Molecular Biology Quiz: tRNA and Translation
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Questions and Answers

Which of the following statements accurately describes the relationship between a tRNA molecule's anticodon loop and its corresponding mRNA codon?

  • The anticodon loop recognizes the mRNA codon based on the sequence of its three bases, but the interaction is not directly involved in the formation of the polypeptide chain.
  • The anticodon loop binds to the mRNA codon through a process of hydrogen bonding, utilizing only the first two bases of the anticodon sequence.
  • The anticodon loop contains a sequence of three bases that are complementary to the mRNA codon, enabling the tRNA to bind to the mRNA. (correct)
  • The anticodon loop interacts with the mRNA codon by forming a transient, non-covalent bond with the mRNA molecule.

    • Which of the following molecules is responsible for catalyzing the covalent bonding of an amino acid to its corresponding tRNA molecule?

  • tRNA synthetase
  • Ribosomal RNA
  • mRNA polymerase
  • Aminoacyl-tRNA synthetase (correct)

    • Which of the following statements correctly describes the role of the TΨC loop in tRNA structure?

  • It is directly involved in the binding of the tRNA to the ribosome.
  • It is essential for the recognition of the tRNA molecule by the aminoacyl-tRNA synthetase.
  • It plays a significant role in the overall structure and stability of tRNA by contributing to the formation of the tertiary structure. (correct)
  • It contains the anticodon sequence that recognizes the mRNA codon.

    • During protein synthesis, where does the process of translation begin on an mRNA molecule?

    <p>At the 5' end of the mRNA molecule, near the start codon (AUG). (D)</p> Signup and view all the answers

    Which of the following is NOT a characteristic of the acceptor arm in tRNA?

    <p>It is involved in the recognition of the mRNA codon. (A)</p> Signup and view all the answers

    Which of the following statements accurately describes the structure of the eukaryotic ribosome?

    <p>The eukaryotic ribosome is composed of a large subunit (60S) and a small subunit (40S), which together form a complex with a sedimentation coefficient of $80S$. (C)</p> Signup and view all the answers

    Which of the following statements accurately describes the role of the D loop in tRNA?

    <p>It is essential for the folding of the tRNA molecule into its cloverleaf structure. (B)</p> Signup and view all the answers

    Which of the following is NOT a true statement about nuclear pore complexes (NPCs)?

    <p>NPCs are responsible for the breakdown of proteins that are imported into the nucleus. (D)</p> Signup and view all the answers

    What is the primary function of signal sequences in proteins?

    <p>To determine the final location of the protein within the cell. (D)</p> Signup and view all the answers

    How do motor proteins like kinesin and dynein differ in their movement along microtubules?

    <p>Kinesin moves towards the plasma membrane, while dynein moves towards the nucleus. (B)</p> Signup and view all the answers

    Which of the following is NOT a type of cellular communication mentioned in the content?

    <p>Synaptic signaling (D)</p> Signup and view all the answers

    Which type of receptor acts as a channel that opens only when a specific signal molecule binds to it?

    <p>Ligand-gated ion channels (D)</p> Signup and view all the answers

    What is the primary role of signal transduction in cellular communication?

    <p>To convert an extracellular signal into an intracellular response. (B)</p> Signup and view all the answers

    Why is it important for mitochondrial membranes to have pores that prevent protons from passing through?

    <p>To maintain the proton gradient that drives ATP synthesis. (B)</p> Signup and view all the answers

    Which of the following is a common characteristic of signal sequences involved in protein transport?

    <p>They are always recognized by a specific protein translocator. (B)</p> Signup and view all the answers

    Why is RuBisCO considered an inefficient enzyme in the Calvin cycle?

    <p>It has a higher affinity for oxygen than carbon dioxide, leading to photorespiration. (D)</p> Signup and view all the answers

    Which of the following is an example of a cellular response to an environmental stimulus?

    <p>All of the above. (D)</p> Signup and view all the answers

    Which of the following statements accurately describes the role of bundle sheath cells in C4 plants?

    <p>They receive a 4-carbon compound from mesophyll cells, which is then decarboxylated to release carbon dioxide for the Calvin cycle. (C)</p> Signup and view all the answers

    What is the primary difference between endocrine and paracrine signaling?

    <p>Endocrine signaling uses hormones that travel through the bloodstream, while paracrine signaling uses local mediators that act on nearby cells. (B)</p> Signup and view all the answers

    What is the primary advantage of crassulacean acid metabolism (CAM) in plants?

    <p>Increased efficiency of carbon fixation in dry environments. (D)</p> Signup and view all the answers

    Which of the following accurately describes the role of phosphatases in signal transduction?

    <p>Phosphatases reverse the phosphorylation of target proteins by removing phosphate groups. (B)</p> Signup and view all the answers

    How do pyrenoids in algae promote efficient carbon fixation?

    <p>They actively transport carbon dioxide or bicarbonate into the chloroplast and concentrate them around Rubisco. (B)</p> Signup and view all the answers

    Which of the following statements correctly describes the mechanism of signal amplification through second messengers?

    <p>Second messengers amplify the signal by triggering a cascade of events, activating multiple downstream enzymes or signaling molecules for each single messenger molecule. (C)</p> Signup and view all the answers

    Which of the following statements about the inner membrane of mitochondria is INCORRECT?

    <p>It is composed of a double layer of phospholipids, similar to the outer membrane. (D)</p> Signup and view all the answers

    Why is the number of mitochondria per cell variable?

    <p>It reflects the energy requirements of the cell. (C)</p> Signup and view all the answers

    What is the primary effect of protein phosphorylation on the target protein?

    <p>Phosphorylation results in a conformational change in the target protein, potentially altering its activity. (B)</p> Signup and view all the answers

    How many turns of the Calvin cycle are required to generate one glucose molecule?

    <p>6 (D)</p> Signup and view all the answers

    Which of the following is NOT a key feature of enzyme-linked receptors?

    <p>Enzyme-linked receptors directly bind to second messengers like cAMP or calcium to initiate downstream signaling. (A)</p> Signup and view all the answers

    How does the olfactory system distinguish between different smells?

    <p>The brain interprets different smells based on the pattern of receptor activation by a complex mixture of odorant molecules. (C)</p> Signup and view all the answers

    What is the primary role of ATP and NADPH in the Calvin cycle?

    <p>To reduce 3-phosphoglycerate (3-PGA) to glyceraldehyde-3-phosphate (G3P). (B)</p> Signup and view all the answers

    Which factor(s) contribute(s) to the occurrence of photorespiration in plants?

    <p>Low carbon dioxide concentration and high oxygen concentration. (A)</p> Signup and view all the answers

    Which of the following is NOT a characteristic of C4 plants?

    <p>They utilize PEP carboxylase, which has a higher affinity for oxygen than carbon dioxide. (D)</p> Signup and view all the answers

    Which of the following is NOT a role of the cytoskeleton?

    <p>Metabolic processes (B)</p> Signup and view all the answers

    Flashcards

    tRNA Structure

    tRNA has a cloverleaf secondary structure and an inverted 'L' tertiary structure.

    Acceptor Arm

    The 3' terminal of tRNA where an amino acid attaches via a hydroxyl group.

    D Loop

    Part of tRNA that aids in its folding.

    Anticodon Loop

    Contains the complementary codon for the amino acid carried by tRNA.

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    TΨC Loop

    Stabilizes the tRNA structure and aids in its function.

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    Aminoacyl-tRNA Synthetase

    Enzymes that attach amino acids to their corresponding tRNA.

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    Translation Stages

    Includes tRNA charging, initiation, elongation, and termination.

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    Translocation

    Ribosome shifts along the mRNA by one codon after polypeptide formation.

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    eEF2

    A factor that facilitates translocation by hydrolyzing GTP to GDP, providing energy.

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    Uncharged tRNA

    tRNA that has released its amino acid, now in the E site of the ribosome.

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    Stop codon

    A codon that signals the termination of protein synthesis.

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    Release factors (RFs)

    Proteins that mediate the final steps of translation termination.

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    Actin filaments

    5-9nm filaments providing cell strength and structure, recyclable as monomers.

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    Plus end of Actin

    The end of an actin filament where monomers are added, aiding cellular movement.

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    Intermediate filaments

    Diverse proteins providing mechanical strength and cell connections, larger than actin.

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    Microtubules

    Hollow tubes with a plus and minus end, part of the cytoskeleton structure.

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    G-protein coupled receptor (GPCR)

    A cell surface receptor that activates G-proteins upon ligand binding, initiating a signaling cascade.

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    Enzyme-linked receptor

    A receptor that becomes an active enzyme upon ligand binding, often associated with tyrosine kinase activity.

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    Second messengers

    Molecules that amplify signals within a cell, allowing a small signal to produce a larger response.

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    Protein phosphorylation

    The addition of a phosphate group to a protein, altering its function and activity.

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    Differentiation

    The process by which a less specialized cell becomes a more specialized cell type.

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    Signal Sequences

    Specific combinations of amino acids that guide protein transport.

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    Nuclear Pore Complex (NPC)

    Proteins that regulate transport in and out of the nucleus through pores.

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    Gated Transport

    Method of transporting proteins through nuclear pores in both directions.

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    Transmembrane Transport

    Movement of proteins into organelles through specific translocator proteins.

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    Motor Proteins

    Proteins that transport cellular components along cytoskeletal filaments.

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    Myosin

    A motor protein that moves along actin filaments for transport.

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    Kinesin

    Motor protein that transports toward the plasma membrane along microtubules.

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    Dynein

    Motor protein that transports toward the nucleus along microtubules.

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    Cell Communication Types

    Includes endocrine, paracrine, and autocrine signaling methods.

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    Receptor Activation

    Specific receptor proteins on the plasma membrane transmit signals when activated by ligands.

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    Carbon Fixation

    The process where CO₂ combines with RuBP to form a 6-carbon compound.

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    RuBisCO

    An enzyme that catalyzes the reaction between CO₂ and RuBP in carbon fixation.

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    3-PGA

    A 3-carbon molecule formed from the cleavage of a 6-carbon compound in carbon fixation.

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    G3P

    A 3-carbon sugar produced from 3-PGA, used to synthesize glucose.

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    Regeneration of RuBP

    The process of converting G3P back to RuBP using ATP to continue the cycle.

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    C4 Plants

    Plants that fix CO₂ into a 4-carbon compound to reduce photorespiration.

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    CAM Plants

    Plants that fix CO₂ at night and store it as malic acid for daytime use.

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    Photorespiration

    A process where RuBisCO fixes oxygen instead of carbon dioxide, reducing efficiency.

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    Mitochondria Structure

    Organelles with inner and outer membranes that create an intermembrane space and internal matrix.

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    Cristae

    Folded structures of the inner mitochondrial membrane that increase surface area for ATP production.

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    Study Notes

    Criteria of Life

    • Life is defined by evolution through natural selection.
    • Living things are separated from their environment by a boundary.
    • Living things are metabolically active, maintaining themselves, growing, and reproducing.
    • Anything made of cells meets the criteria for being considered living.
    • Viruses meet the first two criteria, but only meet the third when inside a cell, creating debate over their status as living organisms.

    Nucleic acids

    • DNA and RNA are polymers composed of a sugar-phosphate backbone and bases.
    • DNA is a double helix with two antiparallel strands, joined by hydrogen bonds from complementary base pairing.
    • Information is read from the 5' end towards the 3' end.

    Amino acids

    • Amino acids have a common structure with a carboxyl group and an amino group.
    • Variations in amino acids are due to differences in the R group on their side chains.
    • There are 20 amino acids that are encoded in the genome and used to make proteins.

    Lipids

    • Lipids are key for membrane formation and energy storage and cell communication.
    • Most lipids are hydrophobic, but some can be amphiphilic (with both hydrophilic and hydrophobic components).

    Sugars

    • Sugars are a primary energy source, and also used for structural support in cells as carbohydrates.
    • Glucose is converted into ATP.

    Genes - Introduction

    • Most of the genome is non-coding DNA, including introns, regulatory regions, and retroviral sequences (transposons).
    • DNA strands are always read from the 5' to 3' end.

    Endosymbiotic Theory

    • Infoldings in the plasma membrane of an ancestral prokaryote led to the development of endomembrane components, including the nucleus and endoplasmic reticulum.
    • In a first endosymbiotic event, an ancestral eukaryote consumed aerobic bacteria, which evolved into mitochondria.
    • A second endosymbiotic event involved the early eukaryote consuming photosynthetic bacteria, which evolved into chloroplasts.

    LECA

    • LECA (Last Eukaryotic Common Ancestor) had a nucleus, mitochondria, Golgi, lysosomes, and a cytoskeleton.
    • It evolved from the endosymbiosis of archaea and proteobacteria.

    Central Dogma

    • Information cannot be transferred from protein to protein or from protein to nucleic acid.
    • The translation of RNA into protein is unidirectional (DNA → mRNA → protein).

    Nucleotides - Structure

    • Nucleotides are composed of a phosphate group(s), a five-carbon sugar (ribose or deoxyribose), and a nitrogenous base.
    • The bases are divided into purines (adenine and guanine) and pyrimidines (thymine, cytosine, and uracil; uracil present in RNA instead of thymine).

    Nucleotides - Strands

    • Polynucleotide chains have nitrogenous bases linked to a sugar-phosphate backbone.
    • Nucleotides are connected by phosphodiester bonds.
    • Complementary base pairing occurs between a pyrimidine and a purine (C-G form 3 bonds, A-T form 2 bonds).

    DNA - Structure

    • The B-form of DNA is a double helix consisting of two antiparallel polynucleotide chains.
    • It has a major groove and a minor groove.
    • The grooves allow proteins to interact with the bases without unwinding the DNA.

    DNA vs RNA

    • DNA stores genetic information and replicates. It has two strands, a deoxyribose sugar, and the bases A, T, C, G.
    • RNA stores genetic information and converts DNA's genetic information to a format for protein building. It has one strand, a ribose sugar, and the bases A, U, C, G.

    Chromatin

    • DNA is packaged with proteins (histones) to form chromatin.
    • Nucleosomes are complexes of DNA and 8 histone proteins.
    • Histones are positively charged; DNA is negatively charged.
    • Euchromatin is open chromatin, unwound from histones, allowing for transcription.
    • Heterochromatin is closed chromatin, tightly wound around histones, usually preventing transcription.
    • Chromatin remodeling is influenced by histone variants, post-translational modifications (e.g., methylation, acetylation), and ATP-dependent chromatin remodeling complexes.

    Cell Cycle

    • The cell cycle has three checkpoints:
      1. Cell Growth Checkpoint (G1) – checks if the cell is large enough to replicate DNA, contains enough prepared material, and if needed enters a resting state (Go).
      1. DNA Synthesis Checkpoint (S) – DNA is replicated, checked for errors.
      1. Mitosis Checkpoint (M) – checks if mitosis (cell division) is completed.

    Semi-conservative DNA Replication

    • DNA replication involves separating parent DNA strands and using each as a template to synthesize a complementary strand.
    • Replication is bidirectional with multiple origins.
    • Linear DNA replication proceeds in the 5' to 3' direction, requires dNTPs and DNA Polymerases and Primase to synthesise strands.
    • dNTPs loose phosphate groups as pyrophosphate as the monomer bonds.

    Replication Accuracy and Mutations

    • DNA polymerase possesses proofreading and exonuclease activities to check for errors during replication.
    • DNA repair mechanisms correct mistakes and damage: Base Excision Repair (BER) fixes single-base damage.
    • Nucleotide Excision Repair (NER) corrects bulky lesions/crosslinks.
    • Mismatch Mediated Repair (MMR) corrects base mismatches.
    • Homologous Recombination (HR) repairs double-strand breaks.
    • Non-Homologous End-Joining (NHEJ) repairs double-strand breaks.
    • Uncorrected errors result in mutations.

    Telomeres

    • Telomeres are nucleotide sequences at the ends of eukaryotic chromosomes that prevent DNA erosion near the end of the molecules.

    Eukaryotic Gene Structure

    • Regulatory regions (promoters, enhancers) affect gene expression, located far from the regulated gene, either increasing or decreasing transcription.
    • Coding regions (transcription start site, exon, intron, termination) contain instructions for coding amino acids.
    • Gene expression is the process of producing RNA and proteins from a gene.

    Ribozymes

    • Ribozymes are catalytic RNAs that function as enzymes; involved in cutting/binding sequences, replicating RNA, and protein synthesis.
    • RNA World hypothesis describes the possibility that RNA was the first genetic material in the early stages of life.

    Transcription - Overview

    • Transcription requires DNA template (with promoter, coding sequences, terminator sequences), transcription machinery (RNA polymerase), and ribonucleotide triphosphates (rNTPs).
    • Transcription starts in a bubble.
    • mRNA is transcribed from the DNA template strand in a 5' to 3' direction.

    Transcription - Unit

    • Promoters, RNA coding region, and terminators are parts of the transcription unit.
    • Upstream sequences are located before the start of transcription.
    • Downstream sequences are located after the start of transcription.

    RNA polymerases

    • RNA Polymerase I transcribes rRNA genes; located in the nucleolus.
    • RNA Polymerase II transcribes mRNA, snRNA, and microRNA genes; located in the nucleoplasm.
    • RNA Polymerase III transcribes tRNA and 5S rRNA genes; located in the nucleoplasm.
    • Mitochondrial RNA polymerase transcribes mitochondrial RNA genes; located within mitochondria.

    Transcription - Initiation

    • Transcription machinery recognises and binds to the promoter to initiate transcription.
    • Accessory proteins (general transcription factors) are needed for transcription.
    • Regulatory proteins bind to DNA to modify chromatin structure.
    • Transcription factors and regulatory elements (enhancers/silencers) influence transcription rates.
    • Abortive initiation involves repeated synthesis and release of short RNA until the polymerase escapes the promoter and transitions into elongation.

    Transcription - Basal Apparatus

    • The basal apparatus consists of RNA polymerase, transcription factors, and a mediator complex and is necessary for transcription initiation.
    • The TATA box and a mediator complex are crucial for correctly positioning RNA polymerase.

    Transcription - Elongation

    • RNA polymerase transcribes the DNA template strand, synthesizing mRNA in a 5' to 3' direction along the template strand in a 3' to 5' direction.
    • DNA moves through a channel in RNA polymerase and makes a sharp turn at the active site.
    • The newly-forming RNA molecule continues to grow with added nucleotides.

    Transcription - Termination

    • There is no specific termination sequence for RNA polymerase II.
    • RNA polymerase II continues synthesizing RNA beyond the coding sequence.
    • Pre-mRNA is cleaved and the extra RNA sequence is degraded in a 5' to 3' direction by Rat1 (exonuclease).
    • Termination occurs when Rat1 reaches the polymerase.

    mRNA - Structure

    • mRNA has a 5' cap, exons, introns, and a 3' poly A tail.
    • The 5' cap is a modified guanine nucleotide, protecting mRNA from degradation and facilitating ribosome binding.
    • The 3' poly A tail is a sequence of adenine nucleotides that increases mRNA stability and facilitates ribosome binding.
    • Introns are non-coding sequences that are removed from pre-mRNA via splicing (removing introns, splicing exons together).
    • Alternative splicing generates multiple protein variations from a single gene.

    Nuclear export of mRNA

    • Mature mRNA forms a ribonucleoprotein complex (mRNP) by associating with specific RNA-binding proteins.
    • The nuclear pore complex (NPC) facilitates mRNA transport between the nucleus and cytoplasm, with specific export receptors.
    • Only correctly processed mRNAs are exported; improperly processed mRNAs are degraded or retained in the nucleus.
    • mRNA export can respond to cellular signals and stress conditions.

    Primary Structure

    • The primary structure of a protein is the linear sequence of amino acids.
    • Peptides form via condensation reactions between the carboxyl group of one amino acid and the amino group of another.

    3D Folding

    • Hydrogen bonding in the peptide backbone causes secondary structure, such as alpha-helices and beta-pleated sheets.
    • Interactions between side chains cause tertiary structures (3D folding of the polypeptide chain).
    • Quaternary structure is a combination of multiple polypeptide chains.
    • Proteins can have discrete domains, each with a specific function.

    Genetic Code

    • A codon is a triplet RNA code with 64 possible combinations (61 sense codons, 3 stop codons).
    • The genetic code is degenerate because more than one codon can specify the same amino acid.
    • Codons must be read in the correct reading frame for the synthesis of polypeptides.

    Transfer RNAs - Purpose

    • tRNAs transport specific amino acids to complementary codons of mRNA on the ribosome.
    • Each tRNA binds only one specific amino acid. (e.g. tRNA Pro binds proline.)

    Transfer RNAs - Structure

    • The secondary structure of tRNA resembles a cloverleaf due to hydrogen bonding between bases.
    • Important regions include acceptor arms, D loops, anticodon loops, and variable loops.

    Ribosomal RNA

    • Ribosomes are complexes of RNA and proteins, made in the nucleolus.
    • Eukaryotic ribosomes are composed of 18S, 5.8S, 5S, and 28S rRNA for the large and small subunit.

    Translation - Overview

    • Ribosomes bind to mRNA near the 5' end to initiate protein synthesis.
    • New amino acids are added at the carboxyl end (C-terminus) of the growing polypeptide chain.
    • This process has three stages: tRNA charging, initiation, elongation, and termination.

    Translation - tRNA Charging

    • Aminoacyl-tRNA synthetases catalyze the binding of amino acids to their corresponding tRNAs using ATP.

    Translation - Initiation

    • mRNA binds to the small ribosomal subunit (SSU).
    • Initiator tRNA binds to the mRNA's start codon.
    • The large ribosomal subunit joins the complex.
    • Initiation factors help facilitate the assembly of the initiation complex.

    Translation - Pioneer Round

    • Cap-binding complex (CBC) helps confirm there are no mistakes in mRNA prior to the large subunit binding.
    • The CBC complex is replaced by other initiation factors when the ribosome is translating the mRNA in a 5' to 3' orientation.

    Translation - Elongation

    • The ribosome moves along the mRNA in a 5' to 3' direction.
    • Charged tRNA molecules enter the A site.
    • A covalent peptide bond forms between amino acids in the A and P sites.
    • The ribosome translocates forward, moving the tRNA from the A site to the P site and the uncharged tRNA from the P site to the E site, where it is released.

    Translation - Termination

    • When a stop codon is reached, release factors enter the A site to break the bond between the last amino acid and the tRNA.
    • The completed polypeptide chain and ribosomal subunits are released.

    Roles of the cytoskeleton

    • The cytoskeleton provides support, strength, controls cell shape, transport, cell division, connecting cells in tissues, and cell movement.

    Actin

    • Actin molecules assemble into actin filaments, sometimes called microfilaments, measuring 5-9 nm in diameter.
    • Actin filaments are dynamic, allowing addition or removal of actin monomers at their ends.
    • Their plus end generally points outward toward the plasma membrane, pushing the membrane during cell movement.

    Intermediate filaments

    • Intermediate filaments are protein fibers that provide mechanical strength and connect cells in tissues.
    • They are intermediate in size compared to actin and microtubules.
    • They form the supporting nuclear lamina.

    Microtubules

    • Microtubules are hollow tubes, composed of tubulin.
    • They have plus and minus ends, with the minus ends typically located at the microtubule organizing center (MTOC) (centrosome) adjacent to the nucleus.
    • Microtubules are dynamic and can grow and shrink at their plus ends.
    • They play roles in cell transport (like carrying vesicles), and cell division (forming the mitotic spindle).

    Cell Migration

    • The cytoskeleton reassembles at new sites in response to chemical signals for cells to move toward or away from these signals.
    • Microtubules in filaments (like flagella and cilia) are arranged as doublets, with dynein proteins operating along these to coordinate the movement of these structures.

    Standard Light Microscopy

    • Techniques for viewing biological specimens: bright-field microscopy, phase-contrast microscopy, Differential Interference Contrast microscopy and staining techniques like Hematoxylin and Eosin for cell structures and Azan trichrome for connective tissues.

    Electron Microscopy

    • Electron microscopes use electrons instead of light to view specimens, producing highly magnified images with much higher resolution than light microscopes, but not capable of viewing live cells.

    Fluorescence Microscopy

    • Fluorescence microscopy is a type of light microscopy that uses fluorescent labels to visualize specific structures or molecules in cells or tissues.
    • Fluorescent proteins (like GFP) are commonly used to track specific molecules, proteins, or cells in living organisms or to stain specific structures within the cells.

    Conversion of light to chemical energy

    • Photosynthesis converts carbon dioxide and water into glucose and oxygen through the absorption and use of light energy. The equation representing this is 6CO2 + 6H2O → C6H12O6 + 6O2.

    The great oxygenation event

    • Cyanobacteria, through photosynthesis, produced oxygen, which led to a mass extinction event in pre-existing anaerobic organisms due to oxygen's toxicity.
    • The reduction in methane, caused by oxygen reacting with it to form carbon dioxide and water, resulted in a major drop in atmospheric temperatures, and a very large decrease in greenhouse gas effect.

    Chloroplasts

    • Chloroplasts contain double membranes and hold thylakoid membranes that are folded into grana where light reactions take place.
    • The stroma is the fluid material surrounding thylakoids, where light-independent reactions (Calvin cycle) occur.

    Pigments - Absorption Spectra

    • Different pigments, like bacteriochlorophyll a, chlorophyll a and b, phytoerythrobilin, and beta-carotene, absorb different wavelengths of light.

    Pigments - Structure and Function

    • Chlorophyll a is the primary pigment in plants absorbing violet, blue, and red light efficiently.
    • Chlorophyll b and carotenoids are accessory pigments that absorb different light wavelengths and pass energy to chlorophyll a or other pigments via resonance energy transfer to the reaction centre.

    Light dependent reaction - Photolysis

    • Photolysis is the splitting of water molecules by light energy via the oxygen evolving complex into protons, oxygen, and electrons.

    Light dependent reaction - Photophosphorylation

    • The light reactions can either occur in a linear fashion (Non cyclic), or a circular fashion (Cyclic).
    • Non-cyclic photophosphorylation produces ATP and NADPH by using light energy and splitting water molecules.
    • Cyclic photophosphorylation generates ATP by using light energy.

    Light-independent reaction - Calvin-Benson Cycle

    • The Calvin Cycle converts carbon dioxide into organic molecules like glucose.
    • The cycle involves carbon fixation, reduction, and regeneration steps.
    • Plants can use the C4 pathway or CAM pathway to minimize photorespiration in conditions of low CO2 or high temperatures.

    Mitochondria - Main Features

    • Mitochondria have an outer and inner membrane, creating an intermembrane space and an internal matrix.
    • The inner membrane folds into cristae, increasing its surface area.
    • The matrix contains enzymes needed for the citric acid cycle.

    Electrons and Protons

    • Oxidation involves the removal of an electron, while reduction involves the addition of an electron.
    • Hydrogen is a proton with an electron.
    • Electron transfer and reactions where protons (H+) are involved are considered redox reactions.

    Glycolysis

    • Glycolysis is a process converting glucose into pyruvate which is an important step for cellular respiration.
    • It results in the production of 2 ATP, 2 NADH, and 2 pyruvate per glucose molecule.
    • The pyruvate molecules enter the mitochondria from cytoplasm via a transport protein.
    • Oxidative decarboxylation removes CO2, producing acetyl-CoA.
    • NAD+ is reduced to NADH and CO2 is released.

    Kreb's (citric acid) cycle

    • Acetyl CoA enters the cycle reacting with oxaloacetate to form citrate (6 carbon molecule).
    • The cycle turns twice for 1 glucose molecule.
    • Outputs from the cycle include 3 NADH, 1 FADH2, 1 ATP, and 2 CO2.

    Oxidative Phosphorylation

    • Electrons from earlier stages (NADH and FADH2) are transferred to the electron transport chain (ETC) at complex I (from NADH) and complex II (from FADH2).
    • An ETC protein complex passes electrons along the chain releasing energy to pump hydrogen ions (H+) from matrix to the intermembrane space creating a proton gradient.
    • Oxygen acts as the final electron acceptor in the ETC; electrons combine with oxygen (O2) and protons forming water (H2O).
    • ATP synthase uses the energy from the proton gradient to make ATP from ADP.

    Chemiosmosis

    • The proton gradient made by the ETC generates a proton-motive force which is used by ATP synthase, an enzyme located in the inner membrane of the mitochondria, to convert ADP to ATP through chemiosmosis.
    • Uncoupling proteins dissipate this energy as heat; this helps with regulation in metabolic pathways involving coenzymes.

    Compartmentalisation

    • Specialized organelles in cells create compartments with specific functions for efficient metabolism.
    • Compartmentalisation allows for high cellular activity without interference between different processes.

    Membrane structure and function

    • Membranes have a fluid-mosaic structure with various proteins and lipids.
    • Controlling transport across the membrane (passive, facilitated, active) also plays an important role in regulating its function.

    Membrane lipids - phospholipids

    • Phospholipids are composed of glycerol and form the plasma membrane bilayer.
    • Sphingolipids are based on the sphingosine molecule and are involved in membrane structure.
    • Different combinations for head groups, hydrocarbon chain length, and saturation, produce a wide diversity of phospholipids.

    Passive transport across membranes

    • Hydrophobic (nonpolar) molecules can simply diffuse through the lipid bilayer.
    • Channel proteins and carrier proteins facilitate the diffusion of polar molecules and ions.
    • Facilitated diffusion (of certain molecules and ions) occurs along the concentration gradient without the expenditure of energy.

    Active transport

    • Cells actively move molecules against their gradient using ATP and protein carriers.
    • Sodium-potassium pumps and other examples are involved in creating gradients.

    Endocytosis

    • Receptor-mediated endocytosis, phagocytosis, and pinocytosis are types of endocytosis (engulfing substances into cells).
    • The cell membrane forms vesicles around external molecules or large particles.

    Exocytosis

    • Exocytosis is the process where materials are transported outside cells by fusing a vesicle with the plasma membrane. These materials can be proteins, hormones, neurotransmitters and other substances.
    • There are two main pathways for exocytosis. The constitutive secretory pathway exports substances constantly whilst the regulated pathway is signal-dependent for releasing substances at specific times.

    Signal sequences

    • Signal sequences are amino acid sequences within proteins that determine their location within a cell (intracellular, membrane or extracellular).
    • Signal peptides can act as signals and are often removed from the mature proteins.

    Transporting proteins within cells – gated transport

    • Proteins moving into the nucleus or being exported from it use gated transport systems.
    • Proteins have signals and gatekeeping proteins confirm their destinations.

    Transporting proteins within cells – transmembrane transport

    • Proteins moving across membranes via transporters.
    • Proteins with specific signal sequences activate translocators in the membrane allowing translocation across the membrane.
    • The signal sequence is often cut off by signal peptidases in the endoplasmic reticulum.

    Transporting proteins within cells – motor proteins

    • Motor proteins (like myosin, kinesin, and dynein) are responsible for moving cargo along filaments; mostly along microtubules or actin filaments.

    Types of information received

    • Cells receive various signals from the environment, including growth factors, death signals, contact with other cells or proteins in the extracellular matrix, hormones, light, odorants, touch, temperature, oxygen levels, pH, and magnetic fields.

    Mechanisms of Communication - Overview

    • Signaling methods include direct cell-cell, endocrine signaling, paracrine signaling, and autocrine signaling.
    • The receptor, signaling molecule/ligand, cellular response and signal cascade pathways are all critical parts of intercellular communication.

    Signal Reception

    • Ligand binding to a receptor changes the protein's conformation.
    • Receptors can be ligand-gated ion channels, G-protein coupled receptors (GPCRs), or enzyme-linked receptors.

    Signal Transduction - Second Messengers

    • Signals are amplified using second messengers (like cAMP, cGMP, IP3, DAG, and Ca2+) within the cell.
    • Adrenaline signaling via cAMP is an example, where adrenaline binds to its receptor inducing a cascade of events leading to a cellular response.

    Signal Transduction - Protein Phosphorylation

    • Kinases (enzymes) add phosphate groups to proteins, changing their structure/activity.
    • Phosphatases remove phosphate groups, reversing the effect.
    • Phosphorylation is a universal signaling mechanism.

    Olfactory Sensing

    • Olfactory receptors bind to volatile odor molecules with different affinities.
    • A pattern of receptor activation is recognized by the brain, producing a specific smell perception.

    Light Sensing

    • Light sensing mechanisms are involved in detecting light signals.

    Dealing with multiple signals

    • Cells can integrate signals from multiple sources and react appropriately, including regulating responses.

    Differentiation

    • Undifferentiated (generalist) cells become specialized cells during differentiation by expressing specific sets of genes, making them functional in a specific location.
    • Differentiation signals from the surrounding environment play a major role in controlling cell specialization.
    • Stem cells are undifferentiated (generalist) cells (totipotent, pluripotent, multipotent) that divide to form daughter cells. The daughter cells can either remain undifferentiated (self-renewal) or differentiate.
    • Cells receive differentiation signals to bind to receptors which trigger an intracellular response, ultimately influencing gene expression.
    • Activation/silencing of specific genes determines the eventual specialised function of the cell.

    Epigenetics and Differentiation

    • The modification of gene expression or activity without changing the DNA sequence is epigenetics.
    • Epigenetic mechanisms, including DNA methylation, histone acetylation, and histone methylation, control the switch between euchromatin (active gene expression) and heterochromatin (inactive gene expression) which in turn affects differentiation.

    The cell cycle

    • The cell cycle describes the progression of a cell through the phases of growth, DNA replication, and division.
    • Single-celled organisms can continuously repeat the cell cycle; whereas, in multicellular organisms, the cell cycle and cell division is strictly controlled. Post-mitotic cells are those that don’t divide further. Senescent cells have lost their capacity to divide due to age-related decline.

    G1 phase

    • The G1 phase of the cell cycle is characterized by significant protein and organelle synthesis.
    • The cell prepares for DNA synthesis during this stage.

    S phase

    • During the S phase, the cell duplicates its DNA by replicating each chromosome to form two identical copies of the same chromosome joined at the centromere.

    G2 phase

    • The G2 phase is characterized by rapid cell growth and preparation for mitosis.
    • The cells check whether the DNA replication was correctly completed and whether the cell is ready for mitosis.

    M phase

    • M-phase (mitosis) is the cell division process; composed of prophase, prometaphase, metaphase, anaphase, and telophase.
    • Kinetochores are protein complexes that bind to the chromosomes to help during mitosis.
    • The process of cell division involves a cleavage furrow formed and eventually the cell splitting into two daughter cells.

    Cell cycle regulation

    • Cell cycle is controlled at specific checkpoints, where the cell makes decisions for either continuing the cycle or stopping to ensure the cell is properly prepared.
    • DNA damage checkpoints halt the cell cycle when genomic damage is detected and need to be repaired. Incomplete DNA replication, not properly assembled chromosomes also halt cell cycles.

    Senescence

    • Telomeres are regions at the ends of chromosomes that shorten each time a cell divides, eventually causing senescence.
    • Telomerase is an enzyme that maintains telomere length, which is absent in normal cells.
    • Senescence (age-related), halt in cell cycle and can also be triggered during cellular stress; senescent cells don’t divide anymore.
    • Cancer cells have indefinite lifespan because they do not undergo senescence and continuously divide.

    Apoptosis vs Necrosis

    • Apoptosis is programmed cell death (essential for normal development and homeostasis); whereas, necrosis is uncontrolled cell death, associated with disease.
    • Apoptosis involves membrane blebbing, fragmentation into smaller bodies and no inflammatory response; whilst necrosis involves loss of membrane integrity, lysis, and inflammatory response.

    Importance of Apoptosis

    • Apoptosis is important for embryonic development, removing damaged/old cells, maintaining homeostasis (balancing cell division), and preventing uncontrolled cell growth (cancer).

    Triggering Apoptosis - Overview

    • Apoptosis is triggered by two main pathways: Receptor-mediated (extrinsic) pathway and mitochondria-mediated (intrinsic) pathway.
    • Caspases are a group of proteases that are activated by cleavage enzymes which cause a cascade-like activation in a system. The effector (executioner) caspases break down cellular components like cytoskeleton and DNA.

    Triggering Apoptosis – DISC Assembly

    • A death-inducing signaling complex (DISC) is formed after a ligand binds to its receptor, causing trimerization of the receptor.
    • Proteins are arranged into a DISC inside the membrane for the activation of procaspase 8. Once removed, procaspase 8 is then activated and proceeds to activate other caspases to trigger apoptosis.

    Role of Mitochondria in apoptosis

    • Cytochrome c release from the inner mitochondrial membrane is a key step in the intrinsic apoptotic pathway.
    • The release of cytochrome c leads to the formation of the apoptosome.
    • The apoptosome activates initiator caspases, which subsequently activate effector caspases, leading to apoptosis.
    • Control of cytochrome c release is determined by anti-apoptotic members of the Bcl-2 family.

    Forming Tissues – Introduction

    • Human bodies are made up of trillions of cells with specialized structures which need to work together in a coordinated way.
    • The infrastructure holding tissues together need to be malleable for cell division and to support changing environments.

    Cell Junctions – Gap Junctions

    • Gap junctions are proteins that are present in the cytoplasms of two cells; linking the cytoplasm of one cell to another, forming channels between the cells.
    • The channels promote efficient communication allowing the exchange of small signalling molecules and metabolites between attached cells.

    Cell Junctions – Tight Junctions

    • Tight junctions form a barrier between cells; preventing the passage of molecules between the cells using transmembrane proteins (Claudins and Occludins) between cells.
    • These cells are attached (anchored) to actin cytoskeleton which gives them structural strength.

    Cell Junctions – Adhering Junctions

    • Cadherins are protein molecules on cell surfaces which aid the connection between cells that have similar cadherin types.
    • Desmosomes link cells via intermediate filaments; they are stronger (wider gap) compared to tight junctions.
    • Adherens junctions connect to the actin filaments and use cadherin and anchor proteins.

    The Extracellular Matrix – Overview

    • ECM is a scaffolding for cells, providing structure support and attachment.
    • The ECM is made by cells.
    • It is composed of ECM proteins, integrins, fibronectin and proteoglycans that link the cells to maintain the extracellular space.

    The Extracellular Matrix – Collagen

    • Collagen is the most abundant protein in the body, providing structural support to tissues.
    • At least 28 different types of collagen exist, with variations in structure and function (redundancy).

    The Extracellular Matrix – Proteoglycans

    • Many types exist; some are heavily glycosylated, with long sugar chains that are helpful in absorbing compressive forces.
    • Hyaluronan is a type of proteoglycan that provides lubrication to the extracellular matrix.

    The Extracellular Matrix – Fibronectin

    • A glycoprotein with binding sites for numerous ECM proteins and cell surface integrins is fibronectin (assists in cell adhesion).

    The Extracellular Matrix – Integrins

    • The cell surface integrins act as receptors that link the cells to the ECM, controlling cell signalling and sensing the environment. They are composed of alpha and beta chains.

    The Extracellular Matrix – Hemidesmosomes

    • Hemidesmosomes attach cells to basement membranes anchoring them to the ECM using integrins and intermediate filaments.

    The Extracellular Matrix – Healing

    • Fibroblasts are the main type of cell involved in repairing and maintaining the extracellular matrix (ECM) for healing processes of injured tissues.
    • After injury, fibroblasts become more active and begin to produce/deposit collagen. Scar tissue formation occurs if wound healing goes incorrectly.

    Multicellularity – Evolution

    • Multicellularity arose many times in evolutionary history via unique evolutionary pathways.
    • Cell grouping and coordination offered advantages like resilience to threats or enhanced resource acquisition with benefits outweighing drawbacks like exploitation vulnerability.
    • Cell colonies, such as biofilms formed by bacteria, slime moulds (dictyostelium amoebae) and algae (chlamydomonas, volvox) can form multicellular aggregates without sharing identical genetic information or being clonal but still work cohesively.

    Bacterial Biofilms

    • Multicellular aggregates are groups of bacteria and archaea.
    • Individual cells join together and attach to surfaces. They work together, secreting proteins that act like the extracellular matrix (ECM) and the microcolonies (groups of cells) can grow and expand into biofilms.

    Social Amoeba (Dictyostelium)

    • Life cycle involves three different stages: ○ Free-living amoeba stage. ○ Aggregating amoeba stage. ○ Spore forming structure (grex).
    • In response to scarce food supply, individual cells aggregate to form a multicellular structure.

    Algae (Chlamydomonas and Volvox)

    • Chlamydomonas is a unicellular algae that uses flagella for mobility.
    • Volvox forms multicellular colonies of thousands of specialized cells (germ cells and somatic cells).

    Robustness - Overview

    • Cells have a range of strategies to cope with a range of stresses.
    • Redundancy and multiple cell/organism pathways is often involved in stress response.

    Robustness - High Temperatures

    • Cells adjust membrane composition and protein function to maintain proper functions in high temperature environments.
    • Heat shock proteins help in assisting protein folding and the cell to more easily recover from this stress.
    • More saturated fatty acids and cholesterol in the membrane are characteristics helpful in maintaining membrane fluidity.

    Robustness - Extreme Heat

    • Organism such as Geogemma barossi survive in extreme temperatures.
    • Cells increase GC content/bases, supercoiling DNA, and creating specialized proteins to cope with high temperatures.

    Robustness - Low Temperatures

    • Cells respond to low temperatures by altering composition in their membranes to prevent being damaged by ice formation.
    • Glycoproteins and glycolipids can protect the membrane from degradation.
    • Some species (e.g. Antarctic fishes) have evolved "anti-freeze" glycoproteins to protect themselves from ice crystal formation.

    Robustness - Low Oxygen

    • Cells respond to low-oxygen availability by halting the cell cycle, switching to glycolysis (anaerobic metabolism), and activating mechanisms to stimulate blood vessel production (angiogenesis).
    • Hypoxia-inducible factors (HIFs) are protein complexes that move into the nucleus in response to low oxygen to regulate gene expression.

    Robustness – Nutrient Deprivation

    • Cells enter a reversible cell-cycle arrest state called quiescence to conserve resources when deprived of nutrients during cellular stress.
    • Autophagy and proteasomes are responses to maintain homeostasis; recycling unwanted/damaged proteins to form new ones.

    Robustness – Toxic Environments

    • Cells encounter different types of toxic agents; however, cells have tolerance mechanisms.
    • Reactive oxygen species (ROS) are highly reactive molecules with unpaired electrons (free radicals). ROS can cause damage and trigger stress or cell death reactions.
    • Cells have protective mechanisms against ROS, like anti-oxidants such as glutathione, and enzymes such as superoxide dismutases and catalase to minimise effects.

    Robustness – Repairing DNA Damage

    • Cells have mechanisms to identify and repair DNA damage to prevent harmful mutations.
    • Extensive DNA damage is a critical trigger for apoptosis.
    • Cancer occurs when DNA repair mechanisms fail, leading to uncontrolled cell growth.

    ONE OF THE QUESTIONS: How do heat shock proteins protect cells from high temperatures?

    • Heat shock proteins assist protein folding.

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