Lecture 13 & 14 Cell metabolism and Bioenergetics Flashcards
What do living entities have to have?
- harness energy
- respire
- grow and develop
- reproduce (biogenesis)
- respond to stimuli
What do cells need to survive? (4 Point)
- Energy
- C-based molecular materials
- Information/instructions
- Catalysts (enzymes)
[1] Energy
How is the energy harnessed in photosynthesis?
Activation of electrons
- light hits leaf and absorbed by chloroplasts
- within chloroplasts there are two photosystems (the excitation of the electrons in these photosystems that allow energy to be harnessed and allows for bonds to be broken or made)
What is the currency of energy?
Electrons (e-)
Why are electrons important?
- negatively charged
- can easily associate with protons
How electrons associate with protons or hydride ions:
Proton: H+
Atomic Hydrogen: e- + H+
Hydride Ion (H-): e- + e- + H+
Electrons generally transfer energy accompanied by _____ . Examples?
Proton (H+)
- NAD+ + H- → NADH
- NADP+ + H- → NADPH
- FAD + H+ + H- → FADH2
Bond breaking is (catabolism/anabolism), and bond making is (catabolism/anabolism).
Bond breaking is catabolism, and bond making is anabolism.
How does energy flow?
Through oxidation (loss) and reduction (gain)
Energy (electron) passes from the _____ , which gets _____ ; to _____ (NAD+/NADP+/FAD), which get _____ .
Energy (electron) passes from the substrate (donor), which gets oxidised; to nucleotide cofactors (NAD+/NADP+/FAD), which get reduced
[1] C-Based Molecular Materials
4 Examples?
- lipids (hydrocarbons) (e.g. CnH2n+1O2)
- carbohydrates (CnH2nOn)
- amino-acids (+NH3– and –COO- termini)
- nucleotides (ribose/deoxyribose + N-base + PO42-)
What are amino acids composed of?
- amino group
- R group side chain (21) : interactions between side chains create the structure and particular function
- carboxyl group
- hygrogen
The fact that there is a a greater combination of how sugars can bind together means what?
greater structural diversity than amino acids/peptides and nucleic acids/DNA or RNA
[3] Catalysts (enzymes)
What is a catalyst? What is a biological catalyst?
Catalysts: Increases the rate of reaction, Lowers the activation energy
Biological catalyst: An enzyme
What is metabolism?
it is the making and breaking of bonds which require energy
The types of metbolism?
Catabolism = Break down (heat loss and creates energy)
Anabolism = Build up
What is a Calorie?
it is the amount of energy to raise the temperature of 1g of water by 1 degree at a pressure of 1 atomosphere
[4] Information / Instruction
What is the central dogma of molecualr biology?
DNA relication (DNA - DNA)
DNA transcription (DNA - RNA)
RNA translation (mRNA - peptide)
Reasons why cells need energy? (6 Points)
- Biosynthesis (formation of new molecules / structures)
- Active transport of solutes (against their concentration / electrochemical gradient)
- Active transport of ions (against the voltage gradient to maintain the membrane potential)
- Mechanical work (physical changes to cell shape e.g. muscle contraction / movement of cell structures e.g. cilia/flagella or the mitotic spindle)
- Heat (by-product of exergonic reactions; c.70% of metabolic energy is used to maintain body temperature)
- Light (bioluminescence) (Green fluorescent protien in Jelly Fish)
How can you define organisms?
Based on the source of energy and carbon required to drive living processes
What does the abbreviation ‘troph’ mean?
nourishment
What does the abbreviation ‘auto’ mean?
Self
What does the abbreviation ‘hetero’ mean?
an(other)
What is an Autotroph?
Organism that can capture energy from sunlight or chemicals and use it to produce its own food from inorganic compounds. Use inorganic carbon such CO2 as their source of carbon (e.g. biosynthesis).
What is a Heterotroph?
Organism that obtains energy from the foods it consumes. Ingest organic carbon molecules to generate energy and building blocks for biosynthesis (e.g. ATP synthesis).
What is a phototroph?
organisms which use energy from photons of light
What is a Photoautotrophs?
Photoautotrophs use light energy to synthesise organic molecules from (inorganic) CO2 = photosynthesis Energy absorbed by photoreceptors and transformed into chemical bond energy (e.g. green plants & photosynthetic bacteria)
What are Photoheterotrophs?
Photoheterotrophs use light energy plus organic substrates to synthesise organic molecules (some bacteria)
What is an example of Photautotrophic “Fuel” Synthesis?
Photosynthesis of glucose:
6 CO2 + 6 H2O + light energy → C6H12O6 + 6 O2
What is an example of photohereotrophs “Fuel” Synthesis and how does this differ from photoautotrophs?
uses light energy to synthesise organic Molecules.
But cannot use CO2 as their sole carbon source.
purple and green non-sulfur bacteria and heliobacteria
Use organic compounds from the environment to satisfy their carbon requirements: carbohydrates, fatty acids and alcohols
What is a Chemoautotroph?
organisms which use energy derived from chemical bonds
What are chemoautotrophs?
use chemical energy to synthesise organic molecules from CO2 (bacteria or archaea living in hostile environments)
Use ferrous iron hydrogen, hydrogen sulfide, elemental sulfur ammonia To generate the energy to synthesise organic molecules from CO2
What are chemoheterotrophs?
use chemical energy plus organic substrates (most animals e.g. Homo sapiens and some plants)
What is Chemoautotroph Fuel Synthesis?
12H2S + 6CO2 → C6H12O6 + 6H2O + 12S
e.g. Purple sulfur bacteria (Chromatiaceae bacteria) Hydrogen sulfide is oxidized to produce granules of elemental sulfur, which can be oxidized to form sulfuric acid.
(blood lakes in texas)
How do you futher subdivide nutritional groups?
Further subdivided on the type of reducing equivalent used to transfer energy
What are Lithotrophs?
Inorganic compounds are used as electron donor.
Litho = rock; troph = eating (Greek)
Lithotrophs generally thrive in inhospitable regions such as the deep ocean and the Earth’s crust
First organisms to have lived on this planet
Lithotrophs:
Fe2+ (ferrous iron) → ?
NH3 (ammonia) → ?
NO2 (nitrite) → ?
S2− (sulfide) → ?
Fe2+ (ferrous iron) → Fe3+ (ferric iron) + e-
NH3 (ammonia) → NO2 (nitrite) + e-
NO2 (nitrite) → NO3 (nitrate) + e-
S2− (sulfide) → S0 (sulfur) + e-
What are Organotrohps?
Organic compounds are used as electron donors
The freed energy is stored as potential energy in:
- ATP
- Carbohydrates
- Lipids
- Proteins
The energy is used for life processes as moving, growth and reproduction
What are examples of Chemoheterotrophic “Fuel” Oxidation?
Complete oxidation of glucose:
Glycolysis: produces ATP and NADH
Citric Acid Cycle: produces NADH and FADH2
Electron Transport Chain: produces ATP
What is the classification of organisms based on their metabolism/Primary Nutritional group?
Heterotrophs eat ____ and other ____.
Heterotrophs eat autotrophs and other heterotrophs
How does the energy transfer work between nutritional groups?
Summary:
Nutritional groups are defined based on what?
- Energy requirement
- Carbon requirement
- Reducing equivalent
What is Bioenergetics?
- The nature (and relevance) of bioenergetics (as relates to cell metabolism)
- Laws of thermodynamics, entropy (degree of disorder) and enthalpy (total heat)
- Fundamental differences between living versus abiotic systems
What Are Thermodynamics?
a branch of physics focused on the relationships between heat/temperature and energy/work (originally in abiotic systems)
What Are Bioenergetics?
a branch of biochemistry concerned with energy flow (applied thermodynamics) in living systems
What is a closed system?
energy remains within that system; can be neither added nor lost from “the system” to that system’s surroundings
What is a open system?
energy can be added to or lost from “the system” to that system’s surroundings (the universe)
What is the First Law Of Thermodynamics?
Law of conservation of energy
What is the Law of conservation of energy?
the total energy of a closed system remains constant – i.e. energy is conserved; it can not be created or destroyed, it can only change form
Potential energy can become kinetic energy and vice versa
What are the Biological Consequences Of The First Law Of Thermodynamics?
• In a “biological system” (cell/tissue/organ/organism):
Energy out = energy in – energy stored
Energy lost = energy in – energy stored
Heat lost = energy in – energy harnessed
If energy in > energy out, will store calories as ____ or ____.
If energy in > energy out, will store calories as glycogen or adipose tissue.
What is the second law of Thermodynamics?
the sum of the entropies of all participating bodies in a closed system must increase (or remain constant)
- Entropy commonly regarded as degree of disorder / chaos
- Entropy = thermal energy unavailable to do work
Do Cells Obey The Second Law of Thermodynamics?
Yes,
- Universe tends towards disorder / chaos
- Cells tend towards order!
- Organisation sacrifices available energy (i.e. it increases entropy!)
Do Living Systems Obey The Second Law of Thermodynamics?
• Organisation sacrifices available energy (i.e. it increases entropy!)
(heat loss in both)
Organisms require a constant supply of energy, how is this provided?
Provided by chemical bond energy in food
- Digestion: Proteins, lipids, carbohydrates broken down into monomers (amino acids, sugars, fatty acids)
- Oxidation of small organic molecules to build new proteins, lipids, carbohydrates
- Can assemble C-based molecular materials = ____
- Can disassemble C-based molecular materials = ____
• Can assemble C-based molecular materials = anabolism
Anabolic reactions require energy
• Can disassemble C-based molecular materials = catabolism
Catabolic reactions liberate energy
Enzymes ____ Activation Energy of Chemical Reactions in Metabolism
Enzymes Lower Activation Energy of Chemical Reactions in Metabolism
Examples of enzymes.
- Oxidoreductase (redox reactions)
- Transferase (transfering chemical group)
- Hydrolase (ryhdrating or loss of water)
- Lyase (breaks chemical bonds)
- Isomerase (changes structure)
- Ligase (can ligate molecules)
What is Activation Energy?
Even when ΔG is negative, need to invest energy (overcome activation energy EA ) for reaction to proceed
What do enzymes do to the activation energy?
For most biochemical reactions, EA is very ___. Which means?
For most biochemical reactions, EA is very high.
High EA stops reaction from occurring spontaneously (in absence of appropriate enzyme)
Substrates / reactants lack sufficient EA so exist in metastable state
How does the Enzyme – Substrate [ES] Complex with the enzyme catalysit work?
- Substrate binds at active site which is specific (or selective or preferential)
- Substrate has a recognised structure and/or consensus sequence
- Two models of ES complex formation
- Second reaction – conversion of the enzyme-substrate complex to an enzyme-product [EP] complex
- In an enzyme protein, involves chemical interactions between substrate and amino-acid side chains in catalytic centre of active site
Enzyme – Substrate [ES] Complex: what is the Lock & key model?
complementary fixed shapes to both E and S
Enzyme – Substrate [ES] Complex: what is the Induced fit model? (more realistic)
E and/or S change conformation as complex forms (e.g. binding of D-glucose to glucokinase)
What does it mean by Coupling chemical reactions in terms of enzymes?
The energetically unfavourable reaction (X to Y) is driven by the energetically favourable reaction (C to D)
The net free energy of the coupled reaction is less than 0
i.e. 𝚫G is overall negative
How can enzymes achieve coupling chemical reactions?
Cofactors
What are Cofactors?
non-protein, organic/inorganic molecule/ion essential for catalysis • May be bound to the enzyme as a prosthetic group (e.g. Zn2+ ion bound to active site of carboxypeptidase)
- Apoenzyme – incomplete and inactive
- Holoenzyme = apoenzyme + cofactor
- Cofactor is unaltered in the course of the reaction!
What are coenzymes? Examples?
small, organic molecule (usually a vitamin derivative) required for catalysis
Examples:
- CoA = coenzyme A = derivative of vitamin B5 (pantothenic acid) – fatty acyl esterification and transport
- Biotin = coenzyme R = vitamin B7 – required by carboxylase enzymes
What are cosubstrates? Examples?
organic molecule required for the main reaction which is changed in the course of that reaction
E.g. Oxidation of a respiratory substrate leads to collateral reduction of a pyridine nucleotide co-substrate
- NAD+ reduced to NADH
- NADP+ reduced to NADPH
- FAD reduced to FADH2
Enzyme metabolism summary:
- Chemical bond energy ____
- Catabolism is ____ bonds and anabolism is ____ bonds can be coupled for energetically ____ reactions
- Enzymes are ____ that ____ the activation energy of a reaction
- Enzymes can use ____, ____ or ____ to drive a reaction
- Cofactors ____ change, cosubstrates ____ change during the enzymatic reaction
- Chemical bond energy is in food
- Catabolism (breaking) and anabolism (making) bonds can be coupled for energetically favourable reactions
- Enzymes are catalysts that lower the activation energy of a reaction • Enzymes can use cofactors, cosubstrates or coenzymes to drive a reaction
- Cofactors do not change, cosubstrates do change during the enzymatic reaction
What is Cellular Energy is Stored as?
Adenosine Trisphosphate (ATP)
What bonds are present in ATP?
- There are different bonds energies within the triphosphate, which determines where you would break the bond
- Y-bond broken for release of energy to create ADP
ADP converstion to ATP
ATP conversion to ADP drives energetically ____ reactions. What does this mean?
ATP conversion to ADP drives energetically unfavourable reactions
- ATP acts as an electron carrier ‘Activated carrier - ready to release energy’
- Provide readily transferable chemical groups
(important to create amino acids - glutamine)
What are other electron carriers?
NADH, NADPH and GTP
involves the transfer of a proton
The Multiple Stepwise Enzyme Reactions in Sugar Oxidation allows for what?
Allows to harness energy at each point and creates new molcules for use in the body.
How is energy harnessed from glucose?
GLYCOLYSIS
- Oxidising sugars
- Produces ATP without O2 (anerobic environment)
- Occurs in most cells-principal source of energy in anaerobic systems
- Uses 2x ATP to make 4x ATP
(net gain 2x ATP)
What is the fermentation process?
Fermentation produces ATP in the absence of oxygen
(e.g yeasts and skeletal muscle)
• Two forms of fermentation reaction
- Releases lactate
- Releases alcohol and CO2
• Converts NADH back to NAD+ for glycolysis
How is energy stored?
High ATP/ADP ratio needs to be maintained
Food energy is stored as:
- Fatty acids (triacylglycerols in adipocytes)
- Glycogen (branched polysaccharides as small granules in many cells)
- Oxidation/gram fat – 2x more energy than glycogen
- 6 fold difference in mass of energy stored in fat against glycogen.
- Glycogen stores: energy for one day
- Fat stores: energy for one month
How is energy stored in plants?
- Only chloroplasts in plants can harness energy through photosynthesis
- Energy needs to be stored and delivered to other cells in the plant
- Two forms of storage: Glucose, & Starch and fat
Glycolosis produces __ ATP
Krebs Cycle produces __ ATP
ETC produces __ ATP
Glycolosis produces 2 ATP
Krebs Cycle produces 2 ATP
ETC produces 34 ATP
Glucose metabolism produces more than just ATP
How does the defective metabolism underly many diseases?
Glycolytic switch: when a cell switches from aerobic to anaerobic metabolism
- Glycolytic switch (Warburg effect) in cancer cells.
- Glycolytic switch in T cells to induce cytokine secretion and inflammation
- Diabetes is the impaired regulation of insulin resulting in abnormal metabolism of carbohydrates and elevated blood glucose levels.
Learning Outcomes:
- Energy can be harnessed from the sun and chemical by autotrophs, which are then ingested by heterotrophs.
- Energy flows through systems in the form of electrons
- Metabolism is a sequence of oxidation and reduction events •Principals of thermodynamics apply to cell metabolism
- Enzymes are used to create order by reducing activation energy of reactions
- Cells can store energy as ATP, glycogen, fatty acids (ATP, glucose, starch in plants)
- Food can be oxidised to release energy to be used by the cell
