Download Exam #1 Review

Exam #1 Review
General Study Suggestions:
1)
Begin by reviewing your lecture notes. If there is anything that you
do not understand, make an appointment with me, attend office
hours or review the content in your book.
2)
Next, carefully review the questions that we discussed during
lecture and the homework questions. **The exam questions will be
similar to the homework questions! 3)
Finally, go through this review as it may serve as a reminder of the
overarching content of the exam. Format and composition:
There will be 25 multiple choice questions. These are followed by 7 - 8 short answer,
matching or fill-in-the-blank questions worth 10 points a piece. All students must
answer #26 regarding Gram-positive and Gram-negative cell wall structure. Then,
choose to answer any four of the remaining questions. Circle the questions that you
would like to answer.
Topics covered by these free response questions:
- Macromolecules
- The cell membrane / transport
- Vocabulary (macromolecules / cell components)
- Basic cell structure and function
The exam is worth 100 points. Your overall score will be determined in one of two ways
depending on which leads to the highest overall total:
1) Multiple Choice Score * 2 + Free Response Score
2) Multiple Choice Score + Free Response Score * 1.5
All of the following is in your notes but here it is in review format:
Microbiology is the study of life forms and agents that are too small to be seen with the
unaided eye. Although humans utilized microorganisms to make bread and beer as early
as 2100 B.C., it was not until 1673 that Antony van Leeuwenhoek, using a hand-crafted
microscope, viewed and thoroughly described these tiny organisms which he called
“animalcules”.
I. The origin of microorganisms (lecture #1)
A. Scientists struggled for over a hundred years to reject the idea of spontaneous
generation and support the idea that all forms of life arise from other living
things of the same kind (biogenesis). Be familiar with all the scientists
involved in this debate and understand their contributions.
Practice: The idea of spontaneous generation postulated that
a. organisms could evolve into the next generation of organisms.
b. organisms could spontaneously combust.
c. organisms could spontaneously arise from other living
organisms.
d. living organisms could arise from nonliving material.
B. Review and understand Koch’s Postulates!
II. Microbiology: Implications and Applications (lecture #1)
A. Fixing nitrogen, replenishing oxygen and degradation (decomposition) are
essential (vital) activities of microorganisms.
B. Microorganisms also have a very big economic impact.
Practice: Microorganisms are involved in
a. Food production
b. Food preservation
c. Production of vaccines
d. Production of antibiotics
e. All of the above
C. Bioremediation - The use of microorganims to clean up waste (e.g. degrade
oil spills, detoxify compounds that are harmful to the environment).
D. Genetic Engineering = Introduction of genes from one organism into another
to give it new features or abilities.
E. Medical Microbiology = The study of disease-causing microorganisms (called
pathogens).
1. In 1906, the three leading causes of death were infectious diseases (cdc.gov)
Now, many infectious diseases have been eradicated.
2. Despite the eradication of many infectious diseases we must fight newly
emerging diseases, the resurgence of old diseases and microorganisms that
are becoming resistant to current treatment techniques. We are also just
beginning to understand that many conditions, such as peptic ulcers, are
caused by bacteria and cancers, such as cervical cancer, are caused by
viruses.
Practice: Which of the following is a reason for the resurgence of old
diseases?
a. A decline in the vaccination of children
b. An increase in international travel
c. both a and b
d. none of the above
F. **Despite the disease-causing potential of some microorganisms, most
microorganisms are not pathogenic. In fact, those covering our body play
a protective role by competing with pathogenic microbes.**
G. Bacteria are good model organisms for study. Why?
III. Macromolecules (proteins, carbohydrates, nucleic acids and lipids)
*Be sure to review and understand the game questions for this section.
A. Proteins
Practice: Which one of the following is NOT a protein
function?
a. Transporting molecules from one location to another.
b. Coordinating motion.
c. Providing the genetic code for all of a cell’s properties.
d. Providing mechanical support in eukaryotic cells.
1. Proteins are composed of 20 standard amino acids. Be familiar with the
general structure of an amino acid (central carbon, amino group, carboxyl group,
hydrogen atom and an R-group.)
*Be able to recognize the names and abbreviations (both 3- and 1-letter) of
these amino acids. I will provide the table with amino acid structures but I
will not provide 1-letter abbreviations or information regarding the nature of
the R group. Thus, be familiar with how amino acids are categorized
according to the nature of their R group.
2. The amino acids are linked together by peptide bonds to form polypeptide
chains. Each amino acid in a polypeptide chain is called a residue.
Practice: What molecule is lost in the formation of a peptide bond?
3. Proteins have three or four levels of structure. The genetically determined
sequence of their amino acids (e.g. Ile-Gly-Met-Phe...) is their primary
structure. The regularly repeating structures (e.g. alpha-helix, beta-sheet and
beta-turn) into which the polypeptide chain folds is called the secondary
structure. The regularly repeating structures fold upon themselves to give a
protein an overall 3-d structure called the tertiary structure. If a protein has
more than one polypeptide chain, the way in which these chains arrange
themselves with respect to one another is called the quaternary structure.
Practice: The helices and sheets of amino acids form a protein’s
a. primary structure
b. secondary structure
c. tertiary structure
d. quaternary structure
What does it mean if a molecule/structure is amphipathic?
ANSWER:
Amphipathic molecules have a dual nature.
B. Carbohydrates
Carbohydrates function as a source of carbon and energy (both immediate and
reserve). They are components of cell walls (glycoproteins and glycolipids) and
some external cell structures (capsule/slime layer).
1. Monosaccharides = simple sugars (glucose, fructose and galactose - 6
carbon monosaccharides, ribose - 5 carbon monosaccharide)
*Be familiar with the structure of glucose and the reaction by which it
forms a ring structure. Be familiar with how the carbon atoms are
numbered in glucose.
Practice: Are monosaccharides likely water soluble?
2. Disaccharide (two sugars) - maltose, lactose, sucrose. Monosaccharide
subunits are joined by a glycosidic linkage.
Practice: What molecule is lost in the formation of a glycosidic
linkage?
3. Oligosaccharides (short chains (2 to 10) of sugars)
4. Polysaccharides (long chains of sugars that often have branches (e.g.
glycogen)) *Glycosidic linkages in straight chain polysaccharides are 1,4
(between the 1st and the 4th carbon). Branched polysaccharides also have
1,6 glycosidic linkages.
Practice: Which is/are TRUE of carbohydrates?
a. They may serve as a source of food.
b. They are hydrophilic.
c. They may be bonded to proteins to form glycoproteins.
d. They are a component of some bacterial capsules.
e. all of the above.
Practice: What is the difference between cellulose and glycogen?
C. Nucleic Acids
1. DNA and RNA - composed of nucleotides which are composed of a 5
carbon sugar, a nitrogenous base and a phosphate group. Practice
numbering the carbon atoms on the 5-carbon sugar. Why are these
numbers so important to understanding the structure of not only
nucleotides but the nucleic acids which they form?
Practice: DNA contains
a. sugars
b. 3’-5’ phosphodiester bonds
c. triacylglycerols
d. peptide bonds
e. c and d
2. Bases
Purines - adenine and guanine (double-ring structure)
Pyrimidines - cytosine, thymine and uracil (single ring)
Practice: Which of the following is found in RNA but not in DNA?
a. adenine
b. cytosine
c. thymine
d. uracil
3. In nucleic acids, the nucleotide subunits are bound covalently (the 5’
phosphate binds to the 3’ hydroxyl). This linkage is termed a 3’,5’phosphodiester linkage.
4. Covalent bonding of many nucleotides forms a single strand of
nucleotides which, in DNA, then binds to a complementary strand via
hydrogen bonds. The complementary strand runs in the opposite direction
(antiparallel) to the first strand. Together they form a double-stranded
helix.
a. A single strand of nucleotides joined by 3’,5’-phosphodiester
bonds always has polarity/directionality. It always has a 3’ end
and a 5’ end.
b. When the H-bonds that hold the two strands of DNA together
are broken, this is called denaturation or melting.
c. **If given a DNA sequence, be sure that you understand how to
determine its correct complimentary sequence!!
D. Lipids
Practice: Which is/are TRUE about lipids?
a. They are a major structural component of all cell membranes.
b. They can serve as energy stores.
c. They function in cell signaling and recognition.
d. All of the above.
1. Triacylglycerols, steroids, sterols, waxes and phospholipids *Know
the basic structure of a triacylglycerol
**Be able to recognize the structure of a phospholipid.
2. ALL CELL MEMBRANES ARE SEMIPERMEABLE
PHOSPHOLIPID BILAYERS. Know how phospholipids come together
to form a PL bilayer. Be able to draw and label the hydrophilic and
hydrophobic portions of a phospholipid bilayer.
Practice: Why are fats packed with power?
IV. Classification and Nomenclature
A. Domains
Practice: Which of the following is/are not domains into which all living
organisms can by classified?
a. Helminths
b. Bacteria
c. Archaea
d. Eucarya
1. Members of the domain Bacteria and Archaea are prokaryotes, they
vary in size but are often 0.3 to 2 micrometers; they are single-celled and
have no membrane-bound nucleus or organelles. Their genetic material is
simply stored in a region called the nucleoid. Prokaryotes are surrounded
by a cell membrane and generally a rigid cell wall. They multiply by
binary fission and some move using flagella. Bacteria differ from archaea
in that their cell wall is composed of peptidoglycan. Archaea have a
different overall cell wall composition that LACKS PEPTIDOGLYCAN.
While bacteria live in all environments, archaea are frequently found in
extreme environments.
2. Members of the domain Eukarya can be either single-celled or
multicellular. They always have a membrane-bound nucleus and
organelles. Some eukaryotic cells have a cell wall but it is NEVER
MADE OF PEPTIDOGLYCAN. On average, eukaryotic cells are larger
than prokaryotic cells (5 to 50 micrometers). Are there exceptions?
B. Nomenclature.
Practice: In binomial nomenclature, the scientific name of an organism
includes its
a. family and genus.
b. first name and last name.
c. genus and species.
d. domain.
**The genus is written first and capitalized followed by the species name, which
is lowercase. Both are either italicized or underlined!! If there is a strain
designation, it follows the species name.
V. Prokaryotic cell structure and function
A. Cell shapes and arrangements
Be able to recognize and or draw all of the cell shapes.
Practice: Which one of the following is not a bacterial cell shape?
a. spirillum
b. coccobacillus
c. coccus
d. oblongccus
*Bacteria that vary their shape are called pleomorphic. Starlike bacterial shapes
can result from bacterial surface extensions called prosthecae.
Know and be able to recognize all of the cell arrangements. What causes these
different cell arrangements?
B. Prokaryotic cell components
**Knowledge of the structure of a bacterial cell is important to
understanding natural host defense systems, synthesis of antimicrobial
substances, identification and characterization of bacteria as well as
ecological / environmental impact.
1. The nucleoid- gel-like mass containing some RNA and protein but
mostly a single, circular, supercoiled piece of dsDNA.
The bacterial chromosome is a single, circular piece of double-stranded (ds)
DNA. If this piece of DNA were cut to form a piece of linear DNA, the linear
piece of DNA would be almost 1,000 times as long as the cell itself. However,
when packaged into the bacterial cell, this DNA takes up only 10% of the
total cell volume. How can this be accomplished?
a. The DNA is tightly packaged within a membrane bound nucleus.
b. The DNA is twisted into a supercoiled form1.
c. The DNA is converted into small circular pieces of dsDNA called
plasmids.
d. none of the above
2. Plasmids - Small, generally circular pieces of DNA that can replicate
on their own (often give a bacterium a new trait such as resistance to an
antibiotic). They are not generally a part of the chromosome =
extrachromosomal. Many plasmids can be transferred from 1 cell to
another (conjugative).
3. Ribosomes - Protein factories (70 S)
Practice: What are the two subunits of the prokaryotic ribosome? Of what
two macromolecules is a ribosome composed? Note that only bacteria and
archaea have 70S ribosomes. Eukaryotes have 80S ribosomes. What is one
important application of this difference?
1 Increasing evidence is showing a larger than once thought role for proteins in condensation as well. 4. Inclusions
a. Generally used for storage (backup food supply) and include granules
that store phosphate, glycogen, and amino acids. Some storage granules
are bound by a single-layered membrane.
b. Microcompartments are thought by some scientists to be functionally
analogous to organelles. These include carboxysomes that store CO2.
c. Magnetosomes
What do magnetosomes allow bacteria to do?
d. Gas vacuoles = aggregates of large numbers of gas vesicles.
Practice: Which one of the following microorganisms is most likely to
have gas vacuoles?
a. Bacillus subtilis (a soil bacterium)
b. Escherichia coli (a gut bacterium)
c. Anabaena flos-quae (an aquatic, photosynthetic cyanobacterium)
5. Cytoplasmic membrane
Practice: Which is not true of the cytoplasmic membrane?
a. it defines the boundaries of the cell.
b. It is a semipermeable barrier.
c. It consists mainly of a fixed, static phospholipid bilayer.
d. It uses proteins as selective gates and sensors.
e. all of the above are true.
*IMPORTANT: There will be a question regarding the cytoplasmic
membrane and the Fluid Mosaic Model.
a. Transport - small hydrophobic molecules and small gas molecules can
diffuse across the membrane (simple diffusion) but large, hydrophilic
molecules and charged molecules require transporters.
b. Energy transfer across the plasma membrane.
Prokaryotic cells that are capable of some type of respiration or
photosynthesis have the components of the electron transport chain
across their membrane. These components are electron carriers.
They transfer electrons from one to the other and this leads to the
ejection of protons. As protons are ejected out of the cell, a proton
gradient forms across the membrane. This proton gradient is called
the proton motive force (PMF). This PMF is like reserve energy (like
a battery). When the protons are allowed to flow back through a
protein into the cell, the reserve energy can be harnessed to make
ATP!! In prokaryotes, this battery-like energy can also be used to
power other cellular processes (e.g. flagella rotation and certain
transport systems).
5. The cell wall
a. Contains peptidoglycan in bacteria. Peptidoglycan contains glycan
chains of alternating NAM and NAG. A tetrapeptide chain is attached to
each NAM (composed largely of unusual amino acids). These
tatrapeptide chains are then joined (directly in most Gram-negative
bacteria, whereas Gram-positive bacteria are more likely to have a
(glycine) peptide interbridge).
b. The peptidoglycan layer in bacteria can be thought of like a wire mesh.
It is very rigid, yet it is porous.
c. Because eucaryotic cells do not contain peptidoglycan, it makes a good
target for antimicrobial substances (penicillin and lysozyme).
Practice: Which is/are true about the cell wall of bacteria?
a. It determines the shape of the bacteria.
b. It prevents the bacteria from bursting in hypotonic solutions.
c. It contains peptidoglycan.
d. It may be targeted by antimicrobials.
e. all are true.
Practice: Draw the cell wall of both a Gram-positive and a Gramnegative bacteria. Be certain to note which molecules are
responsible for the cells’ overall negative charges as well as being
recognized by our body’s immune system. **There will be an
important question about this!**
Practice: What is the difference between teichoic and lipoteichoic acid?
Practice: The cell wall of a Gram-negative bacterium
a. has a thick peptidoglycan layer.
b. has a thin peptidoglycan layer.
c. is characterized by an outer membrane containing LPS.
d. has gel-like fluid between the inner and outer membranes called
the periplasm.
e. b, c and d
f. none of the above.
*Note- An LPS molecule has three regions. The upper region, the O-specific
polysaccharide, is recognized by host defense systems. It also changes in some
bacteria (e.g. Salmonella) allowing them to evade the immune system. The central
region contributes to the negative charge of the cell wall. The lowest lipid A
region is the toxic region that allows LPS to act as an endotoxin (elicits fever and
shock).
Also in Gram-negative cell walls, lipoproteins join the outer membrane to the
peptidoglycan layer. Porin proteins span the outer membrane to form pores
through which small molecules can pass.
d. The cell wall protects bacteria from destruction by osmotic pressure.
Practice: The simple diffusion of water is called
a. permeosis
b. osmosis
c. aquaosis
d. turgorperosis
If the concentration of solutes inside a cell is less than that outside the cell = a
hypertonic enviroment. Water flows out of the cell, the cytoplasmic membrane
shrinks and pulls away from the cell wall (plasmolysis).
Practice: Describe what happens when a cell is placed in a hypotonic
environment.
What is the difference between a spheroplast and a protoplast?
6. Glycocalyx - an outer layer, generally made of polysaccharide that surrounds
some bacteria. If this layer is highly organized then it is called a capsule. If the
layer is irregular, it is called a slime layer.
7. S-layer - an outer protective layer, made of distinctly structured protein or
glycoprotein.
Practice: Both capsules and S-layers
a. are glycocalyx.
b. are structures external to a bacterial cell wall.
c. protect against phagocytosis.
d. b and c
8. Flagella - function in motility - use PMF to spin like propellers, a basal body
anchors the flagella within the cell wall / cytoplasmic membrane, a curved hook
connects the basal body to the filament. The filament extends into the
environment. The filament is made of the protein flagellin. Prokaryotic flagella
spin like propellers.
a. Distribution - monotrichous (polar), amphitrichous, lophotrichous
and Peritrichous flagella.
b. Counterclockwise movement of flagella = a run.
c. Clockwise movement = a tumble.
Practice: A motile bacterium is placed into a medium with a chemical
attractant at the opposite end. Describe the process by which the bacterium
moves towards the attractant. Include a picture.
What is it called when a bacterium moves in response to a chemical
gradient?
7. Pili (fimbriae) - shorter and thinner than flagella, with a hollow core. Allow
for adherence to specific surfaces, movement of populations of cells on solid
media and conjugation. The Prescott book distinguishes between fimbriae and
pili. It terms anything not involved in conjugation as fimbriae.