Ch 3: Energy, Catalysis, and Biosynthesis

Question 1

How is the energy generated for catabolic and anabolic reactions?

Answer 1

Catabolic reactions release energy by breaking down organic molecules through oxidative pathways.

Anabolic reactions use the energy created by catabolic reactions

Question 2

Delta G value

Answer 2

free-energy change for a reaction. Has to be less than 0 for a reaction to happen spontaneously.

Depends on the concentrations of the reacting molecules

Question 3

acetyl CoA

Answer 3

Activated carrier

Question 4

What are the names of some activated carriers?

Answer 4

ATP, NADH, NADPH, acetyl CoA

Question 5

activation energy

Answer 5

the energy that must be acquired by a molecule to undergo a chemical reaction

Question 6

biosynthesis

Answer 6

enzyme-catalyzed process y which complex molecules are formed from simpler substances by living cells (also called anabolism)

Question 7

coupled reaction

Answer 7

linked pair of chemical reactions in which free energy released by one reactions serves to drive another reaction

Question 8

equilibrium constant

Answer 8

the ratio of substrate to product when the rates of the forward and revers actions are equal

Question 9

free energy

Answer 9

G

The energy that can be harnesses to do work, such as driving a chemical reaction

Question 10

free energy change

Answer 10

delta G

The difference in free energy between reactant and product molecules

The larger the difference, the more the reaction has a tendency to occur

Question 11

metabolism

Answer 11

the sum total of chemical reactions that take place in the cells of a living organism

Question 12

NADH/NAD+

Answer 12

NAD+ accepts a hydride ion from a donor molecule producing the activated carrier NADH. Used inteh breakdown of sugar molecules

Question 13

NADPH/NADP+

Answer 13

NADPH is an activated carrier widely used in biosynthetic pathways

Question 14

oxidation

Answer 14

removal of electrons from an atom

Question 15

reduction

Answer 15

addition of electrons to an atom

Question 16

standard free energy change

Answer 16

delta G°

the free energy change measures at a defined temperature, pressure, and concentration

Question 17

What types of functions do proteins perform?

Answer 17

survival, growth, movement, food breakdown, therapeutic drugs

Question 18

Why are so many new therapeutic drugs proteins?

Answer 18

They are highly specific. Most old drugs were small molecules, which could do a lot, much of it unwanted

Question 19

Basic Amino Acid structure

Answer 19

1) alpha carbon
2) amino group
3) carboxyl group
4) side chain

Question 20

What are the groups of amino acids (characterized by side chain features)?

Answer 20

I) Polar
1) negative
2) positive
3) uncharged polar

II) Non-polar

Question 21

Negative Amino acids

Answer 21

Question 22

Positive Amino Acids

Answer 22

Question 23

Uncharged Polar Amino Acids

Answer 23

Question 24

Nonpolar Amino Acids

Answer 24

Question 25

How is protein shape specified?

Answer 25

1) Through variable rotation at two backbone bonds 2) Through non-covalent interactions 3) By hydrophobic proteins coalescing in the interior core

Question 26

How can a folded protein be in a lower energy state than an unfolded one?

Answer 26

Pulling a protein apart disrupts the bonds and takes energy

Question 27

Alpha helix

Answer 27

pulled together by hydrogen bonds on an amine group with oxygen in a neighboring amino acid the R group (side chain) is not involved in the helix, which is why it is so common If there is a stretch of hydrophobic sidechains on an alpha helix, it can cross the plasma membrane

Question 28

Beta sheets

Answer 28

Back-and-forth pleated sheets of folds Stretchs of amino acids will bond to each other (independent of side chains, which is why it is so common) Side chains alternate side of the sheet

Question 29

Protein families

Answer 29

based on chemistry and function, not so much sequence

Question 30

Besides hydrogen bonds/hydrophobic forces, etc, what can help stabilize protein structure?

Answer 30

covalent cross-linkages typically disulfide bonds between two cysteins

Question 31

Answer 31

Try to disrupt the bonding sites by changing one of the amino acids

Question 32

What are the important parts of the structure of antibodies

Answer 32

1) hypervariable loops 2) constant region 3) light chain 4) heavy chain

Question 33

How do antibodies work?

Answer 33

The variable region recognizes different things and bind to them. They either destroy the thing they bind to, or let macrophages know this thing is targeted for destruction

Question 34

Describe an example catalyzing reaction

Answer 34

Asp 52 cutting a sugar molecule in half: Asp 52 acts to stabilize the transition site until a water melecule can come in and take its place, leaving the Asp 52 intact, and the sugar molecule broken

Question 35

Different mechanisms of catalysis:

Answer 35

1) proximity: the enzyme puts hte subtrates together in exactly the formation they'd need to be in 2) electronic stabilization of transition site: when the catalyst binds to the substrate, it rearranges the electrons in the substrate, leaving it in a more favorable state for a reaction 3) positioning: the enzyme strains/changes the shape of the substrate into a position that is more favorable for a reaction

Question 36

Draw an example of a peptide bond between two amino acids

Answer 36

the -COOH group on one links up with the NH2 group of another, loses an H20 and connected the C to the N with a single covalent bond

Question 37

Carbon atoms cycle continuously through the biosphere. What is produced by cell respiration, and what state of carbon does this by-product represent?

Answer 37

CO2, completely oxidized carbon. (The complete oxidation of the carbon atom in glucose)

Question 38

What is true about a cell's energy use and entropy?

Answer 38

The heat released by an animal cell comes from the chemical bond energy present in the food molecules it metabolizes

Question 39

Small molecules diffuse very efficiently through the cell by doing what?

Answer 39

Moving randomly, knocking around by colliding with other molecules

Question 40

What is true and not true of a chemical reaction at equilibrium?

Answer 40

True: ∆G = 0 True: The rates of forward and reverse reactions are equal True: The net concentrations of substrate and product do not change False: Both the forward and reverse reactions have stopped

Question 41

At equilibrium, what is the free energy change for a reaction?

Answer 41

At its lowest point (0)

Question 42

Which of the following represents a carrier in the activated state in which it would be used in a cell? ADP NADP FAD NADH

Answer 42

NADH, which can pass energy in the form of electrons plus a proton to a recipient molecule, generating an oxidized NADH.

Question 43

Which reaction can be driven by the hydrolysis of a molecule of ATP inside a cell?

Answer 43

glucose + fructose --> sucrose (∆G=5.5kcal/mol) the hydrolysis of ATP has a ∆G of about -11 to -13