AP Bio Unit 3

catabolic/exergonic

reactions the release energy

anabolic/endergonic

reactions that consume energy

spontaneous process

a process that leads to an increase in entropy and not require the input of energy to occur

increase in chaos essentially

free energy

the portion of the systems energy that can perform work when the temp and pressure are uniform throughout the system, delta G

for an exergonic reaction, is free energy negative or positive

delta G= g sub final - g sub initial

exergonic reactions have a negative delta g

three main kinds of work that a cell does

chemical, transport, mechanical

molecules that make up ATP

adenine, ribose, 3 phosphate

energy coupling

use of an exergonic process to arise on endergonic one

activation energy (E sub A)

the initial investment of energy for starting a reaction

enzyme

a macromolecule, usually a protein, that acts as a catalyst

substrate

the reactant, what you start with

active site

the physical space on the enzyme where the substrate binds

induced fit

when the substrate enters the active site, the enzyme changes shape to fit more snugly around the substrate; shape change occurs because of interactions between the substrate chemical groups and chemical groups on the side chains of the amino acids forming thee active site

mechanisms to lower activation energy on enzymes

• template on which substrates can come together in the proper orientation for a reaction to occur between them

• enzyme may stretch the substrate molecules, stressing and bending chemical bonds

• the active site may provide a microenvironment that is more conducive to a particular reaction

• direct participation of the active site in the chemical reaction

factors that affect the rate of enzyme action

• initial concentration of substrate

• pH- denaturing if not in optimal range

• temperature- as temp increases, so does kinetic energy with makes more collisions, so denaturing

cofactors

non protein helpers that can bind to the enzyme

coenzymes

cofactors that are organic molecules

competitive inhibitors

binds to the active site and blocked the substrate from bonding

non competitive inhibitor

binds to another site on the enzyme and causes the active site to change shape

allosteric regulation

any case in which a proteins function at one site is affected by the binding of a regulatory molecule to a separate site, can inhibit or stimulate

allosteric activator

bind when the enzyme oscillates into its active form and they help stabilize it in that form

allosteric inhibitor

stabilize the enzyme in its inactive form

cooperativity

a substrate molecules binds to an active site of a multisubunit enzyme and triggers a shape change in all of the subunits

fermentation

a partial degradation of sugars or other organic fuel without oxygen

cellular respiration

includes aerobic and anerobic processes, but originated as a synonym for aerobic respiration

oxidation and reduction

oil rig

• oxidation is less

• reduction is gain

cellular respiration: electron carrier of hydrogen

NAD+

cellular respiration: describe what happens when NAD+ is reduced

dehydrogenases remove 2 hydrogen atoms from the substrate and deliver them to NAD+ so it becomes NADH

what is the function of the electron transport chain in cellular respiration

transfer of electrons from NADH to O2, energy is released a little bit at a time, which is used to generate ATP

cellular respiration: what strongly electronegative atom is the final electron acceptor

oxygen

cellular respiration: explain how the electron transport chain is utilized in oxidative phosphorylation

the energy released at each step of the chain is stored in a form the mitchondrion can use to make ATP from ADP

substrate level phosphorylation

one enzyme transfers a phosphate group from a substrate molecule to ADP, making ATP

products of glycolysis

2 pyruvate, 2 ATP, 2 NADH. process is just sugar splitting

the starting product of glycolysis is what

6 carbon sugar glucose

where does glycolysis occur

cytosol, no oxygen required

products of pyruvate oxidation

2 acetyl coA, 2 CO2, 2 NADH

products of citric acid cycle per molecule of glucose

4 CO2, 6 NADH, 2 ATP, 2 FADH2

cellular respiration: explain what has happened to each of the 6 carbons found in the original glucose molecule

all carbons are converted to CO2

cellular respiration: oxidative phosphorylation

involves the electron transport chain and ATP synthesis, is the final ATP producing stage

why is oxygen the ultimate electron acceptor

bc its very electronegative

two electron carrier molecules that feed the electron transport system

NADH and FADH2

how does ATP synthase use the flow of hydrogen ions to produce ATP

ATP synthase is an ion pump that runs in reverse. the flow of h+ ions through the enzyme turns the rotor, which catalyzes the addition of an inorganic phosphate to the ADP, making ATP

role of the ETC in forming the h+ gradient across the inner mitochondrial membrane

as electrons are dropped off by NADH and FADH2, they release energy as they are passed through the chain, the energy is used to pump protons across the membrane into the intermembrane space

chemiosmosis

energy stored in the form of a H+ gradient across a membrane, used to drive cellular work, like the production of ATP

proton-motive force

the H+ gradient that results from pumping H+ out with the ETC

each NADH can form a maximum of how many ATPs

3 (2.5-3.3)

each FADH2, which donates electrons that activate only two proton pumps, makes how many ATPs

2 (1.5-2)

fermentation allows for the production of ATP without using

oxygen or any electron transport chain

electron acceptor of fermentation

pyruvate

explain alcohol fermentation

1. CO2 is released from pyruvate, making acetaldehyde

2. Acetaldehyde is reduced by NADH to ethanol, regenerating the supply of NAD+

lactic acid fermentation

starts with glucose and yeilds lactate

pyruvate is reduced directly by NADH to form lactate, which regenerates the supply of NAD+

why is pyruvate a key juncture in metabolism

pyruvate is the fork in the pathway of glucose oxidation, if O2 is present, aerobic cellular respiration occurs. If O2 is not present, fermentation occurs

what three organic macromolecules are often utilized to make ATP by cellular respiration

carbohydrates, proteins, fats

whats the difference in energy usage between the catabolic reactions of cellular respiration and anabolic pathways of biosynthesis

• energy is released when carbs, fats, and proteins in the diet and stored in the body are broken down

• biosynthesis uses energy and items present to build necessary molecules

explain how AMP stimulates cellular respiration while citrate and ATP inhibit it

all affect the activity of the enzyme phosphofructokinase, which acts early on in the enzymatic pathway

phosphofructokinase

allosteric enzyme that catalyzes an important step in glycolysis

using oxygen 18 as the basis of your discussion, explain how we know that oxygen released in photosynthesis comes from water

when water containing oxygen 18 is used for photosynthesis, the oxygen product is oxygen 18. when oxygen 18 is in CO2, the oxygen 18 is part of the glucose and water made

light reactions stage of photosynthesis

light absorbed by chlorophyll drives the transfer of electrons and H+ to an acceptor, NADP+, why gets reduced. ATP is generated through phosphorylation

calvin cycle

it incorporates CO2 from the air into organic molecules already present in the chloroplasts, in a process called carbon fixation

absorption spectrum

graph plotting the wavelengths of light best absorbed by chloroplast pigments

action spectrum

plots the rates of photosynthesis versus wavelength

Englemann

used a prism to illuminate algae with different colors of light and used aerobic bacteria as an indicator of where most O2 was being released; therefore more bacteria-more O2= more photosynthesis

photosystem is composed of

reaction center complex surrounded by several light harvesting complexes

photosystems: reaction center complex

includes a pair of chlorophyll a molecules that boost electrons up to a higher energy level and transfers them to the primary electron acceptor

photosystems: light harvesting complex

consists of various pigment molecules bound to proteins, act as an antenna by absorbing photons and passing energy from pigment to pigment until it gets to the reaction center complex

photosystems: primary electron acceptor

a molecule capable of accepting electrons and becoming reduced

P680

refers to the wavelength of light the pigment molecules is best at absorbing

name of chlorophyll at reaction center of photosystem I

P700

linear electron flow

photosynthetic electron transport chain

what is the source of energy that excited the electron in photosystem II

light

what compound is the source of electrons for linear electron flow

water

what is the source of O2 in the atmosphere

water splitting

what does the photosynthetic proton gradient produce in chemiosmosis

ATP

in NADPH production…

NADP+ reductase catalyzes the transfer of the excited electron and H+ to NADP+ to form NADPH

similarities in chemiosmosis between photosynthesis and cellular respiration

• ETCs transform redox energy into proton-motive force. Electrons energy release pumps H+ ions

• ATP synthase is built into the same membrane as the ETC

  • same electron carriers (w/ cytochromes) are similar

• ATP synthase are similar

how is chemiosmosis different in photosynthesis and cellular respiration

1. mitochondria- source of electrons is the organic molecules, like glucose; and H+ ions get pumped OUT of the matrix

2. chloroplasts- source of electrons is water; and H+ ions get pumped INTO the thylakoid space

the carbohydrate directly produced by the Calvin cycle

glyceraldehyde-3-phosphate (G3P), 3 turns of Calvin cycle to net one G3P

carbon fixation of the Calvin cycle

rubisco adds a CO2 to RuBP, the resulting 6 carbon molecule immediately splits into 2 3-phosphoglycerates

enzyme responsible for carbon fixation in Calvin cycle

rubisco

source of reducing power in the Calvin cycle

NADPH

how is the regeneration of RuBP accomplished

3 molecules of ATP are used to rearrange the 5 3-carbon molecules into 3 G3P

photorespiration

on hot, dry days, stomata partially close to conserve water; rubisco starts adding O2 to the Calvin cycle instead of the declining levels of CO2; the resulting 2 carbon compound is split and leaves the cell as CO2

what is meant by a C4 plant

they go through an alternative mode of carbon fixation that results in a 4 carbon compound before entering the Calvin cycle

whats the role of PEP carboxylase in C4 plants

it fixes CO2 to PEP, forming oxaloacetate. Occurs in the mesophyll cells. PEP carboxylase has a higher affinity for CO2 than does rubisco, and no affinity for O2

the C4 pathway does not replace the Calvin cycle but…

works as a CO2 pump that prefaces the Calvin cycle

explain how changes in leaf architecture help isolate rubisco in regions of the leaf that are high in CO2 but low in O2

PEP carboxylase is in the mesophyll cells- it fixes carbon efficiently when there is low CO2 and high O2. The 4 carbon compound then enters the bundle sheath cells and releases CO2- so now the rubisco can bind it because there is a high CO2 concentration

compare and contrast C4 and CAM plants

both plants fix CO2 into 4 carbon compounds and then release it

in C4 plants, the fixing and releasing of CO2 occurs in difference spaces. In CAM plants, it occurs at different times