e3 cell bio

bioenergetics

study of energy flow through a living system

metabolism

Totality of all chemical reactions occuring in every cell

Metabolic pathway

a series of biochemical rxns that converts 1+ substrates into a final product

substrates

reactants in an enzymatically catalyzed rxn

anabolic rxn

Take small simple molecules into larger molecules that requires energy

catabolic rxn

Break down large molecules into smaller molecules & releases energy

energy

ability to do work

kinetic energy

objects in motion

types of kinetic energy

Thermal, electrical, light (photons of light that move thru space), mechanical (kinesin/dynein moving), sound

potential energy

objects that have the potential to move

type of potential energy

chemical

thermodynamics

the study of energy & energy transfer involving physical matter

1st law of thermodynamics

energy cannot be created or destroyed but it can be transferred and transformed

energy transduction

the conversion of energy from one form to the next

2nd law of thermodynamics

Every energy transfer or transformation increases the entropy (disorder) of the universe

some chemical rxns are lost as heat energy

energy being lost as heat…

result is increased entropy (disorder)

spontaneously

rxn CAN occur w/o an additional input of energy

2 main factors that determine spontaneity

• products have lower PE than reactants

• products are less ordered than the reactants

exothermic rxn

reactants had more bond energy than the products

-∆H

endothermic rxn

gain energy from outside

products have more energy than the reactants (+)∆H

enthalpy

the potential energy of the molecules like bond energy

entropy

amt of disorder in a group of molecules & temperature dependent

greater the disorder

the greater the entropy

(+) ∆S

products are more disordered than the reactants

Gibbs free energy

measures the energy available to do useful work

(-)∆G

chemical rxn can occur spontaneously

exergonic rxn

products have less free energy than substrates (-)∆G

endergonic rxn

products have more free energy than the substrates (+)∆G

1 kelvin is

273 C

what is the energy that is used for endergonic rxn?

ATP is used

ATP stands for

adenosine triphosphate

energy coupling

use of an exergonic process to drive an endergonic one

endergonic rxns are

not spontaneous

exergonic rxns

are spontaneous

ATP to ADP ∆G difference value

-7.3 kcal/mol

ATP hydrolysis drives

movement of filaments + creating a concentration gradient

redox rxns

involves loss/gain of electrons

reduced molecule

gains e-

oxidized molecule

loses e-

oxidizing agent

is the reduced molecule

reducing agent

is the oxidized molecule

activation energy

heat energy is used to make/break bonds in a rxn and this determines the speed of the rxn

transition state

most unstable state b/c bonds are being broken/created

enzymes

protein catalysts that speed up rxns by lowering the required Ea

ribozyme

RNA molecule that lowers the Ea

catalyst

a chemical agent that speeds up a rxn w/o being consumed by the rxn

active site

the region of the enzyme that the substrate binds to or catalysis is occuring

cellular respiration

A set of metabolic rxns and processes that take place in the cells of organisms to convert biochemical energy from nutrients into adenosine triphosphate (ATP), and then release waste products

induced fit

the enzyme changes shape slightly as substrate binds

binding sites

bind & orient substrates

catalytic site

reduce chemical Ea

factors that determine active site compatability

shape, size, charge, and noncovalent interactions

Reactant molecules

Enzymes bind w/reactant molecules promoting bond-breaking & bond-forming processes

mechanisms of enzyme catalysis

Substrate orientation

Changing substrate reactivity

Inducing strain in the substrate

Temporary covalent bond

enzyme regulation

Regulation of enzyme activity helps control their environment to meet their specific needs

enzymes can be regulated by

Modifications to temperature and/or pH

Availability of coenzymes or cofactors

Production of molecules that inhibit or promote enzyme function

cofactors

inorganic ions like Fe2+, Mg2+, Zn2+

coenzymes

organic molecules, including folic acid, NAD+, & vitamins

allosteric regulation

a regulatory molecule binds to a protein at an allosteric site & affects the protein’s function at the active site

Competitive inhibitors

substrate and competitor are competing for the same site

Non-competitive allosteric

allosteric inhibitor binds to allosteric site → alters conformation of active site → substrate can’t bind

feedback inhibition

where the end product of the pathway inhibits an upstream step is an important regulatory mechanism in cells

number of ATP made from cell resp

30-32

glucoses gets oxidized

into CO₂

O₂ gets reduced

into H₂O

NAD+

nicotinamide adenine dinucleotide

oxidizing agent during respiration, e’ carrier

3 metabolic pathways

glycolysis, citric acid cycle, oxidative phosphorylation

glycolysis step 1

hexokinase

dehydrogenase

removing 2 H atoms

substrate-level phosphorylation

Take phosphate off a substrate & enough energy is released to stick it on an ADP

1 glucose produces

2 ATPs, 2 NADH, 1 pyruvate

cooperativity

type of allosteric activation that binds a substrate to one active site that affects catalysis in a different active site

enhance enzyme activity

3 stages of metabolism

Stage 1
Stage 2

stage 3

stage 1

digestion of lipids, polysaccharides, proteins

stage 2

glucose→acetyl-CoA

stage 3

TCA cycle

glycolysis happens in…

the cytosol

oxidation of pyruvate & TCA cycle happens in…

the mitochondria

everything past WHAT is doubled in glycolysis

G3P

kinase

phosphate is being covalently linked to something

energy harvesting steps

6, 7, 10

energy investment steps

1 and 3

porins

pore-forming protein that allows passsage of moderate-sized molecules

porin motif

beta-sheet barrel that forms an opening

chemiosmosis

uses kinetic energy from protons falling down its gradient to form ATP from ADP

oxidative phosphorylation

Exergonic proton transport coupled w/endergonic ATP synthase

prosthetic groups

Organic molecules that are associated w/proteins that are easy to reduce (accept e’) & easy to be oxidized for the next step (donate e)

types of prostheic groups

flavins & cytochromes

mobile electron carriers

ubiquinone & cytochrome c

ubiquinone

hydrophobic, diffuse w/the interior of the bilayer

job of Ub

deliver to compelx 3 after receiving e’s from complex 1 or 2

job of cytochrome c

deliver e’s from complex 3 to complex 4

which complexes are coupling sites

complexes 1,3, & 4

protons complexes 1 and 3 pump out

4 H

protons complex 4 pumps out

2 H are pumped out

#of protons per NADH

10

#of protons per FADH₂

6

F1

is the catalytic site of the ATP synthase

F0

is the spinning part of the ATP synthase

ATP synthase

rotary motor enzyme b/c it involves spinning to convert it to mechanical energy