Bio 1105 Test 2 Objectives

Differentiate between kinetic and potential energy

Kinetic energy is moving. Potential energy is in place

Contrast oxidation and reduction reactions

Oxidation is loss and reduction is gain of electrons

Explain the first and second laws of thermodynamics

First Law: Energy is neither created nor destroyed, only transformed

Second Law: Entropy will always increase

Relate free energy changes to the outcome of chemical reactions

If free energy is increased, the reaction is endergonic. This means that the reaction absorbs free energy and is not spontaneous

If free energy is decreased, the reaction is exergonic. This means that the reaction releases free energy and is spontaneous

Contrast the course of a reaction with and without an enzyme catalyst

A catalyst decreases the amount of activation energy required to start the reaction and can speed up the reaction

Discuss the role of enzymes as biological catalysts

Active site of enzyme bonds to substrate and apply stress to distort the bonds and can change shape to maximize contact.

List factors that influence enzyme-catalyzed reaction rates

Temperature

pH

Inhibitors

Distinguish competitive and non-competitive inhibitors

Competitive: Binds to an enzyme's active site, not allowing substrates to bind

Non-competitive (Allosteric inhibitor): Binds to allosteric site on enzyme that changes the shape

Describe the significance of biochemical pathways and feedback inhibition

End product attaches to the allosteric site of the enzyme to change the shape and stop the enzyme chain so that there is not an abundance of products.

Biochemical pathways produce results to ensure homeostasis

Describe the role of ATP in short-term energy storage

ATP creates short-term energy by breaking it’s high energy bonds through ATP hydrolysis

ATP + H2O → ADP + Pi + free energy

Explain how ATP is related to the control of protein activity

ATP hydrolyzes to ADP and free energy that is transferred to the proteins so that they can change shape and become catalysts

Distinguish between autotrophs and heterotrophs

Autotrophs produce their own organic molecules to make energy

Heterotrophs use organic compounds made by other organisms to make energy

Describe the role of electrons and electron carriers in energy metabolism

Solid and membrane bound carriers of electrons that can be easily oxidized and reduced

NAD+ reduced to NADH

NADH oxidized to NAD+

Identify the four stages that comprise the aerobic respiration of glucose and where in the cell each occurs

1. Glycolysis occurs in the cytosol

2. Pyruvate Oxidation occurs in the mitochondrial matrix

3. The Krebs Cycle occurs in the mitochondrial matrix

4. Electron transport chain/ chemiosmosis occurs in the inner membrane

Summarize the key events and products of glycolysis, pyruvate oxidation, and the Krebs cycle

1. Glycolysis produces a net 2 ATP, 2 NADH, and 2 pyruvate

2. Pyruvate Oxidation produces 1 NADH, 1CO2, and 1 Acetyl-CoA per pyruvate (2 pyruvate from glycolysis)

3. The Krebs cycle produces 3 ,NADH, 1 FADH2, 1 ATP, and releases 2 molecules of CO2 per Acetyl-CoA (2 Acetyl-CoA from Pyruvate Oxidation)

4. Electron transport chain produces a proton gradient in the inner membrane to push H+ through the ATP synthase to produce ATP (ETC does not produce ATP. ATP is made from chemiosmosis)

Diagram the flow of electrons through the electron transport chain

Series of electron carriers that are transferred to complexes that pump protons to create a proton gradient and then transfer the electron carrier to the next complex to continue the process. NADH and FADH2 are electron carriers.

Describe how chemiosmosis couples electron transport to ATP synthesis during oxidative phosphorylation

Using the proton gradient created by the ETC, chemiosmosis pumps the H+ protons through the ATP synthase to turn ADP into ATP by oxidative phosphorylation (oxygen is final electron acceptor)

Summarize the energy yield after each stage of aerobic respiration

Glucose -> NADH -> ETC -> proton-motive force -> ATP

Distinguish aerobic respiration, anaerobic respiration, and fermentation

Aerobic respiration requires oxygen. Anaerobic respiration uses inorganic molecules other than O2 as the final electron acceptor.

Fermentation uses organic molecules as the final electron acceptor

Describe how proteins and fats are catabolized to produce energy

Proteins undergo deamination which breaks them down into their amino acids which go into the Krebs cycle.

Fats are broken down into fatty acids through a process called beta-oxidation which creates Acetyl-CoA to go into the Krebs cycle

Describe how photosynthesis and respiration are connected

The products for one are the reactants for another. In photosynthesis, CO2 and H2O are needed to produce O2 and Glucose. In respiration, O2 and Glucose are needed to produce CO2 and H2O

Differentiate between the light-dependent and light-independent reactions

Light-dependent reactions require light and happen in the thylakoid. They capture energy from sunlight to make ATP, reduce NADP+ to NADPH, and produce O2 as a byproduct.

Light-independent reactions do not require light and happen in the stroma. They use ATP and NADPH to create organic materials from CO2

Explain the connection between light energy and photosynthetic pigments

Photosynthesis produces the most energy at red and blue light frequencies because those are the frequencies absorbed by the photosynthetic organisms. Since green light is reflected, that is all we see. When light is absorbed, it excites the electrons in the chloroplast to start photosynthesis.

Describe the structure and compare the functions of the two photosystems in green plants

Photosystem II is responsible for splitting H2O and releasing oxygen.

Photosystem I reduces NADP+ to NADPH. Electrons cycle back to Photosystem II to create a larger proton gradient.

Explain how the light-dependent reactions generate ATP and NADPH

Photons excite electrons in the photosystems which pump H+ protons into the membrane, creating a proton gradient. In NADP reductase, these electrons are used to reduce NADP+ to NADPH. ATP is generated by the proton gradient pushing protons through the ATP synthase.

Describe how the Calvin cycle carries out carbon fixation

The Calvin Cycle (aka C3 photosynthesis)  carries out carbon fixation with the help of the catalyst, Rubisco. Carbon enters the cycle as CO2 and ATP is used to turn it into the sugar, glyceraldehyde-3-phosphate (G3P). For a net generation of 1G3P, the cycle must happen 3 times, using 3CO2 molecules. Part of the product of the Calvin cycle is regenerated into CO2 to complete the cycle.

Explain the mechanisms of photorespiration

Photorespiration occurs in the Calvin cycle where Rubisco adds O2 instead of CO2. This consumes O2 and organic compounds while releasing CO2 without producing ATP or sugar.

Compare carbon fixation in the C3, C4 and CAM pathways

In C3 plants, the initial fixation of CO2 produces a 3-carbon compound.

In C4 plants, CO2 is incorporated into 4-carbon compounds in mesophyll cells using the enzyme PEP carboxylase. These compounds are exported to bundle-sheath cells where the CO2 is used in the calvin cycle.

Crassulacean Acid Metabolism (CAM) plants split photosynthesis into day and night. At night, CO2 is fixed to 4-carbon organic acids. During the day, the calvin cycle uses CO2 to synthesize sugars.

Identify component nucleotides of DNA and describe how they interact using phosphodiester and hydrogen bonds

Adenine attaches to Thymine by two hydrogen bonds. Guanine attaches to Cytosine by three hydrogen bonds. Phosphodiester bonds connect nucleotides to form DNA strands with one end at the 5’ carbon, and the other end at the 3’ carbon of the sugar.

Describe the significance of complementarity for DNA structure and function

Because A is always with T and G is always with C, there are an equal amount of pyrimidines and purines in every DNA strand. This is important because the diameter remains a consistent 2nm

Summarize the key features of the Watson and Crick DNA model

Proposed the double helix model by combining studies from Maurice Wilkins and Rosalind Franklin

Describe the action of DNA polymerase

DNA polymerase synthesizes the new DNA strands.

Explain continuous and discontinuous replication

New DNA is synthesized from the 5’ end to the 3’ end. The leading strand is synthesized from 5’ to 3’ continuously. The lagging strand is also synthesized from 5’ to 3’ but because DNA is antiparallel, it is synthesized in a stop-and-start manner and as such is discontinuous.

List the components required for DNA replication and identify their function

Parent strand (Template)

Building blocks (Nitrogenous Base)

Something to do the copying (DNA Polymerase)

Compare the key features of eukaryotic and prokaryotic replication

Prokaryotic cells have circular DNA. There is one origin of replication and one point of termination which work in opposite directions around the circle.

Eukaryotic cells have linear DNA. There are many origins of replication. DNA is unwound and split into its 5’ and 3’ strands like a zipper. Each end is connected to a newly synthesized complementary strand. Telomerase is needed to secure the ends so they do not shorten.

Describe the function and importance of telomeres and telomerase in eukaryotic replication

Telomeres contain short, repeated DNA sequences that protect the ends of chromosomes from DNA shortening which occurs because the last primer on the lagging strand cannot be fully synthesized.

Telomerase contains the RNA template and extends the parent strand so the lagging strand can be synthesized as normal.

Explain the importance of DNA repair mechanisms and identify examples

Ligase seals the discontinuous parts of the DNA strand (Okazaki Fragments). DNA repair is important because it mitigates the appearance of mutations that could be harmful to the organism.