ENE 487 Final Exam

What do prokaryotes NOT contain?

The mitochondria

What are ribosomes composed of?

RNA and various proteins

What is the phylogenetic tree of life commonly constructed from?

Small subunit of ribosomal RNA

What is the correct sequence of steps to construct the phylogenetic tree of life?

1. DNA Isolation

2. PCR

3. Sequencing

4. Sequence Alignment

What describes a chemoorganotroph?

An organism obtaining energy from organic chemicals

What describes an anaerobe?

An organism that only grows in the absence of oxygen

What describes a chemolithotroph?

An organism obtaining energy from inorganic chemicals

What is the name of the bond between glucose monomers to form glycogen?

Glycosidic

What represents the hydrophobic portion in the cytoplasmic membrane?

Carbon chain of fatty acids

What acts as a template during translation?

Messenger RNA

Which bases are present in RNA?

Uracil, cytosine, adenine, guanine

What do the building blocks of DNA include?

Deoxyribose, phosphate group, a base

Via what do amino acids link together to form proteins?

Peptide bonds between C and N

How is group translocation described?

A series of proteins and chemical modification of the transported substance

What does a gram-positive cell contain?

A thick layer of peptidoglycan

What is a highly heat-resistant strcture?

Endospores

Where are good electron donors found in an electron tower?

Good electron donors are found in couples at the top

What redox couples contain the best electron acceptors?

Ones with a higher (more positive) reduction potential

What is H₂ → 2e^- + 2H⁺?

It is an oxidation

What is the balanced half reaction for nitrite reduction to ammonia?

NO₂^-+6e^-+7H⁺→NH₃+2H₂O

What most closely describes a plasmid?

Circular double stranded DNA

What is true about bacteria and archaea?

Both of them are prokaryotes

What is a facultative aerobe?

An organism able to grow in the presence or absence of oxygen

What is a phototroph?

An organism obtaining energy from light

What is an autotroph?

An organism that obtains carbon from an inorganic source, such as CO₂

What three components form a nucleotide?

A sugar, base, and phosphate group

What elements are found in amino acids?

C, N, O, H, S, Se

What represents the hydrophilic portion in the cytoplasmic membrane?

Phosphate group/glycerol

What does DNA not contain?

DNA does not contain uracil

What step involves rRNA, tRNA, and mRNA?

Translation

What bonds connect two bases in DNA?

Hydrogen bonds

What do the majority of amino acids contain?

Carboxylic acid group and an amino group

What is the cytoplasmic membrade made from?

A phospholipid bilayer

What is simple transport?

A membrane spanning protein only

What is the ABC system?

A substrate binding protein, a membrane spanning transporter, and an ATP hydrolyzing protein

What is the lipopolysaccharide (LPS) layer (also called the outer membrane) a characteristic of?

Gram-negative bacteria

What most closely describes the cell wall?

A component providing structural strength to cells

What is involved in conjugation?

Pili

What is the final outcome of the Gram Stain?

Gram negagtive cells are pink and gram positive cells are purple

What redox couples contain the best electron donors?

Couples with a lower (more negative) reduction potential

Where is the most probable electron acceptor for two redox couples?

The left one on the higher reduction potential couple

i.e. pyruvate/lactate (-0.19 V) and Fe³⁺/Fe²⁺ (+0.77 V)

• Fe³⁺

Where is the most probable electron donor for two redox couples?

The right one on the lower reduction potential couple.

i.e. CO₂/acetate (-0.29 V) and 2H⁺/H₂ (-0.421 V)

• H₂

What always occurs with a reduction?

An oxidation (half reactions)

What is an example of a freely diffusible electron carrier?

NAD⁺/NADH

What is the balanced half reaction for sulfate (SO₄^2-) reduction to sulfite (SO₃^2-)?

SO₄^2-+2H⁺+2e^-→SO₃^2-+H₂O

What is the balanced half reaction for nitrite (NO₂^-) reduction to ammonia (NH₃)?

NO₂^-+6e^-+7H⁺→NH₃+2H₂O

What is the balanced half reaction for sulfate (SO₄^2-) reduction to sulfur (S⁰)?

SO₄^2-+8H⁺+6e^-→S⁰+4H₂O

What is true of oxidation vs fermentation?

Oxidation of glucose produces more energy than the fermentation of glucose

What is true regarding the distance between couples on the electron tower?

The greater the distance on the electron tower between couples, the greater the energy generated

What is needed to calculate actual free energy changes?

Temperature, the concentration of the products and reactants

What applies to ATP hydrolysis to ADP and Pi under standard conditions?

It is an exergonic reaction

What is true about enzymes?

Enzymes increase reaction rates

What are transferases are important for?

The movement of a functional group from one molecule to another

In an enzyme, what binds to the substrate?

The active site

In enzyme kinetics, what does K_m represent?

The subtrate concentration when V = 4*Vmax

What is the equation for V?

V = Vmax[S]/([S]+K_m)

In enzyme kinetics, what occurs in non-competitive inhibition?

An increase in the substrate concentration does not counteract the effect of the inhibitor?

What is the most equired nutrient after carbon?

Nitrogen

What are growth factors typically?

Organic chemicals such as vitamins

What is correct about selective media?

Selective media permits the growth of some organisms, but not others

During which part of the growth cycle are cells typically harvested for use in enzymes experiments?

Exponential phase

What is another term for the generation time?

Doubling time

Which phase of the growth cycle has no net increase or decrease in cells?

Stationary phase

What does not require an exogenous electron acceptor?

Fermentation

In the cytoplasmic membrane, what generates ATP?

ATP synthase

What order are electron carriers in the electron transport chain arranged?

Increasing more positive reduction potentials

In oxidative phosphorylation, why is the cell membrane energized?

A proton gradient

What is a common primary substrate for cometabolism?

Methane

Which two gases can be sparged into groundwater to remediate 1,4-dioxane?

Propane and oxygen

What is the structure of DNA?

Double stranded with hydrogen bonds between bases

What does the term Tm refer to?

The temperature at which half of the DNA molecule is denatured

What term describes the formation of double stranded DNA after cooling?

Annealing

What is a gene described by?

A region of DNA encoding a polypeptide chain or functional RNA

What occurs during replication?

A nucleotide is added to the hydroxyl on the 3’ carbon

What enzyme is critical for transcription?

RNA polymerase

What does DNA polymerase do?

DNA polymerase synthesized DNA and does require a primer

Why is the genetic code degenerate?

Many amino acids have more than one codon

What does the wobble concept in the genetic code refer to?

Unspecific base pairing in the first base of a tRNA

This corresponds to flexibility at the third base of the mRNA codon / first base of the tRNA anticodon

What is the structure of RNA?

One strand, typically with significant secondary structure

What is a codon?

A triplet of bases on mRNA

What is the formation of a stem loop structure useful for?

Signaling the end of transcription

What is a silent mutation often caused by?

A mutation in the third base of a codon

What is it called when DNA released by one cell is taken up by another?

Transformation

What are some electron donors for chemolithotrophs?

H₂, NH₃, H₂S

What does the anaerobic oxidation of hydrogen involve?

The oxidation of hydrogen with nitrate as the electron acceptor

What does the aerobic oxidation of hydrogen involve?

The oxidation of hydrogen with oxygen as an electron acceptor

What is the enzyme sulfite oxidase used for?

To oxidize sulfite

What do iron oxidizers do?

Iron oxidizers oxidize ferrous to ferric iron

What is nitrification?

Microbial conversion of NH₃ to NO₃^-

What are some electron acceptors for anaerobic respiration?

NO₃^-, Fe³⁺, SO₄^2-

What is dissimilative metabolism?

The reduction of chemicals to produce energy

What is incorrect about assimilative metabolism?

Sulfate is reduced to H₂S and excreted

What most closely described denitrifying bacteria?

Microorganisms able to use nitrate as an electron acceptor

What do sulfate reducing bacteria use as the electron acceptor?

Sulfate reducing bacteria use SO₄^2- as their electron acceptor

How are methanogens best described?

Archaea that produce methane

What can perchlorate bioremediation involve?

Reduction of perchlorate to chloride

What generates a sodium motive force?

Acetogenesis

Why are coliforms considered appropriate indicator organisms?

They live in the intestinal tract of humans and their presence indicates fecal contamination

What are enteric organisms?

Organisms that live in the intestinal tract of humans and other animals

What is cholera caused by?

Vibrio cholerae, a bacteria