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BioBiochem > Chapter 2: Cell Structure & Microbiology > Flashcards

Chapter 2: Cell Structure & Microbiology Flashcards

1
Q

The cell theory

A
  1. Cell is the most basic unit of life
  2. All living organisms are composed of 1+ cells
  3. All cells arise from pre existing cells
  4. All cells have the same basic chemical composition
  5. Energy flows within cells
  6. DNA is passed from cell to cell
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2
Q

Types of gradients

A
  1. Chemical concentration gradient: move chemical to low concentration
  2. Electrical gradient: move to ions of opposite charge
  3. Electrochemical gradient: sum of electrical and chemical gradients
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3
Q

Permeability of the membrane

A
  1. Depends on size, polarity and charge
    1a. Small, non polar, not charged pass very easily
    1b. Easiest: gases>hydrophobic>small polar>large polar> amino acid/charged>macromolecule: Can’t pass
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4
Q

Passive transport

A
  1. Simple diffusion: Diffusion through lipid bilayer (likely is small, nonpolar, not charged) and diffusion through nonspecific leakage channels
  2. Facilitated diffusion
    2a. Channel proteins: specific (aquaporins or ion channels)
    2b. Carrier protein: bind more strongly to ligands than channel proteins…when they bind, they undergo a conformational change that transfers binding site from one side of membrane to another
  3. Osmosis:
    3a. Hypertonic: high water area (if cell=swells)
    3b. Hypotonic: low water area
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5
Q

Active transport: against concentration gradient

A
  1. Primary active transport: energy is direct and required
    1a. Na+/K+ pump: 3Na+ out, 2K+ in
  2. Secondary active transport: energy is indirect but required
    2a. Need a cotransporter (transports 2 molecules to same side) to move substance based on a newly made gradient
    2b. ex: Na+ -glucose cotransporter
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6
Q

Directionalities of membrane transport

A
  1. Symport: 2 molecules go same direction
  2. Antiport: molecules move in opposite directions
  3. Uniport: only one molecule is transported
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7
Q

Intrinsic proteins

A
  1. Integral/intrinsic proteins: proteins embedded in membrane permanently
    1a. All transport proteins are integral proteins
    1b. Other integral proteins: receptors, attachment sites, identifiers, adhesive proteins, enzymes etc.
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8
Q

Extrinsic proteins

A
  1. Peripheral /extrinsic proteins: on inner and outer surfaces of membrane…
  2. 3 common mechanisms of attachment:
    2a. hydrophobic extensions: have hydrophobic amino acid loops embedded into the hydrophobic portion of the membrane or a hydrophobic alpha helix attached just beneath the surface
    2b. electrostatic attachments to the surface: peripheral proteins may attach to outside of membrane by ionic bonding to negative phospholipid heads
    2c. Lipid anchors: lipid linked proteins are peripheral proteins covalently bound to a lipid moiety at the hydrophobic portion
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9
Q

Endocytosis and exocytosis

A
  1. Endocytosis:
    1a. Phagocytosis: engulf particles (once engulfed: called a phagosome)
    1b. Pinocytosis: engulf extracellular fluid
    1c. Receptor mediated endocytosis: specific uptake of macromolecules like hormones and nutrients (ex: clathrin mediated endocytosis)
  2. Exocytosis: expelling material out using secretory vesicles from GA
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10
Q

Eukaryotic cells vs prokaryotic cells

A
  1. Eukaryotic: has membrane bound organelles (nucleus, mitochondria, ER, GA, lysosomes), DNA is coiled around histones, RNA gets processed, larger ribosomes (40s, 60s), may have a cell wall (fungi/insects=chitin, plant=cellulose), flagella is made of tubulin, mitosis for sexual reproduction and the genome has linear chromosomes
  2. Prokaryotic: smaller ribosomes (30S, 50s), cell wall is peptidoglycan, flagella is made of flagellin, binary fission for sexual reproduction, genome has circular chromosome
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11
Q

Golgi apparatus

A
  1. Newly synthesized proteins enter cis-Golgi from lumen via transport vesicle …. In cis Golgi: proteins are organized by their signal sequence and carb groups as they are shuttled to trans Golgi ….Specific modified proteins than enter secretory vesicles to be secreted out of GA via exocytosis
  2. Main point: packaging
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12
Q

lysosomes

A
  1. Contain acid hydrolases (proteases, lipases, nucleases, glycosidases) which break down macromolecules
  2. Have an interior of pH 5
  3. Cell death
    3a. If lysosomes leak=apoptosis (natural)
    3b. If lysosomes rupture=necrosis (due to toxins, trauma, infection)
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13
Q

Endoplasmic reticulum

A
  1. RER: has ribosomes for translation
    1a. proteins enter ER lumen by entering secretory pathway (synthesized in ER, sorted and sent to other places)
    1b. Next, in lumen, they are glycosylated: to allow folding processes, prevents proteolysis etc.
  2. SER: Make TAG, cholesterol, detoxify drugs etc.
    2a. Looks like the GA under a microscope
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14
Q

peroxisomes

A
  1. Have catalase that uses hydrogen peroxide to oxidize other organic substances
    1a. Detoxify alcohol
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15
Q

Mitochondria

A
  1. Outer membrane -> intermembrane space -> inner membrane -> matrix
    1a. Matrix contains own circular DNA which is explained by endosymbiotic theory: says bacteria become aerobic and got ingested by a archaea to make eukaryotes
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16
Q

Nucleus

A
  1. Nucleus is membranes bound which has nuclear DNA…is enclosed by nuclear envelope (double phospholipid bilayer) which has nuclear pores so RNA and proteins can exit.
  2. Nucleolus is where rRNA is transcribed to make ribosomes
17
Q

Cellular filaments in cytoskeleton: microtubules

A
  1. Microtubules: made of tubulin to allow for separation of chromosomes in mitosis
    1a. -/alpha end: attached to microtubules organizing centre (MTOC) (ex: centrosomes/2 centrioles) and microtubules grows away from this (+/beta)
    1b. Growth occurs when alpha/beta dimer is bound to GTP…GTP cap prevents spontaneous depolymerization
  2. Make up flagella and cilia
    2a. Axoneme: has 9 pairs of microtubules which forms a circle around 2 lone microtubules (9+2)
    2b. Cross bridges w dynein connect each outer pairs of microtubules to neighbours which cause whip action /fluidity in flagellum or cilia
18
Q

Cellular filaments in cytoskeleton: microfilaments /actin filaments

A
  1. Polymers of actin which play a role in cytokinesis, endocytosis, exocytosis and cytoplasmic streaming
  2. Bind myosin during muscle contraction
    2a. Within a sacromere, the microfilament length is stable bc one end is anchored by Z line and other is capped
19
Q

Cellular filaments in cytoskeleton: intermediate filaments

A
  1. Not dynamic as teh others but serve for structure rigidity … name is dependant on location
  2. ex: keratin
20
Q

Cellular junctions:

A
  1. Tight junctions: Protein complexes that form water tight seal between cells
  2. Desomosomes: joins 2 cells and attach them to cytoskeleton… for attachment and tension resistance
    2a. Hemidesmosomes: anchors cells to ECM
    2b. Adherens junction: cell to cell or cell to matrix anchors
  3. Gap junctions: for cell-cell communication (tunnels)
21
Q

The extracellular matrix

A
  1. Material that surrounds cell and is formed by cell
  2. Include finger nails, bones, cartilage etc
22
Q

Tissues: epithelial

A
  1. Separates connective tissue from fluids inside and outside the body, is avascular but innervated
  2. Formed via 3 germ layers
    2a. Ectoderm: skin
    2b. Mesoderm: pleura, peritoneum, mediastinum, pericardium
    1c. Endoderm: GI. Respiratory, reproductive tract
23
Q

Tissues: connective

A
  1. Glue that holds other tissues in place, but hydrates and diffuses nourishment
  2. 3 components of connective tissues: cells, ground substance, fibers
  3. 2 main types of connective tissue: connective tissue proper (tendons/ligaments) and specialized connective tissue (cartilage, bone, blood, lymph, adipose tissue)
24
Q

Virus

A
  1. Infectious agents that have genetic material (DNA or RNA) surrounded by protein coat/capsid
    1a. If Phospholipid envelope surrounds capsid: nucleocapsid
    1b. Virion (mature virus) has either DNA or RNA but never both
  2. Mature virus=virion …descendants of a virion=progeny
  3. Specific
  4. Not living: can’t replicate on own
  5. Viruses are obligate intracellular parasites that can be made by translation of viral nucleic acids
  6. Can be grown in lab in a tissue culture
25
Q

Bacteriophages

A
  1. Viruses that infect bacteria
  2. Structure: protein capsid head and tail (sheath, tube with collar at top and base plate, spikes, and tail fibres at bottom)
  3. Phages can be virulent (Lytic cycle) or temperate (lysogenic)
26
Q

Viral life cycles: Lytic and lysogenic

A
  1. Viral life cycle
    1a. Attachment/adsorption: to host
    1b. Penetration: of cell membrane & entry of viral material
    1c. Use of host mechanisms to replicate viral components
    1d. New virion self assembly and release of new viral particles: released by cell lysis
  2. 2 replication cycles
    2a. Lytic: virus particles are released and cause cell lysis
    2b. Lysogenic: viral DNA inserts itself into host cell chromosome (virus is dormant/provirus)…provirus can separate from host chromosome during stress and enter Lytic cycle
27
Q

Sub viral particles related to viruses

A
  1. Viroid: infect plants
  2. Prions: misfolded proteins that affect animals
28
Q

Reverse transcriptase for retroviruses

A
  1. Retroviruses contain RNA and reverse transcriptase which enter host cell by fusion and use reverse transcription to form DNA from their RNA template
  2. DNA is then integrated into host which transcribes, translates and assembles new retroviruses to exit host by budding and reinfect new cell hosts
29
Q

Prokaryotes: archaea

A
  1. Nonpathogenic, extremophiles, most are obligate anaerobes, have introns
  2. Their membrane lipids have ether linkage rather than ester linkage between glycerol and fatty acids
30
Q

Prokaryotes: bacteria

A
  1. Types: cocci (sphere), bacilli (rod), spirilli (spiral)
  2. 4 classes: obligate aerobes, obligate anaerobes, faculative anaerobes (goes between O2 and no O2), aerotolerant anaerobes (don’t use O2, but doesn’t mind it)
  3. May possess genes for antibiotic resistance (R factors) or virulence factors
31
Q

Bacterial envelope

A
  1. Protoplast contains cytoplasm and plasma membrane…the bacterial envelopes (cell wall and plasma membrane) function is to prevent the protoplast from bursting
  2. To classify bacteria we use gram staining:
    2a. Gram +: thick peptidoglycan cell wall/purple
    2b. Gram -: thin peptidoglycan cell wall/pink
32
Q

Binary fission & growth of bacteria

A
  1. Asexual reproduction for bacteria: produce 2 identical daughter cells
  2. Growth
    2a. Lag: low growth
    2b. Log: exponential growth
    2c. Stationary: no growth
    2d. Death: exponential depletion
33
Q

Genetic recombination

A
  1. Conjugation: bacteria to bacteria
    1a. Via F plasmid/fertility factor/F factor: codes for sex pilus (bacteria with is F+, bacteria without is F-)
    1b. Copies of plasmid containing genes for sex pilus are not equally distributed to daughter cells which is why some have it and others dont
  2. Transformation: environment to bacteria
  3. Transduction: virus to bacteria via vector
    3a. Generalized transduction: a random piece of bacterial DNA is accidentally incorporated into phage in Lytic cycle and transfers to host
    3b. Specialized transduction: through induction of lysogenic cycle, bacteria DNA near site of integration is excised along with viral DNA and is incorporated into next host
34
Q

Transposons

A
  1. Provide a way for nucleotides to move from one position to another (DNA that are capable of jumping from one place to another along the genome)
  2. Types
    2a. IS elements: transposase genes with inverted repeating sequences
    2b. Complex transposons: transposase gene has regulatory gene and whole transposon has inverted repeats
    2c. Composite transposons: 2 transposase sequences w central region between….inverted repeats flank them
35
Q

Regulation of transcription in prokaryotes

A
  1. The Jacob Monod model of prokaryotic gene defines an operon as a cluster of genes under the control of a single promotor: operator, promotor and genes
  2. Ex: lac operon (code for enzyme that allows E. coli to metabolize lactose when no glucose)
    2a. Positive control: low glucose=high cAMP=binds to CAP=binds upstream of lac operon promotor=transcription of 3 proteins
    2b. Regulation: no lactose=lac repressor binds to operator (regulator site)=no lac genes

BioBiochem (13 decks)

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