positive Wc 9 driven by electrical forces) Both Wc & We negative (driven by both forces)
1. What is the equation for passive diffusion of a charged molecule, what is the membrane potential, what is the valence electron.
2. Chemical force (Wc) & electrical force (We).
4. Voltage & mechanosensory
5. Energy coupling
∙ Uniporter- transports one substance in one direction ∙ Symporter- transports two different substances in the same direction
∙ Antiporter- transport two different substances in opposite directions
∙ Intercellular- between cells
∙ Intracellular- inside cells
1. Is the energy for active transport always provided by ATP? 2. What is another way for things to get inside cells? 3. What are the general types of chemical communication between cells?
4. What do plasma membrane receptors do?
5. What are some of the enzymes affected by GCPR?
GPCR General Pathway
Metabotropic GPCRs Ionotropic
Phosphorylation & gene regulation
Answers 1. Yes
2. Receptor- mediated endocytosis
3. Synaptic, paracrine, endocrine, signal transduction 4. Signal arrives at target cell, signal molecule binds to a receptor protein, the signal binding changes the conformation and exposes its active site, the activated receptor activates a signal transduction pathway to bring about cellular changes.
Steady State- something coming out, something coming in
1. What are two ways to increase cAMP?
2. What is protein phosphorylation?
3. What is the point of receptor tyrosine kinase? 4. Are all receptors on the plasma membrane?
5. What is the purpose of a chaperone? Protein Phosphorylation
Target ATP Protei
Phosphate on protein & ADP (alters shape & function)
Adenylyl cAMP Cyclase
1. Increase adenylyl cyclase activity or decrease
2. The process of covalently attaching a phosphate to a protein which cause a change in conformation.
3. Insulin receptor binds insulin which cause phosphorylation of specific proteins to cause a specific cellular response 4. No
5. It doesn’t allow something to get into the membrane
∙ Metastasis- spread of a tumor to other parts of the body ∙ Potential Energy- stored energy
∙ Kinetic Energy- energy used to do work
∙ Chemical Energy- ATP stored in bonds
∙ Electrical Energy- Sperate charges
∙ Heat Energy- Transfer due to temperature differences ∙ Mechanical Energy- Energy of motion
∙ Light Energy- Electromagnetic radiation stored as photons ∙ Exergonic- Reactions that release free energy due to – ΔG ∙ Endergonic- Reactions that require energy due to + ΔG ∙ Induced Fit- enzyme changes shape when it binds to the substrate, which alters shape of the active site
1. What are special adhesion properties of metastatic cells? 2. What is lost during the growth and development of a tumor? 3. What must be conquered to initiate a reaction?
4. What do enzymes do to a reaction?
5. What might an enzyme do in catalyzing reaction? 6. What does increasing a substrate concentration do?
Hydrolysis (release energy)
1. Less adhesive, penetrate several barriers, invade normal tissues.
3. Activation energy
4. It lowers the energy barrier by bringing reactants together 5. Orientate substrate, induce a strain, add chemical groups 6. Increases the rate and products formed over time
∙ Anabolism- Synthesis (make)
∙ Catabolism- Breakdown (use)
1. What happens at saturation?
2. What is the difference between irreversible & reversible inhibition?
3. What affects the charge of an enzyme? What happens to an enzyme when you increase the temperature?
4. Energy derived from _____________ can be used to drive _____________.
5. What are the 3 steps from glucose to ATP?
6. What can you do with a pyruvate?
Circle of Life
Photosynthet ic Cells
Heterotrophi c cells (us)
1. All enzyme is bound to the substrate.
2. Irreversible- covalent bond forms. Reversible- noncovalent bonds form, competitive inhibitor effect is concentration dependent.
3. pH, it becomes inactive.
4. Catabolism, anabolism.
5. Glycolysis in cytoplasm, citric acid cycle in matric of mitochondria, oxidative phosphorylation across the mitochondria inner membrane.
6. Convert it to acetyl CoA inside the mitochondria to go into citric acid cycle.
1. What is NADH?
2. Is the outer membrane or inner membrane more permeable in mitochondria?
3. What is pmf?
4. What happens to the pmf if the membrane potential is held constant?
5. What are the 3 steps?
6. What happens in the cytoplasm during oxidative phosphorylation?
7. What does mitochondrial electron transport produce? 8. Is oxidation of NADH & FADH2 in the respiratory chain
endergonic or exergonic?
from glucoseOxidati Reductio
∙ Reducing agent
∙ Gets Oxidized (LEO)
∙ Loses electrons
∙ Loses H+ usually
∙ Low Affinity for electrons
∙ Oxidizing Agent
∙ Gets Reduced (GER) ∙ Gains electrons ∙ Gains H+ usually ∙ High affinity for electrons
1. An electron donor that has more energy than ATP. 2. Outer membrane.
3. The proton motive force which provides electrochemical energy.
4. If a change in the pmf occurs, then it is mainly controlled by the changes in the H+ gradient.
5. Electron transport from NADH to O2 produces energy (-ΔG). This energy is used to set up the H+ gradient by pumping H+ against their electrochemical gradient (+ΔG. The energy from the H+ gradient (-ΔG from pmf) is used to make ATP (+ΔG).
6. Glycolysis breaks down sugars into smaller pieces in cytoplasm.
7. A proton gradient across the inner membrane & a higher H+ outside the membrane to generate an inward pmf to provide energy for ATP synthesis in the matrix.
∙ Envelope Membrane- double membranes that aren’t photosynthetic membranes
∙ Thylakoid Membrane- photosynthetic membranes inside chloroplasts
∙ Lumen- aqueous area inside thylakoids
∙ Stroma- aqueous area outside thylakoids
1. How is ATP made?
2. Name one mitochondrial poison.
3. What is non-shivering thermogenesis?
4. What are the two ways to make ATP in the absence of oxidative phosphorylation?
5. What are the 2 main types of anaerobic fermentation?
Anaerobic Energy Production
Sun -> photosynthesis -> glucose -> glycolysis -> pyruvate (3- carbon molecule)
Glucose -> pyruvate (O2 present) -> fermentation -> lactate/ alcohol
1. H+ diffuses through a channel, a subunit rotates, and then the rotation causes the subunit to change its shape to expose active site for ATP synthesis.
3. It is something babies and hibernating organisms do to produce heat.
4. Use sunlight to provide energy to pump protons out through proton gradient & acidophilic bacteria in low pH pond use the pH gradient to make ATP.
5. Fermentation of pyruvate to lactate & fermentation of pyruvate to ethanol.
1. Where does electron transport occur in chloroplast? 2. What are the stages of e-flow in photosynthesis? 3. What does phosphorylation produce?
4. What are the 2 light harvesting centers?
5. Name an inhibitor of photosynthesis.
6.What are the main steps of light reactions?
How do thylakoid membranes harvest light to make NADPH &
Passed along to
(No change in
Emitted as Heat (1)
CO2 + H2O (CH2O)n + O2
1. In the thylakoids.
2. Photolysis, pass electrons from PSII to PSI, pass electrons from PSI to NADPH+.
3. NADPH & ATP (to give to dark reactions to help make carbohydrates).
4. P680 in photosystem II (PSII) & P700 in photosystem I (PSI). 5. DCMU.
6. Light energy is absorbed, electron transport, energy of H+ gradient is used to make ATP in the stroma.
1.Summarize the Calvin Cycle.
2. What is the difference between CAM plants photosynthesis and C3/C4 plants photosynthesis?
3. How is DNA replicated?
4. What is one thing that can happen in 3PG? Where is everything?
1. Light reactions in thylakoid 2. Glucose and oxygen in cytoplasm
3. Carbon dioxide goes into chloroplasts From cytoplasm.
4. Production of ATP & NADPH, Calvin Cycle, Starch synthesis in stroma.
1. First, you need to have enough RuBP to begin the cycle. Carbon dioxide is added to RuBP to make a transient 6
carbon compound which splits into two 3 carbon compounds. Then, 3PG is converted to G3P which uses ATP & NADPH. Finally, some of the G3P is used to regenerate RuBP & the rest goes to make sugars.
2. CAM plants fix carbon dioxide in mesophyll cells a night & then run Calvin cycle during the day. It also has temporal separation.
3. Grow bacteria on “heavy” nitrogen to metabolically label all DNA. Switch the regular “light” nitrogen. Use density gradient centrifugation to separate heavy & light DNA. 4. It can be recycled into RuBP.
∙ Semiconservative Replication- produce molecules with both new and old DNA
∙ Conservative Replication- preserves the original molecules and generates an entirely new molecule
∙ Dispersive Replication- would produce two molecules with old and new DNA interspersed along each strand
∙ Disperse Chromatin- single piece of double stranded DNA with associated proteins, mostly histones
∙ Mitotic Chromosome- paired chromatids
∙ Assay- fuse two cells together and see if the phase that one is in causes the
other to enter that same phase
∙ Eukaryotic Mitotic Chromosome- two long pieces of double stranded DNA bunched up and held together at the centromere
1. What are the three possible models for DNA replication?
2. How can you tell it is replication and not transcription? 3. What is the difference between mitosis and cytokinesis? 4. In what phase do the centrioles replicate?
1. Semiconservative replication, conservative replication, dispersive replication.
2. In replication, A is paired with U. In transcription, A is paired with T and DNA-> RNA.
3. Mitosis is nucleus division and cytokinesis is cell division. 4. S phase.
1. What is MPF?
2. What happens during cell cycle regulation?
3. How is DNA packed into a mitotic chromosome?
4. What are the two parts of a histone?
5. What is the purpose of codensin?
Cell Cycle Checkpoints
1. The maturation promoting factor that stimulates entry into mitosis.
2. Cyclin synthesis begins during G1 and then breaks down when going into S-phase.
3. DNA warps around histones to form nucleosomes, which then compacts loops and forms mitotic chromosomes. 4. Hydrophobic and hydrophilic.
5. It helps compact and supercoil DNA in mitosis.