Metabolism - energy and enzymes

Question 1

metabolism

Answer 1

all of the chemical reactions that occur in an organism that allow it to live

Question 2

metabolic pathway

Answer 2

a cluster of metabolic reactions
Each pathway begins with a specific molecule which is then altered in a series of defined steps resulting in a certain product
Each step of the pathway is catalysed by a specific enzyme

Question 3

catabolism / catabolic pathways

Answer 3

metabolic pathways that release energy by breaking down complex molecules to simpler compounds
degradative processes
cellular respiration is the major catabolic pathway
during catabolic reaction some bonds are broken and others are formed releasing energy and resulting in low energy breakdown products

Question 4

cellular respiration

Answer 4

major catabolic pathway
the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water
energy that was stored in the organic molecules becomes available to do the work of the cell

Question 5

anabolic pathways

Answer 5

consume energy to build complicated molecules from simpler ones (biosynthetic pathways)
e.g. photosynthesis - making sugars from carbon dioxide and water

Question 6

is photosynthesis a catabolic or anabolic papthway

Answer 6

anabolic - making more complex molecules from simpler ones (carbon dioxide and water)

Question 7

how are catabolic and anabolic reactions related

Answer 7

downhill and uphill
the energy released from the downhill reactions of catabolic pathways can be stored and then used to drive the uphill reactions of anabolic pathways

relate to bike riding - downhill - build energy / uphill use energy

Question 8

bioenergetics

Answer 8

the study of how energy flows through living organisms

Question 9

kinetic energy

Answer 9

energy related to the relative motion of objects
movement energy
heat and light energy are forms of kinetic energy

Question 10

thermal energy

Answer 10

kinetic energy associated with the random movement of atoms and molecules
heat energy

Question 11

potential energy

Answer 11

the energy that matter possesses because of its location or structure e.g. chemical energy is a form of potential energy - arrangement of atoms leads to energy release
complex molecules like glucose are high in chemical energy

Question 12

thermodynamics

Answer 12

the study of energy transformations that occur in a collection of matter

Question 13

first law of thermodynamics

Answer 13

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

the principle of conservation of energy

e.g. photosynthesis - convert sunlight to chemical energy is transforming energy not creating it
emu - converts the chemical energy in plants to the kinetic energy of running

Question 14

the second law of thermodynamics

Answer 14

every energy transfer or transformation increases the level of entropy of the universe

increases the amount of disorder (increasing amount of heat) increases randomisation

Question 15

spontaneous/nonspontaneous reactions

Answer 15

spontaneous - energetically favourable / proceeds without requiring an input of energy (increases entropy)
non spontaneous- will happen only if energy is supplied (decreases entropy)

Question 16

exergonic

Answer 16

energy outward
proceeds with a net release of free energy
occur spontaneously

Question 17

endergonic

Answer 17

energy inward
absorbs free energy from its surroundings
nonspontaneous

Question 18

energy coupling

Answer 18

the use of an exergonic process to drive an endergonic one. ATP is responsible for mediating most energy coupling in cells .

Question 19

structure of ATP

Answer 19

ATP contains the sugar ribose with the nitrogenous base adenine and a chain of three phosphate groups(the triphosphate group) bonded to it

Question 20

What is ATP used for in the cell

Answer 20

Energy coupling - drive endergonic reactions

ATP is one of the nucleoside triphosphates used to make RNA

Question 21

ATP to ADP

Answer 21

The bonds between the phosphate groups are broken by hydrolysis - the addition of a water molecule
When the bond holding the terminal phosphate group is broken by the addition of a water molecule a molecule of inorganic phosphate leaves the ATP which then becomes ADP
The reaction is exergonic - releases energy

Question 22

ATP to ADP releases lots of energy - Why

Answer 22

three phosphate groups are negatively charged and crowded together
all negatives together = mutual repulsion
like a spring

Question 23

How does ATP work to drive chemical reactions

Answer 23

with the help of specific enzymes drive chemical reactions that require energy
if the reaction requires more energy than the amount released through hydrolysis of ATP the two reactions can be coupled
this usually involves phosphorylation - the transfer of a phosphate group from ATP to some other molecules

Question 24

phosphorylation

Answer 24

the transfer of a phosphate molecule

Question 25

phosphorylated intermediate

Answer 25

in energy coupling reactions - a phosphate group is transferred from ATP to another molecule such as a reactant. The recipient molecule with the phosphate group covalently bonded to it is then called a phosphorylated intermediate this phosphorylated intermediate is more reactive (less stable) than the original unphosphorylated molecule.

Question 26

How is ATP used in the cell

Answer 26

drives chemical reactions (phosphorylation - ATP to ADP) transport (ATP drives change in the proteins shape and its ability to bind to another molecule) mechanical work - motor proteins

Question 27

How does ATP drive transport work in the cell

Answer 27

hydrolysis of ATP leads to a change in the protein's shape and its ability to bind another molecule Sometimes this occurs via a phosphorylated intermediate

Question 28

How does ATP drive mechanical work

Answer 28

mechanical work is motor proteins walking along cytoskeletal elements ATP binds noncovalently to the motor protein ATP is hydrolysed releasing ADP and P Another ATP can then bind At each stage the motor protein changes its shape and ability to bind to the cytoskeleton resulting in the movement of the protein along the cytoskeleton track

Question 29

ATP cycle

Answer 29

ATP hydrolysis to ADP and Phosphate - yields energy ADP + phosphate = ATP using the energy from exergonic breakdown reactions in the cell ATP hydrolysis releases energy ATP synthesis requires energy The ATP cycle couples the cells energy yielding (exergonic) processes to the energy consuming (endergonic ones) ones

Question 30

How long does the ATP cycle take

Answer 30

astonishing pace | a working muscle cell recycles its entire pool of ATP in less than a minute

Question 31

is the process of ATP formation endergonic or exergonic

Answer 31

endergonic / nonspontaneous / energy must be spent to make it occur cellular respiration provides the energy for the endergonic process of making ATP Plants use light energy to produce ATP

Question 32

How does ATP typically transfer energy from an exergonic to an endergonic reaction in the cell

Answer 32

ATP usually transfers energy to an endergonic process by phosphorylating (adding a phosphate molecule) to another molecule (exergonic process, in turn phosphorylate ADP to regenerate ATP)

Question 33

enzyme

Answer 33

a macromolecule that acts as a catalyst | speeds up a reaction without being consumed by the reaction

Question 34

catalyst

Answer 34

speeds up a reaction

Question 35

activation energy

Answer 35

the energy required to start a reaction the initial investment of energy for starting a reaction All reactions involve bond breaking and bond forming before this can happen the starting molecule must be contorted so that the reaction can proceed to reach this stage requires energy to contort the reactant molecules so the bonds can break

Question 36

energy profile of an exergonic reaction

Answer 36

AB + CD the reactants AB and CD must absorb enough energy from the surroundings to reach the unstable transition state where bonds can break (they are activated) After bonds have broken, new bonds are formed, releasing energy to the surroundings

Question 37

activation energy as a barrier

Answer 37

activation energy provides a barrier that determines the rate of a reaction reactants need enough energy for the reaction to begin in most cases the activation energy required to start the reaction cannot be reached without catalysis

Question 38

catalysis

Answer 38

a process by which a catalyst (e.g. enzyme) selectively speeds up a reaction without itself being consumed

Question 39

how do enzymes catalyse reactions

Answer 39

lowering the activation energy barrier enabling the reactant molecules to absorb enough energy to reach the transition state Can only hasten reactions that would occur anyway

Question 40

substrate

Answer 40

the reactant an enzyme acts on is referred to as the enzyme's substrate The enzyme binds to its substrate forming an enzyme substrate complex While the enzyme and substrate are joined the catalytic action of the enzyme converts the substrate to the product of the reaction

Question 41

enzyme names

Answer 41

most end in 'ase' | e.g. sucrase

Question 42

what enables enzyme specificity

Answer 42

An enzyme can recognise its specific substrate even among closely related compounds enzymes are proteins - proteins have unique three dimensional shapes . The specificity of an enzyme results from its shape which is a consequence of its amino acid sequence

Question 43

active site

Answer 43

the restricted region of the enzyme molecule that binds to the substrate typically a pocket or groove on the surface of the enzyme where catalysis occurs

Question 44

is the active site a stiff structure

Answer 44

no proteins subtly change shape as the substate enters the active site the enzyme changes shape slightly due to interactions between the substrate's chemical groups and those on the active site. This shape change makes the active site fit even more snugly around the substrate

Question 45

induced fit

Answer 45

when the substrate enters the active site the enzyme slightly changes shape to fit more tightly around the substrate the tightening of binding after contact induced fit brings the chemical groups of the active site into positions that enhance their ability to catalyse the chemical reaction

Question 46

catalytic cycle

Answer 46

binding ----catalysis ---product ----binding substrate binds to the active site and is held in place by chemical interactions (hydrogen bonds / ionic bonds) the R groups of the enzyme amino acids catalyse the conversion of substrate to product product departs from the active site the enzyme is free to take another substrate molecule Enzyme emerges in its original form

Question 47

how do enzymes catalyse reactions

Answer 47

1. bring substrates together in the correct orientation 2. enzyme bends and stretches the substrate stressing the chemical bonds to be broken 3. provides a conducive microenvironment e.g. pH 4. amino acids in the active site directly participate in the reaction e.g. bonding

Question 48

what controls the rate of enzyme activity

Answer 48

the concentration of the substrate more substrate molecules - more enzyme activity reaches saturation level where the only way to increase the rate of product formation is to add more enzyme

Question 49

how does heat affect enzyme activity

Answer 49

each enzyme has an optimal temperature at which its reaction rate is greatest higher the temp - substrate particles collide with active sites more often however if to high the protein denatures the optimum temperature allows the greatest number of molecular collisions and the fastest conversion of the reactants to products Most human enzymes have optimal temperatures of about 35-40 degrees

Question 50

how does pH affect enzyme activity

Answer 50

the optimal pH for most enzymes fall in the range of pH 6-8 but there are exceptions e.g. stomach enzymes pepsin

Question 51

cofactors

Answer 51

nonprotein helpers bound to many enzymes many be bound tightly and permanently or loosly and reversibly may be inorganic - zinc/iron / copper may be organic - coenzymes

Question 52

coenzymes

Answer 52

organic molecules that bind to enzymes and act as cofactors (helpers) organic cofactors vitamins act as coenzymes

Question 53

enzyme inhibitors

Answer 53

chemicals that bind to enzymes to inhibit their action some are permanent - bind with covalent bonds some transient - inhibition is reversible e.g. toxins and poisons - Sarin pesticides - DDT antibiotics are inhibitors of specific enzymes in bacteria

Question 54

competitive inhibitors

Answer 54

enzyme inhibitors that work by mimicking normal substrates and competing for admission to the active site block substrates from entering the active site

Question 55

noncompetitive inhibitors

Answer 55

enzyme inhibitors that bind to the enzyme (not at the active site) and cause it to change its shape so that the active site becomes less effective

Question 56

Many spontaneous reactions occur very slowly. Why don't all spontaneous reactions occur instantly

Answer 56

A spontaneous reaction is a reaction that is exergonic. However, if it has a high activation energy that is rarely attained the rate of the reaction may be low

Question 57

allosteric regulation

Answer 57

any case in which a protein's function at one site is affected by binding of a regulatory molecule to a separate site. It may result in either activation or inhibition of an enzyme's activity change the proteins shape and the functioning of its active site by binding to a site elsewhere on the molecule

Question 58

what types of enzymes are allosterically regulated

Answer 58

most enzymes known to be allosterically regulated are constructed of two or more subunits

Question 59

what types of allosteric regulation are there

Answer 59

allosteric inhibition allosteric activation cooperativity

Question 60

how does allosteric inhibition occur

Answer 60

usually enzymes made of two or more subunits inhibiting molecule binds to a regulatory site (the allosteric site) often located where the subunits join shape changes the allosteric inhibitor stabilises the inactive form

Question 61

how does allosteric activation occur

Answer 61

usually for enzymes composed of subunits activator binds to the regulatory site stabilises the active form of the enzyme

Question 62

regulatory site (allosteric site)

Answer 62

on enzymes composed of two or more subunits usually located where the subunits join allosteric activator or inhibitor binds to this site which changes the shape of all the subunits

Question 63

how does ATP act as a allosteric regulator

Answer 63

ATP binds to several catabolic enzymes (catabolic - breaking down) lowering their affinity for substrate and inhibiting their activity ADP acts as an activator This is logical because catabolism functions in generating ATP. If ATP is being used at a high rate (is needed) ADP accumulates and activates the enzymes that speed up catabolism. Vice versa

Question 64

How does cooperativity allosteric activation work

Answer 64

a substrate molecule binding to one active site in a multiunit enzyme triggers a shape change in all active sites One substrate molecules primes an enzyme to act on additional substrate molecules

Question 65

feedback inhibition

Answer 65

the end product of a metabolic pathway binds to the enzyme to inhibit further binding of initial substrate e.g. if product accumulates in the cell - it binds to the enzyme to stop the further production of itself