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Lecture 3: Cellular organisation II – Protein Synthesis and Mitosis (EPBIOL259)

L3.1 Proteins

  • Definition and significance

    • Proteins are polymers of amino acids joined by peptide bonds; they are versatile macromolecules essential for virtually all cellular functions.
    • In humans, proteins underpin much of anatomy and physiology; understanding their structure and behaviour is foundational.
    • Building blocks: amino acids (AAs) and nucleic acids (nucleotides) are the basic building blocks for proteins and nucleic acids, respectively.

  • Functions of proteins (Table 2.6, Saladin et al., 2022)

    • Keratin: strengthens nails, hair, and skin surface (structural).
    • Collagen: structural foundation of bones, cartilage, teeth, and dermis.
    • Communication: hormones and cell-to-cell signals; receptors on receiving cells.
    • Membrane transport: channels and carriers in membranes; regulate passage; involvement in nerve and muscle activity.
    • Catalysis: enzymes as biological catalysts in metabolic pathways (globular proteins).
    • Recognition and protection: immune recognition; antibodies; toxins neutralization; clotting factors.
    • Movement: molecular motors; intracellular transport; muscle contractions and ciliary beating.
    • Cell adhesion: proteins binding cells to each other and extracellular matrix; roles in fertilization and immune cell interactions.

  • Membrane proteins and their roles on the cell surface (Figure 3.3, Saladin et al., 2022)

    • Receptor: binds chemical messengers (e.g., hormones).
    • Enzyme: terminates signal by breaking down messengers.
    • Channel: continuously open channel allowing solutes to pass.
    • Gated channel: opens/closes to regulate solute flow.
    • Cell-identity marker: glycoprotein identifying self versus foreign cells.
    • Cell-adhesion molecule (CAM): binds cells to one another or to extracellular matrix.

  • Amino acids: building blocks of proteins

    • There are 20 amino acids used to build proteins in the human body.
    • Proteins are polymers of amino acids linked by peptide bonds; chains longer than 10–15 amino acids are polypeptides; proteins are typically >50 amino acids.
    • The amino acid sequence determines protein identity and function; the sequence is encoded by the genetic code in DNA.
    • Some proteins require binding of nutrients (ions) for optimal function (e.g., iron in hemoglobin; zinc, magnesium, etc.).
    • General amino acid structure: \mathrm{H_2N{-}CH(R){-}COOH} where R is the side chain that differs among amino acids (e.g., Tyrosine, Arginine shown in examples).
    • Peptide bond formation and dipeptides: two amino acids join to form a dipeptide with the release of water (condensation reaction).
    • Example schematic (illustrative): aa1 + aa2 -> dipeptide + H_2O.

  • Nucleic acids (DNA and RNA) – overview

    • Nucleic acids are organic polymers that carry genetic information and are essential for protein synthesis.
    • DNA (deoxyribonucleic acid): resides in the nucleus; contains genes; typically a double helix with a sugar–phosphate backbone.
    • RNA (ribonucleic acid): carries out the orders given by DNA; ribose sugar; single-stranded; contains uracil instead of thymine.
    • DNA length can range widely; a typical DNA molecule comprises ~$10^6$ to $10^9$ nucleotides per molecule in many organisms.

  • Nucleotides and bases

    • Nucleotide components: monosaccharide (deoxyribose in DNA, ribose in RNA), phosphate group, and one nitrogenous base.
    • Five nitrogenous bases in DNA/RNA:
    • Purines: \text{G (guanine)}, \text{A (adenine)}
    • Pyrimidines: \text{C (cytosine)}, \text{T (thymine)}, \text{U (uracil)}
    • Base-pairing rules in DNA and RNA base-pair interactions: A\text{-}T, \; C\text{-}G in DNA; in RNA, A\text{-}U, \; C\text{-}G (note: RNA uses uracil instead of thymine).

  • DNA structure and RNA structure

    • DNA: two nucleotide chains wound into a double helix; helical backbone formed by alternating sugar (deoxyribose) and phosphate groups.
    • RNA: single nucleotide chain; contains ribose sugar and uracil.

  • Transcription and translation – overview

    • Transcription: DNA → mRNA (gene code copied into mRNA).
    • Translation: mRNA → protein (amino acid sequence assembled by ribosomes using tRNA anticodons).
    • Codons: three-nucleotide units on mRNA that specify specific amino acids; there are 64 possible codons; some codons designate amino acids, others are STOP signals.
    • Ribosomes are the molecular machines that read mRNA and assemble amino acids into polypeptides; tRNA brings amino acids to the ribosome via anticodons that pair with codons on mRNA.

  • L3.1 Nucleic acids – transcription and RNA editing (Transcription details)

    • Transcription starts at a gene (start codon) and involves:
    • Helicase unwinding the DNA double helix exposing the gene bases (A, T, C, G).
    • RNA polymerase reads the gene and creates a complementary mRNA strand (mirror image of the gene code).
    • Complementary base pairing during transcription:
    • For DNA bases encountered by RNA polymerase: \text{T} \rightarrow \text{A}, \quad \text{G} \rightarrow \text{C}, \quad \text{C} \rightarrow \text{G}, \quad \text{A} \rightarrow \text{U}^*
      • Note: in RNA, thymine is replaced by uracil (U); thus A pairs with U in RNA.
    • RNA processing in the nucleus: noncoding segments are removed, coding segments are spliced together to form mature mRNA that exits through nuclear pores into the cytoplasm.
    • Example (from slide): DNA sequence code and its mRNA copy:
    • DNA: 5' - T A C C G T C C A - 3'
    • mRNA: 5' - A U G G C A G G U - 3'

  • L3.1 Transcription practice (Learning Activity B)

    • Questions included:
    • Which complementary base pairs with thymine (T)?
    • Which complementary base pairs with cytosine (C)?
    • Which complementary base pairs with adenine (A)?
    • Complete the complementary mRNA sequence for the given DNA sequence: A T C G T A C C C T G A T T G C G G

  • L3.2 Translation and protein synthesis – key details

    • Translation: mRNA is read by ribosomes in units called codons (three nucleotides).
    • Codons specify specific amino acids; there are 64 codons in total; example: \text{AUG} codes for methionine (start codon).
    • Anticodon: a three-nucleotide sequence on tRNA that is complementary to a codon on mRNA; ensures correct amino acid delivery to the growing polypeptide chain.
    • The process continues until a STOP codon is reached, at which point the ribosome releases the newly formed protein.

  • Protein processing and secretion

    • Proteins destined for lysosomes or secretion:
    • Ribosome–mRNA complexes dock on rough endoplasmic reticulum (RER).
    • The nascent protein enters ER cisterna during assembly; ER enzymes trim or splice certain amino acid segments.
    • Modified proteins are packaged into transport vesicles and bud off the ER toward the Golgi complex.
    • Golgi sorts proteins, may add carbohydrate groups or other components, and then vesicles bud off from the Golgi.
    • Proteins may become lysosomes or be released from the cell via exocytosis.

  • Organelles involved in protein synthesis and secretion (Figure references)

    • Rough endoplasmic reticulum (RER)
    • Golgi apparatus
    • Vesicles (transport and secretory)
    • Ribosomes (on RER or cytoplasmic)

  • L3.1: Amino acids – additional details and example structures

    • Amino acids have a central carbon (alpha carbon) with:
    • An amino group (-NH2)
    • A carboxyl group (-COOH)
    • A distinctive side chain (R group) that determines properties of the amino acid.
    • Illustrated example structures include tyrosine and arginine.
    • Visual note: dipeptide formation involves a peptide bond between amino acids with release of water (H2O).

  • L3.1: Nucleic acids – more about bases and base-pairing

    • DNA base pairing and the double-helix structure are stabilized by hydrogen bonds between complementary bases.
    • RNA bases and their pairing differ from DNA: A pairs with U; C pairs with G.

  • L3.2: The genetic code and translation in more detail

    • The genetic code is read in triplets (codons) on mRNA; 64 total codons map to 20 amino acids plus STOP signals.
    • Start codon: \text{AUG} (codes for methionine) marks where translation begins.
    • Anticodon-codon interaction ensures incorporation of the correct amino acid at the ribosome.
    • Termination occurs at STOP codons; the polypeptide is released and folds into its functional conformation.

  • L3.3 The life cycle of cells

  • Four main questions (learning objectives)

    • Describe how cells synthesize, process, package, and secrete proteins.
    • Describe the stages of a cell’s life cycle and list events that define each stage.
    • Name the stages of mitosis and describe what occurs in each.

  • The life cycle of cells: overview

    • Cell biology posits that all cells arise from existing cells; DNA must be accurately duplicated and equally distributed to two daughter cells.
    • The cell cycle extends from one division to the next and includes four main phases: G1, S, G2, and M.
    • Length of the cell cycle varies by cell type:
    • Fibroblasts: about once per day
    • Stomach and skin cells: rapidly
    • Bone and cartilage: slowly
    • Nerve cells: not dividing (post-mitotic)
    • Interphase comprises G1, S, and G2; M phase is mitosis (and cytokinesis).

  • Cell cycle phases (Interphase)

    • G1 (First Gap Phase)
    • Interval between cell division and DNA replication.
    • Protein synthesis and growth occur; cells perform normal tasks.
    • Begin to replicate centrioles; accumulate materials for DNA replication.
    • S (Synthesis Phase)
    • DNA replication occurs; DNA molecules unzip and duplicate.
    • DNA polymerase synthesizes complementary nucleotides to form two identical DNA strands.
    • G2 (Second Gap Phase)
    • Brief interval between DNA replication and cell division.
    • Centriole replication completes; synthesis of enzymes that control cell division.

  • Mitosis (mitotic phase) and cytokinesis

    • Mitosis consists of four stages: Prophase, Metaphase, Anaphase, Telophase.
    • Cytokinesis overlaps with telophase and completes cell division by splitting the cytoplasm.
    • Summary of stages:
    • Prophase: Chromosomes condense; nuclear envelope breaks down; spindle fibers form from centrioles; centrioles move to opposite poles.
    • Metaphase: Chromosomes align along the cell’s equator; spindle fibers attach to kinetochores and to the plasma membrane.
    • Anaphase: Centromeres split; sister chromatids are pulled to opposite poles; chromatids migrate to poles.
    • Telophase: Chromatids arrive at poles; chromatin decondenses; new nuclear envelopes form; nucleoli reappear; mitotic spindle breaks down.
    • Cytokinesis: Cytoplasm divides; a contractile ring forms a cleavage furrow; two genetically identical daughter cells result; cells re-enter interphase.

  • Mitosis vs meiosis

    • Meiosis purpose: produce reproductive cells (eggs and sperm).
    • Mitosis purpose: growth, tissue repair, and replacement; occurs in most somatic cells.
    • Key phases appear similar in mitosis and meiosis; meiosis includes two rounds of division and homologous recombination (not detailed in this material).

  • Chromosome organization during mitosis

    • Chromatin condenses to chromosomes; each chromosome consists of two sister chromatids joined at the centromere.
    • In humans, there are 23 pairs of chromosomes (46 total) in a typical somatic cell; before division there are 92 chromatids (two chromatids per chromosome).
    • After mitosis, two genetically identical daughter cells are formed.

  • Visual and process references

    • Chromatin → Chromosomes → DNA → Genes progression (conceptual path).
    • Prophase and early/late prophase imagery show chromosomes condensing and spindle formation; metaphase imagery shows alignment at the cell equator; anaphase imagery shows chromatids moving to poles; telophase/cytokinesis imagery shows formation of new nuclei and separation of cells.

  • Consolidated and practice items

    • Learning Activity A: quick review of L3.1 amino acids, nucleic acids, and basic protein concepts.
    • Learning Activity B: transcription and base-pairing questions (as above).
    • Learning Activity C: organelles involved in protein synthesis; the process of converting DNA to mRNA; and converting mRNA to protein.
    • Learning Activity D: multiple-choice style questions about DNA replication timing and mitosis stages.

  • Quick glossary of key terms (L3 Terminology)

    • amino acid, anaphase, centromere, chromatids, chromatid, chromosomes, cleavage furrow, codon, cytokinesis, DNA, double helix, endoplasmic reticulum, exocytosis, Golgi apparatus, interphase, meiosis, metaphase, mitosis, mRNA, nitrogenous bases, nucleic acid, nucleotides, nucleus, polypeptide, prophase, protein synthesis, ribosomes, RNA, rRNA, spindle fibres, telophase, transcription, translation, tRNA, vesicles.

  • Notes on important dates and reminders (course context)

    • Quiz 1 is closed; Quiz 2 is open (due dates provided in the slides).
    • Tutorial times and online options (Tuesdays in GP216; Wednesdays online via ZOOM).

  • Final consolidated takeaways

    • Proteins perform a wide range of cellular functions with structure dictating function.
    • Protein synthesis is a two-step process: transcription (DNA → mRNA) and translation (mRNA → protein).
    • Gene expression includes post-transcriptional processing (introns/exons and splicing) before mRNA leaves the nucleus.
    • The cell cycle coordinates growth, DNA replication, and division; mitosis ensures equal distribution of DNA to two daughter cells.
    • Mitosis is subdivided into Prophase, Metaphase, Anaphase, and Telophase; cytokinesis completes cell division.
    • Understanding base-pairing rules and codon–anticodon interactions is essential for grasping how genetic information is translated into functional proteins.

This set of notes mirrors the content provided in Lecture 3 of EPBIOL259, including proteins, protein synthesis, and the cell cycle with mitosis, as well as the associated terminology and learning activities.