MCB3020 (UF) Bacusmo Exam 3 (not the study guide)

PCR requires all of the following except

DNA ligase

If you start with one double-stranded DNA molecule and you perform SIX cycles of PCR, how many double-stranded copies of the DNA will you have?

64

The most likely source of the Taq polymerase used in PCR is a bacterium that lives in ______.

Hot vents

T/F. PCR can be used to amplify DNA from any source.

True

T/F. During the PCR, the hydrogen bonds of the double-stranded DNA molecules are broken by the enzyme helicase.

False

Genomics is the study of

-the molecular organization of genomes

-the gene products that genomes encode

-the information content of genomes

All of the above

Study of similarities between nucleotide and amino acid sequences among organisms to infer gene function and evolution is called

Comparative genomics

The proteome

Is the entire collection of proteins that an organism can produce

When observing a microbe in which one gene has been deleted, you often find that the product of the missing gene

Broadly affects gene expression and cellular physiology

When two or more genes from the same genome have nucleotide sequences so alike that they most probably arose from gene duplication those genes are called _______.

Paralogs

T/F. Microorganisms do not generally reproduce sexually; therefore, species are usually defined by phenotypic and genotypic similarities.

True

The binomial system of nomenclature assigns each organism a scientific name consisting of

Genus and species

T/F. Molecular methods are so important to the understanding of microbial evolution and taxonomy because they provide the most robust analysis of microbial evolution.

True

The science dealing with classification is called ______.

Taxonomy

T/F. If Microbe A and Microbe B have whole genome similarity of 68%, as determined by DNA-DNA hybridization, they should be considered the same species.

False

T/F. Conjugation is useful for determining relatedness between bacteria at the species level because it never occurs between organisms of different genera.

False

While inspecting the genome sequence of your newly discovered organism, you note that while the genome overall is 50% G + C, there is a cluster of genes comprising about 20,000 bp that is 64% G + C. The best explanation for this is

the 20,000 bp segment is a recent acquisition via horizontal gene transfer.

Which of the following is an example of the use of the binomial system devised by Linnaeus?

Escherichia coli

T/F. Transformation is not useful in determining relatedness between two organisms because it frequently crosses genera.

False

Which of the following facts support the endosymbiotic hypothesis? Select all that apply.

- Mitochondria and chloroplasts have a single circular chromosome.

- Mitochondria and chloroplasts have 70S ribosomes.

Patients who take antibiotics sometimes experience overgrowth of the fungus Candida albicans in their mouths and throats (a condition called thrush). C. albicans is considered part of the normal flora of the gastrointestinal tract but its population is typically limited by the presence of other microorganisms. Based on this evidence, which of the following types of symbiotic relationship do you think occurs between members of the normal flora and C. albicans?

Competition

Several cases of an emerging infectious disease are reported in workers at a research station that borders a tropical rainforest region. The pathogen is identified as a species of bacteria carried by nematodes that infect mosquitos, and disease transmission occurs in a human host following a mosquito bite. Which organisms should be targeted in the treatment of infected patients?

Nematode and bacteria

The chytrid fungus Batrachochytrium dendrobatidis is colonizing frogs across the globe causing massive mortality and even pushing some amphibian species to the brink of extinction. The Batrachochytrium dendrobatidis-frog relationship can be considered which of the following?

Parasitic

Because you have always been fascinated by spiders and bacteria, you decide to study the microbiome of a species of spider that is locally abundant. You are able to cultivate many bacteria from the spiders gut in the lab, and the spiders do not appear to be negatively affected by treatment with antibiotics that you know will inhibit the growth of these bacteria. Based on this evidence, which of the following types of symbiotic relationships do you suspect might be occurring between the spider and the bacteria?

Commensalistic

You have isolated a soil protozoan, which you are now trying to grow in pure culture. You have tried many different types of media but find you can only grow the protozoan if bacteria are also present in the medium. You note that the bacterial population declines as the protozoan population increases. Based on this evidence, which of the following types of symbiotic relationships do you suspect might be occurring between the protozoan and the bacteria?

Predatation

When Alexander Fleming discovered what was to become penicillin, he noticed that wherever mold was growing on plates of Staphylococus sp., there was a zone of inhibition of bacterial growth around the fungi. What type of symbiotic relationship does this describe?

Ammensalistic

Microbes that normally colonize the mouth must be resistant to

mechanical removal through adhesion

The relationship between the bacterium Xenorhabdus nematophila and its nematode host, Steinernema carpocapsae, is classified as cooperation because both organisms benefit and

X. nematophila and S. carpocapsae can be grown separately

Due to the very acidic environment of the gastric contents, the stomach ______.

Contain few viable bacteria per milliliter

The inhalation of cigarette smoke and similar pollutants has a gradual effect on cilia lining the respiratory tract, first causing the beating to slow and eventually stop. How does this change in cilia most directly impact the resistance mechanisms of the host?

Innate host immunity due to mechanical barrier protection would be lost

Which is a primary reason that females are at greater risk of a urinary tract infection than are males?

The urethra is shorter in women, therefore bacteria are closer in proximity to the bladder.

Which of the following is not normally present in the acidic gastric juice

acetic acid

In which of the following areas of the human body do secretions play the greatest role in preventing microbial colonization?

Stomach

The lungs are protected from microorganisms by _________

-Mucociliary blanket

-Lysozyme in mucus

-Phagocytic action in alveolar macrophages

All of the above

Tears protect the eyes by

flushing and lysozyme

Which of the following is a physical barrier in the nonspecific defense of a mammalian host?

Mucous membranes

Lysozyme is an enzyme that lyses _________.

bacteria

T/F. The skin surface is a very favorable environment for colonization by most microorganisms.

False

The human microbiome _______

evolves with humans over time

On which of the following surfaces can biofilms form?

Biotic or abiotic surface

Initial attachment of microorganisms often involves ______.

flagella and is reversible

Which of the following gradients can form in a biofilm?

Oxygen, nutrient, and/or pH gradient

T/F. Colonization specifically refers to the multiplication of a pathogen on or within a host, and includes the resulting tissue invasion and damage.

False

Why are pathogens that are transmitted person-to-person often less virulent than those transmitted by arthropod vectors?

Person-to-person transmission requires the infected host to remain alive long enough to transmit the organism to another susceptible host.

This type of pathogen cannot grow outside a host cell

Obligate intracellular pathogen

Pathogens produce virulence factors primarily to ______.

outcompete host cells for resources

Which of the following must a pathogen possess in order for it to be successful at causing infectious disease?

-Ability to adhere to, colonize, or invade the host

-Ability to be transported initially to the host

-Ability to damage the host

-Ability to exit the host

All of the above

Pathogenicity islands are typically associated with

genes encoding tRNA

The characteristics of a pathogen that determine its virulence include which of the following?

-Infectivity

-Invasiveness

-Pathogenicity

All of the above

Biotechnology

Use of living organisms to create products that are useful to humans

Genetic engineering

The deliberate modification of an organisms genome sequence

Recombinant DNA technology

Set of procedures used to combine genetic material from multiple sources and create DNA sequences that are otherwise not found in biological organisms

Cloning

Generation of a larger number of identical DNA molecules from a single DNA molecule

What are the 5 basic steps of cloning?

1. Isolate DNA to be cloned

2. Use restriction enzymes to "chop up" the DNA into fragments

3. Insert the fragments into a cloning vector, creating recombinant DNA

4. Insert the recombinant DNA into a new host, such as E. coli

5. Culture host cell, growing many identical copies.

Restriction enzymes

A type of endonuclease that allows scientists to cut up DNA at specific sites.

T/F. Restriction enzymes sometimes make staggered cuts, which produce single-stranded DNA sequences known as "sticky ends".

True

What enzyme forms covalent bonds between the cloned gene and the plasmid, creating recombinant DNA?

Ligase

Reverse transcriptase

When double-stranded DNA is created by a single-stranded RNA.

What is the process of constructing cDNA?

1. Apply a short poly- T primer to RNA template

2. Add reverse transcriptase and the 4 nucleotides

3. Add RNaseH to cut up the RNA and regenerate the RNA primers.

4. Add DNA polymerase and DNA ligase to synthesize the new strand

What is the goal of constructing cDNA?

Make DNA from RNA template

Gel electrophoresis

A technique that separates nucleic acids and proteins on the basis of their size and electrical charge.

Why is gel electrophoresis important?

It is important because it determines which fragments are larger than others and tells us the approximate size for each fragment.

1. Nucleic acids have _ charge due to their __ __, so they migrate through the electric field towards the _ electrode.

Negative; phosphate backbones; positive

T/F. Shorter DNA will travel farther in gel electrophoresis because smaller restriction fragments move faster.

True

What dye is used to stain DNA?

Ethidium bromide

PCR

A technique for quickly and easily making many copies of even a very small amount of DNA.

Where does Taq polymerase come from?

Thermophilic bacterium found in hydrothermal vents (Thermus aquaticus)

What are the 4 things required in PCR?

DNA of interest, DNA polymerase, Primers, and deoxyribonucleotide triphosphates

T/F. In PCR, hydrogen bonds of double-stranded DNA molecules are broken by subjecting the DNA to high levels of radiation.

False; under high levels of HEAT

If you perform 6 cycles of PCR on a single double-stranded DNA molecule. How many copies will you have?

64 double-stranded copies (Each cycle the DNA content doubles)

Cloning vector

Provides means for transferring a gene of interest to a host organism during the cloning process

What are the 3 things every "good" cloning vector must have?

An origin of replication, a selectable marker, and unique restriction sites called POLYLINKERS or MCSs

Cloning vector: Plasmids

self-replicating piece of extrachromosomal DNA

What is important to know about plasmids?

It is the most commonly used and it's only in prokaryotes

Cloning vectors: Bacteriophages

A virus that infects bacteria

Cloning vector: Cosmids

A hybrid between a plasmid and a phage

Cloning vector: Artificial chromosomes

Synthetic chromosomes that contain fragments of DNA integrated into a host chromosome

What is a genomic library?

A collection of an organism's entire genomic DNA

How are cloning vector DNA introduced into bacterial hosts?

Transformation: the uptake of naked DNA from the environment

Electroporation

(Related to Transformation) A technique that makes a cell competent to pick up DNA from the environment by applying an electrical shock to it

What are 2 techniques that scientists use to isolate or visualize the protein product of a cloned gene?

Polyhistidine Tagging & Fluorescent labeling

Genomics

Study of the organization of genomes, the information they store, and the gene products they code for.

Sanger sequencing method

-One of the most commonly used methods.

-Requires DNA to be in single-stranded form

-Primer has a sequence that is complementary to 3' end of the region to be copied

-During Sanger sequencing, the addition of dideoxyribonucleotide to the growing strand causes DNA replication to STOP

-If you run the products of the reaction on an electrophoretic gel and read from the bottome to the top you will get the DNA sequence.

Next-generation sequencing technology

-Involves breaking the DNA into pieces. And attaching oligonucleotides to the ends

-These are cheaper and faster methods that produce shorter reads.

Which method is used and why?

Next-generation because they are cheaper and faster

What does functional genomics tell us?

The study of the function of genes

Transcriptome

entire set of mRNA transcripts

Transcriptomics

Study of the transcriptome

Proteome

Entire set of proteins

Proteomics

Study of proteomes

Metagenomics

Study of metagenomes, genetic material recovered from environmental samples

Metatranscriptomics

Study of RNA found in environmental samples

Metabolomics

Study of metabolome, entire set of small-molecule metabolites

Lipidomics

Study of the lipidome, entire set of lipid profile

Glycomics

Study of the glycome, entire set of sugars

DNA microarray analysis

A tool that allows scientists to observe the pattern of DNA expression for thousands of genes at a time

What are the 3 main issues with microarray analysis?

1. Only identifies mRNA molecules

2. Produces some false positives

3. Hard to detect small changes in gene expression

What method was developed to overcome these issues?

RNA- Seq

What is the name of the project that sequences the genomes of a wide variety of cultured microorganisms in order to improve the reference database?

The Genomic Encyclopedia of Bacteria and Archaea Project

Bioinformatics

The study of the genome using computers