Exam 3 Flashcards
What is Biotechnology?
is the manipulation of organisms or their components to make useful products.
What is DNA Sequencing?
Getting to know the order of nucleotides.
What is cytogenetic map?
Each chromosome has a distinct banding pattern, and each band is numbered to help identify a particular region of a chromosome.
What do allele do?
If you have an allele that causes an illness, you can sequence that fragment and you can know where its located on a chromosome and how the DNA sequence looks
what do Generation of fragments require?
enzymes that will cut DNA
sticky ends
pieces of DNA fragments with short strands on each side that are complementary to each other
What are DNA nucleases?
The proteins that cut are molecular
what are different DNA nucleases in the lab generated?
bacteria
the enzymes generated from bacteria are very specific in what_______
DNA sequence can be cut
What is SNP?
single nucleotide polymorphism
The DNA fragments are visualized as ____ on the gel.
bands
DNA is negatively charged so it travels from _______
- to +
the suspect had the SNP the enzymes can only cut at the_______
bottom
what is Gel electrophoresis ?
One indirect method of rapidly analyzing and comparing genomes
During the process of electrophoresis, the ________ functions like a molecular sieve, separating the samples according to their size.
agarose gel
Restriction enzymes specifically recognize and cut short sequences of DNA called
restriction sites
what is the DNA profiling/ DNA fingerprints steps?
- DNA isolation
- Amplification (copying) or markers (fragments) for analysis-PCR
- Sizes of amplified fragments are compared by electrophoresis
- Amplification (copying) or markers (fragments) for analysis-PCR
Genetic profile
An individual’s unique DNA sequence
What is Short tandem repeats (STRs) ?
genetic markers used to analyze current genetic profiles
What is Short Tandem repeats?
4 to 5 nucleotides that are repeated back to back
Respects happened when _____
during meiosis the homologous chromosomes might not line up perfectly because the amount of repeats
_______ are used to amplify and then identify STRs of different lengths.
PCR and gel electrophoresis
DNA profiling has provided ?
- Forensics
- Establishing family
relationships - Identification of
human remains.- Species identification
- Establishing family
What are the two types of genetic markers that can facilitate DNA profiling?
SNPs and STRs
What is Amplifying DNA in Vitro?
The Polymerase Chain Reaction (PCR)
What does SNPs and STRs stand for?
SNPs (single nucleotide polymorphisms)
-STRs (Short tandem repeats)
What is Polymerase chain reaction, PCR?
can produce many copies of a specific target segment of DNA
Three-step cycle; heating, cooling and replication
What is Vivo?
amplification of DNA inside living organisms
What is Vitro?
outside the living body
What is Taq polymerase?
heat-stable DNA polymerase
What Amplifying DNA in Vitro components of?
-DNA: template
-dNTPs: nucleotides (A,T,C, and G), the building bricks of DNA
-Two primers: single stranded DNA that bind to the template to initiate DNA replication
-DNA polymerase: enzyme which binds the dNTPs to the primers
-buffer: to adjust the PH and amount of alt that help the DNA polymerase keep its shape
What are the Steps of Polymerase Chain Reaction (PCR)
- A reaction mixes with dNTPs, a DNA template, copies of the two primers, and Taq polymerase.
- Denaturation-heating the mixture to 95 cells to separate the two strands of the DNA.
- Primer annealing-cooling the mixture allows the primers to bond to complementary sections of single- stranded target DNA homology. It will make hydrogen bonds.
- Extension-heating the mixture to 72 cells causes the Taq polymerase to synthesize the complementary DNA strand from the dNTPs, staring at the primer. Starts adding nucleotides on the primer at the 3-prime end. This is Cycle 1
- Steps 2-4 are repeated to make the necessary number of copies
Requirements of PCR
PCR is possible only when DNA sequence information surrounding the gene of interest is available
What information is critical to the success of polymerase chain reaction (PCR)?
The DNA sequence of the ends of the DNA to be amplified (flanking regions) must be known.
Advantages of PCR
- Can amplify DNA from a small sample
- Results are fast
- Copying only the target sequence
PCR and cellular DNA replication share which of the following characteristics?
extend new strand in 5 to 3 direction
What piece of DNA do we want in making DNA?
genetic markers (SNP, STRS)
How do you open up DNA?
Hot temperature 92 cells
Who discovered tags polymerase?
Kary
What is DNA sequencing?
Knowing the order of nucleotides
What is restriction enzymes?
enzymes used to cut within a DNA molecule
What is Gel electrophoresis?
One indirect method of rapidly analyzing and comparing genomes
What is DNA fingerprinting?
a laboratory technique used to determine the probable identity of a person based on the nucleotide sequences of certain regions of human DNA that are unique to individuals.
What is DNA profiling?
the process where a specific DNA pattern, called a profile, is obtained from a person or sample of bodily tissue
Examples of genetic markers for molecular biology.
SNP, STRS
What is PCR?
a simple and widely used process in which minute amounts of DNA can be amplified into multiple copies.
Ingredients for PCR
dNTPs, a DNA template, copies of the two primers, and Taq polymerase, buffer
What do you need in the tube to run PCR. Name four ingredients.
- DNA template
- primers
- DNA polymerase
- free nucleotides
- buffer
Place the steps in a cycle of PCR in the correct order.
1. Annealing-cool to allow primers to form hydrogen bonds with ends of target sequence.
2. Extension- DNA polymerase adds nucleotides to the 3’ end of each primer.
3. Denaturation-Heat briefly to separate DNA strands.
3,1,2
Look at slide 1
B
What are PCR ingredients?
DNA template, primers, polymerase, free nucleotides, buffer
Vivo
-In vivo means in a living organism
- In vivo uses RNA primers
-In vivo uses helicase to open the DNA double-strand
vitro
-In vitro is in the tube
-In vitro uses DNA primers
-In vitro, uses hot temperature to open the strands
- In vitro amplification we use Taq polymerase
What is Bacteria?
The DNA Toolbox
What is Recombinant DNA?
If we but human gene into a bacteria, then that bacteria will carry recombinant DNA
Is Recombinant DNA done in vitro or in vivo?
vitro (in the tube)
What is Recombinant Organisms?
organism that carry foreign DNA
What is Genetic engineering?
the direct manipulation of genes for practical purposes
What is Biotechnology?
the manipulation of organisms or their genetic components to make useful products
How is DNA mixing possible?
All DNA no matter if you think humans, birds, plants, bacteria we all speak the same language of nucleotide.
What is vivo cloning?
Taking a piece of DNA and putting it into a living organism can help us make multiple copies
What is DNA cloning?
to work directly with specific genes, scientists prepare well-defined DNA segments in multiple identical copies
Which one uses bacteria to make a copy of genes vivo or vitro?
In vivo
PCR is vitro cloning or Vivo cloning?
vitro cloning
What is Plasmids?
are small circular DNA molecules that replicate separately from the bacterial chromosome
What is Recombinant DNA?
Is produce when researchers insert DNA into plasmids. A molecule with DNA from two different sources
What is DNA manipulation?
first extracting the plasmid from bacteria, then cutting open that plasmid with an enzyme that cuts in a very specific spot. Ones its cut you are able to put foreign DNA into it. The foreign DNA is stuck with sticky ends and that is called recombinant plasmid.
Is Vitro cloning is very long or very short?
Very short
steps for Gene cloning
first extracting the plasmid from bacteria, then cutting open that plasmid with an enzyme that cuts in a very specific spot. Ones its cut you are able to put foreign DNA into it. The foreign DNA is stuck with sticky ends and that is called recombinant plasmid. Then you have to put the plasmid back into bacteria and we stress it with heat shock. We need to recover bacteria and lead to multiply. Whenever the bacteria multiplies, the recombinant plasmid will multiply as well we get the clones of a gene. Next day you can extract that plasmid from the bacteria cut that gene of interest out and you will have multiple copies of it
Why is bacteria used?
It takes 20 minutes for bacteria to multiply and we can get many of them in short period of time
What is Cloning Vector?
A plasmid used to clone a foreign gene
Would it matter if I go back to my plasmid and insert the DNA in different ways?
no it wont matter
Gene cloning in vivo steps?
- Plasmid DNA is isolated
- DNA containing the gene of interest is isolated
- Plasmid DNA is treated with restriction enzyme (molecular scissors) That cuts in one place, opening the circle
- DNA with the target gene is put into plasmid
- Plasmid is put into bacteria
- Each time bacteria multiplies, the gene will be multiplied- gene cloning (making many copies)
- Protein of interest is harvested from the genetically modified bacteria
What is Genomic Library?
is made using bacteria is the collection of recombinant vector clones produced by cloning DNA fragments from an entire genome
How are Genomic books made?
You can chop the genome of a species I’m interested in and put every piece into a different vector that will create books like in a library
Why do we have vectors?
Plasmid cant not carry to much cant stick to much DNA. We have vectors for more space
Plasmids capacity space
have a capacity of 15 kb
Phage (lambda)s capacity
have a capacity of 25 kb
Cosmids or Fosmids capacity
Have a capacity of 35-45 kb
Bacterial artificial chromosomes (BAC) capacity
Have a capacity of 50-300 kb
Yeast artificial chromosomes (YAC) capacity
Have a capacity of 300->1500 kb
Human artificial chromosomes (HAC) capacity
Have a capacity of > 2000 kb
What was the first drug approved by the FDA
Making Humulin
Humulin was the first recombinant DNA drug approved by the FDA
Transgenic bacteria uses
- Insulin
- Vaccine
- Human growth
-hormone - Vaccines
bacteria can decompose petroleum and are useful in ______
cleaning up oil spills
Human insulin made in and use?
Made in E. coli and use treatment for diabetes
Human growth, hormone (HIGH) made in and used in?
Made in E.coli and use in treatment for growth defects
Taxol made in and use in?
made in E.coli and use in treatment for ovarian cancer
Erythropoietin (EPO) is made in and use in?
Made in Mammalian cells and made for treatment for anemia
Factor VIII is made in and use in?
Made in Mammalian cells and use for treatment for hemophilia
Tissue Plasminogen activator (TPA) is made in and use for?
made in Mammalian cells and use for treatment for heart attacks and some strokes
Fist modification on plants was made by
European corn
What is Traditional breeding?
when I take related species and let them cross, mate, produce progeny Traditional breeding
How long does radiational breeding take
12-15 years and a lot of space for a new variety
What is Recombinant DNA?
Is when you can take DNA from a fish and put it inside of a strawberry
How much time does Recombinant DNA take and how long does it take and who is crossed and hoe many genes transfer?
-single gene transfer
-Requires 2-3 years
-small space
-crossing unrelated species
What are Two primary concerns with modification of foods?
- Fear that GM foods could be hazardous to human health
- Fear that crops carrying genes from other species might harm the environment
What is Human gene therapy?
is a recombinant DNA procedure that seeks to trat disease by altering the genes of the affected person
How are vectors transfer Genes to Human Cells?
Viruses used as vectors.
1. Normal human gene isolated and cloned
2.Human gene inserted into virus
3. virus injected into patient
What is Crispr
is how bacteria deals with a viral infection
What is Cas9 ?
chops the DNA
What is Guide RNA ?
guides the protein where to go and cut so the right viral DNA is recognized
What is Gene editing?
adding, disrupting, or changing the sequence of specific genes
Agriculture has three methods of breeding. What are there?
- Traditional breeding
- Breeding with genetically modified organisms
- Breeding so far with knocking out undesirable genes (crisper)
All people speak the same language of _____
nucleotides
What are Genes?
the fundamental unit of heredity-made of DNA
A
T
G
C
C
G
T
A
What is a DNA?
is comprised of a polymer (linked string) of chemical subunits called nucleotides
How many nucleotide does humans have?
3 billion nucleotide long DNA
What is Gene expression?
The process of making proteins
How is protein made?
Start with our body we have cells (so many)
-inside the cell there is a nucleus where DNA is found in forms of chromosomes
-DNA is a double-stranded nucleic acid that has coding sequences for making proteins
-proteins are made in the cytoplasm
What is messenger RNA?
translation of information form nucleic to cytoplasm
What is DNA sequencing?
Knowing the order of nucleotides in the given segment of DNA
What is The Human Genome project (HGP)?
the goal of the project was to sequence the human genome
What are the The Mani players for The Human Genome project (HGP)?
National institute of health (NIH)
The U.S. Department of Energy (DOE)
The three people that led the (HGP)
- Francis Collins
- Eric Lander
- Craig Venter
Who started Celera?
Celera
An international consortium was built with the involvement of all those countries which are:
-Great Britain
-US
-Japan
-France
- China
- Germany
When was The end of The Human Genome project?
was April 25, 2003
The DNA of two people of the _____ is 99.9% identical
same sex
How much did the HGP cost U.S. taxpayers?
- $2.7 billion
What did the people get In return for paying for the HGP?
Improvement in human health
-Biotechnology and drugs
- Development industries
What are they trying to do for the future for HGP?
cheaper and shorter time
Why do we sequence human genome?
- Discover gene functions
The Human Genome Project help to discover?
Parkinson disease
Program to ensure that genetic information would be safeguarded, not used in discriminatory ways
- ELSI Focuses on several issues
- Privacy
- Fairness
- Discrimination
Use of genetic information in reproductive decisions
With the Human Genome project we learned:
- Human DNA has about 3 billion base pairs
- 800 phone books
- 200 actionable genes
-Number of genes about 24,000
-Only a small portion of our genes are coding genes (expressed in the form of proteins) (1.5%)
What is Genomics?
is the study of an organism’s complete set of genes and their interactions. They are passed to the next generation.
- Data base available:
-(NCBI) National center for Bioeconomy information
What is deCODE?
Icelandic Genetic Database
Number of genes is not equal to number of ______
proteins
How can we get Genetic profile?
can be obtained by analysis of tissue or body fluids
Laws that protect privacy
- HIPAA (Health Insurance Portability and Accountability ACT) from 1996
- GINA (The Genetic Information Nondiscrimination Act)-bill passed in the spring of 2008
When we study DNA we study
genomics
When we study proteins we study
proteomics
To discover which genes are expressed in certain cells is to_____
identify the mRNAs being made
What is Nucleic acid probes
complementary molecules, of either DNA or RNA
What is In situ hybridization use for?
uses fluorescent dyes attached to probes to identify the location of specific mRNAs in place in the intact organism
What are fluorescent dye or radioactivity used
Probe that are marked with either fluorescent dye or radioactivity are used to determine the localization of different gene expression
When we work with RNA that test, in general, is called
Northern
When we work with proteins that test in general is called
Western
_______are used for studying DNA
Southern
Northerns are useful for studying
RNA
Westerns are used to study
proteins
Northerns and Westerns address
gene expression
What is Reverse transcriptase-polymerase chain reaction (RT-PCR)
is useful for comparing amounts of specific mRNAs in several samples at the same time
What is Complementary DNA (cDNA)
serves as a template for PCR amplification of the gene of interest
What is DNA microarray assays?
compare patterns of gene expression in different tissues, at different times, or under different conditions
Genomics
- DNA world
Transcriptomics
RNA world
(a lot of work is done here in cDNA )
Transcriptomics
cDNA is complementary
RNA, messenger RNA
cDNA is complementary is generated by
reverse transcription
Proteomics
Protein world
Number of genes is not equal to number of
proteins
What is Genomics
is the study of whole set of genes and their interactions
What is Bioinformatic
is the application of computational methods to the storage and analysis of biological data
What is Systems biology
approach can be applied to define gene circuits and protein interaction network
Genome size increases as we move from
bacteria Archaea to plants and animals
Genome size for Bacteria and Archaes
Most are 1-6 MB
Genome size for Eurkarya
Most are 10-4,000 Mb, but a few are much larger
Number of genes of Bacteria and Archaea
1,500-7,500
Number of genes of Eukarya
5,000-40,000
Gene density for Bacteria and Archaea
Higher than in eukaryotes
Gene density for Eukarya
Lower than in prokaryotes (within eukaryotes, lower density is correlated with larger genomes.)
Introns Bacteria and Archaea
Nine in Protein-coding genes (Bacteria)
Present in some genes (Archaea
Introns Eukarya
Present in most genes of multicellular eukaryotes, but only in some genes of unicellular eukaryotes
Other noncoding DNA Bacteria and Archaea
Very little
Other noncoding DNA
Can exist in large amounts; generally more repetitive noncoding DNA in multicellular eukaryotes
coding sequencees we have
1.52%
introns we have
20%
we have non-coding DNA
15%
What is RNA interference
refers to stopping messenger RNA from being translated
What is MicroRNAs (miRNAs)?
are small single-stranded RNA molecules that can bind to mRNA
What is Transposable elements?
move from one site to another in a cell’s DNA they are present in both prokaryotes and eukaryotes
What is Transposons?
Which move by means of a DNA intermediate and require a transposase enzyme
What is Retrotransposons?
which move by means of an RNA intermediate, using a reverse transcriptase
Genetic markers
SNPS
STRS
What is Multigene families
Collection of identical or very similar genes
What is In situ hybridization
to study locally either DNA RNA or protein
Chromatin is the string of DNA wrapped around ______
histones
Chromatin structure is essential for starting
transcription
When chromosome is unpacked DNA is available for
transcription
Histones have arms those arms when they are not unoccupied they will
hug the near by histone molecule
Histone When they are occupied they
can not hug
When histones are hugging We have heterochromatin the gene is turn
off its not available for transcription
When the acetyl groups occupied arms of histones they can not hug. The DNA is exposed. The gene is turn
on
Methyl groups bind directly to
DNA
If I attach a methyl group to DNA and now I want to transcribe it. DNA Methylation blocks transcription and gene is
Turn off
Piwi blocks our expression of genes by attaching to
chromatin
What is Epigenetics
in addition to DNA. Added to either directly to DNA or to histones that regulate gene expression that turn gene of or on. Some of those can be passed to next generation
microRNAs acts during protein synthesis but also can affect chromatin structure causing
epigenetic effect.
Epigenetic tags are whipped out during
zygote formation
