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Biochem/ metab > lecture 7 > Flashcards

lecture 7 Flashcards

1
Q

what is an enzymes activity site?

A

a location on the enzyme where a substrate can bind

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2
Q

What does an activity site do?

A

allows enzymes to reach higher catalytic rates

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3
Q

what does enzyme kinetics measure?

A

the rate that an enzyme can catalyze a rxn

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4
Q

what are the kinetics of the catalysis

A
  1. accelerates the rate
  2. causes chemistry to occur
  3. lowers the free energy of the transition state
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5
Q

is there a difference in between enzyme catalysis and non-enzyme catalysis

A

NO it is the same mechanisms

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6
Q

what are the 4 factors that contribute to enzyme catalysis?

A
  1. proximity and strain
  2. electrostatic
  3. acid-base catalysis
  4. covalent catalysis
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7
Q

describe proximity and strain

A

substrates must come in close proximity to the amino acid residues in the active site and have the correct orientation

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8
Q

what does proximity and strain encourage?

A

the transition state

*done by holding substrates and the prosthetic group in place at the activity site.

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9
Q

what is a prosthetic group?

A

cofactors

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10
Q

describe electrostatic interactions

A

interactions that occur between the 2 molecules
-hydrogen bonds
van der waal
- hydrophobic

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11
Q

what bonds can form at close proximity?

A

hydrogen bonds

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12
Q

how is the strength of the electrostatic interactions determined?

A

opposite of the concentration of water

inverse of the hydration spheres

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13
Q

what is excluded from the activity site and why?

A

water is excluded because it increases the distance from the core of the molecule and prevents it from bonding with the enzyme

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14
Q

what does the interaction between the substrate and amino acid encourage?

A

the stabilization of the transition state

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15
Q

what are the acid/base catalysis amino acids?

A 
Histidine 
aspartate 
tyrosine 
cysteine 
lysine 
arginine
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16
Q

what is unique about Histidine?

A

that at physiological pH is able to act like an acid or a base

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17
Q

how to enzymes use functional groups?

A

to transfer protons efficiently

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18
Q

describe acid/base catalysis

A

when the R group of an amino acid is able to act as

  1. acid–> proton donor
  2. base–> proton acceptor
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19
Q

what is the difference between direct acid-base and indirect acid-base catalysis

A

direct: is able to remove protons directly from the substrate
indirect: the enzyme bound molecule accepts electrons from a molecule that is NOT the substrate and then donates the to an electron acceptor before the molecule can act like a nucleophile

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20
Q

what is covalent catalysis?

A

when a side chain or bound cofactor act as a nucleophile and form an UNSTABLE covalent bond to the substrate

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21
Q

what results from a covalent catalysis?

A

an intermediate is formed (enzyme + substrate) and then H20 as a result
HYDROLYSIS

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22
Q

what are example of covalent catalysis?

A

serine
cystine
protases
topoisomerases

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23
Q

what are Cofactors made up of?

A

proteins/ amino acids

24
Q

what are cofactors?

A

they are the side chains found in the active site (enzymes use but is NOT apart of the enzymes)

25
Q

what are cofactors primarily responsible for?

A

catalyzing proton transfers and nucleophilic substitutions

26
Q

are protein cofactors only used?

A

NO

27
Q

what are the other cofactors

A

no protein cofactors

28
Q

is it required by every enzymatic rxn to have covalently bond cofactors?

A

NO, some require non-covalently bonds

29
Q

what are the types of cofactors?

A

Non-organic(metals)

organic (coenzymes)

30
Q

what are the non-organic cofactors?

A
  1. alkali and alkali earth metals

2. transition metals

31
Q

what is the role of alkali earth metals?

A

structural role

*loosely bound

32
Q

what are examples of alkali earth metals?

A

Na, K, Mg, Ca (group 1 &2)

33
Q

what is the role of transition metals?

A

major role in metabolic catalysis

34
Q

what are example of transition metals?

A

Fe, Cu, Mn (found in the middle of the periodic table

35
Q

what is another term of organic cofactors?

A

Co-enzymes

36
Q

what are examples of coenzymes?

A

vitamines

water-soluble and Lipid soluble

37
Q

what environment do enzymes work best in

A

optimum conditions

38
Q

what are consequences that happen when an enzyme is not in its preferred environment?

A

disruptions to the protein structure which can change the enzyme activity

39
Q

what are the 2 factors that enzymes are most sensitive to?

A

-temperature and pH

40
Q

what happens to enzymes if it is too cold or too hot

A

freeze or denature the enzyme

41
Q

how can the change in pH influence the enyzm3

A
  • charges on the ionizable side chain

- ionizable groups on substrates

42
Q

what are important factors of enzyme regulation?

A
  • rxns take place in a sequence
  • breakdown and biosynthesis of molecules is done in s way that conserves energy
  • metabolism responds to environment
43
Q

what are the 4 ways that enzymes are regulated

A
  1. genetic
  2. covalent
  3. allosteric
  4. compartmentalization
44
Q

what are the 2 ways that enzymes are controlled through genetic control?

A
  1. enzyme induction

2. enzyme repression

45
Q

explain each enzyme induction and repression

A

induction- responds to the changing of metabolism (turns genes on or off)

repression- uses feedback inhibition an end product enzyme signals for an enzyme at the beginning of the pathway to be repressed this turns off genes because the enzymes are not present to activate it

46
Q

explain covalent modification

A

reversible interconversion between enzyme’s active and inactive state

47
Q

what are example of covalent modification methods?

A
  1. phosphorylation
  2. other: methylation, acetylation, ubitintion, sumoylation
  3. zymogens
48
Q

explain zymogens

A

a molecule that is produced and stored in the inactive form and must go through covalent modification to become activated this includes cleavage of peptide bonds

Pepsinogen–> pepsin

49
Q

explain allosteric regulation with respect to structure of the enzyme

A

conformational change in one subunit or protein unit that results in the conformational change in all of the other subunits of the molecule

50
Q

explain allosteric regulation and how the structural changes impact the activity of the enzyme.

A

the structure of the enzyme can turn of the active site of the protein/enzyme or turn off based on if a substrate in bond or not (if so all are not if not then all are off)

51
Q

describe compartmentalization.

A

putting enzymes into compartments to where they can best do their job

52
Q

what are examples of compartmentalization in the cell

A
  1. atp synthesis –> mitochondria

2. protein synthesis–> cytosol

53
Q

what are the 4 benefits of compartmentalization?

A
  1. better control of processes
  2. prevents wasting of resources
  3. microenvironments for enzymes and substrates
  4. separate potential toxins
54
Q

what determines where enzymes are located?

A

needs from the cell

enzymes all go to compartments where they are needed

55
Q

are all compartments they same?

A

no, some have unique properties/ requirements

Ex: lysosomes low pH

Biochem/ metab (4 decks)

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