lecture 7: enzymes and metabolism Flashcards

You may prefer our related Brainscape-certified flashcards:
1
Q

What is metabolism?

A

Thousands of different chemical reactions linked through a NETWORK of metabolic pathways
not isolated pathways, they are all linked
ex: carbohydrate metabolism, amino acid metabolism, lipid metabolism, energy metabolism, etc

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What’s a metabolic pathway?

A

Pathway composed of steps where each step is CATALYZED by a specific ENZYME
- Each step has its own enzyme
- Starting molecule A —> Reaction 1 + Enzyme 1 —> B —> Reaction 2 + Enzyme 2 —> C —> Reaction 3 + Enzyme 3 —> Product D

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

2 types of metabolic pathways

A
  1. Anabolic pathways: builds larger molecules from smaller components
    - Synthesis, building
    - Require inputs of energy —> so, involve ENDERGONIC REACTIONS —> uphill
  2. Catabolic pathways: breakdown of molecules & RELEASE of energy
    - Involve EXERGONIC reactions —> downhill
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Primary vs Secondary metabolism

A
  • Primary = ESSENTIAL for cell SURVIVAL + REPRODUCTION in organisms
    ex: producing ATP
  • Secondary = synthesis of secondary metabolites that are NOT essential for cell survival and reproduction but can HELP an organism survive & reproduction
  • for competition, to increase fitness for evolution, adaptations (ex: colours, flavours in plants and fruits)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

6 types of reactions

A
  1. Oxidation-Reduction
    X + Y —> X- + Y+
  2. Group transfer
    X + YZ —> XZ + Y
  3. Hydrolysis: add H2O to split bond
    HY + H2O —> H-OH + H-Y
  4. Cleavage: split bond without H2O
    XY —> X + Y
  5. Isomerization: transfer into an isomer
    XYZ —> XZY
  6. Condensation/dehydration: remove water to form bond
    X-OH + H-Y —> XY + H2O
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

2 requirements for reactions to happen

A
  1. Right orientation: Need reactants to COLLIDE in a PRECISE ORIENTATION to allow them to interact and create new bonds
  2. Enough energy: Need reactants to have enough KINETIC ENERGY to reach the TRANSITION STARE —> more energy than activation energy
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the transition state?

A
  • Intermediate condition: between braking old bonds and forming new ones
  • Stare where repulsive forces need to be overcame and where there are molecules with a combination of old and new bonds
  • Activation energy (Ea) = amount of energy required for reactants to reach transition state
  • the more unstable the transition state = the bigger Ea = the slower it is to reach Ea = the slower the exergonic reaction proceeds
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

2 characteristics of chemical reactions

A
  1. Direction of reaction (forward or inverse):
    a) Change in potential energy
    b) Change in disorder (entropy)
    —> both determine change in free energy (∆G)
    - Influenced by temperature (not too relevant in bio bc stable temp.) and concentration of reactions and products
  2. Rate
    Governed by:
    a) Temperature
    b) Concentrations of reactants
    c) CATALYSIS —> enzymes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Effect of temperature on rate of chemical reaction?

A

Higher temperature = Higher kinetic energy = More molecules have the change to have enough energy bigger than Ea

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Effect of concentration on rate of chemical reaction?

A

Higher concentration of reactants = More collisions = More chance to collide int he right orientation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are catalysts and what do they do to the rate of chemical reactions?

A
  • Substance that provide an alternate reaction route (mechanism) with a LOWER activation energy —> thus INCREASES RATE of reaction as MORE reactants will have the kinetic energy to reach the transition state
  • Some reactants will still take the original route with a higher Ea
  • Transition state = stabilized —> so required less activation energy bc of the catalyst
  • Speeds up an already spontaneous reaction as even some reactions are spont. they happen too slowly —> need catalyst to speed it up
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

3 characteristics of catalysts important

A
  1. Only required in small amounts
  2. Are NOT consumed in the reaction and can be RECYCLED and used again and again
  3. Do NOT influence the change in free energy & DIRECTION of chemical reaction —> only influence the rate/speed of the chemical reaction
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What are biological catalysts?

A
  • Catalysis = vital function of proteins and some RNAs
  • Protein catalysts = enzymes —> typically increase rate of a reaction 10^8 to 10^13 fold
  • RNA catalysts = ribozymes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Why is catalysis important biologically?

A

Most biological chemical reactions occur at meaningful rates only in the presence of enzymes
- By providing an alternate reaction mechanism with lower activation energy —> more reactants have enough energy—> increase rate of reaction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

6 enzyme groups

A
  • Based on the types of reactions that they catalyze
    1. Oxidoreductases: catalyze oxidation-reduction reactions
    2. Transferases: catalyze transfer of C, N, or P containing groups
    3. Hydrolases: catalyze cleavage of bonds by addition of water
    4. Lyases: catalyze cleavage of C-C, C-O, C-S and certain C-N bonds
    5. Isomerases: catalyze isomerization reactions
    6. Ligases: catalyze formation of bonds in dehydration/condensation reactions
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Specificity of enzymes? Examples?

A

All enzymes have some degree of specificity, range of specificity
- Can be specific for one reaction or a group of similar reactions

Ex:
- Hexokinase: can recognize glucose as reactants, but ALSO other hexoses —> more flexible bc NOT specific for one reaction, but for one TYPE of reaction
- Glucokinase: only recognize glucose as a substrate —> more specific

17
Q

What is the enzyme’s active site?

A
  • Made up of the side chains of amino acids that form a COMPLEMENTARY pocket —> complements substrates’ shape, charge, hydrophilic/phobic characteristics
  • Responsible for specificity and catalysis

—> Substrates bind to enzyme’s active site & forms an enzyme-substrate complex

18
Q

What are kinases?

A

Enzymes that catalyze transfer reactions like phosphorylation

19
Q

What are substrates?

A

Reactants in an enzymatic reaction

20
Q

What is the induced fit model?

A
  • “Lock and key” model
  • When substrates bind to enzymes, enzymes changes shape slightly —> results in increase of the strength of binding & help in catalysis
21
Q

How do enzymes lower the activation energy required to complete the reaction?

A

By:
1. Forming an enzyme-substrate complex: brings substrates CLOSE together in a PRECISE ORIENTATION —> catch them and help them to be in the right orientation
2. Facilitating the formation of the transition state —> by creating alternate route that requires less energy

22
Q

3 steps of enzyme catalysis

A
  1. Initiation: formation of enzyme-substrate complex —> reactants bind to active site in a specific orientation active site has HIGH affinity for reactants
  2. Transition state facilitation: INTERACTIONS between enzyme and substrate LOWER Ea required
  3. Termination: products have LOWER affinity for active site —> then products are released
    - Enzyme is UNCHANGED after the reaction
23
Q

3 characteristics of the transition state facilitation

A
  1. Straining substrate’s bonds by induced fit
  2. Functional groups on side chains can REACT (covalent bonds) with substrate and change substrate’s REACTIVITY
  3. Functional groups on side chains can INTERACT (non-covalent bond) with transition state and STABILIZE it
24
Q

What is enzyme activity?

A

It’s the RATE of an enzyme-catalyzed reaction

25
Q

Enzyme activity/rate of enzyme-catalyzed reaction depends on… (7)

A
  1. Cofactors
  2. Enzyme concentration
  3. Substrate concentration
  4. Affinity (to the substrate/how well they interact)
  5. Temperature
  6. pH
  7. Regulation
26
Q

How can cofactors affect enzyme activity?

A

Some enzymes require cofactors to function normally:
- metal ions: Fe2+, Mg2+, Zn2+
- cosubstrates: organic molecules
- prosthetic groups: tightly bound organic molecules

  • Cofactors = part of active site —> role in STABILIZING the TRANSITION STATE during the reaction —> so lower Ea —> so faster rate
27
Q

How does enzyme concentration affect enzyme activity?

A

The higher the enzyme concentration, the higher the reaction rate
- Increases proportionately, linear graph
- But there’s a limit if there’s too much enzyme and not enough substrate

28
Q

How does substrate concentration affect enzyme activity?

A

The higher the substrate concentration, the higher the reaction rate
- Not linear, hyperbolic graph
- At high substrate concentration = reaction rate PLATEAUS
- Enzyme’s capacity is saturated bc all active sites are taken, so even if increase substrate concentration, enzymes cannot keep up —> it’s already at the maximum reaction speed

29
Q

What is enzyme saturation?

A

When all active site are being used and a maximum reaction rate is reached
- All enzyme-catalyzed reactions show saturation at high substrate concentration
- Reaction rate cannot pass this maximum no matter how large the concentration of substrates gets

30
Q

What would an uncatalyzed reaction look like?

A
  • The higher the substrate concentration, the faster the rate
  • But takes more substrate to get the same rate of a catalyzed reaction —> so all graph lower
  • Linear relationship
31
Q

What does a protein’s affinity for a substance measure?

A

Measure of how STRONGLY it BINDS to the substance
- Proteins are specific in their activities and have the ability to bind specific substances

32
Q

What is Michaelis constant (Km) ?

A

Measure enzyme’s affinity for its substrate
- Km = substrate concentration where V = Vmax/2
- So, the less substrate you need to reach Vmax/2, the higher the affinity
- So, lower Km = higher affinity

33
Q

Why do physical conditions affect enzyme’s function?

A

Enzyme = protein: if changes in structure, there will be changes in function
- Sensitive to changes in physical environment
- All enzymes have optimal conditions: optimum temperature and optimum pH

34
Q

How does temperature affect enzymes’ function?

A

Diff. enzymes = diff. adaptations for diff. environment= diff. optimum temperature
- Higher than optimum T = enzyme denatures and loses function = enzyme has lower activity
- Lower than optimum T = lower kinetic energy = slower = enzyme has lower activity

35
Q

How does pH affect enzyme’s function?

A

Diff. enzymes = Diff. adaptations = Diff. optimum pH
- Higher than optimum pH: enzyme denatures = loses functions = lower activity
- Lower than optimum pH: enzyme denatures = loses functions = lower activity