DNA Damage and Repair

DNA DAMAGE MECHANISMS

Endogenous Agents

• Spontaneous chemical reactions

  1. Deamination: nucleotides lose amine groups
    • Cytosine –> uracil
    • Adenine –> hypoxanthine
  2. Depurination: purine (adenine or guanine) released from DNA
    • Bond between deoxyribose and purine base spontaneously cleaves
    • Produces AP site (apurinic site)

Exogenous Agents

  • Exposure to mutagens (chemicals or radiation)
  1. Pyrimidine dimers: induced by UV light exposure
    • Cyclobutane ring forms between adjacent pyrimidines (often thymines)
    • Distorts the DNA double helix
  2. Alkylation: addition of methyl/ethyl groups to nucleotides
    • -CH3 or –CH2CH3 add to nitrogenous bases at numerous positions
  3. Bulky group addition: exposure to carcinogens
    • i.e. benzo(a)pyrene: aromatic, polycyclic structure can react with purines/pyrimidines at numerous positions
    • Cause distortions in DNA helix

Carcinogen

• Cancer-causing mutagen

CONSEQUENCES OF DNA DAMAGE
• Can increase frequency of mutations
• Mutations: nucleotide substitutions, deletions and insertions

CLINICAL CORRELATIONS

Skin melanomas

• Pyrimidine dimers produce helical distortions that result in skin cancers

Cigarette smoking

• Carcinogens in smoke form covalent bonds with DNA
• Disrupts H-bonding between nucleotides: causes frameshift
• Frameshift changes subsequent codons in DNA strand
• Constant exposure to carcinogens –> lung cancer

REPAIR MECHANISMS
• Mismatch-repair: fixes replication errors missed by DNA Polproofreading (cannot repair damage)
• Base excision repair: deamination, depurination and alkylation
• Nucleotide excision repair: pyrimidine dimers and bulky group addition

Mitosis versus Meiosis

KEY DIFFERENCES BETWEEN MITOSIS AND MEIOSIS

  1. Parent cell types
  • Mitosis: diploid somatic cell
  • Meiosis: diploid germ line cell (reproductive cell precursor)
  1. Tetrad formation (Meiosis only)
  • Prophase I
  1. Crossing over (Meiosis only)
  • Chiasmata: site of genetic recombination, occurs in prophase I
  1. Synaptonemal complex (Meiosis only)
  • Zipper-like protein structure that holds homologues together: specific to meiosis I
  1. Kinetochore orientation
  • Mitosis: sister chromatid kinetochores face opposite poles
  • Meiosis I: sister chromatid kinetochores face the same pole
  • Meiosis II: sister chromatid kinetochores face opposite poles
  1. Genetic variability (Meiosis only)
  • Crossing over (genetic recombination)
  • Random fertilization
  • Independent assortment: each tetrad positions itself on the metaphase plate independently of other tetrads
  • Meiosis produces four genetically distinct haploid daughter cells
  • Mitosis produces two genetically identical diploid daughter cells

Meiosis Part II

HUMAN CELLS

  1. Somatic cells: majority of the body’s cells
  • 46 chromosomes – diploid (2n)
  1. Reproductive cells: sperm and egg cells (gametes)
  • 23 chromosomes – haploid (1n)
  • Diploid germ line cells: precursors for reproductive cells; undergo meiosis

FERTILIZATION

  • 1 egg and 1 sperm fuse to form zygote (2n)
  • Followed by repeated cycles of mitosis to produce multicellular organism (2n)

INTERPHASE

  • Parent cell (2n): two sets of 23 chromosomes
  • Homologous chromosomes: contain the same genes in the same order, each from a different parent (contain different alleles)
  • S-phase: each set of 23 chromosomes duplicates (92 chromosomes total), sister chromatids pair at the centromere

PROPHASE I

  • >90% of meiosis
  • Chromosomes condense
  • Tetrad forms via synapsis: each gene aligns with its homologue (4 chromatids)
  • Synaptonemal complex: zipper-like structure holds chromosomes together until crossing over occurs
  • Crossing over: paternal chromosome crosses over to maternal and vice versa
  • Chiasma (site of crossing over) holds tetrad together after synaptonemal complex disassembles

Other features of this phase:

  • Nuclear envelope fragments
  • Nucleolus disperses
  • Centrosomes move to opposite poles
  • Microtubules form spindle & attach kinetochores of homologous chromosomes

METAPHASE I

  • Tetrads align on metaphase plate
  • Sister chromatids face same pole
  • Homologous chromosomes face opposite poles

ANAPHASE I

  • Homologous chromosomes separate

TELOPHASE I AND CYTOKINESIS

  • Two haploid daughter cells: 1 tetrad in each

PROPHASE II

  • Each cell has one duplicated set of 23 chromosomes

METAPHASE II

  • Sister chromatids line up on metaphase plate and face opposite poles

ANAPHASE II

  • Sister chromatids separate

TELOPHASE II

  • Nuclear envelope reforms
  • Nucleolus reappears
  • Mitotic spindles depolymerize
  • Cleavage furrow

CYTOKINESIS

  • 4 haploid daughter cells
  • Daughter cells genetically distinct from each other and parent cells
  • Each develops into reproductive cell (egg or sperm cells)

CLINICAL CORRELATION
Down’s Syndrome (Trisomy 21): aneuploid gametes

  • Nondisjunction: chromosome 21 fails to separate properly during meiosis I
  • 2 daughter cells with extra chromosome 21 copy
  • 2 daughter cells missing chromosome 21
  • Trisomy 21: gamete with extra chromosome fuses with normal gamete during fertilization = zygote with 3 copies of chromosome 21

Meiosis Part I

HUMAN CELLS

  1. Somatic cells: majority of the body’s cells
  • 46 chromosomes – diploid (2n)
  1. Reproductive cells: sperm and egg cells (gametes)
  • 23 chromosomes – haploid (1n)
  • Diploid germ line cells: precursors for reproductive cells; undergo meiosis

FERTILIZATION

  • 1 egg and 1 sperm fuse to form zygote (2n)
  • Followed by repeated cycles of mitosis to produce multicellular organism (2n)

INTERPHASE

  • Parent cell (2n): two sets of 23 chromosomes
  • Homologous chromosomes: contain the same genes in the same order, each from a different parent (contain different alleles)
  • S-phase: each set of 23 chromosomes duplicates (92 chromosomes total), sister chromatids pair at the centromere

PROPHASE I

  • >90% of meiosis
  • Chromosomes condense
  • Tetrad forms via synapsis: each gene aligns with its homologue (4 chromatids)
  • Synaptonemal complex: zipper-like structure holds chromosomes together until crossing over occurs
  • Crossing over: paternal chromosome crosses over to maternal and vice versa
  • Chiasma (site of crossing over) holds tetrad together after synaptonemal complex disassembles

Other features of this phase:

  • Nuclear envelope fragments
  • Nucleolus disperses
  • Centrosomes move to opposite poles
  • Microtubules form spindle & attach kinetochores of homologous chromosomes

METAPHASE I

  • Tetrads align on metaphase plate
  • Sister chromatids face same pole
  • Homologous chromosomes face opposite poles

ANAPHASE I

  • Homologous chromosomes separate

TELOPHASE I AND CYTOKINESIS

  • Two haploid daughter cells: 1 tetrad in each

PROPHASE II

  • Each cell has one duplicated set of 23 chromosomes

METAPHASE II

  • Sister chromatids line up on metaphase plate and face opposite poles

ANAPHASE II

  • Sister chromatids separate

TELOPHASE II

  • Nuclear envelope reforms
  • Nucleolus reappears
  • Mitotic spindles depolymerize
  • Cleavage furrow

CYTOKINESIS

  • 4 haploid daughter cells
  • Daughter cells genetically distinct from each other and parent cells
  • Each develops into reproductive cell (egg or sperm cells)

CLINICAL CORRELATION

Down’s Syndrome (Trisomy 21): aneuploid gametes

  • Nondisjunction: chromosome 21 fails to separate properly during meiosis I
  • 2 daughter cells with extra chromosome 21 copy
  • 2 daughter cells missing chromosome 21
  • Trisomy 21: gamete with extra chromosome fuses with normal gamete during fertilization = zygote with 3 copies of chromosome 21

Membrane Asymmetry

MEMBRANE COMPONENTS

  • Phospholipids: synthesized on the cytosolic face of the ER
  • Glycolipids
  • Membrane proteins

MEMBRANE SYNTHESIS

  1. Phospholipids are synthesized on the cytosolic face of the ER and glycolipids on the lumenal face of the Golgi apparatus
  2. Vesicles bud from organelles and transport them to cell membrane
  3. Vesicles fuse with cell membrane the lipids they transport retain same orientation unequal distribution of molecules generates curvature
  4. Flippases flip some phospholipids to the extracellular face of bilayer
  5. Glycolipids remain on extracellular face (no flippase action)

TOPOLOGICALLY EQUIVALENT SPACES
Endoplasmic reticulum
Golgi Apparatus
Vesicles
Extracellular space

MEMBRANE LIPIDS DISTRIBUTION

Extracellular layer

  • Phosphatidylcholine: most common, structural
  • Sphingomyelin: less abundant, variable head groups
  • Glycolipids: carbohydrate attached to membrane lipid

Cytosolic layer

  • Phosphatidylethanolamine: small head group that generates curvature
  • Phosphatidylinositol: minor lipid, binds proteins (signal transduction)
  • Phosphatidylserine: binds proteins to membrane
    Variable head groups & fatty acid tail length/saturation

CLINICAL CORRELATION

Apoptosis (programmed cell death)

  • Phosphatidylserine in extracellular leaflet of bilayer is signal for phagocytosis

Membrane Proteins Overview

FREEZE-FRACTURE METHOD

  • Freeze cell and fracture it along cell membrane’s hydrophobic interior
  • Proteins associate with either layer after fracturing
  • More proteins associate with cytosolic layer

INTEGRAL PROTEINS

  • Embedded in the bilayer

Transmembrane proteins: amphipathic, pass through both membrane layers

  • Single pass or multi-pass
  • Alpha helices: hydrophobic side chains
  • Beta barrel: multi stranded beta sheet (i.e. porin proteins)

Monolayer associated

  • Alpha helix
  • Lipid-linked

PERIPHERAL PROTEINS

  • Do not extend into the bilayer
  • Protein-attached: non-covalently bound to transmembrane protein
  • Oligosaccharide-attached: bound to carbohydrate head group of glycolipid

Glycocalyx

  • Oligosaccharide side chains and glycolipids form carbohydrate coat on external surface of cell

MEMBRANE PROTEIN FLUIDITY

  1. Fuse mouse and human cells with surface marker proteins
  2. Marker proteins mix on hybrid cell surface
  • Conclusion: membrane proteins are fluid

MEMBRANE PROTEIN FUNCTIONS

  • Transport ions, nutrients and other substances across membrane
  • Anchor cells to each other, to extracellular matrix or basement membrane
  • Transduce external signals to inside of cell
  • Mediate cell-cell recognition of glycoproteins on adjacent cell surfaces
  • Enzymatically catalyze metabolic pathways

Membrane Structure Overview

PLASMA MEMBRANE

  • Phospholipid bilayer: bilayer that comprises mostly phospholipids
  • Fluid mosaic: mosaic of proteins embedded within a fluid phospholipid bilayer
  • Selectively permeable: some substances move through passively, others use proteins for transport

MEMBRANE COMPONENTS

  • Phospholipids
  • Proteins
  • Cholesterol
  • Carbohydrates

PHOSPHOLIPIDS

  • Amphipathic: hydrophilic head and hydrophobic fatty acid tails
  • Form liposomes in aqueous environment
  • Weak hydrophobic interactions = membrane fluidity
  • Saturated phospholipids: maximize hydrogens in fatty acid tails, no kinks
  • Unsaturated phospholipids: double bond produces kink, increases fluidity

CHOLESTEROL

  • Temperature buffer
  • Moderate temperature: decreases fluidity, lessens lateral movement
  • Low temperature: increases fluidity, prevents solidification

PROTEINS

  • Includes transmembrane proteins that span the bilayer (other types exist)
  • Proteins provide about half the mass of the membrane

CARBOHYDRATES

  • Glycoproteins: branched carbohydrates covalently bound to proteins
  • Glycolipids: carbohydrates covalently bound to lipids (extracellular only)

CLINICAL CORRELATION:

Blood types

  • Carbohydrates on surface of red blood cells must be compatible between donor & recipient in blood transfusion

FUNCTIONS OF THE CELL MEMBRANE

  • Cell communication
  • Import and export of molecules
  • Cell growth
  • Cell motility

Eukaryotes have internal membranes within the cell, prokaryotes do not.

Fluorescence Microscopy

FLUORESCENCE MICROSCOPY APPLICATIONS

Fluorescence recovery after photobleaching (FRAP)

  • Used to study membrane fluidity

Fluorescence resonance energy transfer (FRET)

  • Used to study protein-protein interactions

METHOD

  1. Light passes through excitation filter
  2. Excitation filter filters out undesired wavelengths of light
  3. Mirror deflects light downward toward sample
  4. Light passes through the objective lens and onto specimen of interest
  5. Molecules in sample absorb light & emit light with longer wavelength (fluoresce)
  6. Fluorescent light travels back upward and passes through mirror w/o deflecting
  7. Barrier filter above the mirror lets fluorescent light through
  8. Fluorescence observed

FRAP

  1. Tag membrane proteins with fluorophore (i.e. GFP)
  2. Irreversibly bleach portion of membrane with laser (photobleaching)
  3. Measure rate at which membrane recovers fluorescence (proportional to rate at which tagged molecules diffuse back into bleached area)

FRET

  1. Tag one protein with blue GFP and another with green GFP
  2. Shine violet light on sample

If the proteins interact (i.e they come in close proximity):

  • Blue light from blue GFP excites green GFP
  • Green light observed

If the proteins do not interact:

  • Blue light observed (not absorbed and reemitted by green GFP)