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7.E: Microbial Biochemistry (Exercises)

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    7.1: Organic Molecules

    Biochemistry is the discipline that studies the chemistry of life, and its objective is to explain form and function based on chemical principles. Organic chemistry is the discipline devoted to the study of carbon-based chemistry, which is the foundation for the study of biomolecules and the discipline of biochemistry. Both biochemistry and organic chemistry are based on the concepts of general chemistry.

    Multiple Choice

    Which of these elements is not a micronutrient?

    1. C
    2. Ca
    3. Co
    4. Cu
    Answer

    A

    Which of the following is the name for molecules whose structures are nonsuperimposable mirror images?

    1. structural isomers
    2. monomers
    3. polymers
    4. enantiomers
    Answer

    D

    True/False

    Aldehydes, amides, carboxylic acids, esters, and ketones all contain carbonyl groups.

    Answer

    True

    Two molecules containing the same types and numbers of atoms but different bonding sequences are called enantiomers.

    Answer

    False

    Short Answer

    Why are carbon, nitrogen, oxygen, and hydrogen the most abundant elements in living matter and, therefore, considered macronutrients?

    Identify the functional group in each of the depicted structural formulas.

    Figure A has a C bound to an OH. Figure B has a C double bonded to an O as well as a single bonded OH and R. Figure C has an N bound to an R and two Hs.

    Critical Thinking

    The structural formula shown corresponds to penicillin G, a narrow-spectrum antibiotic that is given intravenously or intramuscularly as a treatment for several bacterial diseases. The antibiotic is produced by fungi of the genus Penicillium. (a) Identify three major functional groups in this molecule that each comprise two simpler functional groups. (b) Name the two simpler functional groups composing each of the major functional groups identified in (a).

    A complex chemical figure begins with a ring of Cs; each C is double bonded to one other C. Off this ring is a CH2, then a C with a double bonded O, then an NH, then a C in a square. This square has Cs in 3 corners and an N in the fourth. The top left C is attached to the previous components discussed here, the bottom left C is double bonded to an O. The top right C is bound to an S, which is bound to a C, which is bound to a CH, which is bound to the N in the square. Back to the C that is attached to the S – this C is bound to two CH3s. The C attached to the N is bound to a C that is double bonded to an O and bound to an OH.

    7.2: Carbohydrates

    The most abundant biomolecules on earth are carbohydrates. From a chemical viewpoint, carbohydrates are primarily a combination of carbon and water, and many of them have the empirical formula (CH2O)n, where n is the number of repeated units. This view represents these molecules simply as “hydrated” carbon atom chains in which water molecules attach to each carbon atom, leading to the term “carbohydrates.”

    Multiple Choice

    By definition, carbohydrates contain which elements?

    1. carbon and hydrogen
    2. carbon, hydrogen, and nitrogen
    3. carbon, hydrogen, and oxygen
    4. carbon and oxygen
    Answer

    C

    Monosaccharides may link together to form polysaccharides by forming which type of bond?

    1. hydrogen
    2. peptide
    3. ionic
    4. glycosidic
    Answer

    D

    Matching

    Match each polysaccharide with its description.

    ___chitin A. energy storage polymer in plants
    ___glycogen B. structural polymer found in plants
    ___starch C. structural polymer found in cell walls of fungi and exoskeletons of some animals
    ___cellulose D. energy storage polymer found in animal cells and bacteria
    Answer

    C, D, A, B

    Short Answer

    What are monosaccharides, disaccharides, and polysaccharides?

    Critical Thinking

    The figure depicts the structural formulas of glucose, galactose, and fructose. (a) Circle the functional groups that classify the sugars either an aldose or a ketose, and identify each sugar as one or the other. (b) The chemical formula of these compounds is the same, although the structural formula is different. What are such compounds called?

    Galactose has 6 carbons with a double bonded O at carbon 1; all other carbons have one OH. The difference between glucose and galactose is the direction of the OH groups. Fructose has 6 carbons with a double bonded O at carbon 2; all other carbons have one OH.

    Structural diagrams for the linear and cyclic forms of a monosaccharide are shown. (a) What is the molecular formula for this monosaccharide? (Count the C, H and O atoms in each to confirm that these two molecules have the same formula, and report this formula.) (b) Identify which hydroxyl group in the linear structure undergoes the ring-forming reaction with the carbonyl group.

    A chain of 5 Carbons. Carbon 1 has a double bonded O and an H. Carbons 2, 3, and 4, each have an OH above the chain and an H below. Carbon 5 has an OH and 2 Hs. The second image is a pentagon. The top point is an O. Moving clockwise, each of the next 3 points are attached to an OH and an H. The last point is attached to an H and a CH2OH.

    The term “dextrose” is commonly used in medical settings when referring to the biologically relevant isomer of the monosaccharide glucose. Explain the logic of this alternative name.

    7.3: Lipids

    Although they are composed primarily of carbon and hydrogen, lipid molecules may also contain oxygen, nitrogen, sulfur, and phosphorous. Lipids serve numerous and diverse purposes in the structure and functions of organisms. They can be a source of nutrients, a storage form for carbon, energy-storage molecules, or structural components of membranes and hormones. Lipids comprise a broad class of many chemically distinct compounds, the most common of which are discussed in this section.

    Multiple Choice

    Which of the following describes lipids?

    1. a source of nutrients for organisms
    2. energy-storage molecules
    3. molecules having structural role in membranes
    4. molecules that are part of hormones and pigments
    5. all of the above
    Answer

    E

    Molecules bearing both polar and nonpolar groups are said to be which of the following?

    1. hydrophilic
    2. amphipathic
    3. hydrophobic
    4. polyfunctional
    Answer

    B

    True/False

    Lipids are a naturally occurring group of substances that are not soluble in water but are freely soluble in organic solvents.

    Answer

    False

    Fatty acids having no double bonds are called “unsaturated.”

    Answer

    False

    A triglyceride is formed by joining three glycerol molecules to a fatty acid backbone in a dehydration reaction.

    Answer

    False

    Fill in the Blank

    Waxes contain esters formed from long-chain __________ and saturated __________, and they may also contain substituted hydrocarbons.

    Answer

    alcohols; fatty acids

    Cholesterol is the most common member of the __________ group, found in animal tissues; it has a tetracyclic carbon ring system with a __________ bond in one of the rings and one free __________group.

    Answer

    steroid; double; hydroxyl

    Critical Thinking

    Microorganisms can thrive under many different conditions, including high-temperature environments such as hot springs. To function properly, cell membranes have to be in a fluid state. How do you expect the fatty acid content (saturated versus unsaturated) of bacteria living in high-temperature environments might compare with that of bacteria living in more moderate temperatures?

    Short Answer

    Describe the structure of a typical phospholipid. Are these molecules polar or nonpolar?

    7.4: Proteins

    Amino acids are capable of bonding together in essentially any number, yielding molecules of essentially any size that possess a wide array of physical and chemical properties and perform numerous functions vital to all organisms. The molecules derived from amino acids can function as structural components of cells and subcellular entities, as sources of nutrients, as atom- and energy-storage reservoirs, and as functional species such as hormones, enzymes, receptors, and transport molecules.

    Multiple Choice

    Which of the following groups varies among different amino acids?

    1. hydrogen atom
    2. carboxyl group
    3. R group
    4. amino group
    Answer

    C

    The amino acids present in proteins differ in which of the following?

    1. size
    2. shape
    3. side groups
    4. all of the above
    Answer

    D

    Which of the following bonds are not involved in tertiary structure?

    1. peptide bonds
    2. ionic bonds
    3. hydrophobic interactions
    4. hydrogen bonds
    Answer

    A

    Fill in the Blank

    The sequence of amino acids in a protein is called its __________.

    Answer

    Primary structure

    Denaturation implies the loss of the __________ and __________ structures without the loss of the __________ structure.

    Answer

    secondary, tertiary, primary

    True/False

    A change in one amino acid in a protein sequence always results in a loss of function.

    Answer

    False

    Critical Thinking

    Heating a protein sufficiently may cause it to denature. Considering the definition of denaturation, what does this statement say about the strengths of peptide bonds in comparison to hydrogen bonds?

    The image shown represents a tetrapeptide. (a) How many peptide bonds are in this molecule? (b) Identify the side groups of the four amino acids composing this peptide.

    A green 5-C chain linked to an NH linked to a black 2 C chain linked to an NH linked to a black 2 C chain linked to an NH linked to a blue 5 C chain.

    7.5: Using Biochemistry to Identify Microorganisms

    Accurate identification of bacteria is essential in a clinical laboratory for diagnostic and management of epidemics, pandemics, and food poisoning caused by bacterial outbreaks. In this section, we discuss a few methods that use biochemical characteristics to identify microorganisms.

    Multiple Choice

    Which of the following characteristics/compounds is not considered to be a phenotypic biochemical characteristic used of microbial identification?

    1. poly-β-hydroxybutyrate
    2. small-subunit (16S) rRNA gene
    3. carbon utilization
    4. lipid composition
    Answer

    B

    Proteomic analysis is a methodology that deals with which of the following?

    1. the analysis of proteins functioning as enzymes within the cell
    2. analysis of transport proteins in the cell
    3. the analysis of integral proteins of the cell membrane
    4. the study of all accumulated proteins of an organism
    Answer

    D

    Which method involves the generation of gas phase ions from intact microorganisms?

    1. FAME
    2. PLFA
    3. MALDI-TOF
    4. Lancefield group testing
    Answer

    C

    Which method involves the analysis of membrane-bound carbohydrates?

    1. FAME
    2. PLFA
    3. MALDI-TOF
    4. Lancefield group testing
    Answer

    D

    Which method involves conversion of a microbe’s lipids to volatile compounds for analysis by gas chromatography?

    1. FAME
    2. proteomic analysis
    3. MALDI-TOF
    4. Lancefield group testing
    Answer

    A

    Fill in the Blank

    A FAME analysis involves the conversion of _______ to more volatile _____ for analysis using ____________.

    Answer

    fatty acids, methyl esters, gas chromatography

    True/False

    MALDI-TOF relies on obtaining a unique mass spectrum for the bacteria tested and then checking the acquired mass spectrum against the spectrum databases registered in the analysis software to identify the microorganism.

    Answer

    True

    Lancefield group tests can identify microbes using antibodies that specifically bind cell-surface proteins.

    Answer

    False

    Short Answer

    Compare MALDI-TOF, FAME, and PLFA, and explain how each technique would be used to identify pathogens.

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