Download Microbiology Study Guide – Exam #2

Microbiology Study Guide – Exam #2
This is a list of general topics you should be prepared to answer questions on for each chapter. This guide
is NOT what you should study but rather is a guide to help organize your studying of the material listed.
Your actual studying should involve the textbook, Powerpoint slides, your notes and other supplemental
material such as Mastering Microbiology. Keep in mind that you will not be tested on material in the book
that was not covered in class, and should know all of the key terms at the end of the Powerpoint slides for
each chapter. Most important, if you have trouble understanding anything, come to my office hour or see
a tutor ASAP. Once you feel like you understand the material in a given chapter, be sure to test yourself
using the chapter questions, Mastering Microbiology, the sample questions on this study guide, or coming
up with your own. If you put in the time and effort and use all the resources available to you, I’m confident
you all can perform very well on the exam.
Chapter 5 (Microbial Metabolism)
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the concept of metabolic pathways, also endergonic vs exergonic, catabolic vs anabolic
how enzymes catalyze (increase the rate of) chemical reactions, activation energy
factors that affect enzyme activity – pH, temperature, substrate concentration
o the concept of denaturation of proteins
enzyme regulation/inhibition (competitive, allosteric, feedback)
basic structure of ATP (ribose, adenine, 3 phosphates), why it is a good energy source in cells
oxidation/reduction, substrate-level phosphorylation
the basic process and products of glycolysis
the basic process, purpose and various products of fermentation
basic process, products of each stage of respiration
o Krebs cycle
o electron transport
o chemiosmosis
the roles of the following in respiration:
o electron carriers (NADH, FADH2)
o electron transport
o H+ gradient
where fatty acids enter the process of cellular respiration
difference between aerobic and anaerobic respiration
sample questions:
1. Compare ATP production in fermentation vs respiration.
2. Describe how feedback inhibition would work to allosterically inhibit a metabolic pathway.
Chapter 6 (Microbial Growth)
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the effects of temperature, pH, osmotic pressure on microbial growth
characterize organisms based on the temperature range in which growth occurs
why oxygen can be harmful to organisms,
o the reactive oxygen species (radicals) that are derived from oxygen
o enzymes organisms produce to protect themselves from these
chemical nutrients needed for microbial growth
general types of growth media and the purpose of each
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o complex vs defined media
o selective vs differential media
how to culture anaerobic organisms
concepts of bacterial growth: binary fission, generation time, arithmetic vs exponential growth
phases of microbial growth: lag, log, stationary, death phases
characteristics of biofilms
methods of determining cell density and the advantages & disadvantages of each
o serial dilution
 concept of a colony forming unit (CFU)
 how to calculate CFU/ml
o filtration
o direct microscopic counts using a counting chamber slide
o spectrophotometry
sample questions:
1. How does osmotic pressure restrict microbial growth?
2. What is the culture density (in CFU/ml) if 0.1 ml of a 1/100,000 dilution yields 78 colonies?
3. What is quorum sensing with regard to biofilm formation?
Chapter 7 (DNA Replication & Gene Expression)
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the process of DNA replication
o basic nucleotide structure (NTPs)
 deoxyribose vs ribose
 nitrogenous bases – adenine, cytosine, guanine, thymine (or uracil in RNA)
the concept of base pairing and why each nitrogenous base pairs with only one partner
 molecular complementarity
 hydrogen bonding
o 5’ and 3’ ends of a DNA or RNA strand – the 5’ to 3’ direction of DNA synthesis
o antiparallel orientation of strands in DNA (or base pairing within RNA)
o the requirement of an origin of replication (Ori)
o concepts of a replication bubble, replication fork
o the roles of the following proteins/enzymes in the replication process (in E. coli)
 helicase
 stabilizing proteins
 gyrase
 primase
 DNA polymerase III
 DNA polymerase I
 DNA ligase
o leading vs lagging strand synthesis
the process of gene expression
o Transcription – synthesis of RNA from a DNA template
 the role of a promoter sequence in a gene
 the roles of RNA polymerase
 coding vs template strands
 the general process of transcription and how it is limited to 1 strand of 1 gene
 5’ to 3’ direction of synthesis (as with DNA)
 new strand is made antiparallel to template strand
o 3 key roles of RNA – mRNA, rRNA, tRNA
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the genetic code & how to determine the amino acid sequence encoded in DNA or RNA
 the concepts of a codon and reading frame
 start codon, stop codons
o differences between DNA and RNA
 deoxyribose vs ribose
 A, C, G and T vs A, C, G and U
 double-stranded vs single stranded
o Translation – production of a polypeptide based on an mRNA sequence
 the roles of ribosomes, mRNA, tRNA
 how translation initiates, elongates, terminates
 ribosomes “read” or move down the mRNA 5’ to 3’
the various types of mutations and how they may affect gene expression
o silent, missense, nonsense, insertion/deletion
horizontal vs vertical gene transfer
the basic methods of gene transfer:
o conjugation
o Hfr conjugation
o Transformation
o transduction
the concept of homologous recombination and its role in gene transfer methods
sample questions:
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What is the promoter of a gene?
How does Hfr conjugation differ from “regular” conjugation?
Describe lagging strand synthesis during DNA replication.
Describe how a single nucleotide insertion in the coding sequence of a gene would affect the
production of the protein (polypeptide) the gene encodes.
Chapter 4B (Methods of Identification)
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how serological testing (antibodies) can be used in the identification of microbes
how phage typing is used in the identification of microbes
how DNA base composition can be used in the identification of microbes
the concept of DNA hybridization
identification techniques that use DNA hybridization
o FISH
o PCR
how ribotyping is used to identify organisms
sample questions:
1. Define “DNA hybridization” and indicate one technique that involves DNA hybridization.
2. What is ribotyping and how is it used to classify organisms?
Extra Credit Article
The Price of Silent Mutations, Scientific American June 2009 by Chamary & Hurst, pp. 46-53.