Module 2 Flashcards
What is anabolism
This is where smaller molecules assemble into larger ones. Energy is required for this process
What is a cell’s metabolism
Chemical reactions inside cells that use and release energy
What is catabolism
This is where larger molecules break down into smaller molecules. Here, energy is released
What is oxidation
Oxidation describes a loss of electrions
What is reduction
Reduction describes a gain in electrons
What are electron carriers
Electron carriers are molecules that transport electrons (or electrons and protons) during cellular processes, such as cellular respiration and photosynthesis. These carriers play a crucial role in energy transfer within cells by accepting and donating electrons, which helps to drive chemical reactions
What are the common electron carriers
NAD+ / NADH
FAD / FADH2
NADP + / NADPH
What is ATP and how does it work
Adenosine triphsphate is the energy which is stored chemically and acts as a rechargable battery
Here, the phosphate bonds are “high energy” bonds
ATP acts as a cellular energy carrier
Energy Storage: ATP stores energy in the bonds between its phosphate groups. The last phosphate group is attached by a high-energy bond, which, when broken, releases energy.
Hydrolysis: ATP is converted to ADP (adenosine diphosphate) and inorganic phosphate (Pi) by a process called hydrolysis, in which a water molecule is used to break the bond between the second and third phosphate groups. This releases energy.
What is heterotrophy
This is where organisms must consume other organisms for food or energy
They are unable to synthesise their own food from inorganic sources, so rely on other organisms for nourishment
What is autotrophy
This describes an organism who can create their own food from inorganic substances. They can convert CO2 into organic compounds, like glucose, using energy from either sunlight or chemical reactions
What are the 2 stages to photosynthesis
First stage: light dependent reactions (Aim to trap sunlight and convert it to chemical energy for later use (ATP and NADPH))
Second stage: Calvin cycle or Light independent reactions (aims to capture CO2 from air and convert into sugars using chemical energy produced in first stage)
Explain the conversion of radiant energy into chemical energy
There are chlorophylls in the chloroplasts which capture light. This travels through the antenna complex through pigment molecules, ultimately reaching the reaction centre
The excitation energy is transferred from one pigment molecule to another through resonance energy transfer (as electron gets excited, when it falls back down, to ground state, it excites the next electron which continues throughout the antenna complex to allow transfer of electrons). This energy from reaction centre is used to excite the P680(PSII) and p700 (PSI) chlorophylls
Explain the overall organisation of the light reactions in photosystems I and II
The light reactions of photosynthesis occur in the thylakoid membranes of chloroplasts, where light energy is captured and converted into chemical energy in the form of ATP and NADPH. These reactions involve two main protein complexes: Photosystem II (PSII) and Photosystem I (PSI), which work together in a coordinated process.
Location: PSII is primarily located in the grana stacks of the thylakoid membranes.
Location: PSI is located in the stroma lamellae of the thylakoid membrane.
Describe ATP synthesis during the light-dependent reactions
In the light-dependent reactions, the movement of hydrogen ions down their concentration gradient is coupled to the production of ATP.
ATP synthesis during the light-dependent reactions of photosynthesis occurs through a process known as photophosphorylation, where light energy is used to generate ATP from ADP and inorganic phosphate (Pi). This process occurs in the thylakoid membrane of the chloroplasts, and it is driven by the proton gradient created during electron transport. Here’s how it works:
Here, the protons are transported from stroma to lumen to create a proton gradient –> H+ move from umen back to stroma via ATP synthase, causing ATP to form
Explain the process of light-dependent reactions / non cyclic phosphorylation
Photons are absorbed by photosystem II (PSII). This excites electrons from PSII, raising them to a higher energy level. These excited electrons are captured by the primary electron acceptor in PSII
PSII then undergoes the splitting of water into oxygen and protons, and electrons. The electrons from water help replenish the electrons lost by PSII, whhile O2 is released as a byproduct.
Energy from PSII pass through the etc to PSI. As electrons move through ETC, their energy is used to pump protons from stroma into thylakoid lumen –> proton gradient across the thylakoid membrane
Proton gradient from ETC drives synthesis of ATP, where protons flow back into stroma through ATP synthase to convert ADP to ATP
In PSI, lijght energy is absorbed by chlorophyll molecues which reexcites the electrons. The excited electrons are picked up by the electron acceptor in PSI
The high energy electrons from PSI are transferred to a protein called ferredoxin which transfers electrons to NADP+, along with protons from stroma to form NADPH. NADPH is used later on in calvin cycle
What is RUbisco? What is its function
It is the most abundant protein on Earth, and exists in chloroplast stroma
Function is to convert CO2 from atmosphere into organic form of carbon found in biology of all organisms. Important for the calvin cycle.
Its function is to attach CO2 to ribulose-1,5-bisphosphate (RuBP) which will then split off into 2 molecules of 3-PGA
In addition to its carboxylase activity, it has oxxygenase activity where it could bind to O2 instead of CO2 –> photorespiration
What is carboxylation done by rubisco
Carboxylation by Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) is the first step in the Calvin cycle of photosynthesis, where carbon dioxide (CO₂) is incorporated into an organic molecule. Rubisco plays a key role in fixing atmospheric CO₂ into a stable compound that can later be used to build sugars.
As part of carboxylation, rubisco acts on RuBP, to form 2 3-PGA molecules. This then turns into G3P molecules.
The carboxylation reaction effectively “fixes” carbon from CO₂ into an organic form (3-PGA) that can then be further processed in the Calvin cycle to eventually produce sugars and other organic compounds.
What is oxygenation which can be done by rubisco
The process of oxygenation by Rubisco is a reaction where Rubisco binds to oxygen (O₂) instead of carbon dioxide (CO₂).
Here, it causes RuBP to bind with O2. This causes the production of 3-PGA and a 2-phosphoglycolate which isn’t helpful and is actually toxic. This requires further processing which is done through photorespiration
Explain photorespiration and describe why its bad
Photorespiration is a method to get rid of the 2-phosphoglycolate.
It ultimately consumes ATP and releases CO2 which is unideal for a plant
What can increase the possibility of photorespiration occurring
When there is a greater concentration of oxygen than carbon dioxide in the atmosphere
Also when there is greater temp
Explain fixation of carbon dioxide in the Calvin (C3) cycle (i.e. explain how the calvin cycle works)
Basically, CO2 enters, and this binds to RuBP, with the assistance of Rubisco as an enzyme. This causes the formation of 2 3-PGA molecules. This is then able to breakdown into G3P. (3 CO2 molecules cause production of six G3P)
Of this six G3P, one is used to be able to create glucose (through formation of sucrose or starch etc)
The rest of the G3P is used for the regeneration of the RuBP. The cycle then continues. As part of this cycle, it consumes the ATP and NADPH which was created from the Light dependent reactions
What % of plant production is lost to photorespiration
25%
Describe the co-evolution of C4 photosynthesis with Earth;s atmosphere overtime
Over time, photosynthetic organisms released significant amounts of O₂ as a byproduct, causing O₂ levels to rise and CO₂ levels to gradually decrease.
The increase in O₂ and decline in CO₂ led to a higher chance of photorespiration, as Rubisco, which has an affinity for both CO₂ and O₂, increasingly bound O₂ instead of CO₂. This caused a wasteful reaction, reducing carbon fixation efficiency in C₃ plants.
The declining CO₂ levels and rising O₂ created selective pressure for plants to adapt to avoid the loss of fixed carbon through photorespiration.
C₄ photosynthesis evolved as a specialized pathway that minimizes photorespiration and increases carbon fixation efficiency under low CO₂ conditions.
Thus, as the atmosphere started having more O2, the C4 photosynthesis started to emerge
Explain how C4 photosynthesis works
This describes a series of metabolic and structural adjustments to exploit PEPcase
In the mesophyll cells, the CO2 is initially fixed by an enzyme called PEPcase to a PEP molecule. This forms a 4C compound
This 4C compound is quickly converted to malate which is transported to bundle sheath cells
The malate is then decarboxylated to release CO2 in the bundle sheath cells. This increases the concentration of CO2 around the RUbisco enzyme in the Bundle sheath cell. This then causes the CO2 to ignore its oxygenase ability, and increases its carboxylase activity, minimising chances of photorespiration
Released CO2 enters calivn cycle, where RUbisco then fixes it to produces sugar, and follows the steps done in C3 photosynthesis
Explain how CAM photosynthesis works
Basically, to be able to get CO2, plants have to open a stomata (which is like an opening to the rest of the world). However, when the environment is too hot, if they do this, they are unlikely to get much CO2, and also will probably lose a lot of its water. As such, there needs to be a solution to this.
CAM photosynthesis works by making the plant open its stomata at night. At night, the air is more damp, and the plant is thus unlikely to lose water. It is then able to absorb the CO2 from the air at night. This CO2 is combined with PEP to form a four carbon molecule called oxaloacetate which then turns into malic acid, and is stored in vacuoles within plant cells overnight
During the day, the stomata closes to conserve water, which is crucial in hot and dry environments
This stored malic acid is transported from vacuoles to chloroplasts where it is then broken down to release CO2, and then the Rubisco does its job
What environments would C3 photosynthesis best suit?
Cool and wet environments.
At higher temps, rubisco affinity for O2 increases relative to CO2, making it more efficient in cooler environments
Also, when stomata opens, there is water loss, but in wet enviros, water is more available –> less water loss
What environments would C4 photosynthesis best suit?
Hot and sunny environments
High light environment because it is enough to fue energy demands of C4 pathway.
Also, at higher temps, there is a higher likelihood of photorespiration happening
What environments would CAM photosynthesis best suit?
Hot and dry environments
Because it is known for being able to save water
A botanist sets up a greenhouse with intense lights and adequate soil water. In this enviro which photosynthesis process has an advantage?
C4 has a relative photosynthetic advantage compared to CAM and C3
This is because C3 is at a disadvantage because it is worse in higher temperatures with intense lighting. CAM is also used to help conserve water, but if theres enough water here, there really isn’t any point
THIS ONE IS STILL A BIT CONFUSING
What is oxidation
Loss of electrons
WHat is reduction
Gain of electrons
In photosynthesis, the C from CO2 is ____ to become glucose
Reduced
Both burning and aerobic respiration releases the same amount of energy, but aerobic respiration does it step-by-step. WHy is this ideal?
Because if all the energy was released in one go –> excess heat –> damage to cell
Also, aerobic respiration allows for more energy to be moved at a time (?!)
Where does glycolysis occur?
It occurs in the cytoplasm
Explain the process of glycolysis
Here, a glucose molecule is broken down into 4 ATP molecules (net 2 ATP gain), 2 pyruvate molecules, and 2 NADH molecules
Doesn’t require any oxygen
Explain what happens with the intermediate reaction
This involves the conversion of pyruvate produced from glycolysis into acetyl CoA. Electrons are removed, and given to NADH electron basket
Overall, 2 NADH and 2 acetyl CoA is produced from the two glucose molecules (i.e. 1 NADH and 1 acetyl CoA per glucose molecule)
Explain what happens in the Krebs Cycle
It uses the acetyl CoA produced from the intermediate reaction and forms 1 ATP molecule, 3 NADH molecules, 1 FADH2 molecule and 2 CO2 molecules
Explain the process of the electron transport chain
Basically the previous electron carriers (NADH and FADH2) oxidise in the matrix, thus turning into NAD+ and FAD. As a result of this, electrons are deposited in one (of four) protein complexes, which assists in bringing the H+ from the matrix to the intermembrane space. As such, the intermembrane space has an extremely high concentration of H+ (protons) from the deposition of the four protein complexes. These e- are then used to react with oxygen and H+ in the matrix to produce H2O.
The creation of ATP occurs with the ATP synthase which allows for H+ to flow through it (via the electrochemical gradient of protons), to ultimately free phosphate and turn ADP to ATP, ultimately producing ATP
This process creates 28-34 ATP per glucose oxidised
WHat are the similarities of mitcohondria and chloroplast structure (very important)
Both membrane bound (double membraned)
Membrane is folded in both
Compartmentalisation
Both produce ATP; mitochondria through oxidative phosophyrlation and chloroplasts through light transport
Both organelles have their own DNA
What are the differences in mitochondria and chloroplast structure (very important)
Internal membrane structure - Mitochondria = inner membrane folded into cristae which increases SA for oxidative phosophyrlation
Chloroplasts =Inner membrane forms network of thylakoid membranes arranged in stacks called grana where light dependent reactions occur
Matrix vs stroma-
Space inside of inner membrane of mitochondria is called matrix. FOr chloroplasts, the space inside inner membrane is called stroma
Mitochondria don’t contain pigments, whilst chloroplasts have thylakoids organised into granum and thylakoid stacks
What are the similarities between mitochondria and chloroplast function/process
Proton gradient used to create ATP through using an ATP synthase
Relies on movement of protons through ATP synthase to provide energy for ATP synthesis
Proteins involved in both functions
What are differences in mitochondria and chloroplast function / process
Source of energy -
ATP synthesis in mitochondria driven by oxidation of nutrients like glucose than cellular respiration. Chloroplast ATP synthesis is driven by light energy from chlorophyll
ETC components -
Mitochondria: ETC involves complexes I-IV. Chloroplasts: involves photosystem I and photosystem II
Final electron acceptors:
Mitochondria: O2 acts as final electron acceptor in ETC, forming water. Chloroplasts: NADP+ acts as final acceptor, forming NADPH which is used in calvin cycle for fixation
Location of ATP synthesis:
Mitochondria: Synthesised in matrix, whilst chloroplasts has ATP synthesised in stroma, which is enclosed by thylakoid membrane
Why do we need proteins to control levels of ATP
We need proteins to act as a asafety valve mechanism to control levels of ATP. Processes aimed at decreasing ATP levels (Because sometimes we don’t need that much ATP)
What proteins can control levels of ATP
Alternative Oxidase
Uncoupling protein
What does Alternative oxidase do
Instead of the electrons being transported from complex 2 to complex 3, they could instead travel through alternative oxidase, and thus stops the journey of the electrons. This decreases the proton gradient further –> decreased ATP synthesis
What does uncoupling protein do
They help dissipate the proton gradient by the electron transport chain as heat rather than using the proton gradient to produce ATP. This is a critical aspect to maintaining a healthy body temperature
This ultimately diverts energy from ATP synthesis to thermogenesis by catalysing a leak of protons across the matrix intermembrane space to the matrix. Provides alternative pathway to reduce pressures other than ATP synthase
What are macronutrients
These are larger than micronutrients in terms of size, and are required by the body in larger amounts to provide energy and various physiological functions.
They serve as fuel and construction elements of tissues.
Examples include carbohydrates, fats and proteins
These provide energy, support growth, regulate bodily processes
What are micronutrients
These are much smaller than macronutrients in terms of size
They are also required in smaller quantities compared to macronutrients
Includes vitamins and minerals. Supports various biochemical reactions and processes, immune function, hormones and enzymes etc
What is the composition of the body
liquids (60% in adults, 70% in infants, 50-55% in elderly people)
Protein (18%)
Fats (16%)
Carbs, minerals etc (6%)
Describe the composition of carbohydrates
Mainly composed of carbon, hydrogen and oxygen
It is a common carbohydrate which is quite long and could branch
carbohydrates are composed of carbon, hydrogen, and oxygen, arranged in simple or complex structures that serve as energy sources, structural materials, and storage molecules.
Could be in the form of monosaccharides, disaccharides, and polysaccharides
What are monosaccharides
Most basic unit of carbs which cant be broken down into smaller sugars
What are disaccharides
Two monosaccharides linked together by a glycosidic bond
What are polysaccharides
Long chains of monosaccharide units linked together, and sometimes branch out
Explain process of glycosidic bond formation
Each monosaccharide contains multiple hydroxyl groups (-OH) attached to its carbon atoms. In formation of glycosidic bonds, a hydroxyl group from one monosaccharide and H atom from hydroxyl group of another react together. In this process, H2O is removed, and oxygen connects the two sugars together
Explain the basic composition of amino acids/proteins
Proteins made up of C , O, N, H atoms They all contain a central carbon, amino group, carboxyl group and H atom, with a side chain group as well
They are linked together by a peptide bond through dehydration between -NH2 of an amino acid and a carboxyl group of another, releasing a water molecule
How many amino acids are found in proteins
20 amino acids
11 non essential
9 essential
Does the bloodstream absorb protein?
No it absorbs amino acids
WHat is the main composition of fats?
Exists through triglycerides
Glycerol; 3 C molecules which is the backbone of trigylcerides
Fatty acids; long chains of C and H atoms with carboxyl group
TYpically contains C, H and O
Where is fat stored
Adipose tissue
Compare and contrast different nutritional sources of protein
Ultimately, as long as we are getting the 9 amino acids we can’t make, our protein synthesis is fine.
Ultimately, when it comes to obtaining amino acids for proteins, the source doesn’t really matter
However, when comparing animal vs plant protein; the plant one actually has more of the essential amino acids (i.e. when comparing soy beans to beef)
Animal based proteins are more digestible, and considered complete proteins (vs plants in comparison) and thus high in essential amino acids and other nutrients as well
How does ATP power cellular processes (2 ways)
ATP stores energy through the high potential energy phosphate groups
When ATP turns into ADP and a free phosphate, this release of a phosphate can be used to power various cellular processes.
2;
If the protein has existing negatively charged regions near the newly added phosphate, these charges can repel each other due to electrostatic forces.
This repulsion can cause the protein to change its shape—for example, pushing different domains of the protein apart or altering its structure in a way that enables or disables its interaction with other molecules.
Conformational Change: The repulsion can force a conformational (shape) change in the protein, leading it to switch from an active to an inactive form, or vice versa.
3:
Puts phosphate on a substrate for enzyme, allowing it to fit into enzymes 3D space –> do it before phosophrylation - by now it can release all energy from there
When enzymes chaneg structure, it can fit into another site of enzyme and facilitate chemical reaction or activate enzyme to catalyse a reaction more effectively
Understand how fats, carbs and proteins can be interconnected via metabolism
Carbs –> fats (Excess glucose –> acetyl CoA –> synthesise fatty acids - lipogenesis)
Fats –> carbs (Glycerol from fat can be used to make glucose)
Carbs –> protein (Intermediaries from glucose metabolism can synthesise non essential amino acids)
Proteins –> carbs (Glucagonic amino acids –. glucose via gluconeogenesis)
Proteins –> fats (ketogenic amino acids –> acetyl CoA –> fatty acids)
