Metabolism Flashcards
What happens in a biological chemical reaction?
For chemical reactions in biological systems (facilitated by enzymes), we call reactant “substrate”: Substrate → Product
What is metabolism?
The sum of all chemical reactions performed by a
cell or organism
What happens to individual reactions during metabolism?
» 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
What are the two types of Metabolic pathways?
Anabolic (biosynthetic) and Catabolic (degradative)
What is an anabolic metabolic pathway?
(biosynthetic)
» Synthesis of more complex compounds and molecules from simpler ones
» eg, sugars from CO2 during photosynthesis, or proteins from amino acids
What is a Catabolic metabolic pathway?
(degradative)
» Breakdown of complex molecules and compounds into simpler ones
» eg, amino acids from proteins, or oxidation of sugars to CO2 during respiration
What is Gibbs free energy (G)
- Energy stored in a system
» Measured in kcal/mol (or kJ/mol) - More complex systems have more G
What does ΔG mean?
Change in system energy
What is the ΔG for Catabolic reactions?
Catabolic reactions » Release energy » “Exergonic” » “Spontaneous” » Gproduct < Gsubstrate, so ΔG<0
What is the ΔG for anabolic reactions?
Anabolic reactions » Require energy » “Endergonic” » “Non-spontaneous” » Gproduct > Gsubstrate, so ΔG>0
What are the three kinds of work a cell performs?
» 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
How is the energy paid for during the different kinds of work a cell does?
Harvesting the energy stored in ATP
What is Adenosine Triphosphate and what is it composed of?
The currency of cells also known as ATP and it is composed of:
» Nucleotide base adenine
» Ribose sugar
» 3 linked phosphate groups
What releases energy in the ATP?
- O-P bonds unstable, and release energy
(exergonic) when broken down
» ATP + H2O → ADP + Pi
» ΔG = -7.3 kcal/mol
Draw the ATP cycle
Do this in your work book, refer to the back for the answer.
What happens in the ATP cycle?
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.
Where does all energy come from?
The sun. Energy flows into an ecosystem as sunlight and ultimately leaves as heat, while the chemical elements essential to life are recycled.
What are enzymes?
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
What do enzymes do?
- 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)
What is an activation energy?
Difference b/w energy level of substrate and transition
state
What is the transition state of a chem reaction?
Transition state is highest energy state
What is the order of a chemical reaction?
Substrate → transition state → product(s)
What is the difference between a catalysed reaction and an uncatalised reaction?
Catalysed has a lower activation evergy for the transition state because an ezyme is being used to speed up the reaction.
Why is it important to living systems that chemical reactions should have activation energies?
Other wise everything would happen at once and we would spontaneously combust because too much energy is being used at the same time.
How do you pay activation energy?
- 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
How do enzymes work?
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
What happens to the enzymes shape after the reaction?
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
Can any enzyme react with any substrates?
Active site is substrate specific
» There is only one correct substrate
» Think “enzyme = lock, substrate = key”
» Pharmaceutical drugs work by “copying the key”
Some enzymes require additional help to perform the biochemical reaction, where do they get it from?
» 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 …
Enzymes require optimum environments, what are some things that affect this environment?
pH, temperature, etc…
Chemical chaos would result if all of a cell’s metabolic pathways were operating all the time, how do cells stop this from happening?
- 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”
What is an inhibitor?
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.
