Chapter 3D

Cell Cycle

  • Series of changes a cell undergoes from formation to reproduction.
  • Two major periods:
    • Interphase: Cell grows and carries out usual activities.
    • Cell division (mitotic phase): Cell divides into two.

Interphase

  • Period from cell formation to cell division.
  • Cell carries out routine activities and prepares for cell division.
  • Nuclear material is in an uncondensed chromatin state.
  • Involves DNA replication.
  • Subphases:
    • G1 (gap 1): Vigorous growth and metabolism.
      • Cells that permanently cease dividing enter G0 phase.
    • S (synthetic): DNA replication occurs.
    • G2 (gap 2): Preparation for division.
DNA Replication
  • Occurs prior to division.
  • Cell makes a copy of DNA.
  • Double-stranded DNA helices unwind and unzip.
    • Replication fork: Point where strands separate.
    • Replication bubble: Active area of replication.
  • Each strand acts as a template for a new complementary strand.
  • RNA starts replication by laying down a short strand (primer).
  • DNA polymerase attaches to primer and adds nucleotides to form a new strand.
    • DNA polymerase synthesizes both new strands at one time (one leading and one lagging strand).
    • DNA polymerase works only in one direction.
      • Leading strand: Synthesized continuously.
      • Lagging strand: Synthesized discontinuously into segments.
  • DNA ligase splices short segments of the discontinuous lagging strand together.
  • End result: Two identical daughter DNA molecules are formed from the original.
  • During mitotic cell division, one complete copy is given to the new cell, and one is retained in the original cell.
  • Semiconservative replication: Each new double-stranded DNA is composed of one old strand and one new strand.

Cell Division (Mitotic Phase)

  • Most cells need to replicate continuously for growth and repair.
    • Skeletal, cardiac, and nerve cells do not divide efficiently; damaged cells are replaced with scar tissue.
  • M (mitotic) phase: Division occurs.
    • Mitosis
    • Cytokinesis
  • Control of cell division is crucial.

Mitosis

  • Division of the nucleus, where duplicated DNA is distributed to new daughter cells.
  • Four stages:
    • Prophase
    • Metaphase
    • Anaphase
    • Telophase
Prophase
  • Early prophase:
    • Chromatin condenses, forming visible chromosomes.
    • Each chromosome and its duplicate (sister chromatids) are held together by a centromere.
    • Centrosome and its duplicate begin synthesizing microtubules, pushing each centrosome to opposite poles of the cell (mitotic spindle).
    • Asters: Microtubules radiating from the centrosome.
  • Late prophase:
    • Nuclear envelope breaks up.
    • Special microtubules attach to a specific area on centromeres (kinetochore), pulling chromosomes to the center (equator) of the cell.
    • Nonkinetochore microtubules push against each other, causing poles of the cell to move farther apart.
Metaphase
  • Centromeres of chromosomes are precisely aligned at the cell’s equator.
  • Metaphase plate: Imaginary plane midway between poles.
Anaphase
  • Shortest phase.
  • Centromeres of chromosomes split simultaneously; each sister chromatid becomes a separate chromosome.
  • Chromosomes are pulled toward their respective poles by motor proteins of kinetochores.
  • Nonkinetochore microtubules continue forcing poles apart.
Telophase
  • Begins when chromosome movement stops.
  • Each set of chromosomes (at opposite ends of the cell) uncoils to form chromatin.
  • New nuclear membranes form around each chromatin mass.
  • Nucleoli reappear.
  • Spindle disappears.

Cytokinesis

  • Begins during late anaphase and continues through mitosis.
  • A ring of actin microfilaments contracts to form a cleavage furrow.
  • Two daughter cells are pinched apart.

Control of Cell Division

  • “Go” and “Stop” signals direct when a cell should and should not divide.
    • Go signals:
      • Critical surface-to-volume ratio of cell.
      • Chemicals (growth factors, hormones).
    • Stop signals:
      • Availability of space.
      • Contact inhibition: Normal cells stop dividing when they come into contact with other cells.
  • Two groups of proteins:
    • Cyclins: Regulatory proteins that accumulate during interphase.
    • Cdks (Cyclin-dependent kinases): Activate cyclins when they bind to them.
      • Cyclin-Cdk complex activates enzyme cascades that prepare the cell for division.
      • Cyclins are destroyed after mitotic cell division, and the process begins again.
  • Checkpoints: Key events where cell division processes are checked and stopped if faulty.
    • G1 checkpoint (restriction point): Most important checkpoint.
      • If a cell does not pass, it enters G0, where no further division occurs.

Protein Synthesis

  • DNA is the master blueprint holding the code for protein synthesis.
    • DNA directs the order of amino acids in a polypeptide.
    • A gene is a segment of DNA that holds the code for one polypeptide.
  • The code is determined by the specific order of nitrogen bases (Adenine, Guanine, Thymine, and Cytosine) in the gene.
    • Code consists of three sequential bases (triplet code).
      • Example: GGC codes for proline, whereas GCC codes for arginine.
      • Each triplet specifies the code for a particular amino acid.
  • Genes are composed of exons and introns.
    • Exons: Part of the gene that actually codes for amino acids.
    • Introns: Noncoding segments interspersed amongst exons.

The Role of RNA

  • RNA is the “go-between” molecule that links DNA to proteins.
    • RNA copies the DNA code in the nucleus, then carries it into the cytoplasm to ribosomes.
  • All RNA is formed in the nucleus.
  • RNA differs from DNA:
    • Uracil is substituted for thymine in RNA.
    • RNA has ribose instead of deoxyribose sugar.
  • Three types of RNA:
    • Messenger RNA (mRNA)
    • Ribosomal RNA (rRNA)
    • Transfer RNA (tRNA)
Messenger RNA (mRNA)
  • Single-stranded.
  • Code from DNA template strand is copied with complementary base pairs, resulting in a strand of mRNA (transcription).
  • mRNA maintains the triplet code (codon) from DNA.
Ribosomal RNA (rRNA)
  • Structural component of ribosomes, the organelle where protein synthesis occurs.
  • Helps to translate message from mRNA into polypeptide.
Transfer RNA (tRNA)
  • Carrier of amino acids.
  • Has special areas that contain a specific triplet code (anticodon) that allows each tRNA to carry only a specific amino acid.
  • Anticodon of tRNA will complementary base-pair with codon of mRNA at ribosome, adding its specific amino acid to growing polypeptide chain (translation).

Protein Synthesis Steps:

  • Transcription
    • DNA information coded in mRNA.
  • Translation
    • mRNA decoded to assemble polypeptides.

Transcription

  • Process of transferring code held in DNA gene base sequence to complementary base sequence of mRNA.
  • Transcription factors (protein complex) activate transcription by:
    • Loosening histones from DNA in the area to be transcribed so the DNA segment can be exposed.
    • Binding to a special sequence of the gene to be transcribed, called the promoter (starting point).
      • Occurs only on the DNA template strand.
    • Mediating binding of RNA polymerase, enzyme that synthesizes mRNA, to the promoter region.
Transcription Phases:
  • Initiation
    • RNA polymerase separates DNA strands.
  • Elongation
    • RNA polymerase adds complementary nucleotides to growing mRNA matching the sequence of bases on the DNA template strand.
    • Short, 12-base-pair segment where DNA and mRNA are temporarily bonded is referred to as a DNA-RNA hybrid.
  • Termination
    • Transcription stops when RNA polymerase reaches a special termination signal code.
Processing of mRNA
  • Newly formed mRNA is edited and processed before translation can begin (pre-mRNA).
  • Introns are removed by special proteins called spliceosomes, leaving only exons (coding regions).

Translation

  • Step of protein synthesis where the language of nucleic acids (base sequence) is translated into the language of proteins (amino acid sequence).
  • Process involves: mRNA, genetic code, tRNA and ribosomes, translating events, and sometimes the rough ER.
Genetic Code
  • Each three-base sequence on DNA (triplet code) is represented by a complementary three-base sequence on mRNA called a codon.
  • There are 64 possible codons (43=644^3 = 64).
  • There are 3 “stop” codons; the rest are codons for amino acids.
  • There are only 20 possible amino acids, meaning some amino acids are represented by more than one codon (redundancy).
    • Redundancy helps protect against transcription errors.
Role of tRNA
  • tRNA binds a specific amino acid at one end (stem); once an amino acid is loaded onto tRNA, the molecule is called aminoacyl-tRNA.
  • Anticodon at the other end (head) is a triplet code that determines which amino acid will be bound at the stem.
    • Example: tRNA with anticodon UAU will only be able to load a methionine amino acid to its stem region.
  • Anticodon of tRNA will bind only to a codon on mRNA that is complementary.
    • Example: if the codon is AUA, only a tRNA with anticodon UAU will be able to bond.
  • Ribosomes coordinate coupling of mRNA and tRNA.
  • Ribosomes contain one binding site for mRNA and three binding sites for tRNA:
    • Aminoacyl site (A site): For incoming aminoacyl-tRNA.
    • Peptidyl site (P site): For tRNA linked to growing polypeptide chain.
    • Exit site (E site): For outgoing tRNA.
Translation Sequence of Events
  • Translation occurs in three phases that require ATP, protein factors, and enzymes:
    • Initiation
    • Elongation
    • Termination
Translation - Initiation
  • Small ribosomal subunit binds to a special initiator tRNA (methionine) and then to the mRNA to be decoded.
    • Ribosome scans mRNA looking for the first methionine codon (start codon).
  • When the anticodon of the initiator tRNA binds to the start codon, the large ribosomal unit can then attach to the small ribosomal unit, forming a functional ribosome.
  • At the end of initiation, the initiator tRNA is in the P site of the ribosome, and the A and E sites are empty.
Translation - Elongation
  • Involves three steps:
    • Codon recognition: tRNA binds to the complementary codon in the A site of the ribosome.
    • Peptide bond formation: Ribosomal enzymes transfer and attach the growing polypeptide chain from tRNA in the P site over to the amino acid of tRNA in the A site.
    • Translocation: The ribosome shifts down three bases of mRNA, displacing tRNAs by one position.
      • tRNA in the A site moves into the P site.
      • tRNA in the P site moves into the E site.
      • tRNA in the E site is ejected from the ribosome.
  • Once the A site is empty, a new tRNA can enter, bringing its amino acid cargo, and the whole process starts over.
  • After a portion of mRNA is “read,” additional ribosomes may attach to the already read part and start another round of translation of the same mRNA.
Polyribosome
  • Multiple ribosome-mRNA complex that produces multiple copies of the same protein.
Translation - Termination
  • When one of the three stop codons (UGA, UAA, UAG) on mRNA enters the A site, translation ends.
  • Protein release factor binds to the stop codon, causing water to be added to the chain instead of another tRNA.
  • The release of the polypeptide chain occurs, as well as the separation of ribosome subunits and degradation of mRNA.
  • The final polypeptide product will be further processed by other cell structures into a functional 3-D protein.
Role of Rough ER in Protein Synthesis
  • A short amino acid segment, called the ER signal sequence, present on a growing polypeptide chain, signals the associated ribosome to dock on the rough ER surface.
  • The signal-recognition particle (SRP) on the ER directs the mRNA–ribosome complex where to dock.
  • Once docked, the forming polypeptide enters the ER.
    • Sugar groups may be added to the protein, and its shape may be altered.
    • The protein is then enclosed in a vesicle for transport to the Golgi apparatus.

Summary: From DNA to Proteins

  • Complementary base pairing directs the transfer of genetic information in DNA into the amino acid sequence of the protein.
  • DNA triplets are coded to mRNA codons.
  • mRNA codons are base-paired with tRNA anticodons to ensure the correct amino acid sequence.
    • The anticodon sequence of tRNA is identical to the DNA sequence, except uracil is substituted for thymine.

Other Roles of DNA

  • DNA codes for other types of RNA:
    • MicroRNA (miRNA)
      • Small RNAs that can bind to and silence mRNAs made by certain exons.
    • Riboswitches
      • Folded RNAs that act as switches that can turn protein synthesis on or off in response to certain environmental conditions.
    • Small interfering RNAs (siRNA)
      • Similar to miRNA but can also be made to silence mRNA from pathogenic sources such as viruses.

Apoptosis, Autophagy, and Proteasomes

Autophagy

  • Cells that have become obsolete or damaged need to be taken out of the system.
  • Autophagy (self-eating) is the process of disposing of nonfunctional organelles and sweeping up cytoplasmic bits by forming autophagosomes, which can then be degraded by lysosomes.

Ubiquitin-Proteasome Pathway

  • Unneeded, misfolded, or damaged proteins can be marked for destruction by a protein called ubiquitin.
  • Proteasomes disassemble ubiquitin-tagged proteins, recycling the amino acids and ubiquitin.

Apoptosis

  • Also known as programmed cell death, causes certain cells (cancer cells, infected cells, old cells) to neatly self-destruct.
  • The process begins with mitochondrial membranes leaking chemicals that activate enzymes called caspases.
  • Caspases cause degradation of DNA and cytoskeleton, which leads to cell death.
  • The dead cell shrinks and is phagocytized by macrophages.

Developmental Aspects of Cells

  • All cells of the body contain the same DNA, but not all cells are identical or carry out the same function.
  • Chemical signals in the embryo channel cells into specific developmental pathways by turning some genes on and others off.
  • The development of specific and distinctive features in cells is called cell differentiation.

Cell Destruction and Modified Rates of Cell Division

  • Organs are well-formed and functional before birth, but cell division is needed for growth.
  • Cell division in adults is needed to replace short-lived cells and repair wounds.
  • Hyperplasia: Accelerated growth that increases cell numbers when needed.
  • Atrophy: A decrease in size that results from loss of stimulation or use.

Cell Aging

  • The mechanism of aging is a mystery, but there are several theories:
    • Wear and tear theory: A lifetime of chemical insults and free radicals have cumulative effects.
    • Mitochondrial theory of aging: Free radicals in mitochondria diminish energy production.
    • Immune system disorders: Autoimmune responses, as well as progressive weakening of the immune response.
    • Genetic theory: Cessation of mitosis and cell aging are programmed into genes.
      • Telomeres: Strings of nucleotides that protect the ends of chromosomes (like caps on shoestrings).
        • Every time a cell divides, the telomere shortens, so telomeres may act like an hour-glass on how many times a cell can divide.
      • Telomerase: An enzyme that lengthens telomeres.
        • Found in germ cells of embryos but absent in adult cells, except for cancer cells.
        • Telomerase makes cancer cells immortal.

Clinical - Homeostatic Imbalance 3.4

  • Progeria is a rare disease that mimics aging.
    • Caused by a defective progerin protein in the nuclear lamina that results in an unstable, abnormal nucleus.
  • The disease appears by age 2.
  • Children with the disease display slow growth, thinning hair, brittle bones, arthritis, and severe cardiovascular disease, with death usually by age 20.
  • Scientists have found a drug that stimulates autophagy that can help cells clear out progerin.