Metabolism

Question 1

What happens in a biological chemical reaction?

Answer 1

For chemical reactions in biological systems (facilitated by enzymes), we call reactant “substrate”: Substrate → Product

Question 2

What is metabolism?

Answer 2

The sum of all chemical reactions performed by a

cell or organism

Question 3

What happens to individual reactions during metabolism?

Answer 3

» catalysed by specific enzymes
» connected into “metabolic pathways”, where the products of one pathway become the substrates for others
• Pathways can be linear, reversible, circular, branched

Question 4

What are the two types of Metabolic pathways?

Answer 4

Anabolic (biosynthetic) and Catabolic (degradative)

Question 5

What is an anabolic metabolic pathway?

Answer 5

(biosynthetic)
» Synthesis of more complex compounds and molecules from simpler ones
» eg, sugars from CO2 during photosynthesis, or proteins from amino acids

Question 6

What is a Catabolic metabolic pathway?

Answer 6

(degradative)
» Breakdown of complex molecules and compounds into simpler ones
» eg, amino acids from proteins, or oxidation of sugars to CO2 during respiration

Question 7

What is Gibbs free energy (G)

Answer 7

• Energy stored in a system
  » Measured in kcal/mol (or kJ/mol)
• More complex systems have more G

Question 8

What does ΔG mean?

Answer 8

Change in system energy

Question 9

What is the ΔG for Catabolic reactions?

Answer 9

Catabolic reactions
» Release energy
» “Exergonic”
» “Spontaneous”
» Gproduct < Gsubstrate, so ΔG<0

Question 10

What is the ΔG for anabolic reactions?

Answer 10

Anabolic reactions
» Require energy
» “Endergonic”
» “Non-spontaneous”
» Gproduct > Gsubstrate, so ΔG>0

Question 11

What are the three kinds of work a cell performs?

Answer 11

» Chemical: endergonic reactions
» Transport: pumping across membranes against the concentration gradient
» Mechanical: contraction of muscle cells, movement of chromosomes during cell division, beating of cilia

Question 12

How is the energy paid for during the different kinds of work a cell does?

Answer 12

Harvesting the energy stored in ATP

Question 13

What is Adenosine Triphosphate and what is it composed of?

Answer 13

The currency of cells also known as ATP and it is composed of:
» Nucleotide base adenine
» Ribose sugar
» 3 linked phosphate groups

Question 14

What releases energy in the ATP?

Answer 14

• O-P bonds unstable, and release energy
  (exergonic) when broken down
  » ATP + H2O → ADP + Pi
  » ΔG = -7.3 kcal/mol

Question 15

Draw the ATP cycle

Answer 15

Do this in your work book, refer to the back for the answer.

Question 16

What happens in the ATP cycle?

Answer 16

Energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. Chemical potential energy stored in ATP drives most cellular work.

Question 17

Where does all energy come from?

Answer 17

The sun. Energy flows into an ecosystem as sunlight and ultimately leaves as heat, while the chemical elements essential to life are recycled.

Question 18

What are enzymes?

Answer 18

Most enzymes are proteins
» Exception: some RNA-based (eg, ribozyme*)
- Enzymes speed up chemical reactions by lowering energy barriers, making life possible.
» “Catalyst” = a substance that increases the rate of a reaction without being consumed by the reaction

Question 19

What do enzymes do?

Answer 19

• Facilitate transformation of initial substance (substrate) into different molecules (products)
• Enzyme names (usually ending in –ase) indicate their function:
  » Lipase = breaks down lipids
  » Protease = breaks down proteins
  » Synthase = enzymes that build molecules
  » Isomerase = enzymes that rearranges a molecule into its isomer (ie, a different form)

Question 20

What is an activation energy?

Answer 20

Difference b/w energy level of substrate and transition

state

Question 21

What is the transition state of a chem reaction?

Answer 21

Transition state is highest energy state

Question 22

What is the order of a chemical reaction?

Answer 22

Substrate → transition state → product(s)

Question 23

What is the difference between a catalysed reaction and an uncatalised reaction?

Answer 23

Catalysed has a lower activation evergy for the transition state because an ezyme is being used to speed up the reaction.

Question 24

Why is it important to living systems that chemical reactions should have activation energies?

Answer 24

Other wise everything would happen at once and we would spontaneously combust because too much energy is being used at the same time.

Question 25

How do you pay activation energy?

Answer 25

- Abiotic
» Heat, pH gradient, sunlight etc ...
- In cells, combination of
» Lowering the energy costs (with enzymes)
• Bringing substrates together
• Putting torque on the substrate
• Providing proper chemical micro-environment
• Adding or removing functional group
» ATP, the cellular energy currency

Question 26

How do enzymes work?

Answer 26

Step 1: Substrate enters active site; enzyme changes shape so that its active site enfolds the substrates (induced fit)
Step 2: Substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds
Step 3: Substrates are converted to products
Step 4: products are released
Step 5: Active site is available to new substrates

Question 27

What happens to the enzymes shape after the reaction?

Answer 27

Enzymatic reaction does not permanently change the enzyme’s chemistry or structure
» Often changes its shape (“conformation”) during the reaction, but reverts back to original conformation once reaction complete

Question 28

Can any enzyme react with any substrates?

Answer 28

Active site is substrate specific
» There is only one correct substrate
» Think “enzyme = lock, substrate = key”
» Pharmaceutical drugs work by “copying the key”

Question 29

Some enzymes require additional help to perform the biochemical reaction, where do they get it from?

Answer 29

» Co-factor = inorganic molecule that assists chemical transformation of substrate → products
• Metal ions, such as iron (Fe2+ and Fe3+), magnesium (Mg2+) and zinc (Zn2+), which help with electron transfer
» Co-enzyme = small organic molecule that assists in chemical transformation
• Vitamin C, ATP, NAD+, NADP+, coenzyme A, etc …

Question 30

Enzymes require optimum environments, what are some things that affect this environment?

Answer 30

pH, temperature, etc…

Question 31

Chemical chaos would result if all of a cell’s metabolic pathways were operating all the time, how do cells stop this from happening?

Answer 31

• Cells regulate enzymes by turning them on or off
  » Natural regulation (methylation, phosphorylation, proteolytic cleavage) is usually reversible
  » Some poisons (eg, nerve gas) or drugs (eg, antibiotics) can cause irreversible enzyme inhibition
• Often the products will act as inhibitor
  » “Feedback inhibition”

Question 32

What is an inhibitor?

Answer 32

Substance which slows down or prevents a particular chemical reaction or other process or which reduces the activity of a particular reactant, catalyst, or enzyme.