BIO EXAM 2

catabolic pathways

release energy by breaking down complex molecules into simpler compounds

anabolic

consume energy to build complex molecules from simpler ones

energy

the capacity to cause change; exists in various forms some of which can perform work

kinetic energy

associated with motion (ex: dam water & turbines)

thermal energy

kinetic energy associated with random movement of atoms or molecules

potential energy

energy that matter possesses because of its location or structure, even if not moving (ex: water BEHIND A DAM)

chemical energy

potential energy available for release in a chemical reaction (ex: catabolic reactions)

first law of thermodynamics

the energy of the universe is constant; it can be transferred and transformed but not created or destroyed

second law of thermodynamics

during energy transfer or transformation; some energy is unusable and lost as heat; every energy transfer increases entropy of universe

entropy

measure of molecular disorder or randomness

exergonic reaction

proceeds with a net release of free energy and occurs spontaneously

endergonic reactions

absorbs free energy from its surroundings and is nonspbonteaneous

types of work a cell does

chemical, transport, and mechanical

chemical work

pushing endergonic reactions

transport work

pumping substances against the direction of spontaneous movement

mechanical work

i.e. movement of blood cells and contraction of muscle cells

energy release via hydrolysis

energy is released from ATP when the terminal phosphate bond is broken; release of energy comes from change to a state of lower free energy

enzyme

a macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction

activation energy (Ea)

the initial energy needed to start a chemical reaction; often supplied in the form of thermal energy

catalyst role

speed up specific reactions by lowering the Ea barrier

substrate

specific reactant that an enzyme acts on

substrate-enzyme complex

enzyme binds to a substrate; while bound turns the substrate into a product

active site

the region of the enzyme where the substrate bonds

induced fit

brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

saturated enzyme

all enzyme molecules have their active sites engaged; reaction rate can be sped up by adding more enzyme

effects on enzyme activity

temperature and PH; chemicals that specifically influence the enzyme

cofactor

non-protein enzyme helpers; can be nonorganic or organic (coenzyme)

competitive enzyme inhibitor

mimics substrate and binds to an enzymes active site and competes with it

noncompetitive enzyme inhibitor

binds to another part of the enzyme, causing the enzyme to change shape which makes the active site less effective

cell regulation of enzymatic activity

direct regulation; switching on and off the genes that encode specific enzymes

allosteric regulation

occurs when a regulatory molecule binds to a protein at one site and affects the enzymes function; can inhibit or activate

enzyme complex active form

binding of an activator stabilizes the active form

enzyme complex inactive form

binding of an inhibitor stabilizes the inactive form

feedback inhibition

the end product of a metabolic pathway shuts down the pathway; prevents cell from wasting chemical resources

potential energy

comes from attraction between negatively charged electrons and positively charged nucleus

fermentation

extension of glycolysis that allows continuous generation of ATP by substrate level phosphorylation

oxidation-reduction reactions

the relocation of electrons during chemical reactions releases energy stored in organic molecules

reducing agent

electron donor

oxidizing agent

electron acceptor

shift of energy in reaction

an electron LOSES potential energy when it shifts from a less electronegative atom towards a more electronegative atom

nicotinamide adenine dinucleotide (NAD+/NADH)

electron carrier of hydrogen; coenzyme

NAD+

most versatile electron acceptor in cellular respiration

stages of cellular respiration

glycolysis → pyruvate oxidation & citric acid cycle → oxidative phosphorylation and chemiosmosis

oxidative phosphorylation

powered by redox reactions; generates almost 90% of ATP

substrate-level phosphorylation

occurs when an enzyme transfers a phosphate group directly from a substrate to ATP

glycolysis

glucose is split into 3 carbon sugars → sugars are oxidized → remaining molecules form pyruvate

glycolosis energy investment phase

cell spends ATP, an investment that is paid with interest later on

glycolysis energy payoff phase

ATP is produced by substrate-level phosphorylation and NAD+ is reduced to NADH by e- released from oxidation of glucose

glycolysis STEP 1

glucose becomes less stable and has to stay in cell (ATP to ADP) → glucose transformed by hexokinase to glucose 6-phosphate

glycolysis STEP 2

glucose 6-phosphate transformed by phosphoglucoisomerate to fructose 6-phosphate

glycolysis STEP 3

fructose 6-phosphate transformed by phosphofructokinase to fructose 1-6 bisphosphate; transfers phosphate group from ATP to opposite end of sugar (ATP to ADP)

glycolysis STEP 4 + 5

fructose 1-6 biphosphate transformed by aldolase to dihydroxyacetone and glyceraldehyde 3-phosphate; reversible conversion between products (only need g3p)

glycolysis STEP 6

glyceraldehyde 3-phosphate transformed by triose-phosphate-dehydrogenase to 1,3 biphosphoglycerate; some energy is released so phosphate is added ( 2 NAD+ to 2 NADH + 2 H+)

glycolysis STEP 7

1,3 biphosphoglycerate transformed by phosphoglycerokinase to 3-phosphoglycerate; substrate level phosphorylation to make ATP (2 ADP to 2 ATP)

glycolysis STEP 8

3-phosphoglycerate transformed by phosphoglyceromutase to 2-phosphoglycerate; remaining phosphate group relocated

glycolysis STEP 9

2-phosphoglycerate transformed by enolase to phosphoenolpyruvate; extracts water molecule and yields PEP

glycolysis STEP 10

phosphoenolpyruvate transformed by pyruvatekinase to pyruvate; phosphate group transferred from PEP to ADP (2 ADP to 2 ATP

oxidation of pyruvate

pyruvate enters the mitochondrion via active transport and is converted to acetylene coA

reactions catalyzed by pyruvate oxidation

pyruvate’s carboxyl group is fully oxidized and given off as co2; remaining two carbon fragment oxidized and electron transferred to NAD+; coA is attached to two carbon intermediate forming acetyl coA

citric acid cycle STEP 1

oxaloacetate → citrate via acetyl coA adding 2-carbon group

citric acid cycle STEP 2

citrate → isocitrate via removing one H2O and adding another

citric acid cycle STEP 3

isocitrate → a-ketogluterate; reduces NAD+ to NADH and resulting compound loses a co2 molecule

citric acid cycle STEP 4

a-ketogluterate → succinyl coA; another co2 is lost and resulting compound is oxidized (NAD+ to NADH)

citric acid cycle STEP 5

succinyl coA → succinate; coA displaced by a phosphate group (GDP to GTP → ADP to ATP)

citric acid cycle STEP 6

succinate → fumarate; two hydrogens transferred to FAD making FADH, succinate is oxidized

citric acid cycle STEP 7

fumarate → malate; addition of water molecule rearranges bonds in substrate

citric acid cycle STEP 8

malate → oxaloacetate; substrate is oxidized reducing NAD+ to NADH and regenerating oxaloacetate

net production of glycolysis and citric acid cycle

4 ATP, 6 NADH, and 4 FADH

electron transport chain

drop in free energy as electrons travel down the chain

chemiosmosis

the process of using energy stored in an H+ gradient (protein motive force) across a membrane to drive ATP synthesis

net production of glycolysis

2 NADH, 2 pyruvate, 2 ATP

respiration energy flow

glucose → NADH → electron transport chain → protein motive force → ATP

alcohol fermentation

pyruvate is converted to ethanol in 2 steps → removal of co2 and reduction of acetaldehyde to ethanol

lactic acid fermentation

pyruvate is reduced directly to NADH to form lactate, regeneration of NAD+ with no release of co2

obligate anaerobes

carry out only fermentation or anaerobic respiration, cannot even survive in the presence of oxygen

facultative anaerobes

can make enough ATP to survive using either fermentation or aerobic respiration

photosynthesis

transforms the energy of sunlight into chemical energy stored in sugars and other organic molecules

stomata/stoma

holes through which co2 enters the leaf and o2 exits

thykaloids

membrane system made up of connected sacs, suspended in the stroma (two membranes surrounding fluid)

stages of photosynthesis

light reactions and the callvin cycle

light reactions

occurs in the thylakoids and involves the split of H2O, the release of O2, the reduction of NADP to NADPH, and the generation of ATP from ADP via photophosphorylation

calvin cycle

occurs in the stroma, begins with carbon fixation, and makes sugar from co2, using ATP and NADPH

photons

discrete particles that light consists of

pigments

substances that absorb visible light; different pigments absorb different wavelengths, those that are not absorbed are reflected or transmitted

photosystem

consists of a reaction-center complex surrounded by light harvesting complexes

reaction-center complex

holds a special pair of chlorophyll a molecules and a primary e- acceptor that accepts energy from the excited chlorophyll

light-harvesting complex

consists of various pigments bound to proteins that transfer energy of photons to the reaction center

photosystem II (PSII)

functions first, contains chlorophyll a and b, absorbs light at 680nm

photosystem I (PSI)

best at absorbing at 700nm, has 110 cofactors, and electrons received are used to produce NADPH

linear electron flow STEP 1

photon hits a pigment and energy is based among pigment molecules until reaching the p680 pair of chlorophyll a molecules

linear electron flow STEP 2

an excited electron is transferred to primary electron acceptor

linear electron flow STEP 3

an enzyme splits H2O, electrons are transferred from H+ atoms to P680

linear electron flow STEP 4

each electron “falls” down the electron transport chain from PSII to PSI

linear electron flow STEP 5

energy released pumps H+ into thylakoid space → H+ gradient drives ATP synthesis through chemiosmosis

linear electron flow STEP 6

light energy excites P700, which loses an e- to an electron acceptor

linear electron flow STEP 7

each e- falls down the ETC from PSI to the protein ferredoxin

linear electron flow STEP 8

e- from ferredoxin are transferred to NADP+ reducing it to NADPH

cyclic electron flow

electrons cycle from ferredoxin to the PSI reaction center, produces ATP but not NADPH

calvin cycle

builds sugar from smaller molecules by using ATP and reducing power of electrons carried by NADPH; carbon enters the cycle as co2 and leaves as G3P

phases of the calvin cycle

carbon fixation, reduction, and regeneration of co2 acceptor