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Chapter 10: Molecular Biology of the Gene, Chapter 12: DNA Technology and…
Chapter 10: Molecular Biology of the Gene
The Structure of the Genetic Material
Experiments showed that DNA is the genetic material
Alfred Hershey and Martha Chase showed that certain phages reprogram host cells to produce more phages by injecting their DNA
Bacteriophages
: viruses that exclusively infect bacteria (aka
phages
)
DNA and RNA are polymers of nucleotides
Nucleotides
: A building block of nucleic acids, consisting of a 5-carbon sugar covalently bonded to a nitrogenous base and one or more phosphate groups
Polynucleotides
: A polymer made up of many nucleotide monomers covalently bonded together
Sugar-phosphate backbone
: In polynucleotide the alternating chain of sugar and phosphate to which nitrogenous bases are attached
Deoxyribonucleic acid (DNA
): A double-stranded helical nucleic acid molecule consisting of nucleotide monomers with deoxyribose sugar and the nitrogenous bases-
Thymine
(T): a single-ring nitrogenous base
Cytosine
(C): a single-ring nitrogenous base
Adenine
(A): a double-ring nitrogenous base
Guanine
(G): a double-ring nitrogenous base
Uracil
(U): a single ring-nitrogenous base (found in RNA)
Capable of replication, DNA is an organism's genetic material
DNA is a double-stranded helix
Double helix
: Two polynucleotide strands wrapped around each other. Hydrogen bonds between bases hold the strands together. Each base pairs with a complementary partner: A with T, G with C
DNA Replication
DNA replication depends on specific base pairing
Separation of DNA strands starts DNA replication. it uses each strand as a template to assemble new nucleotides into a complementary strand.
Semiconservative mode
l: Type of DNA replication in which the replicated double helix consists of one old strand, derived from the old molecule and one newly made strand
DNA replication proceeds in two directions at many sites simultaneously
DNA polymerases
: A large molecular complex that assembles DNA nucleotides into polynucleotide using a preexisting strand as a template. The cell makes one daughter strand as a continuous piece. The other strand is made as a series of short pieces which are then connected by the enzyme
DNA ligase
The Flow of Genetic Information from DNA to RNA to Protein
Genes control phenotypic traits through the expression of proteins
DNA --> RNA --> protein
Transcription
: The synthesis of RNA on a DNA template.
Translation
: The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of language from nucleotides to amino acids
Gene
: a small unite of hereditary information consisting of a specific nucleotide sequence in DNA.
The genetic code dictates how codons are translated into amino acids
Organisms use an identical genetic code to convert mRNA codons transcribed from a gene tot he amino acid sequence of a polypeptide.
Genetic Code
: The set of rules that dictates the amino acid translations of each mRNA nucleotide triplet
Ribosomes build polypeptides
Ribosomes
: A cell structure condition of RNA and protein organized into two subunits and function as the site of protein synthesis in the cytoplasm
Ribosomal RNA (rRNA)
: The type of ribonucleic acid that with proteins makes ribosomes
Genetic information written in codons is translated into amino acid sequences
Triplet code
: A set of 3-nucleotide words that specify the amino acids from polypeptide chains
Codons
: a 3-nucleotide sequence in mRNA that specifies a particular amino acid or polypeptide termination signal
Transcription produces genetic messages in the form of RNA
RNA polymerase
: A large molecular complex that links together the growing chain of RNA nucleotides during transcription, using DNA as a template.
Promoter
: A specific nucleotide sequence in DNA located near the start of a gene that is binding site for RNA polymerase and the place where transcription begins
Terminator
: A sequence of nucleotides in DNA that marks the end of a gene, by signaling RNA polymerase to release the newly made RNA molecule and then to depart from the gene
An initiation codon marks the start of an mRNA message
An mRNA molecule binds to a small ribosomal subunit.
Start codon
: 3-nucleotide sequence (AUG) to which an initiation tRNA molecules binds-starting translation of genetic information
A large ribosomal subunit binds to the small subunit creating a functional ribosome.
P site
: a binding site for tRNA that holds the tRNA carrying the growing polypeptide chain
Elongation adds amino acids to the polypeptide chai until a stop codon terminates translation
The anticodon of an incoming tRNA molecule pairs with the mRNA codon in the A site of the ribosome.
The polypeptide separates from the tRNA and the P site and attaches by a new peptide bond to the amino acid carried by the tRNA in the A site. The ribosome catalyzes the formation of the peptide bond, adding one more amino acid to the chain.
The P site tRNA leaves the ribosome, and the ribosome translocated the remaining tRNA from the A site to the P site The codon and anticodon remain hydrogen-bonded, and the mRNA and tRNA move as a unit.
Stop codon
: On mRNA, one of 3 triples (UAG, UAA, UGA) that signal gene translation to stop
Eukaryotic RNA is processed before leaving the nucleus as mRNA
Messenger RNA (mRNA)
:The type of ribonucleic acid that encodes genetic information from DNA and conveys it to ribosomes, where the information is translated into amino acid sequences
Introns
: An internal, noncoding region of a gene that does not become part of the final messenger RNA molecule and is therefore not expresses
Exons
: The part of a gene that becomes part of the final mRNA and is therefore expressed
RNA Splicing
: The removal of introns and joining of exons forming an mRNA molecule with a continuous coding sequence; happens before mRNA leaves the nucleus
Transfer RNA molecules serve as interpreters during translation
Transfer RNA (tRNA)
: A type of ribonucleic acid that functions as an interpreter in translation. Each tRNA molecule has a specific anticodon, pieces up a specific amino acid and conveys the amino acid to the appropriate codon on mRNA.
Anticodon
: On a tRNA molecule, a specific sequence of three nucleotides that is complementary to a codon triplet on mRNA
Mutations can affect genes
Mutation
: A change in the genetic information of a cell; occurs in either DNA or RNA of a virus
Silent mutation
: a mutation in a gene that changes a codon to one that codes from the same amino acid as the original codon
Missense mutation
: A change in the nucleotide sequence of a gene that alters the amino acid sequence of the resulting polypeptide. In a missense mutation, a codon is changed from encoding one amino acid to encoding a different amino acid
Nonsense mutation
: change an amino acid codon into a stop codon.
Frameshift mutation
: A change in the genetic material that invokes the insertion or deletion of one or more nucleotides in a gene, resulting in a change in the triplet grouping of nucleotides.
Mutagens
: A chemical or physical agent that interacts with DNA and causes a mutation
The Genetics of Viruses and Bacteria
Viral DNA may become part of the host chromosome
Virus
: A microscopic particle capable of infecting cells of living organisms and inserting its genetic material.
Capsid
: the protein shell that encloses a viral genome
Lytic cycle
: A type of viral replication cycle resulting in the release of new viruses by lysis of the host cell
Lysogenic cycle
: A type of bacteriophage replication cycle in which the viral genome is incorporated into the bacterial host chromosomes as a prophage. New phages are not produced and the host cell is not killed or lysed unless the viral genome leaves the host chromosome
The phage DNA enters the bacterium. 2. It then forms a loop and either goes 1 of two ways
lytic cycle, the DNA immediately turns the cell into a virus -producing factory
the cell lyses and releases its viral products which could effect other cells
in the lysogenic cycle the DNA is inserted into the bacterial chromosomes.
Prophage
: Phage DNA that has inserted by genetic recombination into the DNA of a bacterial chromosome
Every time the cell divides, it replicates the phage DNA along with its own chromosomes and passes the copies on to the daughter cell
Many viruses cause disease in animals and plants
The viral envelope fuses with the cell's membrane allowing the protein-coated RNA to enter the cytoplasm
Enzymes digest the protein coat
an enzyme that entered the cell as part of the virus uses it's RNA genome as a template for making complementary strands of RNA
they serve as mRNA for the making of new viral proteins and they serve as templates for synthesizing new viral genome
the new coat proteins assemble around the new viral RNA
the viruses leave the cell by cloaking themselves in the host cell's plasma membrane
Emerging viruses threaten human health
Emerging viruses
: A virus that has appeared suddenly or has recently come to the attention of medical scientists
HIV
: The retrovirus that attacks the human immune system and causes AIDS
AIDS
: The late stages of HIV infection, characterized by a reduced number of T cells and the appearance of characteristic opportunistic infections
The AIDS virus makes DNA on an RNA template
Retrovirus
: An RNA virus that reproduces by means of a DNA molecule. It reverse-transcribes its RNA into DNA, inserts the DNA into a cellular chromosome, and then transcribes more copies of the RNA from the viral DNA. HIV is a retrovirus
Reverse transcriptase
: An enzyme encoded and used by retroviruses that catalyzes the synthesis of DNA on an RNA template
Reverse transcriptase uses the RNA as a template to make a DNA strand
it then adds a second, complementary DNA strand
the new double-stranded viral DNA enters the cell's nucleus and inserts itself into the chromosomal DNA
The host's RNA polymerase transcribes the incorporated DNA into RNA
which can be translated into viral proteins.
New virus assemble form these components leave the cell and infect other cells
Prions are infectious proteins
Prions
: An infection from a protein that may multiply by converting related proteins to more prions. Prions cause several related diseases in different animals, includes scrapie in sheep and mad cow disease.
Bacteria can transfer DNA in three ways
Transformation
: The incorporation of new genes into a cell from DNA that the cell takes up fro the surrounding environment.
Transduction
: The transfer of bacterial genes from one bacterial cell to another by a phage
Conjugation
: The union (mating) of two bacterial cells or protists cell and the transfer of DNA between the two molecules
Bacterial plasmids can serve as carriers for gene transfer
F factor:
A piece of DNA that can exist as a bacterial plasmid. The F factor carries genes for making sex pili and other structures needed for conjugation, as well as a site where DNA replication can start. F stands for fertility
F factor integrated
the F factor is integrated into the donor bacterium's chromosomes
when the ell conjugates wit a recipient cell, the donor chromosome starts replication at the F Factor's origin of replication
Once inside the recipient cell, the transferred donor genes can recombine with the corresponding part of the recipient chromosomes by crossing over.
F factor plasmid
the F factor can exist as a plasmid: a small circular DNA molecule separate from the bacterial chromosomes
When the donor cell mates with a recipient cell, the F factor replicates and at the same time transfers one whole copy of itself in linear rather than curricular form to the recipient cell.
the transferred plasmid reforms a circle in the recipient cell and the cell becomes a donor
Plasmid
: a small ring of independently replicating DNA separate from the main chromosomes; found in yeasts and bacteria
R plasmid
: A bacterial plasmid that carries genes for enzymes that destroy particular antibiotics thus making the bacterium resistant to the antibiotics
Chapter 12: DNA Technology and Genomics
Gene Cloning and Editing
Reverse transcriptase can help make genes for cloning
Reverse transcriptase
: An enzyme encoded and used by retroviruses the catalyzes the synthesis of DNA on an RNA template
Complementary DNA (cDNA)
:A DNA molecule made in-vitro using mRNA as a template and the enzyme reverse transcriptase
the chosen cells transcribe their genes within the nucleus producing mRNA. Occurs in test tube.
Single-stranded DNA transcripts are made from the mRNA using reverse transcriptase
Another enzyme is added to break down the mRNA
DNA polymerase is used to synthesize a second DNA strand
Enzymes are used to cut and paste DNA
Restriction enzymes
: A bacterial enzyme that cuts up foreign DNA, protecting bacteria against intruding DNA.
Restriction site
: A specific sequence on a DNA strand that is recognized as a cut site by a restriction enzyme.
Restriction fragments
: Molecules of DNA produced from a longer DNA molecule cut up by a restriction enzyme.
Genes can be cloned in recombinant plasmids
Biotechnology
: The manipulation of living organisms of their components to make useful products
DNA Technology
: Methods used to study and or manipulate DNA, including recombinant DNA technology
Recombinant DNA
: A DNA molecules that has been manipulated in the laboratory to carry nucleotide sequences derived from two sources
Genetic engineering
: The direct manipulation of genes for practical purposes
Plasmids
: A small ring of independently replicating DNA separate from the main chromosomes.
DNA cloning
: the production of many identical copies of a target segment of DNA.
Vector
: A piece of DNA that is used to move genes from one cell to another
DNA ligase
: Used in genetic engineering to paste a specific piece of DNA containing a gene of interest into a bacterial plasmid or other vector
Clone
: to produce genetically identical copies of a cell, organism or DNA molecule
Gene cloning
: The production of multiple copies of genes
Isolate two kinds of DNA: a bacterial plasmid that will serve as the vector
The DNA from another organism that includes the gene that codes for protein V along with other unwanted genes.
Both the plasmid and the gene V source DNA are treated with an enzyme that cuts DNA. AN enzyme is chosen that cleaves the plasmid in only one place
the source DNA is cut into many fragments. only one of which carries the gene V
The cut DNA from both sources are mixed .
The enzyme DNA ligase joins the two DNA molecules by way of covalent bond
The recombinant plasmid is taken up by a bacterium through transformation
The bacterium reproduces
Harvested proteins may be used directly
Nucleic acid probes can label specific DNA segments
Nucleic acid probe
: A radioactive or fluorescent labeled single-stranded nucleic acid molecule used to find a specific gene or other nucleotide sequence within a mass of DNA
New techniques allow a specific gene to be edited
The CRISPR-Cas9 system allows researchers to target a specific gene in a living cell for removal and editing
Genetically Modified Organisms
Recombinant cells and organisms can mass produce gene products
Bacteria, yeast, cell cultures, and whole animals can be genetically modified to make products for medical and other uses
DNA technology has changed the pharmaceutical industry and medicine
Treating Diseases
Diagnosing Diseases
Preventing Diseases
Vaccine
: a harmless variant or derivative of a pathogen that is used to stimulate the immune system to mount a lasting defense against that pathogen, preventing disease
Genetically modified organisms are transforming agriculture
Genetically modified organisms (GMOs)
: An organism that has acquired one or more genes by artificial means.
Transgenic organism
: An organism that contains genes from another species
With the help from a restriction enzyme and DNA ligase, the gene fro the desired trait is inserted into a modified version of the plasmid
Then the recombinant plasmid is put into a plant cell, where the DNA carrying the new gene integrates into one of the plant's chromosomes.
the recombinant cell is cultured and grown into a plant
The use of genetically modified organisms raises questions and concerns
Human Safety
Environmental Safety
Labeling
Scientists are investigating the potential risks to human and environmental health posed by DNA technologies
Gene therapy may someday help treat a variety of diseases
Gene therapy
: A treatment for a disease in which the patient's defective gene s supplemented or altered
A gene from a healthy person is cloned, converted to an RNA version and then inserted into the RNA genome of a harmless virus
Bone marrow cells are taken from the patient and infected with the recombinant virus
The virus inserts a DNA version of its genome into the cell's DNA
The engineered cells are then injected back into the patient
DNA Profiling
The analysis of genetic markers can produce a DNA profile
Forensics
: The scientific analysis of evidence for crime scene investigations and other legal proceedings
DNA profiling
: The Analysis of DNA samples to determine whether they cam from the same individual
DNA samples are isolated from the crime scene, suspects, victims, or other evidence
selected markers from each DNA sample are amplified producing a large sample of DNA fragments
The amplified DNA markers are compared providing data about which samples are from the same individual
The PCR method is used to amplify DNA sequences
Polymerase chain reaction (PCR)
: a teqnique by which a specific segment of a DNA molecule can be targeted and quickly amplified in the laboratory
Primers
: Short artificially created, single-stranded DNA molecules that bind to each need of a target sequence during a PCR procedure
The reaction mixture is heated to separate the strands of the DNA double helices
The strands are cooled. As they are cooled, the primer molecules hydrogen bond to their target sequences on either end of the target DNA
A heat-stable DNA polymerase builds new DNA strands by extending the primers
Gel electrophoresis sorts DNA molecules by size
Gel electrophoresis
: A method that separates macromolecules - usually proteins or nucleic acids - on the basis of size, electrical charge or other physical properties.
DNA profiling has provided evidence in many forensic investigations
The applications of DNA profiling include helping to solve crimes, establishing paternity and identify victims
Sort tandem repeat analysis is used fo DNA profiling
Repetitive DNA
: DNA that consists of nucleotide sequences that are present in multiple copies in the genome
Short tandem repeat (STR)
: A series of short DNA sequences that are repeated many times in a row in the genome
STR analysis
: A method of DNA profiling that compares the lengths of short tandem repeats selected from specific sites within the genome
Genomics and Bioinformatics
Small segments fo DNA can be sequenced directly
Next and third generation sequencing machines can quickly determine the sequence of relatively close stretches of DNA
Genomics is the scientific study of whole genomes
Genomics
: The study of heredity. Modern genetics began with the work of Mendel in the 19th century
The Human Genome Project
revealed that most of the human genome does not consist of genes
A massive endeavor to determine the nucleotide sequence of all DNA in the human genome and identify the location and sequence of every gene
The whole-genome shotgun
method of sequencing a genome can provide a wealth of data quickly
A method for determining the DNA sequence of an entire genome. After a genome is cut into small fragments, each fragment is sequence and then placed in the proper order
The field of bioinformatics is expanding our understanding of genomes
Bioinformatics
: the application of computational methods to the storage and analysis of biological data
Proteomics
: The study of whole sets of proteins and their interactions
Genomes hold clues to human evolution
The comparison of genomic sequences between humans and our nearest evolutionary relatives provides insight into human evolution
Chapter 11: How Genes Are Controlled
Control of Gene Expression
Proteins interacting with DNA turn prokaryotic genes on or off in response to environmental change
Gene regulation
: The turning on and off of genes within a cell in response to environmental stimuli or other factors
Gene Expression
: The process whereby genetic information flows from genes to proteins; the flow of genetic information from the genotype to the phenotype
The lac Operon: an inducible operon that is usually turned off but can be stimulated by lactose
Promoter
: A specific nucleotide sequence in DNA located near the start of a gene that is the binding site for RNA polymerase and the place where transcription begins
Operator
: A sequence of nucleotides near the start of an operon to which an active repressor protein can attach. the binding of a repressor prevents RNA polymerase from attaching to the promoter and transcribing the genes of the operon,. The operator sequence thereby acts as a switch that can turn all the genes in an operon on or off as a single functional unit.
Operon
: A unit of genetic regulation common in prokaryotes; a cluster of genes with related functions, along with he promoter and operator that control their function
Repressor
: When transcription is turned off because a protein binds to the operator and physically blocks the attachment of RNA polymerase to the promotor
Regulatory gene
: a gene located on the outside of the operons, coding for the repressor
Other kinds of Operons:
Activators
: proteins that turn operons on by binding to DNA and stimulating gene transcription
Chromosome structure and chemical modifications can affect gene expression
Differentiation
: The specialization in the structure and function of cells that occurs during the development of an organism; results from selective activation and deactivation of the cell's genome
DNA Packing
Histones
: A small protein molecule important in DNA packing in the eukaryotic chromosome. Eukaryotic chromatin consists of roughly equal parts of DNA and histone protein
Nucleosome
: Bead like unit of DNA packing in a eukaryotic cell; consists of DNA would twice around a protein core made up of eight histone molecules
Chemical modifications and Epigenetic Inheritance
Epigenetic inheritance
: The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence of a genome, such as the chemical modification of histone proteins or DNA bases
X Inactivation
X chromosome inactivation
: In female mammals, the inactivation of one X chromosome in each somatic cell
Barr body
: A dense body formed from a deactivated X chromosome found in the nuclei of female mammalian cells
Complex assemblies of proteins control eukaryotic transcription
Transcription factors
: A protein that functions in initiation or regulating transcription. Transcription factors bind to DNA or to other proteins hat bind to DNA
Enhancers
: A eukaryotic DNA sequence that helps stimulate the transcription of a gene at some distance from it. An enhancer functions by means of a transcription factor call an activator
Eukaryotic RNA may be spliced in more than one way
Alternative RNA splicing
: A type of regulation at the RNA processing level in which multiple mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns
Later stages of gene expression are also subject to regulation
Breakdown of mRNA
Initiation of translation
Protein processing
Noncoding RNAs play multiple roles in controlling gene expression
Functional RNAs
micro RNAs (MiRNAs)
: Degrade complimenting mRNAs and block translation of partially complementing mRNAs
Small interfering RNAs (siRNAs)
: RNA interference of translation, formation of centromere, methylation for gamete formation
RNA interference (RNAi)
: The blocking of gene expression by siRNAs
Multiple mechanisms regulate gene expression in eukaryotes
DNA unpacking
Transcription
Splicing
Addition of a cap and tail
Flow through nuclear envelope
Breakdown of mRNA
Translation
Cleavage modification, activation
Breakdown of Protein
Cell signaling and waves of gene expression direct animal development
Homeotic gene
: A master control gene that determines the identity of a body structure of a developing organism, presumably by controlling the developmental fate of groups of cells 1. occur in the ovaries and involve communication between an unfertilized egg cell and cells adjacent to it in its follicle. 2. location of a specific type of mRNA at the end of the egg. 3. after the egg is fertilized and laid, repeated rounds of mitosis transform the zygote into an embryo. The embryo makes proteins that diffuse through its cell layers. chemical signals between cells help drive the process of development. 4. the outcome is a mutation
Researchers can monitor the expression of specific genes
Nucleic acid hybridization
: The base pairing of one strand of a nucleic acid to a complementary sequence on another strand.
DNA microarray
: tiny amounts of a large number of different single-stranded DNA fragments on a glass slide
Signal transduction pathways convert messages received at the cells surface
Signal transduction pathway
: A series of molecular changes that converts a signal on a target cell's surface to a specific response inside the cell
The cell sends a message secretes a signaling molecule
The molecule binds to a specific receptor protein embedded in the target cells plasma membrane.
The binding activates the first in a series of relay proteins within the target cell. Each relay molecule activates another
The last relay molecule in the series activates a transcription factor
This triggers transcription of a specific gene
Translation of the mRNA produces a protein
Cloning of Plants and Animals
Biologists can clone animals via nuclear transplantation
Nuclear transplantation
The nucleus is removed from an egg cell
A somatic cell from an adult donor is added
the cell grows in culture to produce a blastocyst
The blastocyst is implanted in a surrogate
a clone of the donor is born
Plant cloning shows that differentiated cells may retain all of their genetic potential
Totipotent
: Describing a cell that can five rise to all of the different types of cells within an organism
Clone
: To produce genetically identical copies of a cell, organism, or DNA molecules
Regeneration
: The regrowth of body parts from pieces of an organism
Therapeutic cloning can produce stem cells with great medical potential
Embryonic stem cell (ES cells)
: Cell in the early animal embryo that differentiates during development to give rise to all the different kinds of specialized cells in the body
Therapeutic cloning: Producing ES cells to treat diseases
Adult stem cells
: A cell present in adult tissues that generates replacements for non dividing differentiated cells. Adult stem cells are capable of differentiating into multiple cell types, but that are not as developmentally flexile as embryonic stem cells
The Genetic Basis of Cancer
Cancer results from mutations in genes that control cell division
Oncogene
: A cancer causing gene; usually contributes to malignancy by abnormally enhancing the amount or activity of a growth factor made y the cell
Proto-oncogene
: A normal gene that, through mutation, can be converted to a cancer-causing gene
Tumor-Suppressor Genes: A gene whose product inhibits cell division, which prevents uncontrolled cell growth, A mutations that deactivates a tumor-suppressor gene may lead to cancer
Multiple genetic changes underlie the development of cancer
DNA changes
an oncogene is activated
a tumor suppressor gene is inactivated
A second tumor suppressor gene is inactivated
Cellular changes
Increased cell division
Growth of a benign tumor
Growth of a malignant tumor
Faulty proteins can interfere with normal signal transduction pathways
Lifestyle choices can reduce the risk of cancer
Carcinogens
: A cancer causing agent, either high-energy radiation or chemicals
Chapter 8: The Cellular Basis of Reproduction
The large, complex chromosomes of eukaryotes duplicate with each cell division
Chapter 9: Patterns of Inheritance
Sex-linked genes exhibit a unique patten of inheritance
Chapter 8: The Cellular Basis of Reproduction
Growing out of control, cancer cells produce malignant tumors
Chapter 9: Patterns of Inheritance
Many inherited traits in humans are controlled by a single gene
Chapter 9: Patterns of Inheritance
Mendel's Laws: The study of genetics has ancient roots
Chapter 2: The Chemical Basis of Life
Chemical Bonds
Chapter 4: A Tour of the Cell
Eukaryotic cells are partitioned into functional compartments
Chapter 5: The Working Cell
A specific enzyme catalyzes each cellular reaction
Chapter 3: The Molecules of Cells
THe nucleic acids DNA and RNA are information-ric polymers fo nucleotides
Melissa Weythman
Bio&160
Dr Hoffman