Topic 5

Question 1

Nitrogen fixation

Answer 1

N2 + 3H2 > NH3

Question 2

At what environments do industrial processes do N fix?

Answer 2

~200 atmospheres and 400 degrees Celcius

Question 3

At what environments do bacteria fix N?1

Answer 3

Atmospheric pressure, ambient temperature

Question 4

2 ways a reaction can be accelerated?

Answer 4

Adding heat

Adding catalyst

Question 5

3 ways enzymes are proteins?

Answer 5

• primary, secondary, tertiary, quaternary structure
• typically globular
• structure determined by same forces

Question 6

3 ways enzymes are catalysts?

Answer 6

• accelerate reaction rates
• regenerate at the end of reaction
• highly specific (no side reactions)

Question 7

Enzyme Nomencclature

Answer 7

end in -ase

substrate (or product) chemical rxn

Question 8

A reaction will only proceed if…

Answer 8

free E of products is less than free E of reactants

Question 9

When G is negative

Answer 9

Reaction is exergonic, thermodynamically favourable, spontaneous

Question 10

When G is positive

Answer 10

Reaction is endergonic, thermodynamically unfavourable, and non-spontaneous

Question 11

how is the speed of a biochemical reaction determined?

Answer 11

activation energy barrier

Question 12

At what point in the reaction is there highest free energy?

Answer 12

Transition state

Question 13

T/F do enzymes affect G of reaction

Answer 13

FALSE, enzymes do not affect

Question 14

How do enzymes reduce free energy? (4)

Answer 14

1. remove substrates from aqueous solutions
2. proximity and orientation
3. taking part in reaction mechanism
4. stabilizing transitions state

Question 15

Active sites (4)

Answer 15

• where catalysis occurs (small portion of protein)
• key amino acids located in active site (binding and catalysis)
• determines affinity, speciality and rate
• complementary to substrate/transition state (shape, hydrophobic interactions, H bonds, ion pairs)

Question 16

Where is the active site in a lysosome?

Answer 16

3D cleft/crevice

Question 17

Lock and Key model

Answer 17

active site matches shape of substrate contributing to affinity and specificity

Question 18

Desolvation

Answer 18

exclusion of water,

Question 19

3 advantages of desolvation

Answer 19

1. removal of water shell accelerates reactions
2. enhances polar interactions
3. prevents side reactions

Question 20

Induced Fit Model

Answer 20

enzymes change shape when substrate binds
closes off active site
brings catalytic groups together

Question 21

orientation

Answer 21

chemical reactions only occur if substrates come together in right orientation

Question 22

proximity

Answer 22

active sites bind substrates close to each other

Question 23

3 types of catalysis

Answer 23

acid/base, covalent, metal ion

Question 24

how are catalysis reactions acheived

Answer 24

amino acids or cofactors

Question 25

Acid/Base catalysis

Answer 25

R groups of amino acids act as acids or bases depending on state of protonation

Question 26

Covalent catalysis

Answer 26

de-protonated R groups of amino acids act as nucleophiles

Question 27

Review classification of cofactors tree

Answer 27

and examples btw

Question 28

holoenzyme

Answer 28

prosthetic group and tertiary structure

Question 29

apoenzyme

Answer 29

tertiary structure without prosthetic group

Question 30

3 ways transition state is stabilized

Answer 30

• binding TS lowers G
• parts of protein interact with unstable transition state
• enzyme active sites

Question 31

the more tightly an enzyme binds to TS ….

Answer 31

the greater the catalytic activity of the enzyme

Question 32

TS analogs are ____ inhibitors

Answer 32

potent

Question 33

potent inhibitors

Answer 33

binds to enzyme with higher affinity compared to substrate

rational basis for drug design

Question 34

Km gets ___ as affinity ____

Answer 34

smaller, increases

Question 35

Mechanisms that affect intrinsic activity of enzyme

Answer 35

competitive inhibition, allostery, reversible covalent modification, ionic signals

Question 36

Allostery (allosteric enzymes)

Answer 36

modify metabolic processes with allosteric effectors because enzyme activity may be cooperative

Question 37

Reversible covalent modification

Answer 37

modify proteins in tertiary amino acid residue, increase or decrease activity of target

Question 38

mechanisms that change amount of enzyme available,

Answer 38

regulation of gene expression, changes in sub cellular localization (regulate access of enzyme and substrate)

Question 39

competitive inhibitors

Answer 39

bind reversibly
resemble substrate or TS but DO NOT react
physically block = less active sites, lower reaction rate, increase in Km

Question 40

how to overcome inhibition

Answer 40

increase substrate concentration (no change in Vmax)

Question 41

Competitive inhibitors decrease _____ affinity (increase Km)

Answer 41

decrease

Question 42

T state

Answer 42

low activity, allosteric inhibitor favours

Question 43

R state

Answer 43

high activity, allosteric activators favours

Question 44

most common type of reversible modification

Answer 44

phosphorylation

Question 45

Phosphorylation

Answer 45

increases size, polarity, and charge

Question 46

____ catalyze phosphoryaltion

Answer 46

protein kinase

Question 47

______ catalyze dephosphorylation by ____

Answer 47

protein phosphatase, hydrolysis

Question 48

which amino acids are usually phosphorylated (ones with OH)

Answer 48

ser, tyr, thr