Study Guide 2 for Bio 103L at Duke

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What is the cell?: It is the basic unit of all organisms
What are the cell's basic features?: 1) A pattern of organization unique to each group of organisms

2) Capacity for independent reproduction of organismal traits (totipotency)
What primarily limits cell size?: The surface-area/volume ratio' surfaces required for efficient metabolism and maintenance of order
What is the difference between Eukaryotic cells and Prokaryotic cells?: Eukaryotic cells are larger and utilize compartmentalization to maintain higher surface-area/volume ratio. They also have internal membranes, including membrane-bound organelles such as nucleus, and are larger.

Prokaryotic cells are smaller, lack extensive internal membrane and organelles (may have nucleoid region through and mesosomes).
What kind of cells are viruses?: TRICK QUESTION! Viruses are acellular by definition.
What are the three basic shapes of bacterial cells?: 1) Bacilli
2) Cocci
3) Spirilli
What is a pleomorphic cell?: A cell who has a variable shape
What are some common types of arrangements of cell groupings?: pairs, chains, filaments
What does it mean when that a cell membrane is differentially permeable?: It means that small and/or hydrophobic molecules move across but...

Larger,polar or charged molecules require a transport pathway.
What is the cytoplasmic cell membrane structure composed of?: A lipid bilayer involving phospholipids.
Do membranes have proteins? If so, to what extent?: Yes they have proteins. They are 40-75% composed of proteins. Proteins include many enzyme systems which facilitate tranport of large molecules.
What kind of picture of the cell does the fluid mosaic model paint?: It depcits the cell membrane as a dynamic structure.
What is one of the primary functions of the cell membrane in regards to other molecules?: It is responsible for the transport of said molecules into and out of the cell.
What are the two broad categories of transport methods?: 1) Diffusion (passive or facilitated)

2) Active transport (requires energy)
What is passive diffusion?: Molecules go in the cell because of a higher chemical gradient existing outside the cell
What is facilitated diffusion?: It is when the cell membrane utilizes carrier proteins to obtain saturated kinetics of uptake.
What is active transport?: It involves the transport of compounds against their free energy gradients and require an energy source.
What does primary active transport in bacteria use for an energy source?: They use proton (H+) pumping ATPase to set up a proton motive force across the cell membrane. This drives the uptake of other compounds by secondary active transport.
What is group translocation?: It is unique to prokaryotes and couples metabolism with transport.
What are some of the other functions of cell membrane proteins other than transport?: Secretion of extracellular enzymes, electron transfer during oxidative phosphorylation (i.e. ATP synthesis) and photosynthesis, and a role in cell division.
What is the primary function of the cell wall?: To prevent the cell from bursting from osmotic shock.
What is the cell wall made of?: It is composed of a porous polymer layef called Peptidoglycan (murien, mucopeptide)
What do the three main types of bacterial shapes actually look like?: Bacilliary- rodshaped
Coccoid- round
Spirilloid- spiral shaped
Wha is a more general desciption of the physical quality of cell walls?: They are rigid, multilayered sheets
What is the structure of peptidoglycan (a component of the cell wall): glycan polymers (polysaccharide) of alternating N-acetylglucosamine and
N-acetylmuramic acid (both amino sugars), connected by β-1,4 linkages.
What is muramic acid attached to in the peptidoglycan structure?: Muramic acid attached to tetra-peptide chain; tetrapeptides are cross-linked
(interbridged) via peptide bonds to form a lattice structure.
What is the difference in the amino acid composition of the tetrapeptides in gram-negative and gram-positive bacteria?: D- + L-alanine, D-glutamic acid, L-lysine in gram positive bacteria
diaminopimelic acid in gram negative bacteria.
What is the difference between the ways in which lysozyme and penicillin act to reduce wall stability in the structure of peptidoglycan?: Penicillin acts to prevent cross-linking of peptide lattice; its primary effect is on growing cells.

Lysozyme breaks down Beta-1,4 linkage of glycan in full grown and young cells.
What is a spheroplast?: A cell in which the cell wall is partially removed by lysozyme under the proper osmotic conditions
What is a protoplast?: It is a cell whose cell wall is completely absent after being exposed to lysozyme under the proper osmotic conditions
Describe the specifics of the Gram positive cell wall structure: Gram positive walls consist of a thick layer of murein (>90%) and are resistant to decolorizing agents (alcohol). Wall matrix of gram+ bacteria also contains teichoic acids, acidic polymers made of gylcerol phosphate, amino acids, and a polyhydroxy alcohol (ribitol)
Describe the specifics of the Gram NEGATIVE cell wall structure: Gram negative cell walls are biochemically more complex - only 10% is murein,
teichoic acids are absent; instead, an outer membrane (cell envelope) is present,
composed of phospholipids, polysaccharides and proteins. Outer surface covered with
lipopolysaccharides (LPS) with unique immunological and toxic properties (endotoxin &
O-antigen). A Gram negative cell thus actually has two cell membranes. The cell
envelope functions as a molecular sieve and repels many molecules, such as some
antibiotics (e.g., penicillin). As a result, gram negative bacteria are often less sensitive to
certain antibiotics. Most pathogenic bacteria are gram negative.
What kind of bacteria have modified or no cell walls?: Archaebacteria and mycoplasmas?
Describe the cell walls of Archaebacteria: Most Archaea have no murein (although some have a related
pseudopeptidoglycan). The nature of Archaea cell walls varies considerably among different species and some have wall that only have proteinaceous material in them.
Describe the cell walls of mycoplasms: TRICK QUESTION!! Mycoplasmas lack cell walls entirely; the cell membrane is more rigid; however, due to incorporation of sterols (obtained from the eukaryotic host cell). Mycoplasmas and Archaea are not inhibited by penicillin.
What is a capsule?: The outermost layer of many prokaryotic organisms that is usually made up of polysaccharides but sometimes proteins. It is usually slimy or gummy. Functions include protection against dessication, phagocytosis; often associated with pathogenicity, also a site for attachment of bacteriophages, and for attachment of bacterium to substrate (e.g., plaque bacteria). Capsule may
also be less tightly bound (slime layer or glycocalyx).
What are pili?: Pili (fimbriae) - short hair-like, cylindrical structures. Functions include attachment,conjugation, receptor site for phage.
What are flagallae?: Flagellae - confer motility, may be polar or peritrichous. Composed of flagellin, forming helical subunits, growth at tip. Bacterial flagellum consists of a single filament. Attached to cell via a set of rings and basal body (Gram negative bacteria have second set of rings on outer
membrane). Function similar to electric motor shaft. Energy derived from proton motive force. Many flagellated bacteria exhibit chemotaxis in response to a stimulus gradient.
Describe the bacterial chromosome: single, circular, supercoiled DNA. Although unbound by a
nuclear envelope, the chromosome is contained within a nucleoid region. Histones are absent in bacteria (although some may have histone-like protein).
What is a plasmid?: extrachromosomal (circular) DNA that contains supplemental genetic information.
Describe ribosomes.: site of translation (protein synthesis); roughly 10,000 per cell. Composed of ribosomal RNA, and protein. Composed of two subunits defined by their sedimentation velocity, 30S and 50S, which combine to form a single 70S ribosome. 70S ribosome function is affected by several antibiotics which block protein synthesis (e.g., streptomycin and erythromycin).
Describe storage bodies: metachromatic granules (volutin) -- contain polyphosphate. Cytoplasmic
inclusions contain other storage products, including carbohydrate sources like poly-betahydroxybutyric
acid (PHB). Other stored compounds can include elemental sulfur and iron
oxide which are formed in response to nutrient limitations.
Describe spores: many types are present; Endospores are a highly specialized, layered structure
composed of murein and calcium dipicolinate (very heat resistant).
What is a difference in location between eukaryotic DNA and prokaryotic DNA: Eukaryotic DNA resides in the nucleus which is delimited by a double membrane (nuclear
envelope).
What is a difference in the structure of the Eukaryotic DNA?: Chromosomes are composed of chromatin -- linear DNA plus protein (histones). Chromatin is packaged into nucleosomes, consisting of tightly coiled DNA and histones ("beads on a string").
What is a difference between eukaryotic and prokaryotic ribosomes?: Eukaryotic ribosomes are larger and denser (80S). The small ribosomal subunit (40S)
contains longer 18S RNA; the larger subunit (60S) has 25-28S RNA. RNA transcription in eukaryotes is localized within the nuceolus (which is not present in bacteria).
What about eukaryotic mitochondria and chloroplasts in regards to ribosomes and DNA?: Mitochondria and chloroplasts also have ribosomes, of the prokaryotic type (70S) (they also have small circular DNA, which supports the endosymbiotic theory of their origin).
What antibiotics are eukaryotic ribosomes not affected by?: Eukaryotic ribosomes are not affected by streptomycin or erythromycin.
What are some distinctive features of eukaryotic flagallae and cilia?: Eukaryotic flagellae and cilia are more complex, with a '9+2'arrangement of microtubules. Movement is also driven by ATP, but achieved by 'sliding' of filaments past each other.
Explain the endomembrane system of eukaryotes: Eukaryotic cells contain an endomembrane system -- an extensive set of membranes used for intracellular trafficking and communication. Includes nuclear envelope, smooth and rough ER, golgi and vacuoles, among others.
Describe the cytoskeleton of eukaryotes: Cytoskeleton of eukaryotes is composed of microtubules, intermediate filaments, and
microfilaments. Provides internal rigidity and structure to the cell as well as being involved in
both intra- (cytoplasmic streaming) and extracellular (pseudopodia in amoebae) movement.

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