Chapter 8- Microbial metabolism

Question 1

Metabolism

Answer 1

Describes all of the chemical reactions inside a cell

Question 2

Exergonic reactions

Answer 2

Reactions that are spontaneous and release energy

Question 3

Endergonic reactions

Answer 3

Reactions that require energy to proceed

Question 4

Anabolism

Answer 4

Refers to endergonic metabolic pathways involved in biosynthesis, where simple molecular building blocks are converted into complex molecules, through the use of cellular energy. Molecular energy is stored in the bonds of complex molecules and can be harvested to produce high energy molecules that are used to drive anabolic pathways

Question 5

Catabolism

Answer 5

Refers to exergonic pathways that break down complex molecules into simpler ones. Molecular energy is stored in the bonds of complex molecules and is released in catabolic pathways

Question 6

Autotrophs

Answer 6

Organisms that convert inorganic carbon dioxide into organic carbon compounds. Plants and cyanobacteria are examples

Question 7

Heterotrophs

Answer 7

Use complex organic carbon compounds as nutrients, which are provided to them by autotrophs. This includes many organisms, like humans and many prokaryotes like E. coli

Question 8

Phototrophs

Answer 8

Organisms who use light as their energy source. They get their energy from electron transfer from light

Question 9

Chemotrophs

Answer 9

Obtain energy for electron transfer by breaking chemical bonds. Includes organotrophs and lithotrophs

Question 10

Organotrophs

Answer 10

Chemotrophs that obtain energy from organic compounds. Humans, fungi, and many prokaryotes are examples

Question 11

Lithotrophs

Answer 11

Chemotrophs that get energy from inorganic compounds, like hydrogen sulfide and reduced iron. Only microbes get their energy this way

Question 12

Oxidation reactions

Answer 12

Reactions that remove electrons from donor molecules- this means the donor molecules are oxidized. Transferring energy in the form of electrons allows energy to be transferred incrementally

Question 13

Reduction reactions

Answer 13

Reactions that add electrons to acceptor molecules, reducing them

Question 14

Redox reactions

Answer 14

Electrons move from one molecule to another, so oxidation and reduction occur together. These pairs of reactions are called oxidation-reduction reactions

Question 15

Electron carriers

Answer 15

A class of compounds that bind to and shuttle high energy electrons between compounds in pathways. The 3 main electron carriers are from the B vitamin group and are derivatives of nucleotides. They include nicotinamide adenine dinucleotide (NAD), nicotine adenine dinucleotide phosphate (NADP), and flavin adenine dinucleotide (FAD).

Question 16

NAD+/NADH

Answer 16

The most common mobile electron carrier used in catabolism. NAD+ is the oxidized form of the molecule, NADH is the reduced form of the molecule. It is typically used in energy extraction from sugars during catabolism in chemoheterotrophs

Question 17

NADP+/NADPH

Answer 17

NADP+ is the oxidized form of an NAD+ variant that contains an extra phosphate group. It is another important electron carrier than forms NADPH when reduced. It plays an important role in anabolic reactions and photosynthesis

Question 18

FAD/FADH2

Answer 18

FAD is the oxidized form and FADH2 is the reduced form. It is typically used in energy extraction from sugars during catabolism in chemoheterotrophs

Question 19

Adenosine triphosphate (ATP)

Answer 19

Used as the energy currency of the cell. Living cells use ATP to safely store energy released during catabolism and release it for use as needed.

Question 20

Adenosine monophosphate (AMP)

Answer 20

A molecule located at the heart of ATP. It is composed of an adenine molecule bonded to a ribose molecule and a phosphate group. Ribose is 5 carbon sugar found in RNA, and AMP is one of the nucleotides in RNA

Question 21

Adenosine diphosphate (ADP)

Answer 21

A molecule formed when a second phosphate group is added to AMP. Adding a phosphate group is done through a process called phosphorylation, which requires energy

Question 22

High energy phosphate bonds

Answer 22

Phosphate groups are negatively charged and therefore repel one another when they are arranged in series, like they are in ATP and ADP. This makes ATP and ADP inherently unstable, so the bonds between the phosphate groups are considered high energy

Question 23

What happens when the high energy phosphate bonds are broken?

Answer 23

When one phosphate is released, it is considered inorganic phosphate. Two connected phosphate groups, called pyrophosphate, can also be released from ATP in the process called dephosphorylation. During dephosphorylation, energy is released to drive endergonic reactions

Question 24

Catalysts

Answer 24

A substance that helps speed up a chemical reaction. Catalysts are reusable because they are not used or changed during reactions

Question 25

Enzymes

Answer 25

Proteins that act as catalysts for biochemical reactions inside cells. They play a role in controlling cellular metabolism

Question 26

Activation energy

Answer 26

The energy needed to form or break chemical bonds and convert reactants to products. Enzymes work by lowering the activation energy of a chemical reaction, by binding to reactant molecules and holding them in a way that speeds up the reaction

Question 27

Substrates

Answer 27

The chemical reactants that an enzyme binds to

Question 28

Active site

Answer 28

The location within the enzyme where the substrate binds

Question 29

Induced fit of an enzyme

Answer 29

The amino acids near an enzyme’s active site create a specific chemical environment that makes it suitable for a substrate to bind. This makes an enzyme very specific. When an enzyme binds to the substrate, the structure of the enzyme changes slightly to create a good fit between the intermediate (transition) state and the the active site. The enzyme essentially molds itself to fit the substrate. There is a specifically matched enzyme for each substrate and therefore each chemical reaction, but some enzymes can act on several different structurally related substrates

Question 30

How does temperature influence enzyme activity?

Answer 30

Increasing temperature can increase reaction rates, but high temperatures can cause enzymes to denature. Increasing or decreasing the temperature outside of a specific range can affect the chemical bonds within the active site, making them less likely to bind to substrates

Question 31

How does pH influence enzyme activity?

Answer 31

Enzymes function best in a certain pH range. If the pH is too acidic or basic, the enzyme can denature. Amino acid side chains have acidic or basic properties that are best for catalysis, so they are sensitive to pH changes

Question 32

How does substrate concentration influence enzyme activity?

Answer 32

Enzyme activity increases when the concentration of substrates is higher. Activity will increase until it reaches a saturation point, where there is no more substrate for the enzyme to bind to. Enzymes are optimized to work best in the conditions that their organisms live. Human enzymes work best at 37 degrees Celsius

Question 33

Cofactors and coenzymes

Answer 33

Cofactors are inorganic ions like iron and magnesium that help stabilize enzyme conformation and function. DNA polymerase, which helps build DNA molecules, requires a zinc ion to function. Coenzymes are reusable organic helper molecules that are required for enzymes to function. Dietary vitamins are examples

Question 34

Apoenzyme

Answer 34

An enzyme that lacks a necessary cofactor or coenzyme, and is therefore inactive. An apoenzyme becomes a holoenzyme once it’s bound to a cofactor or coenzyme.

Question 35

Holoenzyme

Answer 35

An enzyme with a necessary associated cofactor or coenzyme, which is therefore active. It is able to bind to a substrate

Question 36

Competitive inhibitor

Answer 36

A molecule similar enough to a substrate that it can compete with the substrate for binding to the active site by simply blocking the substrate from binding. The inhibitor concentration needs to be about equal to the substrate concentration for it to be effective. Sulfa drugs are one example. They bind to the active site of an enzyme in the bacterial folic acid synthesis pathway, blocking folic acid synthesis. Bacteria can’t grow because the need folic acid to make DNA, RNA, and proteins. Humans aren’t affected because we get folic acid from our diets

Question 37

Allosteric site

Answer 37

A location on an enzyme other than an active site

Question 38

Noncompetitive (allosteric) inhibitor

Answer 38

Binds to the enzyme at an allosteric site and still manages to block substrate binding at the active site by inducing a conformational change. This reduces the affinity of the enzyme for its substrate. Only one inhibitor molecule is needed for effective inhibition of the enzyme, so the concentration of inhibitors needed for allosteric inhibition is lower than the concentration needed for competitive inhibition

Question 39

Allosteric activators

Answer 39

Bind to locations on an enzyme other than the active site, inducing a conformational change that increases the affinity of the enzyme’s active site for the substrate

Question 40

Feedback inhibition of enzyme activity

Answer 40

Involves the use of a pathway product to regulate its own further production. When the cell senses an abundance of specific products, it slows down production during anabolic or catabolic reactions. Allosteric control is an important mechanism used to accomplish this.