Lecture 4 - Molecules, Energy, and Biosynthesis Flashcards
what are the four biomolecules
- lipids
- carbohydrates
- proteins
- nucleic acid
diverse group of water-insoluble biological molecules
lipids
energy stores
fats
major components of membrane
- phospholipids
- sterols
- sugar molecules
- polyhydroxy aldehydes and ketones with the general formula of (CH2O)n
carbohydrates
most complex and most abundant organic molecules containing at least one carboxyl group and one amino group
proteins
store and express genomic information
nucleic acids
carries coded information
DNA
arranged DNA
genes
instrumental in translating the coded message of DNA into sequences of amino acids during synthesis of protein molecules
RNA
process of increasing the rate of reaction with the use of a catalyst
catalysis
any substance that increases rate of reaction upon addition to a certain reaction
catalyst
- catalyst of biochemical reactions
- neither used up in the reaction nor do they appear as reaction products
- proteins of very specific amino acid composition and sequence
enzymes
how are enzymes denatured and precipitated
salts, solvents, other reagents
effect of enzymes on energy of activation
lower
- kinetic energy required to bring the reactants into position to interact
- measured as the number of calories required to bring all the molecules in a mole of reactant at a given temperature to a reactive state
activation energy / free energy of activation
how do enzymes hasten reactions
lower activatiion energy
each enzyme is specific for a certain __
substrate
example of enzyme specificity
- stereospecific
- single product
- specific bonds
- reaction in which the stereochemistry of the reactants controls the outcome of the reaction
- one stereoisomer of certain reactant produces one stereoisomer of a certain product, whereas a different stereoisomer of the same reactant produces a different stereoisomer of the same product
stereospecific
molecules that are chemically identical but whose functional groups are attached in different configurations around central carbon atoms
stereoisomer
hydrolyses any peptide bond in which the carbonyl group belongs to a phenylalanine, tyrosine, or tryptophan residue
chymotrypsin
what does chymotrypsin hydrolyses
- phenylalanine
- tyrosine
- tryptophan residue
what does chymotrypsin reduce
- energy used up by cell
- build-up of toxic by-products
- highly specific nature of most enzyme
- arises from the close and complementary fit between enzymes and substrate in a special portion of the enzyme surface
- substrate can fit like a lock-and-key mechanism
active site
Different models of the active site
- lock-and-key model
- induced-fit model
- early theory for enzyme action
- enzyme-substrte have specific shape to fit exactly into another
lock-and-key model
- enzymes are flexible structures
- active site can change the shape to fit the substrate
- better, widely accepted theory
induced-fit model
catalytic potency of an enzyme
enzyme activity
number of reactions catalyzed per second by the enzyme
turnover number
enzymatic reaction
- substrate to active site
- enzyme-substrate complex (ES) formation
- product separates from enzyme
- free enzyme can form another ES
how do enzymes accelerate reactions
- hold substrates in close proximity to enhance probability of a reaction
- form unstable intermediate that readily undergoes second reaction
- presence of protons donors and acceptors in active site
Factors affecting enzyme activity
- temperature
- pH
increase in temperature
- increase average molecular velocity
- increase no. of molecular collisions per unit
- increase probability of successful interaction
as velocities increase, the molecules possess __ __ __ and thus are more likely to react upon collision
higher kinetic energies
as temperature increases, reaction rate __ __
initially increases
as temperature increases further, reaction rate __
decreases
why does the reaction rate decrease when the temperature increases further
onset of denaturation
where is the reaction rate maximal
optimal temperature
what happens when there is drop in pH
exposes more positive sites on an enzyme for interaction with negative groups on a substrate molecule
what happens when there is rise in pH
binding of positive groups on a substrate to negative sites on the enzymes
- facilitates enzyme reactions but is not required
- small organic compounds or metals primarily used to support the action of enzymes
Cofactors
small organic molecules that act as cofactors
coenzymes
- enzyme minus its cofactor
- cannot function without its cofactor/coenzyme
apoenzyme
ex. of cofactors
vitamins
cofactor + apoenzyme
holoenzyme
Six major classes of enzymes
- oxidoreductases
- transferases
- hydrolases
- lyases
- isomerases
- ligases
type of reaction of oxidoreductases
oxidation-reduction
type of reaction of transferases
group transfer
type of reaction of hydrolases
hydrolysis reactions (transfer of function groups to water)
type of reaction of lyases
addition or removal of groups to form double bonds
type of reaction of isomerases
isomerization (intramolecular group transfer)
type of reaction of ligases
ligation of two substrates at the expense of ATP hydrolysis
example of oxidoreductases
lactate dehydrogenase
example of transferases
nucleoside monophosphate kinase (NMP kinase)
example of hydrolases
chymotrypsin
example of lyases
fumarase
example of isomerases
triose phosphate isomerase
example of ligases
aminoacyl-tRNA synthetase
where does the rate at which an enzymatic reaction proceeds depend on
concentrations of
- substrate
- product
- active enzymes
molecules that interact with enzymes (temporary or permanent) in some way and reduce the rate of an enzyme-catalyzed reaction or prevent enzymes to work in a normal manner.
Enzyme inhibitors
irrevirsible enzyme inhibition
toxins
two types of enzyme inhibition
- competitive inhibition
- noncompetitive inhibition
- caused by molecules that react directly with the active site of the enzyme
- can be reversed by an increase in substrate concentration
- most are substrate analogs
competitive inhibition
how is competitive inhibition reversed
increase in substrate concentration
- caused by molecules that bind to a region(s) of the enzyme outside the active site
- reversed by dilution or removal of inhibitor
- chemical structure typically differs from that of the substrate
noncompetitive inhibition
how is noncompetitive inhibition reversed
dilution or removal of inhibitor
regulation of metabolic reactions
- control of enzyme synthesis
- regulated by modulator molecules
how is enzyme synthesis controlled
modulation of rate of transcripton
when are enzyme synthesized
only when needed
distinct from the active site
allosteric site
how is enzyme activity controlled by modulator molecules
by binding to the allosteric site affecting affinity of enzyme for its substrate
acts as the regulatory enzyme
first enzyme
inhibit the activity of the first enzyme
end product of pathway
what is the end product of the pathway
allosteric inhibitor
several cation cofactors act as __ __ for some enzymes
allosteric activators
example of where ATP is used for
- biosynthesis
- mechanical work
- transport work
two kinds of energy-yielding metabolic pathways in animal tissues
- aerobic metabolism
- anaerobic metabolism
- food molecules are completely oxidized to carbon dioxide and water by molecular energy
- energy yield is far greater
aerobic metabolism
- food molecules are oxidized incompletely to lactic acid (lactate)
- absence of oxygen
anaerobic metabolism
products of aerobic respiration
- CO2
- water
- ATP
products of anaerobic respiration
- Mammalian muscle - lactic acid (and ATP)
- Yeast and some plants - ethanol and CO2 (and ATP)
net ATP produced in aerobic respiration
32 ATP molecules
net ATP produced in anaerobic respiration
2 ATP molecules
