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Biology 160 Exam 2 Study
Guide
Chapter 6: Lipids, Membranes, and transport Biological Molecules: Lipids and Membranes Learning Outcomes · Be familiar with related scientific terminology and chemical structure and properties of the various lipids. · Compare and contrast the structures and functions of saturated and unsaturated fats. Describe how each affects the fluidity and permeability of the plasma membrane. · Describe the role of cholesterol in biological systems- both in steroid hormone production and how it affects the fluidity and permeability of the plasma membrane.. · Describe the molecular structure of phospholipids and the roles phospholipids play in cells. Biological Molecules: Lipids and Membranes Questions
- How are lipids defined? Are they made of discrete monomer units that are linked together to form massive polymers? What is a hydrocarbon? a) Any organic substance that does not dissolve in water, but dissolves well in nonpolar solvents b) Lipids include fatty acids, oils, waxes, steroids, and phospholipids c) Lipids are not composed of discrete subunits like polysaccharides but are still macromolecules. d) Lipids are primarily hydrocarbons CH 2 a. No charge (nonpolar) b. Energy source c. Insulation in animals- d. Cell membranes e) Hydrocarbon chains in lipids are called isoprene – a five carbon compound that has only carbons bonded to hydrogens+
- What is a saturated fat and what is an unsaturated fat? How are they different? How are they the same? Why is one solid at room temperature and why is one liquid? a) Saturated fat a. The hydrocarbon chain is a straight chain b. Comes from animals i. Butter, beeswax c. Carbons are packed tightly together and form a solid d. Has a carboxyl group at the end of the hydrocarbon chain b) Unsaturated fat a. The hydrocarbon chain has a bend in it (a double bond) b. The bend does not allow the carbons to be packed tightly thus causing the fatty acid to be a liquid
c. Comes from plants i. Safflower oil d. Unsaturated lipids may prevent heart disease and is good for your diet e. Has a carboxyl group at the end of the hydrocarbon chain c) The fluidity of sat. and unsat. fats depends on how long the hydrocarbon chain length
- What is a triglyceride? How are the fatty acid tails linked to the glycerol molecule (what reaction takes place)? What linkage forms? a) Triglyceride has 3 fatty acid tails, and provides energy storage and insulation in animals b) Fats form through dehydration reactions c) Ester linkages – join fatty acids and glycerol to form a fat or phospholipid
- What is a steroid and why are they considered to be a lipid? What is the function of cholesterol? Estrogen? Testosterone? What is common to the structure of these molecules? ● Steroid is a group of lipids with 4 rings; defined as lipid because they are made largely of carbon and hydrogen atoms, and they are water insoluble.
- Be able to define the effect each of the following has on membrane permeability: short length of fatty acid tails, unsaturated fatty acid tails, long length of fatty acid tails, and saturated fatty acid tails. Further, what effect does cholesterol have on membrane permeability? How do we know? What experiments have been done with liposomes? ● Double bonds in a hydrocarbon chain can cause a “kink” in the hydrocarbon chain preventing: close packing of hydrocarbon tails, reduces hydrophobic interactions, membranes are much more permeable. ● Membranes containing phospholipids with longer tails are less permeable ● Cholesterol reduces membrane permeability ○ Experiment with liposome has been done ■ Construct liposomes with different amounts of cholesterol and measured glycerol movement ● Short and Unsaturated tails=higher permeability ● Long and Saturated tails= Lower permeability
- What is the sandwich model vs. the fluid mosaic model of membrane structure? What is the freeze-fracture technique and how did it allow scientists to rule out the sandwich model? ● Sandwich Model: consist of just membrane proteins on cell interior and exterior ○ Hydrophilic proteins cover/coat both sides of lipid bilayer ● Fluid- mosaic Model: Has peripheral and integral proteins ○ “At Least some proteins span the membrane instead of being found only on the outside of the lipid bilayer”
Freeze-Fracture Preparations Allow Biologists to View Membrane
Proteins. The nature of the membrane model was solved with the
freeze-fracture electron microscopy technique for visualizing the
surface of plasma membranes (used alongside the SEM). Biologists
can freeze-fracture and split membranes down the middle.
- What is a peripheral protein and what is an integral or transmembrane protein? How can we use detergents to isolate an integral protein?
● Peripheral membrane proteins are membrane
proteins that adhere only temporarily to the
biological membrane with which they are associated.
These proteins attach to integral membrane
proteins , or penetrate the peripheral regions of the
lipid bilayer
- What is an ion channel and what is CFTR and what role does it play in cystic fibrosis?
● Ion channels create tiny openings in the membrane.
They only allow specific ions to pass through
● If ion channel does not function, chloride ion will not
enter lungs which results in thick-sticky mucus.
● CTFR is a protein channel that allows chloride ions to
pass thru the membrane and into airway. Pts. with
Cystic Fibrosis lack or have dysfunctioning CTFR
proteins, reducing the number of chloride ions in the
airway and increasing thickness of mucus.
- What is the path of protein production in a cell? What is the endomembrane system? How are proteins sorted and sent to the correct destination in a cell?
The endomembrane system:
–Proteins made in the RER
–Move to the Golgi apparatus for processing
–Travel to the correct destination
–Contain special signal sequences that target them to the appropriate
organelles
- What organelles do we see in eukaryotic cells and what are the basic functions of each?
enclosed in a nucleus
Eukaryotic cytoplasm is compartmentalized into a larger number of
distinct organelles
- Are there any real “generalized cells” or are cells specialized to carry out particular functions? Explain. Cells cannot really be generalized because each one must have the right parts/organelles to function correctly. For example, a muscle cell will probably have lots of mitochondria in order to produce a bunch of ATP needed for the muscle to do its work. A cell that needs lots of protein making would contain many endoplasmic reticulum to get the job done. Energy and Enzymes Learning objectives: · Define a chemical reaction and the role of energy and entropy in determining if a reaction will be spontaneous or not. · Use ATP hydrolysis to explain how endergonic reactions can become spontaneous by coupling them to exergonic reactions. · Explain how temperature, concentration, entropy, and potential energy affect the rate of a chemical reaction. · Describe the function of enzymes and their importance in living systems. · Explain how the activity of an entire metabolic pathway can be regulated by a single product molecule via feedback inhibition. Questions:d
- What is the definition of energy and what are the different forms of energy discussed in lecture? Kinetic? What does kinetic energy “look” like on a big scale and what about on a molecular scale? Potential? What does potential energy look like on a big scale and what about on a molecular scale? Chemical energy? Is chemical energy a form of kinetic or potential energy? ● Energy is the capacity to do work and cause change ● Kinetic Energy- energy of motion ○ Molecular level is thermal energy ● Potential Energy- energy that an object possesses as a result of its location or structure ○ Molecular level chemical energy is stored ● Chemical energy is potential energy because of its energy available for release in a chemical reaction
- What does electron position tell you about potential energy? ● Amount of potential energy in an electron is based on its position relative to positive and negative charges
● Electrons closer to negative charges and farther from positive charge have higher potential energy
- Imagine you are a molecule at the top of a waterfall. What type of energy do you possess? What happens if you then “fall” down the waterfall? Are there any energy transformations occurring and if so, what kind? Is the transformation 100% efficient? Why or why not? ● Potential energy while at the top of waterfall ● Kinetic energy while falling ● Transformation 100% effective??? The transformation would not be 100% efficient because other forms of energy also “appear,” such as sound and heat.
- Be familiar with basic concepts regarding the first and second law of thermodynamics. For example, be able to answer the following: Can organisms “make” energy? How can organisms convert one form of energy to another? What is entropy? Why is it increasing? What is heat energy and why does it contribute to entropy? Can organisms make use of heat energy? ● First Law of Thermodynamics- energy cannot be created or destroyed, it can only be transferred and transformed ● Second Law of Thermodynamics- total entropy always increases in isolated systems ● Entropy- amount of disorder ○ When the products of a chemical reaction become less ordered than the reactant molecules- entropy increases
- Which is more efficient: a car “burning” fossil fuels or a cell “burning” glucose? Why/how can a cell be more efficient? What are the products of a car burning fuel and a cell burning glucose? A cell “burning” glucose is more efficient. It releases energy slower and in steps allowing the energy to capture more and have a better transformation. A car uses combustion and all the energy is used at once -- causing heat and not much energy to be captured.
- Know the difference between exergonic and endergonic reactions. Define exergonic and endergonic reactions and be able to describe which one involves making bonds and energy input and which one involves breaking bonds and energy release? Are exergonic reactions always spontaneous? Why or why not? a) Exergonic: When energy (heat) is released, it is a spontaneous reaction( catabolism), but an exergonic reaction may still require an input of some amount of activation energy to get started. b) Endergonic: a reaction that requires energy input to occur is not spontaneous(anabolism)
- What is the relative potential energy of reactants versus products in a exergonic and an endergonic reaction? ● Exergonic - products have less potential energy than reactants (the energy difference
b) When the phosphate is cleaved, you can either describe it as the phosphate being released as an inorganic phosphate, or you can demonstrate that the reactions are paired so that it ultimately returns to the ATP and the energy release/usage is balanced c) Phosphate can act as an allosteric activator (if I’m remembering correctly, please verify!),” verified” meaning that it would bind to the enzyme outside of the active site, changing the shape of the enzyme so that it can accept the substrates. It can also bind to a substrate or reactant directly, as part of a step process… The new bond is easy to break, and the energy released from breaking that bond and breaking ATP in the first place to have the phosphate provide the activation energy for the actual reaction.
- What is the importance of NAD+/NADH, FAD+/FADH2, and NADP+/NADPH? Why are they called electron carriers and how do they act as both an electron acceptor and then an electron donor? Answer???
–Readily donates electrons to other molecules
–Is called an electron carrier
–Has reducing power
- What is ATP? What about its structure makes it a molecule with high potential energy? How is it a renewable source of energy? ● Adenosine triphosphate
● High potential energy due to the phosphate group ( 4 negative
charges in its 3 phosphate groups repel each other)
● Composed of adenine, ribose, and three phosphate groups
- What is an enzyme and what role(s) do they play in chemical reactions of living things? What is activation energy? How do enzymes lower it? What does it mean if I say “enzymes orient substrates/reactants and stabilize the transition state molecule”? What is a transition state molecule and how do enzymes help the molecule reach transition state? ● Protein catalyst- typically catalyze only one reaction ● They speed up the chemical reaction that are required for life ● Activation Energy- amount of free energy required to reach the intermediate condition, or transition state
● Transition State facilitation- between the substrate and active site R- groups lower the activation energy ● Enzymes function best at some particular temperature and pH ○ Rate of enzyme-catalyzed reaction depends on ■ Substrate concentration ■ Temperature ■ pH ■ Enzyme’s intrinsic affinity for the substrate
- What is an active site? Why is shape so critical to an enzymes function? As catalysts, are enzymes changed or “used up” in the reactions that they catalyze? What does it mean if we say that enzymes are “saturable”? ● The site on the enzyme, where the substrate binds. ● The shape determines what substrates can bind to that enzyme ● Catalysts are not used up in the reaction
● Saturable: The rate of the reaction is limited by the amount of
Substrate present and Enzyme available
- What effect does temperature and pH have on an enzymes shape? What are cofactors, coenzymes, and prosthetic groups and how can they affect an enzymes shape and therefore activity? ● Cofactors - inorganic (metal) ions necessary for an enzyme to work ● Coenzymes - organic molecules, transfer electrons between enzymes ● Prosthetic Groups - non-amino acid atoms/molecules, stays attached ● Temperature affects the movement of the substrates and enzymes and pH affects the enzyme’s shape and reactivity
- What is competitive inhibition? What is an allosteric regulator? What is allosteric inhibition and what is allosteric activation? What is feedback inhibition? ● Competitive inhibition - molecule similar in size & shape to the substrate competes w/ the substrate for access to the active site ● Allosteric regulator - molecule changes enzyme shape by binding to the enzyme at a location other than the active site (can activate or deactivate enzyme)
- What is a metabolic pathway and how does feedback inhibition work to regulate most metabolic pathways? ● Metabolic Pathway ○ A series of reaction ○ Each catalyzed by a different enzyme ● Feedback inhibition: when an enzyme in a pathway is inhibited by the product of that pathway → product can shut down pathway when the product is no longer needed Cellular Respiration Learning objectives: · Summarize the four steps of cellular respiration.
i. NADH and FADH2 bring the electron to the electron transport chain and we are therefore oxidized when they donate the electrons to the ETC ii. Inner membrane
- Explain the following statement: Energy is harvested in the electron transport chain when electrons “flow” from high energy carriers to low energy carriers and finally to oxygen. These electrons are releasing energy as they fall from their highly negative charge, it’s like the energy (sound and heat) being harvested as something falls down a waterfall but on a cellular scale.
- What is substrate level phosphorylation? Do we see this happening in cellular respiration? When or in what phase? What is oxidative phosphorylation? Do we see this happening in cellular respiration? When or in what phase? ● Substrate Level Phosphorylation: enzyme-catalyzed reactions that result in the production of ATP; when ATP is made in glycolysis or citric acid cycle (1,3) ● Oxidative Level Phosphorylation: when ATP is made in E.T.C (4)
- How is the establishment of H+ gradient tied to ATP production? What is meant by proton motive force and chemiosmosis? What is ATP synthase and how does this channel protein produce ATP from ADP+Pi? ● The H+ passes through ATP synthase which creates energy(hydroelectric dam), that is used for the synthesis of ATP from ADP. ● Proton motive force is the flow of H+ through ATP synthase
● ATP synthase: acts as a molecular motor. – Catalyze the phosphorylation
of ADP to ATP
- Why is oxygen needed for the continued working of the ETC? What is anaerobic respiration and what types of organisms are capable of this? ● Oxygen is needed because it accepts the H+ from ATP synthase and is the final electron acceptor/produces more ATP ● Anaerobic respiration: use other electron acceptors other than oxygen to generate less ATP in oxygen poor environments. (Organisms → some prokaryotes)
- What types of products will inhibit glycolysis and Citric acid cycle? ATP
- What is fermentation? Under what circumstances do humans ferment? Is it a benefit under certain conditions/cellular needs? What is the product of human fermentation? What is the product of yeast fermentation? ● Metabolic pathway that regenerates NAD+^ from NADH ● Glycolysis can produce ATP in the absence of oxygen ● Fermentation occurs in the absence of oxygen. Fermentation in the human body can occur in muscles ● The product of human fermentation is lactate ● Yeast fermentation produces ethanol
- How can other fuels be used in our cells (proteins and fats for example)? How are they used to generate ATP?
Basically anything with C-H bonds is usable for energy because we can break the C- H bonds to release energy Beyond the scope of our class.
- What are other ways that cells can use metabolism (ways other than energy production)? What are precursors? ● a chemical that is transformed into another compound, as in the course of a chemical reaction, and therefore precedes that compound in the synthetic pathway: Cholesterol is a precursor of testosterone. Photosynthesis Learning objectives: ● Summarize how the light-capturing reactions and the Calvin cycle transform light energy to chemical energy. ● Explain how light energy is captured and used to drive an endergonic redox reaction. ● Describe how ATP and NADPH are produced during the light-capturing reactions of photosynthesis. ● Explain the role of the Calvin cycle in photosynthesis and compare it with the role of the C4 cycle. **Questions:
- What is the overall equation of Photosynthesis?**
- 6 CO^2 +^6 H^^2 O^ + light^ energy^ → Glucose ( C 6 H 12 O 6 )+ 6 O 2 How does it compare to the equation for Cellular Respiration?
- Glucose +^6 O^2 → 6 H^^2 O^ +^6 C^ O^2 +^ ATPenergy Is cellular respiration exergonic or endergonic overall?
- Cellular Respiration = EXERGONIC ( oxidizes sugar → CO^2 )
Glucose + 6 O 2 → 6 H 2 O + 6 C O 2 + ATPenergy
Is photosynthesis exergonic or endergonic overall?
- Photosynthesis = ENDERGONIC ( reduces CO^2 → sugar )
6 CO 2 + 6 H 2 O + light energy → ( C 6 H 12 O 6 ¿+ 6 O 2
2. What are Autotrophs and Heterotrophs?
4. What are chloroplasts? - Chloroplasts → chlorophyll-containing organelles bound by a double membrane where photosynthesis occurs. - Found in plants & photosynthetic protists What pigments are found in the chloroplasts? - Pigments are molecules that absorb only certain wavelengths of light - other wavelengths are either reflected or transmitted. Pigments have colors because we see the wavelengths they do not absorb. Chlorophyll absorbs strongly in the blue/red regions, which makes plants look green (reflect green light). - Chlorophyll a & b, caratenoids 5. What are stomata? - Stomata → tiny openings or pores used by plants for gas exchange - Mostly found on the under-surface of plant leaves. - They consist of two guard cells that open/close Why must they be open during photosynthesis? - When a leaf’s CO2 concentration is low during photosynthesis, the stomata open & allow atmospheric CO2 to diffuse into the cells chloroplasts. What gases are exchanged through these pores? - CO 6. Why are plants green? - Plants are green because green light from chlorophyll is reflected. What color(s) of the visible light spectrum is/are reflected by chlorophyll? - Green.
What color(s) is/are absorbed?
- Red & blue are absorbed. 7. Why do leaves turn red, yellow, and orange in the fall?
- When chlorophyll degenerates, carotenoids remain. What are carotenoids?
- Carotenoids → class of accessory pigments that are found in chloroplasts & absorb wavelengths of light not absorbed by chlorophyll.
- Typically appear yellow, orange, or red.
- Includes carotenes & xanthophylls (not important) What colors are absorbed and what colors are reflected or transmitted?
- Carotenoids absorb blue & green light; they reflect/transmit yellow, orange, & red light. What important roles do the carotenoids play in increasing photosynthesis?
- Carotenoids absorb wavelengths of light that are not absorbed by chlorophyll.
- This results in an extended range of wavelengths that can drive photosynthesis. What role do they play in protecting the chlorophyll molecules?
- Carotenoids “quench” free-radicals by accepting or stabilizing unpaired electrons. What is an Absorption Spectrum and what is an Action Spectrum?
- Absorption Spectrum - a graph to study pigments; it plots the wavelength of light absorbed by pigment molecules.
- Action Spectrum - shows the rate of photosynthesis vs. wavelength. 8. What happens to electrons when pigments absorb sunlight energy?
- When pigments absorb sunlight energy → electrons become “excited” & raised to a higher energy level. What are the three possible outcomes?
- Drop down to a lower energy state → fluorescence
- Excite an electron in a nearby pigment → inducing resonance
- Be transferred to an electron acceptor in a redox reaction Describe what happens when electrons fall back down to their ground state.
- The excess energy is given off as HEAT & FLUORESCENCE (light) Describe what happens in Resonance****.
- When a red or blue photon strikes a pigment molecule in the Antenna Complex, the energy is absorbed & an electron is “excited” in response. This energy (but not the electron itself) is passed to a nearby chlorophyll molecule, where another electron is excited in response.
11. What is photophosphorylation and how does it occur in photosynthesis? - Photophosphorylation is the production of ATP molecules by ATP synthase using the PMF (Proton Motive Force) generated as light-excited electrons flow through an Electron Transport Chain during photosynthesis. 12. What is the main purpose of the Calvin cycle? - The main purpose of the Calvin Cycle is to produce SUGARS for plants from co2 and by using ATP What is Rubisco and what is this enzymes role in the Calvin cycle? - Rubisco is a CO2 fixing enzyme. It is found in all photosynthetic organisms that use the Calvin Cycle to fix carbon, and is thought to be the most abundant enzyme on earth! Rubisco is inefficient because it catalyzes the addition of CO2 to RuBP and catalyzes the addition of O2 to RuBP. What happens when Rubisco binds to CO2? - Slows the rate of CO2 reduction What happens when Rubisco binds to O2? - One of the products undergoes a process called Photorespiration. What is photorespiration and why is it such a problem in C3 plants? - Photorespiration undoes Photosynthesis by consuming energy & releasing fixed CO2. When photorespiration occurs, the rate of photosynthesis declines drastically. Carbon fixation is favored over photorespiration when CO2 concentration is high & O2 concentration is low.
What are stomata and why must they close on hot, dry days?
- Stomata are leaf structures where gas exchange occurs.
- They consist of 2 guard cells that change shape to open or close.
- On hot, dry days, leaf cells lose a lot of water to evaporation through the stomata
- They close the openings & half photosynthesis or risk death from dehydration. How does this closing affect Rubisco’s activity?
- Closing the stomata causes CO2 delivery (and photorespiration) to stop. Oxygen levels increase as cellular respiration continues and increases rate of photorespiration. What conditions favor photosynthesis and CO2 fixation?
- Open stomata favors photosynthesis On the other hand, what conditions favor photorespiration and O2 fixation?
- Closed stomata favor photorespiration 13. What is the basis of C4 photosynthesis and how has this novel type of photosynthesis solved the issue of photorespiration?
- C4 plants divide the process between the mesophyll and the bundle sheath cells. The process that occurs in the mesophyll cells are the light-dependent reactions & help fixate CO2 into malate. The malate is then transferred through the respiration pump, which helps prevent O2 from getting into the Calvin Cycle. The C4 pathway occurs mostly in plants from hot, dry habitats. It limits the damaging effects of photorespiration by spatially separating carbon fixation and the Calvin Cycle. What is PEP carboxylase and why does it not fix O2?
- PEP Carboxylase is an enzyme that catalyzes addition of CO2 to phosphoenolpyruvate (a 3-C compound that forms a 4-C organic acid). It fixes CO2. What reaction does it carry out?
- PEP + CO2 = 4-Carbon + Pi What happens to the product of PEP carboxylase reaction and where does decarboxylation take place?
- The 4-Carbon product enters the Calvin Cycle, which takes place in the bundle sheath. Why do we say that “C4 plants have solved the issue of photorespiration by spatially separating CO2 fixation from the Calvin cycle reactions”?
- C4 plants start off with a 4-Carbon molecule instead of a 3-Carbon molecule, and they use photorespiration pump → allows less O2 to enter the system & overall makes the system more efficient.
