week 9-12

Question 1

The ‘Central Dogma of
Molecular Biology

Answer 1

describes the flow of genetic information in cells: DNA → RNA → Protein.

DNA stores genetic information.
Transcription: DNA is copied into mRNA.
Translation: mRNA is used to synthesize proteins at the ribosome.
This process is typically one-way, though exceptions like reverse transcription (in retroviruses) allow for some reversal of flow. The Central Dogma is essential for understanding how genetic information directs protein synthesis and cell function.

Question 2

Proteomics

Answer 2

the study of the proteome, which consists of all the proteins expressed by a genome at any given time. Unlike the genome, which is stable, the proteome is dynamic and changes in response to environmental factors or cellular conditions. Proteins are responsible for various cellular functions and structural roles. Proteomics helps us understand how proteins contribute to traits (phenotype) and how their expression changes in response to different factors, at levels ranging from whole organisms to individual cells.

Question 3

Proteome

Answer 3

The Proteome is the PROTEins expressed by a genOME at any one
time.
*The Proteome is constantly changing as cells respond to environmental
conditions
*It may be as complex as a whole organism, a tissue or a single cell type

Functional Diversity Resides in the
Proteome

Question 4

PTMs

Answer 4

a single gene may give rise to more than one functional
protein due to the influence of chemical or physical
modifications to proteins
* PTMs are additions or subtractions to translated proteins
that can alter the chemical structure of a protein and
therefore modify its function
* PTMs can act as molecular ‘switches’ to turn on (or off)
enzyme activity
* By influencing structure, a PTM may influence how
proteins interact with other protein

Question 5

Specific Example of PTM

Answer 5

Methylation – Methyl groups on several amino acids (Lys, Arg)

Question 6

Post-translational modifications (PTMs) are classified into enzymatic and non-enzymatic types

Answer 6

Enzymatic PTMs involve specific enzymes adding or removing groups, such as:
Kinases (add phosphate) and phosphatases (remove phosphate).

Non-enzymatic PTMs occur without enzymes, including:
Oxidation (e.g., cysteine oxidation by reactive oxygen species).

These modifications regulate protein function and are important in cellular responses.

Question 7

What are the functions of PTMs?

Answer 7

Alter protein structure/function relationship
› Influence protein-protein, protein-DNA, protein-ligand interactions
› Activate or repress activity (recycling)
› ‘Mark’ proteins for degradation/removal of a ‘signal’ peptide

Question 8

Protein-Protein [ Protein-Biomolecule] Interactions

Answer 8

Proteins often interact with each other or other biomolecules (like DNA, RNA, or small molecules) to perform their functions. These interactions can result in the formation of protein complexes, where proteins may serve structural roles (e.g., support or transport) or enzymatic roles (e.g., catalysis). Protein complexes are temporary and enable various cellular processes.

protein tertiary structure and protein-protein interactions are largely determined by
hydrophobic interactions, charge-based interactions and hydrogen-bond
interactions, with other influences including disulfide bon

Question 9

Examples of how PTMs can potentially alter
structure / function

Answer 9

A PTM alters charge-based interactions within protein
structure inhibiting the ability of an enzyme to bind it’s
substrate (or vice versa)
* A PTM alters hydrophobic interactions (e.g. by
increasing hydrophilicity) opening up a binding site for a
partner protein
* A PTM causes a protein to unfold and be targeted by
degradative processes

Question 10

Reactive oxygen and reactive nitrogen species
(ROS/RNS) induce oxidative stress and PTM

Answer 10

Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are free radicals that can cause oxidative stress by reacting with cellular components like proteins and DNA. They are produced continuously in biochemical processes and play roles in immune responses, such as macrophages using ROS to kill pathogens. However, excess ROS or compromised antioxidant defense systems can cause cellular damage. Defense proteins like superoxide dismutase (SOD), catalase, peroxiredoxins, and glutathione peroxidase help mitigate oxidative stress.

Question 11

Antioxidants like Glutathione (GSH), Superoxide Dismutase (SOD), and Catalase (Kat) help remove reactive oxygen species (ROS) and protect cells from oxidative stress.

Answer 11

Glutathione (GSH): A tripeptide (glutamate-cysteine-glycine) that neutralizes free oxygen by oxidizing cysteine. A healthy cell maintains a GSH to GSSG (oxidized glutathione) ratio of 400:1.

Question 12

the role of Cys redox PTMs

Answer 12

Redox signaling
* Protect against ‘over’ or irreversible oxidation

Question 13

Cell signaling

Answer 13

biochemical mechanism through which cells sense environmental signals and initiate responses that involve the genome. The process involves the activation of membrane-bound or cytosolic receptors by extracellular stimuli. Key features of cell signaling include:

Receptors: Membrane receptors, like G-Protein Coupled Receptors (GPCRs) and Receptor Tyrosine Kinases (RTKs), detect external signals.
Transduction: Activated receptors can function as transcription factors or regulate downstream pathways through protein phosphorylation or second messengers.
Phosphorylation Cascade: Protein kinases add phosphate groups to proteins, activating or deactivating them, while phosphatases remove phosphate groups, regulating protein activity and amplifying the signal.

Question 14

GPCR signaling involves:

Answer 14

Activation: External signals (e.g., epinephrine) bind to GPCRs, causing them to activate G-proteins.
G-Protein Activation: The G-protein exchanges GDP for GTP, becoming active.
Signal Transduction: Active G-protein regulates effector enzymes (e.g., adenylate cyclase), generating second messengers like cAMP.
Biological Effects: This signaling controls processes like glycogen breakdown, lipid hydrolysis, and heart rate increase in response to stress.
Termination: The signal ends when GTP is hydrolyzed to GDP, and second messenger levels are regulated.

Question 15

Epinephrine-induced β-adrenergic signaling activates protein kinase A (PKA) through the production of cAMP. PKA then transmits the signal by phosphorylating target proteins. Key points:

Answer 15

Phosphorylation: A rapid, reversible, and coordinated process that amplifies the signal.
Signal Amplification: A single kinase activation can trigger the phosphorylation of many proteins.
PKA Activation: PKA phosphorylates key proteins, such as glycogen phosphorylase, which breaks down glycogen into glucose, enabling the body to respond to stress.

Question 16

Protein kinases

Answer 16

Protein kinases add phosphate groups to specific sites on proteins, altering their function by introducing a negative charge. They can phosphorylate multiple sites and proteins, either specifically or broadly. Some kinases activate or deactivate other kinases, amplifying the signal and regulating cellular responses.

Question 17

Signal amplification in GPCR

Answer 17

occurs when the activation of a GPCR by a substrate leads to the activation of multiple adenylyl cyclase enzymes. Each active adenylyl cyclase produces several cAMP molecules, which activate PKA. PKA, in turn, activates many targets, amplifying the signal and leading to the activation of thousands of glycogen-degrading enzymes in the liver. This amplification process magnifies the cellular response to the initial signal.

Question 18

In GPCR signaling, PKA not only activates enzymes but also induces gene transcription. The process involves:

Answer 18

Activation of the GPCR.
Activation of adenyl cyclase by Gs and production of cAMP.
cAMP activates PKA, leading to the dissociation of PKA’s catalytic subunits, which then translocate to the nucleus.
PKA phosphorylates CREB (cAMP response element binding protein).
Phosphorylated CREB forms a complex with CBP/P300, enabling it to bind to CRE (cAMP response elements) in the promoters of cAMP-regulated genes, promoting their transcription.
This pathway allows for the long-term effects of signaling, including changes in gene expression.

Question 19

Self-inactivation is crucial for terminating G-protein signaling, ensuring that signals like epinephrine, which are intended to be short-acting, don’t persist longer than needed.

Key steps in the termination of signaling include:

Answer 19

cAMP degradation: PKA activation is mediated by cAMP. To stop signaling, cAMP is degraded into AMP by cyclic nucleotide phosphodiesterase (cAMP phosphodiesterase).
G-protein inactivation: GTP bound to the Gs α-subunit is hydrolyzed to GDP upon signal withdrawal, leading to the inactivation of Gs.
Inhibitory G-protein (Gi): An increase in Gi, which inhibits adenyl cyclase, further reduces cAMP production.
These mechanisms ensure that the signaling pathway is shut down efficiently after its purpose is fulfilled.

Question 20

Phosphoprotein phosphatases

Answer 20

remove phosphate groups from target proteins in response to cellular signals.

Question 21

Oxytocin

Answer 21

(the ‘love hormone’) response is
via GPCR signaling
* Oxytocin is a neuropeptide hormone produced in the
hypothalamus and released by the pituitary gland
* Binds to a GPCR that activates G-protein ‘q’ (Gq)
activation by GTP and binding to membrane-associated
phospholipase C (PLC), initiating phosphatidylinositol
signaling
* PIP2 (phosphatidylinositol 4,5-bisphosphate) is cleaved
by PLC to diacylglycerol (DAG) and inositol 1,4,5-
trisphosphate; IP3)
* IP3 acts as the second messenger and initiates calcium
release from the ER, while DAG and Ca 2+ stimulate
protein kinase C (PKC

Question 22

week 9 summary

Answer 22

• Signalling involves the binding of a signal molecule (e.g. hormone) to a
  specific receptor (GPCRs and others)
• Activated receptor results in disassociation of an enzyme activating protein (A
  G-protein) which in turn activates a membrane-localized enzyme (adenyl
  cyclase)
• A second messenger (cAMP) activates protein kinases (PKA) that amplify the
  signal without altering protein expression
• Activated kinases phosphorylate multiple target proteins at consensus motifs
  to alter their structure / function
• Activated kinase signal transduction ultimately leads to a change in gene
  transcription
• Feedback mechanisms exist to dampen and ultimately stop the response
  upon reduction or removal of the stimulus

Question 23

What is the primary function of Gq in oxytocin signaling?

a) To activate protein kinase A (PKA)
b) To activate phospholipase C (PLC)
c) To release calcium from the endoplasmic reticulum (ER)
d) To bind to diacylglycerol (DAG)

Answer 23

to activate phospholipase C (PLC)

Question 24

Which of the following molecules is generated when phospholipase C cleaves PIP2?

a) cAMP and calcium
b) DAG and IP3
c) cAMP and PKA
d) ATP and IP3

Answer 24

DAG and IP3

Question 25

What is the role of IP3 in oxytocin signaling?

a) It activates protein kinase C (PKC)
b) It promotes the synthesis of oxytocin
c) It triggers calcium release from the endoplasmic reticulum (ER)
d) It binds to G-protein Gq

Answer 25

It triggers calcium release from the endoplasmic reticulum (ER)

Question 26

Receptor Tyrosine Kinases (RTKs):

Answer 26

RTKs are a family of ~60 membrane receptors that mediate extracellular signal transduction via autophosphorylation.

Question 27

RTK structure:

Answer 27

Extracellular ligand-binding domain.
Single transmembrane domain.
Intracellular tyrosine kinase domain.
They are activated by ligand binding (e.g., epidermal growth factor (EGF) or insulin).
Ligand binding induces receptor dimerization, activating the tyrosine kinase domain, which autophosphorylates tyrosine residues and provides docking sites for downstream signaling proteins.

Question 28

Insulin Signaling via RTKs:

Answer 28

Insulin is produced by pancreatic β-cells and binds to the insulin receptor (INSR) on target cells (liver, muscle, fat).
The insulin receptor is a dimer consisting of two α-chains and two β-chains. Binding activates the intracellular kinase domain, leading to phosphorylation of tyrosine residues.
Insulin receptor substrate-1 (IRS-1) is phosphorylated, triggering downstream signaling pathways, including:
MAPK signaling (Ras/Raf): Activation of Ras leads to Raf, then to ERK, which stimulates gene expression.
PI3K/Akt signaling: Activation of PI3K produces PIP3, which activates Akt, leading to effects such as glucose uptake and gene expression.

Question 29

Insulin Signaling Pathways

Answer 29

MAPK signaling: ERK enters the nucleus, phosphorylates transcription factors (e.g., Elk1), and stimulates gene expression like glucose transporters.
PI3K/Akt signaling: Akt phosphorylates various targets, such as FOXO transcription factors, to regulate gene expression and glucose metabolism.
GLUT4 translocation: Akt phosphorylates TBC1D4, enabling GLUT4 vesicles to move to the cell surface for glucose uptake.

Question 30

Termination of Insulin Signaling

Answer 30

Phosphatases (e.g., PTEN) deactivate signaling by removing phosphates from proteins.
Endocytosis of the insulin receptor complex leads to receptor degradation, reducing sensitivity to insulin.
Ser/Thr phosphatases (e.g., PP2A, PHLPP) also inhibit Akt signaling.
Ubiquitination and degradation of IRS proteins can also downregulate insulin signaling.

Question 31

Research Insights

Answer 31

Phosphoproteomics provides insights into the temporal dynamics of insulin signaling.
Ongoing research reveals new signaling pathways and mechanisms involved in insulin action and metabolic regulation.

Question 32

week 10 summary

Answer 32

RTKs, like the insulin receptor, mediate complex signaling pathways that lead to diverse physiological effects.
Cross-talk between pathways can modulate insulin signaling outcomes.
New insights into insulin signaling mechanisms are continuously being discovered.

Question 33

What is the main function of the insulin receptor (INSR) in insulin signaling?
A) To bind glucose and initiate its uptake into cells
B) To activate intracellular signaling pathways by autophosphorylation of tyrosine residues
C) To break down insulin into inactive fragments
D) To bind and activate MAPK signaling pathways directly

Answer 33

To activate intracellular signaling pathways by autophosphorylation of tyrosine residues

Question 34

Which of the following is a direct consequence of Akt activation in insulin signaling?
A) Inhibition of glucose transport
B) Phosphorylation of FOXO transcription factors leading to gene expression modulation
C) Activation of the insulin receptor kinase domain
D) Degradation of IRS proteins

Answer 34

phosphorylation of FOXO transcription factors leading to gene expression modulation

Question 35

How is the insulin receptor signaling terminated?
A) By the binding of insulin receptor antagonists that prevent activation
B) Through the phosphorylation of insulin receptor substrate-1 (IRS-1) by PKA
C) By endocytosis and lysosomal degradation of the insulin receptor complex
D) Through the activation of PI3K and subsequent activation of Akt

Answer 35

By endocytosis and lysosomal degradation of the insulin receptor complex

Question 36

Two-Component Regulatory Systems (TCS):

Answer 36

TCSs are used by bacteria to respond to environmental changes.

Components:
Histidine Kinase (HK): A sensor protein with a ligand-binding domain that initiates signaling by autophosphorylation.
Response Regulator (RR): Receives the phosphate group and acts as a transcription factor to regulate gene expression.

Process:
Signal sensing: A ligand binds to the HK, which auto-phosphorylates at a histidine residue.
Signal transfer: The phosphate group is transferred to a specific aspartic acid residue in the RR.
Gene regulation: The RR binds to target gene promoters to activate or repress transcription.

ATP-Dependent Process: Phosphorylation of HK is an ATP-driven process that enables the transfer of phosphate to RR, affecting gene expression.

Question 37

Functions and Types of TCS:

Answer 37

TCS Functions: Control virulence, stress responses, and environmental adaptability in bacteria.

Phosphorelay Systems: Some TCSs involve intermediary proteins (e.g., phosphorelay proteins) to transfer the signal between HKs and RRs.

Histidine Kinase Structure:
Highly conserved regions: Transmembrane region (TMR), His phosphorylation (Dhp), and ATP-binding domain.
Variable regions: Sensor domain (ligand-specific) and signal transducing domain.
Response Regulators: Composed of:
Receiver Domain: Contains the phosphorylation site (Asp).
Output Domain: DNA-binding domain that targets specific promoters.

Question 38

Model TCS - PhoP-PhoQ in Salmonella (S. enterica):

Answer 38

PhoP-PhoQ System: A model system for understanding TCSs.
Activated by environmental signals such as low magnesium (Mg2+), low pH, and antimicrobial peptides.
Involves changes in gene expression related to virulence, Mg2+ transport, acid stress resistance, and iron uptake.
Mutations in PhoP or PhoQ reduce virulence in animal models.
Regulation of Gene Expression:
At low Mg2+: PhoP-PhoQ activates genes for Mg2+ uptake (e.g., mgtA).
At low pH: PhoP-PhoQ activates other transcription factors like rstA, affecting iron uptake.
Interaction with Other TCSs: PhoP-PhoQ can activate other TCSs like PmrA/PmrB under low Mg2+ conditions, impacting LPS modification and antimicrobial peptide resistance.

Question 39

Regulons and Regulomes:

Answer 39

Regulon: A group of genes regulated by a single regulatory protein.
Methods for Studying Regulons:
Gene Knock-out: Identifies proteins whose expression is promoted or repressed by the regulator.
Gene Over-expression: Identifies proteins whose abundance is increased or decreased by the regulatory protein.
Proteomics: Two-dimensional gel electrophoresis (2-DE) can be used to identify proteins regulated by TCSs.

Question 40

Case Study - SarA Regulon in Staphylococcus aureus:

Answer 40

SarA: A global regulator in S. aureus controlling virulence factor expression.
It can both activate and repress target genes.
Genetic knock-out of sarA helps to identify the proteins regulated by SarA (SarA regulon).
Proteomic Analysis: Helps identify proteins positively or negatively regulated by SarA.

Question 41

week 10 summary

Answer 41

Bacterial Signaling: Bacteria use TCSs to sense environmental changes and regulate gene expression in response to those changes.
Applications: Understanding TCSs and their regulons is important for studying bacterial virulence, stress responses, and potential therapeutic targets.

Question 42

What is the main function of bacterial two-component regulatory systems (TCSs)?

A) To transport proteins across the bacterial membrane
B) To detect and respond to environmental stimuli
C) To produce ribosomal RNA
D) To synthesize phospholipids for membrane formation

Answer 42

To detect and respond to environmental stimuli

Question 43

In bacterial two-component regulatory systems, what is the role of the response regulator (RR)?

A) To initiate autophosphorylation of the histidine kinase
B) To bind to a specific ligand in the periplasm
C) To bind to DNA and regulate gene transcription
D) To transport ions across the cell membrane

Answer 43

To bind to DNA and regulate gene transcription

Question 44

Which bacterial TCS is used as a model for studying bacterial response to environmental changes, and is involved in virulence factor regulation in Salmonella?

A) PhoP-PhoQ
B) GlnB-GlnK
C) ArcA-ArcB
D) FsrA-FsrB

Answer 44

PhoP-PhoQ

Question 45

Light Reactions of Photosynthesis:

Answer 45

Photosynthesis converts sunlight into chemical energy, driving life on Earth. The light-dependent reactions produce ATP and NADPH, which are used to synthesize carbohydrates from CO₂ and H₂O.
Light-dependent reactions occur in the thylakoid membranes of chloroplasts, while carbon-assimilation reactions take place in the stroma.

Question 46

Sunlight as Energy:

Answer 46

Sunlight is the primary source of energy for photosynthesis, and plants absorb specific wavelengths of light, which excite electrons in pigments.

Question 47

Chromophores & Energy Transfer:

Answer 47

Pigments like chlorophyll absorb light energy, causing excitation of electrons. Energy is transferred in four ways: heat, fluorescence, exciton transfer, or charge transfer.

Question 48

Pigments:

Answer 48

Chlorophyll (a and b) is the main pigment, coordinating a Mg atom.
Carotenoids are accessory pigments, absorbing light at different wavelengths and protecting against reactive oxygen species (ROS).
Phycobilins are used by cyanobacteria and red algae for light capture.

Question 49

Light Harvesting Complexes (LHC):

Answer 49

Photosynthetic pigments are bound to proteins forming light-harvesting complexes (LHC). These complexes funnel absorbed light to reaction centers.

Question 50

Charge Separation & Electron Transport:

Answer 50

Light absorption leads to charge separation. Excited electrons are transferred to an electron transport chain, leading to proton pumping and ATP synthesis. The Z-scheme describes the flow of electrons from H₂O to NADP+, producing O₂.

Question 51

Photosystems:

Answer 51

There are two types of photosystems in plants:
PSI (Photosystem I): Absorbs light at 700 nm.
PSII (Photosystem II): Absorbs light at 680 nm. Electrons flow through both systems, with cyclic and non-cyclic electron transport affecting the ATP and NADPH production.

Question 52

Structure of Photosystems:

Answer 52

PSII: Dimeric structure with Mn₄CaO₅ complex for water-splitting.
PSI: Trimeric structure, involved in electron transfer to NADP+.

Question 53

Integration of PSI and PSII:

Answer 53

The Z-scheme describes how light energy is converted into chemical energy via electron flow from H₂O to NADP+, generating ATP and O₂ in the process.

Question 54

Which of the following is not common to the processes
associated with the production of ATP in both the chloroplast
and mitochondrion?
a. Electron donation from water.
b. Electron transport through a series of electron carriers.
c. Build-up of a proton gradient across an internal membrane.
d. Utilisation of proton motive force to drive ATP synthesis.
e. Catalysis by an F-type ATP synthase.

Answer 54

Electron donation from water.

Question 55

Which of the following statements about carotenoids in the
light reactions of plant photosynthesis is incorrect?
a. Carotenoids are known as accessory pigments.
b. Carotenoids have absorption spectra that complement those of the
chlorophylls.
c. Carotenoids protect the photosynthetic machinery from singlet oyxgen.
d. The molecular structures of beta-carotene and lutein are closely
related.
e. All antenna molecules in a photosystem are carotenoids.

Answer 55

All antenna molecules in a photosystem are carotenoids.

Question 56

For the Z-scheme describing the light reactions of
photosynthesis in plants, which of the following statements is
incorrect?
a. The units of the y-axis of the Z-scheme are electron volts.
b. Photosystem I is the oxygen-evolving complex.
c. Electrons are transferred from H 2 0 to NADP + .
d. Both photosystem I and photosystem II evolved from bacterial
photosystems.
e. The cytochrome b 6 f complex links photosystem II to photosystem I.

Answer 56

The oxygen-evolving complex is part of Photosystem II (PSII), not Photosystem I (PSI). This complex is responsible for splitting water molecules into oxygen, protons, and electrons, a process called photolysis, which occurs in PSII.

Question 57

Carbon Fixation and the Calvin Cycle:

Answer 57

Calvin Cycle: Converts CO₂ into organic molecules in three stages:
CO₂ fixation: CO₂ is fixed by RuBisCO to ribulose-1,5-bisphosphate (RuBP).
Reduction: 3-phosphoglycerate is reduced to triose phosphate.
Regeneration: RuBP is regenerated using most of the triose phosphate molecules produced.
RuBisCO: The enzyme responsible for CO₂ fixation, found in plants, algae, and cyanobacteria. It’s one of the most abundant enzymes in the biosphere, though it has a low catalytic rate. It is activated by carbamoylation and requires a magnesium ion.
Triose Phosphate Fate: Most triose phosphates regenerate RuBP; the remainder is used to form glucose, sucrose, or starch.

Question 58

NADPH and ATP Usage:

Answer 58

Each triose phosphate requires 6 NADPH and 9 ATP to be synthesized in the Calvin cycle, which are produced by the light reactions (photosynthesis).

Question 59

Photorespiration:

Answer 59

Photorespiration: A wasteful process where RuBisCO oxygenates RuBP, leading to the formation of 2-phosphoglycolate (wasteful). This occurs because of the high O₂ concentration in the atmosphere, and it consumes energy and reduces biomass accumulation.
Photorespiration is a metabolic cycle (glycolate pathway) involving chloroplasts, peroxisomes, and mitochondria, which recovers most of the lost carbon but still results in some carbon loss as CO₂.

Question 60

C₄ Photosynthesis:

Answer 60

C₄ Pathway: Involves fixing CO₂ into oxaloacetate by PEP carboxylase in mesophyll cells, and then transporting malate to bundle-sheath cells where RuBisCO fixes CO₂. This minimizes photorespiration.
Metabolic Cost: C₄ photosynthesis is more energy-intensive (5 ATP per CO₂) compared to C₃ photosynthesis (3 ATP per CO₂), but it is more efficient in hot environments where photorespiration is a problem.

Question 61

week 11 summary

Answer 61

The Calvin cycle is critical for CO₂ assimilation, using energy from light reactions (NADPH and ATP) to produce triose phosphates.
Photorespiration is a challenge for plants, but C₄ plants have evolved to reduce this cost by spatially separating the CO₂ fixation and RuBisCO activities.

Question 62

Where are the 13 enzymes of the reductive pentose
phosphate pathway located?
a. The peroxisomal matrix
b. The chloroplast thylakoid membrane
c. The chloroplast stroma
d. The mitochondrial intermembrane space
e. The mitochondrial matrix

Answer 62

The chloroplast stroma

Question 63

Which of the following is not a property of RuBisCO?
a. RuBisCO fixes CO 2 .
b. RuBisCO is the most abundant protein in plant leaves.
c. RuBisCO has an extremely low turnover number.
d. Plant RuBisCO is comprised of a total of 16 subunits (8 large and 8
small).
e. Ribulose 1,5-bisphosphate is an inhibitor of RuBisCO.

Answer 63

Ribulose 1,5-bisphosphate is an inhibitor of RuBisCO.

Question 64

Which of the following statements on C 3 and C 4 plants is
incorrect?
a. C 4 plants use PEP carboxylase to catalyse the initial fixation CO 2 .
b. The first stable intermediate in C 3 plants for the fixation of CO 2 is 3-
phosphoglycerate.
c. C 4 plants spatially separate PEP carboxylase and RuBisCO in two cell
types.
d. C 3 plants require high light intensity to grow normally.
e. RuBisCO has the unfortunate property that it can take O2 as an
alternative substrate to CO 2 .

Answer 64

C 3 plants require high light intensity to grow normally

Question 65

Nutrient Assimilation and the Nitrogen Cycle:

Answer 65

Nutrient assimilation involves converting mineral nutrients into organic compounds like amino acids and cofactors.
Nitrogen (N₂) is essential for plant growth but is not directly available to most organisms. Nitrogen must be fixed from the atmosphere by specific bacteria or archaea.
Industrial nitrogen fixation (Haber-Bosch process) is energy-intensive.
The nitrogen cycle includes processes like nitrification (conversion of ammonia to nitrate), denitrification (reduction of nitrate to N₂), and anammox (anaerobic conversion of ammonia and nitrite to N₂).

Question 66

Nitrogen Assimilation:

Answer 66

Nitrogen assimilation requires a lot of ATP: 12 ATP per amide N for nitrate reduction, and about 10 ATP for nitrogen fixation in symbiotic plants.
Plants and bacteria reduce nitrate (NO₃⁻) and nitrite (NO₂⁻) to ammonia (NH₄⁺) using nitrate reductase and nitrite reductase, enzymes involved in the process.
Ammonium toxicity: High levels of NH₄⁺ are toxic as they dissipate pH gradients across membranes, leading to stress in plants and animals. Plants store excess NH₄⁺ in vacuoles.

Question 67

Nitrogen Fixation:

Answer 67

Nitrogen fixation is catalyzed by the nitrogenase complex in nitrogen-fixing bacteria. This process requires anaerobic conditions because O₂ inactivates nitrogenase.
Free-living and symbiotic bacteria (like those in legume root nodules) fix nitrogen, converting N₂ into ammonia (NH₃), which is then assimilated into organic compounds.

Question 68

Incorporating Ammonium into Amino Acids:

Answer 68

Glutamine synthetase (GS) and glutamate synthase (GOGAT) are key enzymes that incorporate ammonium into amino acids.
GS: Catalyzes the formation of glutamine from glutamate and ammonium.
GOGAT: Uses glutamine to produce glutamate, with NADH or ferredoxin as electron donors.
Aminotransferases transfer an amino group from glutamate to other molecules, forming different amino acids.

Question 69

Sulfur Assimilation:

Answer 69

Sulfur assimilation begins with the uptake of sulfate (SO₄²⁻) from the soil. Plants reduce sulfate to cysteine (Cys) via several enzyme-catalyzed steps.
The reduction process changes sulfur’s oxidation state from +6 (in sulfate) to -4 (in cysteine), requiring 10 electrons.
ATP sulfurylase catalyzes the activation of sulfate, preparing it for reduction. The process involves enzymes like glutathione and ferredoxin to facilitate further reductions.

Question 70

week 12 summary

Answer 70

Nitrogen and sulfur assimilation in plants are complex, energy-consuming processes involving several enzymes.
Nitrogen fixation requires anaerobic conditions and a high-energy input, while sulfur assimilation involves sulfate reduction to cysteine, a critical amino acid for plants.

Question 71

Which of the following statements on the nitrogen cycle is
incorrect?
a. Nitrification is the oxidation of NH 3 to NO 2- and then to NO 3- .
b. Nitrate and nitrite reductase catalyse the reduction of NO 3- and NO 2-
to NH 3 .
c. Anammox bacteria convert N 2 to NH 3 and NO 2- anaerobically.
d. The oxidation state of nitrogen varies from -3 (in NH 4+ ) to +5 (in
NO 3- ).
e. Anaerobic bacteria use NO 3- and NO 2- as the terminal electron
acceptor.

Answer 71

Anammox bacteria convert N₂ to NH₃ and NO₂- anaerobically.

Explanation: Anammox bacteria perform an anaerobic process that converts NH₃ (ammonia) and NO₂- (nitrite) into N₂ (nitrogen gas), not the other way around. This process is called anaerobic ammonium oxidation (anammox).

Question 72

Which of the following is not a feature of nitrogen assimilation
in plants?
a. Each subunit of nitrate reductase contains FAD, haem and a Mo atom
complexed to a pterin.
b. NAD(P)H provides the electrons for the reduction of NO 3- and NO 2- .
c. Ferredoxin provides the electrons for the reduction of NO 2- to NH 4+ .
d. The reducing equivalents used by nitrite reductase are derived from
the carbon assimilation reactions of photosynthesis.
e. Nitrite reductase is a single polypeptide.

Answer 72

the reducing equivalents used by nitrite reductase are derived from the carbon assimilation reactions of photosynthesis.

Explanation: The reducing equivalents used by nitrite reductase are actually derived from ferredoxin (which is reduced during photosynthesis), not directly from the carbon assimilation reactions of photosynthesis.

Question 73

Which of the following statements on sulfur assimilation in
plants is incorrect?
a. Plants absorb sulfur from the soil in the form of SO 42- .
b. Before any sulfur reductive reactions can proceed, SO 42- needs to be
activated.
c. APS is an abbreviation for 5¢-adenylylsulfate.
d. The final molecular form in plant sulfur assimilation is a sulfide.
e. Serine is converted to O-acetylserine as the precursor for cysteine.

Answer 73

the final molecular form in plant sulfur assimilation is a sulfide.

Explanation:
In plant sulfur assimilation, the final molecular form is not a sulfide. Instead, the sulfur from sulfate (SO₄²⁻) is reduced and incorporated into cysteine.

Question 74

Secondary Metabolites

Answer 74

Definition and Function
Secondary metabolites are non-essential for basic growth but vital for defense, attraction, and competition.
Categories: terpenes, phenolics, and nitrogen-containing compounds.

Question 75

Terpenes

Answer 75

Largest class, derived from isoprene units.
Biosynthesis pathways: Mevalonic acid and Methylerythritol phosphate (MEP) pathways.
Functions:
Defense (e.g., toxic monoterpenes in conifers).
Constituents of essential oils (e.g., menthol in peppermint).
Classes based on isoprene units: monoterpenes, sesquiterpenes, diterpenes, triterpenes, tetraterpenes.

Question 76

Phenolics

Answer 76

Contain a phenol group; derived from phenylalanine via the shikimic acid pathway.
Functions:
Defense against herbivores/pathogens.
UV protection, pollinator attraction.
Structural roles (e.g., lignin in cell walls).
Subtypes: Flavonoids (e.g., anthocyanins for pigmentation), tannins, lignins.

Question 77

Nitrogen-Containing Compounds

Answer 77

Include alkaloids and cyanogenic glycosides.
Functions:
Alkaloids: Defense, physiological effects on animals (e.g., morphine, nicotine).
Cyanogenic glycosides: Release toxic cyanide when broken down.

Question 78

Plant Hormones
Definition

Answer 78

Chemical messengers influencing growth, metabolism, and morphogenesis.
Functions through specific signal transduction pathways.

Question 79

Major plant Hormones and Functions

Answer 79

Auxins: Promote cell elongation, root formation, and phototropism (e.g., indole-3-acetic acid).
Gibberellins: Promote stem elongation, seed germination, and flowering.
Cytokinins: Stimulate cell division, delay senescence, and affect meristem activity.
Ethylene: Regulates fruit ripening, stress responses, and seedling growth.

Question 80

How many carbon atoms is the structure of a tetraterpene
based on?
a. 4
b. 8
c. 20
d. 40
e. 80

Answer 80

Terpenes are built from isoprene units, each containing 5 carbon atoms.
A tetraterpene is made of 8 isoprene units, so:
8
×
5
=
40
8×5=40 carbon atoms.

Question 81

Which of the following is not a feature of phenolic compounds
in plants?
a. The protein amino acid phenylalanine is an intermediate in the
biosynthesis of most plant phenolics.
b. The most important pathway for converting carbohydrates to aromatic
amino acids is the shikimic acid pathway.
c. The building blocks of lignin are coniferyl, coumaryl and sinapyl
alcohols.
d.
e. Anthocyanidins are anthocyanins that lack the sugar group

Answer 81

The flavonoids are a group of anthocyanins.

flavonoids are not a subgroup of anthocyanins; rather, anthocyanins are a subgroup of flavonoids.

Question 82

Which of the following is a gaseous plant hormone or group
of plant hormones?
a. Gibberellins
b. Auxins
c. Cytokinins
d. Strigolactones
e. Ethylene

Answer 82

e. Ethylene