Midterms: Biotechnology

Fermentation

Anaerobic process that involves breakdown of organic compounds to generate energy.

Fermentation

Any process that produces yeast and bacteria biomass.

Biotransformation

Transformation by cells of a compound added to the medium of a commercially valuable compound.

Bioreactor

Large Chambers where fermentation takes places.

Enzymes

The most common product produced by microbes.

Detergent

Largest application of industrial enzymes.

Mannanase

Enzyme that remove stains containing guar gum

Subtilisin

Enzyme secreted in large amount of bacillus amyloiquefaciens.

Nucleic Acid Isolation

separation of the DNA or RNA from the other components of the cell.

Guanidine isothiocyanate

Potent protein denaturant that isolates RNase activity.

Spectrophotometry

Determination of DNA Concentration and Purity technique that uses DNA standards (different concentrations) and UV-VIS/Nanodrop.

Fluorometer

Determination of DNA Concentration and Purity technique that utilizes fluorescent dyes that are specific to the target molecule. It accurately quantifies DNA, RNA, and protein even at low concentration and minimizes effect of contaminants.

Microfluidics

This provides sizing, quantitation and quality check of DNA, RNA, Protein and cells. It employs microchannel-based elecrophoretic cell technology.

Maxam-Gilbert method

It involves labeling the 5"‘ end of DNA fragments followed by chemical cleaving at random sites.

Sanger chain termination method

This technique involves enzymatic termination of DNA synthesis at random sites using dideoxynucleotide.

Pyrosequencing

Sequencing technique that uses in vitro DNA amplification method known as emulsion PCR. This requires no cloning.

Chemiluminescence

Sequencing by synthesis measures the release of inorganic phosphate by __.

Illumina (Solexa) sequencing

Sequencing technique in which DNA stranded molecules are attached to single molecule arrays or flow cell.

Shotgun sequencing

Sequencing Technique in which genomic DNA is cut into small fragments (~1Kb or less) and inserted into a universal cloning vector to create small insert libraries, random clones are sequenced.

Shotgun

it means random or redundant.

GEL ELECTROPHORESIS

Biotech technique that involves the movement of electrically charged molecules in an electrical field. Allows molecular separation based on: size and net charge.

GEL ELECTROPHORESIS

most common method for separation & visualization of DNA.

Inversely

DNA migrates towards the anode (+) at a rate _____ proportional to its molecular weight.

EtBr (Ethidium Bromide)

the stain used in gel electrophoris.

red-orange

EtBr in UV light emits this color (flourescence) at 590 nm detected by he naked eye.

Buffer

It provides ions that carry a current through the gel, and to maintain a constant pH.

Tris-Acetate EDTA

common running buffer for agarose.

Tris-Borate EDTA

stronger buffering capacity vs. TAE; can be used for agarose or PAGE.

microwave

Agarose solution is cooked in ___.

Snaking or Reptation

Refers to the end-on movement of DNA through the agarose gel.

Southern or Norther Blotting

includes the transfer of DNA/RNA fragments from an elecrophoresis gel to a membrane support

DNA

Target molecule of Southern Blot technique

RNA

Target molecule of Northern Blot Technique

Protein

Target molecule of Western Blot technique

electroblotting

most reliable method for polyacrylamide

Radiolabels

detection is by autoradiography; less popular because of safety considerations but the most sensitive; 32P can detect single copy genes in only 0.5 μg of DNA; high sensitivity means detection of low concentrations of probe-target hybrid.

Non-radioactive labels

safer than radiolabels; does not require dedicated rooms, glasswares, and equipment but not as sensitive.

Hybridization

ssDNA (probe) can base pair to a second (DNA or RNA) molecule that contains a complementary sequence (target).

BIOTECHNOLOGY

any biology-based technology that makes use of an organism or any of its parts to make or modify a product, or improve plants, animals, microorganisms.

1979

The year of establishment of the UPLB Biotech (National Institute of microbiology and Biotechnology)

2011

Completion of Golden Rice Confined Field Testing/Establisment of the Philippine Genome Center

2021

Year of commercial release of Golden Rice

2022

Year of commercial release of BT talong

1944

Discovery of DNA as hereditary material

1953

The year when Watson and Crick discovered the Double Helix Structure of DNA

1973

The year when Cohen and Boyer discovered the DNA-Recombiinant technology

1994

Year of release of FlavrSavr Tomato

1997

Dolly the Sheep was born(?)

2000

The 1st draft of the Human Genome.

1996

First Greenhouse trial of BT Corn and Congressional hearing for GM Rice.

1998

Papaya Biotechnology Network Established to developed a PRSV resistant and delayed ripening Papaya.

1999-2001

Field Testing of BT Corn

2002

Release of BT Corn/Issuance of AO no. 8

2006

HErbicite-Tolerannt GM Corn/ National Biosafety Framework

2009

BT eggplant limited Trial Completion

2010

BT cotton confined Field testing completion

2011

Completion of Golden Rice COnfine Field Testing/Establishment of the Ph Genome Center.

2012

Lawsuit was filed against the Commercialization of BT eggplant.

Nucleic Acids

Chemical repositories of genetic information

Nucleic Acids

Biopolymers of nucleotides linked together by phospodiester bonds,

DNA
RNA

Two forms of Nucleic Acid

Phosphate
Purine or Pyramidine Base
Pentose

Three components of Nucleotide Structure

Phosphate Groups

Form the backbone of the polynucleotide together with the pentose

Phosphate Groups

Imparts (–) charge to the DNA hence enabling DNA to associate with the positively charged histones.

Phosphodiester bonds

sugar and phosphate groups are linked together by

Hydrogen Bonds

Two complimentary strands of DNA are held together by __

Chargaff’s Rule

This rule states that #A = #T ; #C = #G

hydrophobic interactions

Base pair stacking maximizes ___ to stabilize the DNA structure

DNA

1

RNA

2

POLYPETIDES

3

Proteins

4

Phenotype

5

Replication

6

Reverse Transcription

7

Transcription

8

Translation

9

Replication

Process by which DNA makes identical copies of itself; the Synthesis of DNA.

S-phase

Replication occurs during what phase of the cell cycle in preparation for cell division.

DnaA Protein

The protein responsible for opening duplex at specific sites in origin.

DnaB Protein (DNA helicase)

The protein that unwinds the DNA double helix.

SSBP (Sing strand DNA-binding proteins)

The protein that binds to ssDNA and keeps them separated.

DNA Topoisomerase (DNA gyrase)

The protein that relieves torsional strain brought about by DNA unwinding.

RNA Primer

Responsible for providing the free 3’ —OH group where deoxyribonucleotides will be added.

RNA Primer

It is need because the major DNA replicating enzyme can only extend a pre-existing DNA strand and cannot initiate a nucleotide DNA.

DnaA Protein
DnaB Protein (DNA helicase)
SSBP (Single strand DNA-binding proteins)
DNA Topoisomerase (DNA gyrase)
RNA Primers
RNA Primase

Proteins required during the initiation stage of DNA replication.

RNA Primase

The enzyme responsible for the catalyzation of the synthesis of the RNA.

DNA Polymerase III

This protein catalyzes chain elongation from 5’ to 3’ direction with respect to the daughter DNA strand.

dATP
dGTP
dCTP
dTTP

the deoxyribonucleoside triphosphates.

DNA Polymerase I

This protein proofreads the daughter DNA for mismatches.

DNA Polymerase I

This protein exercises RNA primers and fills in gaps with deoxyribonucleotides until only one phosphodiester bond remains to be formed.

DNA ligase

This enzyme catalyzes formation of phospodiester bond to seal nich in the sugar phoesphate backbone.

DNA Polymerase III
DNA Polymerase I
DNA ligase

The proteins required during the elongation stage of DNA Replication.

Termination

The stage of DNA Replication in which the entire length of the DNA molecule has been duplicated already.

two daughter strands

Products of termination stage of DNA Replication.

Semi-conservative

The characteristic of DNA replication that refers to the daughter DNA molecules containing one strand from the parent and one newly synthesized strand.

Bidirectional

The characteristic of DNA replication that refers to the occurrence of DNA replication in two opposite directions about the origin of replication.

Semidiscontinuous

The characteristic of DNA Replication that refers to the synthesis of new DNA strand always occurs from the 5’ to 3’ direction with respect to the DNA strand being synthesized.

Leading strand

that stand that elongates continuously.

Lagging strand

the strand that elongates discontinuously.