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Bio1MGC > Metabolism - energy and enzymes > Flashcards

Metabolism - energy and enzymes Flashcards

1
Q

metabolism

A

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

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2
Q

metabolic pathway

A

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

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3
Q

catabolism / catabolic pathways

A

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

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4
Q

cellular respiration

A

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

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5
Q

anabolic pathways

A

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

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6
Q

is photosynthesis a catabolic or anabolic papthway

A

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

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7
Q

how are catabolic and anabolic reactions related

A

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

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8
Q

bioenergetics

A

the study of how energy flows through living organisms

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9
Q

kinetic energy

A

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

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10
Q

thermal energy

A

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

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11
Q

potential energy

A

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

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12
Q

thermodynamics

A

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

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13
Q

first law of thermodynamics

A

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

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14
Q

the second law of thermodynamics

A

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

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

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15
Q

spontaneous/nonspontaneous reactions

A

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

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16
Q

exergonic

A

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

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17
Q

endergonic

A

energy inward
absorbs free energy from its surroundings
nonspontaneous

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18
Q

energy coupling

A

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

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19
Q

structure of ATP

A

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

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20
Q

What is ATP used for in the cell

A

Energy coupling - drive endergonic reactions

ATP is one of the nucleoside triphosphates used to make RNA

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21
Q

ATP to ADP

A

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

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22
Q

ATP to ADP releases lots of energy - Why

A

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

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23
Q

How does ATP work to drive chemical reactions

A

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

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24
Q

phosphorylation

A

the transfer of a phosphate molecule

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25
Q

phosphorylated intermediate

A

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.

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26
Q

How is ATP used in the cell

A

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

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27
Q

How does ATP drive transport work in the cell

A

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

28
Q

How does ATP drive mechanical work

A

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

29
Q

ATP cycle

A

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

30
Q

How long does the ATP cycle take

A

astonishing pace

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

31
Q

is the process of ATP formation endergonic or exergonic

A

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

32
Q

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

A

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)

33
Q

enzyme

A

a macromolecule that acts as a catalyst

speeds up a reaction without being consumed by the reaction

34
Q

catalyst

A

speeds up a reaction

35
Q

activation energy

A

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

36
Q

energy profile of an exergonic reaction

A

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

37
Q

activation energy as a barrier

A

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

38
Q

catalysis

A

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

39
Q

how do enzymes catalyse reactions

A

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

40
Q

substrate

A

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

41
Q

enzyme names

A

most end in ‘ase’

e.g. sucrase

42
Q

what enables enzyme specificity

A

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

43
Q

active site

A

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

44
Q

is the active site a stiff structure

A

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

45
Q

induced fit

A

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

46
Q

catalytic cycle

A

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

47
Q

how do enzymes catalyse reactions

A
  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
48
Q

what controls the rate of enzyme activity

A

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

49
Q

how does heat affect enzyme activity

A

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

50
Q

how does pH affect enzyme activity

A

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

51
Q

cofactors

A

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

52
Q

coenzymes

A

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

53
Q

enzyme inhibitors

A

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

54
Q

competitive inhibitors

A

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

55
Q

noncompetitive inhibitors

A

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

56
Q

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

A

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

57
Q

allosteric regulation

A

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

58
Q

what types of enzymes are allosterically regulated

A

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

59
Q

what types of allosteric regulation are there

A

allosteric inhibition
allosteric activation
cooperativity

60
Q

how does allosteric inhibition occur

A

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

61
Q

how does allosteric activation occur

A

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

62
Q

regulatory site (allosteric site)

A

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

63
Q

how does ATP act as a allosteric regulator

A

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

64
Q

How does cooperativity allosteric activation work

A

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

65
Q

feedback inhibition

A

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

Bio1MGC (11 decks)

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