Bio 2 Exam 3

metabolism

totality of an organism’s chemical rxns, manages material + energy resources of the cell

metabolic pathway

a specific molecule is altered in a series of defined steps, resulting in a certain product

consists of: starting material, enzymes 1, 2, and 3, intermediates, and final product

catabolic reaction

metabolic pathways that release energy by breaking down complex molecules into simpler compounds, “downhill”, ex. cell respiration

anabolic reaction

metabolic pathways that consume energy to build complicated molecules from simpler ones, “uphill”, ex. photosynthesis, amino acids → polypeptide

energy

capacity to cause change

kinetic energy

associated with motion

thermal energy

associated with random movement (constant motion)

heat

energy in transfer from one object to another

potential energy

possessed by matter due to location or structure

chemical energy

possessed by molecules due to arrangement of electrons in bonds

1st law of thermodynamics

Principle of conservation of energy → energy can be transferred + transformed, but cannot be created nor destroyed (energy of the universe is constant)

2nd law of thermodynamics

only a small amount of chemical energy of food foes to kinetic, some is converted to thermal and leaves as heat

with each energy transfer, the universe becomes more disordered (increased entropy)

spontaneous

processes that can lead to ab increase in entropy, can proceed w/o energy input, energetically favorable

free energy (G)

the portion of a system’s energy that can perform work when temp. + pressure are uniform in a system (living cell)

delta G of a spontaneous rxn

negative delta G value, loss of free energy

delta G of a stable system

negative

delta G of an unstable system

positive

system @ equilibrium

state of max stability (lowest possible delta G)

system moving towards equilibrium

process is spontaneous and can perform work

exergonic

negative delta G, spontaneous, net release of free energy, energy outward, ex. cell resp

endergonic

positive delta G, non-spontaneous, absorbs free energy from surroundings, energy inward, ex. photosynthesis

equilibrium in a closed system

will reach equilibrium and do no work

equilibrium in an open system

metabolism is never at equilibrium, if it does reach equilibrium the cell dies

Three main types of work a cell does

Chemical, transport, mechanical

ATP and chemical work

creation of a phosphorylated intermediate (less stable, ^ free energy), coupled rxns, negative delta G and spontaneous

ATP and transport work

direct phosphorylation of a protein by ATP hydrolysis, shape change and binding change ex. transport pump

ATP and mechanical work

ATP minds motor protein, hydrolyzes and changes shape, and the protein moves

energy coupling

mediated by ATP, use of an exergonic process to drive an endergonic one

hydrolysis of ATP

ATP to ADP releases and inorganic phosphate, exergonic, negative delta G

proteins and ATP hydrolysis

proteins harness the energy released during ATP hydrolysis to perform cell work

ATP Cycle

ATP Synthesis (ADP+P) endergonic

ATP Hydrolysis (ATP→ADP+P) exergonic

chemical work

pushes endergonic rxns that would not occur spontaneously

transport work

pumping substances across membranes and against the direction of spontaneous moving

mechanical work

beating of cilia, contraction of muscle cells, movement of chromosomes during cell reproduction

exergonic rxn parts

reactants having higher energy that the products, unstable transition state at the peak of Ea

P-

R-

enzyme fucntion

catalysis, lower Ea, same delta G, speed up rxns

Enzyme substrate interaction

substrate→induced fit→lowered Ea speeds rxn up→products→enzyme w/ active site

4 ways enzymes lower Ea

1) active site provides template

2) active site clutches substrate and distorts its bonds→ transition state

3) active site creates microenvironment

4) amino acids in active site participate in rxn

Saturation of enzymes

all enzymes molecules have active site engaged (there is a limit)

Optimal enzyme conditions

create the Mose active shape ex. temp and pH

cofactor

small, nonprotein helper (often inorganic) ex. Zn, Fe

coenzyme

organic cofactor ex. vitamins

competitive inhibitor

binds the active site

noncompetitive inhibitor

binds away from active site + alters enzyme shape so substrates no longer fit

Cell regulation of metabolic pathways

1) switching on and off transcription of enzyme genes

2) regulate enzyme activity

allosteric regulation

binding to a site elsewhere on the molecule

allosteric activator

stabilizing active form of enzyme (enhancing activity)

allosteric inhibitor

stabilizing the inactive form of enzyme (enhancing inactivity)

cooperativity

active sites open once one substrate binds

feedback inhibition

supply and demand, product goes back to the beginning and inhibits pathway

Enzyme organization in a cell

enzymes and localized

energy behavior

flow

chemical behavior

cycle

fermentation in general

partial degradation of sugars or other organic fuel without the use of oxygen

aerobic respiration in general

oxygen is consumed as a rattan along with other organic fuel, also called cell resp, much more efficient that fermentation

anaerobic respiration

other substance is used in the place of oxygen

cell respiration equation

C₆H₁₂O₆ + 6 O₂ → 6 CO₂ + 6 H₂O + energy (heat and ATP) delta G= -686 kJ/mol

oxidation

loss of electrons

reduction

gain of electrons

oxidizing agent

e- acceptor

reducing agent

e- donor

__ is reduced in cell resp

oxygen (oxidizing agent)

__ is oxidized in cell resp

glucose (reducing agent)

e- carriers and stored energy cycle

NADH→stored energy, dehydrogenase enzyme allows easy cycling between oxidized and reduced forms

NADH role in ETC

NADH passes e- to the ETC

Glycolysis process

sugar splitting, e- carriers strip off e-

1 glucose (6C) → 2 pyruvate (3C)

occurs in cytosol (cytoplasm)

produces a little ATP via substrate-level phosphorylation

Glycolysis Phases

1. Energy Investment phase- Glucose → 2 G3P (3C) (key intermediate) *uses 2 ATP

2. Energy Payoff phase- 2 G3P → 2 pyruvate (3C) + 4 ATP

Glycolysis inputs

1 glucose, 2 ATP, 4 ADP, 2 NAD+

Glycolysis outputs

4 ATP, 2 NADH, 2 pyruvate, 2 ADP

Net ATP: 2

Pyruvate oxidation process

2 pyruvate in cytosol→2 acetyl CoA (2C) + 2CO₂

pyruvate dehydrogenase strips off carbons

occurs in mitochondrial matrix

Pyruvate oxidation inputs

2 pyruvate (3C), 2 NAD+, 2 S-CoA (coenzyme A)

Pyruvate oxidation outputs

2 NADH, 2 Acetyl CoA (2C), 2 CO₂

Citric acid cycle process

8 steps catalyzed by a specific enzyme

occurs in the mitochondrial matrix

CA cycle Step 1

Acetyl CoA (2C) and oxaloacetate (4C) join → citrate (6C)

CA cycle Step 2

citrate rearranged→ isocitrate

CA cycle Steps 3-4

2 NAD+ → 2 NADH

2 CO₂ out

S-CoA (coenzyme A) in → Succinyl CoA (4C) out

CA cycle Step 5

Substrate level phosphorylation → 1 ATP

CA cycle Step 6

FAD reduced → FADH₂ e- carrier

CA cycle Step 8

NAD+ → NADH

regenerate oxaloacetate

Citric acid cycle inputs

2 Acetyl CoA, 2 oxaloacetate, 6 NAD+, 2 FAD, 2 ADP

Citric acid cycle outputs

6 NADH, 2 FADH₂, 2 ATP, 2 oxaloacetate, 4 CO₂

Electron Transport chain (cell resp) process

no ATP generated

multiprotein complexes I, II, III, IV w/ coenzymes and cofactors

carry out sequential redox rxns

Oxidative phosphorylation

2 parts: 1. ETC 2. Chemiosmosis

produces a lot of ATP

occurs in the inner mitochondrial membrane

Complex I

coenzyme FMN accepts e- from NADH and passes e- to Fe-S protein

Complex II

coenzyme FMN accepts e- from FADH₂ and passes e- to Fe-S protein

Fe-S protein e- passing

e- from Fe-S proteins and passed to coenzyme Q (small, mobile, hydrophobic e- carrier)

Complexes III and IV

contain cytochrome (cyt) proteins + cofactor of heme w/ Fe

e- energy use in ETC

used to establish a H+ gradient

Complexes I, III, IV

pump H+ from low to high concentration

Chemiosmosis process

H+ gradient drives cell work (ATP synthesis), spins ATP synthase and produces ATP

occurs in the inner mitochondrial membrane

ETC inputs

8 NADH + 4 FADH₂ OR 10 NADH + 2 FADH₂, 6 O₂, H+ in matrix (low)

ETC outputs

8 NAD+ and 4 FAD OR 10 NAD+ and 2 FAD, 6 H₂O, H+ gradient across inner mito membrane (high)

Chemiosmosis inputs

H+ gradient, 26-28 ADP

Chemiosmosis outputs

26-28 ATP, H+ in matrix (low)

Substrate-level phosphorylation

a little ATP produced, (CA cycle and glycolysis)

role of O₂ in the ETC

terminal e- acceptor

ATP synthase

H+ flow through a channel in the stator and bind one by one to binding sites on the rotor, shape change leads to a spin of the internal rod, activates catalytic sites in the catalytic knob

fermentation defined

extends glycolysis, no ETC

2 types: lactic acid & alcohol

produces 2 ATP

anaerobic respiration

uses ETC, but no oxygen

produces ~30 ATP

aerobic respiration (cell respiration) steps

glycolysis, pyruvate oxidation, citric acid cycle, oxidative phosphorylation

~30-32 ATP