AP Bio Unit 3 Test

Substrate

Reactant that is changed by the enzyme

Active site

Where the substrate binds, matches shape and chemical properties of the substrate

Enzyme-substrate complex

When the enzyme and substrate are bound together, like a lock and key

What is an enzyme?

Enzymes are biological catalysts that speed up chemical reactions in the body so they go fast enough to maintain homeostasis, made of protein, reusable

Induced Fit

When substrate binds, the enzyme undergoes a conformational change and surrounds the substrate to catalyze and speed up the chemical reaction, enzyme returns to its original shape once the reaction is complete

Activation Energy

Certain amount of energy needed for all chemical reactions to occur

How do enzymes work?

Enzymes lower the activation energy, making it go faster, does not add or take away energy from the reaction

Energy and metabolism

The combination of chemical reactions that synthesize and hydrolyze biomolecules for energy storage and release in an organism

Catabolism

Break down biological polymers into monomers to help generate ATP, exergonic

Anabolism

Build up monomers into biological polymers for energy storage, endergonic

Exergonic reactions

There is a net release of free energy

Endergonic reactions

Requires a net investment of free energy into the bonds between the monomers

Reaction coupling

Exergonic reactions release free energy that is used by endergonic reactions so they can occur

Enzymes in the digestive system

Mouth, stomach, and small intestines, help break down food, amylase is an example in the mouth that breaks down starch, pepsin is a stomach enzyme that breaks down proteins

Cofactors

Enzyme sidekicks, typically metal ions/iron, bound within enzyme molecule

Coenzymes

Enzyme sidekicks, organic molecules (vitamins), bind near the active site and assist reactions

Denaturation of enzymes

Enzymes have ideal conditions, changes to pH & temp can stop enzyme from working (can’t bind to substrate)

Enzyme names

Indicate substrate or chemical reaction involved, end in -ase

Control group

Generates date under conditions with no treatment or manipulations, generates data under normal/unchanged conditions, baseline data

Experimental test (group)

Generates data under abnormal/unknown conditions, generates data under treated/manipulated conditions, results compared with control test results to determine impacts of manipulation

Negative control

Not exposed to the experimental treatment or any treatment with any effect

Positive control

Exposed to a treatment with effect, not exposed to experimental treatment

Controlled variable

Aspects of an experiment that could be changed but are intentionally not, helps isolate & identify impact of intentional change/treatment, also known as constants

Enzymes and the cell environment

Enzymes have to be in optimal conditions to work at their most efficient, enzymes outside the conditions will be less efficient and have a lower reaction rate, enzymes in extreme conditions will denature, optimal conditions depend on the organism

Factors that affect enzyme efficiency

Enzymes have a maximum rate at which they can catalyze reactions, this is different for each enzyme, enzyme efficiency is a measure of how close to that maximum rate they are working, optimal temp & pH, substrate concentration, enzyme concentration, product concentration, presence of inhibitors

Suboptimal temperatures

Lack of energy decreases the amount of collisions between the enzyme and substrate, reaction rate slows or stops, heating the enzyme back up will fix it

Above optimal temperatures

Too much energy available, extra energy causes amino acid side chains to move faster which disrupts weak interactions between amino acid side chains, this disrupts secondary and tertiary structure of enzyme which leads to denaturation, reaction rate is zero

Raising the pH of enzyme, more basic

Substances with basic pH’s have a high concentration of OH- ions, these ions break hydrogen bonds and ionic interactions which denatures the enzyme, because it disrupts secondary and tertiary structures

Lowering the pH of enzyme, more acidic

Substances with acidic pH’s have a high concentration of H+ ions, these ions break hydrogen bonds and ionic interactions which denatures the enzyme, because it disrupts secondary and tertiary structures

Effect of substrate concentration of enzyme efficiency

Decreasing substrate concentration will slow the reaction rate, increasing substrate concentration will increase the reaction rate, rate can only increase up to the maximum rate for that enzyme

Competitive inhibition

Inhibitor and substrate have similar shapes and compete for the active site of the enzyme, stops substrate from binding and inhibits the enzyme

Non-competitive inhibition

Inhibitor binds to a different place on the enzyme called the allosteric (other) site, changes shape of enzyme which prevents the substrate from binding

How to see optimal temperature or pH from a graph

Find the peak on the graph

Negative feedback inhibition

Metabolic pathways have multiple steps where each step is catalyzed by a separate reaction, sometimes an intermediate or a final product of the pathway will act as an inhibitor of enzymes in the pathway

Effect of enzyme concentration on reaction rate

Less enzyme means a slower reaction rate because it gives less opportunities for substrates to collide with active sites, more enzyme means a faster reaction rate because it gives more opportunities of collisions

Energy

Life requires free and available energy, ability to re-arrange a collection of matter, growth, development, metabolism, and reproduction all require energy

Forms of energy

Kinetic, potential, activation

1st law of thermodynamics

Energy can be transferred and transformed, but it cannot be created or destroyed, energy can be changed from one form to another

2nd law of thermodynamics

Energy cannot be changed from one form to another without a loss of usable energy, each energy transfer or transformation increases the entropy (disorganization) of the universe

Exergonic reactions

Reactions with a net release of free energy, delta g is negative, favored, spontaneous occur without much input of energy

Endergonic reactions

Reactions that absorb free energy, delta g is positive, unfavored, example is photosynthesis

Adenine triphosphate structure

Adenine, ribose, 3 phosphate groups

ATP Hydrolysis

When energy is needed, one of the phosphate bonds is broken, giving off energy and turning the molecule into ADP, exergonic and provides free energy, increases entropy

Synthesis of ATP

To store energy, the third phosphate group is added back on, this happens by the work of enzymes

Autotrophs

Capture energy and transform that energy into energy sources usable by all cells

Photosynthesis chemical equation

6CO2 + 6H2O → C6H12O6 + 6O2

Origins of photosynthesis

Ancestral prokaryotes were first to evolve use, photosynthesis introduced oxygen into early earth’s atmosphere, eukaryotes evolved photosynthesis from endosymbiosis

Where do light dependent reactions occur

Thylakoid membrane

What are the three main parts of light dependent reactions

Electron transport chain, photolysis, chemiosmosis

Inputs of light dependent reactions

NADP+, ADP, H2O

Outputs of light dependent reactions

NADPH, ATP, O2

Electron transport chain first excitement light dependent reactions

Light strikes electron in chlorophyll in photosystem II, electron is excited and moves through series of proteins to photosystem I, energy from moving electron is used to actively transport H+ ions from stroma to lumen which makes an H+ ion gradient

Electron transport chain second excitement light dependent reactions

Electron out of energy once it hits photosystem I, another photon of light hits the electron and re excites it, electron is captured by NADP+ and H+ ion to reduce NADP+ into NADPH, NADPH is transported and used in light independent reactions

Photolysis light dependent reactions

Water is struck by a photon of light and broken into O2, H+ ions and electrons, electrons are used to replenish photosystem II and O2 is released as a waste product, H+ ions help maintain concentration gradient

Chemiosmosis light dependent reactions

H+ ions from concentration gradient diffuse through a channel in ATP synthase, energy of diffusion allows ATP synthase to phosphorylate ADP into ATP, ATP is transported and used to power light independent reactions

Where do light independent reactions occur

Stroma of the chloroplast

Inputs of light independent reactions

CO2, NADPH, ATP

Outputs of light independent reactions

Glucose, NADP+, ADP

How do light independent reactions work

NADPH and ATP are oxidized and energy released from this is used by the enzyme RuBisCo to reduce and fix inorganic carbon from CO2 into an organic form in glucose, regenerates NADP+ and ADP back to the light dependent reactions, must occur twice before one glucose molecule is produced

Factors that affect the rate of photosynthesis

Light, temperature, CO2, minerals

Photosynthesis as an oxidation-reduction process

CO2 is reduced (gains H+ and e-) water is oxidized (loses H+ and e-)

Chloroplast structure

Inner membrane (thylakoid membrane) folded and stacked into grana, stroma: liquid that surrounds the thylakoid membranes

Chlorophylls

Red and blue light are absorbed and used, green light is reflected or transmitted, pigment that absorbs light energy for light dependent reactions

Photosystems

Collection of pigments, serve as a light trap, embedded in thylakoid membrane, PSI and PSII

Origins of aerobic cellular respiration

Ancestral prokaryotes were the first to evolve the use of it, it was advantageous because it allowed them to process oxygen without dying, eukaryotic cells that perform aerobic respiration evolved as a result of endosymbiosis

What is cellular respiration

Process that organisms use to convert chemical energy stored in the bonds of glucose into usable chemical energy in ATP, all living organisms utilize it

Aerobic

With oxygen, main purpose is to generate ATP for use in cellular processes that maintain homeostasis

Anaerobic respiration

Without oxygen, also known as fermentation, main function is to regenerate the electron carrier NAD+ for use in glycolysis

Electron carriers

Molecules that can be both oxidized and reduced, move high energy electrons from various steps of aerobic respiration to the electron transport chain, for cellular respiration they are NAD+/NADH and FADH/FADH2

Glycolysis

Anaerobic, occur in cytoplasm to oxidize glucose into 2 molecules of pyruvate, requires reduction of 2 NAD+ to NADH, NADH is used in later steps, requires breakdown of two ATP molecules, but makes 4 ATP, net gain of 2 ATP

Why must glycolysis occur before any form of respiration can occur

Produces pyruvate which is precursor for anaerobic and aerobic respiration, glycolysis must occur, all living organisms use glycolysis

Anaerobic respiration/Fermentation examples

Alcohol fermentation, lactic acid fermentation

Cellular respiration equation

C6H12O6 + 6O2 → 6CO2 + 6H2O + ATP

Aerobic respiration in a nutshell

Potential chemical energy in the bonds of glucose is converted into usable chemical energy in the bonds between the phosphates in ATP

Steps of aerobic respiration

Glycolysis, pyruvate oxidation, citric acid cycle (krebs cycle), ETC and oxidative phosphorylation

Pyruvate oxidation

Cellular respiration, pyruvate is converted to acetyl-coA as it is transported from the cytoplasm, across the mitochondrial membranes, and into the matrix, goes to Citric acid cycle, CO2 is breathed out as waste

Citric acid cycle

Cellular respiration, aka Krebs cycle, acetyl-coA goes through a series of exergonic chemical reactions that reduce NAD+ to NADH and FADH to FADH2

Electron transport chain cellular respiration, where does it occur?

Inner mitochondrial membrane

Electron transport chain cellular respiration

NADH and FADH2 are oxidized, releasing electrons and energy, NAD+ and FADH are recycled back into the cell environment, electrons move through ETC losing energy until they combine with O2 and H+ ions to form water as a waste product, energy released is used to maintain H+ gradient

Oxidative phosphorylation cellular respiration

Coupled with ETC, H+ ions diffuse through ATP synthase (an enzyme) from the matrix to the intermembrane space, energy from this diffusion is used to phosphorylate ADP into ATP, generates 32-34 ATP

Energy not captured from oxidation of NADH during ETC is given off as what

Heat

Where do prokaryotes (bacteria) do cellular respiration?

Cellular membranes/cytoplasm

Where does glycolysis take place?

Cytoplasm

Where does pyruvate oxidation take place?

Matrix of the mitochondria

Where does krebs cycle/citric acid cycle take place?

Mitochondrial matrix

Oxidation

Loss of electrons loss of hydrogens (OIL)

Reduction

Gain of electrons gain of hydrogens (RIG)