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Cell Biology > Ch 3: Energy, Catalysis, and Biosynthesis > Flashcards

Ch 3: Energy, Catalysis, and Biosynthesis Flashcards

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1
Q

How is the energy generated for catabolic and anabolic reactions?

A

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

Anabolic reactions use the energy created by catabolic reactions

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2
Q

Delta G value

A

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

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3
Q

acetyl CoA

A

Activated carrier

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4
Q

What are the names of some activated carriers?

A

ATP, NADH, NADPH, acetyl CoA

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5
Q

activation energy

A

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

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6
Q

biosynthesis

A

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

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7
Q

coupled reaction

A

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

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8
Q

equilibrium constant

A

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

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9
Q

free energy

A

G

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

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10
Q

free energy change

A

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

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11
Q

metabolism

A

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

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12
Q

NADH/NAD+

A

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

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13
Q

NADPH/NADP+

A

NADPH is an activated carrier widely used in biosynthetic pathways

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14
Q

oxidation

A

removal of electrons from an atom

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15
Q

reduction

A

addition of electrons to an atom

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16
Q

standard free energy change

A

delta G°

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

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17
Q

What types of functions do proteins perform?

A

survival, growth, movement, food breakdown, therapeutic drugs

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18
Q

Why are so many new therapeutic drugs proteins?

A

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

19
Q

Basic Amino Acid structure

A

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

20
Q

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

A

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

II) Non-polar

21
Q

Negative Amino acids

A
22
Q

Positive Amino Acids

A
23
Q

Uncharged Polar Amino Acids

A
24
Q

Nonpolar Amino Acids

A
25
Q

How is protein shape specified?

A

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

26
Q

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

A

Pulling a protein apart disrupts the bonds and takes energy

27
Q

Alpha helix

A

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

28
Q

Beta sheets

A

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

29
Q

Protein families

A

based on chemistry and function, not so much sequence

30
Q

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

A

covalent cross-linkages

typically disulfide bonds between two cysteins

31
Q
A

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

32
Q

What are the important parts of the structure of antibodies

A

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

33
Q

How do antibodies work?

A

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

34
Q

Describe an example catalyzing reaction

A

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

35
Q

Different mechanisms of catalysis:

A

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

36
Q

Draw an example of a peptide bond between two amino acids

A

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

37
Q

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

A

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

38
Q

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

A

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

39
Q

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

A

Moving randomly, knocking around by colliding with other molecules

40
Q

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

A

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

41
Q

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

A

At its lowest point (0)

42
Q

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

A

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

43
Q

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

A

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

Cell Biology (24 decks)

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