Biotechnology test 1

Using living organisms, or the products of living organisms, for human benefit to make a product or solve a problem

a) Human, animal/plant physiology

b) Mathematics

c) Molecular and call biology

d) Immunology

e) Computer Science

f) Chemical engineering

g) Genetics

h) Bioinformatics

i) Biochemistry

A) ability to identify and copy/clone a gene of interest

B) technique enabling DNA to be combined from different sources

C) altering an organism's DNA

D) international effort to identify all human genes and their loci

1) Microbial

2) Agricultural 

3) Animal

4) Forensic

5) Bioremediation

6) Aquatic

7) Medical

-use of microorganisms to make valuable products & applications

-create better enzymes

-simplify manufacturing and production processes

-make vaccines & batch amounts of proteins for human medicine

-make more efficient decontamination processes for industrial waste removal

They extracted and purified it from pigs and cows

• 1)
• -genetically engineer plants to make valuable products 

• 2) 
• -be more environmentally friendly and yield more per acre (genetically engineered)

-resistance to diseases and insects

-drought-resistant and tolerant to cold temperatures

-foods with higher protein or vitamin content

-drugs developed and grown as plant products

• 1)
• -genetically engineer animals to make valuable products

-used "bioreactors" for producing medically valuable proteins

-used as model organisms

-organismal cloning

2) Way to achieve large scale production of therapeutic proteins from animals for use in humans

3) Goats and Atryn

1) Disrupt a gene in the animal and then look at what functions are affected in the animal due to the knockout.

-It helps determine the role and function of the gene

2) Rats and mice

-Analysis and application of biological evidence as DNA sequence data to detect an organisms unique DNA pattern.

• -Uses scientist utilize DNA finger printing to: 
• a) solve crimes

b) determine paternity

c) identify human remains

d) track and confirm organisms that spread disease

e) determine identity of mystery meats

-Use of living organisms to process, degrade, and clean up naturally occurring or human-made pollutants in the environment

-The use of biotechnology to process and degrade a variety of natural and human-made substances. Particularly those that contribute to environmental pollution.

-Adding nutrients to stimulate growth of bacteria to clean up an oil spill

• -Scientists utilize living organisms to:
• a) break down oil

b) degrade human waste (wastewater treatmant)

c) degrade hazardous materials

d) bioaccumulate heavy metals

-Use of aquatic organisms such as finfish,shellfish, marine bacteria and aquatic plants for biotechnology applications

-Raising finfish or shellfish in controlled conditions for use as food sources

• Scientists utilize living aqautic organisms to:
• a) genetically engineer disease-resistant strains of oysters

b) develop vaccines against viruses of salmon and other finfish

c) genetically engineer salmon to overproduce growth hormone

d) obtain rich and valuable sources of new genes (bio prospecting)

-Use of organisms to improve the entire spectrum of human health and medicine

• Scientists utilize organisms or their products to provide:
• a) diagnosis of health and illness

b) preventative medicine

c) treatment of human diseases

d) gene therapy

-CAR (chimeric antigen receptor) T-cell therapy is a type of cancer immunotherapy treatment

• Prokaryotic Cells
• -True bacteria (eubacteria)

-Archaebacteria

-No nucleus; DNA located in the cytoplasm. No organelles

• Eukaryotic Cells
• -Protists, fungi, plant, animals cells

-DNA enclosed in a membrane-bound cytoplasm.Nucleus. Many organelles.

A) Dies

B) Lives

C) Lives

D) Dies

Process by which bacteria take in DNA from the surrounding

• 1)
• a) Pentose (5-carbon) sugar called deoxrubose

b) A nitrogenous base

c) Phosphate molecule

• 2)
• a) Adenine

b) Thymine

c) Guanine

d) Cytosine

• 3) RNA uses Uracil instead of Thymine for its bases
• -In it's 2' it has an OH group instead of H

• 1)
• Purines:
• a) Adenine
• b) Guanine

• Pyrimidines:
• a) Thymine 
• b) Cytosine
• c) Uracil

• 2)
• Purines: are two or more rings connected together

pyrimidines are just one ring

1) Consist of two strands that join together and warp around each other to form a double helix

2) Bond that holds nucleotides together in a strand

3) it connects each strand by its polarity of 5'end and 3' end

1) Hydrogen bond

2) Due to the antiparallel force from their polarity being reversed to each other

1) strings of DNA wrapped around DNA-binding proteins called histones

2) tightly coiled arrangement of DNA & proteins

3) sex cells contain a single set of 23 chromosomes 

• 4) one copy of newly replicated chromosome
• -sister chromatids are exact replicas of each other

• 5) region consisting of intertwined DNA and protein
• -delineates sister chromatid into 2 arms-p and q

• 6) proteins that attach chromosomes to microtubules
• -located at centromere

• 7) highly conserved repetitive nucleotide sequence
• -enables cells to divide without losing genes
• -attaches chromosomes to nuclear envelope

1) way to study chromosome number and basic aspects of chromosome structure

2) sequence of nucleotides that provides cells with instructions to synthesize a protein or type of RNA 

• 3) not all genes are templates to produce a protein
• ex. genes involved in making tRNA\

4) all of the DNA in an organism's cell

5) Map out or identify all the genes in the human body

1) Mitosis

2) A process where one cell divides to form two daughter cells

-Prior to mitosis DNA replication must occur which happens during interphase

3) Meiosis

4) Parent cell divides to create 4 daughter cells 

-DNA replication must occur prior to meiosis

5) A fertilized egg which has the complete set of 46 chromosomes

1) Where meiosis 1 creates a haploid cell

2) DNA replication results in one original (parental) DNA strand and one newly synthesized DNA strand

3) Enzyme breaks the hydrogen bonds between complimentary base pairs that hold the two DNA strands together, "unzips" DNA

4) Enzymes synthesize RNA primers; known as an RNA polymerase

5) Enzyme that synthesizes new strands of DNA

1) Unwinding the DNA

-Helicase unzips the DNA two strands then the single-strand binding proteins bind to the complementary strand of DNA and prevent them from base pairing and reforming a double helix

2) Adding RNAprimers

- RNA primers start the replication process because they serve as binding site for DNA Polymerase

3) Copying the DNA

-DNA polymerase enzyme binds to the RNA primers

-Reads/Scans in one direction 3 to 5

-Works/Synthesizes in one direction 5 to 3

1) RNA primers are replaced with DNA nucleotides using DNA Pol

-Shot Okazaki fragments are synthesized as DNA Pol works on lagging strand

2) Lagging is discontinuous and Leading is continuous

1) Genes are copied (transcribed from DNA code into RNA code

2) RNA code (exact copies of genes) is read into protein

3) Exxplainsthat DNA codes for RNA, which codes for protein

1) Binds to a promoter region

-Unwinds DNA helix

-Copies "works" one strand of DNA into RNA

-Template strands is read 3'-5' & works 5'-3'

2) Are DNA binding proteins that can bind to promoters

-Help RNA Pol find the promoter

-Can speed up or stop transcription

3) Are DNA nucleotides that play role in transcription

-Regulatory sequences; bind regulatory proteins (activators)

1) Genes are copied (transcribed) from DNA code into RNA code

2) RNA code (exact copies of genes) is read into protein

• 3) Explains that DNA codes for RNA, which codes for protein
• Ex. DNA>RNA>Protein

• 1) Bind to a promoter region
• -unwinds DNA helix

-copies "works" one strand of DNA into RNA

-template strand is read 3'-5' and works 5'-3'

b) Are DNA binding proteins that can bind to promoters

-help RNA Pol find the promoter

-can speed up or stop transcription

c) are DNA nucleotides that play role in transcription

-regulatory sequences; bind regulatory proteins (activators)

Are the RNA polymerase and newly formed strand RNA are released from DNA molecule

a) copy of gene (acts as messenger by carrying genetic code from nucleus to cytoplasm where info is read into protein)

b) molecules that transport amino acids to ribosomes during protein synthesis

c) short single-stranded RNA molecules and are components of ribosomes

1) The production of immature and not fully functional mRNA

• 2)
• a) Addition of a 5' cap- guanine base containing methyl group allows ribosome recognition

b) Splice out DNA not coding for proteins (introns)

-retain the protein coding sequence of the gene (exons)

-alternative splicing-multiple proteins produced from single gene

c) 3' Poly A tail- 100-300 adenine nucleotides added to protect mRNA from RNA degrading enzymes

-increases its stability and availability for translation

1) By genetic code a universal language of genetics used by virtually all living organisms

2) Three nucleotides units of mRNA

3) AUG

4) UGA, UAA,UAG

1) Aggregates containing rRNA and protein

-Contains 2 subunits small (18S) and large (28S)

-Associate to form 2 grooves A (aminoacyl) and P (peptidly)

-E site where tRNA molecules leave the ribosome

2) small molecules that folds into cloverleaf ctructure

-Has site for amino acid attachment by the enzyme aminoacyl tRNA synthetase

• -Opposite end of tRNA is anticodon
• -Aminoacyl "charged" tRNA binds to the A site of ribosome
• -Each tRNA anticodon to its complementary codon

1) Initiation- is the recruitment of ribosome to mRNA and recognition of the start codon

2) Elongation- is the stepwise addition of amino acids to the growing protein chain

3) Termination- is the process by which a completed polypeptide and mRNA is released from the ribosome

-Protein factors around start codon help guide small ribosome subunits to mRNA

-Small subunit binds to 5' end of mRNA by recognition of 5' Cap

-Small ribosome subunit moves along the mRNA until the start codon is found

-Small subunit waits for correct tRNA (initiator tRNA)

-Now large subunit binds to complex containing: mRN; initiation factors; small subunit; and initiator tRNA

1) tRNA, carrying that correct amino acid, enters the ribosome at the A site, one at a time as the mRNA code is read

2) Catalyzes formation of peptide bond between 2 AA's attached to their tRNAs

3) Ribosomes shifts forward 5' to 3' tRNA and protein move into P site

-Ribosome encounters the stop codon near the end of mRNA

-Releasing factor proteins interact with the stop codon to terminate translation

-Ribosomal subunits come apart and release the mRNA, and newly formed protein

Refers to the production of mRNA by a cell and sometimes protein.

-All cells of an organism contain the same genome.

-Not all genes will be turned on at the same time some will be upregulated while others will be silenced or downregulated

1) how genes can be turned on and off in response to different signals

• 2)
• -Chromatin domains

-Transcription

-Post-transcriptional modification

-RNA transport

-Translation

-Post-translational modification

-mRNA degradation

-Protein degradation

1) Controlling the amount of mRNA transcribed from a particular gene as a way to turn genes on or off

2) DNA sequence located upstream from gene

-Found in TATA box and CAAT box

3) DNA binding proteins

4) Genes that bind specific regulatory sequences next to the promoter

1) Enhancers: DNA sequences which are often located upstream of promoter that can bind to activators.

2) Activators: regulatory receptor protein complex (activators) binds to androgen response element (specific enhancer)

-Clusters of several related genes located together and controlled by a single promoter

-Operator-region within promoter 

-Regulate gene expression in response to their nutrient requirments

a) Codes for Beta Galactosidase (B Gal) 

-Breaks down lactose to glucose and galactose

b) Codes for permease

-A membrane protein that transports lactose into the cell

c) Codes for Transacetylase

-Has a protective function

d) Codes for repredor protein

• 2) 
• a) Lactose, it acts as an inducer by binding to the repressor protein and changes its shape so it falls off the operator and allows RNA Pol transcribe the 3 genes

b) Glucose, the repressor stays bound and prevents transcription

a) Non-coding RNA mechanisms of gene silencing

b) Begin in the cytoplasm

-derived  from long double stranded RNA

-binds to mRNA and regulates gene expression cleaving mRNA

-silences specific target mRNA (single gene); no translation

c) Begins in the nucleus

-initially single stranded non-coding RNA

-miRNA silence gene expression by inhibiting translation of mRNA or causing degradation of mRNA

-a single miRNA can regulate the expression of many genes

1) Change in the nucleotide sequence of DNA 

-Can effect cells by changing the properties of the protein which affects the trait

-Can spontaneous or induced by environmental factors including X-rays and UV

• 2)
• Transitions mean purines turning into other purines  and pyrimidines turning into other pyrimidines 

Transversion pyrimidines turning into purines and purines turning into pyrimidines 

a) Where a change in the gene doesn't have any effect in the sequence

b) A mutation that causes a single nucleotide to be changed causing the following amino acid to have a different function 

c) A mutation that causes an early stop codon to be read

d) A manual insertion or deletion of a single nucleotide

1) inherited or acquired

2) Passed onto offspring through gametes

-Can cause birth defects or inherited diseases because the mutation is present in the genome of all the offspring's cells

3) Occur in the genome of somatic cells

-Are not passed along to offspring

-These mutations can lead abnormalities in cell growth and ultimately become cancerous

1) 99.9%

2)Most have no obvious effect; other mutations strongly influence cell functions, behavior, and susceptibility to genetic diseases

3) By SNPs ( single nucleotide polymorphism)-are bad when they occur in exons and change protein structure so ultimately can change protein function

1) Modifications in chromatin structure which do not involve mutations in DNA and histones

• 2)
• -Some are reversible; some are long-lasting

-These changes vary between call types in the body and in normal and diseased tissues

-Diet and environment can influence epidenome

-Involved in patterns of gene expression during development

a) Typically acts to repress gene transcription

b) Increases levels of gene transcription

c) Mechanisms of gene silencing

1) Denatures proteins and solubilizes denatured proteins

2) Is called the aqueous layer and contains DNA & RNA

1) A genetically identical copy of a cell or organism; also the process of making copies of a gene, cell, or organism

2) DNA cutting enzymes (molecular scissors)

3) Circular form of self-replicatingDNA

-Can be manipulated to carry and clone other pieces of DNA

1) Cuts DNA by cleaving the phosphodiester bond that joins adjacent nucleotides in a DNA strand

2) Binds to, recognizes, and cuts DNA within a specific sequence of bases

3) Reads the same forward and backwards on opposite strands of DNA

a) Restriction enzymes that cut DNA to create DNA fragments with overhanging single strands ends

b) Restriction enzymes that cut DNA to generate fragments with double-stranded ends

-yield is significantly lower ligating

-can insert in the opposite orientation desired

-blunt ends are always compatible with each other

-Preferred for cloning; DNA fragments with sticky ends can be easily joined together because they base pair with each other by forming weak hydrogen bonds

-DNA ligase is used to form a covalent bond between the sugar-phosphate residue of adjacent nucleotides to join the two molecules together

1) Wells

2) Charge & size

3) Large fragments move slower and small fragments move after through the gel

4) Ficolland tracking dye. It prevents DNA from escaping well and o monitors DNA samples during migration in gel

5) 0.5% is used to get a variety of DNA bases while 2% is used to get a specific estimate base pair from the DNA

1) Small circular pieces of DNA found primarily in bacteria

2) Pieces of DNA that can accept, carry, and replicate other pieces of DNA

1: Treat bacterial cells with calcium chloride, while chilled on ice for 30 minutes

2: Add plasmid DNA to cells chilled on ice

3: Heat the cell and DNA mixture (30 sec @ 42C)

4: Plasmid DNA enters bacterial cells and is replicated to express their genes

1) Apply brief pulse of high voltage electricity to create tiny holes in bacteria cell wall that allow the DNA to enter

• 2) 
• a) Rapid

b) Requires fewer cells

c) Can be used to introduce DNA into other cells types

d) More efficient process

1) Is process designed to facilitate the identification of recombinant bacteria from bacteria that contain plasmid without foreign DNA, while preventing the growth of non-transformed bacteria

2) Transformed cells are cultured on plates containing antibiotics to identify transformed bacteria from non-transformed bacteria

-Does not select for plasmid containing foreign DNA (recombinant plasmid) vs. recircularized plasmid with no DNA insert

• 1) 
• -DNA is cloned into plasmid restriction site within lacZ gene

-When it is interrupted by an insert gene, the lacz gene cannot produce functional Beta-galactosidase

• 2)
• -White colony = non-functional lacZ = clone = genetically identical bacteria cells each h containing copies of the recombinant plasmid

-Blue colony = functional lacZ

- Clone human insulin DNA sequence inserted into a plasmid and the bacteria cells were then used to synthesize the protein product of the cloned gene

-Can generate lots of pure protein via this technique

a) Small enough to be separated from chromosomal DNA of host plasmid

b) Site for DNA replication that allow plasmid to replicate independently from host chromosomes

c) Number of plasmid in the cell; normally small (recombinant plasmids have high copy numbers)

d) Recognition sites for several restriction enzymes in which DNA insert is cloned into

e) Enables selection of transformed colonies

f) Used for transcription in vitro and in vivo

g) Flank ends of multiple coloning site