Foundations of Bio 1 Exam 3

created by Raccoon_Pope on Quizlet. for Dr Zapanta BIOSC0150

Energy

the capacity to do work(change)

Chemical reactions occur when _____ have enough ______ to combine or change bonding partners

atoms, energy

Kinetic energy

energy of motion

Potential energy

stored energy based on position

Thermal energy

kinetic energy of molecular motion

temperature

measure of the average molecular motion of a system

Heat

H
thermal energy transferred between objects at different temperaturess

Chemical energy

potential energy that can be stored in chemical bonds

First Law of thermodynamics

energy can not be created nor destroyed, no difference in total amount of energy

Second Law of thermodynamics

systems tend to proceed from a state of order to a state of disorder
when energy is converted, some becomes unusable, lost to disorder

Electrical energy

separation of charged

Heat energy

transfer due to temperature difference

Light energy

electromagnetic radiation stored as photons

Mechanical energy

energy of motion

entropy

S
measure of disorder in a system
when products of chemical reaction become less ordered than reactant molecules, entropy increases

enthalpy

H
total energy transferred in a biological system
potential energy of the molecule and effect of molecule on surrounding temperature and pressure

Exothermic

H

Endothermic

H>0
absorbs heat energy

Gibbs Free energy

amount of energy able to do work
if 0, no work occurs
takes into account total energy and entropy

Gibbs Free energy equation

ΔG = ΔH - TΔS

Delta G equation

G=Gproducts-Greactants

Exergonic reaction

release free energy
G

reactions tend to be spontaneous when ______ increases

entropy

Endergonic reaction

consume free energy
G>0
requires input of energy

a spontaneous reaction happens _________ and input of energy

without

Reversible reaction

reaction that can progress to a state of equilibrium
rate of forward and reverse reaction are equal
quantities of reactants and products remain constant NOT equal

Equilibrium can be altered by changing concentrations of _______ and _______

reactants, products

work cant be done at

equilibrium

If a gibbs free energy value is closer to 0...

the reaction is readily reversible, meaning its almost at equilibrium

If a gibbs free energy value is far from 0...

the reaction and equilibrium are functionally irreversible, basically cant happen

Energetic coupling

allows chemical energy released from one reaction to drive another
energy released from exergonic reactions are used to create endergonic reactions

What are the 2 characteristics of ATP that account for the free energy released?

1. Negative charge on phosphate groups cause repulsion, and the energy needed to get them close enough is stored in the P-O bond
2. Free energy of products is lower than reactants

Activation energy is the energy that is needed to

start a reaction

the transition state is the human invented model of an ________ in a reaction with a _____ energy that _____ be isolated

intermediate, high, cannot

If G is negative, the reaction _____ ________

is spontaneous

If G is positive, the reaction _____ ______

isn't spontaneous

A spontaneous reaction

will occur without an input of energy

Just because reactions are spontaneous doesn't mean they

occur fast or quickly

increasing the temperature of a reaction (increases/decreases) the rate

increases

an example of a spontaneous reaction is the breakdown of

glucose

Catalyst

biological molecule that increases the rate of a reaction by lowering the activation energy

Enzyme

biological catalyst
made of multiple peptides(proteins)
have all 4 structures(primary, secondary, etc)
some RNA catalysts exist(ribozymes)

substrate

reactant in an enzyme catalyzed reaction
binds to the enzymes active site

active site

location on an enzyme where the main substrate binds and the main reaction takes place

When an enzyme and substrate bind together they form the

enzyme-substrate complex(ES)

The enzyme substrate complex can be bound

noncovalently or with temporary covalent bonds

induced fit

when an enzyme undergoes a conformational change when the substrate binds to the active site, helps the substrate have a better fit into the enzyme

enzymes help facilitate the formation of the

transition state

in a regular reaction, the enzyme (is/is not) consumed

is not

(T/F) Enzymes bring substrates into the right formation and the right orientation

True

Enzymes induce ________ strain and make substrates (more/less) reactive by adding _________ groups or altering ______

physical, more, chemical, charge

The rate of enzymic reactions depends on the

substrate concentration

Saturation

when the amount of substrate is so great, the reaction can't go any faster, so the rate levels off

cofactors

inorganic ions that help with enzymic reactions
Zn2+, Mg2+, Fe2+
charged
reversibly interact with enzymes and substrates

coenzymes

organic ions that help with enzymic reactions
NADH
FAD
CoA
reversibly interact with enzymes and substrates
bind and be released

prosthetic groups

non amino acid molecules
Heme
Retinal
permanantly bound to enzymes

Acid base catalysis

transfer of protons H+

covalent catalysis

temporary covalent bond between substrate and amino acid side chain

metal ion catalysis

transfer of electrons e-

what serves as the proton donors/acceptors in acid base catalysis?

amino acids in the active site

What and where allows temporary covalent bonding in covalent catalysis?

amino acid residue in the active site

What plays the major role in metal ion catalysis and how?

cofactors(metal ions) bind and change orientation of substrate in the active site

Enzymes have optimal

pH and temperature

if temperature is too high, an enzyme

will degrade(breakdown)

if a temperature is too low, an enzyme

will not react

enzymes are regulated because

cellular conditions are constantly changing and we dont always need enzyme products

3 types of regulation

reversible inhibition
allosteric regulation
covalent modification

enzyme inhibitors are

small molecules that slow the rate of reaction
they interfere with product forming and release
reversible ones associate/dissociate rapidly
irreversible inhibitors(suicide inhibitors) dissociate slowly if at all and are usually manmade

types of reversible inhibitors

competitive inhibition
noncompetitive inhibition
uncompetitive inhibition

competitive inhibition

inhibitor competes directly with the substrate to bind to active site
prevents substrate binding
forms enzyme-inhibitor complex(EI)
resembles substrate
increasing substrate concentration overpowers the inhibitor

noncompetitive inhibition

inhibitor can bind to both active site and different binding site on enzyme substrate complex
binding to active site prevents substrate binding
binding to binding site prevents product formation
increasing substrate concentration has no difference

uncompetitive inhibition

inhibitor binds at binding site on enzyme substrate complex not active site
causes conformational change allowing inhibitors to bind and stopping products from being made
increasing substrate concentration has no difference

irreversible inhibition

completely ruins the enzymes, so body has to make more

allosterism

binding of molecule to protein at one site affects another site

allosteric regulation

regulator binds before substrate
allosteric activation
allosteric inhibition

allosteric activation

activator binds, causes conformational change in enzyme to better fit substrate, causes product formation

allosteric inhibition

inhibitor binds, causes conformational change in enzyme to not fit substrate, stops product formation

the most common covalent modification is

phosphorylation

feedback inhibition

when an enzyme in a metabolic pathway is turned off by the product it forms due to a surplus of said product
stops product from being made when their is enough

covalent modification

chemical change in the enzymes primary structure that alters the function
can increase or decrease function
chemical groups added covalently

metabolism

sum of all chemical reactions in an organism

intermediates

species in pathways that allow them to be linked

metabolic pathway

series of catalyzed enzymic reactions that start with a specific molecule and form a characteristic product

catabolic pathway

breakdown of large molecules into smaller ones
exergonic
make ATP

anabolic pathway

creation of small molecules to make larger ones
endergonic
require ATP

(T/F) Metabolic pathways aren't linked through intermediate molecules

False

Why can metabolic pathways be turned off and on?

to regulate catabolic and anabolic reactions

Metabolic homeostasis

state of balance of metabolites in a cell(NOT EQUILIBRIUM)

Mechanisms of regulation include

changing amount of active enzymes, amount of enzyme activity by covalent modification, substrate availability, and feedback through allosteric regulators

feedback can also be

positive

redox reaction

chemical reaction involving the transfer of electrons

oxidation

loss of electrons

reduction

gain of electrons

redox events are always

coupled

the more reduced a molecule, the (greater/lesser) the free energy

greater

each electron is usually accompanied by a

proton

NADH

important electron carrier in redox reactions
based off nucleotide

NAD+

oxidized form of NADH

FADH2

important electron carrier in redox reactions
based off nucleotide
3 carbon rings can be protonated

glucose

primary energy molecule that is essential for all metabolism