Chapter 2: Cell Structure & Microbiology

Question 1

The cell theory

Answer 1

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

Question 2

Types of gradients

Answer 2

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

Question 3

Permeability of the membrane

Answer 3

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

Question 4

Passive transport

Answer 4

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

Question 5

Active transport: against concentration gradient

Answer 5

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

Question 6

Directionalities of membrane transport

Answer 6

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

Question 7

Intrinsic proteins

Answer 7

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.

Question 8

Extrinsic proteins

Answer 8

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

Question 9

Endocytosis and exocytosis

Answer 9

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

Question 10

Eukaryotic cells vs prokaryotic cells

Answer 10

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

Question 11

Golgi apparatus

Answer 11

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

Question 12

lysosomes

Answer 12

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)

Question 13

Endoplasmic reticulum

Answer 13

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

Question 14

peroxisomes

Answer 14

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

Question 15

Mitochondria

Answer 15

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

Question 16

Nucleus

Answer 16

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

Question 17

Cellular filaments in cytoskeleton: microtubules

Answer 17

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

Question 18

Cellular filaments in cytoskeleton: microfilaments /actin filaments

Answer 18

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

Question 19

Cellular filaments in cytoskeleton: intermediate filaments

Answer 19

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

Question 20

Cellular junctions:

Answer 20

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)

Question 21

The extracellular matrix

Answer 21

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

Question 22

Tissues: epithelial

Answer 22

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

Question 23

Tissues: connective

Answer 23

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)

Question 24

Virus

Answer 24

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

Question 25

Bacteriophages

Answer 25

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)

Question 26

Viral life cycles: Lytic and lysogenic

Answer 26

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

Question 27

Sub viral particles related to viruses

Answer 27

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

Question 28

Reverse transcriptase for retroviruses

Answer 28

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

Question 29

Prokaryotes: archaea

Answer 29

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

Question 30

Prokaryotes: bacteria

Answer 30

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

Question 31

Bacterial envelope

Answer 31

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

Question 32

Binary fission & growth of bacteria

Answer 32

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

Question 33

Genetic recombination

Answer 33

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

Question 34

Transposons

Answer 34

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

Question 35

Regulation of transcription in prokaryotes

Answer 35

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