Bio 1610 Exam 2 USU

Energy is the capacity to cause change, do work, or move matter against opposing forces. It exists in various forms. Contrast kinetic energy with potential energy.

Kinetic energy is associated with the relative motion of objects, whereas potential energy refers to an object not presently moving; it is the energy that matter possesses because of its location or structure.

Which type of energy does water behind a dam have? A mole of glucose? Diffusion of ions through an ion channel?

Water behind a dam has potential energy. A mole of glucose also has potential energy, although more significantly, glucose has chemical energy, a term biologists use to refer to the potential energy available for release in a chemical reaction. Diffusion of ions through an ion channel is kinetic energy.

What are the two laws of thermodynamics?

1st law: Energy can be transferred and transformed, but it cannot be destroyed. The amount of energy in the universe is constant.

2nd Law: Every energy transfer or transformation increases the entropy (MOLECULAR DISORDER) of the universe. During every energy transfer or transformation, some energy is converted to thermal energy and released as heat, becoming unavailable to do work.

What is free energy?

Portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system.

- G.

For an exergonic reaction, is ΔG negative or positive?

An exergonic reaction proceeds with a net release of free energy. Because the chemical mixture loses free energy, ∆G is negative for an exergonic reaction.

Is cellular respiration an endergonic or exergonic reaction? Is photosynthesis endergonic or exergonic? What is the energy source behind it?

Cellular respiration is an exergonic reaction. Photosynthesis is an enedergonic reaction. Plants get the required energy to make a mole of glucose from the environment by capturing light energy from the sun and converting its energy into chemical energy.

What is the difference between catabolic and anabolic pathways?

Catabolic: the cellular process of breaking down large molecules into smaller ones, RELEASING energy.

Anabolic: build larger molescules from smaller ones, REQUIRES energy.

What is energy coupling? How does it drive energonic reactions in cells?

In cellular metabolism, energy coupling is the use of energy released from an exergonic reaction to drive endergonic reactions.

E.G. Protons diffusing across the gradient is an exergonic process used to drive the endergonic process of creating ATP

When the terminal phosphate bond is broken, a molecule of inorganic phosphate P, is formed, and energy is ___________. Is this reaction endergonic or exergonic?

- Released

- Exergonic

What is a catalyst?

A chemical agent that selectively increases the rate of a reaction without being consumed by the reaction.

What is activation energy (EA )?

Activation energy is the amount of energy that reactants must absorb before chemical reaction will start; also called free energy of activation.

Enzyme

A macromolecule serving as a catalyst, a chemical agent that changes the rate of a reaction without being consumed by the reaction. Most enzymes are proteins.

Substrate

The reactant on which an enzyme works.

Active site

Typically, a pocket or groove on the surface of the enzyme where the substrate binds and catalyst occurs.

Products

A material resulting from a chemical reaction.

What is meant by induced fit?

The slight change in shape of the active site of an enzyme so that it binds more snugly to the substrate.

How is protein structure involved in enzyme specificity?

Enzyme are proteins, and proteins are macro-molecules with unique three-dimensional configuration. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequences. The specificity of an enzyme is attributed to a compatible fit between the shape of its active site and the shape of the substrate.

What is a cofactor?

Any nonprotein molecule that is required for the proper functioning of an enzyme. Can be permenantly bound to the active site or may bind loosely and reversibly along with the substrate, during catalyst. Cofactors of some enzymes are inorganic such as the metal atoms, zinc, copper, and iron in ionic form.

What is a coenzyme?

An organic molecule serving as a cofactor. Most vitamins are important in nutrition because they act as coenzyme or raw materials from which coenzyme are made.

Human enzyme that functions well in pH 2. Where is it found?

Pepsin, a digestive enzyme found in the human stomach.

Why can extremes of pH or very high temps affect enzyme activity?

The 3-D structure of proteins are sensitive to their environments. As a consequence, each enzyme works better under some conditions rather than others, because these optimal conditions favor the most active shape for the enzyme molecule.

Competitive inhibitors

Substances that reduce the activity of an enzyme by entering the active site in place of the subsrtate, whose structure mimics.

Noncompetitive inhibitor

Substances that reduce the activity of an enzyme by binding to a location away from the active site. This changes the enzymes shape in such a way that the active site becomes much less effective at catalyzing conversion of substrate to product.

Describe feedback inhibition as a mechanism to control metabolic pathways.

The end product of a metabolic pathway often serves to inhibit the production of more of its own molecules. This preserves raw materials for biosynthesis.

Fermentation

A partial degradation of sugars or other other organic fuels that occurs without the use of oxygen.

Aerobic respiration

Consumes oxygen as a reactant along with organic fuel.

What are the products of glucose oxidation? (cellular respiration)

The breakdown of glucose in cellular respiration yields carbon dioxide, water, and energy.

Redox reactions

The loss of electrons from one substance is called OXIDATION, and the addition of electrons to another substance is known as REDUCTION.

When compounds lose electrons, they _______; when compounds gain electrons, they ______ energy.

-Lose

-Gain

What electron carrier is hydrogen transferred to first?

NAD+

What happens when NAD+ is reduced? NAD+ is the ___ form, and NADH is the ___ form.

The enzymatic transfer of 2 electrons and 1 proton (H+) from an organic molecule in food to NAD+ reduces the NAD+ to NADH; the second proton (H+) is released. NAD+ is the oxidized (low energy) form, NADH is the reduced (high energy) form.

What is the function of the electron transport chain in cellular respiration?

Shuttles electrons down a series of redox reactions that release energy used to make a proton gradient, that is ultimately used to generate ATP.

What is the final electron acceptor in the electron transport chain?

Oxygen

How is the electron transport chain utilized in oxidative phosphorylation?

This mode of ATP synthesis is powered by the redox reactions of the electron transport chain. The energy released in each step in the electron transport chain provides the energy to maintain the chemiosmotic gradient that powers the ATP synthase complex.

Where does each stage of cellular respiration occur?

GLYCOLYSIS: cytoplasm

PYRUVATE OXIDATION: mitochondria

CITRIC ACID CYCLE: mitochondria

PHOSPHORYLATION: mitochondria

Glycolysis

Sugar-splitting (cutting)

Glycolysis is a series of reactions that ultimately splits glucose into pyruvate. Glycosis occurs in almost all living cells, serving as the starting point for fermentation or cellular respiration. Oxygen is not required.

The starting product of glycosis is the six-carbon sugar _____ and the ending products are two _____ -carbon molecules of _______.

- Glucose

- 3

- Pyruvate

In glycolysis, whats the difference between the energy investments and energy payoff phases? What are the inputs and outputs?

Energy investments: invest 2 ATP to phosphorylate glucose

Energy payoff: oxidize G3P to create NADH and generate 4 ATP from substrate level phosphorylation.

Input: 2 ATP, glucose, 2 NAD+

Output: 4 ATP, 2NADH, 2 pyruvate.

Used 2 ATP, gained 4 ATP, sum of 2 ATP is gained in glycolysis.

6 Carbons found in original glucose molecule

6 molecules of CO2 released containing the six carbons in the original glucose molecule. 2 molecules are released from the conversion of pyruvate to acetyl CoA and 4 molecules are released from the citric acid cycle.

Citric Acid Cycle (Krebs Cycle)

-NADHs formed: 3 from each Acetly-CoA

-Lost carbons when oxidized: 2

Carbons lost where: CO2

FADH2 formed: 1/acetyl-CoA

ATP formed: 1/acetyleCoA

How many times does this cycle occur for each molecule of glucose: 2

Where is most of the energy at this point in cellular respiration?

NADH and FADH2

What's oxygens role in cellular respiration?

Oxygen is extremely electronegative. It is the final electron acceptor.

Oxygen stabilized the electrons by combining with 2 hydrogen ions to form what compound?

H2O

What is the electron acceptor in fermentation?

NAD+

What 3 organic macromolecules are often utilized to make ATP by cellular respiration?

Proteins, carbs, and fats

Where do the light reactions take place chloroplasts?

The thylakoid membrane; Calvin cycle in the stroma

First process of photosynthesis

The light reactions are the steps of photosynthesis that convert solar energy to chemical energy. Water is split, providing a source of electrons and protons (hydrogen ions, H+) and giving off O2 as a by-product. Light absorbed by chlorophyll drives a transfer of the electrons and hydrogen ions to an acceptor called NADH+ (nicotinamide adenine dinucleotide phosphate), where they are temporarily stored.

Calvin Cycle

The cycle begins by incorporating CO 2from the air into organic molecules already present in the chloroplast. This initial incorporation of carbon into organic compounds as known as carbon fixation. The Calvin cycle then reduces the fixed carbon to carbohydrate by the addition of electrons.The reducing power is provided by NADPH, which acquired its 21 cargo of electrons in the light reactions. To convert CO2 to carbohydrate, the Calvin cycle also requires chemical energy in the form of ATP, which is also generated by the light reactions

What is the relationship between the light reaction and Calvin cycle?

Light reactions provide ATP and NADPH to the calvin cycle. This is the energy needed to build glucose molecules. Calvin cycle provides NADP+ and ADP back to the light cycle to be reused.

Correlation between an absorption spectrum and action spectrum

Absorption spectrum: range of a pigments ability to absorb various wavelengths of light; also a graph of range.

Action Spectrum: a graph that profiles the relative effectiveness of different wavelengths of radiation in driving photosynthesis

Photosystem II (PSII) has at its reaction center a special pair of chloropyll a molecule called P680. Why is it named this?

These molecules are best at absorbing light energy at 680 nm.

What is the name of the chlorophyll a at the reaction center of PS II? P680+ may be the strongest biology oxidizing agent. Why is this necessary? What molecule is it oxidizing?

P680; it is pulling electrons from the oxygen atom in water, which does not want to be oxidized. It obtains electrons from the oxygen atom in a water molecule, so it must have a greater affinity for electrons than oxygen has.

What is the source of O2 in the atmosphere?

Splitting of water

As electrons fall from photosystem II to photosystem I, the cytochrome complex uses the energy to pump ions. This builds a proton gradient that is used in chemiosmosis to produce what molecule?

Hydrogen; ATP

In photo-system I, NADP+ reductase catalyzes the transfer of the excited electron and H+ to NADP+ to form

NADPH

1. Photo-phosphorylation is most similar to what process in cellular respiration?

2. What is the source of energy that excites the electron in photosystem II?

3. Where do the electrons come from that replace the excited electrons in photosystems II?

4. Where do electrons have the highest potential energy?

- Oxidative phosphorylation

- Light

- Water

- End of PS I

Which wavelengths of light are best for supporting plant growth and why?

Red & blue because chlorophyll pigments absorb those specific wavelengths.

Why are plants green?

Pigments in the plants absorb most colors, except green. Green is reflected, thus our eyes see that color.

The carbohydrate produced directly from the Calvin cycle is not glucose, but the three-carbon compound. Each turn of the Calvin cycle fixed one molecule of CO2; therefore, it will take turns of the Calvin cycle to net one G3P

glyceraldehyde 3-phosphate (G3P) 3 turns

The enzyme responsible for carbon fixation in the Calvin cycle, and possibly the most abundant protein on Earth is:

Rubisco

In phase two, the reduction stage, what molecule will donate electrons, and therefore is the source of reducing power?

NADPH :0

The net production of one G3P requires ___ molecules of ATP and ___ molecules of NADPH.

9;6

What is the main purpose of the calvin cycle?

To fix CO2 into organic sugars. This will be used to power cellular respiration and build plant matter.

Where does the CO2 that the calvin cycle fixes come from?

The atmosphere

What happens when a plant undergoes photo-respiration?

Photo-respiration is a metabolic process in which the plant consumes oxygen and ATP, releases carbon dioxide, and decreases photosynthetic output. For photorespiration to occur, C3 plants will close their stomata on hot dry days and produce less sugar because of declining levels of CO2. Rubisco is capable of easily binding O2 in place of CO2.

Compare and contrast C4 with CAM plants. How do they prevent photorespiration?

Both C4 and CAM plants thrive in hot, dry conditions. Both have evolved methods to reduce water loss and to "fix" carbon dioxide in an intermediate compound before it enters the Calvin cycle.

In C4 plants, the initial steps of carbon fixation followed by transfer of CO2 to the Calvin Cycle are separated structurally by 2 different types of cells.

Cam plants, the two steps occur at different times (temporal separation of steps) but in the same cell.

What is an example of CAM plants? C4 plants? C3 plants?

CAM: cactus, C4: corn, C3: apple tree

Interphase

The cell grows; in preparation for cell division, the chromosomes are duplicated, with the genetic material (DNA) copied precisely.

Mitosis

The chromosome copies are separated from each other and moved to opposite ends of the cell.

Cytokinesis

The cell divides into two daughter cells, genetically identical to each other and to the parent cell.

Why do cells need to divide?

- Asexual reproduction for new organisms (cloning)

- Growth and development for multicellular organisms

- Tissue-renewal and repair replaces cells that die.

What is apoptosis?

programmed cell death. -When it is damaged or infected.

-When it has reached the end of its functional life

What is chromatin?

The entire complex of DNA and proteins that is the building material of chromosomes. Chromatin will vary in its degree of condensation during the process of cell division.

How many chromosomes are in a human SOMATIC cell?

There are 46 chromosomes in a human somatic cell.

- Somatic cells include any cell in the body except for reproductive.

What is a gamete?

A reproductive cell, either sperm or egg. There are 23.

Chromosome

A cellular structure carry genetic material, found in the nucleus of eukaryotic cells. Each chromosome consist of one very long DNA molecule and associated proteins. (A bacterial chromosome usually consists of a singular circular DNA molecule and associated proteins. Found in nucleoid region, which is NOT membrane bounded.

Chromatid

One of two identical joined copies of the original chromosome

Centromere

In a duplicated chromosome, the region on each sister chromatid where they are most closely attached to each other by proteins that bind specific DNA sequences; this close attachment causes a constriction in the condensed chromosome.

What is mitosis? How is it different from cytokinesis?

Mitosis, the division of the genetic material in the nucleus, is usually followed immediately by cytokinesis, the division of the cytoplasm.

When in DNA synthesized?

S-phase of interphase

Cell cycle and each phase

G1: "first gap", the first part of interphase. Metabolic activity and growth occurs in this phase.

S: "Synthesis", the second phase of interphase. DNA synthesis occurs in preparation for mitosis. Metabolic activity and growth still occur.

G2: "Second gap", the last part of interphase. Metabolic activity, growth, and preparation for cell division occur.

M: Mitosis distributes the daughter chromosomes to daughter nuclei, the cytokinesis divides the cytoplasm, producing 2 daughter cells.

Which part of the cell cycle is longest in duration?

Interphase

Many of the events of mitosis depend on the mitotic spindle. In animal cells, the assembly of spindle microtubules starts at the centrosome. What is another name for centrosome? What is its function?

-Microtubule-organizing center

-Centrosomes are regions in animal cells that organize the microtubules of the spindle. Each centrosome contains two centrioles.

G2 of interphase

nucleoli are present. Two centrosomes have formed for microtubule organization.

-Chromosomes duplicated during S phase

Prophase

Chromatin starts to condense to chromosomes, nucleoli disappear, mitotic spindle begins to form and centrioles migrate towards to poles; duplicated chromosomes look like 2 identical sister chromatids.

Prometaphase

Nuclear envelope disappears; kinetochore forms

Metaphase

Chromosomes align at the metaphase plate' centrosomes at each pole. Chromosomes arranged as sister chromatids.

Anaphase

Sister chromatids become daughter chromosomes as they are pulled towards each pole; cohesion proteins holding sister chromatids together broken.

Telophase

Nuclear envelope reform; nucleoli reappear; chromosomes become less condensed.

Cytokinesis

Divsiion of cytoplasm, cleavage furrow pinches cell into 2.

Cytokinesis in an animal cell

occurs by a process known as cleavage. The first sign of cleavage is the appearance of a cleavage furrow, a shallow groove in the cell surface near the old metaphase plate. On the cytoplasmic side of the furrow is a contractile ring of act in microfilaments associated with molecules of the protein myosin. The act in microfilaments interact with the myosin molecules, causing the ring to contract. The contraction of the dividing cell's ring of microfilaments is like the pulling of a drawstring. The cleavage furrow deepens until the parent cell is pinched in two, producing two completely separated cells, each with its own nucleus and share of cytosol, organelles, and other subcellular structures.

Binary fission

A method of asexual reproduction by "division in half". Involves the DNA replication machinery copying the origin of replication, producing 2 origins. One cell moves rapidly to the opposite end of the cell, which elongates and divides once DNA replication is complete.

What controls the cell cycle?

Molecules present in the cytoplasm during S or M phase control the progression to those phases.

What is a cell cycle checkpoint?

A control point in the cell cycle where stop and go-ahead signals can regulate the cycle.

What is the order of checkpoints and their function?

1. G1: if a cell receives the go-ahead signal at this checkpoint, the cell will continue.

2. G2: Mitosis is promoted

3. M: The kinetochores must all be attached to spindle fibers during metaphase. This will activate an enzyme (separase), which allows the sister chromatids to seperate, and anaphase will proceed.

What is the G0 phase?

G0 phase is a nondividing state occupied by cells that have left the cell cycle, sometimes reversibly, such as liver cells. Most cells of the human body are in this phase.

What is transformation? What is metastasis?

-Transformation is the conversion of a normal animal cell to a cancerous cell

-Metastasis is the spread of cancer cells to locations distant from their original site.

Cancer

When cells escape the checkpoints and divide uncontrollably

What kinds of drugs are most effective against cancer cells?

Ones that only target rapidly dividing cells

Gene

A discrete unit of hereditary info consisting of a specific nucleotide sequence in DNA (or RNA in some viruses)