Chapter 5 - Ground Rules Of Metabolism

Question 1

Energy

Answer 1

Capacity to do work.

Question 2

Kinetic Energy

Answer 2

Energy of Motion

Question 3

First Law of Thermodynamics

Answer 3

Energy cannot be created or destroyed.

Question 4

Entropy

Answer 4

Tendency of energy to spontaneously disperse.

Increases until heat is evenly distributed throughout system.

Question 5

Second Law of Thermodynamics

Answer 5

Entropy tends to increase.
Energy tends to spread out spontaneously.
Related to Chem. Bonding in that covalent bonds between atoms decrease movement, thus decreasing entropy.

Question 6

Potential Energy

Answer 6

Stored Energy.
Stored in chemical bonds.
Resists entropy.

Question 7

Reaction

Answer 7

Any process by which a chemical change occurs.

Question 8

Reactants

Answer 8

Molecules entering a reaction.

Question 9

Products

Answer 9

Molecules remaining at reaction’s end.

Question 10

Free Energy

Answer 10

Amount of energy available to do work. 
Bond energy(energy required to break a bond)/entropy contribute to free energy.

Question 11

Endergonic Reactions

Answer 11

Reactants have less free energy that products.

Do not proceed without an energy input.

Question 12

Exergonic Reactions

Answer 12

Reactants have greater free energy than products.
End with net release of free energy.
Cells run these to access free energy of molecules.
Example: Aerobic Resp. (converts glucose + oxygen = CO2 and H2O for a net energy output)

Question 13

Why doesn’t Earth burst into flame?

Answer 13

The molecules of life release energy when combined with Oxygen.
Example: Wood is cellulose (MOL). A spark initiates a reaction converting cellulose and oxygen in air to water and carbon dioxide. The reaction is exergonic, releasing enough energy to continue the same reaction with cellulose and oxygen molecules, causing a fire to keep burning following being lit.
Earth does not burst into flame because energy is required to break the bonds in any reaction.<– Activation Energy

Question 14

Activation Energy

Answer 14

Minimum amount of energy required to start a chemical reaction.
Analagous to a hill that rewctants must climb before coasting toward the products.
Different amounts of activation energy are required to start endergonic and exergonic reactions. Amount varies with reaction.

Question 15

ATP (Adenosine Triphosphate)

Answer 15

Functions as energy carrier by accepting energy given off by exergonic reactions and delivering it to endergonic reactions.
“Currency” of cell’s energy economy.
Nucleotide with 3 phosphate holding immense energy in their bonds. When phosphates of ATPs are transferred to each other, energy is moved along with the phosphate.<–Phosphorylation

Question 16

Phosphorylation

Answer 16

The transfer of a phosphate group from an ATP to another molecule. This is the “net energy input” required in endergonic reactions.

Question 17

ATP/ADP Cycle

Answer 17

Cycle of using and replenishing ATP.

When ATP loses a phosphate, ADP forms. ATP reforms when ADP binds to a phosphate in an endergonic reaction.

Question 18

Catalysis

Answer 18

Process in which an enzyme makes a reaction run much faster than it would on its own.
Enzyme is unchanged by participating in reaction.
Most enzymes are proteins; some are RNAs. Each kind recognizes specific reactants (substrates) and alters them in a specific way.

Question 19

Substrate

Answer 19

Specific reactants in a reaction.
Altered in a specific way by enzymes.
Enzymes are so specific because of their active sites.

Question 20

Active Site

Answer 20

Pockets where substrates bind and reactions proceed.
Complementary in size, shape, polarity, and charge to substrate of enzyme. <–reason for specificity of enzymes relative to substrates.

Question 21

Transition State

Answer 21

State where substrate bonds reach their breaking point and reaction runs spontaneously to product.
Lowering of Activation energy causes change bringing on transition state.
HOW TO LOWER ACTIVATION ENERGY:

Helping substrates get together by binding at active site(increases chance of substrates reacting with each other)

Orienting substrates favoring reaction (positioning bound substrates at active site aligns them for reaction)

Inducing fit between molecule and substrate(since active site isn’t perfectly complementary to substrate, interaction with substrate causes enzyme to change shape to better fit the substrate. Improved fit results in stronger bond, or bring on the transition state better/faster.

Shutting out water molecules:
Metabolism occurs in water-based fluids, but water can sometimes interfere with certain reactions, so active sites of those enzymes participating in those reactions repel water.

Question 22

HOW TO LOWER ACTIVATION ENERGY:

Answer 22

Helping substrates get together by binding at active site(increases chance of substrates reacting with each other)

Orienting substrates favoring reaction (positioning bound substrates at active site aligns them for reaction)

Inducing fit between molecule and substrate(since active site isn’t perfectly complementary to substrate, interaction with substrate causes enzyme to change shape to better fit the substrate. Improved fit results in stronger bond, or bring on the transition state better/faster.

Shutting out water molecules:
Metabolism occurs in water-based fluids, but water can sometimes interfere with certain reactions, so active sites of those enzymes participating in those reactions repel water.

Question 23

Effects of tempterature, pH, and salinity on enzymes

Answer 23

Temp: adding heat energy boosts free energy, bringing a reaction closer to its activation energy. More temp increases with reaction rate, but too high temp makes an enzyme denature.
pH: most enzymes in human body tolerate optimal pH between 6 and 8 (blood is 7.35). Some enzymes can tolerate harsher conditions(pepsin in stomach acid; pH 2)
Salinity: too much or too little salt disrupts H bonding holding an enzyme in 3-D shape.

Question 24

Cofactors

Answer 24

Atoms or molecules (EXCLUDING PROTEINS) that assoc. with enzymes and are necessary for their function. Some are metal ions.
Organic molecules that are cofactors: coenzymes
Example: Catalyse (enzyme). (also an antioxidant)
Has 4 hemes. Iron atom at center of each heme is cofactor, pulling on substrate’s electrons, bringing on trans. state.

Question 25

Coenzyme

Answer 25

A cofactor that is an organic molecule. (Vit C)
Can be tightly bound to enzyme or participate as separate molecules. ARE modified by participating in reactions. Typically regenerated in other reactions.
Example: NAD+ becomes NADH by accepting electrons/hydrogen atoms in a reaction. Regenerated when NADH gives up E/Hs in another reaction.

Question 26

Antioxidant

Answer 26

Stops other molecules from reacting with oxygen, since oxygen reactions often produce free radicals (atoms or moluecules with unpaired electrons), which attack the structure of biological molecules.

Question 27

Free Radical

Answer 27

Atoms or molecules with unpaired electrons.
Often form in oxygen reactions and other normal metab. reactions.
Damage structure of biological molecules.
Amt.s are reduced by antioxidants.

Question 28

Metabolic Pathway

Answer 28

A series of step-wise reactions in which organic substances are built, rearranged, or broken.
Can be linear (run from reactant to product) or cyclic (last step generates reactant for first).

Question 29

How does a cell adjust the types and amounts of molecules it produces?

Answer 29

Reactions can run in reverse, with some products becoming reactants. The rates of forward and rev. reactions depends on the concentration of reactants and products. A high conc. of reactants pushes the reaction forward, while a high conc. of products pushes it in the reverse direction.
Other mechanisms for actively regulate enzymes. Certain molecules in cells govern how fast enzyme molecules are made, or influence activity of completed enzymes. End product of a pathway may inhibit an enzyme in the seriess shape, inhibiting or enhancing its function.

Question 30

Feedback Inhibition

Answer 30

Method by which and end product of a series of enzymatic reactions inhibits activity of an enzyme in the series.

Question 31

Allosteric Site

Answer 31

Regions of an enzyme other than the active site where regulatory molecules bind. Allosteric regulator molecules change the shape of enzymes and enhance (bring active site to surface) or inhibit(block active site) the enzyme’s activities.

Question 32

Redox Reaction

Answer 32

One molecule accepts electrons (becomes reduced in charge), and the donor molecule becomes oxidized.
Also known as Electron Transfers.
Comprise most of the steps incrementally releasing energy in manageable amounts from organic molecules in cells.

Question 33

Electron Transfer Chain

Answer 33

Organized series of reactions in which membrane-bound arrays of enzymes and other molecules give up and accept molecules in turn. Harvest energy given off by electrons as they drop to lower energy levels as they progress through the chain.
Electrons are delivered to chains in photosynthesis and aerobic respiration by coenzymes. Energy release in those steps helps drive ATP synthesis.

Question 34

Concentration

Answer 34

Amount of a solute that is dissolved in a given amount of fluid.

Question 35

Concentration Gradient

Answer 35

A difference in solute concentration between adjacent regions of solution.
Solute molecules tend to move “down” a concentration gradient (from higher to lower concentration) because molecules/ions are constantly in motion, so crowded molecules collide more and move out of a higher-concentrated region.

Question 36

Diffusion

Answer 36

Net movement of molecules/ions in response to a concentration gradient. Essential way for substances to move into, through, and out of cells.
Rate of diffusion depends on:
Size: smaller molecules diffuse more quickly(require less energy to move than larger ones)
Temperature: molecules move faster at higher temps, so faster diffusion
Steepness of concentration gradient: molecules collide more as they travel across gradient
Charge: can affect rate/direction of diffusion. Positively charged substances diffuse toward a region with an overall negative charge.
Pressure: squeezes molecules together, causing more collisions and faster diffusion.

Question 37

Tonicity

Answer 37

Total concentration of solutes in fluids separated by a selectively permeable membrane.
Allows water to cross it. <–diffusion of water across a membrane: osmosis.
Example: lipid bilayer

Question 38

3 ways to describe tonicity:

Answer 38

Hypotonic: fluid with lower overall concentration of solutes
Hypertonic: fluid with higher solute concentration
Isotonic: fluids with same overall concentration
Water flows from hypotonic to hypertonic fluid. Diffusion continues until fluids are isotonic relative to each other.
If solute concentration in a cell changes enough, cell’s enzymes cease to function.

Question 39

Turgor

Answer 39

Pressure exerted by a fluid against containing structure.
Usually caused by osmosis as water enters a cell. If enough pressure in a cell, osmosis into the cell stops. That amount of turgor is osmotic pressure

Question 40

Osmotic Pressure

Answer 40

Amount of turgor required to stop osmosis.
Keeps walled cells plump.
If soil dries out(becomes hypertonic), hypotonic plant cell loses water, causing cytoplasm to shrink and turgor to decrease, causing plant to wilt.

Question 41

Membrane transport proteins

Answer 41

Help molecules and ions other than gases/water/small nonpolar molecules cross a lipid bilayer. Each protein helps a specific ion/molecule. Specificity means that the materials entering a cell are determined by the proteins embedded in the bilayer.

Question 42

Passive Transport

Answer 42

Movement of a solute through a PTP(pass trans prot) driven only by solute’s concentration gradient.
AKA facilitated diffusion. Solute binds to pass trans prot and is released on other side of membrane.
EXAMPLE: Glucose Transporter
Changes shape upon binding to molecule of glucose. Shape change moves molecule to other side of membrane, where it detached. Transporter reverts to original shape. Some do not change shape and are permanently open channels; others open and close in response to stimulus such as shift in electrical charge/binding to sign. molecule.

Question 43

Active Transport

Answer 43

The act of a trans prot using energy to pump a solute against the concentration gradient in a cell membrane. After solute binds to transporter, energy input (phosphate-group transfer from ATP) changes protein shape, causing release of the solute on the other side of the membrane.
Example: Calcium pump, which moves calc ions across cell membs. Calc ions are messengers in cells. Many enzymes have allosteric sites to bind with with calc ions. Presence of these ions is very regulated. Pumps in euk cells’ membs keep concentration of calc ions 10K times higher than in EXC fluid.
Active trans prots include cotransporters

Question 44

Cotransporter

Answer 44

Active Transport Proteins moving 2 substances simultaneously in the same or opp directions across a membrane.
Almost all body cells have Sodium-Potassium pumps. Sodium ions (Na+) in cytoplasm diffuse into pump’s open channel and bind to interior. A phosphate group transfer from ATP causes shape of pump to change, making the pump open a channel release Na+ into extracellular fluid. Then Potassium ions (K+) from EXC fluid diffuse into channel and bind to its interior. Sodium-potassium pump releases Phosphate group and reverts to original shape, where channel opens back to cytoplasm and releases the K+.

Question 45

When a lipid bilayer is disrupted, such as when part of the plasma membrane pinches off as a vesicle, it seals itself. Why?

Answer 45

Disruption exposes nonpolar fatty acid tails to watery surroundings, they rearrange spontaneously into a lipid bilayer.

Question 46

Membrane Trafficking

Answer 46

Formation/movement of vesicles.

Requires ATP and involves motor proteins.

Question 47

Exocytosis

Answer 47

A vesicle moves to the cell surface, and the protein studded lipid bilayer of its membrane fuses with the cell’s plasma membrane. As exocytic vesicle loses its identity, contents are released into EXC fluid. Main process by which new patches of cell membrane form.

Question 48

Endocytosis

Answer 48

Small patch of plasma membrane balloons inward, pinching off as it sinks farther into the cytoplasm. Membrane patch becomes outer boundary of endocytic vesicle. Contents of vesicle are delivered to an organelle or stored in cytoplasm.
THREE types of endocytosis:
Phagocytosis (cell eating)
Phagocytic cells such as amoebas engulf microorganisms/cell debris/other particles. Microfilaments form a mesh under plasma memb, which forces cytoplasm and some plasma membrane out upon contraction. The bulging lobe is a pseudopod, which engulfs a target and two of which merge as a vesicle that sinks into the cytoplasm and fuses with a lysosome. The vesicle’s contents are broken down by lysosomal enzymes, and remaining molecular bits are recycled by the cell or expelled through exocytosis.

Pinocytosis: the cell takes in dissolved materials (liquid content of vescicle is slowly released into cytosol)

Receptor mediated endocytosis: receptor prots in coated (clarithin) pits in memb bind to specific molecules (ligands) which are then enclosed in a coated vesicle.

Question 49

How do plasma membranes form?

Answer 49

Membrane proteins and lipids are made and modified in the ER and become part of vesicles transporting them to Golgi Bodies for final modifications. The finished proteins/lipids are repackaged as new vesicles that travel to and fuse with the plasm membrane.

In cells no longer growing, plasma membrane area remains relatively constant. Membrane lost by endocytosis is replaced by exocytosis.