Biochemical Basics Flashcards

11
Q

A chemical substance that cannot be broken down further using standard chemical techniques is known as:

A

An element

For example, carbon (C) is an element. Atoms of a particular element always have the same number of protons. For example, all carbon atoms have 6 protons!

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13
Q

What is the difference between an atom, a molecule, and a compound?

A
  • An atom is the fundamental unit of matter. Atoms contain protons, neutrons, and electrons.
  • A molecule is a group of two or more atoms, connected by chemical bonds (for example, O2).
  • A compound is a molecule that contains atoms of more than one element (for example, H2O).
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14
Q

Which of the following are contained within the nucleus of a typical atom?

  • Protons
  • Neutrons
  • Electrons
A

A typical atomic nucleus contains protons and neutrons. Electrons are not found in the nucleus; instead, they are located in regions (“shells”) surrounding the nucleus.

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15
Q

Isotopes are atoms with the same number of:

A

protons

Isotopes are atoms with the same number of protons, meaning that they must represent the same element. Isotopes differ in their number of neutrons.

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16
Q

Define:

ionic bond

A

A chemical bond that forms due to the transfer of specific electrons from one atom to another, with one atom losing an electron and the other gaining it.

The atom that gains electrons is given a negative charge, while the atom that gives up electrons is given a positive charge.

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17
Q

Define:

covalent bond

A

A chemical bond that forms via the sharing (not complete transfer) of electrons.

When the electrons are shared unequally, the bond is polar covalent. For example, H2O contains two polar covalent bonds between H and O, because these atoms have different electronegativities (attraction to electrons in a bond).

When the electrons are shared equally, the bond is nonpolar covalent. For example, O2 contains a nonpolar covalent bond between the two O atoms, which have the same electronegativity.

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18
Q

What is the chemical formula for water, and is the water molecule polar or nonpolar?

A

Water has a formula of H2O, and it is polar.

The water molecule (shown here) is bent due to the presence of two lone pairs on the central oxygen atom. Oxygen is more electronegative than hydrogen, so the oxygen atom will carry a partial negative charge, while the hydrogen atoms will be partially positive. Molecules with asymmetrical charge distributions like this one are polar.

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19
Q

How do hydrogen bonds differ from ionic or covalent bonds?

A

Hydrogen bonds are intermolecular, which means they occur between two or more different molecules. Ionic and covalent bonds are intramolecular, meaning they connect atoms within a single molecule.

Hydrogen bonds are attractive forces.

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21
Q

Define:

a hydrophilic compound

A

One that is attracted to water.

Since water is polar, it tends to attract other polar compounds.

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22
Q

Define:

a hydrophobic compound

A

One that is repelled by water.

Since water is polar, it tends to repel nonpolar compounds. A classic example is an oil slick on the top of the ocean. Oil is nonpolar, so it is not attracted to the ocean water, and the two liquids do not mix.

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23
Q

Define:

macromolecule

A

A molecule that contains an extremely large number of atoms.

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24
Q

Name the four main types of organic macromolecules that are found in living organisms.

A
  1. Carbohydrates
  2. Lipids
  3. Proteins
  4. Nucleic acids

Carbohydrates are commonly known as sugars, and lipids are commonly known as fats.

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25
Q

What is the general chemical formula for a typical carbohydrate?

A

(CH2O)n

Where n is an integer.

This can be easily remembered, since H2O represents water. Carbohydrates are simply “hydrated carbons.” Note that a few rare carbohydrates, like deoxyribose, have formulas that differ from this rule.

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27
Q

Define a monosaccharide and give two common examples.

A
  • A carbohydrate that contains only a single sugar subunit.
  • Classic examples: glucose and fructose.
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28
Q

Define a disaccharide and give three common examples.

A
  • A carbohydrate that consists of two sugar subunits, joined by a bond called a glycosidic linkage.
  • Classic examples: maltose, lactose, and sucrose.
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29
Q

Define a polysaccharide and give three common examples.

A
  • A carbohydrate that consists of a polymer (or long chain) of many sugar subunits.
  • Classic examples: glycogen, starch, and cellulose.
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31
Q

What type of reaction occurs when two carbohydrate subunits combine to form a disaccharide?

A

A dehydration reaction.

Dehydration reactions involve the combination (or condensation) of smaller reactants to form a larger product. This occurs along with the loss of a water molecule.

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32
Q

What is the molecular formula for glucose?

A

C6H12O6

Glucose is a six-carbon monosaccharide (meaning that it contains only one sugar subunit).

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33
Q

What is the molecular formula for sucrose?

A

C12H22O11

Sucrose is a disaccharide, meaning that it consists of two sugar subunits. Specifically, these subunits are glucose and fructose.

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34
Q

The main component of plant cell walls is classified as which of the four main types of organic macromolecule?

A

Carbohydrates

Plant cell walls are composed of cellulose, which is a polysaccharide, or carbohydrate polymer.

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35
Q

Protein molecules are composed of smaller subunits known as:

A

Amino acids

Amino acids are the monomers, or individual subunits, that make up protein molecules. Adjacent amino acids are held together by peptide bonds.

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36
Q

Which two functional groups are found in all amino acids?

A
  1. amine
  2. carboxylic acid

Each amino acid also contains a specific side chain.

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37
Q

A laboratory technician is analyzing the composition of a plasma protein. Which elements could he expect to find in this protein’s structure?

A
  • carbon
  • hydrogen
  • oxygen
  • nitrogen

Sulfur also may be present, depending on the particular amino acids in the structure. Some proteins also contain trace amounts of selenium.

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38
Q

Which would be expected to have a higher molecular weight: a dipeptide or a polypeptide?

A

polypeptide

A dipeptide is the smallest form of peptide and contains only two amino acids bound together. Polypeptides typically consist of long strings of amino acids, making them significantly heavier; a polypeptide can include up to around 50 amino acids in total.

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40
Q

Name the four levels of protein structure.

A
  • Primary structure
  • Secondary structure
  • Tertiary structure
  • Quaternary structure
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41
Q

Define:

the primary structure of a protein

A

It is simply its linear amino acid sequence.

Primary structure is often written using either a one- or a three-letter abbreviation for each amino acid (for example, “Gly-Pro-Ile-Cys…” or “GPIC…”).

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43
Q

Define:

the secondary structure of a protein

A

Refers to the folding of the amino acid chain into repetitive structures due to hydrogen bonding between backbone groups.

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44
Q

What functional group is present in all peptide bonds?

A

amides

In fact, they are sometimes alternatively known as amide linkages.

A peptide bond forms when the amine group of one amino acid attacks the carbonyl carbon of another.

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45
Q

Define:

the tertiary structure of a protein

A

Refers to its large-scale three-dimensional shape.

Tertiary structure is determined by interactions between side chains and by hydrophobic interactions (the tendency for nonpolar groups to avoid facing the watery environment).

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46
Q

Define:

the quaternary structure of a protein

A

It is present only in proteins that are composed of multiple subunits. This level of structure refers to interactions between subunits.

For example, hemoglobin (shown here) consists of four separate subunits, held together by various interactions and attractive forces.

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47
Q

Define:

lipids

A

A class of organic macromolecule characterized by their nonpolar (non-water-soluble) nature.

Most notably, lipids include triglycerides (fats), oils, steroids, waxes, and phospholipids.

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48
Q

What type of lipid is pictured here?

A

triglyceride

A triglyceride is commonly known simply as a fat. It consists of three fatty acid molecules attached to a three-carbon glycerol backbone.

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49
Q

The diagram below depicts a fatty acid. Is this fatty acid saturated, monounsaturated, or polyunsaturated?

A

polyunsaturated

Saturated fatty acids have carbon chains that include only single bonds, while unsaturated fatty acids include one or more double bonds in their chains. Since this fatty acid contains three carbon-carbon double bonds, it is polyunsaturated. (To be monounsaturated, a fatty acid must include only one double bond in its carbon chain.)

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50
Q

What functional groups are present in a typical fatty acid?

A

A carboxylic acid (COOH) group attached to a hydrocarbon chain.

Fatty acids can combine with glycerol to form triglycerides, or fat. Fatty acids can also be broken down to provide cells with energy.

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51
Q

What type of lipid would be expected to be most predominant in a eukaryotic cell membrane?

A

phospholipids

The cell membrane (in both eukaryotes and prokaryotes) is composed mainly of phospholipids in the form of a “bilayer,” or double layer.

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52
Q

A typical phospholipid includes both a polar “head” region and two nonpolar “tails.” What term describes this property of having both polar and nonpolar regions?

A

amphipathic

Specifically, the polar “head” region includes phosphate, which is charged; this charge is what gives the head group its polarity. The two “tails” consist of fatty acids, which are largely nonpolar due to their long hydrocarbon chains.

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53
Q

What class of lipid is derived from the molecule below and plays a vital role in the endocrine system?

A

steroid hormones

Steroid hormones are derived from cholesterol (shown here). These lipid molecules can be easily spotted due to their structures, which include four fused rings.

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54
Q

Structures like that shown below are found in which of the four major classes of organic macromolecules?

A

Nucleic acids

The structure pictured here is a nucleotide, as is evident from its nitrogenous base, sugar, and phosphate group. Nucleotides are the monomers (“building blocks”) that form nucleic acids, including DNA and RNA.

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55
Q

A student is analyzing an unknown biomolecule. He knows that the molecule includes covalent bonds and that it is not a lipid. He is also certain that the molecule contains carbon, hydrogen, and phosphorus, although it may also include other elements. This biomolecule is most likely a:

A

Nucleic acid

All four of the main classes of organic macromolecule include covalent bonds, so that piece of information is unhelpful. However, only nucleic acids and (some) lipids can contain phosphorus. Since we are told that this molecule is not a lipid, it must be a nucleic acid.

56
Q

Define:

nucleic acids

A

A class of organic macromolecule, which consists of long chains of nucleotide monomers and are involved in the storage and transmission of genetic material.

57
Q

Define:

metabolism

A

It collectively refers to the biological processes that occur within cells. Specifically, these processes either generate energy through the breakdown of molecules or use energy to build molecules.

Metabolism is also known as “cellular respiration.”

58
Q

Define:

catabolism

A

It is the biological breakdown of molecules into smaller units. Catabolic processes are accompanied by the generation of energy.

The opposite of this class of metabolic reactions is anabolism.

59
Q

Define:

anabolism

A

It is the creation of larger biomolecules from smaller units. Anabolic processes require energy input.

The opposite of this class of metabolic reactions is catabolism.

60
Q

What broad distinction separates aerobic and anaerobic respiration?

A

Aerobic respiration requires oxygen, while anaerobic respiration does not require oxygen.

As part of metabolism, both processes involve the breakdown of biological molecules and the eventual release of energy.

61
Q

Which metabolic process occurs in the cytosol regardless of the presence or absence of oxygen?

A

Glycolysis

Glycolysis is a biochemical process that forms pyruvate from the breakdown of glucose. The pathway produces 2 NADH and a net total of 2 ATP per glucose molecule.

62
Q

Describe the net reaction of glycolysis.

A

C6H12O6 + 2NAD+ + 2 Pi + 2 ADP ⇒ 2 pyruvate + 2 ATP + 2 NADH + 2 H2O + 2 H+

While glycolysis only produces a net of two ATP molecules, it generates a total of four. However, two molecules of ATP are used as reactants in early glycolytic steps.

63
Q

Which metabolic process immediately follows glycolysis in oxygen-poor conditions?

A

Fermentation

This process takes place when O2 is too scarce to facilitate the entry of glycolytic products into the Krebs cycle.

Fermentation can produce either ethanol or lactic acid, depending on the species.

64
Q

The conversion of pyruvate to lactic acid, often referred to simply as “fermentation,” produces no ATP. However, it is still necessary in anaerobic conditions. What purpose does this process serve?

A

Fermentation regenerates NAD+ by oxidizing NADH and reducing pyruvate.

NAD+ is necessary for glycolysis, but cannot be regenerated by the electron transport chain under anaerobic conditions. Fermentation serves to produce NAD+, reducing buildup of NADH and allowing glycolysis to continue.

65
Q

What are the substrates and products of pyruvate decarboxylation?

A

Pyruvate, a three-carbon molecule, is the substrate. CO2, NADH, and acetyl-CoA are the ultimate products.

66
Q

Two glucose molecules undergo glycolysis, producing pyruvate. How many molecules of NADH will be produced simply from the decarboxylation of these pyruvate products?

A

4 NADH molecules

During glycolysis, the initial two glucose molecules will be converted into four molecules of pyruvate. For every molecule of pyruvate that is decarboxylated by pyruvate dehydrogenase, one molecule of NADH is formed.

67
Q

Which metabolic process generates both NADH and FADH2?

A

The Krebs cycle produces the electron carriers NADH and FADH2, as well as an ATP equivalent (either ATP or GTP).

The Krebs cycle, also known as the citric acid cycle, involves the cyclic transformation of organic molecules. It occurs in the mitochondrial matrix.

68
Q

How many molecules of NADH and FADH2, respectively, are produced during one turn of the Krebs cycle?

A

One full cycle produces 3 NADH molecules and 1 FADH2.

Other products include carbon dioxide, which is released as waste, and one molecule of GTP.

69
Q

Which metabolic process takes place along the inner mitochondrial membrane?

A

The electron transport chain (ETC) uses a series of complexes along the inner mitochondrial membrane. These molecules support a chain of oxidation-reduction reactions, ultimately resulting in the oxidization of NADH and FADH2 and the reduction of O2.

The transport of electrons through the chain creates a proton gradient that provides the energy to convert ADP to ATP.

70
Q

Which metabolic process is facilitated by the proton gradient within the mitochondria?

A

ATP synthesis

After establishment of the gradient, proton concentration in the intermembrane space is high. When possible, these protons will move down their gradient and reenter the matrix; this can only occur if they pass through ATP synthase, an enzyme. As this process occurs, ATP synthase uses this energy to convert ADP to ATP.

71
Q

Which of the following molecules are necessary substrates for the electron transport chain?

  • glucose
  • O2
  • NADH
  • pyruvate
  • CO2
A

NADH is a required substrate, and O2 must be present as the final electron acceptor in the chain.

Glucose and pyruvate, though linked to NADH production, are not directly necessary for the electron transport chain. CO2 is a waste product of cellular respiration.

72
Q

Which of the following molecules are necessary substrates for fermentation?

  • ethanol
  • lactate
  • pyruvate
  • NADH
  • NAD+
A
  • Pyruvate
  • NADH

Ethanol, lactate, and NAD+ are all products of fermentation.

73
Q

Which of the following molecules are products of glycolysis?

  • glucose
  • ATP
  • NAD+
  • pyruvate
  • O2
A
  • ATP
  • pyruvate

NADH, though not listed here, is another glycolytic product. Glucose and NAD+ are consumed in glycolysis, while O2 is not involved. Remember that glycolysis is an anaerobic process.

74
Q

Which of the following molecules are products of the Krebs cycle?

  • NADH
  • acetyl-CoA
  • pyruvate
  • FADH2
  • NAD+
A

The Krebs cycle produces NADH and FADH2, which are electron carriers that are later used.

Acetyl-CoA and NAD+ are consumed in the Krebs cycle, while pyruvate is not directly involved.

75
Q

Which two processes of cellular metabolism take place in the cytoplasm?

A
  1. Glycolysis
  2. Fermentation

Note that fermentation only takes place in anaerobic conditions.

All other processes take place in the mitochondria.

76
Q

Which two processes of cellular metabolism take place in the mitochondrial matrix?

A
  1. The Krebs cycle
  2. Pyruvate decarboxylation

The electron transport chain is also a mitochondrial process, but occurs along the inner membrane, not within the matrix itself.

77
Q

Which enzymes are responsible for the metabolism of proteins?

A

Proteases

also called peptidases

Proteins are cleaved into amino acids. Depending on their identity, these amino acids can be converted to acetyl-CoA, pyruvate, or other metabolic intermediates.

78
Q

What homeostatic change occurs in the blood when the cells are in oxygen debt?

A

Acidosis

or low pH

This is the result of excess CO2 and the buildup of lactic acid in muscles during anaerobic respiration.

Note that normal plasma pH is 7.4.

79
Q

The majority of glucose molecules enter the cell via which transport method?

A

facilitated diffusion

This occurs with the assistance of a family of transport proteins.

This process is promoted by high plasma glucose levels, which creates a concentration gradient that drives glucose into the cells. It is also promoted by the activity of insulin, which increases the number of glucose transporters on the membranes of certain cell types.

80
Q

Which reaction is the rate-limiting step of glycolysis?

A

The phosphorylation of fructose 6-phosphate.

This reaction is catalyzed by the enzyme phosphofructokinase-1 (PFK-1). For this reason, PFK-1 is sometimes called the rate-limiting enzyme of glycolysis.

81
Q

Of AMP, ATP, and citrate, which is most likely to serve as an allosteric activator of PFK-1?

A

AMP

The other two molecules are inhibitors.

You can figure this out logically: “activate” means “stimulate.” Glycolysis should be stimulated when available energy is low (to make more) and inhibited when it is high. High AMP concentrations imply that cellular ATP is low.

82
Q

What is the chemical formula of glucose?

A

C6H12O6

Broadly, glucose is a carbohydrate; specifically, it is a monosaccharide.

83
Q

Which two molecules can be created by the fermentation of pyruvate?

A
  • ethanol
  • lactate

Alcohol fermentation, which takes place in yeast and certain bacteria, involves the reduction of pyruvate to ethanol. Lactic acid fermentation, which takes place in human muscle cells as part of anaerobic respiration, involves the reduction of pyruvate to lactate.

84
Q

Which metabolic process immediately follows glycolysis and produces acetyl-CoA?

A

Pyruvate decarboxylation

Under aerobic conditions, pyruvate (a three-carbon molecule) is converted to a two-carbon acetyl group. This group then attaches to coenzyme A.

85
Q

What is the initial substrate of the Krebs cycle, and with which molecule does it first react?

A

Acetyl-CoA, a two-carbon compound, is the substrate entering the cycle. It immediately reacts with oxaloacetate to form a six-carbon compound (citrate).

Coenzyme A is released in this process and can be used again.

86
Q

The electron transport chain functions to produce a proton gradient. Into which mitochondrial region are these protons pumped?

A

Protons are pumped from the mitochondrial matrix to the intermembrane space.

87
Q

Define:

catalyst

A

A molecule that increases the rate of a reaction without being consumed itself.

Catalysts change the kinetics of a reaction, not the thermodynamics. In other words, they lower the activation energy without altering the equilibrium or free energy change of a reaction.

88
Q

Define:

enzyme

A

A biological catalyst that structurally facilitates a chemical reaction. Like all catalysts, enzymes increase the rate of a chemical reaction without being consumed.

Most enzymes are proteins, but RNA molecules called ribozymes also have enzymatic activity.

89
Q

Why are enzymes generally ineffective catalysts over a broad temperature range?

A

Enzymes must be at a certain optimal temperature to maintain their structure.

The structure of an enzyme, especially in relation to its active site, is essential to its function as a catalyst. Like other proteins, enzymes denature, or lose their original conformations, above a certain temperature. However, reactions generally progress more slowly at low temperatures, further narrowing the range of optimal activity.

90
Q

What effect does a reduced activation energy have on reaction kinetics?

A

A lowered activation energy increases the reaction rate.

Each reaction must overcome an activation energy barrier to progress from reactants to products. When this barrier is lower, reactants are more likely to collide with sufficient energy, speeding up the reaction.

91
Q

Why are enzymes generally ineffective catalysts over a broad pH range?

A

Enzymes can only maintain their functional structure at a certain optimal pH.

The structure of an enzyme, especially in relation to its active site, is essential to its function as a catalyst. The active site often contains positively or negatively charged groups, which contribute to the specificity of the site. Changes in pH can affect these sites, reducing enzyme activity.

92
Q

At the molecular level, why are prolonged, high fevers dangerous to human health?

A

At higher-than-optimal temperatures, most human enzymes lose function and cannot support necessary biological processes.

Most human enzymes function most efficiently at an optimal temperature of 37 ºC. While these enzymes can remain active at slightly higher temperatures, their function is impaired.

93
Q

Enzymes are usually limited to acting on a single substrate or class of substrate molecules. What term describes this quality?

A

Specificity

The substrate(s) that can be accommodated by an enzyme are determined by the shape of its active site. For example, proteases are specific to protein substrates, while lipases act on lipid-based substrates.

94
Q

What major limitation prevents the lock-and-key model from being fully accurate?

A

It wrongly portrays all enzymes as being rigid and inflexible.

In reality, the active site of an enzyme can change its conformation to facilitate binding to the substrate.

95
Q

What is the difference between cofactors and coenzymes?

A
  • Cofactors are a broad group of compounds that are required for the proper functioning of enzymes.
  • Coenzymes are a class of small, organic cofactors.

Cofactors can also be inorganic substances, such as ions.

96
Q

Many coenzymes are derived from molecules like niacin and riboflavin, which must be consumed as part of the diet. What category describes these molecules?

A

Vitamins

Vitamins are often used to synthesize coenzymes, which are non-protein organic compounds that are essential for proper enzyme function.

97
Q

Phosphofructokinase, a glycolytic enzyme, is allosterically inhibited by ATP. What common homeostatic process does this example demonstrate?

A

This is an example of negative feedback. In such processes, increased concentration of a product decreases the rate of the reaction that forms that product.

Glycolysis involves the breakdown of glucose to form ATP, among other products. If increased amounts of ATP are already present, glycolysis will slow.

98
Q

Define:

bioenergetics

A

This is the study of energy transformations within organisms. Specifically, it concerns the energy released and used during the formation and breaking of chemical bonds.

Bioenergetics is closely related to thermodynamics, especially Gibbs free energy.

99
Q

What single comparison between reactants and products can be made to determine whether a reaction will proceed?

A

The change in Gibbs free energy, or ΔG, determines reaction spontaneity.

A negative ΔG means the reaction will be spontaneous, while a positive ΔG denotes a nonspontaneous reaction.

100
Q

What term can be used to describe a thermodynamically favorable reaction?

A

exergonic

In such reactions, ΔG is always negative, meaning that free energy is released.

The opposite type of reactions are endergonic. In these processes, ΔG is positive and the reaction will not proceed spontaneously.

101
Q

How will the free energy diagram of a catalyzed reaction differ from that of an uncatalyzed reaction?

A

The catalyzed reaction will have a lower activation energy.

Note that the overall change in free energy will be the same for the catalyzed and uncatalyzed reactions.

102
Q

Define:

substrate

A

A specific molecule that an enzyme acts upon, usually via interactions with the enzyme’s active site.

For example, starch is the substrate of salivary amylase. This means that amylase, an enzyme, catalyzes a reaction involving starch as a reactant.

103
Q

What is the functional significance of the active site?

A

It is the structural component where enzyme-substrate interactions take place.

In other words, the active site is the catalytic region of an enzyme. It is structured to facilitate the binding of its substrate, often through the presence of certain amino acid residues.

104
Q

How does the lock-and-key model explain enzyme-substrate specificity?

A

it posits that a substrate will fit perfectly into the active site of its corresponding enzyme, without any conformational changes taking place.

In this model, the active site is the “lock” and its complementary substrate is the “key.”

105
Q

How does the induced fit model explain enzyme-substrate specificity?

A

It posits that active sites are flexible. When a substrate approaches the enzyme, the conformation of the active site will change to better fit the substrate.

The induced fit model is a more recent adaptation of the lock-and-key model.

106
Q

Define:

allosteric site

A

A region of an enzyme, separate from the active site, where molecules can bind and affect enzyme function.

Allosteric binding can either facilitate or inhibit the binding of substrate to the active site.

107
Q

How does a competitive inhibitor alter an enzyme-catalyzed reaction?

A

It binds to an enzyme on its active site, inhibiting the reaction.

Specifically, these inhibitors compete with the substrate and block it from binding the active site.

108
Q

How does a noncompetitive inhibitor alter an enzyme-catalyzed reaction?

A

It binds to an enzyme on a region outside of its active site, inhibiting the reaction.

Specifically, these inhibitors bind an allosteric site, inducing a structural change in the enzyme that decreases its efficiency. Substrates can still enter the enzyme’s active site.

109
Q

What class of substrate is common to maltase, sucrase and lactase?

A

disaccharides

Maltase breaks down maltose into two glucose molecules. Sucrase cleaves sucrose into glucose and fructose, and lactase breaks down lactose into glucose and galactose.

110
Q

What molecule is shown below, and what is its biological role?

A

This molecule is adenosine triphosphate (ATP), the major form of cellular energy.

ATP consists of three phosphate groups bound to the ribonucleoside adenosine. The cleavage of the third phosphate bond facilitates the release of energy, which the cell harnesses to drive biological processes.

111
Q

What name is given to the bonds circled in the structure below?

A

phosphoanhydride bonds

These phosphoanhydride bonds exist between phosphate groups on molecules like ATP (shown) and ADP.

The name of these bonds comes from the reaction that forms them: dehydration (removal of H2O). Predictably, they can be broken by the reverse reaction, hydrolysis (addition of H2O).