Thẻ ghi nhớ: UF Asghari MCB3020 Exam 3 | Quizlet

Biotechnology

Use of part or whole microorganisms to make products

Recombinant DNA technology

combines genes from different sources into a single DNA molecule

rDNA (recombinant DNA)

DNA molecule artificially created with segments originating from different organisms

PCR

Amplifies specific DNA sequences, generating millions of copies from a small sample

RT (reverse transcription)

Process to synthesize cDNA from from an RNA template using the enzyme reverse transcriptase

cDNA

Complementary DNA. DNA synthesized from an mRNA template

Vector

self-replicating DNA molecule used to transplant foreign DNA into cell

Examples of Vectors

Plasmids, Transposons, Virus, plaque, cosmids, artificial chromosomes

Restriction Enzymes

Recognizes and cuts specific sequences of DNA. Creates blunt ends or sticky (staggered) ends

Blotting

Used to detect specific DNA fragments seperated through gel electrophoresis.

1. Extract and fracture DNA

2. Place fragments into gel electrophoresis to seperate them

3. Transfer fragment(s) to nitrocellulose membrane and expose to probe for specific gene

Genomic Library

All the DNA derived from a single organism. Constructed from fragmenting source DNA and cloning each fragment into seperate vectors to find genes with specific functions

Recombinant Plasmid

Plasmid with foreign DNA inserted into it. Created with foreign DNA cut by restriction enzyme. Sometimes, PCR is used to amplify foreign DNA before insertion. Foreign DNA is then inserted into the Plasmid.

Genomic Fingerprinting

Used to analyze and compare DNA patterns unique to an individual or species.

1. Isolating DNA

2. Amplifying specific regions using PCR

3. Separating DNA fragments by gel electrophoresis to produce a unique banding pattern or "fingerprint."

Autonomous (self) Replication

DNA molecule, like a plasmid, replicates independently of the host cell's chromosomal DNA, using its own origin of replication

Plasmids Strengths

Circular DNA molecules that replicate independently in bacterial cells, used for small gene insertions; easy to manipulate and introduce into bacteria via transformation

Phages strengths

Viruses that infect bacteria, used for cloning larger DNA fragments; have a high capacity for foreign DNA but require specialized techniques for handling.

Cosmids Strengths

Hybrid vectors that combine features of plasmids and bacteriophages, capable of cloning larger fragments than plasmids, but still replicating within bacterial cells; used for larger gene libraries

TI Plasmid

A plasmid of a tumor-inducing bacterium (Agrobacterium tumefaciens) that integrates a segment of its DNA into the host chromosome of a plant; frequently used as a carrier for genetic engineering in plants.

Protoplast

Plant, bacterial, or fungal cell that has had its cell wall removed

Protoplast Fusion

Two protoplasts from different species or strains are fused together, often using chemical agents or electric fields. Has genetic material of both parents.

Therapeutics resulting from Biotechnology

- creation of human enzymes such as insulin

- subunit vaccines made from pathogen proteins in GMO yeast

- creation of DNA vaccines: nonpathogenic viruses carrying genes for specific pathogen

- Gene therapy

- CRISPR gene editing to correct genetic mutations

Gene silencing

Process that stops or reduces expression of a specific gene.

Whole Genome shotgun-sequencing

genome is randomly fragmented into small pieces, which are then sequenced and assembled using computational methods to reconstruct the entire sequence

cas9

RNA-guided endonuclease that cuts both strands of target DNA

cas9 Genome editing

Alters genomes in vivo. Direct modification of DNA in any cell into which DNA can be introduced and expressed

Genomics

Study of the genome

Structural genomics

study of the physical characteristics of the genome

Functional Genomics

Study of how the genome functions

Comparative Genomics

Study that compares the genomes of different organisms

Bioinformatics

The use of computers, software, and mathematical models to process and integrate biological information (genomes) from large data sets

In silico analysis

analysis carried out by a computer

Annotation

determines locations of genes on newly sequenced genome (in regards to bioinformatics)

Proteomics

Study of the Proteome: entire collection of proteins an organism produces

Functional Proteomics

study of protein function that determines what actually occurs in the cell

Structural Proteomics

Study of the 3D structure of proteins

Paralogs

2 or more duplicate genes in the same genome.

Orthalogs

2 or more genes found very similar in different organisms; predicted to have the same function

DNA Microarray System

technology used to detect and measure the expression of thousands of genes simultaneously by hybridizing labeled cDNA or RNA samples to a grid of DNA probes fixed on a solid surface

Comparative genomics analysis of pathogenic microbes

comparing the genomes of different strains or species of pathogens to identify genetic differences, understand virulence factors, and uncover potential targets for treatment or vaccine development.

2D Gel Electrophoresis

Seperates proteins through charge and size; Proteins separated (charge) through their isoelectric point - point at which protein has no net pH (= positive and negative charges)

Human Microbiome

the complete collection of microorganisms in the human body's ecosystem

Methanogens

Archaea that produce methane. Important in C cycle.

Bioprospecting

exploration of natural resources (microbes) to develop new products (compounds) for different purposes

High-throughput Screening (HTS)

quickly tests and analyzes thousands of compounds or biological samples for specific activity, typically in drug discovery, by automating the process and using microplates and readout technologies to detect results

Impact of chemolithotrophs

Use inorganic compounds carbon source, ATP production, and source of electrons. Do not need any existing life to survive. Impact local nutrient cycles, convert inorganic -> organic

Carbon cycle & Microbes

Microbes cause decomposition, releasing CO2 from dead organisms. Cyanobacteria and Algae fix CO2 through photosynthesis. Methanogens turn organic C into CH4

Nitrogen cycle and microbes

Nitrogen fixation through symbiotic bacteria and free-living bacteria in soil. Nitrobacter also converts nitrite into nitrate (usuable -> usable). Denitrification by soil microbes turns nitrates and nitrites into N2 (unsuable)

BOD

Biochemical oxygen demand

Overall purpose of sewage treatment

Reducing BOD load before release

Three stages of the sewage treatment process

1. Primary treatment: Physical removal of large particles and debris.

2. Secondary treatment: Biological treatment to degrade organic matter using microorganisms. Removes the most BOD

3. Tertiary treatment: Advanced filtration and chemical treatment for further purification.

Anaerobic Sludge Digestion

Turns solid waste into CH4 gas which is used for power. Removes BOD. Part of the Secondary sewage treatment.

Septic Tank

Device for primary (mechanical) treatment of sewage. Microbes in septic tank breaddown BOD and the liquid portion from septic tank is released.

Composting

a process that allows the organic material in solid waste to be decomposed and reintroduced into the soil, often as fertilizer. Microbes help this process through anaerobic decomposition

Bioremediation

Use of microorganisms or their products for the removal of toxic waste, i.e. oil spill w oil eating bacteria

Three basic principles of antimicrobial therapy

1: Selective toxicity - destroy target w/o any side effects (damaging human)

2: Reach the site of infection at inhibitory concentrations.

3: Penetrate and bind to target, avoiding inactivation and extrusion.

Origin of antibiotics

Common metabolic products of aerobic (soil) bacteria and fungi.

- Bacillus & Actinomycetes

- Penicillium fungi

Why do some microorganisms produce antibiotics?

to inhibit or kill competing microbes in their environment, giving them an advantage

Chemotherapeutic Agents

substances used to treat infections or diseases

Inhibitors of Cell Wall Synthesis

Blocks enzyme that catalzes the formation of peptide cross links in peptidoglycan (transpeptidase)

Penicillin and Cephalosporin

Inhibitors of cell wall synth. with β-lactam ring present. Penicillin has many different forms; methicillin can treat MRSA.

Inhibitors of Protein Synthesis (translation)

Target and bind to different parts of bacterial 70S Ribosome. Either the 30S or 50S subunits

Chloramphenicol

Inhibitor of Protein Synth. Attacks 50S subunit and stops peptide bond formation

Erythromycin

Inhibitor of Protein Synth. Attacks the 50S subunit, stopping the elongation of the polypeptide chain

Streptomycin

Inhibitor of Protein Synth. Attacks the 30S subunit, causes misreading of mRNA.

Tetracycline

Inhibitor of Protein Synth. attacks the 30S subunit, inhibiting the attachment of aminoacyl-tRNA to the ribosome. Used for treating severe acne.

Antimetabolites

Inhibits synthesis of essential metabolites through competition for enzyme binding sites. Usually manmade

Sulfanilamide

Antimetabolite. competes w Para-aminobenzoic acid (PABA), stopping folic acid synth.

Trimethoprim

Antimetabolite. Interferes with folic acid synth. by competing with dihydrofolate reductase (DHFR), blocking 2 steps in the folic acid pathway.

- used to treat UTI

Inhibitors of Nucleic Acid Synthesis (Replication and Transcription)

antimicrobial agents that disrupt the synthesis of DNA or RNA in microbes by targeting enzymes like DNA gyrase or RNA polymerase, which are essential for replication and transcription

Ciprofloxacin

disrupts DNA replication by targeting topoisomerases

Rifamycin

Inhibits RNA transcription by targeting RNA polymerase. Used to treat tuberculosis

Beta-Lactam ring

Portion of the penicillin and cephalosporin molecule that breaks bacterial cell walls. Can be resisted by bacteria with the beta-lactamase enzyme

Therapeutic dose

drug lvl required for clinical treatment

Therapeutic Index

ratio of toxic dose to therapeutic dose. The higher the better (toxic/therapeutic).

Selective Toxicity

Selectively destroying pathogen w/o damaging host

How antibiotic resistance can spread through a bacterial population

Drug resistance exchanged through Horizontal gene transfer (HGT), specifically conjugation. Also can be spread through Resistant 'R' Plasmids and compositive 'jumping' transposons

Antifungal drugs

Affect fungal sterols or ergosterols within plasma membrane. Either Polyenes - disrupt cell membrane function, or azoles - disrupt cell membrane synthesis

Nyastatin

Antifungal drug - Polyene. Most common/used antifungal drug

Amphotericin B

Antifungal drug - Polyene. Produced by Streptomyces. Toxic to kidneys

Imidazole

Antifungal drug - Azole. Treats cutaneous mycoses

Triazole

antifungal drug - Azole. Treats systemic fungal infections

Chloroquine

Antiprotozoa drug. Treats malaria by preventing the microbe's detoxification of the heme group in blood

Metronidazole

Antiprotozoa drug. Treats anaerobic infections - entamoeba & trichomonas

Antiviral drugs

Developed from small molecules that inhibit virus-specific enzymes and replication cycle processes.

- Usually either limits the duration or lessens severity of illness. Does not cure

Entry & Fusion inhibitors

Antiviral.

Entry: Blocks virus from binding to cell receptors

Fusion: Blocks fusion of virus and cell at receptor

Tamiflu

Antiviral. Anti-influenza agent. Inhibits neuraminidase - stops virus from spreading by altering surface of viral cells

- treats A & B flu virus infection

Acyclovir

Antiviral. Structural analog that resembles guanine. Inhibits herpes and shingles replication

Sofosbuvir

Hep. C Antiviral. Nucleotide analog that blocks HepC Virus RNA polymerase (transcription)

Ledipasvir & Velpatasvir

Hep. C Antiviral. Target viral enzyme needed for replication

Azidothymidine (AZT)

HIV antiviral. Reverse transcriptase (RT) inhibitor. Blocks creation of viral DNA from viral RNA (from viral capsule)

Ritonavir

HIV antiviral. Viral Protease inhibitor. Blocks transcription of viral DNA

Interferons

Produced by viral-infected cells to inhibit further spread of the infection

Imiquimod

Antiviral. Promotes interferon production in viral-infected cells

Amantadine

Antiviral. Stops virus from uncoating, disrupting viral replication. Used for Influenza A virus

Vancomycin

Inhibits Cell wall synth. Important for treatment of antibiotic resistant staphylococcal, enterococcal, and MRSA infections

MRSA

methicillin-resistant staphylococcus aureus

Teixobactin

Inhibits Cell wall synth. Works against gram + bacteria

Isoniazid (INH)

Inhibits Cell wall synth. Inhibits mycolic acid synth. in mycobacteria (tuberculosis)

Aminoglycosides

Inhibitor of protein synthesis. Bonds to bacterial 30S subunit causing misreading of mRNA and inhibiting protein synthesis. Gram - bacteria.

Macrolides

Inhibitor of protein synthesis. Bonds to bacteria 50S subunit blocking the elongation of the peptide chain