chapter 9 study questions hth 245

fecal transplantation

a process whereby feces from a donor is administered into the intestinal tract of the recipient. used to colonize the digestive tract w bacteria that may be missing from the recipient's microbiota

hypothesis

a proposed explanation for a phenomenon that can be tested experimentally using the scientific method

repressor

a protein that turns the expression of a particular gene off

origin of replication

a sequence of DNA that denotes where replication should start

codon

a series of three nucleotides on mRNA that relates to anticodons

anticodon

a series of three nucleotides on tRNA that relate to codons on mRNA

terminator sequences

a site on DNA marking the end point of transcription

promoter site

a site on a gene strand that marks the beginning of mRNA transcription

attenuated strain

a weakened strain of a virus or microbe that can be used in a vaccine to stimulate an immune response but not the illness

insertion mutation

addition of one (or more) nucleotides; can occur naturally during DNA replication or are intentionally introduced through genetic engineering techniques

disease triangle model

addresses the interactions among the host, infectious agent, and environment

inducible enzymes

enzymes that are synthesized in the presence of inducers

Next generation DNA sequencing

extremely fast DNA sequencing techniques that can be used to sequence entire genomes in a day

prebiotics

foods that promote growth of probiotic bacteria ingested to promote balance of human gut microbiota

homologous recombination

form of genetic recombination where similar or identical nucleotide sequences are exchanged between DNA molecules during replication

recombinants

formation of novel viruses or cells through genetic recombination

GRAS stands for ___ microbes for the development of microbiota-based therapies

generally regarded as safe

operon

group of functionally related genes that act as "on and off" switches that are controlled by the same regulatory sequences (promoter)

A ___ is the entire set of genes of a host, in addition to the genes of its microbiota

hologenome

the integration of donor DNA fragments into a complementary region of a donor's chromosome is called ____

homologous recombination

dysbiosis

imbalance of microbiota, in particular gut microbiota, which can result in disease

mutagen

physical or chemical agents that cause mutations in DNA

the transfer structure of a bacterium used in conjugation is a(n)

pilus

specialized transduction

process whereby a fragment of bacterial DNA is recombined with phage DNA and packaged into its head. the recombinant phage DNA is introduced into another susceptible bacterium and may become incorporated into the bacterial genome as a provirus

recombination

production of offspring with different traits from the parents due to exchange of genetic material.

A(n) ___ is bacteriophage DNA incorporated into the chromosome of its host bacterium

prophage

which expression describes transcription: mRNA to protein DNA to mRNA DNA to protein DNA comingling

DNA to mRNA

a bacterium with the F plasmid integrated into its chromosome is called a(n)

F+

(a) List the three main types of genetic recombinations or genetic material transfer processes. (b) Discuss how a pathogenic bacterium could become antibiotic-resistant through one of these processes (HINT: Figure 9.18).

1. Conjugation: mating contact between donor and recipient bacteria via F gene integrated into the donor chromosome and conjugation pilus (F+ donor that has the F plasmid to F- recipient, Hfr to F-: plasmids to chromosomes in the same donor, rarely Hfr to F+) 2. Transformation: uptake of naked DNA from the environment. Requires competent recipient bacteria. 3. Transduction: bacteriophage-mediated transfer of DNA. DNA carried by bacteriophage moves from donor to recipient bacteria. Generalized transduction is the result of bacterial donor chromosomal DNA fragments taken up by a bacteriophage following lysis of the bacterial host cell. Specialized transduction is the result of bacteriophage DNA carried along with excised bacterial donor DNA fragments following lysis of the bacterial host cell. A pathogenic bacterium could become antibiotic resistant through transformation if dead bacteria leaves cell debris and is degraded. This leaves the dead cell's DNA naked and exposed, including extra-chromosomal plasmids. There could be a plasmid that has an antibiotic resistant gene on it, which another bacterium may uptake.

(a) List the different types of mutations. (b) Which types are the most serious and why?

1. Point: substitution of one nucleotide for another 2. Nonsense: one nucleotide changes in amino acid leading to an early stop codon 3. Missense: one nucleotide changes in a codon, leading to a different amino acid 4. Insertion: addition of one nucleotide leads to a shift or change in the reading frame of codons 5. Deletion: deletion of one nucleotide leads to a shift or change in the reading frame of codons Missense, deletions, and insertions may change the reading frame of the codons, resulting in a different amino acid sequence and mutated protein

What are the three major differences between RNA and DNA?

1. RNA contains uracil instead of thymine 2. RNA is single-stranded, and DNA is double stranded 3. DNA is transcribed into RNA. RNA is translated into proteins

F (fertility) factor

A DNA F plasmid in a bacterium that allows plasmid DNA to be transferred from one bacterium to another through conjugation. aka sex factor

Deoxyribose

A five-carbon sugar molecule that alternates with phosphate groups to form the backbone of DNA

with reference to RNA, which is correct: A-T U-U U-T A-U

A-U

genetically modified organisms (GMOs)

An organism whose genetic material has modified using molecular biology techniques through the introduction of foreign DNA from another organism to confer the expression of new traits that were not present in the original organism

Why are 'defective' phages so named? Provide an example.

Bacterial DNA gets packaged into the bacteriophage protein coat, which is the capsid, which results in "defective" phages. They contain only bacterial DNA or a combination of both bacterial and bacteriophage DNA. When the defective phage infects another recipient cell, the bacterial DNA from the first host bacterium becomes part of the genome of the second bacterial cell; homologous recombination by transduction. So, rather than injected their own DNA into bacteria, they are injecting the DNA of other bacteria. An example could be if a bacteriophage with its accidentally packaged foreign bacterial DNA infects other bacteria and transfers antibiotic resistant genes into the new host bacteria.

___ is the hereditary material of a cell

DNA

transduction

DNA recombination process whereby bacterial DNA from one bacterium is introduced into another bacterium by a bacteriophage

generalized transduction

DNA recombination process whereby bacterial DNA from one bacterium is introduced into another bacterium by a bacteriophage. The DNA may or may not be incorporated into the recipient bacterium's chromosome

Compare and contrast generalized and specialized transduction.

Generalized transduction is a genetic recombination process in which a bacteriophage packages a fragment of chromosomal DNA during the course of a lytic infection of a host bacterium and the resultant defective bacteriophage transfers the packaged host chromosomal DNA fragment into a recipient bacterium. The donor DNA fragment is integrated into the chromosome of the transduced/recombinant recipient host bacterium Specialized transduction is a genetic recombination process in which a bacteriophage DNA is integrated as a prophage (part of the chromosome now) into the chromosome of a donor bacterium. At some point, the prophage is activated into a productive/lytic replication cycle. New phages are released during lysis. On occasion, during break out or assembly and release of phage particles a phage will also package a small fragment of DNA from the chromosome that was flanking either side of the excised integrated prophage DNA. The bacteriophage then attaches to a new host recipient bacterium and transfers the packaged host chromosomal DNA fragment along with the phage DNA into the recipient host bacterium. The donor DNA fragment is integrated along with phage DNA into the chromosome of the transduced/recombinant recipient host bacterium.

synthetic biology

Uses genetic engineering to produce unnatural biological molecules from "scratch" -"designer BAC" or "designer genes"

transposon

a DNA segment that can change its position or "jump" to different locations within a genome

lytic bacteriophage

a bacteriophage that has a lytic replication cycle, thus destroyed the infected bacterial host cell upon the release of the new bacteriophages

mutation

a change in DNA that is transferred to subsequent generations

inducer

a chemical or protein whose presence turns on the expression of a particular gene

What is the role of chromosomes in gene expression

a chromosome consists of long strands of DNA. prokaryotes usually have one chromosome. Genes are specific segments of the DNA that are expressed and code for certain proteins.

high-throughput sequencing

a fast, inexpensive DNA sequencing technique that is particularly well suited to sequencing large genomes rather quickly

prophage

a fragment of phage DNA integrated into a bacterial chromosome

point mutation

a genetic process in which one nucleotide is replaced with another nucleotide; simplest mutation; can occur naturally or through genetic engineering

disease biomarkers

a measurable protein that indicates the presence of the disease biological or pathological processes, such as inflammatory proteins or signal proteins that evoke inflammation that can be targeted with therapeutic intervention (anti-inflammatory proteins that bind to and that block their activity)

discuss Mutations

a mutation is a change in the nucleotide sequence. some have little consequence, some have huge consequence. rarely are they beneficial. Most errors through transcription and translation are fixed, but some slip through. they can occur spontaneously or through chemical or physical agents called mutagens.

ribose

a pentose sugar that is component of RNA

Synthetic gene circuit

an application in synthetic biology in which bacteria are engineered to perform tasks in a designed, logical manner. probiotic bacteria can be engineered to produce therapeutic proteins that bock the progression of disease

proofreading

an error-correcting process by DNA polymerases that occurs during DNA replication

biotechnology

area of molecular biology that uses living microbes to develop new products

a(n) ___ microbe or virus is a weakened strain of a pathogen that can no longer cause disease but can be used in vaccine applications

attenuated

F+ bacteria

bacteria that contain an F plasmid or fertility factor

F- bacteria

bacteria that do not posses a fertility factor or F plasmid but can act as a recipient of the F plasmid through conjugation with an F+ bacterium

Hfr bacteria

bacteria that exhibit a much higher frequency of DNA recombination with F- bacteria

competent

bacterial cells that are able to take up DNA from the environment resulting in genetic transformation

peptide bonds

bonds formed between amino acids during protein synthesis

temperate bacteriophages

capable of lysogenic cycle

transcription factors

cell proteins that direct RNA polymerase to transcribe DNA into RNA

semiconservative

characteristic of DNA replication where one strand of each new DNA is derived from a template strand within the original

antiparallel

characteristic of the DNA double helix whereby the two complementary strands run in opposite directions alongside each other

redundant

characteristic of the genetic code whereby most amino acids are coded for by more than one codon.

bacterial cells must be ___ in order to take up foreign DNA through the cell wall via transformation

competent

which of the following is not a characteristic of DNA: double stranded antiparallel complementary contains uracil

contains uracil

protein

critical structural and non structural roles in all living things as building blocks and workhorses of cells

GRAS (Generally Regarded As Safe)

designation of the Food and Drug Administration that a bacteria used to produce a food product are considered safe for human consumption

bacterial ___ refers to a variety or different types of bacteria

diversity

probiotics

live microorganisms that are ingested to improve or restore the balance of gut microbiota

sanguivores

mammals that feed on the fresh blood of other mammals

biocontainment

management practices implemented to control spread of microbes

amino acids

nitrogen-containing molecule that is the building block of protein

Pyrimidines

one of the two types of bases. C and T

purines

one of two types of bases. A and G

vector

organism that is a carrier of a pathogen

bloodborne pathogens

pathogens that are present in human blood and can cause disease in humans such as HIV

which of the following is a macromolecule that constitutes about 50% of the dry weight of an organism: DNA RNA proteins lipids/membranes

proteins

virulence factors

proteins such as toxins or capsules that enable a pathogen to cause an infection and disease

enzymes

proteins that act on specific biological substrates

discuss Recombination

recombination in eukaryotes is different because it is vertical and involves the fusion of male and female gametes, each carry half the number of chromosomes. but bacteria reproduce ASEXUALLY, so reproduction and recombination are separate. recombination occurs through transformation, transduction, and conjugation. these are horizontal.

dna replication fork

region during replication of DNA where the DNA double helix is open and the single stranded DNA is exposed, acting as a template

deletion mutation

removal of one (or more) nucleotides in DNA; can occur naturally during replication or in genetic engineering

gene

segments of DNA that encode proteins

autoinducer

signaling molecule produced when a population of cells reaches a certain density. plays a role in quorum sensing by bacteria

____ allows for bioengineering of unnatural life through the assembly of natural biological molecules

synthetic biology

anticodons refer to

tRNA

metagenomics

the analysis of the genetic material obtained from environmental samples

blood meal

the blood ingested by a blood sucking insect

cytoplasm

the fluid that is enclosed by a cell wall in prokaryotes and contained by the plasma membrane in eukaryotes

hologenome

the genome of an organism as well as the genomes of all of its associated symbiotic microbes

human genome project

the mapping of the genes located on the 23 pairs of human chromosomes

microbiota

the microbes inhabiting a particular body site of a living organism

microbiome

the microbes that form a community in a particular environment

Discuss the importance, objective, and utility of synthetic biology

the objective of synthetic biology is: Uses genetic engineering to produce unnatural biological molecules from "scratch" and possible create life or assemble naturally occurring biological molecules into systems that function unnaturally as a result of modifying existing systems of genetic material. it is important to be able to manipulate genes for their beneficial use. We have made a number of useful products in medicine, agriculture, and more. Understanding how to manipulate genes can help with forestalling epidemics and pandemics "designer BAC" or "designer genes"

F plasmid

the plasmid DNA or fertility factor that is present in F+ bacteria

chromosomes

the structure in which DNA is organized

complementary

the two strands of DNA contain complementary base pairs held together with h bonds AT CG

___ is the transfer of DNA into mRNA

transcription

conjugation

transfer of DNA from donor to recipient via physical contact Requires cell-to-cell contact -ssDNA is transferred from donor to recipient -Donor requires F factor -Donors are F+ (Have F plasmid (Shigella to E. coli) and produce sex pilus) -Recipient is F- HFr cells: plasmids to chromosomes in same donor (can make it even more virulent)

the uptake of naked DNA is called

transformation

____ is a term used for protein synthesis

translation

Jumping genes are also called __________

transposons

transformation

uptake of naked DNA into competent cells

live vaccines

vaccines that consist of a live, replication-competent weakened or attenuated virus

gigantobacteria

very large bacteria; often have multiple copies of chromosomes

repression

when a gene is turned off

deforestation

widespread clearance of forests and conversion of forestland to non-forest use. will expand the range of infectious diseases