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human metabolism - summary notes > OC1 - the role of enzymes in human metabolism > Flashcards

OC1 - the role of enzymes in human metabolism Flashcards

1
Q

what is human metabolism?

A

human metabolism is every single biochemical reaction in the human body

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2
Q

what are anabolic reactions (basic)?

A

build simple molecules into complex molecules
require energy

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3
Q

what are catabolic reactions (basic)?

A

breakdown complex molecules into simple molecules
release energy

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4
Q

what are the nutrients for metabolism?

A

water
vitamins - coenzymes
minerals - cofactors
carbohydrates - glucose
lipids (fats)
proteins - enzymes

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5
Q

what is the structure of an amino acid?

A

diagram
amino group, variable R group, carboxyl group

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6
Q

what is the structure of a dipeptide?

A

condensation reaction between two amino acids to remove a water molecule
peptide bond

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7
Q

what is a zwitterion?

A

amino acids at a physiological pH (7.2)
diagram

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8
Q

what is the primary protein structure?

A

the sequence of amino acids in a polypeptide chain held together by peptide bonds

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9
Q

what is the secondary protein structure?

A

alpha-helices and beta-pleated sheets held together by hydrogen bonds

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10
Q

what is the tertiary protein structure?

A

interactions between R-groups that give the protein its 3D arrangement - Van Der Waals, hydrophobic interactions, ionic bonds, hydrogen bonds, disulphide bridges between cysteine and methionine

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11
Q

what is the quaternary protein structure?

A

more than one polypeptide chain/subunit exhibiting all previous bonds

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12
Q

what is the biological function of enzymes?

A

enzymes are biological catalysts that increase the rate of a reaction, by lowering the activation energy required for the reaction. enzymes remain unchanged during the reaction.
enzymes are sensitive to pH and temperature changes and they are specific in the reactions they catalyse.

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13
Q

what is an active site?

A

enzymes possess an active site
where chemical reactions take place
where substrates bind
crevice in the 3D structure
non-polar environment - excludes water
unique combination of R-groups creates a very specific chemical environment

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14
Q

how does a substrate bind to an enzyme?

A

substrate binds to an enzyme at its active site where it is held by many weak, non-covalent bonds - hydrogen bonds, ionic interactions, hydrophobic interactions, Van Der Waals
the tertiary arrangement of amino acid side chains in the active site is complementary to those on the substrate allowing these bonds to form.

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15
Q

what is the ‘lock and key model’ of substrate binding?

A

the substrate binds to the enzymes active site exactly as they are complementary in shape to each other

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16
Q

what is the ‘induced fit model’ of substrate binding?

A

substrate and enzyme are not complementary so binding of a substrate to an enzymes active site induces a conformational change in the enzymes active site to bind the substrate more tightly
reactions can only take place after induced fit has occurred
the bonds in the enzyme-substrate complex are under stress as they are not in their natural conformation, this lowers the activation energy required for the reaction
allows the possibility that more than one specific substrate can bind to one enzyme

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17
Q

what is the hexokinase induced fit example?

A

performs the first step in glycolysis using an ATP molecule to start the process
transfers a phosphate from ATP to glucose forming glucose-6-phosphate
changes shape by induced fit following ATP and glucose binding to form the enzyme-substrate complex closing over the ATP and glucose substrates

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18
Q

what is the citrate synthase induced fit example?

A

oxaloacetate binds first inducing a conformational change and creating a binding site for acetyl coenzyme A
oxaloacetate and acetyl CoA are now in close proximity to each other and citrate synthase can catalyse the condensation reaction between them

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19
Q

what is Gibbs free energy?

A

the energy available for work in a reaction
most metabolic enzymes have small ΔG values - close to zero
overall energy released during reaction
ΔG = ΔH - TΔS

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20
Q

what is enthalpy?

A

total energy change in the system

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21
Q

what is entropy?

A

measure of disorder of a system

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22
Q

what is enzyme kinetics?

A

‘how a substrate binds to an enzyme and is converted into a product’

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23
Q

what is the transition state?

A

enzyme-substrate complex is not a substrate or a product
has the highest free energy making it a rare and unstable intermediate
enzymes decrease the free energy of the transition state - more molecules will have the necessary for the reaction to occur and products will be made at a faster rate.

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24
Q

what is the activation energy?

A

the minimum energy required for a reaction to proceed. substrate must overcome the activation energy before it is converted into a product.

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25
Q

what is the michaelis-menten equation?

A

Vo = Vmax x [s] / Km + [s]
Vmax - maximum velocity
[s] - substrate concentration
Km - the substrate concentration when half of the active sites are filled (1/2Vmax)

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26
Q

what is the relationship between Km and affinity?

A

high Km = low affinity - more substrate needed for half of the active sites to be filled
low Km = high affinity - less substrate needed for half of the active sites to be filled

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27
Q

what is the axis points on a lineweaver- burke plot?

A

Vmax = 1/y-intercept
Km = -1/x-intercept

28
Q

what is the relationship between inhibitors and Km and Vmax?

A

non-competitive inhibitor: Km is unaffected, Vmax is reduced
competitive inhibitor: Km is increased, Vmax is unaffected.

29
Q

what are isoenzymes?

A

enzymes which differ in amino acid sequence but catalyse the same chemical reaction
display different kinetic parameters/ different regulatory properties
allows fine tuning of metabolism to meet the particular needs of a given tissue

30
Q

what is the example of an isoenzyme?

A

creatine kinase (CK)
CK-BB - the brain
CK-MB - cardiac tissue
CK-MM - skeletal tissue

31
Q

what factors affect enzyme activity?

A

temperature
pH
competitive inhibitors
non-competitive inhibitors

32
Q

what is denaturation?

A

the process in which a protein loses its native shape due to a disruption of weak chemical bonds/interactions caused by an external stress or compound rendering the protein biologically inactive.
denaturation can be reversible as the primary protein structure is still intact - renaturation

33
Q

what happens during pH denaturation?

A

a change in pH will alter the acidic and basic groups on amino acid side chains in a proteins active site by altering the equilibrium point of ionisation rendering the protein inactive but maintaining its 3D arrangement

34
Q

what happens during temperature denaturation?

A

enzymes have an optimum temperature of 37-40ºC. an increase in temperature above the optimum will provide too much kinetic energy which causes the atoms to vibrate making them thermally unstable, this increase in energy overcomes the hydrogen bonds holding the enzymes active site together changing its shape therefore rendering the protein non-functional.

35
Q

what are inhibitors?

A

decrease enzyme activity
competitive
non-competitive

36
Q

what is a competitive inhibitor?

A

bind to the enzyme at its active site, competing with the substrate
initial rate of reaction is affected by the presence of the inhibitor. Maximum rate of reaction can be achieved as the inhibitor can be out-competed by very high substrate concentrations.

37
Q

what is a non-competitive inhibitor?

A

bind to the enzyme at an allosteric site inducing a conformational change to the enzymes active site so the substrate can no longer bind
all enzyme molecules with bound inhibitor do not convert substrate to product
maximum reaction rate is never achieved
cannot be reversed by increasing substrate concentration

38
Q

what factors affect rate of reaction?

A

temperature
pH
substrate concentration

39
Q

what is the affect of temperature on rate of reaction?

A

as the temperature increases the rate of reaction increases until the maximum rate of reaction is achieved at the optimum temperature
as the temperature increases beyond the optimum, bonds that stabilise the tertiary structure are broken as the increase in kinetic energy causes the molecules to vibrate so the enzyme loses its 3D shape and the active site is altered.
substrate can no longer bind to the enzyme as it has been denatured

40
Q

what is the affect of pH on rate of reaction?

A

each enzyme has its own optimum pH where the rate of reaction is maximum
changes in pH can affect the ionic and hydrogen bonds responsible for the specific tertiary shape of enzymes, extremes of pH break these bonds and denature the enzyme

41
Q

what is the affect of low substrate concentration on rate of reaction?

A

low product concentration per unit time

42
Q

what is the affect of increasing substrate concentration on rate of reaction?

A

more product formation, increased reaction rate
a further increase leads to maximum product formation and maximum rate of reaction

43
Q

what is the affect of excess substrate concentration on rate of reaction?

A

no further increase in product formation. maximum rate of reaction is maintained
enzyme concentration is the limiting factor

44
Q

what are complex enzymes?

A

require cofactors for activity
apoenzyme + cofactor > holoenzyme
apoenzyme - inactive protein
cofactor - non-protein
holoenzyme - active

45
Q

what is a simple enzyme?

A

only protein

46
Q

what is a cofactor?

A

inorganic ions that are tightly bound to the enzyme and are essential for its activity.
e.g. Zn2+, Fe2+, Mg2+

47
Q

what is a coenzyme?

A

organic helper molecules that bind directly to the enzymes surface creating a binding site for the substrate. e.g. CoA, NAD+.
loosely bound

48
Q

what is a prosthetic group?

A

a specific type of coenzyme
tightly bound - covalently bonded
e.g. haem group

49
Q

what are the modes of enzyme regulation?

A

allosteric regulation
end-product feedback
covalent modification
gene induction
mRNA degradation
proteolytic activation

50
Q

what is allosteric regulation?

A

modulator binds to an enzymes allosteric site transmitting a conformational change to the enzymes active site so the affinity for the substrate is altered

51
Q

what are activators/inhibitors?

A

activators - increase enzyme activity
inhibitors - decrease enzyme activity

52
Q

what are allosteric proteins?

A

contain distinct regulatory sites and multiple function sites
show the porperty of cooperativity

53
Q

what is cooperativity?

A

activity at one functional site alters the activity at other functional sites.

54
Q

what is end-product feedback?

A

a form of allosteric regulation using non-competitive inhibition

55
Q

what is the process of end-product feedback?

A

the end-product in a stepwise enzymatic reaction binds to an earlier enzyme by acting as a non-competitive inhibitor preventing a substrate from binding by inducing a conformational change to the enzymes active sire rendering the enzyme biologically inactive and therefore inhibiting product formation halting the reaction pathway.

56
Q

what is the advantage of end-product feedback?

A

this avoids unnecessary accumulation of end product and prevents wasteful conversions

57
Q

what is covalent modification?

A

when covalent bonds are made or broken in an enzyme which causes a conformational change to either activate or inactivate the enzymes, changing the concentration of active enzyme and therefore the reaction rate.

58
Q

what are methods of covalent modification?

A

phosphorylation/dephosphorylation
histone modification

59
Q

what is phosphorylation?

A

the addition of a phosphate (PO4) group to a protein molecule through a condensation reaction using kinase enzymes
addition of a phosphoryl group results in the addition of two negative charges to a modified protein, meaning that new electrostatic interactions can be formed resulting in altered substrate binding and catalytic activity
the reverse reaction is dephosphorylation - removal of a phosphate group by phosphatase enzymes

60
Q

what are examples of phosphorylation?

A

cyclin-dependant kinases
G-protein/ protein kinase A

61
Q

what is histone modification?

A

conversion from transcriptionally active euchromatin to inactive heterochromatin is controlled by post-translational modification - acetylation and methylation - of the histone packaging proteins, this alters the density of chromatin to allow or deny access for RNA polymerase.

62
Q

what happens in the lac operon when there is no lactose?

A

when lactose is absent the lac operon is switched off.
the regulator gene produces the repressor protein which binds to the operator, so RNA polymerase cannot bind to the promoter and structural genes are not transcribed so there is no translation of structural proteins therefore there are no enzymes for lactose breakdown.

63
Q

what happens in the lac operon when there is lactose?

A

when lactose is present the lac operon is switched on.
the regulator gene produces the repressor protein and it binds to lactose which causes a conformational change in the repressor protein so it cannot bind to the operator, so RNA polymerase can bind to the promoter and structural genes are now transcribed so there is translation of structural proteins therefore there are enzymes available for the breakdown of lactose.

64
Q

what is the difference between allosteric regulation and gene induction?

A

allosteric regulation is faster as effectors are in close proximity to enzymes so they can bind and regulate activity
gene induction/modification relies on hormones to regulate the rate of enzyme synthesis

65
Q

what is mRNA degradation?

A

mRNA molecules have lifetimes between 3 and 8 minutes
mRNA is protected from degradation in the cytoplasm by a 5’cap and a 3’ poly A tail
during the process of degradation the 3’ poly A tail is gradually shortened by exonucleases

66
Q

what is proteolytic activation (proteolytic cleavage)?

A

the enzymatic hydrolysis of one or more peptide bonds

67
Q

what are zymogens?

A

inactive form of the enzyme
activated by proteolytic cleavage

human metabolism - summary notes (3 decks)

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