Download 2 Pts. each

-2 Pts. each1. For each of the 5 terms below give a brief definition and a brief statement of the
significance for microbiology:
Tyndall Effect
The Tyndall Effect is the scattering of light by particles in the atmosphere.
These particles may be viable microorganisms, or may have microorganisms attached, i.e.
absence of a demonstrable Tyndall effect indicates that air is essentially sterile.
Endotoxin
Refers to the Lipid A component of lipopolysaccharide (LPS) from the outer membrane of
Gram-negative Bacteria. Release of endotoxin in the host may cause severe symptoms.
Transpeptidase
Transpeptidases are the periplasmic enzymes responsible for forming the peptide crosslinks
between new and old glycan strands. they are the targets for β-lactam antibiotics.
Transcription-Translation Coupling
Unlike eukaryotes, in bacteria, ribosomes begin translating the 5ʼ end of an mRNA while
the 3ʼ end of the mRNA is still being transcribed. This essentially eliminates processing of
the RNA transcript.
Molecular Clock
A molecular clock is a gene (DNA), RNA, or protein whose sequence accumulates substitutions
at a constant rate over time. This allows determining the time since the divergence between
two branches of a phylogenetic tree.
2.
A. (5 pts.)
Give the complete scientific name of the organism that is the source of the enzyme used in
PCR;
Thermus aquaticus
the name of investigator who isolated it;
Thomas Brock
and the location/environment from which it was first isolated
Hot spring in Yellowstone Natl. Park
B. (5 pts.)
Pasteur’s experiments with “swan-necked” flasks were intended to answer specific objections
made by proponents of spontaneous generation to the earlier experiments done by
Spallanzani. Explain briefly the significance of the flasks in relation to Spallanzani’s
experiments and to the criticisms they elicited.
Spallanzani used SEALED flasks. His experiments were criticized on the grounds that
heating somehow altered the property of the air in the vessels so that it could not support
life. Pasteurʼs flasks were open to the atmosphere. Extraneous organisms were excluded
by the tortuous path in the neck, not by sealing.
3.
A. (5 pts.)
Scientists believe that oxygen first appeared in the atmosphere several billion years ago due
to the evolution of a specific microbial group. What is the general name for this group?
Cyanobacteria
What specific cellular mechanism "invented" by this group was responsible for oxygen
production?
Photosystem II / Oxidation ("Splitting") Water (1 pt. for "photosymnthesis")
B. (5 pts.)
Current thinking on the origin of life suggests that, contrary to the Stanley Miller-Harold
Urey concept, the first organisms:
were not mesophiles, but thermophiles or hyperthermophiles
were not organotrophs, but lithotrophs or chemolithotrophs (accepted chemotrophs)
were not heterotrophs, but autotrophs
4.
A. (6 pts.)
Phospholipids occur in the plasma membrane of Gram-negative bacteria, as well as in the
outer membrane. The outer monolayer of the outer membrane is primarily composed of a
different molecular component.
What is the name of this component?
Lipopolysaccharide
In as much detail as you can, describe the molecular structure of this outer membrane
component. You may use text, a diagram, or both.
“lipid A”: Fatty acid chains esterified to a di-phosphorylated disaccharide (Glucosamine)
“Core Polysaccharide”: branched, phosphorylated polysaccharide chain
“O-Specific Polysaccharide (or O-specific Antigen): highly variable chain of hexose
sugars, may be branched.
B. (4 pts.)
Give 2 examples of aqueous solutes that would freely diffuse across plasma membranes at
rates fast enough that we would not expect them to need transport proteins.
water, O2, N2 etc.
Give 2 examples of aqueous solutes that freely diffuse across plasma membranes at rates too
slow enough that we would expect transport proteins would be needed.
ions, carbohydrates, amino acids, etc.
5.
A.
(5 pts.) Give a brief, general description of the class of enzymes known as
“lysozymes”.
Lysozymes catalyze hydrolysis of the beta 1,4 gloycoside bond between sugars in the
glycan strands of peptidoglycan. Weakening of the cell wall leads to osmotic lysis of the
cell.
How would the result of lysozyme treatment be altered by the presence of high
sucrose concentration?
In high sucrose prevents osmotic lysis i.e. stabilizes spheroplast.
B.
In the diagram below, an arrow and a circle are used to indicate a particular
structure within the molecule. The structure is called:
Beta-Lactam Ring (2/3 for "penicillin")
Describe the significance of this structure.
Structural mimic of the peptide bond in the NAM-NAG pentapeptide substrate for
transpeptidase enzymes. Transpeptidases cleave the ring and form a permanent covalent
complex, inactivating the enzyme.
6. In the diagram, add labels that will indicate clearly and precisely to location of the:
Flagellar filament
Flagellin protein monomers
L Ring
MS Ring
Mot proteins
Fli Proteins
Lipopolysaccharide (LPS)
Peptidoglycan
Path and Direction of Proton (H+) Flow
H+
7.
According to the model of bacterial chemotaxis presented in class, and in the text, which
protein or proteins from the list below undergo alternate phosphorylation and
dephosphorylation?
CheA
CheY
CheB
Which protein or proteins from the list below undergo alternate methylation and
demethylation?
Transducer MCP Metrhyl-accepting-chemotaxis protein (=transducer)
Which protein or proteins from the list below is a trans-membrane proton channel?
Mot
Transducer MCP Metrhyl-accepting-chemotaxis protein (=transducer)
CheA
CheB
CheR
CheW
CheY
CheZ
Fli
Mot
8.
A.
(5 pts.)Highly expressed genes are generally located near the origin of replication in
many bacterial genomes. Explain how this genomic location can lead to higher levels of gene
expression.
The copy number of genes near the origin of replication is increased under conditions of
dichotomous repliction.
B.
(5 pts.) Define the terms pan genome and core genome. Give an example of a type of
gene that would be found in each.
Each individual strain of a bacterial species shares a common or "core" array of genes with all
other strains of that species. The core genome includes most or all "housekeeping genes"; genes
essential for basic cell functions such as replication, transcription and translation.
Each strain also has a unique and variable set of adjunct genetic sequences, either in the
bacterial chromosome or in extrachromosomal elements such as plasmids, that is called the
"pan" genome. The pan genome often includes (inessential) genes that allow the cell to adapt to
special circumstances. The pan genome consists of plasmids, viral genomes and chromosomal
islands.
9.
A.
(5 pts.) The evolution of antibiotic-resistant bacteria by the process of “transferrable
drug resistance” is an enormous clinical problem. Which 2 of the mechanisms listed below are
the most important contributors to the evolution of transferrable drug resistance?
Plasmid-mediated Conjugation X
Specialized Transduction
Generalized Transduction
Transformation
Transposable Elements (Transposons)
B.
X
(5 pts.) Describe the process (or event) that converts F+ to Hfr strain.
Homologous recombination between similar IS elements or transposons present in both
the cellular genome and the F plasmid.
What can an Hfr strain do that an F+ strain cannot?
Transfer genes of the bacterial cellular genome to a recipient strain.
10.
A.
(5 pts.) You are given an unlabeled graph of an Arrhenius plot for a microorganism.
Indicate by drawing on the graph the specific location/s of the following parameters:
a.) the extent of the normal growth range (i.e. the “Arrhenius” range)
b.) the optimum temperature
B. (5 pts.) Describe the phenomenon called the "heat shock response" and its mode of
regulation.
Heat shock response involves a global control network of many genes.
Above the normal growth range a specific set of proteins are expressed at significantly
higher levels than they are at lower temperatures.
This response is regulated in part by two alternate sigma factors which direct
transcription of these gene products.
Some of the heat shock proteins are necessary for survival at elevated temperatures.
11. Give three characteristics that would allow you to recognize the presence of a
chromosomal island in a bacterial genome.
i.) the genes are not present in closely related strains or groups ii.) the %GC of the island is different than the genome as a whole. iii.) the pattern of synonomous codon preference is different from the majority of genes in the genome. iv.) the DNA sequences at the island boundaries are similar to sequences found in lysogenic virus genomes or in transposable elements. v.) genes in islands do not code for essential basic cell functions