Molecules Chapter 14

reaction energy

-The reaction energy is the energy difference between the reactants and products. an energy input is required to break the chemical bonds in the reactants. Energy is released when bonds are formed in the products. The net difference between the energy input and output determines whether a reaction produces energy (exothermic) or absorbs energy (endothermic). In many cases, such as combustion of a fuel, an exothermic reaction releases energy in the form of heat.

reaction pathway example

-The substitution reaction between OH and CH3Br provides an example of a reaction pathway. -The reaction is initiated when the OH ion collides with CH3Br in the correct orientation. -In this reaction, the transition state has a trigonal bipyramidal geometry. The transition state structure is different from the structures of the reactants and the products. -The product of the reaction, methanol, CH3OH, has a tetrahedral geometry, but the orientation of the C—H bonds is inverted as a result of the reaction.

What happens when a lactose-intolerant person ingests lactose?

Lactose passes into the large intensine, where it is used by bacteria as a fuel for fermentation reactions -Because of this enzyme deficiency, lactose is not digested in the small intestine. The intact sugar is too large to be absorbed through the walls of the intestine. Instead, lactose passes into the large intestine, which contains large amounts of bacteria. The bacteria use lactose as a chemical fuel for a fermentation reaction, which converts lactose into lactic acid. Molecules produced via fermentation reactions can stimulate the flow of water into the intestine, leading to diarrhea. Bacteria in the large intestine also use the lactose for other chemical reactions. Some of these reactions produce gases—methane and hydrogen—that cause sensations of bloating.

Evolution of Lactase Persistent Culture

Milk was safer to drink that water Pastoralists: culture centered around cows Different gene mutations in different regions Independently evolved to be lactose persistent (ability to digest milk after childhood) -Lactose intolerance in adults is the ancestral human condition. Lactase persistence arose as the result of a genetic mutation in the promoter region, which left the gene expression switch in the ON position into adulthood. The ability to digest lactose provided a survival advantage, so the mutation was preserved via natural selection. Lactase persistence is an example of geneculture co-evolution.

chemical demonstration of catalyst

hydrogen peroxide and potassium iodine (KI) mixed to decompose H2O2 into water and oxygen, generating bubbles. KI acts as a catalyst since H2O2 decomposes very slowly on its own.

energy diagram

label activation energy transition state reaction energy reactants products activation energy -The rate of a chemical reaction depends on the height of the activation energy. A small activation energy enables a faster reaction rate; a large activation energy produces a much slower rate.

What chemical reaction is catalyzed by the enzyme called lactase?

lactose --> glucose + galactose Hydrolysis of glycosidic bond (adds water) -lactose is composed of two sugar units, glucose and galactose, which are joined by a C—O—C chemical linkage (a glycosidic bond). Lactase catalyzes a reaction that uses an H2O molecule to break the glycosidic bond and release the smaller sugar units (Figure 14.17). This bond-breaking process is called a hydrolysis reaction (hydro refers to water and lysis means "to break")

what step is necessary to initiate the chemical reaction that burns gasoline in a car engine?

must overcome an energy barrier (activation barrier) for reaction to occur -Most reactions have an energy barrier that prevents the reactants from immediately converting into the products. This barrier is called the activation energy for the reaction. Overcoming the activation energy requires an input of energy like a spark.

name one drug that works by inhibiting enzyme function

penicillin --> transpeptidase

what type of biological molecule is used for most types of enzymes? what is the exception?

proteins ribozymes

restriction enzyme

recognizes specific sequences of DNA and cut DNA strand at this region if mutation is an altered form of this sequence, it won't be cut

catalytic cycle

the enzyme binds the substrate to form the enzyme-substrate complex the enzyme stabilizes the transition state the enzyme releases the products -Step 1: The substrate binds to the active site of the enzyme. Step 2: Binding interactions between the enzyme and the substrate form an enzyme-substrate complex. These interactions typically occur in the form of hydrogen bonds or electrical charge attractions between the substrate and amino acids in the enzyme's active site. Step 3: The enzyme binds the transition state structure and lowers its energy. To function as an effective catalyst, the enzyme binds the transition state more tightly than it binds the reactants or the products. This tight binding stabilizes the high-energy transition state, which lowers the activation energy for the reaction and increases its rate. Step 4: The transition state is converted into products, which are then released by the enzyme. The active site is now empty, and it can catalyze another reaction by binding a new substrate.

transition state for enzyme-catalyzed reaction vs structure of the substrate

_/------\ \ /---------\ \____ vs ------\_____/ \ \_________

stickase diagram

_______ substrate /\ transition state ____ ____ products - Note that the structure of the transition state is distinct from the structures of the reactants and the products.

enzyme

a biological catalyst that increases the rate of a chemical reaction

AIDs and HIV

acquired immunodeficiency syndrome human immunodeficiency virus

lactase

an enzyme that helps with digestion and breaks lactose into glucose and galactose

catalyst diagram

catalyst lowers energy of activation accelerates rate of reaction lowers activation energy stabilized transition state no change to reaction energy -A catalyst increases the rate of a chemical reaction without being permanently altered. -A catalyst accelerates a chemical reaction by lowering the activation energy. If the energy barrier is lowered, then the reaction proceeds more quickly because the barrier is easier to overcome. -Therefore, a catalyst can lower the activation energy by chemically binding the transition state and reducing its energy. Atoms in the catalyst form stabilizing chemical interactions with the transition state, which lowers its energy.

HIV protease enzyme essential for HIV replication

cuts long polypeptide chain into smaller components smaller chains form proteins used to create protective shell within HIV

what happens when you put hydrogen peroxide on a cut? write a chemical reaction to describe this process

decomposes into water & oxygen gas & produces bubbles 2H2O2 --> 2H2O + O2

why are enzymes essential for the function of living cells

enzymes increase the rate of chemical reactions within cells without enzymes, these reactions would be too slow to sustain life (eg digestion, ATP)

-ase

general suffix of enzyme

what do we mean by saying that the reaction produces an inversion of the structure from reactant to product?

hydrogen bonds inverted the side they connect to -Note that the orientation of the C—H bonds has flipped during the course of the reaction, analogous to an umbrella turning inside-out in a strong wind. This effect is called inversion of configuration; it is a characteristic of this type of reaction

IN DNA gel electrophoresis, what size of DNA fragments move fastest through the gel?

short

transition state

short-lived and unstable state that is formed during the conversion of reactants into products -In a chemical reaction, the state that exists briefly between reactants and products is called the transition state

what final step is necessary in order to visualize the DNA fragments in the gel?

stained with SYBR safe & illuminated with UV light energy transilluminator to fluoresce the light larger, more visible small, more faint

explain how HIV protease inhibitors function as a transition state analog

the enzyme binds the drug very tightly because of its structural similarity to the transition state when the drug is bound, the enzyme is not able to perform its usual catalytic function

what is the biological role of the enzyme called catalase?

turns 20 million H2O2 molecules into water and oxygen per second. (H2O2 is very reactive and dangerous to cells)

what is the role of the active site of an enzyme?

where the catalytic reaction occurs

On/Off Lactase gene switch

On: transcription factor binds to a promoter region in DNA which activates the production of lactase Off: transcription factor not bound, no lactase production

reaction pathway

3d molecular structure of reactants, transition state, and products reactants: tetrahedral transition state: trigonal bipyramidal (bond being formed, bond being broken) products: inverted tetrahedral -Note that the molecular structure of the transition state differs from the structures of the reactants and the products.

What happens when a lactose-tolerant person ingests lactose?

After lactase has decomposed lactose, the glucose & galactose are absorbed through the walls of the intestine & enter the bloodstream - Individuals who can digest milk have an ample supply of lactase, which is attached to the walls of the small intestine. Lactase catalyzes the breakdown of lactose into glucose and galactose. After being released by the enzyme, the two smaller sugars are absorbed through the walls of the intestine and enter the bloodstream, which circulates them around the body to be used as nutrients.

cofactor

In some cases, the enzyme requires assistance from an auxiliary molecule or ion, which is called a cofactor

activation energy

energy barrier between reactants and products

why is it necessary for the enzyme to release the products in order for the catalytic cycle to repeat itself?

it frees the active site so it can catalyze another reaction

name one human disorder that is caused by enzyme deficiency

lactose intolerance PKU tay-sachs disease

lock-key model

only a specific substrate (the key) will fit into the precise shape of the enzyme -The lock-and-key model describes the enzyme as the lock and the substrate as the key. An enzyme selects only one substrate among many possible options because of complementary chemical interactions between the active site and the substrate.

induced fit model

the enzyme changes its shape during the process of binding the substrate -In the induced fit model, the enzyme changes its shape upon binding the substrate. This shape change allows the enzyme to bind the substrate more tightly by generating a larger number of complementary chemical interactions.

Lactose intolerance

the inability to digest lactose sugar in milk

what demonstration was used in class to illustrate induced fit binding?

throwing a baseball- when caught, hands change shape to wrap around the ball to firmly grasp it